Index (Intact core API Documentation)

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absolutePath - Variable in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: absolute path file
AbstractEditBean - class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean.: Generic edit bean.
AbstractEditBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean
AbstractEditKeyBean - class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean.: Generic edit bean with keys.
AbstractEditKeyBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean: Default constructor; the internal key is set to a default value.
AbstractEditKeyBean(long) - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean: Constructs with given key.
AbstractEditorAction - class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction.: Super class for all Editor related action classes.
AbstractEditorAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
AbstractEditorDispatchAction - class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction.: The super class for all the dispatch actions.
AbstractEditorDispatchAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction
AbstractEditViewBean - class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean.: This super bean encapsulates behaviour for a common editing session.
AbstractEditViewBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
AbstractIntDisplayWrapper - class uk.ac.ebi.intact.application.editor.struts.view.experiment.AbstractIntDisplayWrapper.: This class is the super class for all the decorator classes for Interactions.
AbstractIntDisplayWrapper() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.experiment.AbstractIntDisplayWrapper
AbstractPredictAction - class uk.ac.ebi.intact.application.predict.struts.framework.AbstractPredictAction.: Super class for all the Predict action classes.
AbstractPredictAction() - Constructor for class uk.ac.ebi.intact.application.predict.struts.framework.AbstractPredictAction
AbstractResulltAction - class uk.ac.ebi.intact.application.search2.struts.controller.AbstractResulltAction.: Perform the common behaviour of the result Action.
AbstractResulltAction() - Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.AbstractResulltAction
AbstractSequenceManager - class uk.ac.ebi.intact.persistence.AbstractSequenceManager.
AbstractSequenceManager(PersistenceBroker) - Constructor for class uk.ac.ebi.intact.persistence.AbstractSequenceManager: Public constructor
AbstractViewBean - class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean.: Abstract class containing some basic operations useful to display beans for Intact.
AbstractViewBean(String, String) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean: Construst an instance of this class with help link.
ac - Variable in class uk.ac.ebi.intact.model.IntactObjectImpl: The unique accession number of an object.
ac - Variable in class uk.ac.ebi.intact.util.IntactStatistics: Specify the ac of the field retrieved.
acc - Variable in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean: 2 items to full the two columns of the displayed table.
AccessionSimilarityAction - class uk.ac.ebi.intact.application.intSeq.struts.controller.AccessionSimilarityAction.: This class provides the actions required for the SRSSearchResults page.
AccessionSimilarityAction() - Constructor for class uk.ac.ebi.intact.application.intSeq.struts.controller.AccessionSimilarityAction
acquire(String, String) - Method in class uk.ac.ebi.intact.application.editor.util.LockManager: Obtains a lock.
ADD_INTERACTION_NETWORK - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
add(String, Object) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet: Allows to add a key / value pair.
addActiveInstance(Component) - Method in class uk.ac.ebi.intact.model.InteractorImpl
addActiveInstance(Component) - Method in interface uk.ac.ebi.intact.model.Interactor
addActiveInstance(Component) - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
addAlias(Alias) - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
addAlias(Alias) - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl: Adds an alias to the object.
addAlias(Alias) - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
addAnnot(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction: Action for adding a new annotation.
addAnnotatedObject(AnnotatedObject) - Method in class uk.ac.ebi.intact.model.Reference
addAnnotation(Annotation) - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
addAnnotation(Annotation) - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
addAnnotation(Annotation) - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
addAnnotation(CommentBean) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Adds an annotation.
addBindingDomain(Feature) - Method in class uk.ac.ebi.intact.model.Component
addCachedClass(Class) - Method in class uk.ac.ebi.intact.business.IntactHelper: cache to be used for caching by shortLabel.
addCachedClass(Class) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
addCachedClass(Class) - Method in interface uk.ac.ebi.intact.persistence.DAO: adds a class to a set of classes that should be cached.
addCentralProtein(Node) - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
addChild(CvDagObject) - Method in class uk.ac.ebi.intact.model.CvDagObject
addComponent(Component) - Method in class uk.ac.ebi.intact.model.InteractionImpl
addComponent(Component) - Method in interface uk.ac.ebi.intact.model.Interaction
addComponent(Component) - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
addCriteria(CriteriaBean) - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: Add a new criteria to the interaction network
addEdge(EdgeI) - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
addEdge(EdgeI) - Method in class uk.ac.ebi.intact.simpleGraph.Graph
addError(String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Adds an error with given key.
addError(String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: Adds an error with given key.
addError(String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: Adds an error with given key.
addError(String) - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Adds an error with given key.
addError(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Adds an error with given key and value.
addError(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: Adds an error with given key and value.
addError(String, String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: Adds an error with given key and value.
addError(String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Adds an error with given key and value.
addEvidence(Evidence) - Method in interface uk.ac.ebi.intact.model.BasicObject
addEvidence(Evidence) - Method in class uk.ac.ebi.intact.model.BasicObjectImpl
addEvidence(Evidence) - Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
addExperiment(Experiment) - Method in class uk.ac.ebi.intact.model.InteractionImpl
addExperiment(Experiment) - Method in interface uk.ac.ebi.intact.model.Interaction
addExperiment(Experiment) - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
addExperiment(ExperimentBean) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Adds an Experiment.
addExperimentToHold(Collection) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Adds an Experiment bean to hold if the new experiment doesn't already exists in the experiment hold collection and in the current experiment collection for this interaction.
addFeature(Feature) - Method in class uk.ac.ebi.intact.model.ProteinImpl
addFeature(Feature) - Method in interface uk.ac.ebi.intact.model.Protein
addFeature(Feature) - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
addHighlightOption(String, Object) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI: Add a new option in the option set.
That new option is referenced by its name
addHighlightOption(String, Object) - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
addInteraction(Interaction) - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Adds an Interaction.
addInteraction(Interaction) - Method in class uk.ac.ebi.intact.model.Experiment
addInteractionNetwork(InteractionNetwork, Interactor, int) - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.GraphHelper: Create or extend an interaction network by using the given Interactor as a central node.
addInteractionToHold(Collection) - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Adds an Interaction to hold if the new interaction doesn't already exists in the interaction hold collection and in the current interaction collection for this experiment.
addMessage(String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Adds an Message with given key.
addMessage(String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: Adds an error with given key.
addMessage(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Adds an Message with given key and value.
addMessage(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: Adds an error with given key and value.
addModification(Modification) - Method in class uk.ac.ebi.intact.model.ProteinImpl
addModification(Modification) - Method in interface uk.ac.ebi.intact.model.Protein
addModification(Modification) - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
addNewAlias(AnnotatedObject, Alias) - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: add (not update) a new Xref to the given Annotated object and write it in the database.
addNewAlias(AnnotatedObject, Alias) - Method in class uk.ac.ebi.intact.util.UpdateProteins
addNewAnnotation(AnnotatedObject, Annotation) - Method in class uk.ac.ebi.intact.util.UpdateProteins: Add an annotation to an annotated object.
addNewXref(AnnotatedObject, Xref) - Method in class uk.ac.ebi.intact.util.InsertGo: Add a new xref to an annotatedObject.
addNewXref(AnnotatedObject, Xref) - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: add (not update) a new Xref to the given Annotated object and write it in the database.
addNewXref(AnnotatedObject, Xref) - Method in class uk.ac.ebi.intact.util.UpdateProteins
addNewXref(AnnotatedObject, Xref) - Method in class uk.ac.ebi.intact.util.GoaTools
addNode(Interactor) - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: add the initialization part to the super class method
addNode(Interactor) - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
addNode(Interactor) - Method in class uk.ac.ebi.intact.simpleGraph.Graph
addNode(NodeI) - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
addNode(NodeI) - Method in class uk.ac.ebi.intact.simpleGraph.Graph
addNodes(BufferedReader, DagNode, Class, IntactHelper, String, int) - Static method in class uk.ac.ebi.intact.util.DagNode: Read new nodes from the input, add nodes to the aParent node.
addObject(Object) - Method in class uk.ac.ebi.intact.util.ObjectSet
addParent(CvDagObject) - Method in class uk.ac.ebi.intact.model.CvDagObject
addProduct(Product) - Method in class uk.ac.ebi.intact.model.InteractorImpl
addProduct(Product) - Method in interface uk.ac.ebi.intact.model.Interactor
addProduct(Product) - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
addProtein(Protein) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Adds an Protein.
addProteinToUpdate(ProteinBean) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Adds a Protein bean to update.
addRange(Range) - Method in class uk.ac.ebi.intact.model.Feature
addReference(Reference) - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
addReference(Reference) - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
addReference(Reference) - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
addReleased(Product) - Method in class uk.ac.ebi.intact.model.InteractionImpl
addReleased(Product) - Method in interface uk.ac.ebi.intact.model.Interaction
addReleased(Product) - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
addSelected() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm: True if Add button is pressed.
addSelected() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm: True if add radio button is selected.
addToCurrentExperiment(Experiment) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Adds the experiment to the currently edited/added experiment list.
addToCurrentExperiment(Experiment) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
addToCurrentInteraction(Interaction) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Adds the interaction to the currently edited/added interaction list.
addToCurrentInteraction(Interaction) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
addToRecentList(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Adds the current edit object to the recent edited item list.
addToRecentList(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
addToRecentList(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
addToSearchCache(Collection) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Collection of AnnotatedObjects to add to the search cache.
addToSearchCache(Collection) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
addVisited(BasicObject) - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI: record that a Component has been visited during graph exploration.
addVisited(BasicObject) - Method in class uk.ac.ebi.intact.simpleGraph.Graph: record that a Component has been visited during graph exploration.
addXref(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction: Action for adding a new xref.
addXref(Xref) - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
addXref(Xref) - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl: Adds an xref to the object.
addXref(Xref) - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
addXref(XreferenceBean) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Adds an xref.
adjust(float, float) - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension: Widen the size if the new coordinate is out of the usable space.
adjustCadre(float, float, float, float) - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension: Adjust width and height according to components size.
Alias - class uk.ac.ebi.intact.model.Alias.: An alternative name for the object.
Alias(Institution, AnnotatedObject, CvAliasType, String) - Constructor for class uk.ac.ebi.intact.model.Alias: Create a new Alias for the given Annotated object
ALL_INTERACTIONS_DATA - Static variable in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
ancestors() - Method in class uk.ac.ebi.intact.model.CvDagObject: TODO comments
AnnotatedObject - interface uk.ac.ebi.intact.model.AnnotatedObject.
AnnotatedObjectImpl - class uk.ac.ebi.intact.model.AnnotatedObjectImpl.: Represents an object with biological annotation.
AnnotatedObjectImpl() - Constructor for class uk.ac.ebi.intact.model.AnnotatedObjectImpl: no-arg constructor provided for compatibility with subclasses that have no-arg constructors.
AnnotatedObjectImpl(String, Institution) - Constructor for class uk.ac.ebi.intact.model.AnnotatedObjectImpl: Constructor for subclass use only.
AnnotatedObjectProxy - class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy.
AnnotatedObjectProxy() - Constructor for class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
AnnotatedObjectProxy(InvocationHandler) - Constructor for class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
AnnotatedObjectProxy(PBKey, Identity) - Constructor for class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
Annotation - class uk.ac.ebi.intact.model.Annotation.: Funtional description of an object.
ANNOTATION_cDNA - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_cDNA_BAIT_3_UTR - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_cDNA_BAIT_5_UTR - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_cDNA_PREY_3_UTR - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_cDNA_PREY_5_UTR - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_CONFIDENCE - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_NEED_TO_BE_REVISITED - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
ANNOTATION_ORIENTATION - Static variable in class uk.ac.ebi.intact.util.InsertComplexGiot
Annotation(Institution, CvTopic) - Constructor for class uk.ac.ebi.intact.model.Annotation: Creates a valid Annotation instance.
AnnotationDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction.: Dispatcher action which dispatches according to the button title.
AnnotationDispatchAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction
annotations - Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
apply(Collection, InteractionNetwork) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour: Apply the implemented behaviour to a set of nodes.
applyBehaviour(Node) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.VisibleHighlightmentBehaviour: Apply the implemented behaviour to the specific Node of the graph.
applyBehaviour(Node) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour: Apply the implemented behaviour to the specific Node of the graph
applyBehaviour(Node) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.ColorHighlightmentBehaviour: Apply the implemented behaviour to the specific Node of the graph.
ATTRIBUTE_COLOR_LABEL - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the color of a Label.
ATTRIBUTE_COLOR_NODE - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the color of a Node.
ATTRIBUTE_COORDINATE_X - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The X coordinate of a Node int the image.
ATTRIBUTE_COORDINATE_Y - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The Y coordinate of a Node int the image.
ATTRIBUTE_HEIGHT - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the heigth of the image graph.
ATTRIBUTE_KEY_CLICKED - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants: The name of the attribute in the session which represents the element selected in the external application which allows to highlight.
ATTRIBUTE_KEYS_LIST - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants: The name of the attribute in the session which represents the list of elements selected component in the external application which allows to highlight.
ATTRIBUTE_LABEL - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the label of a Node.
ATTRIBUTE_LENGTH - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the width of the image graph.
ATTRIBUTE_NAME - Static variable in class uk.ac.ebi.intact.model.Constants: The name of an attribute set in the session.
ATTRIBUTE_OBJECTTYPE - Static variable in class uk.ac.ebi.intact.model.Constants: The name of an attribute set in the session.
ATTRIBUTE_SEARCH - Static variable in class uk.ac.ebi.intact.model.Constants: The name of an attribute set in the session.
ATTRIBUTE_SOURCE_URL - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants: The name of the HTTP attribute to describe the URL of the highlight source.
ATTRIBUTE_VISIBLE - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The attribute which allows to access the visibility of a Node

B

BaseException - exception uk.ac.ebi.intact.application.editor.exception.BaseException.: This is the common superclass for all application.exception; This class and its subclasses support the chained exception facility.
BaseException() - Constructor for class uk.ac.ebi.intact.application.editor.exception.BaseException: Default constructor.
BaseException(String) - Constructor for class uk.ac.ebi.intact.application.editor.exception.BaseException: Constructor with a message.
BaseException(Throwable) - Constructor for class uk.ac.ebi.intact.application.editor.exception.BaseException: Constructor that takes a root exception.
BasicGraph - class uk.ac.ebi.intact.simpleGraph.BasicGraph.: Common properties for objects in the SimpleGraph package.
BasicGraph() - Constructor for class uk.ac.ebi.intact.simpleGraph.BasicGraph
BasicGraphI - interface uk.ac.ebi.intact.simpleGraph.BasicGraphI.: A simple graph package for temporary processing, for example to prepare output for graph analysis packages.
BasicObject - interface uk.ac.ebi.intact.model.BasicObject.
BasicObjectImpl - class uk.ac.ebi.intact.model.BasicObjectImpl.: New class which factors out owner and evidences from IntactObject.
BasicObjectImpl() - Constructor for class uk.ac.ebi.intact.model.BasicObjectImpl: Protected constructor for use by subclasses
BasicObjectImpl(Institution) - Constructor for class uk.ac.ebi.intact.model.BasicObjectImpl
BasicObjectProxy - class uk.ac.ebi.intact.model.proxy.BasicObjectProxy.
BasicObjectProxy() - Constructor for class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
BasicObjectProxy(InvocationHandler) - Constructor for class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
BasicObjectProxy(PBKey, Identity) - Constructor for class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
BeanStreamReader - class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader.: Allow to iterate through the line or the resource describe by a given URL.
BeanStreamReader(String, Class) - Constructor for class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader
BeanStreamReader(String, Class, int) - Constructor for class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader
begin() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
begin() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
begin(int) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Used to begin a transaction.
begin(int) - Method in interface uk.ac.ebi.intact.persistence.DAO: Used to begin a transaction.
BENCHMARK_LOGGER_NAME - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: The name of the benchmark logger
BI_DIRECTIONAL_ORIENTATION - Static variable in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
BIgOFFSET - Static variable in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config: BigOffset is the left and bottom part of the image (text-area)
BINARY_INTERACTIONS_DATA - Static variable in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
BinaryDetailsViewBean - class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean.: Displays a binary view for a collection of Protein.
BinaryDetailsViewBean.BinaryData - class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean.BinaryData.
BinaryDetailsViewBean.BinaryData() - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean.BinaryData
BinaryDetailsViewBean(Collection, String, String) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean: Construct an instance of this class for given collection of object.
binaryInteractions - Variable in class uk.ac.ebi.intact.util.IntactStatistics
BinaryResultAction - class uk.ac.ebi.intact.application.search2.struts.controller.BinaryResultAction.: Performs the binary view for Proteins.
BinaryResultAction() - Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.BinaryResultAction
BioSource - class uk.ac.ebi.intact.model.BioSource.: Represents a biological source.
BioSource(Institution, String, String) - Constructor for class uk.ac.ebi.intact.model.BioSource: Creates a valid BioSource (ie a source organism) instance.
BioSourceAction - class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceAction.: The action to handle tax id for a bio source.
BioSourceAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceAction
bioSourceFactory - Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
BioSourceFactory - class uk.ac.ebi.intact.util.BioSourceFactory.: That class his hidding the logic which allow to get a valid biosource from a taxid.
BioSourceFactory(IntactHelper) - Constructor for class uk.ac.ebi.intact.util.BioSourceFactory
BioSourceFactory(IntactHelper, Institution) - Constructor for class uk.ac.ebi.intact.util.BioSourceFactory
BioSourceFactory(IntactHelper, Institution, int) - Constructor for class uk.ac.ebi.intact.util.BioSourceFactory
BioSourceSubmitAction - class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceSubmitAction.: Handles when the user enters a value for tax id.
BioSourceSubmitAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceSubmitAction
BioSourceViewBean - class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean.: BioSource edit view bean.
BioSourceViewBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
BlastException - exception uk.ac.ebi.intact.application.intSeq.exception.BlastException.: This class manages the Blast exceptions.
BlastException() - Constructor for class uk.ac.ebi.intact.application.intSeq.exception.BlastException
BlastException(String) - Constructor for class uk.ac.ebi.intact.application.intSeq.exception.BlastException: Constructor with a message.
BlastException(String, Exception) - Constructor for class uk.ac.ebi.intact.application.intSeq.exception.BlastException: Constructor with a message.
boundDomainAc - Variable in class uk.ac.ebi.intact.model.Feature
broker - Variable in class uk.ac.ebi.intact.application.synchron.XmlDumper
broker - Variable in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: reference to the PersistenceBroker
buildChunkIndex(Object, String, int, int, int, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder: Display the chunk index.
buildCompactElem(Object) - Method in class uk.ac.ebi.intact.util.XmlBuilder: Provides a 'compact' expansion of an object.
buildFileData(Collection) - Method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator: Creates the necessary file data from the DB information, using the specified DataBuilder.
buildFullElem(Object) - Method in class uk.ac.ebi.intact.util.XmlBuilder: Provides a 'complete' expansion of an object.
buildInteractionsOnly(Collection, int) - Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder: Produces an XML Document which contains only an interactionList.
buildPartialElem(Object, Collection) - Method in class uk.ac.ebi.intact.util.XmlBuilder: Provides a 'partial' expansion of an object.
buildWithReflection(ClassDescriptor, Map) - Method in class uk.ac.ebi.intact.persistence.IntactRowReaderImpl: Method used by the main OJB code in RowReaderDefaultImpl to generate an object via reflections.
buildXml(Collection) - Method in class uk.ac.ebi.intact.util.XmlBuilder: This method builds an XML Document for a Collection of objects.
buildXml(Object) - Method in class uk.ac.ebi.intact.util.XmlBuilder: Convenience method to build a Document for one object only.
BusinessConstants - class uk.ac.ebi.intact.business.BusinessConstants.: Constants used for the business package.
BusinessConstants() - Constructor for class uk.ac.ebi.intact.business.BusinessConstants

C

CalcBinaryInteractions - class uk.ac.ebi.intact.application.goDensity.setupGoDensity.CalcBinaryInteractions.: Calculates binary interactions from Intact
CalcBinaryInteractions() - Constructor for class uk.ac.ebi.intact.application.goDensity.setupGoDensity.CalcBinaryInteractions
CalcBinInteractionData - class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.CalcBinInteractionData.: CalcBinInteractionData can be used to generate binary interactions from intAct core model.
CalcBinInteractionData(IntactHelper, boolean, boolean, boolean) - Constructor for class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.CalcBinInteractionData: Constructor of CalcBinaryInteractionData
The parameter CalcBinaryInteractionData(helper, true, true, false) is for us at the moment the best way to generate BinaryInteractions with biological significant sense.
CallingSrs - class uk.ac.ebi.intact.application.intSeq.business.CallingSrs.: This class allows to retrieve AC and Description fields from the SRS engine, with the SPTr database.
CallingSrs() - Constructor for class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: constructor by default
CallingSrs(String) - Constructor for class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: constructor which allows to check if the protein topic exists in IntAct.
CallingSrs(String, String) - Constructor for class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: constructor which allows to call the SRS engine in case of lack of the request in IntAct
CallingSrsIF - interface uk.ac.ebi.intact.application.intSeq.business.CallingSrsIF.: Interface which provides methods specific to a user request, to return SRS results from this query.
cancelEdit() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
cancelEdit() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
CancelFormAction - class uk.ac.ebi.intact.application.editor.struts.action.CancelFormAction.: This action handles the event when the user clicks on Cancel button (common to all the editors).
CancelFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.CancelFormAction
cancelUpdate(Object) - Method in class uk.ac.ebi.intact.business.IntactHelper: Cancels the update for the given object.
CELLS - Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: The name for the CV cell list.
centerSelected() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm: True if center radio button is selected.
characters(char[], int, int) - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
ChartBuilder - class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder.: Construction of the Chart out of a IntactStatistics collection.
ChartBuilder() - Constructor for class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
checkExperiments() - Method in class uk.ac.ebi.intact.util.SanityChecker: Performs checks on Experiments.
checkExperimentsPubmedIds() - Method in class uk.ac.ebi.intact.util.SanityChecker: Performs checks on Experiments.
checkInteractions() - Method in class uk.ac.ebi.intact.util.SanityChecker: Performs Interaction checks.
checkInteractionsBaitAndPrey() - Method in class uk.ac.ebi.intact.util.SanityChecker: Performs Interaction checks.
checkProteins() - Method in class uk.ac.ebi.intact.util.SanityChecker: Performs checks against Proteins.
Chrono - class uk.ac.ebi.intact.util.Chrono.
Chrono() - Constructor for class uk.ac.ebi.intact.util.Chrono
ChunkedSingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean.: Class allowing to handle the chunked view for a single AnnotatedObject.
ChunkedSingleViewBean(AnnotatedObject, String, String, int, int) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean: Constructs an instance of this class from given AnnotatedObject.
CLASS_INFO - Static variable in class uk.ac.ebi.intact.model.Constants: used as a servlet context parameter name to refer to reflection data for the intact classes
classifyExperiments(String) - Static method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator: Classify experiments matching searchPattern into a data structure according to species and experiment size.
cleanErrorMessages() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
cleanErrorMessages() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccess
cleanErrorMessages() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl: Clean message list
cleanErrorMessages() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccess: Clean message list
cleanUp() - Method in class uk.ac.ebi.intact.util.SanityChecker: tidies up the DB statements.
clear() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Deletes all the links to sub objects of the current edit object.
clear() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
clear() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
clearCache() - Method in class uk.ac.ebi.intact.business.IntactHelper: Wipe the whole cache.
clearCache() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
clearCache() - Method in interface uk.ac.ebi.intact.persistence.DAO: wipe the whole cache.
clearErrors() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Clear error container.
clearErrors() - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: Clear error container.
clearErrors() - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Clear error container.
ClearErrorsTag - class uk.ac.ebi.intact.application.commons.struts.taglibs.ClearErrorsTag.: That class allows to clear from the request scope (in pageRequest) any errors collected by struts.
ClearErrorsTag() - Constructor for class uk.ac.ebi.intact.application.commons.struts.taglibs.ClearErrorsTag
clearExperimentToHold() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Clears all the experiments on hold.
clearInteractionToHold() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Clears all the interactions on hold.
clearMessages() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Clear Message container.
clearTransactions() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Clears any pending xrefs and annotations stored in the transaction containers.
clearTransactions() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
clearTransactions() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
ClickAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickAction.: Implementation of Action that validates a centered submisson (from a link).
ClickAction() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickAction
ClickBehaviourAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickBehaviourAction.: Implementation of Action that update in the session the current behaviour of a user click on the interaction network.
ClickBehaviourAction() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickBehaviourAction
ClickBehaviourForm - class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm.: This form captures the user action of the sideBarClickBehaviour.jsp.
ClickBehaviourForm() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm
clickBehaviourIsAdd() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
clickBehaviourIsAdd() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser: is the current behaviour is to Add when the user click on the image map
clickBehaviourIsCenter() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
clickBehaviourIsCenter() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser: is the current behaviour is to Center the view when the user click on the image map
close() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: closes a DAO (connection).
close() - Method in interface uk.ac.ebi.intact.persistence.DAO: closes a DAO (connection).
close() - Method in class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader
closeCon() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools: close jdbc connection
closeConnection() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser: Closes the connection to the database.
closeData(Iterator) - Method in class uk.ac.ebi.intact.business.IntactHelper: Closes result data.
closeHelper() - Method in class uk.ac.ebi.intact.util.InsertComplexMerck: Close the database connexion if it has been opened.
closeHelper() - Method in class uk.ac.ebi.intact.util.InsertComplex: Close the database connexion if it has been opened.
closeResults(Iterator) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Method to release result resources (eg result set).
closeResults(Iterator) - Method in interface uk.ac.ebi.intact.persistence.DAO: Method to release result resources (eg result set).
closeStore() - Method in class uk.ac.ebi.intact.business.IntactHelper: close the data source.
Collector - class uk.ac.ebi.intact.application.synchron.Collector.: Purpose: collects XML files from others IntAct nodes
Collector() - Constructor for class uk.ac.ebi.intact.application.synchron.Collector
ColorAction - class uk.ac.ebi.intact.application.goDensity.struts.controller.ColorAction.: If user wants to change the state of color-settings of the figure for the session, this Action is called by two radio-buttons (images!).
ColorAction() - Constructor for class uk.ac.ebi.intact.application.goDensity.struts.controller.ColorAction
ColorHighlightmentBehaviour - class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.ColorHighlightmentBehaviour.: Behaviour class allowing to change the color of highlighted proteins.
ColorHighlightmentBehaviour() - Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.ColorHighlightmentBehaviour
command - Variable in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: command line required to manage the blast program.
CommentBean - class uk.ac.ebi.intact.application.editor.struts.view.CommentBean.: Bean to store data for comments (annotations).
CommentBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Default constructor.
CommentBean(Annotation) - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Instantiate an object of this class from an Annotation object.
CommentBean(Annotation, long) - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Instantiates with given annotation and key.
commit() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
commit() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
commit() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Commits (finishes) a transaction.
commit() - Method in interface uk.ac.ebi.intact.persistence.DAO: Commits (finishes) a transaction.
compare(Object, Object) - Method in class uk.ac.ebi.intact.util.ShortLabelComparator: This method compares the two object parameters based on their short label values.
compare(Object, Object) - Method in class uk.ac.ebi.intact.util.InteractorComparator: This method compares two Components and orders them according to the short label alphabetic ordering of their Interactors.
compareTo(Object) - Method in class uk.ac.ebi.intact.util.IntactStatistics: Compares this object with the specified object for order.
Complex - class uk.ac.ebi.intact.model.Complex.: TODO comments
Complex() - Constructor for class uk.ac.ebi.intact.model.Complex
complexInteractions - Variable in class uk.ac.ebi.intact.util.IntactStatistics
Component - class uk.ac.ebi.intact.model.Component.: The specific instance of an interactor which participates in an interaction.
Component(Institution, Interaction, Interactor, CvComponentRole) - Constructor for class uk.ac.ebi.intact.model.Component: Creates a valid Component instance.
componentAc - Variable in class uk.ac.ebi.intact.model.Feature
Config - class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config.: Some goDensity specific Settings
CONFIG_DIR - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: The key to access configuration directory.
CONFIG_FILE - Static variable in class uk.ac.ebi.intact.persistence.AbstractSequenceManager
Config() - Constructor for class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config
Constants - class uk.ac.ebi.intact.application.hierarchView.business.Constants.: Manifest constants for the interaction network components.
Constants - class uk.ac.ebi.intact.application.intSeq.business.Constants.
Constants - class uk.ac.ebi.intact.application.search2.business.Constants.
Constants - class uk.ac.ebi.intact.application.statisticView.business.Constants.: Constants for the statisticView application.
Constants - class uk.ac.ebi.intact.model.Constants.: Basic constants file.
Constants() - Constructor for class uk.ac.ebi.intact.application.hierarchView.business.Constants
Constants() - Constructor for class uk.ac.ebi.intact.application.intSeq.business.Constants
Constants() - Constructor for class uk.ac.ebi.intact.application.search2.business.Constants
Constants() - Constructor for class uk.ac.ebi.intact.application.statisticView.business.Constants
Constants() - Constructor for class uk.ac.ebi.intact.model.Constants
contains(Object) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps: test, if key is already added
containsKey(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet: test, if Key2HashSet already contains the String "key"
contextDestroyed(ServletContextEvent) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
contextInitialized(ServletContextEvent) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
CONTRACT_NODES - Static variable in class uk.ac.ebi.intact.util.XmlBuilder: identifies a contract request
contractSelected() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm: True if Contract All button is pressed.
Crc64 - class uk.ac.ebi.intact.util.Crc64.: Crc64 checksum computation.
Crc64() - Constructor for class uk.ac.ebi.intact.util.Crc64
CREATE_INTERACTION_NETWORK - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants: Action allowed to create an interaction network
create(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.SidebarDispatchAction: Creates a new CV object for a topic.
create(Collection) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method provides a create operation for intact objects.
create(Object) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
create(Object) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
create(Object) - Method in class uk.ac.ebi.intact.business.IntactHelper: Convenience method to create a single object in persistent store.
create(Object) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: creates a single object in persistent store.
create(Object) - Method in interface uk.ac.ebi.intact.persistence.DAO: creates a single object in persistent store.
create(String, String) - Static method in class uk.ac.ebi.intact.application.predict.business.PredictUser: Factory method to create different instances of Predict user instances depending on the JDBC subprotocol.
CreateException - exception uk.ac.ebi.intact.persistence.CreateException.: Exception class to provide more meaningful error messages.
CreateException() - Constructor for class uk.ac.ebi.intact.persistence.CreateException
CreateException(String) - Constructor for class uk.ac.ebi.intact.persistence.CreateException
CreateException(String, Exception) - Constructor for class uk.ac.ebi.intact.persistence.CreateException: this constructor is used typically to pass on extra failure information from excpetions thrown elsewhere, eg from within other APIs
CreateFile() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: Create a file, checking some important points before: if it already exists, and if it is readable.
createIntactUser(HttpSession, HttpServletRequest) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Create a new IntactUser and store it in the session.
A datasource is also initialised inside the IntactUser.
createInteractionShortLabel(String, String) - Method in class uk.ac.ebi.intact.util.InsertComplexGiot: Creata an interaction shortlabel.
CreateWriter() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: if the PutInFile method needs to be managed in a loop, the FileWriter has to be created only once.
CriteriaBean - class uk.ac.ebi.intact.application.commons.search.CriteriaBean.: Holds the criteria who gave a search result.
CriteriaBean(String, String) - Constructor for class uk.ac.ebi.intact.application.commons.search.CriteriaBean
curator - Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl: The curator who has last edited the object.
curatorAc - Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
CvAliasType - class uk.ac.ebi.intact.model.CvAliasType.: The type of the alias.
CvAliasType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvAliasType: Creates a valid CvAliasType instance.
cvAliasTypeAc - Variable in class uk.ac.ebi.intact.model.Alias
CvCellCycle - class uk.ac.ebi.intact.model.CvCellCycle.: TODO comments
CvCellCycle(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvCellCycle: Creates a valid CvCellCycle instance.
cvCellCycleAc - Variable in class uk.ac.ebi.intact.model.BioSource
CvCellType - class uk.ac.ebi.intact.model.CvCellType.: TODO comments
CvCellType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvCellType: Creates a valid CvCellType instance.
cvCellTypeAc - Variable in class uk.ac.ebi.intact.model.BioSource
CvCompartment - class uk.ac.ebi.intact.model.CvCompartment.: The subcellular compartment.
CvCompartment(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvCompartment: Creates a valid CvCompartment instance.
cvCompartmentAc - Variable in class uk.ac.ebi.intact.model.BioSource
CvComponentRole - class uk.ac.ebi.intact.model.CvComponentRole.: The role of the specific substrate in the interaction.
CvComponentRole(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvComponentRole: Creates a valid CvComponentRole instance.
CvDagObject - class uk.ac.ebi.intact.model.CvDagObject.: Controlled vocabulary class for CVs which are organised in a Directed Acyclic Graph (DAG).
CvDagObject() - Constructor for class uk.ac.ebi.intact.model.CvDagObject: no-arg constructor which will hopefully be removed later...
CvDagObject(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvDagObject: Creates a valid CvDagObject instance.
CvDatabase - class uk.ac.ebi.intact.model.CvDatabase.: Represents an external database and contains all the information necessary to retrieve an object from it by a given primary identifier.
CvDatabase(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvDatabase: Creates a valid CvDatabase instance.
cvDatabaseAc - Variable in class uk.ac.ebi.intact.model.Xref
CvDevelopmentalStage - class uk.ac.ebi.intact.model.CvDevelopmentalStage.: TODO comments
CvDevelopmentalStage(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvDevelopmentalStage: Creates a valid CvDevelopmentalStage instance.
cvDevelopmentalStageAc - Variable in class uk.ac.ebi.intact.model.BioSource
CvDynaForm - class uk.ac.ebi.intact.application.editor.struts.view.cv.CvDynaForm.: The form to edit bio experiment data.
CvDynaForm() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.cv.CvDynaForm
CvEvidenceType - class uk.ac.ebi.intact.model.CvEvidenceType.: TODO comments
CvEvidenceType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvEvidenceType: Creates a valid CvEvidenceType instance.
cvEvidenceTypeAc - Variable in class uk.ac.ebi.intact.model.Evidence
CvFeatureIdentification - class uk.ac.ebi.intact.model.CvFeatureIdentification.: TODO comments
CvFeatureIdentification(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvFeatureIdentification: Creates a valid CvFeatureIdentification instance.
cvFeatureIdentificationAc - Variable in class uk.ac.ebi.intact.model.Feature
CvFeatureType - class uk.ac.ebi.intact.model.CvFeatureType.: TODO comments
CvFeatureType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvFeatureType: Creates a valid CvFeatureType instance.
CvGoDag - class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag.: CvGoDag represents a GO graph within IntAct.
Furthermore, the method todb():void can be used, to store the GO-graph in an external table, which can be used for fast & direct access (FastGoDag.java).
CvGoDag() - Constructor for class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag: Constructor retrieve the root element of GO hierarchy (of typ CvGoNode) from the database.
CvGoNode - class uk.ac.ebi.intact.model.CvGoNode.: Controlled vocabulary class for GeneOntology.
CvGoNode() - Constructor for class uk.ac.ebi.intact.model.CvGoNode: This constructor should be replaced as it could result in objects with invalid state.
CvIdentification - class uk.ac.ebi.intact.model.CvIdentification.: The method by which the Interactors have been detected.
CvIdentification(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvIdentification: Creates a valid CvIdentification instance.
CvInteraction - class uk.ac.ebi.intact.model.CvInteraction.: he method by which the Interaction has been determined.
CvInteraction(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvInteraction: Creates a valid CvInteraction instance.
CvInteractionType - class uk.ac.ebi.intact.model.CvInteractionType.: The type of interaction.
CvInteractionType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvInteractionType: Creates a valid CvInteractionType instance.
CvJournal - class uk.ac.ebi.intact.model.CvJournal.: TODO Represents ...
CvJournal(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvJournal: Creates a valid CvJournal instance.
CvModificationType - class uk.ac.ebi.intact.model.CvModificationType.: Represents a type of modification.
CvModificationType(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvModificationType: Creates a valid CvModificationType instance.
cvModificationTypeAc - Variable in class uk.ac.ebi.intact.model.Modification
CvObject - class uk.ac.ebi.intact.model.CvObject.: Represents a controlled vocabulary object.
CvObject() - Constructor for class uk.ac.ebi.intact.model.CvObject: no-arg constructor provided for compatibility with subclasses that have no-arg constructors.
CvObject(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvObject: Constructor for subclass use only.
CvProductRole - class uk.ac.ebi.intact.model.CvProductRole.: The role of the product.
CvProductRole(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvProductRole: Creates a valid CvProductRole instance.
cvProductRoleAc - Variable in class uk.ac.ebi.intact.model.Product
CvProteinForm - class uk.ac.ebi.intact.model.CvProteinForm.: TODO comments
CvProteinForm(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvProteinForm: Creates a valid CvProteinForm instance.
CvReferenceQualifier - class uk.ac.ebi.intact.model.CvReferenceQualifier.: Terms in this controlled vocabulary qualify the association between an AnnotatedObject and a Reference.
CvReferenceQualifier(String, Institution) - Constructor for class uk.ac.ebi.intact.model.CvReferenceQualifier: Creates a valid CvReferenceQualifier instance.
cvReferenceQualifierAc - Variable in class uk.ac.ebi.intact.model.ReferenceQualifier
CvTissue - class uk.ac.ebi.intact.model.CvTissue.: TODO comments
CvTissue(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvTissue: Creates a valid CvTissue instance.
cvTissueAc - Variable in class uk.ac.ebi.intact.model.BioSource
CvTopic - class uk.ac.ebi.intact.model.CvTopic.: Controlled vocabulary for description topics.
CvTopic(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvTopic: Creates a valid CvTopic instance.
CvViewBean - class uk.ac.ebi.intact.application.editor.struts.view.cv.CvViewBean.: The CV edit view bean.
CvViewBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.cv.CvViewBean
CvXrefQualifier - class uk.ac.ebi.intact.model.CvXrefQualifier.: Terms in this controlled vocabulary class qualify the association between AnnotatedObject and Xref.
CvXrefQualifier(Institution, String) - Constructor for class uk.ac.ebi.intact.model.CvXrefQualifier: Creates a valid CvXrefQualifier instance.
cvXrefQualifierAc - Variable in class uk.ac.ebi.intact.model.Xref

D

DagNode - class uk.ac.ebi.intact.util.DagNode.: Auxiliary class to insert GO Dag nodes from a GO dag formatted flat file.
DAO - interface uk.ac.ebi.intact.persistence.DAO.: This interface defines the methods available from a Data Access Object (DAO) implementation.
DAOFactory - class uk.ac.ebi.intact.persistence.DAOFactory.: This class is a factory for providing data sources from which a data source connection can be obtained.
DAOFactory() - Constructor for class uk.ac.ebi.intact.persistence.DAOFactory
DAOSource - interface uk.ac.ebi.intact.persistence.DAOSource.: This interface defines the functionality usually provided by a specific data source, eg Castor, oracle etc.
DATA_NOT_LOADED - Static variable in class uk.ac.ebi.intact.util.StatisticsDataSet
DATA_SOURCE - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants: Used as a key to identify a datasource class - its value is deifned in the web.xml file as a servlet context parameter
DATA_SOURCE - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Used as a key to identify a datasource class - its value is deifned in the web.xml file as a servlet context parameter
DatabaseEmptyException - exception uk.ac.ebi.intact.application.goDensity.exception.DatabaseEmptyException.: If database for goDensity is still empty within same tables
DatabaseEmptyException() - Constructor for class uk.ac.ebi.intact.application.goDensity.exception.DatabaseEmptyException
DatabaseEmptyException(String) - Constructor for class uk.ac.ebi.intact.application.goDensity.exception.DatabaseEmptyException
DATABASES - Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: The name for the database list.
DataBuilder - interface uk.ac.ebi.intact.application.dataConversion.DataBuilder.: Interface defining the operations required to generate flat files.
DataConversionException - exception uk.ac.ebi.intact.application.dataConversion.DataConversionException.: Created by IntelliJ IDEA.
DataConversionException() - Constructor for class uk.ac.ebi.intact.application.dataConversion.DataConversionException
DataConversionException(String) - Constructor for class uk.ac.ebi.intact.application.dataConversion.DataConversionException
DataConversionException(String, Exception) - Constructor for class uk.ac.ebi.intact.application.dataConversion.DataConversionException
DATASOURCE - Static variable in class uk.ac.ebi.intact.model.Constants: used as a key to identify a datasource class - its value is deifned in the web.xml file as a servlet context parameter
DataSourceException - exception uk.ac.ebi.intact.persistence.DataSourceException.: Custom exception class to handle errors occurring with eg opening/closing a connection to a data source.
DataSourceException() - Constructor for class uk.ac.ebi.intact.persistence.DataSourceException
DataSourceException(String) - Constructor for class uk.ac.ebi.intact.persistence.DataSourceException
DataSourceException(String, Exception) - Constructor for class uk.ac.ebi.intact.persistence.DataSourceException
dateFormater - Static variable in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
dateFormater - Static variable in class uk.ac.ebi.intact.util.StatisticsDataSet
DB - Static variable in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config
DB_FILE_KEY - Static variable in class uk.ac.ebi.intact.model.Constants: used as a key to identify a DB filename (for Castor) the value is defined in the web.xml file
DB_NAME_KEY - Static variable in class uk.ac.ebi.intact.model.Constants: used as a key to identify a DB name - value defined in web.xml file
dbPopulate(boolean) - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.CalcBinInteractionData: populate database with binary interaction data - but only if bait and prey are annotated by go.
DbTools - class uk.ac.ebi.intact.application.goDensity.business.data.DbTools.: This class is used for db-connection (it's a Singleton!)
DEFAULT_BORDER - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
DEFAULT_EGO_URL - Static variable in class uk.ac.ebi.intact.util.GoServerProxy
DEFAULT_MAX_CENTRAL_PROTEIN - Static variable in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
delAnnotation(CommentBean) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Removes an annotation
delete() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: This method clears the view of the current edit object, remove it from the search cache, deletes from the experiment list (if the current edit is an instance of an Experiment class), tand finally delete the current edit object.
delete() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction: Action for deleting the selected annotation.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction: Action for deleting the selected annotation.
delete(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction
delete(Object) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
delete(Object) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
delete(Object) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method provides a delete operation.
deleteAllElements(Collection) - Method in class uk.ac.ebi.intact.business.IntactHelper: Delete all elements in a collection.
DeleteFile() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: Delete a file which isn't used anymore.
DeleteFormAction - class uk.ac.ebi.intact.application.editor.struts.action.DeleteFormAction.: This action handles the event when the user clicks on the Delete button to delete the current edit record.
DeleteFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.DeleteFormAction
delExperiment(ExperimentBean) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Removes an Experiment
delInteraction(Interaction) - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Removes an Interaction
delProtein(int) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Removes a Protein from given position.
delXref(XreferenceBean) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Removes a xref.
DensityImage - class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage.: Image rendering class for go-go-densities
DensityImage(GoGoDensity[][], boolean) - Constructor for class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage: constructor for a density image
DensityImageServlet - class uk.ac.ebi.intact.application.goDensity.business.image.DensityImageServlet.
DensityImageServlet() - Constructor for class uk.ac.ebi.intact.application.goDensity.business.image.DensityImageServlet
deploy() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager: deploy the web service according to collected data (ie deployment file name).
des - Variable in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
desacreaseDepth() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
desacreaseDepth() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser: Desacrease the depth of the interraction network up to the defined minimum.
description - Variable in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean: The description to be returned to the server.
deserialize(byte[]) - Static method in class uk.ac.ebi.intact.util.Serializer: simple method to deserialize an array of bytes.
deserialize(String) - Method in class uk.ac.ebi.intact.util.fileParsing.SerializationHelper
DetailsResultAction - class uk.ac.ebi.intact.application.search2.struts.controller.DetailsResultAction.: Performs the details view for Proteins.
DetailsResultAction() - Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.DetailsResultAction
DetailsViewBean - class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean.: Class allowing to handle the view for a collection of AnnotatedObject.
DetailsViewBean(Collection, String, String) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean: Constructs an instance of this class from given collection.
DIR_INPUT_BLAST - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
DIR_OUTPUT_BLAST - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
DIR_OUTPUT_WGETZ - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
DIR_OUTPUT_WGETZ_SEQ - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
disableCaching() - Method in class uk.ac.ebi.intact.util.NewtServerProxy
DispatcherAction - class uk.ac.ebi.intact.application.search2.struts.controller.DispatcherAction.: This class provide a bridge between the search process and the result.
DispatcherAction() - Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.DispatcherAction
DisplayAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplayAction.: Action allowing to display an interaction network.
DisplayAction() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplayAction
displayCookieContent() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag: For Debugging Purpose.
DisplayHighlightOptions - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHighlightOptions.: That class allows to include HTML code to Displays current highlight source options.
DisplayHighlightOptions() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHighlightOptions
DisplayHttpContentTag - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHttpContentTag.: That class allow to initialize properly the HTTPSession object with what will be neededlater by the user of the web application.
DisplayHttpContentTag() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHttpContentTag
DisplayInteractionNetworkTag - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayInteractionNetworkTag.: That class allows to display in the browser the current interaction network and the associated HTML MAP.
DisplayInteractionNetworkTag() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayInteractionNetworkTag
DisplaySourceAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplaySourceAction.: Implementation of Action that allows to save in the context the selected source URL.
DisplaySourceAction() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplaySourceAction
DisplaySourceTag - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplaySourceTag.: That class allow to initialize properly in the session the sources to display according to the current central protein.
DisplaySourceTag() - Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplaySourceTag
displayStatistics() - Method in class uk.ac.ebi.intact.util.InsertComplexGiot
displayStatistics() - Method in class uk.ac.ebi.intact.util.GoaTools
DisplayStatisticsBean - class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean.: Use for the <display:> tag in order to display one line of a table.
DisplayStatisticsBean(String, int, String) - Constructor for class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
displayUnmappedIds() - Method in class uk.ac.ebi.intact.util.InsertComplexGiot
DocumentationIntegrityChecker - class uk.ac.ebi.intact.util.DocumentationIntegrityChecker.: Allows to check if the IntAct documentation is ready to be generated by checking if a section is used several times.
DocumentationIntegrityChecker() - Constructor for class uk.ac.ebi.intact.util.DocumentationIntegrityChecker
DocumentationTag - class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag.: Allows to display a javascript link pointing on the intact documentation directly on the right section.
DocumentationTag() - Constructor for class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
doEndTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.SaveErrorsTag: In case some errors (ActionErrors) are discovered, let's save them in the session for later displaying.
doEndTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.RestoreErrorsTag: In case some errors (ActionErrors) are discovered, let's save them in the session for later displaying.
doEndTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag: Display the link to the documentation page with eventually the section.
doEndTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.ClearErrorsTag: Clear any Struts errors stored in the pageContext.
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag: Save the hierarchView search context in a cookie
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.RestoreContextFromCookieTag: Restore the context if needed.
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplaySourceTag: Called when the JSP encounters the end of a tag.
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayInteractionNetworkTag: Called when the JSP encounters the end of a tag.
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHttpContentTag: Called when the JSP encounters the end of a tag.
doEndTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHighlightOptions: Called when the JSP encounters the end of a tag.
doGet(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.commons.util.LoggingInitServlet
doGet(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.goDensity.business.image.DensityImageServlet: Servlet allowing to get image data, rasterize into JPEG and send to the browser the image by taking care of the MIME type.
doGet(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSServlet: doGet - the "main" method of a servlet.
doGet(HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.business.servlet.GenerateImage: Servlet allowing to get image data, rasterize into JPEG and send to the browser the image by taking care of the MIME type.
doIt() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorTopicsGenerator: This method does the actual writing of the resource file.
doLookup(List, String, IntactUserI) - Method in interface uk.ac.ebi.intact.application.commons.search.SearchHelperI: Search in the IntAct data for a colleciton of object (type=searchClass).
doLookup(List, String, IntactUserI) - Method in class uk.ac.ebi.intact.application.commons.search.SearchHelper
doLookup(String, String, IntactUserI) - Method in interface uk.ac.ebi.intact.application.commons.search.SearchHelperI: Search in the IntAct data for a colleciton of object (type=searchClass).
doLookup(String, String, IntactUserI) - Method in class uk.ac.ebi.intact.application.commons.search.SearchHelper
doLookupSimple(String, String, IntactUserI) - Method in interface uk.ac.ebi.intact.application.commons.search.SearchHelperI: Peforms a simple search in the IntAct data for given search class and value.
doLookupSimple(String, String, IntactUserI) - Method in class uk.ac.ebi.intact.application.commons.search.SearchHelper
doSimilaritySearch(String, HttpServletRequest) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: Perform the similarity search operation.
Check the protein sequence and similarity search program parameters.
doStartTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.SaveErrorsTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.RestoreErrorsTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.ClearErrorsTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.RestoreContextFromCookieTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplaySourceTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayInteractionNetworkTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHttpContentTag: Skip the body content.
doStartTag() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHighlightOptions: Skip the body content.
draw() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.DrawGraph: drawing process, call methods to draw nodes, edges ...
DrawGraph - class uk.ac.ebi.intact.application.hierarchView.business.image.DrawGraph.: Purpose : ------- This class allows to tranform a graph to an image (binary content)
DrawGraph(InteractionNetwork, String) - Constructor for class uk.ac.ebi.intact.application.hierarchView.business.image.DrawGraph: Constructor
DuplicateLabelException - exception uk.ac.ebi.intact.business.DuplicateLabelException.: Exception class to provide more meaningful error messages.
DuplicateLabelException() - Constructor for class uk.ac.ebi.intact.business.DuplicateLabelException
DuplicateLabelException(String, String) - Constructor for class uk.ac.ebi.intact.business.DuplicateLabelException

E

Edge - class uk.ac.ebi.intact.simpleGraph.Edge.
Edge() - Constructor for class uk.ac.ebi.intact.simpleGraph.Edge
EdgeI - interface uk.ac.ebi.intact.simpleGraph.EdgeI.: An edge in the binary graph representation of an Interaction network.
edit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction: Action for editing the selected annotation.
edit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction: Action for editing the selected annotation.
edit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction
Editable - interface uk.ac.ebi.intact.model.Editable.: An editiable class must implement this marker interface.
EDITOR_ERROR - Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction: The global Intact error key.
EDITOR_SERVICE - Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants: The key to store an Intact Service object.
EDITOR_TOPICS - Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants: To access intact types.
EditorActionServlet - class uk.ac.ebi.intact.application.editor.struts.framework.EditorActionServlet.: This is Intact editor specific action servlet class.
EditorActionServlet() - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.EditorActionServlet
EditorChoiceAction - class uk.ac.ebi.intact.application.editor.struts.action.EditorChoiceAction.: This action is responsible for choosing the editor.
EditorChoiceAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.EditorChoiceAction
EditorConstants - interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants.: Contains constants required for the editor.
EditorExceptionHandler - class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorExceptionHandler.: Extends the struts default exception handler to Editor specific behaviour.
EditorExceptionHandler() - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorExceptionHandler
EditorMenuFactory - class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory.: The menu factory to generate various menus.
EditorMenuFactory(IntactHelper) - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: Construst with an Intact helper.
EditorService - class uk.ac.ebi.intact.application.editor.business.EditorService.: This class provides the general editor services common to all the users.
EditorSwitchAction - class uk.ac.ebi.intact.application.editor.struts.action.util.EditorSwitchAction.: This action class is responsible for selecting which to editor to display.
EditorSwitchAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.util.EditorSwitchAction
EditorTopicsGenerator - class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorTopicsGenerator.: This utility class generates EditorTopics.properties file using the classes in the AnnotatedObject package.
EditorTopicsGenerator(String, String) - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorTopicsGenerator: Constructor that accepts root to the class directory to search for AnnotatedObject and the destination to write the properties.
EditUser - class uk.ac.ebi.intact.application.editor.business.EditUser.: This class stores information about an Intact Web user session.
EditUser(String, String) - Constructor for class uk.ac.ebi.intact.application.editor.business.EditUser: This constructor for Seralization test class.
EditUser(String, String, String, String) - Constructor for class uk.ac.ebi.intact.application.editor.business.EditUser: Constructs an instance of this class with given mapping file and the name of the data source class.
EditUserI - interface uk.ac.ebi.intact.application.editor.business.EditUserI.: Provides methods specific to a user editing an Annotated object.
EditViewBeanFactory - class uk.ac.ebi.intact.application.editor.struts.framework.util.EditViewBeanFactory.: The factory class to create edit view beans.
EditViewBeanFactory(IntactHelper) - Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.EditViewBeanFactory: Creates the factory with an instnce of the Intact helper.
EGO_QUERY - Static variable in class uk.ac.ebi.intact.util.GoServerProxy
ElementNotParseableException - exception uk.ac.ebi.intact.application.graph2MIF.exception.ElementNotParseableException.: This Exception should be thrown, if an error occours, but the above Element has to determine if it is an fatal one or PSI Format without this Element would also be valid.
ElementNotParseableException() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.ElementNotParseableException
ElementNotParseableException(String) - Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.ElementNotParseableException
EmptyTopicsException - exception uk.ac.ebi.intact.application.editor.exception.EmptyTopicsException.: Exception thrown for any problems with IntactTypes resource file.
EmptyTopicsException(String) - Constructor for class uk.ac.ebi.intact.application.editor.exception.EmptyTopicsException: Constructor with a message.
enableCaching() - Method in class uk.ac.ebi.intact.util.NewtServerProxy
enableCaching(int) - Method in class uk.ac.ebi.intact.util.NewtServerProxy
endDocument() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
endElement(String, String, String) - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler: Called when the end of a tag is encoutered.
endPrefixMapping(String) - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
equals(Object) - Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.editor.util.LockManager.LockObject: Compares obj with this object according to Java's equals() contract.
equals(Object) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
equals(Object) - Method in class uk.ac.ebi.intact.model.ReferenceQualifier: Equality for ReferenceQualifiers is currently based on equality for CvReferenceQualifiers and References.
equals(Object) - Method in class uk.ac.ebi.intact.model.ProteinImpl: Equality for Proteins is currently based on equality for Interactors, the sequence and the crc64 checksum.
equals(Object) - Method in class uk.ac.ebi.intact.model.InteractionImpl: Equality for Interactions is currently based on equality for Interactors, CvInteractionType, kD and Components.
equals(Object) - Method in class uk.ac.ebi.intact.model.InteractorImpl: Equality for Interactors is currently based on equality for AnnotatedObjects, BioSources and Products.
equals(Object) - Method in class uk.ac.ebi.intact.model.Range: Equality for Ranges is currently based on equality for Modification, position from and position to (ints).
equals(Object) - Method in class uk.ac.ebi.intact.model.Product: Equality for Product is currently based on equality for stoichiometry, CvProductRole, Interaction and Interactor.
equals(Object) - Method in class uk.ac.ebi.intact.model.Component: Equality for Components is currently based on object identity (i.e.
equals(Object) - Method in class uk.ac.ebi.intact.model.Modification: Equality for Modifications is currently based on equality for CvModificationType and Range.
equals(Object) - Method in class uk.ac.ebi.intact.model.Reference: Equality for References is currently based on equality for author, title and Xrefs.
equals(Object) - Method in class uk.ac.ebi.intact.model.Alias: Equality for Aliases is currently based on equality for CvAliasTypes and names.
equals(Object) - Method in class uk.ac.ebi.intact.model.Annotation: Equality for Annotations is currently based on equality for CvTopics and annotationText (a String).
equals(Object) - Method in class uk.ac.ebi.intact.model.Person
equals(Object) - Method in interface uk.ac.ebi.intact.model.Interaction
equals(Object) - Method in interface uk.ac.ebi.intact.model.Interactor
equals(Object) - Method in interface uk.ac.ebi.intact.model.Protein
equals(Object) - Method in class uk.ac.ebi.intact.model.Xref: Equality for Xrefs is currently based on equality for CvDatabases and primaryIds.
equals(Object) - Method in class uk.ac.ebi.intact.model.Institution: Equality for Institutions is currently based on equal shortLabels and fullNames.
equals(Object) - Method in class uk.ac.ebi.intact.model.Experiment: Equality for Experiments is currently based on equality for AnnotatedObjects and BioSources only.
equals(Object) - Method in class uk.ac.ebi.intact.model.BioSource: Equality for BioSources is currently based on equality for AnnotatedObjects and taxIds (String representation of an integer).
equals(Object) - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
equals(Object) - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl: Equality for AnnotatedObjects is currently based on equality for Xrefs, shortLabels and fullNames.
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
equals(Object) - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
equals(Object) - Method in class uk.ac.ebi.intact.simpleGraph.Edge
equals(Object) - Method in class uk.ac.ebi.intact.simpleGraph.Node
equals(Object) - Method in interface uk.ac.ebi.intact.simpleGraph.NodeI
equals(Object) - Method in class uk.ac.ebi.intact.util.Key
equals(Object, Object) - Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean: True if both objects are null or object i is equal to object 2.
equals(Object, Object) - Static method in class uk.ac.ebi.intact.util.Utilities: compares two objects.
ERROR - Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
ERROR - Static variable in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean: Identifier for an error bean.
evalueMin - Variable in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: E-Value initialized at "0" to make a test afterwards.
Evidence - class uk.ac.ebi.intact.model.Evidence.: TODO comments TODO what to do with this ?
Evidence() - Constructor for class uk.ac.ebi.intact.model.Evidence
ExecBlast() - Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: FillSeqFileConcatCommand 1) creates and full the input file, and also complete the command line.
ExecFinalCommand(boolean) - Method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: This method decides which command will be executed (Wgetz or Getz) and put the file in the provided directory: to organize the numerous generated files into two separate directories.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction: This method dispatches calls to various methods using the 'dispatch' parameter.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction: Action for submitting the edit form.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.ResultAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.FillResultFormAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.FillCvFormAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.EditorChoiceAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.DeleteFormAction: Action for cancelling changes to the current edit.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.CancelFormAction: Action for cancelling changes to the current edit.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction: This method dispatches calls to various methods using the 'dispatch' parameter.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.biosrc.FillBioSrcFormAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceSubmitAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionLinkAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionHoldAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.FillExperimentFormAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.ExperimentSubmitAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinSearchAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction: This method dispatches calls to various methods using the 'dispatch' parameter.
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.InteractionSubmitAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.FillInteractionFormAction
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentHoldAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.security.LogoutAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.security.LoginAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.goDensity.struts.controller.goInputAction: Action execute
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.goDensity.struts.controller.goChildrenAction: Action execute
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.goDensity.struts.controller.InitAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.goDensity.struts.controller.ColorAction: Action execute
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.SourceAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.SearchAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.InteractionNetworkAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.InitAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.HighlightmentAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplaySourceAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.DisplayAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickBehaviourAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.controller.ClickAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.intSeq.struts.controller.SequenceSimilarityAction: Execute method with the Struts 1.1 release Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.intSeq.struts.controller.ProteinSearchAction: Execute method with the Struts 1.1 release Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.intSeq.struts.controller.AccessionSimilarityAction: Execute method with the Struts 1.1 release Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.predict.struts.action.WelcomeAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.predict.struts.action.PredictionAction: Collects Top 50 Pay-As-You-Go protein results from database for each species and places them in results bean Species info is collected in species bean These are called from the success jsp page
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.WelcomeAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.DispatcherAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.AbstractResulltAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.statisticView.struts.controller.FilterAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it).
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.util.HeaderSwitchAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it), with provision for handling exceptions thrown by the business logic.
execute(ComponentContext, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.action.util.EditorSwitchAction: Process the specified HTTP request, and create the corresponding HTTP response (or forward to another web component that will create it), with provision for handling exceptions thrown by the business logic.
execute(Exception, ExceptionConfig, ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorExceptionHandler
EXP - Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants: Forward to the experiment editor from the interaction editor.
EXPAND_NODES - Static variable in class uk.ac.ebi.intact.util.XmlBuilder: Identifies an expand request
expandSelected() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm: True if Expand/Contract button is pressed.
EXPANSION_ALL - Static variable in class uk.ac.ebi.intact.business.BusinessConstants: Expand a complex to all pairwise interactions.
EXPANSION_ALL - Static variable in class uk.ac.ebi.intact.model.Constants: Expand a complex to all pairwise interactions.
EXPANSION_BAITPREY - Static variable in class uk.ac.ebi.intact.business.BusinessConstants: Expand a complex into all bait-prey pairs.
EXPANSION_BAITPREY - Static variable in class uk.ac.ebi.intact.model.Constants: Expand a complex into all bait-prey pairs.
Experiment - class uk.ac.ebi.intact.model.Experiment.: Represents one experiment.
EXPERIMENT_DATA - Static variable in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
Experiment(Institution, String, BioSource) - Constructor for class uk.ac.ebi.intact.model.Experiment: Creates a valid Experiment instance.
ExperimentAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentAction.: Invoked when Delete button is pressed in the experiment form to delete an experiment from an Interaction.
ExperimentAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentAction
ExperimentBean - class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean.: Bean to store data for an Experiment (in an Interaction).
ExperimentBean(Experiment) - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean: Instantiate an object of this class from a Experiment instance.
ExperimentChunkedSingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean.: View bean responsible for the chunked display of a single experiment.
ExperimentChunkedSingleViewBean(AnnotatedObject, String, String, Integer, Integer) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean: THe Integer parameter are needed to be able to access the constructor by reflexion.
ExperimentDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentDispatchAction.: The action class to search an Experiment (in the context of an Interaction).
ExperimentDispatchAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentDispatchAction
ExperimentDynaForm - class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentDynaForm.: The form to validate experiment data.
ExperimentDynaForm() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentDynaForm
ExperimentException - exception uk.ac.ebi.intact.application.editor.exception.validation.ExperimentException.: Thrown when the validation for an experiment fails.
ExperimentException() - Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.ExperimentException: Default constructor.
ExperimentException(String) - Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.ExperimentException: Construst with given message key
experimentExists(ExperimentBean) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: True if given experiment exists in this object's experiment collection.
ExperimentHoldAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentHoldAction.: Invoked when either Add/Hide button is pressed in the form for holding experiments yet to add to the Interaction.
ExperimentHoldAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentHoldAction
experimentNumber - Variable in class uk.ac.ebi.intact.util.IntactStatistics
EXPERIMENTS - Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: The name for the experiment list.
ExperimentSingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.ExperimentSingleViewBean.: View bean responsible for the display of a single experiment.
ExperimentSingleViewBean(AnnotatedObject, String, String) - Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.ExperimentSingleViewBean: Construct an instance of this class for given object.
ExperimentSubmitAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.ExperimentSubmitAction.: An action to handle Experiment specific events.
ExperimentSubmitAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.ExperimentSubmitAction
ExperimentViewBean - class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean.: Experiment edit view bean.
ExperimentViewBean() - Constructor for class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
exportBioLayout() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: Create a String giving informations for the bioLayout EMBL software the informations are just pairwise of protein label.
exportTlp() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: Create a String giving informations for the Tulip treatment the informations are : - the number of nodes, - the whole of the edges and nodes associeted for each edge, - the label of each node.

F

factory(Class) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditViewBeanFactory: Returns a view bean constructed from given class.
FAILURE - Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants: Used in various action classes to define where to forward to on different conditions.
FAILURE - Static variable in class uk.ac.ebi.intact.application.predict.struts.framework.AbstractPredictAction: The key to failure action.
FastGoDag - class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag.: Represents GO-Graph (hierarchy) with fast and direct JDBC access to db.
Feature - class uk.ac.ebi.intact.model.Feature.: TODO comments
Feature() - Constructor for class uk.ac.ebi.intact.model.Feature: Deprecated. Use the full constructor instead
FileGenerator - class uk.ac.ebi.intact.application.dataConversion.FileGenerator.: This class is the main application class for generating a flat file format from the contents of a database.
FileGenerator(IntactHelper, DataBuilder) - Constructor for class uk.ac.ebi.intact.application.dataConversion.FileGenerator
fileInput - Variable in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: the both ManagerFiles -> 1 input file and 1 output file for each execution of BLAST or FASTA
fileName - Variable in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
fileOutput - Variable in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
FillBioSrcFormAction - class uk.ac.ebi.intact.application.editor.struts.action.biosrc.FillBioSrcFormAction.: Populates BioSource form for display.
FillBioSrcFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.biosrc.FillBioSrcFormAction
FillCvFormAction - class uk.ac.ebi.intact.application.editor.struts.action.FillCvFormAction.: Fills the form with values for ac, short label and full name.
FillCvFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.FillCvFormAction
filledProteinFastaFile(String) - Method in class uk.ac.ebi.intact.util.ProteinFastaDownload: This method * delete all files in the directory * creates the proteinFastaDownload File and full it with the search result * calls the format database method at the end to make available the process with a sequence analysis algorithm like Blast or Fasta
FillExperimentFormAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.FillExperimentFormAction.: Populates experiment form for display.
FillExperimentFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.FillExperimentFormAction
FillInteractionFormAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.FillInteractionFormAction.: Populates Interaction form for display.
FillInteractionFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.FillInteractionFormAction
FillResultFormAction - class uk.ac.ebi.intact.application.editor.struts.action.FillResultFormAction.: Sets up the editor form type using the selected editor topic.
FillResultFormAction() - Constructor for class uk.ac.ebi.intact.application.editor.struts.action.FillResultFormAction
fillSearchResult(DynaBean) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Popluate the given form with search result.
fillSearchResult(DynaBean) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
FillSeqFileConcatCommand(String, boolean) - Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: This method creates a random file name in the good directory: input files and output files are managed in two different directories.
FilterAction - class uk.ac.ebi.intact.application.statisticView.struts.controller.FilterAction.: Implementation of Action that validates a visualize submisson.
FilterAction() - Constructor for class uk.ac.ebi.intact.application.statisticView.struts.controller.FilterAction
FilterBean - class uk.ac.ebi.intact.application.statisticView.struts.view.FilterBean.
FilterBean(String, String) - Constructor for class uk.ac.ebi.intact.application.statisticView.struts.view.FilterBean
FilterForm - class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm.: Form bean for the main form of the view.jsp page.
FilterForm() - Constructor for class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
finalize() - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag: close all sql-statements properly - should be called once FastGoDag instance is not needed any more -> don't trust the automatic finalisation!
finalize() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools: if instance of DbTools.java is no longer in use
FIND_MORE_DETAILS - Static variable in class uk.ac.ebi.intact.model.Constants: The name to identify that a search is required for detailed objects (ie not from a search JSP).
find(Object) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
find(Object) - Method in interface uk.ac.ebi.intact.persistence.DAO: This method performs an object-based search.
find(String, String, String) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: This method searches the DB based on the information in the parameters.
find(String, String, String) - Method in interface uk.ac.ebi.intact.persistence.DAO: This method performs a simple search based on the object type to search over, the parameter name and the search value.
findBySQL(String, String) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: This method allows submission of a query by straight SQL string.
findBySQL(String, String) - Method in interface uk.ac.ebi.intact.persistence.DAO: This method allows submission of a query by straight SQL string.
findColumnValues(String, String[]) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: This method provides a means of obtaining particular values of a persistent object without retrieving the whole object itself.
findColumnValues(String, String[]) - Method in interface uk.ac.ebi.intact.persistence.DAO: This method provides a means of obtaining particular values of a persistent object without retrieving the whole object itself.
finishTransaction() - Method in class uk.ac.ebi.intact.business.IntactHelper: ends a busines transaction.
flybaseDatabase - Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
formatProteinFastaFile(File) - Method in class uk.ac.ebi.intact.util.ProteinFastaDownload: If we need to format the protein database in a Fasta format file, before processing a biological software like Blast or Fasta, the corresponding command line must be runned by this method.
FORWARD_ACC_ERROR - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: command error from the page which display the list of accession number.
FORWARD_BINARY_ACTION - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Forward to the Action responsible for setting up a view when using the search box
FORWARD_DETAIL - Static variable in class uk.ac.ebi.intact.model.Constants: Used in various action classes to define where to forward to on different conditions.
FORWARD_DETAILS_ACTION - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Forward to the Action responsible for setting up a view when using the search box
FORWARD_DISPATCHER_ACTION - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Key to the dispatcher action.
FORWARD_END_SESSION - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: the key to forward on the welcome session when a session is put down.
FORWARD_ERROR - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: The key to some errors.
FORWARD_FAILURE - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: command error from the page which display the list of accession number.
FORWARD_FAILURE - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Used in various action classes to define where to forward to on different conditions.
FORWARD_FAILURE - Static variable in class uk.ac.ebi.intact.model.Constants: Used in various action classes to define where to forward to on different conditions.
FORWARD_MATCHES - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Used as a key to identify a page to display when matches are found from a search.
FORWARD_NO_MATCHES - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Used as a key to identify a page to display when no matches are found from a search.
FORWARD_NO_MATCHES - Static variable in class uk.ac.ebi.intact.model.Constants: used as a key to identify a page to display when no matches are found from a search
FORWARD_RESULT - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: Forward to the result page which another template of the idseq page.
FORWARD_RESULTS - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Forward to the Action responsible for setting up a view when clicking on a link
FORWARD_SESSION_LOST - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Forward to the results page.
FORWARD_SINGLE_ACTION - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Forward to the Action responsible for setting up a view when clicking on a link
FORWARD_SUCCESS - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: The key to success action.
FORWARD_SUCCESS - Static variable in class uk.ac.ebi.intact.model.Constants: Used in various action classes to define where to forward to on different conditions.
FORWARD_SUCCESS_ID - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: The key to success ProteinSearchAction action.
FORWARD_SUCCESS_SEQ - Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants: The key to success SequenceSimilarityAction action.
FORWARD_WARNING - Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants: Used as a key to identify a page to display when warning are raised from a search.
ForwardConstants - interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants.: Forward constants for the editor.
fullName - Variable in class uk.ac.ebi.intact.model.Institution: TODO comments
fullName - Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl: The full name or a minimal description of the object.
fusion(FusionableGraph) - Method in class uk.ac.ebi.intact.application.graph2MIF.conversion.FusionableGraph: Fusion a graph to the current one.
For each edge of the new graph we check if it exists in the current one.
If the edge already exists : continue.
If not, we check if the two Nodes of the edge already exists in the current graph : if the node exists, update the edge with its reference
if not add it to the current graph finally we add the up-to-date edge to the current graph
fusion(InteractionNetwork) - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: Fusion a interaction network to the current one.
For each edge of the new network we check if it exists in the current one.
If the edge already exists : continue.
If not, we check if the two Nodes of the edge already exists in the current network : if the node exists, update the edge with its reference
if not add it to the current network finally we add the up-to-date edge to the current network
FusionableGraph - class uk.ac.ebi.intact.application.graph2MIF.conversion.FusionableGraph.: Extention of a Graph allowing to fusion two Graph.
FusionableGraph() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.conversion.FusionableGraph

G

geneNameAliasType - Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
geneNameSynonymAliasType - Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
generateFile(String) - Method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator: Generates the file from the previously created data.
GenerateImage - class uk.ac.ebi.intact.application.hierarchView.business.servlet.GenerateImage.: Purpose:
For a bean given in the session, forward an image to be displayed.
GenerateImage() - Constructor for class uk.ac.ebi.intact.application.hierarchView.business.servlet.GenerateImage
generatePsiData(String, String) - Static method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator: Generates a PSI MI formatted file for a searchPattern.
generateTables() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools: generation of all the tables for goDensity
generateXYChart(StatisticsBean, int, String, String, String, HttpSession, PrintWriter) - Static method in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
getAbstractViewBean(Collection, IntactUserIF, String) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.SingleResultAction
getAbstractViewBean(Collection, IntactUserIF, String) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.DetailsResultAction
getAbstractViewBean(Collection, IntactUserIF, String) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.BinaryResultAction
getAbstractViewBean(Collection, IntactUserIF, String) - Method in class uk.ac.ebi.intact.application.search2.struts.controller.AbstractResulltAction
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns accession number.
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.AbstractIntDisplayWrapper
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean
getAc() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the accession number
getAc() - Method in class uk.ac.ebi.intact.model.SequenceChunk
getAc() - Method in interface uk.ac.ebi.intact.model.IntactObject
getAc() - Method in class uk.ac.ebi.intact.model.IntactObjectImpl
getAc() - Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy: Implements IntactObject's methods
getAc() - Method in class uk.ac.ebi.intact.simpleGraph.Node
getAc() - Method in interface uk.ac.ebi.intact.simpleGraph.NodeI
getAc() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the timestamp
getAcc() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean: returns the accession number
getAcc() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.ProteinDecorator: Transform the accession number contained by the SrsResultBean bean beiing displayed by the Display:* tag into a link.
getAcLink() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns a link to the search application.
getAction() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntHoldDisplayWrapper
getAction() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntDisplayWrapper
getAction() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.AbstractIntDisplayWrapper: Subclasses must provide the implementation for this method.
getAction() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
getAction() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm
getAction() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm
getActiveInstances() - Method in class uk.ac.ebi.intact.model.InteractorImpl
getActiveInstances() - Method in interface uk.ac.ebi.intact.model.Interactor
getActiveInstances() - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
getAddBioSourceMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
getAddDatabaseMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
getAdditionalCg1() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getAdditionalCg2() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getAddProteinRoleMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns the add menu for a Protein role.
getAddTopicMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the add menu for annotations.
getAddXrefMenus() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the add menu for xrefs.
getAliases() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getAliases() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getAliases() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getAll() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet: Allows to get all HashSets for all keys and all keys itself.
getAllChilds() - Method in class uk.ac.ebi.intact.model.CvGoNode: This CvGoNode can have children - the equivalent method is implemented in the super class CvDagObject by "getChilds" method
This method should provide ALL children (subchildren) of the node,
that means also the children of the children of the children etc.
getAllChilds(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
getAllChilds(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag
getAllProteinIntAct(IntactHelper) - Method in class uk.ac.ebi.intact.util.ProteinFastaDownload: get all protein sequences in a Fasta format (in a String object)
getAnEntry(String) - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: From a given URL, returns a string of a SPTR entry.
getAnEntry(String) - Method in class uk.ac.ebi.intact.util.UpdateProteins
getAnnotatedObject() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the Annotated object.
getAnnotatedObjects() - Method in class uk.ac.ebi.intact.model.Reference
getAnnotation(CommentBean) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns an Annotation constructed from the given bean.
getAnnotation(CommentBean) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getAnnotation(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Updates the internal annotation with the new values from the form.
getAnnotations() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns a collection of CommentBean objects.
getAnnotations() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getAnnotations() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getAnnotations() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getAnnotationText() - Method in class uk.ac.ebi.intact.model.Annotation
getApplicationPath() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getApplicationPath() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getApplicationPath() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
getAuthorizedBehaviour(String) - Static method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator: Create a collection of LabelValueBean object specific of an highlightment method from a properties file
getAuthors() - Method in class uk.ac.ebi.intact.model.Reference
getBait() - Method in class uk.ac.ebi.intact.model.InteractionImpl: Returns the first components marked as bait.
getBait() - Method in interface uk.ac.ebi.intact.model.Interaction
getBait() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getBait3utr() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getBait5utr() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getBaitOther() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getBaitPrey() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getBehaviour() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getBehaviour() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getBehaviour() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm: Return the behaviour value.
getBinaryInteractions(List, boolean) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag: For a Set of GoIds the
- possible binary Interactions and
- all real existing Interactions which (could) occur in or within the two goIds are calculated and encapsulated in GoGoDensities.
getBinaryViewBean(Collection, String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory: Returns the appropriate view bean for given Collection object.
getBindingDomains() - Method in class uk.ac.ebi.intact.model.Component
getBioSource() - Method in class uk.ac.ebi.intact.model.InteractorImpl
getBioSource() - Method in interface uk.ac.ebi.intact.model.Interactor
getBioSource() - Method in class uk.ac.ebi.intact.model.Experiment
getBioSource() - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy: Implements AnnotatedObject methods
getBioSourceAc() - Method in class uk.ac.ebi.intact.model.InteractorImpl
getBioSourceAc() - Method in interface uk.ac.ebi.intact.model.Interactor
getBioSourceAc() - Method in class uk.ac.ebi.intact.model.Experiment
getBioSourceAc() - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
getBioSourceByName(String) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method is used for searching by scientific name (provided that name is unique).
getBioSourceByTaxId(String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Searches for a BioSource given a tax ID.
getBioSources() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
GetBooleanIntactId() - Method in interface uk.ac.ebi.intact.application.intSeq.business.CallingSrsIF: check if the protein topic still corresponds to an Intact entry.
GetBooleanIntactId() - Method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: later, a method will allow to look for an IntAct entry from a protein topic (no SRS process in this case)
getBoundDomain() - Method in class uk.ac.ebi.intact.model.Feature
getBoundDomainAc() - Method in class uk.ac.ebi.intact.model.Feature
getBufferedImage() - Method in class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage
getBytesFromFile(File) - Method in class uk.ac.ebi.intact.util.fileParsing.SerializationHelper
getCategory() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoResponse
getCategory() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
getCconf() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getCellType() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
getCellTypeMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean: The cell type menu list.
getCentralInteractors() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCentralProtein() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCentralProteinAC() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCentralProteins() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCg1() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getCg2() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getChildren() - Method in class uk.ac.ebi.intact.model.CvDagObject
getChilds(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
getChilds(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag
getChunkedSingleViewBean(AnnotatedObject, String, String, int, int) - Method in class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory
getChunkIndexHtml(Writer, AnnotatedObject, Set, String, String, int, int, int, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager
getClassLoader() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getClassLoader() - Method in interface uk.ac.ebi.intact.persistence.DAOSource
getClassName(String) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the class name associated with the given topic.
getColumnData(String, String[]) - Method in class uk.ac.ebi.intact.business.IntactHelper: Allows access to column data rather than whole objects.
GetCommandExecResponse() - Method in interface uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearchIF: keep inform the action whether the command line was executed well or not.
GetCommandExecResponse() - Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: keep inform the Action Class whether the command line was executed well or not.
getCommandMessage() - Method in class uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException: Keeps inform about the srs execution.
getCommandMessage() - Method in class uk.ac.ebi.intact.application.intSeq.exception.BlastException: Keeps inform about the blast execution.
getComponent() - Method in class uk.ac.ebi.intact.model.Feature
getComponent(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getComponent1() - Method in class uk.ac.ebi.intact.simpleGraph.Edge
getComponent1() - Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
getComponent2() - Method in class uk.ac.ebi.intact.simpleGraph.Edge
getComponent2() - Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
getComponentAc() - Method in class uk.ac.ebi.intact.model.Feature
getComponents() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getComponents() - Method in interface uk.ac.ebi.intact.model.Interaction
getComponents() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getComponents() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getComponentsByRole(CvComponentRole) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for components given a role.
getComputedTlpContent(String) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.TulipClient: allows to compute a tlp content
getComputedTlpContent(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
getComputedTlpContent(String, String) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccess
getComputedTlpContent(String, String) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl: get the computed TLP content from tulip
getComputedTlpContent(String, String) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccess: get the computed TLP content from tulip
getCon() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools
getConfig() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getConfig() - Method in interface uk.ac.ebi.intact.persistence.DAOSource
getContent(String, String) - Static method in class uk.ac.ebi.intact.util.PropertyLoader: get the content of the property file int a String
getContextPath() - Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
getCount() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
getCountPossibleIAs() - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
getCoutInteractions() - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
getCrc64() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getCrc64() - Method in interface uk.ac.ebi.intact.model.Protein
getCrc64() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getCrc64(String) - Static method in class uk.ac.ebi.intact.util.Crc64: Returns the crc64 checksum for the given sequence.
getCreated() - Method in interface uk.ac.ebi.intact.model.IntactObject
getCreated() - Method in class uk.ac.ebi.intact.model.IntactObjectImpl
getCreated() - Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
getCriteria() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCurator() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getCurator() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getCurator() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getCuratorAc() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getCuratorAc() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getCuratorAc() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getCurrentCentralProteinCount() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getCurrentDepth() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getCurrentDepth() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getCurrentDocument() - Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder: Used to obtain a PSI Document object that is initialised and ready for use when for example later appending lists.
getCurrentExperiments() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns a list of currently edited/added experiments.
getCurrentExperiments() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getCurrentInteractions() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns a list of currently edited/added interactions.
getCurrentInteractions() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getCurrentSelection(String[]) - Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction
getCvAliasType() - Method in class uk.ac.ebi.intact.model.Alias
getCvCellCycle() - Method in class uk.ac.ebi.intact.model.BioSource
getCvCellCycleAc() - Method in class uk.ac.ebi.intact.model.BioSource
getCvCellType() - Method in class uk.ac.ebi.intact.model.BioSource
getCvCellTypeAc() - Method in class uk.ac.ebi.intact.model.BioSource
getCvCompartment() - Method in class uk.ac.ebi.intact.model.BioSource
getCvCompartmentAc() - Method in class uk.ac.ebi.intact.model.BioSource
getCvComponentRole() - Method in class uk.ac.ebi.intact.model.Component
getCvComponentRoleAc() - Method in class uk.ac.ebi.intact.model.Component
getCvDatabase() - Method in class uk.ac.ebi.intact.model.Xref
getCvDatabaseAc() - Method in class uk.ac.ebi.intact.model.Xref
getCvDevelopmentalStage() - Method in class uk.ac.ebi.intact.model.BioSource
getCvDevelopmentalStageAc() - Method in class uk.ac.ebi.intact.model.BioSource
getCvEvidenceType() - Method in class uk.ac.ebi.intact.model.Evidence
getCvEvidenceTypeAc() - Method in class uk.ac.ebi.intact.model.Evidence
getCvFeatureIdentification() - Method in class uk.ac.ebi.intact.model.Feature
getCvFeatureIdentificationAc() - Method in class uk.ac.ebi.intact.model.Feature
getCvFeatureType() - Method in class uk.ac.ebi.intact.model.Feature
getCvGoNode(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag: get a single CvGoNode by a GoId String
getCvIdentification() - Method in class uk.ac.ebi.intact.model.Experiment
getCvIdentificationAc() - Method in class uk.ac.ebi.intact.model.Experiment
getCvInteraction() - Method in class uk.ac.ebi.intact.model.Experiment
getCvInteractionAc() - Method in class uk.ac.ebi.intact.model.Experiment
getCvInteractionType() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getCvInteractionType() - Method in interface uk.ac.ebi.intact.model.Interaction
getCvInteractionType() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getCvInteractionTypeAc() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getCvInteractionTypeAc() - Method in interface uk.ac.ebi.intact.model.Interaction
getCvInteractionTypeAc() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getCvJournal() - Method in class uk.ac.ebi.intact.model.JournalRef
getCvJournalAc() - Method in class uk.ac.ebi.intact.model.JournalRef
getCvModificationType() - Method in class uk.ac.ebi.intact.model.Modification
getCvModificationTypeAc() - Method in class uk.ac.ebi.intact.model.Modification
getCvProductRole() - Method in class uk.ac.ebi.intact.model.Product
getCvProductRoleAc() - Method in class uk.ac.ebi.intact.model.Product
getcvProductRoleAc(String) - Method in class uk.ac.ebi.intact.model.Product
getCvProteinForm() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getCvProteinForm() - Method in interface uk.ac.ebi.intact.model.Protein
getCvProteinForm() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getCvProteinFormAc() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getCvProteinFormAc() - Method in interface uk.ac.ebi.intact.model.Protein
getCvProteinFormAc() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getCvReferenceQualifier() - Method in class uk.ac.ebi.intact.model.ReferenceQualifier
getCvReferenceQualifierAc() - Method in class uk.ac.ebi.intact.model.ReferenceQualifier
getCvTissue() - Method in class uk.ac.ebi.intact.model.BioSource
getCvTissueAc() - Method in class uk.ac.ebi.intact.model.BioSource
getCvTopic() - Method in class uk.ac.ebi.intact.model.Annotation
getCvTopicAc() - Method in class uk.ac.ebi.intact.model.Annotation
getCvXrefQualifier() - Method in class uk.ac.ebi.intact.model.Xref
getCvXrefQualifierAc() - Method in class uk.ac.ebi.intact.model.Xref
getDagMenu(String, int) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: Returns a menu for given name without leading '.' characters.
getDAO() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource: This method returns a connection to the data source, ie in this case a broker instance which provides database connection.
getDAO() - Method in interface uk.ac.ebi.intact.persistence.DAOSource: This method returns a connection to the data source.
getDAO(String, String) - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource: Returns a connection to the data source, and connects to it using the supplied username and password.
getDAO(String, String) - Method in interface uk.ac.ebi.intact.persistence.DAOSource: Returns a connection made using the specified user details.
getDAOSource(String) - Static method in class uk.ac.ebi.intact.persistence.DAOFactory: This method returns a specific data source instance
getData() - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean.BinaryData
getDatabase() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the database name.
getDatabaseLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Returns the database with a link to show its contents in a window.
getDatabaseName() - Method in interface uk.ac.ebi.intact.application.commons.business.IntactUserI: The name of the database connected to.
getDatabaseName() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getDatabaseName() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getDatabaseName() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getDatabaseName() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getDatabaseName() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
getDataSourceName() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getDataSourceName() - Method in interface uk.ac.ebi.intact.persistence.DAOSource
getDbData(String) - Method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator: Obtains the data from the dataSource, in preparation for the flat file generation.
getDbInfo(String) - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser: Returns a list of beans created from ia_payg database.
getDbInfoSQL(String) - Method in class uk.ac.ebi.intact.application.predict.business.PredictUserPg
getDbInfoSQL(String) - Method in class uk.ac.ebi.intact.application.predict.business.PredictUserOra
getDbInfoSQL(String) - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getDbName() - Method in class uk.ac.ebi.intact.business.IntactHelper: Provides the database name that is being connected to.
getDbName() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Provides the database name that is being connected to.
getDbName() - Method in interface uk.ac.ebi.intact.persistence.DAO: Provides the database name that is being connected to.
getDbRelease() - Method in class uk.ac.ebi.intact.model.Xref
getDbUserName() - Method in class uk.ac.ebi.intact.business.IntactHelper: Provides the user name that is connecting to the DB.
getDbUserName() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Provides the user name that is connecting to the DB.
getDbUserName() - Method in interface uk.ac.ebi.intact.persistence.DAO: Provides the user name that is connecting to the DB.
getDefaultChoice() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getDefaultSource() - Static method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator: create a LabelValueBean object corresponding to the default source if it exists
getDefaultXrefQualifier() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the default xref qualifier.
getDensity() - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity: The proportion between all possilbe interactions for the two GoIds and the real existing interactions can be expressed as the density.
getDeploymentFile() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
getDes() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean: returns the description
getDescription() - Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Returns the annotated text.
getDescription() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceDecorator: Send back the desciption of the source and in case it doesn't exists, give a meaningfull message.
getDescription() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
getDescription() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
getDescription() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.ProteinDecorator: Send back the description corresponding to the accession number, and in case it doesn't exists, give a meaningfull message.
getDescription() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
getDeserializer(String, Class, QName) - Static method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate: Get Custom Deserializer
getDetailsViewBean(Collection, String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory: Returns the appropriate view bean for given Collection object.
getDirectHighlightUrl() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceDecorator: Transform the label and value data contained by the LabelValueBean beiing displayed by the Display:* tag into a link.
getDirectHighlightUrl() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
getDisplayableClassName(Class) - Static method in class uk.ac.ebi.intact.business.IntactHelper: From the real className of className, gets a displayable name.
getDisplayableClassName(Object) - Static method in class uk.ac.ebi.intact.business.IntactHelper: From the real className of an object, gets a displayable name.
getDisplayableClassName(String) - Static method in class uk.ac.ebi.intact.business.IntactHelper: From the real className of className, gets a displayable name.
getEdges() - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
getEdges() - Method in class uk.ac.ebi.intact.simpleGraph.Graph
getEditClass() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the edit class.
getEditDatabaseMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
getEditorMenus() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the editor specific menus.
getEditProteinRoleMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns the edit menu for a Protein role.
getEditState() - Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean: Returns the status of the editing state.
getEditTopicMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the topic menu for editing an existing annotation.
getEditXrefMenus() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the edit menu for xrefs.
getEmail() - Method in class uk.ac.ebi.intact.model.Person
getEmptyLink() - Static method in class uk.ac.ebi.intact.application.commons.util.XrefHelper: Returns the identifier for the empty primary id link.
getEntryCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the number of entry found in the given URL
getEntryCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getEntryProcessededCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the number of entry successfully processed.
getEntryProcessededCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getEntrySet() - Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder: Provides the set of PSI entries currently generated.
getEntrySkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the number of entry skipped during the process.
getEntrySkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getErrorFileName() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: return the filename in which have been saved all Entries which gaves us processing errors.
getErrorFileName() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getErrorMessages(boolean) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.TulipClient: Get the list of messages produce in the web service
getErrorMessages(boolean) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
getErrorMessages(boolean) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccess
getErrorMessages(boolean) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl: Allows the user to get messages produced byte the web service
getErrorMessages(boolean) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccess: Allows the user to get messages produced byte the web service
getErrors() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: return the error set
getEvidences() - Method in interface uk.ac.ebi.intact.model.BasicObject
getEvidences() - Method in class uk.ac.ebi.intact.model.BasicObjectImpl
getEvidences() - Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
getExperiment() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean
getExperiment(int) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns an ExperimentBean at given location.
getExperimentBySource(BioSource) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for an experiment given a specific BioSource.
getExperimentList() - Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder: Provides access in Document format to the current Experiment List.
getExperiments() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns a collection of ExperimentBean objects.
getExperiments() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getExperiments() - Method in interface uk.ac.ebi.intact.model.Interaction
getExperiments() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getExperiments() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getExperimentsByInstitution(Institution) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for Experiments given an Institution.
getExpressedIn() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getExpressedIn() - Method in class uk.ac.ebi.intact.model.Component
getExpressedInAc() - Method in class uk.ac.ebi.intact.model.Component
getFeatures() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getFeatures() - Method in interface uk.ac.ebi.intact.model.Protein
getFeatures() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
GetFileName() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: to get the file name only
getFilterKey() - Method in class uk.ac.ebi.intact.application.editor.exception.validation.ValidationException
getFirstNames() - Method in class uk.ac.ebi.intact.model.Person
getFirstpage() - Method in class uk.ac.ebi.intact.model.JournalRef
getFirstRow() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean: Retrieve the eldest data of the Statistics table
getFormOf() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getFormOf() - Method in interface uk.ac.ebi.intact.model.Protein
getFormOf() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getFormOfAc() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getFormOfAc() - Method in interface uk.ac.ebi.intact.model.Protein
getFormOfAc() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getFragmentend() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator: Send back the both fragment ends, for the query and the subject
getFragmentstart() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator: Send back the both fragment starts, for the query and the subject
getFtpAddress() - Method in class uk.ac.ebi.intact.model.IntactNode
getFtpDirectory() - Method in class uk.ac.ebi.intact.model.IntactNode
getFtpLogin() - Method in class uk.ac.ebi.intact.model.IntactNode
getFtpPassword() - Method in class uk.ac.ebi.intact.model.IntactNode
getFullName() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Return the full name.
getFullName() - Method in class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper: Returns the full name.
getFullName() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getFullName() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean
getFullName() - Method in class uk.ac.ebi.intact.application.predict.struts.view.ResultBean
getFullName() - Method in class uk.ac.ebi.intact.model.Institution
getFullName() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getFullName() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getFullName() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getFullName() - Method in class uk.ac.ebi.intact.util.NewtServerProxy.NewtResponse
getGNLine(String) - Method in class uk.ac.ebi.intact.util.InsertComplexGiot
getGoaBrowser() - Method in class uk.ac.ebi.intact.util.GoaTools
getGoId() - Method in class uk.ac.ebi.intact.model.CvGoNode
getGoId() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoResponse
getGoid(CvObject, String) - Static method in class uk.ac.ebi.intact.util.GoTools: Return an identifier to be used in the go flat file format for the goid: element.
getGoId1() - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
getGoId2() - Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
getGoIds() - Method in class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm: getter
getGoIdTokens(String) - Static method in class uk.ac.ebi.intact.application.goDensity.struts.business.GoTokenizer
getGoProxy() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the Go server proxy assigned for the current session.
getGoProxy() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getGoTermFullname(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
getGoTermShort(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
getGraph(String, Integer) - Static method in class uk.ac.ebi.intact.application.graph2MIF.GraphFactory: getInteractionNetwork retrieves a interactionnetwork (graph) from a given queryString and depth.
getHeader() - Method in class uk.ac.ebi.html.Helper
getHeaderBody() - Method in class uk.ac.ebi.html.Helper
getHelper() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getHelper() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getHelper() - Method in class uk.ac.ebi.intact.util.TestCaseHelper: provides a way to use the same helper object that is used to create/remove the example test data.
getHelpLink() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getHelpLink() - Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
getHelpLink() - Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean: Returns the help section.
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.ProteinSingleViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.InteractionSingleViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.ExperimentSingleViewBean
getHelpSection() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean
getHelpTag() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the help tag for the current view bean.
getHelpTag() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getHelpTag() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the help tag link for the current view bean; subclasses must override this method to return the help tag (if necessary) or else the link to the CV editor is returned.
getHelpTag() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
getHelpTag() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
getHelpTag() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
getHelpURL(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the relative link to the help page.
getHierarchViewProp(String) - Method in class uk.ac.ebi.intact.application.search2.business.IntactServiceImpl
getHierarchViewProp(String) - Method in interface uk.ac.ebi.intact.application.search2.business.IntactServiceIF: Returns a hierarchy view property for given key as a String.
getHighlightMap() - Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean: Returns the higlight map.
getHighlightmentBehaviour(String) - Static method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour: Provides a implementation of HighlightmentBehaviour from its name. for example you have an implementation of this abstract class called : ColorHighlightmentBehaviour.
getHighlightmentSource(String) - Static method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource: Provides a implementation of HighlightmentSource by its name.
getHighlightmentSources() - Static method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator: create a collection of LabelValueBean object from a properties file
getHighlightOption(String) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI: Get the value associated to the option name.
getHighlightOption(String) - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getHoldDate() - Method in class uk.ac.ebi.intact.model.SubmissionRef
getHoldExperiment(int) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns an ExperimentBean from a collection of 'hold' experiments at given location.
getHoldExperiments() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns a collection of ExperimentBean objects on hold.
getHoldInteractionCount() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Returns the number of interactions in the hold interaction collection.
getHoldInteractions() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Returns a collection of Interaction objects on hold.
getHost() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean: Instructs the bean to create an HTML content for the object that it wraps.
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.ProteinDetailsViewBean: Building the Protein view in the comtext of the wrapped Proteins' Experiment.
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.InteractionDetailsViewBean
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean: Build a copy the Experiment object - don't copy the interactions.
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean: Building the Protein view in the comtext of the wrapped Proteins' Experiment.
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean
getHTML(Writer) - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean
getHtml(Writer, Collection, Set, String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager: Write the HTML code related the the collection of object given in the the writer.
getHtml(Writer, Object, Set, String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager: Write the HTML code related the the single object given in the the writer.
getHtmlCodeOption(HttpSession) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource: Return the html code for specific options of the source to be integrated in the highlighting form.
getHtmlCodeOption(HttpSession) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource: Return the html code for specific options of the source to integrate int the highlighting form.
getHtmlVersion(String, String, String) - Static method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag: Returns HTML code snippet for use in non JSP pages.
getId() - Method in class uk.ac.ebi.intact.application.editor.util.LockManager.LockObject
getId() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
getId() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate: -------------------------------------------------------- Methods - Accessors
getId() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceDecorator: Transform the label and value data contained by the LabelValueBean beiing displayed by the Display:* tag into a link.
getId() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
getId() - Static method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch: Returns the unique id based on the current time; the ids are unique for a session.
getId() - Static method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: Returns the unique id based on the current time; the ids are unique for a session.
getId() - Method in interface uk.ac.ebi.intact.simpleGraph.BasicGraphI
getId() - Method in class uk.ac.ebi.intact.simpleGraph.BasicGraph
getIdent() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
getIdentMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: The idetification menu list.
getImageBean() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getImageBean() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getImageBean() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.DrawGraph: Create an Container with the image and the HTML MAP code.
getImageData() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
getImageDimension() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: Return the object ImageDimension which correspond to the graph
getImageHeight() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
getImageMap(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage
getImageWidth() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
getInstance() - Static method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the only instance of this class using the default resources file.
getInstance() - Static method in class uk.ac.ebi.intact.application.editor.util.MenuManager: Returns only instance of this class.
getInstance() - Static method in class uk.ac.ebi.intact.application.editor.util.LockManager
getInstance() - Static method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag: get a instance of FastGoDag -> it's a singleton
getInstance() - Static method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools
getInstance() - Static method in class uk.ac.ebi.intact.application.predict.util.PredictLogger: Returns the only instance of this class.
getInstance() - Static method in class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory: Returns the only instance of this class.
getInstance() - Static method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager: Returns the only instance of this class.
getInstance() - Static method in class uk.ac.ebi.intact.util.StatisticsDataSet
getInstance(String) - Static method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the only instance of this class using given resources file.
getInstance(String) - Static method in class uk.ac.ebi.intact.util.StatisticsDataSet
getInstitution() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the Institution.
getInstitution() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getInstitution() - Method in class uk.ac.ebi.intact.business.IntactHelper: Allow the user not to know about the it's Institution, it has to be configured once in the properties file: ${INTACTCORE_HOME}/config/Institution.properties and then when calling that method, the Institution is either retreived or created according to its shortlabel.
getInstitution() - Method in class uk.ac.ebi.intact.model.Person
getInstitutionAc() - Method in class uk.ac.ebi.intact.model.Person
getInstitutions() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getIntactacc() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator: Transform the intact accession number contained by the SimilarityResultBean beiing displayed by the Display:* tag into a link, which will refer to the Search Application.
getIntactService() - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Returns the only instance of Intact Service instance.
getIntactTypes() - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns a collection of Intact types.
getIntactUser(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction: Returns the Intact User instance saved in a session for given Http request.
getIntactUser(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction: Returns the Intact User instance saved in a session for given Http request.
getIntactUser(HttpSession) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction: Returns the Intact User instance saved in a session.
getIntactUser(HttpSession) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Returns the Intact User instance saved in a session.
getIntactUser(HttpSession) - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Returns the Intact User instance saved in a session.
getInteger(String) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Retrieves the resource for given key from the editor resource file as an int.
getInter() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
getInteraction() - Method in class uk.ac.ebi.intact.model.Product
getInteraction() - Method in class uk.ac.ebi.intact.model.Component
getInteractionAc() - Method in class uk.ac.ebi.intact.model.Product
getInteractionAc() - Method in class uk.ac.ebi.intact.model.Component
getInteractionAc(String) - Method in class uk.ac.ebi.intact.model.Product
getInteractionLimit() - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: A convenient method to return the interaction limit for JSPs.
getInteractionMenus(int) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: Returns the menus for the Interaction editor.
getInteractionNetwork() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getInteractionNetwork() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getInteractionPageLimit() - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: A convenient method to return the interaction per page limit for JSPs.
getInteractions() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Returns a collection of Interactions for the current experiment.
getInteractions() - Method in class uk.ac.ebi.intact.model.Experiment
getInteractions() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getInteractionsByType(CvInteractionType) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for interactions given a type.
getInteractionType() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
getInteractionTypeMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: The interaction type menu list.
getInteractor() - Method in class uk.ac.ebi.intact.model.Product
getInteractor() - Method in class uk.ac.ebi.intact.model.Component
getInteractor() - Method in class uk.ac.ebi.intact.simpleGraph.Node
getInteractorAc() - Method in class uk.ac.ebi.intact.model.Product
getInteractorAc() - Method in class uk.ac.ebi.intact.model.Component
getInteractorAc(String) - Method in class uk.ac.ebi.intact.model.Product
getInteractorBySource(Class, BioSource) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method is used for obtaining an interactor given a specific BioSource and the subclass of Interactor that is to be searched for.
getInteractorList() - Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder: Provides access in Document format to the current Interactor List.
getInteractors(IntactHelper) - Method in class uk.ac.ebi.intact.model.CvGoNode
getInteractors(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
getInteractors(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag
getInterMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: The interaction menu list.
getItemCount() - Method in class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader
getJDBCConnection() - Method in class uk.ac.ebi.intact.business.IntactHelper: Gets the underlying JDBC connection.
getJDBCConnection() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO: Method to get a direct SQL connection which can be used by JDBC
getJspPath() - Static method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag: The path to the JSP documentation page.
getKD() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
getKD() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getKD() - Method in interface uk.ac.ebi.intact.model.Interaction
getKD() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy: Implements Interaction's methods
getKey() - Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean: Returns the key assigned to this bean.
getKey() - Method in class uk.ac.ebi.intact.util.Key
getKeyMethodMap() - Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction: Provides the mapping from resource key to method name.
getKeyMethodMap() - Method in class uk.ac.ebi.intact.application.editor.struts.action.SidebarDispatchAction: Provides the mapping from resource key to method name.
getKeyMethodMap() - Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionDispatchAction: Provides the mapping from resource key to method name.
getKeyMethodMap() - Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentDispatchAction: Provides the mapping from resource key to method name.
getKeys() - Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
getKeys() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getKeys() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getKeysFromIntAct(String, HttpSession) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource: Return a collection of keys specific to the selected protein and the current source.
getKeysFromIntAct(String, HttpSession) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource: Return a collection of keys specific to the selected protein and the current source.
getLabel() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
getLabel() - Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterBean
getLabel() - Method in interface uk.ac.ebi.intact.simpleGraph.BasicGraphI
getLabel() - Method in class uk.ac.ebi.intact.simpleGraph.BasicGraph
getLastCheckId() - Method in class uk.ac.ebi.intact.model.IntactNode
getLastProvidedDate() - Method in class uk.ac.ebi.intact.model.IntactNode
getLastProvidedId() - Method in class uk.ac.ebi.intact.model.IntactNode
getLastRow() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean: Retrieve the latest data of the Statistics table
getLastTimestamp() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean: Retrieve the latest timestamp of the Statistics table
getLine() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getLineBrowser() - Method in class uk.ac.ebi.intact.util.InsertComplexGiot
getLineSeparator() - Method in class uk.ac.ebi.intact.util.ProteinFastaDownload: get the line separator string.
GetLineSeparator() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: get the line separator string.
getLink(String, String) - Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean: Returns a link to display a read only window.
getLoadMethods() - Method in class uk.ac.ebi.html.Helper: Returns the value previously set by setLoadMethods
getLock() - Method in class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper
getLock(String) - Method in class uk.ac.ebi.intact.application.editor.util.LockManager: Returns the lock object for given id if it exists.
getLockDate() - Method in class uk.ac.ebi.intact.application.editor.util.LockManager.LockObject
getLocks() - Method in class uk.ac.ebi.intact.application.editor.util.LockManager: Returns a clone of the current locks.
getLogger() - Method in class uk.ac.ebi.intact.business.IntactHelper
getLogger() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getLogger() - Method in interface uk.ac.ebi.intact.persistence.DAOSource: Returns the log destination being used for this data source
getMapCode() - Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
getMaxCentralProtein() - Static method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
getMaxChunk() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean
getMaximalDepth() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getMenu(String, int) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory: Returns a menu for given name.
getMenuFactory() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Allows access to menu factory.
getMenuList(Class, IntactHelper) - Method in class uk.ac.ebi.intact.application.editor.util.MenuManager: Return a Vector of all shortLabels of the class, e.g.
getMessageArgs() - Method in class uk.ac.ebi.intact.application.editor.exception.BaseException: Returns an array of arguments to pass to place holders application resources file.
getMessageKey() - Method in class uk.ac.ebi.intact.application.editor.exception.BaseException: Returns the message key
getMessages() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm: return the error set
getMethod() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
getMethodClass() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getMethodClass() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getMethodLabel() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getMethodLabel() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getMIF(Graph) - Method in class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2UnfoldedMIF: The only public function.
getMIF(Graph) - Method in class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2FoldedMIF: The only public function.
getMIF(String, Integer, Boolean) - Method in class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSService: getMIF is the only method which is necessary for access.
getMIF(String, Integer, Boolean) - Method in interface uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWS: getMIF is the only method which is necessary.
getMinimalDepth() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getModification() - Method in class uk.ac.ebi.intact.model.Range
getModificationAc() - Method in class uk.ac.ebi.intact.model.Range
getModifications() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getModifications() - Method in interface uk.ac.ebi.intact.model.Protein
getModifications() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
getMoreRecentStatisticsDate() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
getMw() - Method in class uk.ac.ebi.intact.model.Complex
getName() - Method in class uk.ac.ebi.intact.model.Alias
getName() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoResponse
getName() - Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
getNestedMessage() - Method in class uk.ac.ebi.intact.application.dataConversion.DataConversionException
getNestedMessage() - Method in class uk.ac.ebi.intact.business.IntactException
getNestedMessage() - Method in class uk.ac.ebi.intact.persistence.UpdateException: this method obtains any information from within nested exceptions that have been passed on.
getNestedMessage() - Method in class uk.ac.ebi.intact.persistence.SearchException
getNestedMessage() - Method in class uk.ac.ebi.intact.persistence.CreateException: this method obtains any information from within nested exceptions that have been passed on.
getNestedMessage() - Method in class uk.ac.ebi.intact.persistence.DataSourceException
getNestedMessage() - Method in class uk.ac.ebi.intact.persistence.TransactionException
getNewSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Returns a session and create a new one if necessary.
getNewtProxy() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the Newt server proxy assigned for the current session.
getNewtProxy() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getNextSequence() - Method in class uk.ac.ebi.intact.persistence.PostgresSequenceManager
getNextSequence() - Method in class uk.ac.ebi.intact.persistence.OracleSequenceManager
getNextSequence() - Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: Called by the vendor specific implementation to obtain the SQL statement which allows to get the next unique ID.
getNode1() - Method in class uk.ac.ebi.intact.simpleGraph.Edge
getNode1() - Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
getNode2() - Method in class uk.ac.ebi.intact.simpleGraph.Edge
getNode2() - Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
getNodes() - Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
getNodes() - Method in class uk.ac.ebi.intact.simpleGraph.Graph
getNorient() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getNumberOfBinaryInteractions() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of interactions with two interactors, now available in the IntAct Database
getNumberOfComplexInteractions() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of interactions with more than two interactors, now available in the IntAct Database
getNumberOfExperiments() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of experiments now available in the IntAct Database
getNumberOfGoTerms() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of terms in the Controlled Vocabulary table now available in the IntAct Database
getNumberOfInteractions() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: Returns the number of interactions for this experiment.
getNumberOfInteractions() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of interactions now available in the IntAct Database
getNumberOfProteins() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the number of proteins now available in the IntAct Database
getObject() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
getObjectByAc(Class, String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Return an Object by ac for given class.
getObjectByAc(Class, String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getObjectByAc(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Return an Object by classname and ac.
getObjectByKey(Object) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
getObjectByLabel(Class, String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Return an Object by classname and shortLabel.
getObjectByLabel(Class, String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getObjectByLabel(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Return an Object by classname and shortLabel.
getObjectByLabel(String, String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Return an Object by classname and shortLabel.
getObjectByLabel(String, String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getObjectByName(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method retrieves an intact object, given a class and the object's full name (provided that name is unique).
getObjectByValue(Object) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
getObjectByXref(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Searches for a unique Object by classname and Xref.
getObjects() - Method in class uk.ac.ebi.intact.util.ObjectSet
getObjectsByAlias(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for objects by any alias with the specified name.
getObjectsByAlias(Class, String, CvAliasType) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for objects by any alias with the specified name.
getObjectsByAlias(Class, String, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for objects by any alias with the specified name.
getObjectsByXref(Class, String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Searches for objects by classname and Xref.
getOrderedNodes() - Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork: return a list of nodes ordered
getOrganism() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
getOrganism() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getOrganism() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
getOrganismMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean: The organism menu list.
getOrganismMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: The organism menu list.
getOwner() - Method in class uk.ac.ebi.intact.application.editor.util.LockManager.LockObject
getOwner() - Method in interface uk.ac.ebi.intact.model.BasicObject
getOwner() - Method in class uk.ac.ebi.intact.model.BasicObjectImpl
getOwner() - Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
getOwner(String) - Method in class uk.ac.ebi.intact.application.editor.util.LockManager: Returns the owner for given id if it exists.
getOwnerAc() - Method in interface uk.ac.ebi.intact.model.BasicObject
getOwnerAc() - Method in class uk.ac.ebi.intact.model.BasicObjectImpl
getOwnerAc() - Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
getOwnerPrefix() - Method in class uk.ac.ebi.intact.model.IntactNode
getP1() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getP2() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getParameters() - Method in class uk.ac.ebi.intact.model.Evidence
getParentAc() - Method in class uk.ac.ebi.intact.model.SequenceChunk
getParentAc() - Method in class uk.ac.ebi.intact.model.Alias
getParentAc() - Method in class uk.ac.ebi.intact.model.Xref
getParents() - Method in class uk.ac.ebi.intact.model.CvDagObject
getParsingExceptions() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives all Exceptions that have been raised during the last processing.
getPassword() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getPassword() - Method in interface uk.ac.ebi.intact.persistence.DAOSource
GetPathFile() - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: to get the absolute path of a file
getPercentage() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the percentage identity
getPercentageidentity() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator: Send back the percentage identity retrieved in the fasta output file and in case it doesn't exists, give a meaningfull message.
getPort(Class) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator: For the given interface, get the stub implementation.
getPosFrom() - Method in class uk.ac.ebi.intact.model.Range
getPostalAddress() - Method in class uk.ac.ebi.intact.model.Institution
getPosTo() - Method in class uk.ac.ebi.intact.model.Range
getPredictUser(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.predict.struts.framework.AbstractPredictAction: Returns the Intact User instance saved in a session for given Http request.
getPrey3utr() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getPrey5utr() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getPreyBait() - Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
getPrimaryId() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the primary id.
getPrimaryId() - Method in class uk.ac.ebi.intact.model.Xref
getPrimaryIdLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the primary id as a link.
getPrimaryIdLink(Xref) - Static method in class uk.ac.ebi.intact.application.commons.util.XrefHelper: Return the primary id as a link.
getProducts() - Method in class uk.ac.ebi.intact.model.InteractorImpl
getProducts() - Method in interface uk.ac.ebi.intact.model.Interactor
getProducts() - Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
getProperties(String) - Static method in class uk.ac.ebi.intact.util.Utilities: Initialise parameters from the properties file.
getProperty(String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: returns a value stored in a properties file.
getProperty(String, String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: eturns a value stored in a properties file, eventually a default value.
getProtein() - Method in class uk.ac.ebi.intact.model.Feature
getProtein(int) - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns a ProteinBean at given location.
getProteinAc() - Method in class uk.ac.ebi.intact.model.Feature
getProteinByXref(Xref) - Method in class uk.ac.ebi.intact.business.IntactHelper: Search for Protein given a cross reference.
getProteinCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of all potential protein (i.e.
getProteinCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getProteinCreatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of created protein
getProteinCreatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getProteinParseException() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the last protein parse exception.
getProteinParseException() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getProteins() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns a collection of ProteinBean objects.
getProteins() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getProteinSkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of protein which gaves us errors during the processing.
getProteinSkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getProteinsSrsUrl(String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
getProteinUpdatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of updated protein
getProteinUpdatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getProteinUpToDateCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of up-to-date protein (i.e.
getProteinUpToDateCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getProtocol() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm
getPubMedLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean: Returns the pubmed id as a link.
getPubmidId() - Method in class uk.ac.ebi.intact.model.JournalRef
getQualifier() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the reference qualifier.
getQualifierLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Returns the qualifier with a link to show its contents in a window.
getQuery() - Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
getQueryFragmentBegin() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the start of the query fragment
getQueryFragmentEnd() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the end of the query fragment.
getQueryString() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getQueryString() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getQueryString() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
GetRandFileName(Object) - Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles: Generate a file name randomly, with a long added at the end of the name.
getRange() - Method in class uk.ac.ebi.intact.model.Modification
getRangeAc() - Method in class uk.ac.ebi.intact.model.Modification
getRanges() - Method in class uk.ac.ebi.intact.model.Feature
getRank() - Method in class uk.ac.ebi.intact.application.predict.struts.view.ResultBean
getReadOnly() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: False as this object is editable.
getReadOnly() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
getRealClassName() - Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy: Return the class of the real subject.
getRealClassName(Object) - Static method in class uk.ac.ebi.intact.business.IntactHelper: Gives the Object classname, give the real object class name if this is a VirtualProxy class
getRealIntactObject(IntactObject) - Static method in class uk.ac.ebi.intact.business.IntactHelper: Returns the real object wrapped around the proxy for given object of IntactObjectProxy type.
getReference() - Method in class uk.ac.ebi.intact.model.ReferenceQualifier
getReference() - Method in class uk.ac.ebi.intact.model.SubmissionRef
getReferenceAc() - Method in class uk.ac.ebi.intact.model.ReferenceQualifier
getReferenceAc() - Method in class uk.ac.ebi.intact.model.SubmissionRef
getReferences() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getReferences() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getReferences() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getRejected() - Method in class uk.ac.ebi.intact.model.IntactNode
getRelatedExperiment() - Method in class uk.ac.ebi.intact.model.Experiment
getRelatedExperimentAc() - Method in class uk.ac.ebi.intact.model.Experiment
getRelatedExperiments(Object) - Method in class uk.ac.ebi.intact.business.IntactHelper: Used to obtain the Experiments related to a search object.
getRelations(BasicObject) - Method in class uk.ac.ebi.intact.business.IntactHelper: This method obtains the nearest neighbours (ie the next level of related objects) to a given intact object.
getReleased() - Method in class uk.ac.ebi.intact.model.InteractionImpl
getReleased() - Method in interface uk.ac.ebi.intact.model.Interaction
getReleased() - Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
getReleaseNumber() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the release number.
getResource(String) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Retrieves the resource for given key from the editor resource file.
getRole() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getRoot() - Method in class uk.ac.ebi.intact.model.CvDagObject: TODO coments
getRootCause() - Method in class uk.ac.ebi.intact.application.dataConversion.DataConversionException
getRootCause() - Method in class uk.ac.ebi.intact.application.editor.exception.BaseException: Return the root exception, if one exists.
getRootCause() - Method in class uk.ac.ebi.intact.business.IntactException
getRootCause() - Method in class uk.ac.ebi.intact.persistence.UpdateException
getRootCause() - Method in class uk.ac.ebi.intact.persistence.SearchException
getSearchClass() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getSearchClass() - Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
getSearchCritera() - Method in interface uk.ac.ebi.intact.application.commons.search.SearchHelperI: Return a collection of search criteria.
getSearchCritera() - Method in class uk.ac.ebi.intact.application.commons.search.SearchHelper
getSearchQuery() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the latest search query.
getSearchQuery() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getSearchResult() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the search result as a list.
getSearchResult() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getsearchResults() - Method in class uk.ac.ebi.intact.persistence.ObjectSearch: Returns the entire result vector
getSearchString() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm
getSearchString() - Method in class uk.ac.ebi.intact.persistence.ObjectSearch: Returns the search string used to get the result set.
getSearchUrl() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getSearchUrl() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getSearchURL(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the relative link to the search application.
getSearchURL(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.predict.business.PredictService: Returns the relative link to the search application.
getSearchUrl(String, boolean) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getSearchUrl(String, boolean) - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getSearchValue() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getSearchValue() - Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
getSecondaryId() - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Return the secondary id.
getSecondaryId() - Method in class uk.ac.ebi.intact.model.Xref
getSection() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
getSelectedChunk() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getSelectedChunk() - Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
getSelectedChunk() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean
getSelectedKey() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getSelectedKey() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getSelectedTopic() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
getSelectedTopic() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getSequence() - Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
getSequence() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
getSequence() - Method in class uk.ac.ebi.intact.model.ProteinImpl
getSequence() - Method in interface uk.ac.ebi.intact.model.Protein
getSequence() - Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy: Implements Protein's methods
getSequenceChunk() - Method in class uk.ac.ebi.intact.model.SequenceChunk
GetSequenceFasta() - Method in interface uk.ac.ebi.intact.application.intSeq.business.CallingSrsIF: return the sequence, which allows to run a multi-alignment algorithm (like Fasta or Blast).
GetSequenceFasta() - Method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs: Wgetz execution + parsing of the WGETZ output file get the sequence one by one in a fasta format string because the SequenceSimilarityAction requires a protein sequence in a String format (don't forget that the Fasta Format is required)
getSequenceIndex() - Method in class uk.ac.ebi.intact.model.SequenceChunk
getSequenceSrsUrl(String) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
getSerializer(String, Class, QName) - Static method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate: Get Custom Serializer
getService() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction: Returns the only instance of Intact Service instance.
getService() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction: Returns the only instance of Intact Service instance.
getSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction: Returns the session from given request.
getSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction: Returns the session from given request.
getSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction: Returns the session from given request.
getSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction: Returns the session from given request.
getSession(HttpServletRequest) - Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction: Returns the session from given request.
getShallowCopy(Experiment) - Static method in class uk.ac.ebi.intact.model.Experiment: Builds a SHALLOW copy of the Experiment parameter.
getShortLabel() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns the short label.
getShortLabel() - Method in class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper: Returns the short label.
getShortLabel() - Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.AbstractIntDisplayWrapper: Returns the topic with a link to show its contents in a window.
getShortLabel() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getShortLabel() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean
getShortLabel() - Method in class uk.ac.ebi.intact.model.Institution
getShortLabel() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getShortLabel() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getShortLabel() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy: Implements AnnotatedObject's methods
getShortLabel() - Method in class uk.ac.ebi.intact.util.NewtServerProxy.NewtResponse
getShortLabelLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getShortLabelLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean: Returns the topic with a link to show its contents in a window.
getShortLabelLink() - Method in class uk.ac.ebi.intact.application.predict.struts.view.ResultBean
getSingleViewBean(AnnotatedObject, String, String) - Method in class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory: Returns the appropriate view bean for given basic object.
getSource(String) - Static method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator: create a LabelValueBean object corresponding to the default source if it exists
getSourceBrowserUrl() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
getSourceExperimentAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean: Returns the AC of the source experiment.
getSourceURL() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
getSourceURL() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getSourceUrls(Collection, Collection, String) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource: Return a collection of URL corresponding to the selected protein and source eg.
getSourceUrls(Collection, Collection, String) - Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource
getSpAc() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getSpecieLink() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getSpecies() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser: Returns a list of tax ids for species from the database.
getSpeciesSQL() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUserPg
getSpeciesSQL() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUserOra
getSpeciesSQL() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getSpliceProteinsByXref(String) - Method in class uk.ac.ebi.intact.business.IntactHelper: Searches for splice objects by primaryId.
getSpliceVariantCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of all potential splice variant (i.e.
getSpliceVariantCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSpliceVariantCreatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of created splice variant
getSpliceVariantCreatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSpliceVariantProteinCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSpliceVariantSkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of splice variant which gaves us errors during the processing.
getSpliceVariantSkippedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSpliceVariantUpdatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of updated splice variant
getSpliceVariantUpdatedCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSpliceVariantUpToDateCount() - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: Gives the count of up-to-date splice variant (i.e.
getSpliceVariantUpToDateCount() - Method in class uk.ac.ebi.intact.util.UpdateProteins
getSPTRProteins(String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Gets SPTR Proteins via SRS.
getSPTRProteins(String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getStart() - Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
getStatisticBean() - Method in class uk.ac.ebi.intact.util.StatisticsDataSet: Return the data collected, this is the only public method.
getStatisticBean(String, String) - Method in class uk.ac.ebi.intact.util.StatisticsDataSet: Return the data collected, this is the only public method.
getStatistics() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
getStoichiometry() - Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
getStoichiometry() - Method in class uk.ac.ebi.intact.model.Product
getStoichiometry() - Method in class uk.ac.ebi.intact.model.Component
getStop() - Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
getSubjectFragmentBegin() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the start of the subject fragment
getSubjectFragmentEnd() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean: returns the end of the subject fragment.
getSubmissionRef() - Method in class uk.ac.ebi.intact.model.Reference
getSubmissionRefAc() - Method in class uk.ac.ebi.intact.model.Reference
getSurName() - Method in class uk.ac.ebi.intact.model.Person
getTarget() - Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
getTaxId() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
getTaxId() - Method in class uk.ac.ebi.intact.model.BioSource
getTaxId() - Method in class uk.ac.ebi.intact.util.NewtServerProxy.NewtResponse
getTelephone() - Method in class uk.ac.ebi.intact.model.Person
getTimestamp() - Method in class uk.ac.ebi.intact.util.IntactStatistics: returns the timestamp
getTissue() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
getTissueMenu() - Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean: The tissue menu list.
getTitle() - Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
getTitle() - Method in class uk.ac.ebi.intact.model.Reference
getTopic() - Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Returns the topic.
getTopic(Class) - Method in class uk.ac.ebi.intact.application.editor.business.EditorService: Returns the topic name for given class.
getTopicLink() - Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean: Returns the topic with a link to show its contents in a window.
getTulip() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator
getTulip() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessService
getTulip(URL) - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator
getTulip(URL) - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessService
getTulipAddress() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator
getTulipAddress() - Method in interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessService
getUndeploymentFile() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
getUniqueId(Class, String) - Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: returns a unique int for class clazz and field fieldName.
getUniqueLong(Class, String) - Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: Returns a long id unique across all classes.
getUniqueObject(Class, String) - Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: Returns an id unique across all classes.
getUniqueShortLabel(IntactHelper, Class, String, String, String) - Static method in class uk.ac.ebi.intact.util.GoTools: Generate a label which is unique in targetClass and resembles label.
getUniqueShortLabel(String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns a unique short label.
getUniqueShortLabel(String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getUniqueShortLabel(String, String) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns a unique short label.
getUniqueShortLabel(String, String) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getUniqueString(Class, String) - Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager: Returns an id unique across all classes.
getUpdated() - Method in interface uk.ac.ebi.intact.model.IntactObject
getUpdated() - Method in class uk.ac.ebi.intact.model.IntactObjectImpl
getUpdated() - Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
getUpToDateTaxid(String) - Method in class uk.ac.ebi.intact.util.BioSourceFactory: Gives a valid taxid.
getUrl() - Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
getUrl() - Method in class uk.ac.ebi.intact.model.Institution
getUrl(String) - Method in class uk.ac.ebi.intact.util.InsertComplexGiot
getUrl(String) - Method in class uk.ac.ebi.intact.util.UpdateProteinsI: From a given sptr AC, returns a full URL from where a flatfile format SPTR entry will be fetched.
getUrl(String) - Method in class uk.ac.ebi.intact.util.UpdateProteins
getUser() - Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
getUser() - Method in interface uk.ac.ebi.intact.persistence.DAOSource
getUserName() - Method in interface uk.ac.ebi.intact.application.commons.business.IntactUserI: Returns the Intact user.
getUserName() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getUserName() - Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
getUserName() - Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
getUserName() - Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
getUserName() - Method in class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
getValidBioSource(String) - Method in class uk.ac.ebi.intact.util.BioSourceFactory: Create or update a BioSource object from a taxid.
getValue() - Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
getValue() - Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterBean
getValueByKey(String) - Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet: Allows to get the related HashSet by the unique key.
getView() - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns the user's current edit view.
getView() - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getWrappedObject() - Method in class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean: Typically subclasses will return a more 'interesting' instance than Object
getWrappedObjects() - Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean: Typically subclasses will return a more 'interesting' instance than Object
getX() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
getX() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
getXref() - Method in class uk.ac.ebi.intact.model.Feature
getXref(EditUserI) - Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean: Updates the internal xref with the new values from the form.
getXref(XreferenceBean) - Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI: Returns a new instance of Xref constructed from the given bean.
getXref(XreferenceBean) - Method in class uk.ac.ebi.intact.application.editor.business.EditUser
getXrefAc() - Method in class uk.ac.ebi.intact.model.Feature
getXrefAc() - Method in class uk.ac.ebi.intact.model.Reference
getXrefs() - Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean: Returns a collection Xref objects.
getXrefs() - Method in interface uk.ac.ebi.intact.model.AnnotatedObject
getXrefs() - Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
getXrefs() - Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
getXrefs() - Method in class uk.ac.ebi.intact.util.TestCaseHelper
getY() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
getY() - Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
GiotLineBean - class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean.
GiotLineBean(String) - Constructor for class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
GoaTools - class uk.ac.ebi.intact.util.GoaTools.
GoaTools() - Constructor for class uk.ac.ebi.intact.util.GoaTools
GoaTools(String) - Constructor for class uk.ac.ebi.intact.util.GoaTools
GoaTools(String, IntactHelper) - Constructor for class uk.ac.ebi.intact.util.GoaTools
goChildrenAction - class uk.ac.ebi.intact.application.goDensity.struts.controller.goChildrenAction.: Action for discovering children of a GO term.
goChildrenAction() - Constructor for class uk.ac.ebi.intact.application.goDensity.struts.controller.goChildrenAction
goDatabase - Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
GoFlatfile2Set - class uk.ac.ebi.intact.application.goDensity.business.data.GoFlatfile2Set.: GoFlatfile2Set can be used to parse a GO flatfile
GoFlatfile2Set() - Constructor for class uk.ac.ebi.intact.application.goDensity.business.data.GoFlatfile2Set
goFlatfile2Set(String) - Static method in class uk.ac.ebi.intact.application.goDensity.business.data.GoFlatfile2Set: used to parse a GO flatfile and returns all GO:IDs as Strings in a Set.
GoGoDensity - class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity.: GoGoDensity represents a repository for a set of data, which consist of: - goId1 - goId2 - possible Interactions between and under these two goIds - existing Interactions between and under these two goIds
GoGoDensity(String, String, int, int) - Constructor for class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity: Constructor
GoHighlightmentSource - class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource.: Interface allowing to wrap an highlightment source.
GoHighlightmentSource() - Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource
GOID_FLAG - Static variable in class uk.ac.ebi.intact.util.GoServerProxy
GoIdNotInDagException - exception uk.ac.ebi.intact.application.goDensity.exception.GoIdNotInDagException.: If GO:ID is not in DAG
GoIdNotInDagException() - Constructor for class uk.ac.ebi.intact.application.goDensity.exception.GoIdNotInDagException
GoIdNotInDagException(String) - Constructor for class uk.ac.ebi.intact.application.goDensity.exception.GoIdNotInDagException
goInputAction - class uk.ac.ebi.intact.application.goDensity.struts.controller.goInputAction.: goInputAction is used when user paste some goIds in the text field and press "submit" button.
goInputAction() - Constructor for class uk.ac.ebi.intact.application.goDensity.struts.controller.goInputAction
goInputForm - class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm.: Form bean for the goInputAction
goInputForm() - Constructor for class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm
GoServerProxy - class uk.ac.ebi.intact.util.GoServerProxy.: The proxy to the Go server.
GoServerProxy.GoHandler - class uk.ac.ebi.intact.util.GoServerProxy.GoHandler.: Parse the XML output given by the EGO web site.
GoServerProxy.GoHandler() - Constructor for class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
GoServerProxy.GoIdNotFoundException - exception uk.ac.ebi.intact.util.GoServerProxy.GoIdNotFoundException.
GoServerProxy.GoIdNotFoundException(String) - Constructor for class uk.ac.ebi.intact.util.GoServerProxy.GoIdNotFoundException
GoServerProxy.GoIdNotFoundException(String, Exception) - Constructor for class uk.ac.ebi.intact.util.GoServerProxy.GoIdNotFoundException
GoServerProxy.GoResponse - class uk.ac.ebi.intact.util.GoServerProxy.GoResponse.
GoServerProxy.GoResponse(String, String, String) - Constructor for class uk.ac.ebi.intact.util.GoServerProxy.GoResponse
GoServerProxy() - Constructor for class uk.ac.ebi.intact.util.GoServerProxy
GoServerProxy(String) - Constructor for class uk.ac.ebi.intact.util.GoServerProxy: Constructs an instance of this class using the URL to connect to the Newt server.
GoTokenizer - class uk.ac.ebi.intact.application.goDensity.struts.business.GoTokenizer.: Tokenizer for GO:ID terms.
GoTokenizer() - Constructor for class uk.ac.ebi.intact.application.goDensity.struts.business.GoTokenizer
GoTools - class uk.ac.ebi.intact.util.GoTools.: Utilities to read and write files in GO format
GoTools() - Constructor for class uk.ac.ebi.intact.util.GoTools
Graph - class uk.ac.ebi.intact.simpleGraph.Graph.: A simple graph class for temporary processing, for example to prepare output for graph analysis packages.
GRAPH_PROPERTIES - Static variable in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
GRAPH_PROPERTY_FILE - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
Graph() - Constructor for class uk.ac.ebi.intact.simpleGraph.Graph
Graph2FoldedMIF - class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2FoldedMIF.: This class gives IntAct the possibillity to give out a graph to MIF-PSI-Format in XML.
Graph2FoldedMIF() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2FoldedMIF: Contructor without parameter - strict MIF will be produced or Exception will be thrown
Graph2FoldedMIF(Boolean) - Constructor for class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2FoldedMIF: Contructor with parameter
GRAPH2MIF_PROPERTIES - Static variable in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
GRAPH2MIF_PROPERTY_FILE - Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
Graph2MIFConsole - class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFConsole.: Graph2MIFConsole This is a stand alone client of Graph2MIF (without WebService).
Graph2MIFConsole() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFConsole
Graph2MIFWS - interface uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWS.: Graph2MIFWS Interface This is the interface of The graph2MIF-WebService.
Graph2MIFWSClient - class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFWSClient.: Graph2MIFWSClient This is an example implementation of accessing the WebService "Graph2MIFWS" for export of the IntAct Database as PSI-MIF Format.
Graph2MIFWSClient() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFWSClient
Graph2MIFWSService - class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSService.: Graph2MIFWSService Implementation This is the implementation of The graph2MIF-WebService.
Graph2MIFWSService() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSService
Graph2MIFWSServlet - class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSServlet.: Graph2MIFServlet This is a Servlet for retrieving a MIF Document using a URL-Call directly.
Graph2MIFWSServlet() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSServlet
Graph2UnfoldedMIF - class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2UnfoldedMIF.: This class gives IntAct the possibillity to give out a graph to MIF-PSI-Format in XML.
Graph2UnfoldedMIF() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2UnfoldedMIF: Contructor without parameter - strict MIF will be produced or Exception will be thrown
Graph2UnfoldedMIF(Boolean) - Constructor for class uk.ac.ebi.intact.application.graph2MIF.conversion.Graph2UnfoldedMIF: Contructor with parameter
GraphFactory - class uk.ac.ebi.intact.application.graph2MIF.GraphFactory.: Graph producer.
GraphFactory() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.GraphFactory
GraphHelper - class uk.ac.ebi.intact.application.hierarchView.business.graph.GraphHelper.: Allows to retreive an interraction network from intact API
GraphHelper(IntactUserI) - Constructor for class uk.ac.ebi.intact.application.hierarchView.business.graph.GraphHelper: basic constructor - sets up (hard-coded) data source and an intact helper.
GraphI - interface uk.ac.ebi.intact.simpleGraph.GraphI.: A simple graph class for temporary processing, for example to prepare output for graph analysis packages.
GraphNotConvertableException - exception uk.ac.ebi.intact.application.graph2MIF.exception.GraphNotConvertableException.: This Exception should be thrown, if a fatal Error occours - so the PSIFormat will NOT be valid without this mising Element
GraphNotConvertableException() - Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.GraphNotConvertableException
GraphNotConvertableException(String) - Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.GraphNotConvertableException




H

handle(ActionMapping, ActionForm, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction
Subclass must override this to provide to handle the event.
handle(ActionMapping, ActionForm, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.InteractionSubmitAction
 
handleDispatch(ActionMapping, ActionForm, HttpServletRequest, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction
Subclass must override this to provide to handle the event.
handleDispatch(ActionMapping, ActionForm, HttpServletRequest, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.biosrc.BioSourceSubmitAction
 
handleDispatch(ActionMapping, ActionForm, HttpServletRequest, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.ExperimentSubmitAction
 
handleDispatch(ActionMapping, ActionForm, HttpServletRequest, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.InteractionSubmitAction
 
hasDuplicates(ProteinBean) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
True if given protein bean already exists among current saved proteins.
hasErrors(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction
Returns true if errors in stored in the request
hasErrors(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if errors in stored in the request
hasGivenResults() - 
Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
 
hashCode() - 
Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
 
hashCode() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.ReferenceQualifier
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
Remember that hashCode and equals methods has to be develop in parallel
 since : if a.equals(b) then a.hoshCode() == b.hashCode()
 The other way round is NOT true.
hashCode() - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Range
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Product
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Component
This class overwrites equals.
hashCode() - 
Method in class uk.ac.ebi.intact.model.Modification
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Reference
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Alias
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Annotation
This class overwrites equals.
hashCode() - 
Method in class uk.ac.ebi.intact.model.Person
 
hashCode() - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
hashCode() - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
hashCode() - 
Method in interface uk.ac.ebi.intact.model.Protein
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.Xref
This class overwrites equals.
hashCode() - 
Method in class uk.ac.ebi.intact.model.Institution
This class overwrites equals.
hashCode() - 
Method in class uk.ac.ebi.intact.model.Experiment
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.BioSource
 
hashCode() - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
This class overwrites equals.
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
hashCode() - 
Method in class uk.ac.ebi.intact.simpleGraph.Node
 
hashCode() - 
Method in class uk.ac.ebi.intact.util.Key
returns a cached value, rather than re-computing for every call
hasLock(String) - 
Method in class uk.ac.ebi.intact.application.editor.util.LockManager
Checks the existence of given lock.
hasShortLabel() - 
Method in class uk.ac.ebi.intact.util.NewtServerProxy.NewtResponse
 
hasSourceUrlToDisplay() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
hasSourceUrlToDisplay() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
hasTime() - 
Method in class uk.ac.ebi.intact.util.Chrono
 
HeaderSwitchAction - class uk.ac.ebi.intact.application.editor.struts.action.util.HeaderSwitchAction.
This action class is responsible for appending the class type to the header.
HeaderSwitchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.util.HeaderSwitchAction
 
height() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
 
HELP_TITLE - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The default help link.
helper - 
Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
Helper - class uk.ac.ebi.html.Helper.
This class is provided to help generate EBI specific HTML pages from within
     a Java program.
Helper() - 
Constructor for class uk.ac.ebi.html.Helper
 
hideExperimentToHold(ExperimentBean) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
Hides an Experiment bean from hold.
hideInteractionToHold(Interaction) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
Hides an Interaction bean from hold.
HIGHLIGHTING_PROPERTIES - 
Static variable in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
HIGHLIGHTING_PROPERTY_FILE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
HighlightmentAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.HighlightmentAction.
Implementation of Action that validates an highlightment submisson.
HighlightmentAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.HighlightmentAction
 
HighlightmentBehaviour - class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour.
Abstract class allowing to deals with the Highlightment behaviour,
 the implementation of that class would just specify the behaviour
 of one node of the graph.
HighlightmentBehaviour() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour
 
HighlightmentForm - class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm.
Form bean for the highlightment form of the view.jsp page.
HighlightmentForm() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm
 
HighlightmentSource - class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource.
Abstract class allowing to wrap an highlightment source.
HighlightmentSource() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource
 
HighlightProteins - class uk.ac.ebi.intact.application.hierarchView.highlightment.HighlightProteins.
Allows to perfoem the highlightment according to data stored in the user session
HighlightProteins() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.HighlightProteins
 
HOST - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
HtmlBuilder - class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder.
This class generates an HTML view of search results.
HtmlBuilder(Writer, Set, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
Instantiate a new view object
HtmlBuilderManager - class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager.

 This class gives the access to the HtmlBuilder methods by calling the appropriate one
 according to the objects (one or a collection) given.
htmlView(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
The default html view for an AnnotatedObject.
htmlView(BinaryDetailsViewBean.BinaryData) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
Displays a interaction partner table for BinaryData data structure.
htmlView(BioSource) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvComponentRole) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvDatabase) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvIdentification) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvInteraction) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvInteractionType) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvTopic) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(CvXrefQualifier) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
TODO as to be refined
htmlView(Experiment) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
HTML view of an experiment.
htmlView(Interaction) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
HTML view of an Interaction object.
htmlView(InteractionImpl) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
HTML view of an InteractionProxy object.
htmlView(Protein) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
HTML view of a Protein object.
htmlView(ProteinImpl) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
HTML view of a ProteinProxy object.
HttpProxyManager - class uk.ac.ebi.intact.util.HttpProxyManager.
Setup the HTTP proxy setting in the current JVM.
HttpProxyManager.ProxyConfigurationNotFound - exception uk.ac.ebi.intact.util.HttpProxyManager.ProxyConfigurationNotFound.
 
HttpProxyManager.ProxyConfigurationNotFound(String) - 
Constructor for class uk.ac.ebi.intact.util.HttpProxyManager.ProxyConfigurationNotFound
 
HttpProxyManager() - 
Constructor for class uk.ac.ebi.intact.util.HttpProxyManager
 
HV_PROPS - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The name of the hierarchView properties file.



I

IDENTIFICATIONS - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the identification list.
identityXrefQualifier - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
Describe wether an Xref is related the primary SPTR AC (identityCrefQualifier)
 or not (secondaryXrefQualifier)
ignorableWhitespace(char[], int, int) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
ImageBean - class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean.
 
ImageBean() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
 
ImageDimension - class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension.
Storage of the image dimension, allow to keep the heigth, width, border soze ...
ImageDimension() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
initialize all coordinate to zero
IMAGeSIZE - 
Static variable in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config
Imagesize x and y
importDataToImage(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Send a String to Tulip to calculate coordinates
 Enter the obtained coordinates in the graph.
increaseDepth() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
increaseDepth() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Increase the depth of the interraction network up to the defined maximum.
INFORMATIONAL - 
Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
init() - 
Method in class uk.ac.ebi.intact.application.commons.util.LoggingInitServlet
You should include the folowing lines in your web.xml file to load that
 servlet on Tomcat startup.
init() - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.EditorActionServlet
 
init() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
Set the default value of user's data
init() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Set the default value of user's data
init() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Initialization of the interaction network
 Record the nodes in a list which allows to keep an order ...
init() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
Initialize the web service manager by reading the properties file
 and setting needed files names.
init() - 
Method in class uk.ac.ebi.intact.application.predict.struts.framework.PredictActionServlet
 
init() - 
Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactActionServlet
 
init(ServletConfig) - 
Method in class uk.ac.ebi.intact.application.goDensity.struts.business.InitFastGoDag
 
InitAction - class uk.ac.ebi.intact.application.goDensity.struts.controller.InitAction.
Implementation of Action that initialise the application.
InitAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.InitAction.
Implementation of Action that validates a centered submisson (from a link).
InitAction() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.struts.controller.InitAction
 
InitAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.InitAction
 
InitFastGoDag - class uk.ac.ebi.intact.application.goDensity.struts.business.InitFastGoDag.
 
InitFastGoDag() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.struts.business.InitFastGoDag
 
InitForm - class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm.
Form bean for the main form of the view.jsp page.
InitForm() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm
 
initHighlightMap() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
 
initHighlightMap() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean
 
initHighlightMap() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean
 
initNodeDisplay(NodeI) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
initialisation of one Node about its color, its visible attribute
initNodes() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Allow to put the default color and default visibility for each
 protein of the interaction network
INPUT_OUTPUT_DIR - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
Manager files ------- to arrange files in their directory.
insert(String, String, String) - 
Method in class uk.ac.ebi.intact.util.InsertComplexMerck
 
insert(String, String, String) - 
Method in class uk.ac.ebi.intact.util.InsertComplex
 
InsertComplex - class uk.ac.ebi.intact.util.InsertComplex.
Insert complex data for Ho and Gavin publications.
InsertComplex() - 
Constructor for class uk.ac.ebi.intact.util.InsertComplex
basic constructor - sets up intact helper and protein factory
insertComplex(String, ArrayList, String, String, String) - 
Method in class uk.ac.ebi.intact.util.InsertComplexMerck
Inserts a complex into the database
 If the complex already exists, it is skipped!
insertComplex(String, String, Vector, String, Experiment, String) - 
Method in class uk.ac.ebi.intact.util.InsertComplex
Inserts a complex into the database
 If the complex already exists, it is skipped!
InsertComplexGiot - class uk.ac.ebi.intact.util.InsertComplexGiot.
Insert of the Giot data in IntAct
InsertComplexGiot(String, String, String, IntactHelper) - 
Constructor for class uk.ac.ebi.intact.util.InsertComplexGiot
 
InsertComplexMerck - class uk.ac.ebi.intact.util.InsertComplexMerck.
Insert binary iteraction data (customize to MERCK format).
InsertComplexMerck() - 
Constructor for class uk.ac.ebi.intact.util.InsertComplexMerck
basic constructor - sets up intact helper and protein factory
insertComponent(Interaction, String, CvComponentRole) - 
Method in class uk.ac.ebi.intact.util.InsertComplex
Insert a Component object linking an Interactor to an Interaction.
insertComponent(Interaction, String, String, CvComponentRole) - 
Method in class uk.ac.ebi.intact.util.InsertComplexMerck
Insert a Component object linking an Interactor to an Interaction.
insertDefinition(Hashtable, IntactHelper, String, Class, boolean) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Insert a GO term into IntAct.
InsertGo - class uk.ac.ebi.intact.util.InsertGo.
Create GO crossreferences for Protein objects.
InsertGo() - 
Constructor for class uk.ac.ebi.intact.util.InsertGo
basic constructor - sets up (hard-coded) data source and an intact helper
insertGoDag(Class, IntactHelper, String, String) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Read a GO DAG file from the given URL,
 insert or update DAG into aTargetClass.
insertGoDefinitions(Class, IntactHelper, String, String) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Read a GO definition flat file from the given URL,
 insert or update all terms into aTargetClass.
InsertGoFromFlatfile - class uk.ac.ebi.intact.application.goDensity.setupGoDensity.InsertGoFromFlatfile.
Insert GO Term from flatfile (e.g.
InsertGoFromFlatfile() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.setupGoDensity.InsertGoFromFlatfile
 
insertSimpleProtein(String, CvDatabase, String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Creates a simple Protein object for entries which are not in SPTR.
insertSimpleProtein(String, CvDatabase, String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
Creates a simple Protein object for entries which are not in SPTR.
insertSPTrProteins(InputStream, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Inserts zero or more proteins created from SPTR entries which are retrieved from a Stream.
insertSPTrProteins(InputStream, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
 
insertSPTrProteins(String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Inserts zero or more proteins created from SPTR entries which are retrieved from an SPTR Accession number.
insertSPTrProteins(String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
 
insertSPTrProteins(String, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Inserts zero or more proteins created from SPTR entries which are retrieved from an SPTR Accession number.
insertSPTrProteins(String, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
 
insertSPTrProteinsFromURL(String, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Inserts zero or more proteins created from SPTR entries which are retrieved from a URL.
insertSPTrProteinsFromURL(String, String, boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
 
Institution - class uk.ac.ebi.intact.model.Institution.
Represents the contact details for an institution.
Institution(String) - 
Constructor for class uk.ac.ebi.intact.model.Institution
This constructor ensures creation of a valid Institution.
institutionAc - 
Variable in class uk.ac.ebi.intact.model.Person
 
INTACT_ERROR - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
The global Intact error key.
INTACT_ERROR - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
The global Intact error key.
INTACT_ERROR - 
Static variable in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
The global Intact error key.
INTACT_ERROR - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction
The global Intact error key.
INTACT_HELPER - 
Static variable in class uk.ac.ebi.intact.model.Constants
used as a servlet session parameter name to refer to an intact helper instance
INTACT_LOG_FILE - 
Static variable in class uk.ac.ebi.intact.model.Constants
used as a servlet context parameter name to refer to the path of
 a log file
INTACT_MESSAGE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
The global Intact message key.
INTACT_MESSAGE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
The global Intact message key.
INTACT_SERVICE - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
The key to store an Intact Service object.
INTACT_SERVICE - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The key to store an Intact Service object.
INTACT_TYPES_FILE - 
Static variable in class uk.ac.ebi.intact.model.Constants
used as a key to identify an intact object types property file -
 its value is defined in the web.xml file as a servlet context parameter
INTACT_USER - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The key to access an Intact user.
INTACT_USER - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
The key to access a user session object.
INTACT_USER - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The key to access a user session object.
IntactActionServlet - class uk.ac.ebi.intact.application.search2.struts.framework.IntactActionServlet.
This is Intact specific action servlet class.
IntactActionServlet() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.framework.IntactActionServlet
 
IntactBaseAction - class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction.
Super class for all hierarchView related action classes.
IntactBaseAction - class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction.
Super class for all Intact related action classes.
IntactBaseAction - class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction.
Super class for all Intact related action classes.
IntactBaseAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
 
IntactBaseAction() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
 
IntactBaseAction() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction
 
IntactBaseForm - class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm.
Super class for all hierarchView related form classes.
IntactBaseForm() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
 
IntactDailyRollingFileAppender - class uk.ac.ebi.intact.util.logging.IntactDailyRollingFileAppender.
 
IntactDailyRollingFileAppender() - 
Constructor for class uk.ac.ebi.intact.util.logging.IntactDailyRollingFileAppender
 
intactDatabase - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
IntactException - exception uk.ac.ebi.intact.business.IntactException.
Exception class to provide more meaningful error messages.
IntactException() - 
Constructor for class uk.ac.ebi.intact.business.IntactException
 
IntactException(String) - 
Constructor for class uk.ac.ebi.intact.business.IntactException
 
IntactException(String, Exception) - 
Constructor for class uk.ac.ebi.intact.business.IntactException
 
IntactHelper - class uk.ac.ebi.intact.business.IntactHelper.
This class implements the business logic for intact.
IntactHelper() - 
Constructor for class uk.ac.ebi.intact.business.IntactHelper
Shortcut constructor
IntactHelper(DAOSource) - 
Constructor for class uk.ac.ebi.intact.business.IntactHelper
Constructor - requires a datasource to be provided.
IntactHelper(DAOSource, String, String) - 
Constructor for class uk.ac.ebi.intact.business.IntactHelper
Constructor allowing a helper instance to be created with a given
 username and password.
IntactHelper(Map, DAOSource) - 
Constructor for class uk.ac.ebi.intact.business.IntactHelper

  This constructor allows creation of an IntactHelper with a
 Map of java classnames to PropertyDescriptor information.
IntactNode - class uk.ac.ebi.intact.model.IntactNode.
TODO comments
IntactNode() - 
Constructor for class uk.ac.ebi.intact.model.IntactNode
 
IntactObject - interface uk.ac.ebi.intact.model.IntactObject.
 
IntactObjectImpl - class uk.ac.ebi.intact.model.IntactObjectImpl.
This is the top level class for all intact model object.
IntactObjectImpl() - 
Constructor for class uk.ac.ebi.intact.model.IntactObjectImpl
Protected constructor for use by subclasses - used to set
 the creation data for instances
IntactObjectProxy - class uk.ac.ebi.intact.model.proxy.IntactObjectProxy.
 
IntactObjectProxy() - 
Constructor for class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
IntactObjectProxy(InvocationHandler) - 
Constructor for class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
IntactObjectProxy(PBKey, Identity) - 
Constructor for class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
IntactRowReaderImpl - class uk.ac.ebi.intact.persistence.IntactRowReaderImpl.
Row Reader class specific to Intact.
IntactRowReaderImpl() - 
Constructor for class uk.ac.ebi.intact.persistence.IntactRowReaderImpl
 
IntactServiceIF - interface uk.ac.ebi.intact.application.search2.business.IntactServiceIF.
The business interface for the Web Intact application.
IntactServiceImpl - class uk.ac.ebi.intact.application.search2.business.IntactServiceImpl.
Implments the IntactService interface.
IntactServiceImpl(String) - 
Constructor for class uk.ac.ebi.intact.application.search2.business.IntactServiceImpl
Constructs an instance with given resource file.
IntactSrsException - exception uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException.
This class manages the SRS exceptions.
IntactSrsException() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException
 
IntactSrsException(String) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException
Constructor with a message.
IntactSrsException(String, Exception) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException
Constructor with a message.
IntactStatistics - class uk.ac.ebi.intact.util.IntactStatistics.
This class represents the Statistics table in the database.
IntactStatistics() - 
Constructor for class uk.ac.ebi.intact.util.IntactStatistics
 
IntactUser - class uk.ac.ebi.intact.application.hierarchView.business.IntactUser.
This class stores information about an Intact Web user session.
IntactUser(String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Constructs an instance of this class with given mapping file and
 the name of the data source class.
intactUserExists(HttpSession) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Says if an IntactUser object is currently available in the session.
IntactUserI - interface uk.ac.ebi.intact.application.commons.business.IntactUserI.
This interface defines methods common to all Intact WEB applications.
IntactUserI - interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI.
This interface stores information about an Intact Web user session.
IntactUserIF - interface uk.ac.ebi.intact.application.search2.business.IntactUserIF.
This interface represents an Intact user.
IntactUserImpl - class uk.ac.ebi.intact.application.search2.business.IntactUserImpl.
This class stores information about an Intact Web user session.
IntactUserImpl(String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
Constructs an instance of this class with given mapping file and
 the name of the data source class.
IntDisplayWrapper - class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntDisplayWrapper.
This class is a decorator of the Interaction objects that we keep in our
 List.
IntDisplayWrapper() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntDisplayWrapper
 
Interaction - interface uk.ac.ebi.intact.model.Interaction.
 
INTERACTION_TYPES - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the interaction type list.
interactionAc - 
Variable in class uk.ac.ebi.intact.model.Product
 
InteractionAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionAction.
Invoked when Delete/Edit Interaction button is pressed to delete/edit
 an Interaction.
InteractionAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionAction
 
InteractionDetailsViewBean - class uk.ac.ebi.intact.application.search2.struts.view.details.InteractionDetailsViewBean.
Displays a collection of Interactions in the context of their Experiment.
InteractionDetailsViewBean(Collection, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.details.InteractionDetailsViewBean
Construct an instance of this class for given collection of object.
InteractionDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionDispatchAction.
The action class to search an Interaction (in the context of an Experiment).
InteractionDispatchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionDispatchAction
 
InteractionDynaForm - class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionDynaForm.
The form to validate interaction info data.
InteractionDynaForm() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionDynaForm
 
InteractionException - exception uk.ac.ebi.intact.application.editor.exception.validation.InteractionException.
Thrown when the validation for an interaction fails.
InteractionException() - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.InteractionException
Default constructor.
InteractionException(String) - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.InteractionException
Construst with given message key
InteractionHoldAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionHoldAction.
Invoked when either Add/Hide button is pressed in the form for holding
 interactions yet to add to the Experiment.
InteractionHoldAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionHoldAction
 
InteractionImpl - class uk.ac.ebi.intact.model.InteractionImpl.
Represents an interaction.
InteractionImpl(Collection, Collection, CvInteractionType, String, Institution) - 
Constructor for class uk.ac.ebi.intact.model.InteractionImpl
Creates a valid Interaction instance.
InteractionLinkAction - class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionLinkAction.
Links to an interaction button from an experiment.
InteractionLinkAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionLinkAction
 
InteractionNetwork - class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork.
 
InteractionNetwork(Interactor) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Constructor
InteractionNetworkAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.InteractionNetworkAction.
Implementation of Action that perform hndling of the current interaction network.
InteractionNetworkAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.InteractionNetworkAction
 
InteractionNetworkForm - class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm.
This form captures the user action of the sideBarGraph.jsp.
InteractionNetworkForm() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm
 
InteractionNetworkReadyToBeDisplayed() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
InteractionNetworkReadyToBeDisplayed() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Allows the user to know if an interaction network will be displayed
InteractionNetworkReadyToBeHighlighted() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
InteractionNetworkReadyToBeHighlighted() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Allows the user to know if an interaction network is ready to be highlighted.
interactionNumber - 
Variable in class uk.ac.ebi.intact.util.IntactStatistics
 
InteractionProxy - class uk.ac.ebi.intact.model.proxy.InteractionProxy.
 
InteractionProxy() - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
InteractionProxy(InvocationHandler) - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
InteractionProxy(PBKey, Identity) - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
INTERACTIONS - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the interaction list.
InteractionSingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.InteractionSingleViewBean.
View bean responsible for the display of a single Interaction.
InteractionSingleViewBean(AnnotatedObject, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.InteractionSingleViewBean
Construct an instance of this class for given object.
InteractionSubmitAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.InteractionSubmitAction.
An action to handle Interaction specific events.
InteractionSubmitAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.InteractionSubmitAction
 
InteractionViewBean - class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean.
Interaction edit view bean.
InteractionViewBean() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
interactor - 
Variable in class uk.ac.ebi.intact.simpleGraph.Node
 
Interactor - interface uk.ac.ebi.intact.model.Interactor.
 
interactorAc - 
Variable in class uk.ac.ebi.intact.model.Product
 
InteractorComparator - class uk.ac.ebi.intact.util.InteractorComparator.
This class provides a specific Comparator for  'hidden' Interactors, based on short label.
InteractorComparator() - 
Constructor for class uk.ac.ebi.intact.util.InteractorComparator
 
InteractorImpl - class uk.ac.ebi.intact.model.InteractorImpl.
Defines a generic interacting object.
InteractorImpl() - 
Constructor for class uk.ac.ebi.intact.model.InteractorImpl
no-arg constructor provided for compatibility with subclasses
 that have no-arg constructors.
InteractorImpl(String, Institution) - 
Constructor for class uk.ac.ebi.intact.model.InteractorImpl
Constructor for subclass use only.
InteractorProxy - class uk.ac.ebi.intact.model.proxy.InteractorProxy.
 
InteractorProxy() - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
InteractorProxy(InvocationHandler) - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
InteractorProxy(PBKey, Identity) - 
Constructor for class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
interproDatabase - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
IntHoldDisplayWrapper - class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntHoldDisplayWrapper.
This class is a decorator for the Interaction objects in the hold section.
IntHoldDisplayWrapper() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.experiment.IntHoldDisplayWrapper
 
INTSEQ_PROPERTIES - 
Static variable in class uk.ac.ebi.intact.application.intSeq.business.Constants
Properties files in which you'll find all command lines, URLs use
 to run intSeq.
isActive() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
checks to see if a transaction is currently in progress.
isActive() - 
Method in interface uk.ac.ebi.intact.persistence.DAO
checks to see if a transaction is currently in progress
isaOrPartOf(String, String) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
test, if goId1 equals goId2 or
 if goId1 is a child or subchild of goId2
isAutoSave() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
checks to see if object saving automatically is turned on
isAutoSave() - 
Method in interface uk.ac.ebi.intact.persistence.DAO
checks to see if object saving automatically is turned on
isAutoSaveSet() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
 
isAutoSaveSet() - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
 
isCachedClass(Class) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
isClosed() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
checks to see if a transaction is closed.
isClosed() - 
Method in interface uk.ac.ebi.intact.persistence.DAO
checks to see if a transaction is closed
isEditing() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Returns the state of editing.
isEditing() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
isEmptyError() - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
answer the question : "is the error set empty ?"
isErrorsEmpty() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Specify if an the error set is empty.
isErrorsEmpty() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
Specify if an the error set is empty.
isGoIdInDag(Set) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
Test, if one or more of the goIds is not in contained in dag.
isInitialized() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
Tells is the Manager is properly initialized.
isInSameGraphPath(Set) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
test all goIds of a Set of GoIds, which are in the same graph path
isInSameGraphPath(String, String) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
test, if goId1 is in the same graph path of goId2
isInTransaction() - 
Method in class uk.ac.ebi.intact.business.IntactHelper
 
isLocalTransactionControl() - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
If true, each protein is updated in a distinct transaction.
isLocalTransactionControl() - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
If true, each protein is updated in a distinct transaction.
isMajor(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
 
isMenuType(Class) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
True if clazz is a menu type
isMessagesEmpty() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Specify if an the Message set is empty.
isMessagesEmpty() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
Specify if an the error set is empty.
isMinor(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
 
isoformComment - 
Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
isoFormParentXrefQualifier - 
Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
isoformSynonym - 
Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
isPersistent() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
True if the current edit object is persistent.
isPersistent() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
isPersistent(Object) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
True if given object is persistent.
isPersistent(Object) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
isPersistent(Object) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Wrapper for uk.ac.ebi.intact.persistence#DAO(Object)
isPersistent(Object) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
checks to determine if a given object is persistent or not
isPersistent(Object) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
checks to determine if a given object is persistent or not.
isPropertyEmpty(DynaActionForm, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if given property is empty.
isPropertyEmpty(String) - 
Static method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if given value is empty.
isPropertyNull(DynaActionForm, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if the property for given name is null.
isPropertyNullOrEmpty(DynaActionForm, String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if the property for given name is empty.
isRunning() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
Tells is the web service is running.
isSelected() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
isSourceFromAnExperiment() - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
True when this bean is constructed from an experiment.
isUserValid(String, String) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
validates a username and password against the datastore.
isUserValid(String, String) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
validates a username and password against the datastore.
isUserVerified(String, String) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
validates a user's credentials against the data store.
isVisited(BasicObject) - 
Method in interface uk.ac.ebi.intact.simpleGraph.GraphI
return true if a Component has been visited during graph exploration.
isVisited(BasicObject) - 
Method in class uk.ac.ebi.intact.simpleGraph.Graph
return true if a Component has been visited during graph exploration.
iteratorFind(String, String, String) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
This method provides a means to obtain an Iterator for search results.
iteratorFind(String, String, String) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
This method provides a means to obtain an Iterator for search results.
iterSearch(String, String, String) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Search which provides an Iterator rather than a Collection.



J

JDBC_TX - 
Static variable in class uk.ac.ebi.intact.business.BusinessConstants
used to identify a JDBC transaction type.
JDO - 
Static variable in class uk.ac.ebi.intact.model.Constants
Name of the database engine being used
JournalRef - class uk.ac.ebi.intact.model.JournalRef.
TODO Represents ...
JournalRef(Institution, String, String, Integer, String, CvJournal) - 
Constructor for class uk.ac.ebi.intact.model.JournalRef
 



K

Key - class uk.ac.ebi.intact.util.Key.
This class provides a wrapper around a String object
 for use with java Maps.
Key(String) - 
Constructor for class uk.ac.ebi.intact.util.Key
 
Key2HashSet - class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet.
Key2HashSet with unique (!) Values for a key.
Key2HashSet() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
default Constructor
KeyNotFoundException - exception uk.ac.ebi.intact.application.goDensity.exception.KeyNotFoundException.
If key is not found
KeyNotFoundException() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.exception.KeyNotFoundException
 
KeyNotFoundException(String) - 
Constructor for class uk.ac.ebi.intact.application.goDensity.exception.KeyNotFoundException
 



L

label - 
Variable in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
The label to be displayed to the user.
LabelValueBean - class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean.
Simple JavaBean to represent label-value pairs for use in collections
 that are utilized by the <form:options> tag.
LabelValueBean(String, String, String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
Construct a new LabelValueBean with the specified values.
LARGESCALESIZE - 
Static variable in class uk.ac.ebi.intact.application.dataConversion.FileGenerator
 
LAST_VALID_SEARCH - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The most recent user-defined search (ie not from a CvObject link).
length() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
 
load(String) - 
Static method in class uk.ac.ebi.intact.util.PropertyLoader
Allows to get a set of property or null from a property file.
loadFile(String) - 
Method in class uk.ac.ebi.intact.application.synchron.XmlLoader
unmarshall the XML file xmlFile @xmlFile
localTransactionControl - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
If true, each protein is updated in a distinct transaction.
LOCK_MGR - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The lock manager.
lock(CvObject) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Locks the given object for write access.
lock(Object) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
Locks the specified object to a transaction for WRITE.
lock(Object) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
Locks the given object for write access.
LockManager - class uk.ac.ebi.intact.application.editor.util.LockManager.
The lock manager keeps a track of edit objects.
LockManager.LockObject - class uk.ac.ebi.intact.application.editor.util.LockManager.LockObject.
 
log(SQLException) - 
Method in class uk.ac.ebi.intact.application.predict.util.PredictLogger
Logs the SQL exception using the logger
log(String) - 
Method in class uk.ac.ebi.intact.application.predict.util.PredictLogger
Logs a string.
log(Throwable) - 
Method in class uk.ac.ebi.intact.application.predict.util.PredictLogger
Logs an exception.
logger - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
 
logger - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
 
logger - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
 
logger - 
Static variable in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
 
logger - 
Static variable in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
logger - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction
 
logger - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
 
logger - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilderManager
 
logger - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
LOGGER - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorDispatchAction
The logger for Editor.
LOGGER - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
The logger for Editor.
LOGGER - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The name of the logger.
LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants
The name of the logger specific of hierarchView
LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.application.intSeq.business.Constants
The name of the logger specific of intSeq
LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.application.search2.business.Constants
Name of the Log4J logger
LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.application.statisticView.business.Constants
The name of the logger specific of statisticView
 cf.
LoggingInitServlet - class uk.ac.ebi.intact.application.commons.util.LoggingInitServlet.
Inititialize the Logger with the log4J properties file.
LoggingInitServlet() - 
Constructor for class uk.ac.ebi.intact.application.commons.util.LoggingInitServlet
 
LoginAction - class uk.ac.ebi.intact.application.editor.struts.security.LoginAction.
Implements the logic to authenticate a user for the editor application.
LoginAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.security.LoginAction
 
loginTime() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
 
loginTime() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
logoff() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Logs off from the application.
logoff() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
logoffTime() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
 
logoffTime() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
LogoutAction - class uk.ac.ebi.intact.application.editor.struts.security.LogoutAction.
The class is called by struts framework when the user logs off from editor
 application.
LogoutAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.security.LogoutAction
 
lookup(String, String) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Utility method to handle the logic for lookup, ie trying AC, label etc.
lookup(String, String) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 



M

main(String[]) - 
Static method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator
Main method for the PSI application.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorTopicsGenerator
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools
main
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.SetupGoDensityTables
import of the go graph within intact (CvGoNodes) to goDensity specific tables
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.PrecalcGoGoDensities
Import CvGoNodes from a GO flatfile.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.InsertGoFromFlatfile
Import CvGoNodes from a GO flatfile.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.CalcBinaryInteractions
Calculates binary interactions according to the arguments.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFWSClient
main Method, which will be called if the client is started.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFConsole
main Method, which will be called if the client is started.
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.TulipClient
TEST METHOD    *
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.predict.util.PredictPg
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.predict.util.PredictOra
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.synchron.XmlLoader
This main method is only
 used for test, and has to be deleted later
 with method init and constructor XmlLoader()
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.synchron.XmlDumper
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.application.synchron.Collector
Calls init() to initialise some fields
 calls getIntactNodes and retrieves an ObjectSet of IntactNode objects
 For each IntactNode object it calls getXmlFiles().
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.SanityChecker
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.ProteinFastaDownload
This utilitie allows to download all protein sequences being in the IntAct database

 With a call to this class, it should download all IntAct sequences into a file in
 fasta format: the fasta header contains the IntAct ac, and the protein sequence behind.
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.ProteinExport
D E M O
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.InsertGo
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.InsertComplexMerck
Read complex data from flat file and insert it into the database.
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.InsertComplexGiot
D E M O
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.UpdateProteins
D E M O
 
 Could be use for loading from a .txl file
 ./scripts/javaRun.sh UpdateProteins file:///homes/user/mySPTRfile.txl
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.InsertComplex
Read complex data from flat file and insert it into the database.
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.GoaTools
D E M O
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Load or unload Controlled Vocabularies in GO format.
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.DocumentationIntegrityChecker
 
main(String[]) - 
Static method in class uk.ac.ebi.intact.util.fileParsing.SerializationHelper
D E M O
makePersistent(Collection) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
This method performs a simple creation for a number of objects.
makePersistent(Collection) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
This method performs an object creation operation for a collection of
 objects provided as parameters.
ManageBlastResult(String, String, String, String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
ManageBlastResult can be called from different action classes, to manage the execution
 of the command line provided and to retrieve alignment results from the parsing.
ManagerFiles - class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles.
This class is a base class which allows to manage the file operations like opening,
 reading, writing, parsing, deleting.
ManagerFiles() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
constructor by default
ManagerFiles(String, Object) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
constructor which allows us to create a random file name,
 this application is multi-user.
ManagerFiles(String, String) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
constructor which passes a hard file name in parameter
ManagerFilesBlast - class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast.
This class inherits the ManagerFiles class.
ManagerFilesBlast() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast
constructor by default
ManagerFilesBlast(String, Object) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast
constructor which allows us to create a random file name,
 this application is multi-user.
ManagerFilesBlast(String, String) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast
constructor which passes a hard file name in parameter
ManagerFilesSrs - class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesSrs.
This class inherits the ManagerFiles class.
ManagerFilesSrs() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesSrs
constructor by default
ManagerFilesSrs(String, Object) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesSrs
constructor which allows us to create a random file name,
 this application is multi-user.
ManagerFilesSrs(String, String) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesSrs
constructor which passes a hard file name in parameter
MAPPING_FILE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants
Used as a key to identify a mapping filename (for Castor).
MAPPING_FILE_KEY - 
Static variable in class uk.ac.ebi.intact.business.BusinessConstants
used as a key to identify a mapping filename (for Castor)
 the value is defined in the web.xml file
MAPPING_FILE_KEY - 
Static variable in class uk.ac.ebi.intact.model.Constants
used as a key to identify a mapping filename (for Castor)
 the value is defined in the web.xml file
MappingFile - 
Static variable in class uk.ac.ebi.intact.application.synchron.XmlLoader
 
MappingFile - 
Static variable in class uk.ac.ebi.intact.application.synchron.XmlDumper
 
MATCH - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants
Used as a key to identify a page to display when matches are found
 from a search.
match(String, String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
from a given string and a given pattern(string), to find all matches.
match(String, String) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
from a given string and a given pattern(string), to find all matches.
matchWithIntactId - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
 
MAX_CACHED_ITEM - 
Static variable in class uk.ac.ebi.intact.util.NewtServerProxy
 
MAX_CHUNK_IN_INDEX - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.view.html.HtmlBuilder
 
MAX_CHUNK_SIZE - 
Static variable in class uk.ac.ebi.intact.application.search2.business.Constants
Number of items to display when the display is chunked.
MAX_ID_LEN - 
Static variable in class uk.ac.ebi.intact.util.InsertGo
 
maxChunk - 
Variable in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean
Max count of chunk we can display out of the wrapped object
maximalDepthReached() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
maximalDepthReached() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
says if the current depth is maximal
MAXIMUM_DATA_AVAILABILITY - 
Static variable in class uk.ac.ebi.intact.util.StatisticsDataSet
 
MAXIMUM_DISPLAYABLE_INTERACTION - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction
 
MAXIMUM_DISPLAYABLE_PROTEIN - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction
 
MenuManager - class uk.ac.ebi.intact.application.editor.util.MenuManager.
Management of the list of shortLabel of the IntAct object.
MIFSerializeException - exception uk.ac.ebi.intact.application.graph2MIF.exception.MIFSerializeException.
This Exception should be thrown, if there the DOM-Object could not be serialized
MIFSerializeException() - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.MIFSerializeException
 
MIFSerializeException(String) - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.MIFSerializeException
 
minimalDepthReached() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
minimalDepthReached() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
says if the current depth is minimal
Modification - class uk.ac.ebi.intact.model.Modification.
An amino acid modification.
Modification(Institution, Range, CvModificationType) - 
Constructor for class uk.ac.ebi.intact.model.Modification
 
modifyCollection(Collection, InteractionNetwork) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.VisibleHighlightmentBehaviour
Select all the graph's protein which are not in the given collection.

 The aim of that behaviour is to display only se selected protein, so we
 have to set the VISIBLE flag of all other proteins to false.
modifyCollection(Collection, InteractionNetwork) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.HighlightmentBehaviour
Allow to apply a modification on the collection of protein to highlight.
modifyDoc(Document, Collection, int) - 
Method in class uk.ac.ebi.intact.util.XmlBuilder
This method allows for modification of a given Document.
MONO_DIRECTIONAL_ORIENTATION - 
Static variable in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
 
MultipleResultException - exception uk.ac.ebi.intact.application.hierarchView.exception.MultipleResultException.
Thrown when the user query give several interactors.
MultipleResultException() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.MultipleResultException
 
MultipleResultException(String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.MultipleResultException
 
MyHashtable - class uk.ac.ebi.intact.application.goDensity.business.data.MyHashtable.
Subclassing Hashtable to provide a more elegant toString - that's all ;-)
MyHashtable() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.business.data.MyHashtable
 
myInstitution - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
The owner of the created object



N

NEW_LINE - 
Static variable in class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFWSClient
 
NEW_LINE - 
Static variable in class uk.ac.ebi.intact.application.graph2MIF.client.Graph2MIFConsole
 
NEW_LINE - 
Variable in class uk.ac.ebi.intact.model.IntactObjectImpl
This is used in toString() in order to be platform compatible.
NEW_LINE - 
Static variable in class uk.ac.ebi.intact.util.InsertComplexMerck
 
NEW_LINE - 
Static variable in class uk.ac.ebi.intact.util.InsertComplex
 
newPsiDoc(boolean) - 
Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder
Creates an initialised PSI Document object.
NewtServerProxy - class uk.ac.ebi.intact.util.NewtServerProxy.
The proxy to the Newt server.
NewtServerProxy.NewtResponse - class uk.ac.ebi.intact.util.NewtServerProxy.NewtResponse.
 
NewtServerProxy.TaxIdNotFoundException - exception uk.ac.ebi.intact.util.NewtServerProxy.TaxIdNotFoundException.
 
NewtServerProxy.TaxIdNotFoundException(int) - 
Constructor for class uk.ac.ebi.intact.util.NewtServerProxy.TaxIdNotFoundException
 
NewtServerProxy() - 
Constructor for class uk.ac.ebi.intact.util.NewtServerProxy
Deafult constructor.
NewtServerProxy(URL) - 
Constructor for class uk.ac.ebi.intact.util.NewtServerProxy
Constructs an instance of this class using the URL to connect to the
 Newt server.
NO_CHUNK_SELECTED - 
Static variable in class uk.ac.ebi.intact.application.search2.business.Constants
 
NO_MATCH - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants
Used as a key to identify a page to display when no matches are found
 from a search.
NO_ORIENTATION - 
Static variable in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
 
NoDataException - exception uk.ac.ebi.intact.application.statisticView.business.data.NoDataException.
 
NoDataException() - 
Constructor for class uk.ac.ebi.intact.application.statisticView.business.data.NoDataException
 
Node - class uk.ac.ebi.intact.simpleGraph.Node.
A simple node class for temporary processing, for example to prepare output for graph analysis packages.
Node(Interactor) - 
Constructor for class uk.ac.ebi.intact.simpleGraph.Node
 
NodeI - interface uk.ac.ebi.intact.simpleGraph.NodeI.
 
NoGraphRetrievedException - exception uk.ac.ebi.intact.application.graph2MIF.exception.NoGraphRetrievedException.
This Exception should be thrown, if there were occoured a exception while retrieving the graph
NoGraphRetrievedException() - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.NoGraphRetrievedException
 
NoGraphRetrievedException(String) - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.NoGraphRetrievedException
 
NoInteractorFoundException - exception uk.ac.ebi.intact.application.graph2MIF.exception.NoInteractorFoundException.
This Exception should be thrown, if there were no interactors found for the ac.
NoInteractorFoundException() - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.NoInteractorFoundException
 
NoInteractorFoundException(String) - 
Constructor for class uk.ac.ebi.intact.application.graph2MIF.exception.NoInteractorFoundException
 
NONE - 
Static variable in class uk.ac.ebi.intact.util.StatisticsDataSet
 
normalizeMenuItem(String) - 
Static method in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
A utility method to normalizes a menu item
NucleicAcid - class uk.ac.ebi.intact.model.NucleicAcid.
A nucleic acid sequence.
NucleicAcid() - 
Constructor for class uk.ac.ebi.intact.model.NucleicAcid
 



O

OBJECT_TX - 
Static variable in class uk.ac.ebi.intact.business.BusinessConstants
used to identify an object-level transaction.
ObjectBridgeDAO - class uk.ac.ebi.intact.persistence.ObjectBridgeDAO.
This class provides an ObjectBridge-specific Data Access Object, which
 effectively wraps up an ObjectBridge broker object.
ObjectBridgeDAO(PersistenceBroker) - 
Constructor for class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
ObjectBridgeDAOSource - class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource.
This class effectively wraps an ObjectBridge broker factory instance and abstracts
  away the details of the ObjectBridge creation mechanism.
ObjectBridgeDAOSource() - 
Constructor for class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
 
objects - 
Variable in class uk.ac.ebi.intact.util.ObjectSet
 
ObjectSearch - class uk.ac.ebi.intact.persistence.ObjectSearch.
This class contains methods for performing specific object searches for
 particular intact object types, based on an object's id or name.
ObjectSearch() - 
Constructor for class uk.ac.ebi.intact.persistence.ObjectSearch
Default Constructor.
ObjectSet - class uk.ac.ebi.intact.util.ObjectSet.
Represents a set of IntAct objects
ObjectSet() - 
Constructor for class uk.ac.ebi.intact.util.ObjectSet
 
OJB_LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
 
OJB_LOGGER_NAME - 
Static variable in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
open() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
opens a DAO (connection).
open() - 
Method in interface uk.ac.ebi.intact.persistence.DAO
opens a DAO (connection).
OptionGenerator - class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator.
Allows to create some collection to populate option list in HTML form.
OptionGenerator() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.OptionGenerator
 
OracleSequenceManager - class uk.ac.ebi.intact.persistence.OracleSequenceManager.
This sequence manager accesses a database sequence object to
 get the next unique id, leaving the management of the sequence
 to the database.
OracleSequenceManager(PersistenceBroker) - 
Constructor for class uk.ac.ebi.intact.persistence.OracleSequenceManager
 
ORGANISMS - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the host oragnism list.
outputProcessManagement(Object, boolean) - 
Method in class uk.ac.ebi.intact.util.ProteinFastaDownload
This method manages the output stream of a process:
 limited buffer size: the process needs that a bufferReader
 reads the screen output stream and the error output stream.
OutputProcessManagement(Object, boolean) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
This method manages the output stream of a process:
 limited buffer size: the process needs that a bufferReader
 reads the screen output stream and the error output stream.



P

PageValueBean - class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean.
This bean class is for constructing value parameter for HTML buttons.
PageValueBean(String) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
Constructs from a string.
PageValueBean(String, String, String) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
Constructs from given values for major, minor and ac components.
PARAMETER_SEARCH_AC - 
Static variable in class uk.ac.ebi.intact.model.Constants
The name of a parameter from a form submission.
PARAMETER_SEARCH_NAME - 
Static variable in class uk.ac.ebi.intact.model.Constants
The name of a parameter from a form submission.
paramSearch(String, String, String, boolean, boolean) - 
Method in interface uk.ac.ebi.intact.business.SearchI
This method provides a means of searching intact objects, within the constraints
 provided by the parameters to the method.
paramSearch(String, String, String, boolean, boolean) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
 
ParamTest(int, ArrayList) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
This method tests if the evalue is smaller than the constant defined in the web.xml file,
 which means that the alignment is acceptable.
parseColor(String, int, int, int) - 
Static method in class uk.ac.ebi.intact.application.hierarchView.business.image.Utilities
Parse a string (number separated by comma) and create a Color Object
 The string has to be initialized
parseGoDefs(String) - 
Method in class uk.ac.ebi.intact.util.InsertGo
Reads a GO definition file from a URL.
parseKeys(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource
Parse the set of key generate by the source and give back a collection of keys.
parseKeys(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource
Parse the set of key generate by the source and give back a collection of keys.
parseOutputFile(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl
Parse the Tulip conputed TLP file to grab coordinates of each protein

 Here is the format of the section to parse :

 (property  0 layout "viewLayout"
 (default "(105.000000,966.000000,359.000000)" "()" )
 (node 1 "(215.500000,7.000000,0.000000)")
 (node 2 "(57.500000,-288.000000,0.000000)")
 (node 3 "(40.500000,191.000000,0.000000)")
 (...)
 )
ParseWithReAllFollow(String, String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method allows to parse one line with one Regular Expression in JAVA and to
 retrieve all items described in this RE, except the whole line.
ParseWithReOneGroup(String, String, int) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method allows to parse one line of a file with a Regular Expression in JAVA
 and to retrieve only one item of this line.
PARSING_BEGIN_FRAGMENT_QUERY - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
PARSING_BEGIN_FRAGMENT_SUBJECT - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
PARSING_END_FRAGMENT_QUERY - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
PARSING_END_FRAGMENT_SUBJECT - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
PARSING_ID - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
WU BLAST
 regular expressions to parse the standard blast output file (-m 0 and wu-blast output file)
 
PARSING_PERCENTAGE - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
PARSING_TABLE_BLAST_FILE - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
NCBI BLAST
 regular expression to parse the table blast output file (-m 9 ~ ncbi blast option)
 
PARSING_TABLE_FASTA_FILE - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
FASTA
 regular expression to parse the table fasta output file (-m 9 ~ ncbi fasta option)
 
PARSING_TABLE_WGETZ_AC - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
WGETZ (to run SRS)
 regular expression to parse the table wgetz ouput file (+-vn3+-ascii option = 4 columns)

  SWALL:A1AF_CAVPO        P22324  Alpha-1-antiproteinase F precursor (Alpha-1-antitrypsin) (Alpha-1- proteinase inhibitor) (APF) (Fragment).
parsingExceptions - 
Variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
perform(String, String, HttpSession, InteractionNetwork) - 
Static method in class uk.ac.ebi.intact.application.hierarchView.highlightment.HighlightProteins
Constructor
 Allow to modify the current graph to highlight a part of this.
persist() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Persists the object the user is editing.
persist() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
persist(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Persists the current state to the persistent system.
persistOthers(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Persist any sub objects of the edited object.
persistOthers(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
Person - class uk.ac.ebi.intact.model.Person.
Represents the contact details of a person.
Person() - 
Constructor for class uk.ac.ebi.intact.model.Person
Deprecated. Use the full constructor instead
postalAddress - 
Variable in class uk.ac.ebi.intact.model.Institution
Postal address.
PostgresSequenceManager - class uk.ac.ebi.intact.persistence.PostgresSequenceManager.
This sequence manager accesses a database sequence object to
 get the next unique id, leaving the management of the sequence
 to the database.
PostgresSequenceManager(PersistenceBroker) - 
Constructor for class uk.ac.ebi.intact.persistence.PostgresSequenceManager
Public constructor
precalcDensity(int) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
precalculate all densities for binaryInteractions between various go-nodes.
precalcDensity(Set) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
precalculation of the go densities by a set of go-ids
PrecalcGoGoDensities - class uk.ac.ebi.intact.application.goDensity.setupGoDensity.PrecalcGoGoDensities.
Precalculation of GO-GO-Densities according to a goFlatfile (e.g goSlim.ontology)
PrecalcGoGoDensities() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.setupGoDensity.PrecalcGoGoDensities
 
PredictActionServlet - class uk.ac.ebi.intact.application.predict.struts.framework.PredictActionServlet.
The predict action servlet class.
PredictActionServlet() - 
Constructor for class uk.ac.ebi.intact.application.predict.struts.framework.PredictActionServlet
 
PredictConstants - interface uk.ac.ebi.intact.application.predict.struts.framework.PredictConstants.
Defines constants required for the Predict application.
PREDICTION - 
Static variable in interface uk.ac.ebi.intact.application.predict.struts.framework.PredictConstants
The key for the prediction results.
PredictionAction - class uk.ac.ebi.intact.application.predict.struts.action.PredictionAction.
Implementation of Action that validates a user access.
PredictionAction() - 
Constructor for class uk.ac.ebi.intact.application.predict.struts.action.PredictionAction
 
PredictLogger - class uk.ac.ebi.intact.application.predict.util.PredictLogger.
The logger for the Predict application.
PredictLogger() - 
Constructor for class uk.ac.ebi.intact.application.predict.util.PredictLogger
 
PredictOra - class uk.ac.ebi.intact.application.predict.util.PredictOra.
Runs the PAYG algorithm for Oracle database.
PredictPg - class uk.ac.ebi.intact.application.predict.util.PredictPg.
Runs the PAYG algorithm for Postgres database.
PredictService - class uk.ac.ebi.intact.application.predict.business.PredictService.
This class provides the general services common to all the users.
PredictService() - 
Constructor for class uk.ac.ebi.intact.application.predict.business.PredictService
 
PredictUser - class uk.ac.ebi.intact.application.predict.business.PredictUser.
The super class for a predict user.
PredictUser() - 
Constructor for class uk.ac.ebi.intact.application.predict.business.PredictUser
Default constructor.
PredictUserOra - class uk.ac.ebi.intact.application.predict.business.PredictUserOra.
This class implements Predict user for an Oracle database.
PredictUserOra() - 
Constructor for class uk.ac.ebi.intact.application.predict.business.PredictUserOra
 
PredictUserPg - class uk.ac.ebi.intact.application.predict.business.PredictUserPg.
This class implements Predict user for a Postgres database.
PredictUserPg() - 
Constructor for class uk.ac.ebi.intact.application.predict.business.PredictUserPg
 
PrepareBufferedReader() - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method prepares the buffered reader, to put the file managed
 in a buffer, which allow to work on its content and parse it.
prepareSequenceStm(Class) - 
Method in class uk.ac.ebi.intact.persistence.AbstractSequenceManager
Prepare a statement to retrieve the next unique ID
 from a database sequence object.
printStackTrace() - 
Method in class uk.ac.ebi.intact.application.editor.exception.BaseException
Print both the normal and root stack traces to the std err.
printStackTrace(PrintStream) - 
Method in class uk.ac.ebi.intact.application.editor.exception.BaseException
Print both the normal and root stack traces.
printStackTrace(PrintWriter) - 
Method in class uk.ac.ebi.intact.application.editor.exception.BaseException
Print both the normal and root stack traces.
printTime(long) - 
Method in class uk.ac.ebi.intact.util.Chrono
 
printTimeInMinutes(long) - 
Method in class uk.ac.ebi.intact.util.Chrono
 
printTimeInSeconds(long) - 
Method in class uk.ac.ebi.intact.util.Chrono
 
process(String) - 
Method in class uk.ac.ebi.intact.util.InsertComplexGiot
 
processExperiments(Collection) - 
Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder
Generate the PSI xml for a list of experiments
processExperiments(Collection) - 
Method in interface uk.ac.ebi.intact.application.dataConversion.DataBuilder
Builds some file data for a specific Intact object.
processingInstruction(String, String) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
processLargeExperiment(Experiment, String) - 
Static method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator
 
processWsddFile(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
process the WSDD file given in parameter.
produceImage(IntactUserI) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Produces image accordingly to the interaction network stored in the user :
 Any errors are stored in the ActionErrors object.
Product - class uk.ac.ebi.intact.model.Product.
Describes products of an interaction.
Product() - 
Constructor for class uk.ac.ebi.intact.model.Product
Deprecated. Use the full constructor instead (when it exists)
PROPERTY_FILE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants
Where to find the property file
PropertyLoader - class uk.ac.ebi.intact.util.PropertyLoader.
Allow to create a set of properties from a file.



    example : 


   let's say the onfig/database.properties file contains :

   database.login=username

   

   ---

   

   
Protein - interface uk.ac.ebi.intact.model.Protein.
 
PROTEIN_DATA - 
Static variable in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
Data to extract from the IntactStatistics
proteinAc - 
Variable in class uk.ac.ebi.intact.model.Feature
 
ProteinBean - class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean.
Bean to store data for an Interactor (Protein).
ProteinBean(Component) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
Instantiate an object of this class from a Component instance.
ProteinBean(Protein) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
Instantiate an object of this class from a Protein instance.
ProteinCoordinate - class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate.
 
ProteinCoordinate - class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate.
Purpose : 

 Allows to store for a single protein its coordinates.
ProteinCoordinate() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
 
ProteinCoordinate(int) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
 
ProteinCoordinate(int, float, float) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
-------------------------------------------------------- Constructors
ProteinDecorator - class uk.ac.ebi.intact.application.intSeq.struts.view.utils.ProteinDecorator.
Decorator which should be used by the display:table tag in order to display properly
 accession numbers with their description.
ProteinDecorator() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.ProteinDecorator
 
ProteinDetailsViewBean - class uk.ac.ebi.intact.application.search2.struts.view.details.ProteinDetailsViewBean.
Displays a collection of Protein in the context of their Experiment.
ProteinDetailsViewBean(Collection, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.details.ProteinDetailsViewBean
Construct an instance of this class for given collection of object.
ProteinDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction.
The action class for editing a Protein.
ProteinDispatchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction
 
ProteinExport - class uk.ac.ebi.intact.util.ProteinExport.
 
ProteinExport() - 
Constructor for class uk.ac.ebi.intact.util.ProteinExport
 
ProteinFastaDownload - class uk.ac.ebi.intact.util.ProteinFastaDownload.
This util class retrieves protein sequences from IntAct

 It downloads all IntAct sequences in fasta format into a file "proteinFastaDownload":
              * the fasta header contains the IntAct ac
              * the protein sequence follows (from the next line)

 like that:

          >ac
          seq...........................
ProteinFastaDownload() - 
Constructor for class uk.ac.ebi.intact.util.ProteinFastaDownload
 
ProteinImpl - class uk.ac.ebi.intact.model.ProteinImpl.
Represents a protein or peptide.
ProteinImpl(Institution, BioSource, String) - 
Constructor for class uk.ac.ebi.intact.model.ProteinImpl
Creates a valid Protein instance.
ProteinNotFoundException - exception uk.ac.ebi.intact.application.hierarchView.exception.ProteinNotFoundException.
Thrown when we don't find a protein by its AC
ProteinNotFoundException() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.ProteinNotFoundException
 
ProteinNotFoundException(String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.ProteinNotFoundException
 
proteinNumber - 
Variable in class uk.ac.ebi.intact.util.IntactStatistics
 
ProteinProxy - class uk.ac.ebi.intact.model.proxy.ProteinProxy.
 
ProteinProxy() - 
Constructor for class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
ProteinProxy(InvocationHandler) - 
Constructor for class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
ProteinProxy(PBKey, Identity) - 
Constructor for class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
ProteinSearchAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinSearchAction.
The action class to search a Protein.
ProteinSearchAction - class uk.ac.ebi.intact.application.intSeq.struts.controller.ProteinSearchAction.
This action provides the actions required for the SRS Search page,
      --to do a request on the SP-Tr public database by SRS, if the IntAct entry doesn't exist.
ProteinSearchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinSearchAction
 
ProteinSearchAction() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.controller.ProteinSearchAction
 
ProteinSearchDynaForm - class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinSearchDynaForm.
The form to search for Proteins.
ProteinSearchDynaForm() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinSearchDynaForm
 
ProteinSearchForm - class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm.
This form captures the user action of the srsSearch.jsp.
ProteinSearchForm() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm
 
ProteinSingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.ProteinSingleViewBean.
View bean responsible for the display of a single protein.
ProteinSingleViewBean(AnnotatedObject, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.ProteinSingleViewBean
Construct an instance of this class for given object.
proteinToHightlight(HttpSession, InteractionNetwork) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource
Create a set of protein we must highlight in the graph given in parameter.
proteinToHightlight(HttpSession, InteractionNetwork) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource
Create a set of protein we must highlight in the graph given in parameter.
proteinTopic - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
protein feature which has been captured by the user
PROTOCOL - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
PROXY_PROPERTIES_FILE - 
Static variable in class uk.ac.ebi.intact.util.HttpProxyManager
 
PsiDataBuilder - class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder.
PSI-specific implementation of DataBuilder interface.
PsiDataBuilder() - 
Constructor for class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder
 
put(Object, Object) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
adds an Object by a certain value Object.
PutInFile(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesSrs
This method overrides the PutInFile method.
PutInFile(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method allows to write a string, more or less long, in a file
 which has been created before.



Q

QUALIFIERS - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the qualifier list.
query(InputStream, String) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy
Queries the ego (http://www.ebi.ac.uk/ego) server with given GO term id.
query(int) - 
Method in class uk.ac.ebi.intact.util.NewtServerProxy
Queries the Newt server with given tax id.
query(String) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy
Queries the ego (http://www.ebi.ac.uk/ego) server with given GO term id.



R

Range - class uk.ac.ebi.intact.model.Range.
TODO comments
Range(int, int) - 
Constructor for class uk.ac.ebi.intact.model.Range
 
rangeAc - 
Variable in class uk.ac.ebi.intact.model.Modification
 
readBean() - 
Method in class uk.ac.ebi.intact.util.fileParsing.BeanStreamReader
 
readExternal(ObjectInput) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Used for serialization via Externalizable.
ReadingFile() - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method allows to recover the file content in a String.
recent(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionDispatchAction
Process the specified HTTP request, and create the corresponding
 HTTP response (or forward to another web component that will create
 it).
recent(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentDispatchAction
Process the specified HTTP request, and create the corresponding
 HTTP response (or forward to another web component that will create
 it).
REDIRECTION - 
Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
Reference - class uk.ac.ebi.intact.model.Reference.
TODO COMMENTS
Reference() - 
Constructor for class uk.ac.ebi.intact.model.Reference
This constructor exists only for the benefit of subclasses so that
 they can call the BasicObject no-arg constructor.
Reference(Institution, String, String) - 
Constructor for class uk.ac.ebi.intact.model.Reference
 
referenceAc - 
Variable in class uk.ac.ebi.intact.model.ReferenceQualifier
 
referenceAc - 
Variable in class uk.ac.ebi.intact.model.SubmissionRef
 
ReferenceQualifier - class uk.ac.ebi.intact.model.ReferenceQualifier.
This class qualifies the association between an AnnotatedObject and a
 Reference.
ReferenceQualifier(Reference, CvReferenceQualifier) - 
Constructor for class uk.ac.ebi.intact.model.ReferenceQualifier
 
references - 
Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
refreshDbConnection() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.FastGoDag
test if the connection to db is still available and if not,
 it reconnect to the db - used my default where ever sql-statements are used.
release() - 
Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
release(String) - 
Method in class uk.ac.ebi.intact.application.editor.util.LockManager
Removes given lock.
releaseAllLocks(String) - 
Method in class uk.ac.ebi.intact.application.editor.util.LockManager
Release all the locks held by given owner.
releaseLock() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Releases the lock held by the user.
releaseLock() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
remove(Object) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
removes an object from persistent store.
remove(Object) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
removes an object from persistent store.
removeActiveInstance(Component) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
removeActiveInstance(Component) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
removeActiveInstance(Component) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
removeAlias(Alias) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
removeAlias(Alias) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
removeAlias(Alias) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
removeAnnotatedObject(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.model.Reference
 
removeAnnotation(Annotation) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
removeAnnotation(Annotation) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
removeAnnotation(Annotation) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
removeBindingDomain(Feature) - 
Method in class uk.ac.ebi.intact.model.Component
 
removeChild(CvDagObject) - 
Method in class uk.ac.ebi.intact.model.CvDagObject
 
removeComponent(Component) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
removeComponent(Component) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
removeComponent(Component) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
removeEvidence(Evidence) - 
Method in interface uk.ac.ebi.intact.model.BasicObject
 
removeEvidence(Evidence) - 
Method in class uk.ac.ebi.intact.model.BasicObjectImpl
 
removeEvidence(Evidence) - 
Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
 
removeExperiment(Experiment) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
removeExperiment(Experiment) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
removeExperiment(Experiment) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
removeFeature(Feature) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
removeFeature(Feature) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
removeFeature(Feature) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
removeFormBean(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Removes the obsolete form bean.
removeFromCache(Object) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Removes given object from the cache.
removeFromCache(Object) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
removeFromCache(Object) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
Removes the given object from the cachce; hence, cancelling any changes
 to the object.
removeFromCurrentExperiment(Experiment) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Removes the current experiment from the currently edited/added
 experiment list.
removeFromCurrentExperiment(Experiment) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
removeFromCurrentInteraction(Interaction) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Removes the current interaction from the currently edited/added
 interaction list.
removeFromCurrentInteraction(Interaction) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
removeFromRecentList(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Removes the current edit object from the recent edited item list.
removeFromRecentList(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
removeFromRecentList(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
removeInteraction(Interaction) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
removeModification(Modification) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
removeModification(Modification) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
removeModification(Modification) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
removeObject(Object) - 
Method in class uk.ac.ebi.intact.util.ObjectSet
 
removeParent(CvDagObject) - 
Method in class uk.ac.ebi.intact.model.CvDagObject
 
removeProduct(Product) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
removeProduct(Product) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
removeProduct(Product) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
removeRange(Range) - 
Method in class uk.ac.ebi.intact.model.Feature
 
removeReference(Reference) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
removeReference(Reference) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
removeReference(Reference) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
removeReleased(Product) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
removeReleased(Product) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
removeReleased(Product) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
removeUnsavedProteins() - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
Removes all the unsaved proteins for the current protein collection.
removeXref(Xref) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
removeXref(Xref) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
removeXref(Xref) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
replace(String, String, String) - 
Static method in class uk.ac.ebi.intact.util.SearchReplace
Perform a search replace on a text.
RepositoryFile - 
Static variable in class uk.ac.ebi.intact.application.synchron.XmlDumper
 
reset() - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean
Resets the internal key.
reset() - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Resets fields to blanks, so the addXref form doesn't display
 previous values.
reset() - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean
Resets fields to blanks, so the addAnnotation form doesn't display
 previous values.
reset() - 
Method in class uk.ac.ebi.intact.util.Chrono
 
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm
Reset all properties to their default values.
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
Reset all properties to their default values.
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm
Reset all properties to their default values.
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm
 
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.WelcomeForm
Reset all properties to their default values.
reset(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
Reset all properties to their default values.
reset(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Resets with the bean using an existing Annotated object.
reset(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
reset(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
reset(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
reset(Class) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Resets the bean with the current edit class.
reset(Class) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
reset(Class) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
reset(Class) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
reset(Object) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Resets the bean with given object.
resetCriteria() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
remove all existing criteria from the interaction network
resetHighlightOptions() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
Clear all highlight options.
resetHighlightOptions() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
ResetOjbCacheServlet - class uk.ac.ebi.intact.application.commons.util.ResetOjbCacheServlet.
When called that servlet is reseting the OJB cache of the calling application.
ResetOjbCacheServlet() - 
Constructor for class uk.ac.ebi.intact.application.commons.util.ResetOjbCacheServlet
 
resetSourceURL() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
resetSourceURL() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
resetUserInfo(String, String) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
changes the username and password details used for connection.
RestoreContextFromCookieTag - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.RestoreContextFromCookieTag.
That tag allows to restore the eventual user context of the user
 from a cookie which has been created and updated by SaveContextInCookieTag.
RestoreContextFromCookieTag() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.RestoreContextFromCookieTag
 
RestoreErrorsTag - class uk.ac.ebi.intact.application.commons.struts.taglibs.RestoreErrorsTag.
That class allows to restore in the request scope any errors saved
 in the session scope via the tag <intact:saveErrors>.
RestoreErrorsTag() - 
Constructor for class uk.ac.ebi.intact.application.commons.struts.taglibs.RestoreErrorsTag
 
RESULT - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants
Forward to the result page.
ResultAction - class uk.ac.ebi.intact.application.editor.struts.action.ResultAction.
The action when the the user selects an entry from a list to edit an object.
ResultAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.ResultAction
 
ResultBean - class uk.ac.ebi.intact.application.predict.struts.view.ResultBean.
 
ResultBean(Protein, int) - 
Constructor for class uk.ac.ebi.intact.application.predict.struts.view.ResultBean
 
ResultDisplayWrapper - class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper.
This class is the wrapper class for the display library to display
 results from a search page.
ResultDisplayWrapper() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.ResultDisplayWrapper
 
ResultParsing(ArrayList, int) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFilesBlast
This method parses a wu-blast output file, to retrieve the accession number of each result,
 the percentage identity with the query, start and end of the both aligned fragments.
ResultParsing(ArrayList, int) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method parses a file with only one item requiered and returns the list of this
 item possibly retrieved in several lines.
ResultParsingTableFile(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
This method parses a file from one Regular Expression given.
resultWgetzQuery - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
 
RetrieveAccDes() - 
Method in interface uk.ac.ebi.intact.application.intSeq.business.CallingSrsIF
request result: return a list of accession numbers and its own description.
RetrieveAccDes() - 
Method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
Wgetz execution + parsing of the WGETZ output file
RetrieveParseResult() - 
Method in interface uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearchIF
return the file which contains all Blast results from the user's request.
RetrieveParseResult() - 
Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
In case of a good blast execution, the output blast file would be parsed.
returnToExperiment(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Returns true if the next forward action is back to the experiment editor.
ROLES - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the role list.
rollback() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
 
rollback() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
rollback() - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
rollback a transaction.
rollback() - 
Method in interface uk.ac.ebi.intact.persistence.DAO
rollback a transaction.
rootCauseExists() - 
Method in class uk.ac.ebi.intact.application.dataConversion.DataConversionException
 
rootCauseExists() - 
Method in class uk.ac.ebi.intact.business.IntactException
 
RunSimilaritySearch - class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch.
This class manages the multiple alignment algorithm command line, defined in
 the web.xml file (it can be wu-blast, ncbi-blast or fasta).
RunSimilaritySearch(String, String, double) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
constructor which retrieves the Evalue minimum, required to validate the results,
 in addition to the command line and the protein sequence.
RunSimilaritySearchIF - interface uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearchIF.
Interface which provides methods specific to check if the multiple alignment command
 has been well executed, and to retrieve the result list, made of arrays with:
              * the accession number
              * the percentage identity
              * the start of the query fragment
              * the start of the subject fragment
              * the end of the query fragment
              * the end of the subject fragment


S

SameGraphPathException - exception uk.ac.ebi.intact.application.goDensity.exception.SameGraphPathException.
2 GO:IDs are in the same graph path of a graph (DAG)
SameGraphPathException() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.exception.SameGraphPathException
 
SameGraphPathException(String) - 
Constructor for class uk.ac.ebi.intact.application.goDensity.exception.SameGraphPathException
 
sanityCheck(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Performs sanity check on a bean.
sanityCheck(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
sanityCheck(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
SanityChecker - class uk.ac.ebi.intact.util.SanityChecker.
Utility class to perform some sanity checks on the DB.
SanityChecker(IntactHelper, PrintWriter) - 
Constructor for class uk.ac.ebi.intact.util.SanityChecker
 
SAVE - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean
The saving state.
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction
Action for saving an edited annotation.
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction
Action for saving the edit form.
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.AnnotationDispatchAction
Action for saving an edited annotation.
save(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ProteinDispatchAction
 
saveComment(CommentBean, CommentBean) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Replaces an existing annotation bean with a new bean.
SaveContextInCookieTag - class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag.

 That tag allows to save in a cookie (stored in the client side)
 all needed data to restore later the user context.
SaveContextInCookieTag() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag
 
saveErrors(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Saves the errors in given request for  tag.
saveErrors(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.framework.IntactBaseAction
Saves the errors in given request for  tag.
saveErrors(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.search2.struts.framework.IntactBaseAction
Saves the errors in given request for  tag.
SaveErrorsTag - class uk.ac.ebi.intact.application.commons.struts.taglibs.SaveErrorsTag.
That class allows to save in the session scope any ActionErrors
 available in the request scope (in pageRequest)
SaveErrorsTag() - 
Constructor for class uk.ac.ebi.intact.application.commons.struts.taglibs.SaveErrorsTag
 
saveImage(String) - 
Method in class uk.ac.ebi.intact.application.goDensity.business.image.DensityImage
save the jpg image to a specified path
saveMessages(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Saves the Messages in given request for  tag.
saveMessages(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm
Saves the Messages in given request for  tag.
saveOptions(HttpServletRequest, HttpSession) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.HighlightmentSource
Allows to update the session object with options stored in the request.
saveOptions(HttpServletRequest, HttpSession) - 
Method in class uk.ac.ebi.intact.application.hierarchView.highlightment.source.GoHighlightmentSource
Allows to update the session object with parameters' request.
saveXref(XreferenceBean, XreferenceBean) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Replaces an existing xref bean with a new bean.
SEARCH - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants
Forward to the search page.
SEARCH_BY_AC - 
Static variable in class uk.ac.ebi.intact.model.Constants
a specific data store column  - better in a config file!!
SEARCH_BY_NAME - 
Static variable in class uk.ac.ebi.intact.model.Constants
a specific data store column - better in a config file!!
SEARCH_CLASSES - 
Static variable in class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction
The search order.
SEARCH_CRITERIA - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The search criteria key to display in the results JSP.
SEARCH_DETAIL - 
Static variable in class uk.ac.ebi.intact.model.Constants
The name of an attribute set in the session, holding more detailed search info.
SEARCH_PARAM - 
Static variable in class uk.ac.ebi.intact.model.Constants
session parameter used to identify the search criterion (ac or name)
SEARCH_PROPERTIES - 
Static variable in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
SEARCH_PROPERTY_FILE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
SEARCH_RESULTS - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The label used to identify the search results Collection (often saved in a request)
SEARCH_STRING - 
Static variable in interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants
 
SEARCH_VALUE - 
Static variable in class uk.ac.ebi.intact.model.Constants
The parameter name used to identify a value submitted for a search.
search(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.SidebarDispatchAction
Searches the CV database according to search criteria from the Form
 object.
search(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.experiment.InteractionDispatchAction
 
search(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.ExperimentDispatchAction
 
search(Object) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Deprecated. This should not be used with the new model, as applications should
 not use no-arg constructors.
search(String, String, String) - 
Method in interface uk.ac.ebi.intact.application.commons.business.IntactUserI
This method provides a means of searching intact objects, within the constraints
 provided by the parameters to the method.
search(String, String, String) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
search(String, String, String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
search(String, String, String) - 
Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
 
search(String, String, String) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
 
search(String, String, String) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
This method provides a means of searching intact objects, within the constraints
 provided by the parameters to the method.
search1(String, String, String) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
This method provides a means of searching intact objects, within the constraints
 provided by the parameters to the method.
search1(String, String, String) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
SearchAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.SearchAction.
Implementation of Action that validates a visualize submisson.
SearchAction - class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction.
This class provides the actions required to carry out search operations
 for intact via a web-based interface.
SearchAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.SearchAction
 
SearchAction() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.SearchAction
 
searchBySQL(String, String) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Allows search by raw SQL String.
SearchConstants - interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants.
Contains constants required for the Search application.
SearchException - exception uk.ac.ebi.intact.application.editor.exception.SearchException.
Exception thrown for searching the database.
SearchException - exception uk.ac.ebi.intact.persistence.SearchException.
Exception class to provide more meaningful error messages.
SearchException() - 
Constructor for class uk.ac.ebi.intact.persistence.SearchException
 
SearchException(String) - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.SearchException
Constructor with a message.
SearchException(String) - 
Constructor for class uk.ac.ebi.intact.persistence.SearchException
 
SearchException(String, Exception) - 
Constructor for class uk.ac.ebi.intact.persistence.SearchException
 
SearchForm - class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm.
Form bean for the main form of the view.jsp page.
SearchForm() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
 
SearchHelper - class uk.ac.ebi.intact.application.commons.search.SearchHelper.
Performs an intelligent search on the intact database.
SearchHelper(Logger) - 
Constructor for class uk.ac.ebi.intact.application.commons.search.SearchHelper
Create a search helper for which all the log message will be written by the provided logger.
SearchHelperI - interface uk.ac.ebi.intact.application.commons.search.SearchHelperI.
Interface describing how to search data in IntAct.
SearchI - interface uk.ac.ebi.intact.business.SearchI.
 
SearchOptionTab(String, ArrayList) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
This method splits the command line according to the spaces,
 and retrieve an item in it.
SearchReplace - class uk.ac.ebi.intact.util.SearchReplace.
Managment of search replace with regular expression.
SearchReplace() - 
Constructor for class uk.ac.ebi.intact.util.SearchReplace
 
searchResults - 
Variable in class uk.ac.ebi.intact.persistence.ObjectSearch
A vector of objects that match the search criterai
searchSelected() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
True if Search button is pressed.
searchString - 
Variable in class uk.ac.ebi.intact.persistence.ObjectSearch
The query string used to search for the objects
searchValue - 
Variable in class uk.ac.ebi.intact.persistence.ObjectSearch
The search string to be used
secondaryXrefQualifier - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
SELECT_LIST_ITEM - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The list item to indicate a selection is required.
selectCvObject(IntactHelper, String, Hashtable, Class) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Select an appropriate CvObject for update if it exists.
selectCvObject(IntactHelper, String, String, String, Class) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Select an appropriate CvObject for update if it exists.
SELECTED_SPECIE - 
Static variable in class uk.ac.ebi.intact.application.predict.business.PredictUser
 
selectedChunk - 
Variable in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean
The chunk we will wisplay
SeqIdConstants - interface uk.ac.ebi.intact.application.intSeq.struts.framework.SeqIdConstants.
Contains constants required for the IntSeq application.
sequence - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
protein sequence written in the input file
SequenceChunk - class uk.ac.ebi.intact.model.SequenceChunk.
Represents a crossreference to another database.
SequenceChunk() - 
Constructor for class uk.ac.ebi.intact.model.SequenceChunk
 
SequenceChunk(int, String) - 
Constructor for class uk.ac.ebi.intact.model.SequenceChunk
 
SequenceSimilarityAction - class uk.ac.ebi.intact.application.intSeq.struts.controller.SequenceSimilarityAction.
This action provides the actions required for the Similarity Search page.
SequenceSimilarityAction() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.controller.SequenceSimilarityAction
 
SequenceSimilarityForm - class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm.
This form captures the user action of the similaritySearch.jsp.
SequenceSimilarityForm() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
SerializationHelper - class uk.ac.ebi.intact.util.fileParsing.SerializationHelper.
That class .
SerializationHelper() - 
Constructor for class uk.ac.ebi.intact.util.fileParsing.SerializationHelper
 
serialize(Object, String) - 
Method in class uk.ac.ebi.intact.util.fileParsing.SerializationHelper
 
serialize(Serializable) - 
Static method in class uk.ac.ebi.intact.util.Serializer
simple method to serialize an object.
serializeDeserialize(Serializable) - 
Static method in class uk.ac.ebi.intact.util.Serializer
performs serialization and then deserialization.
Serializer - class uk.ac.ebi.intact.util.Serializer.
Simple utility class for checking serialization for objects.
Serializer() - 
Constructor for class uk.ac.ebi.intact.util.Serializer
 
SERVER_ERROR - 
Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
SERVER_PATH - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The key to access the server path.
SERVICE - 
Static variable in interface uk.ac.ebi.intact.application.predict.struts.framework.PredictConstants
The key to access the service handler.
service(HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.commons.util.ResetOjbCacheServlet
Clear the OJB cache of the calling application.
SESSION_KEY - 
Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
SessionExpiredException - exception uk.ac.ebi.intact.application.commons.exception.SessionExpiredException.
Throws when a session is expired.
SessionExpiredException - exception uk.ac.ebi.intact.application.editor.exception.SessionExpiredException.
Throws when a session is expired.
SessionExpiredException - exception uk.ac.ebi.intact.application.hierarchView.exception.SessionExpiredException.
Thrown when the user session is expired.
SessionExpiredException() - 
Constructor for class uk.ac.ebi.intact.application.commons.exception.SessionExpiredException
 
SessionExpiredException() - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.SessionExpiredException
 
SessionExpiredException() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.SessionExpiredException
 
SessionExpiredException(String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.exception.SessionExpiredException
 
setAc(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setAc(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the ac column.
setAc(String) - 
Method in class uk.ac.ebi.intact.model.SequenceChunk
 
setAc(String) - 
Method in interface uk.ac.ebi.intact.model.IntactObject
 
setAc(String) - 
Method in class uk.ac.ebi.intact.model.IntactObjectImpl
Deprecated. No replacement - should not be used by applications
setAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
setAcc(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
Set the accession number field.
setAction(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
Sets the action.
setAction(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm
Sets the action.
setAction(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm
Sets the action.
setActiveInstances(Collection) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
setActiveInstances(Collection) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
setActiveInstances(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
setAliases(Collection) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setAliases(Collection) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setAliases(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setAnnotatedObject(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Sets the annotated object for the bean.
setAnnotation(Collection) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setAnnotation(Collection) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setAnnotation(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setAnnotationText(String) - 
Method in class uk.ac.ebi.intact.model.Annotation
 
setApplicationPath(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setAuthors(String) - 
Method in class uk.ac.ebi.intact.model.Reference
 
setAutoSave(boolean) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
 
setAutoSave(boolean) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
sets whether or not auto saving is turned on
setAutoSave(boolean) - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
Defines whether or not data are saved automatically
setAutoSave(boolean) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
sets whether or not auto saving is turned on
setBehaviour(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setBehaviour(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setBehaviour(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm
Set the behaviour value.
setBindingDomains(Collection) - 
Method in class uk.ac.ebi.intact.model.Component
 
setBioSource(BioSource) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
setBioSource(BioSource) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
setBioSource(BioSource) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setBioSource(BioSource) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
setBioSourceAc(String) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
setBioSourceAc(String) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
setBioSourceAc(String) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setBioSourceAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
setBoundDomain(Feature) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setBoundDomainAc(String) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setCellType(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
setClickBehaviour(ClickBehaviourForm) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setClickBehaviour(ClickBehaviourForm) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setComponent(Component) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setComponent1(Component) - 
Method in class uk.ac.ebi.intact.simpleGraph.Edge
 
setComponent1(Component) - 
Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
 
setComponent2(Component) - 
Method in class uk.ac.ebi.intact.simpleGraph.Edge
 
setComponent2(Component) - 
Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
 
setComponentAc(String) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setComponents(Collection) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setComponents(Collection) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setComponents(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setConditionAcSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
setConditionNameSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
setConfig(Map) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
This method sets up the configuration of ObjectBridge, based on
 the content of the configuration file whose name is passed
 in as a parameter.
setConfig(Map) - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
sets the configuration data for the data source.
setCount(int) - 
Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
 
setCrc64(String) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setCrc64(String) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setCrc64(String) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setCreated(Date) - 
Method in interface uk.ac.ebi.intact.model.IntactObject
 
setCreated(Date) - 
Method in class uk.ac.ebi.intact.model.IntactObjectImpl
 
setCreated(Date) - 
Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
setCurator(Person) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setCurator(Person) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setCurator(Person) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setCuratorAc(String) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setCuratorAc(String) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setCuratorAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setCurrentDepth(int) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setCurrentDepth(int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setCvAliasType(CvAliasType) - 
Method in class uk.ac.ebi.intact.model.Alias
 
setCvCellCycle(CvCellCycle) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvCellCycleAc(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvCellType(CvCellType) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvCellTypeAc(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvCompartment(CvCompartment) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvCompartmentAc(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvComponentRole(CvComponentRole) - 
Method in class uk.ac.ebi.intact.model.Component
 
setCvComponentRoleAc(String) - 
Method in class uk.ac.ebi.intact.model.Component
 
setCvDatabase(CvDatabase) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setCvDatabaseAc(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setCvDevelopmentalStage(CvDevelopmentalStage) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvDevelopmentalStageAc(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvEvidenceType(CvEvidenceType) - 
Method in class uk.ac.ebi.intact.model.Evidence
 
setCvEvidenceTypeAc(String) - 
Method in class uk.ac.ebi.intact.model.Evidence
 
setCvFeatureIdentification(CvFeatureIdentification) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setCvFeatureIdentificationAc(String) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setCvFeatureType(CvFeatureType) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setCvIdentification(CvIdentification) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setCvIdentificationAc(String) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setCvInteraction(CvInteraction) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setCvInteractionAc(String) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setCvInteractionType(CvInteractionType) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setCvInteractionType(CvInteractionType) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setCvInteractionType(CvInteractionType) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setCvInteractionTypeAc(String) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setCvInteractionTypeAc(String) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setCvInteractionTypeAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setCvJournal(CvJournal) - 
Method in class uk.ac.ebi.intact.model.JournalRef
 
setCvJournalAc(String) - 
Method in class uk.ac.ebi.intact.model.JournalRef
 
setCvModificationType(CvModificationType) - 
Method in class uk.ac.ebi.intact.model.Modification
 
setCvModificationTypeAc(String) - 
Method in class uk.ac.ebi.intact.model.Modification
 
setCvProductRole(CvProductRole) - 
Method in class uk.ac.ebi.intact.model.Product
 
setCvProteinForm(CvProteinForm) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setCvProteinForm(CvProteinForm) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setCvProteinForm(CvProteinForm) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setCvProteinFormAc(String) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setCvProteinFormAc(String) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setCvProteinFormAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setCvReferenceQualifier(CvReferenceQualifier) - 
Method in class uk.ac.ebi.intact.model.ReferenceQualifier
 
setCvReferenceQualifierAc(String) - 
Method in class uk.ac.ebi.intact.model.ReferenceQualifier
 
setCvTissue(CvTissue) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvTissueAc(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setCvTopic(CvTopic) - 
Method in class uk.ac.ebi.intact.model.Annotation
 
setCvTopicAc(String) - 
Method in class uk.ac.ebi.intact.model.Annotation
 
setCvXrefQualifier(CvXrefQualifier) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setCvXrefQualifierAc(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setDatabase(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets the database name.
setDbRelease(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setDebugOnScreen(boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Allows to displays on the screen what's going on during the update process.
setDebugOnScreen(boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
 
setDeploymentFile(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
 
setDepthToDefault() - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setDepthToDefault() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setDes(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
Set the description field.
setDescription(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean
Sets the annotated text.
setDescription(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setDescription(String) - 
Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
 
setDestinationExperiment(HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.AbstractEditorAction
Sets the destination experiment to edit.
setDirectHighlightUrl(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setDocumentLocator(Locator) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
setEditState(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean
Sets this bean's edit state.
setEmail(String) - 
Method in class uk.ac.ebi.intact.model.Person
 
setEvidences(Collection) - 
Method in interface uk.ac.ebi.intact.model.BasicObject
 
setEvidences(Collection) - 
Method in class uk.ac.ebi.intact.model.BasicObjectImpl
 
setEvidences(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
Implements BasicObject's methods
setExperiments(Collection) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setExperiments(Collection) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setExperiments(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setExpressedIn(BioSource) - 
Method in class uk.ac.ebi.intact.model.Component
 
setExpressedIn(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
 
setExpressedInAc(String) - 
Method in class uk.ac.ebi.intact.model.Component
 
setFeatures(Collection) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setFeatures(Collection) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setFeatures(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setFile(String, boolean, boolean, int) - 
Method in class uk.ac.ebi.intact.util.logging.IntactDailyRollingFileAppender
Over definition of that method inherited from FileAppender.
SetFileName(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
 
setFirstNames(String) - 
Method in class uk.ac.ebi.intact.model.Person
 
setFirstpage(String) - 
Method in class uk.ac.ebi.intact.model.JournalRef
 
setFormOf(Protein) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setFormOf(Protein) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setFormOf(Protein) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setFormOfAc(String) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setFormOfAc(String) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setFormOfAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setFromGoServer(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets Secondary id and Qualifier values from the Go Server using PrimaryId.
setFtpAddress(String) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setFtpDirectory(String) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setFtpLogin(String) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setFtpPassword(String) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setFullName(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Sets the full name.
setFullName(String) - 
Method in class uk.ac.ebi.intact.model.Institution
 
setFullName(String) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setFullName(String) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setFullName(String) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setGoIds(String) - 
Method in class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm
setter
setHeaderScript(String) - 
Method in class uk.ac.ebi.html.Helper
Sets a string to be embedded in page <head>
                 You need the appropriate tags (i.e.
setHelpLink(String) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
 
setHelpLink(String) - 
Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
 
setHighlightMap(Set) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
 
setHoldDate(Date) - 
Method in class uk.ac.ebi.intact.model.SubmissionRef
 
setHost(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm
 
setId(int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
 
setId(int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
 
setId(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setId(String) - 
Method in interface uk.ac.ebi.intact.simpleGraph.BasicGraphI
 
setId(String) - 
Method in class uk.ac.ebi.intact.simpleGraph.BasicGraph
 
setIdent(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
setImageBean(ImageBean) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setImageBean(ImageBean) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setImageData(BufferedImage) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
 
setImageHeight(int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
 
setImageWidth(int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
 
setInstitution(Institution) - 
Method in class uk.ac.ebi.intact.model.Person
 
setInstitutionAc(String) - 
Method in class uk.ac.ebi.intact.model.Person
 
setInter(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
setInteraction(Interaction) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
Sets the interaction for this bean.
setInteraction(Interaction) - 
Method in class uk.ac.ebi.intact.model.Product
 
setInteraction(Interaction) - 
Method in class uk.ac.ebi.intact.model.Component
 
setInteractionAc(String) - 
Method in class uk.ac.ebi.intact.model.Component
 
setInteractionAcSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
Sets the search string based on an interaction accessionNumber
setInteractionNameSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
setInteractionNetwork(InteractionNetwork) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setInteractionNetwork(InteractionNetwork) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setInteractions(Collection) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setInteractionType(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
setInteractor(Interactor) - 
Method in class uk.ac.ebi.intact.model.Product
 
setInteractor(Interactor) - 
Method in class uk.ac.ebi.intact.model.Component
TODO document that non obvious method
setInteractorAc(String) - 
Method in class uk.ac.ebi.intact.model.Component
 
setKD(Float) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
setKD(Float) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setKD(Float) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setKD(Float) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setKey(String) - 
Method in class uk.ac.ebi.intact.util.Key
 
setKeys(Collection) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setKeys(Collection) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setLabel(String) - 
Method in interface uk.ac.ebi.intact.simpleGraph.BasicGraphI
 
setLabel(String) - 
Method in class uk.ac.ebi.intact.simpleGraph.BasicGraph
 
setLastCheckId(int) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setLastProvidedDate(Timestamp) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setLastProvidedId(int) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setLayout(ComponentContext) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Sets the layout in given context.
setLayout(ComponentContext) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
setLayout(ComponentContext) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
setLayout(ComponentContext) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
setLoadMethods(String) - 
Method in class uk.ac.ebi.html.Helper
Sets the javascript to call on loading the page the surrounding html tags are generated - just javascript please!
setLocalTransactionControl(boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
If true, each protein is updated in a distinct transaction.
setLocalTransactionControl(boolean) - 
Method in class uk.ac.ebi.intact.util.UpdateProteins
If true, each protein is updated in a distinct transaction.
setLogger(Logger) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
 
setLogger(Logger) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
setLogger(Logger) - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
allows a logging destination to be specified
setLogger(Logger) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
allows a logging destination to be specified
setLogger(Logger) - 
Method in class uk.ac.ebi.intact.util.UpdateProteinsI
Set the updateprotein logger and those of 3rd party tools.
setLogger(Logger) - 
Method in class uk.ac.ebi.intact.util.BioSourceFactory
Set a logger to keep track of the internal processing.
setMapCode(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean
 
setMenuFactory(EditorMenuFactory) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Sets the menu factory to create menus.
setMessageArgs(String[]) - 
Method in class uk.ac.ebi.intact.application.editor.exception.BaseException
The arguments to pass to place holders in the application resources file.
setMessageKey(String) - 
Method in class uk.ac.ebi.intact.application.editor.exception.BaseException
Sets the message key.
setMethod(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
 
setMethodClass(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setMethodClass(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setMethodLabel(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setMethodLabel(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setModification(Modification) - 
Method in class uk.ac.ebi.intact.model.Range
 
setModificationAc(String) - 
Method in class uk.ac.ebi.intact.model.Range
 
setModifications(Collection) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setModifications(Collection) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setModifications(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setMoleculeAcSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
setMoleculeNameSearch() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
setMw(float) - 
Method in class uk.ac.ebi.intact.model.Complex
 
setName(String) - 
Method in class uk.ac.ebi.intact.model.Alias
 
setNode1(NodeI) - 
Method in class uk.ac.ebi.intact.simpleGraph.Edge
 
setNode1(NodeI) - 
Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
 
setNode2(NodeI) - 
Method in class uk.ac.ebi.intact.simpleGraph.Edge
 
setNode2(NodeI) - 
Method in interface uk.ac.ebi.intact.simpleGraph.EdgeI
 
setNumberOfBinaryInteractions(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setNumberOfComplexInteractions(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setNumberOfExperiments(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setNumberOfGoTerms(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setNumberOfInteractions(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setNumberOfProteins(int) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setObject(String) - 
Method in class uk.ac.ebi.intact.application.statisticView.business.data.DisplayStatisticsBean
 
setObjects(Vector) - 
Method in class uk.ac.ebi.intact.util.ObjectSet
 
setOrganism(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
setOrganism(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
setOut(Writer) - 
Method in class uk.ac.ebi.html.Helper
Set the Writer to output the page to.
setOwner(Institution) - 
Method in interface uk.ac.ebi.intact.model.BasicObject
 
setOwner(Institution) - 
Method in class uk.ac.ebi.intact.model.BasicObjectImpl
 
setOwner(Institution) - 
Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
 
setOwnerAc(String) - 
Method in interface uk.ac.ebi.intact.model.BasicObject
 
setOwnerAc(String) - 
Method in class uk.ac.ebi.intact.model.BasicObjectImpl
 
setOwnerAc(String) - 
Method in class uk.ac.ebi.intact.model.proxy.BasicObjectProxy
 
setOwnerPrefix(String) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setParameters(String) - 
Method in class uk.ac.ebi.intact.model.Evidence
 
setParentAc(String) - 
Method in class uk.ac.ebi.intact.model.SequenceChunk
 
setParentAc(String) - 
Method in class uk.ac.ebi.intact.model.Alias
 
setParentAc(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setPassword(String) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
Used to define a password which overrides any default supplied via config data.
setPassword(String) - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
Used to define a password which overrides any default supplied via config data.
SetPathFile(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.ManagerFiles
 
setPercentage(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the percentage identity column.
setPosFrom(int) - 
Method in class uk.ac.ebi.intact.model.Range
 
setPostalAddress(String) - 
Method in class uk.ac.ebi.intact.model.Institution
 
setPosTo(int) - 
Method in class uk.ac.ebi.intact.model.Range
 
setPrimaryId(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets the primary id.
setPrimaryId(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setProducts(Collection) - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
setProducts(Collection) - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
setProducts(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractorProxy
 
setProtein(Protein) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setProteinAc(String) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setProtocol(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm
 
setPubmidId(Integer) - 
Method in class uk.ac.ebi.intact.model.JournalRef
 
setQualifier(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets the reference qualifier.
setQueryFragmentBegin(int) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the start of the query fragment.
setQueryFragmentEnd(int) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the end of the query fragment.
setQueryString(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setQueryString(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setQueryString(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
 
setRange(Range) - 
Method in class uk.ac.ebi.intact.model.Modification
 
setRangeAc(String) - 
Method in class uk.ac.ebi.intact.model.Modification
 
setReference(Reference) - 
Method in class uk.ac.ebi.intact.model.ReferenceQualifier
 
setReference(Reference) - 
Method in class uk.ac.ebi.intact.model.SubmissionRef
 
setReferenceAc(String) - 
Method in class uk.ac.ebi.intact.model.ReferenceQualifier
 
setReferenceAc(String) - 
Method in class uk.ac.ebi.intact.model.SubmissionRef
 
setReferences(Collection) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setReferences(Collection) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setReferences(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setRejected(int) - 
Method in class uk.ac.ebi.intact.model.IntactNode
 
setRelatedExperiment(Experiment) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setRelatedExperimentAc(String) - 
Method in class uk.ac.ebi.intact.model.Experiment
 
setReleased(Collection) - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
setReleased(Collection) - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
setReleased(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.InteractionProxy
 
setReleaseNumber(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets the release number.
setRole(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
 
setSearchClass(String) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
 
setSearchClass(String) - 
Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
 
setsearchResults(Collection) - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
Sets a vector of the search results to be paged.
setSearchString(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm
 
setSearchValue(String) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
 
setSearchValue(String) - 
Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
 
setSecondaryId(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Sets the secondary id.
setSecondaryId(String) - 
Method in class uk.ac.ebi.intact.model.Xref
 
setSection(String) - 
Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
setSelected(boolean) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setSelectedChunk(int) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
 
setSelectedChunk(int) - 
Method in interface uk.ac.ebi.intact.application.search2.business.IntactUserIF
 
setSelectedKey(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setSelectedKey(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setSelectedTopic(String) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
 
setSelectedTopic(String) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
setSequence(IntactHelper, String) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
If there is existing sequence (and chunks), reuse existing chunk
 in order to save AC.

 The update is canceled if the sequence is null or the same.
setSequence(IntactHelper, String) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setSequence(IntactHelper, String) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setSequence(IntactHelper, String, String) - 
Method in class uk.ac.ebi.intact.model.ProteinImpl
 
setSequence(IntactHelper, String, String) - 
Method in interface uk.ac.ebi.intact.model.Protein
 
setSequence(IntactHelper, String, String) - 
Method in class uk.ac.ebi.intact.model.proxy.ProteinProxy
 
setSequence(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.RunSimilaritySearch
 
setSequence(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
setSequenceChunk(String) - 
Method in class uk.ac.ebi.intact.model.SequenceChunk
 
setSequenceIndex(int) - 
Method in class uk.ac.ebi.intact.model.SequenceChunk
 
setShortLabel(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Sets the short label.
setShortLabel(String) - 
Method in class uk.ac.ebi.intact.model.Institution
 
setShortLabel(String) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setShortLabel(String) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setShortLabel(String) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setSourceBrowserUrl(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
setSourceExperimentAc(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
Set the AC of the source experiment.
setSourceURL(String) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
setSourceURL(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
 
setSpecie(String) - 
Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
 
setStart(String) - 
Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
 
setStoichiometry(float) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean
 
setStoichiometry(float) - 
Method in class uk.ac.ebi.intact.model.Product
 
setStoichiometry(float) - 
Method in class uk.ac.ebi.intact.model.Component
 
setStop(String) - 
Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
 
setSubjectFragmentBegin(int) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the start of the subject fragment.
setSubjectFragmentEnd(int) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
Set the end of the subject fragment.
setSubmissionRef(SubmissionRef) - 
Method in class uk.ac.ebi.intact.model.Reference
 
setSubmissionRefAc(String) - 
Method in class uk.ac.ebi.intact.model.Reference
 
setSurName(String) - 
Method in class uk.ac.ebi.intact.model.Person
 
setTaxId(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
setTaxId(String) - 
Method in class uk.ac.ebi.intact.model.BioSource
 
setTelephone(String) - 
Method in class uk.ac.ebi.intact.model.Person
 
setTimestamp(Timestamp) - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
setTissue(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
setTitle(String) - 
Method in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 
setTitle(String) - 
Method in class uk.ac.ebi.intact.model.Reference
 
setTopic(String) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.CommentBean
Sets the topic.
setTopMenuItem(String) - 
Method in class uk.ac.ebi.html.Helper
set the tab to which this page belongs
                 
                 if it starts with "internal/" an internal page is generated,
                 current meaningful topMenuItems are:
                         "internal/seqdb/introduction","internal/seqdb/organisation",
                         "internal/seqdb/projects", "internal/seqdb/curators", 
                         "internal/seqdb/computing" and "internal/seqdb/release"
                         
                 else an external page is generated, current meaningful internal menuitems are:
                         "aboutebi", "groups", "services", "tools", "databases", "submissions"
                 
                 default is to use the stylesheets and images in /services
setUndeploymentFile(String) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
 
setUnLoadMethods(String) - 
Method in class uk.ac.ebi.html.Helper
Sets the javascript to call on leaving the page
                 the surrounding html tags are generated - just javascript please!
                 Also note that it isn't good practice to annoy people with popups and such at this point!
setup() - 
Static method in class uk.ac.ebi.intact.util.HttpProxyManager
Setup the HTTP proxy.
setUp() - 
Method in class uk.ac.ebi.intact.util.TestCaseHelper
 
setup(PrintStream) - 
Static method in class uk.ac.ebi.intact.util.HttpProxyManager
Setup the HTTP proxy.
setUpdated(Date) - 
Method in interface uk.ac.ebi.intact.model.IntactObject
 
setUpdated(Date) - 
Method in class uk.ac.ebi.intact.model.IntactObjectImpl
 
setUpdated(Date) - 
Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
 
SetupGoDensityTables - class uk.ac.ebi.intact.application.goDensity.setupGoDensity.SetupGoDensityTables.
Insert of the go graph in goDensity specific tables (database)
SetupGoDensityTables() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.setupGoDensity.SetupGoDensityTables
 
setUrl(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
 
setUrl(String) - 
Method in class uk.ac.ebi.intact.model.Institution
 
setUser(String) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource
Used to specify a user for connecting to the persistent store.
setUser(String) - 
Method in interface uk.ac.ebi.intact.persistence.DAOSource
Used to specify a user for connecting to the persistent store.
setView(Object) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Sets the view using given object.
setView(Object) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
setWrappedObject(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean
 
setWrappedObjects(Collection) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean
 
setX(float) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
 
setX(float) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
 
setXref(Xref) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setXrefAc(String) - 
Method in class uk.ac.ebi.intact.model.Feature
 
setXrefAc(String) - 
Method in class uk.ac.ebi.intact.model.Reference
 
setXrefs(Collection) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
setXrefs(Collection) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
setXrefs(Collection) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
setY(float) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate
 
setY(float) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate
 
SEVERE_WARN - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.EditorConstants
The key for the severe warning messages.
sgdDatabase - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
shortLabel - 
Variable in class uk.ac.ebi.intact.model.Institution
The name of the institution.
shortLabel - 
Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
Short name for the object, not necessarily unique.
ShortLabelComparator - class uk.ac.ebi.intact.util.ShortLabelComparator.
This class provides a specific Comparator for use with AnnotatedObjects.
ShortLabelComparator() - 
Constructor for class uk.ac.ebi.intact.util.ShortLabelComparator
 
ShortLabelException - exception uk.ac.ebi.intact.application.editor.exception.validation.ShortLabelException.
Thrown when the validation for an experiment fails.
ShortLabelException() - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.ShortLabelException
 
shortLabelExists(String) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Check for duplicity of short label for the current edit object.
shortLabelExists(String) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean
The graph buttons are not displayed by default.
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean
Graph buttons are shown.
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.ProteinSingleViewBean
Graph buttons are shown.
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.InteractionSingleViewBean
Graph buttons are shown.
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.ExperimentSingleViewBean
Graph buttons are shown.
showGraphButtons() - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean
Graph buttons are shown.
SidebarDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.SidebarDispatchAction.
Action class for sidebar events.
SidebarDispatchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.SidebarDispatchAction
 
SimilarityDecorator - class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator.
Decorator which should be used by the display:table tag in order to display properly
 accession numbers, with their percentage identity with our query and the coordinates with
 the matched fragment.
SimilarityDecorator() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityDecorator
 
SimilarityResultBean - class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean.
Bean to display a result object from the aligment.
SimilarityResultBean() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
constructor by default.
SimilarityResultBean(String, String, int, int, int, int) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SimilarityResultBean
constructs an instance of this class for a given object, composed with 6 items.
SingleResultAction - class uk.ac.ebi.intact.application.search2.struts.controller.SingleResultAction.
Performs the single view for Proteins.
SingleResultAction() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.SingleResultAction
 
SingleViewBean - class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean.
Class allowing to handle the view for a single AnnotatedObject.
SingleViewBean(AnnotatedObject, String, String) - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean
Constructs an instance of this class from given AnnotatedObject.
size() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
 
sizeEdges() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Return the number of edge
sizeNodes() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork
Return the number of node
skippedEntity(String) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
SmallMolecule - class uk.ac.ebi.intact.model.SmallMolecule.
TODO comments
 TODO is this going to have anything in it ?
SmallMolecule() - 
Constructor for class uk.ac.ebi.intact.model.SmallMolecule
 
SMALlOFFSET - 
Static variable in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config
SmallOffset is the right and top area of the image
SMALLSCALELIMIT - 
Static variable in class uk.ac.ebi.intact.application.dataConversion.FileGenerator
 
SourceAction - class uk.ac.ebi.intact.application.hierarchView.struts.controller.SourceAction.
Implementation of Action that validates an highlightment submisson.
SourceAction() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.controller.SourceAction
 
SourceBean - class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean.
Simple JavaBean to represent a GO source data.
SourceBean(String, String, String, String, boolean, String) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
 
SourceDecorator - class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceDecorator.
Decorator which should be used by the display:table tag in order to display properly
 highlight sources.
SourceDecorator() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceDecorator
 
srsCommand - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
 
srsError - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
the first idea is that there will be none error during the SRS running
SrsResultBean - class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean.
Bean to display a result object from srs.
SrsResultBean() - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
constructor by default.
SrsResultBean(String, String, String) - 
Constructor for class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
constructs an instance of this class for a given object, composed with 2 items.
srsUrl - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
 
start() - 
Method in class uk.ac.ebi.intact.util.Chrono
 
startDocument() - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
startEditing() - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Starts editing session.
startEditing() - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
startElement(String, String, String, Attributes) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
startPrefixMapping(String, String) - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoHandler
 
startTransaction(int) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
starts a business level transaction.
StatisticsBean - class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean.
Bean which allows you to hold the data to display in the view.
StatisticsBean(ArrayList, String, String) - 
Constructor for class uk.ac.ebi.intact.application.statisticView.business.data.StatisticsBean
 
StatisticsDataSet - class uk.ac.ebi.intact.util.StatisticsDataSet.
 
stop() - 
Method in class uk.ac.ebi.intact.util.Chrono
 
stringSearch(String, String, boolean, boolean) - 
Method in interface uk.ac.ebi.intact.business.SearchI
Searches objects by searchString in all "relevant" fields.
stringSearch(String, String, boolean, boolean) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Not Yet Fully Implemented.
StrutsConstants - class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants.
Manifest constants for the hierarchView application.
StrutsConstants() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
subGraph(InteractionNetwork, int, Collection, int) - 
Method in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
Returns a subgraph centered on startNode.
subGraph(InteractionNetwork, int, Collection, int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Returns a subgraph centered on startNode (stored in the interaction network).
subGraph(Interactor, int, Collection, int, Graph) - 
Method in interface uk.ac.ebi.intact.business.SearchI
Returns a subgraph centered on startNode.
subGraph(Interactor, int, Collection, int, Graph) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Returns a subgraph centered on startNode.
SubmissionRef - class uk.ac.ebi.intact.model.SubmissionRef.
TODO Represents ...
SubmissionRef(Institution, String, String, Reference, Date) - 
Constructor for class uk.ac.ebi.intact.model.SubmissionRef
 
submissionRefAc - 
Variable in class uk.ac.ebi.intact.model.Reference
 
submit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction
Action for submitting the edit form.
submit(ActionMapping, ActionForm, HttpServletRequest, HttpServletResponse) - 
Method in class uk.ac.ebi.intact.application.editor.struts.action.interaction.SubmitAction
 
SubmitAction - class uk.ac.ebi.intact.application.editor.struts.action.interaction.SubmitAction.
An action to handle when an Interaction is submitted.
SubmitAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.interaction.SubmitAction
 
SubmitDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction.
Dispatcher action which dispatches according to 'dispatch' parameter.
SubmitDispatchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.SubmitDispatchAction
 
SubmitFormAction - class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction.
Dispatcher action which dispatches to various submit actions.
SubmitFormAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.SubmitFormAction
 
SUCCESS - 
Static variable in interface uk.ac.ebi.intact.application.editor.struts.framework.util.ForwardConstants
The key to success action.
SUCCESS - 
Static variable in class uk.ac.ebi.intact.application.predict.struts.framework.AbstractPredictAction
The key to success action.
SUCCESSFUL - 
Static variable in class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag
 



T

tearDown() - 
Method in class uk.ac.ebi.intact.util.TestCaseHelper
 
TERM_DATA - 
Static variable in class uk.ac.ebi.intact.application.statisticView.business.graphic.ChartBuilder
 
termNumber - 
Variable in class uk.ac.ebi.intact.util.IntactStatistics
 
TestCaseHelper - class uk.ac.ebi.intact.util.TestCaseHelper.
Helper class for setting up/tearing down objects used for test cases.
TestCaseHelper() - 
Constructor for class uk.ac.ebi.intact.util.TestCaseHelper
 
theUser - 
Variable in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
 
timestamp - 
Variable in class uk.ac.ebi.intact.util.IntactStatistics
Specify the date of the object storing.
TISSUES - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The name for the Tissues.
toDb() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag
stores the GO dag to a external table, which only stores the go hierarchy,
 which is used by FastGoDag
toGoDag(int, CvDagObject, String) - 
Method in class uk.ac.ebi.intact.model.CvDagObject
TODO comments
toGoDag(String) - 
Method in class uk.ac.ebi.intact.model.CvDagObject
Create the GO flat file representation of the current object and all its descendants.
toGoString(CvObject, String) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Return a single CvObject as a GO flatfile formatted string
TOPICS - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.framework.util.EditorMenuFactory
The names (edit/add) for the topic list.
toString() - 
Method in class uk.ac.ebi.intact.application.commons.search.CriteriaBean
 
toString() - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.PageValueBean
 
toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.binaryInteractions.GoGoDensity
 
toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.dag.CvGoDag
 
toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
 
toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.MyHashtable
 
toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
toString Method for Key2HashSet
   

   Example output:

   key: ac2  ->  values: [10, 30, 20] 

   key: ac1  ->  values: [2, 1]       

toString() - 
Method in class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm
 
toString() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
 
toString() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.SourceBean
Return a string representation of this object.
toString() - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
Return a string representation of this object.
toString() - 
Method in class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm
 
toString() - 
Method in class uk.ac.ebi.intact.model.InteractionImpl
 
toString() - 
Method in class uk.ac.ebi.intact.model.CvGoNode
 
toString() - 
Method in class uk.ac.ebi.intact.model.InteractorImpl
 
toString() - 
Method in class uk.ac.ebi.intact.model.Alias
 
toString() - 
Method in class uk.ac.ebi.intact.model.Annotation
 
toString() - 
Method in interface uk.ac.ebi.intact.model.Interaction
 
toString() - 
Method in interface uk.ac.ebi.intact.model.Interactor
 
toString() - 
Method in class uk.ac.ebi.intact.model.Xref
 
toString() - 
Method in class uk.ac.ebi.intact.model.Institution
 
toString() - 
Method in class uk.ac.ebi.intact.model.Experiment
 
toString() - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
toString() - 
Method in interface uk.ac.ebi.intact.model.BasicObject
 
toString() - 
Method in interface uk.ac.ebi.intact.model.IntactObject
 
toString() - 
Method in class uk.ac.ebi.intact.model.IntactObjectImpl
 
toString() - 
Method in class uk.ac.ebi.intact.model.BasicObjectImpl
 
toString() - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 
toString() - 
Method in class uk.ac.ebi.intact.model.proxy.IntactObjectProxy
A call to this method should materialize the real object.
toString() - 
Method in class uk.ac.ebi.intact.persistence.ObjectSearch
 
toString() - 
Method in class uk.ac.ebi.intact.simpleGraph.Node
 
toString() - 
Method in class uk.ac.ebi.intact.simpleGraph.Graph
 
toString() - 
Method in class uk.ac.ebi.intact.util.IntactStatistics
 
toString() - 
Method in class uk.ac.ebi.intact.util.GoServerProxy.GoResponse
 
toString() - 
Method in class uk.ac.ebi.intact.util.DagNode
 
toString() - 
Method in class uk.ac.ebi.intact.util.Chrono
 
toString() - 
Method in class uk.ac.ebi.intact.util.fileParsing.beans.GiotLineBean
 
TransactionException - exception uk.ac.ebi.intact.persistence.TransactionException.
Specific exception class for handling transaction errors
  that may be thrown from a DAO.
TransactionException() - 
Constructor for class uk.ac.ebi.intact.persistence.TransactionException
 
TransactionException(String) - 
Constructor for class uk.ac.ebi.intact.persistence.TransactionException
 
TransactionException(String, Exception) - 
Constructor for class uk.ac.ebi.intact.persistence.TransactionException
 
TulipAccess - interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccess.
 
TulipAccess - interface uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccess.
Purpose : 

 Allows the user to send a TLP file to Tulip and get back the coordinate of the nodes.
TulipAccessImpl - class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl.
Purpose : 

 Allows the user to send a TLP file to Tulip and get back the node's coordinate.
TulipAccessImpl() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.TulipAccessImpl
 
TulipAccessService - interface uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessService.
 
TulipAccessServiceLocator - class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator.
 
TulipAccessServiceLocator() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator
 
TulipClient - class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.TulipClient.
Provide an access to the Tulip web service.
TulipClient() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.TulipClient
 
TulipSoapBindingStub - class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub.
 
TulipSoapBindingStub() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
 
TulipSoapBindingStub(Service) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
 
TulipSoapBindingStub(URL, Service) - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipSoapBindingStub
 
TwoMaps - class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps.
TwoMaps.java represent a data structure, which allow to map unique keys
 to one Object (like a Hashtable) AND in addition it allows to get back
 all key Objects for a certain value.
TwoMaps() - 
Constructor for class uk.ac.ebi.intact.application.goDensity.business.data.TwoMaps
standard void constructor
TYPE_MAP - 
Static variable in class uk.ac.ebi.intact.model.Constants
holds the object type to class mapping within the servlet context



U

uk.ac.ebi.html - package uk.ac.ebi.html
 
uk.ac.ebi.intact.application.commons.business - package uk.ac.ebi.intact.application.commons.business
 
uk.ac.ebi.intact.application.commons.exception - package uk.ac.ebi.intact.application.commons.exception
 
uk.ac.ebi.intact.application.commons.search - package uk.ac.ebi.intact.application.commons.search
 
uk.ac.ebi.intact.application.commons.struts.taglibs - package uk.ac.ebi.intact.application.commons.struts.taglibs
 
uk.ac.ebi.intact.application.commons.util - package uk.ac.ebi.intact.application.commons.util
 
uk.ac.ebi.intact.application.dataConversion - package uk.ac.ebi.intact.application.dataConversion
 
uk.ac.ebi.intact.application.editor.business - package uk.ac.ebi.intact.application.editor.business
The classes implementing the business logic of the CvEdit application are
in this package.
uk.ac.ebi.intact.application.editor.exception - package uk.ac.ebi.intact.application.editor.exception
This package includes exception classes for the CvEdit application.
uk.ac.ebi.intact.application.editor.exception.validation - package uk.ac.ebi.intact.application.editor.exception.validation
 
uk.ac.ebi.intact.application.editor.struts.action - package uk.ac.ebi.intact.application.editor.struts.action
This package contains classes related to the Controller component of the MVC framework.
uk.ac.ebi.intact.application.editor.struts.action.biosrc - package uk.ac.ebi.intact.application.editor.struts.action.biosrc
 
uk.ac.ebi.intact.application.editor.struts.action.experiment - package uk.ac.ebi.intact.application.editor.struts.action.experiment
 
uk.ac.ebi.intact.application.editor.struts.action.interaction - package uk.ac.ebi.intact.application.editor.struts.action.interaction
 
uk.ac.ebi.intact.application.editor.struts.action.util - package uk.ac.ebi.intact.application.editor.struts.action.util
 
uk.ac.ebi.intact.application.editor.struts.framework - package uk.ac.ebi.intact.application.editor.struts.framework
This package contains common classes required for the MVC framework.
uk.ac.ebi.intact.application.editor.struts.framework.util - package uk.ac.ebi.intact.application.editor.struts.framework.util
This package contains utility methods common for the struts framework.
uk.ac.ebi.intact.application.editor.struts.security - package uk.ac.ebi.intact.application.editor.struts.security
The classes required for the security of the application are in this
package.
uk.ac.ebi.intact.application.editor.struts.view - package uk.ac.ebi.intact.application.editor.struts.view
This package contains classes belonging to the View component of the MVC
framework.
uk.ac.ebi.intact.application.editor.struts.view.biosrc - package uk.ac.ebi.intact.application.editor.struts.view.biosrc
 
uk.ac.ebi.intact.application.editor.struts.view.cv - package uk.ac.ebi.intact.application.editor.struts.view.cv
 
uk.ac.ebi.intact.application.editor.struts.view.experiment - package uk.ac.ebi.intact.application.editor.struts.view.experiment
 
uk.ac.ebi.intact.application.editor.struts.view.interaction - package uk.ac.ebi.intact.application.editor.struts.view.interaction
 
uk.ac.ebi.intact.application.editor.util - package uk.ac.ebi.intact.application.editor.util
 
uk.ac.ebi.intact.application.goDensity.business.binaryInteractions - package uk.ac.ebi.intact.application.goDensity.business.binaryInteractions
 
uk.ac.ebi.intact.application.goDensity.business.dag - package uk.ac.ebi.intact.application.goDensity.business.dag
 
uk.ac.ebi.intact.application.goDensity.business.data - package uk.ac.ebi.intact.application.goDensity.business.data
 
uk.ac.ebi.intact.application.goDensity.business.image - package uk.ac.ebi.intact.application.goDensity.business.image
 
uk.ac.ebi.intact.application.goDensity.exception - package uk.ac.ebi.intact.application.goDensity.exception
 
uk.ac.ebi.intact.application.goDensity.setupGoDensity - package uk.ac.ebi.intact.application.goDensity.setupGoDensity
 
uk.ac.ebi.intact.application.goDensity.struts.business - package uk.ac.ebi.intact.application.goDensity.struts.business
 
uk.ac.ebi.intact.application.goDensity.struts.controller - package uk.ac.ebi.intact.application.goDensity.struts.controller
 
uk.ac.ebi.intact.application.goDensity.struts.view - package uk.ac.ebi.intact.application.goDensity.struts.view
 
uk.ac.ebi.intact.application.graph2MIF - package uk.ac.ebi.intact.application.graph2MIF
The classes of the Graph2MIF application are in this package.
uk.ac.ebi.intact.application.graph2MIF.client - package uk.ac.ebi.intact.application.graph2MIF.client
This package contains the example clients of graph2MIF.

  You should easiely be able to copy the important lines for creating imports methods to you local application.
uk.ac.ebi.intact.application.graph2MIF.conversion - package uk.ac.ebi.intact.application.graph2MIF.conversion
 
uk.ac.ebi.intact.application.graph2MIF.exception - package uk.ac.ebi.intact.application.graph2MIF.exception
 
uk.ac.ebi.intact.application.hierarchView.business - package uk.ac.ebi.intact.application.hierarchView.business
Some utility classes and packages.
uk.ac.ebi.intact.application.hierarchView.business.graph - package uk.ac.ebi.intact.application.hierarchView.business.graph
Contains classes to specialize the generic Graph class, and so give a specific behaviour
like TLP export.
uk.ac.ebi.intact.application.hierarchView.business.image - package uk.ac.ebi.intact.application.hierarchView.business.image
Image producing framework.
uk.ac.ebi.intact.application.hierarchView.business.servlet - package uk.ac.ebi.intact.application.hierarchView.business.servlet
Some Servlets used to :
  - display the produced picture on the browser.
uk.ac.ebi.intact.application.hierarchView.business.tulip - package uk.ac.ebi.intact.application.hierarchView.business.tulip
Client and Server side of the Tulip web service.
uk.ac.ebi.intact.application.hierarchView.business.tulip.client - package uk.ac.ebi.intact.application.hierarchView.business.tulip.client
Make the task to access the web service easier for the client.
uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated - package uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated
 
uk.ac.ebi.intact.application.hierarchView.business.tulip.webService - package uk.ac.ebi.intact.application.hierarchView.business.tulip.webService
Server side of the web service, Interface and implementation of the web service tasks.
uk.ac.ebi.intact.application.hierarchView.exception - package uk.ac.ebi.intact.application.hierarchView.exception
 
uk.ac.ebi.intact.application.hierarchView.highlightment - package uk.ac.ebi.intact.application.hierarchView.highlightment
Generic framework to highlight part of an interaction network.
uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour - package uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour
What modification do we apply to the interaction network.
uk.ac.ebi.intact.application.hierarchView.highlightment.source - package uk.ac.ebi.intact.application.hierarchView.highlightment.source
From what do we select the proteins to highlight.
uk.ac.ebi.intact.application.hierarchView.struts - package uk.ac.ebi.intact.application.hierarchView.struts
This package provides struts related classes.
uk.ac.ebi.intact.application.hierarchView.struts.controller - package uk.ac.ebi.intact.application.hierarchView.struts.controller
 
uk.ac.ebi.intact.application.hierarchView.struts.framework - package uk.ac.ebi.intact.application.hierarchView.struts.framework
 
uk.ac.ebi.intact.application.hierarchView.struts.taglibs - package uk.ac.ebi.intact.application.hierarchView.struts.taglibs
 
uk.ac.ebi.intact.application.hierarchView.struts.view - package uk.ac.ebi.intact.application.hierarchView.struts.view
 
uk.ac.ebi.intact.application.hierarchView.struts.view.utils - package uk.ac.ebi.intact.application.hierarchView.struts.view.utils
 
uk.ac.ebi.intact.application.intSeq.business - package uk.ac.ebi.intact.application.intSeq.business
The classes implementing the business logic of the IntSeq application are
in this package.
uk.ac.ebi.intact.application.intSeq.exception - package uk.ac.ebi.intact.application.intSeq.exception
This package includes exception classes for the IntSeq application.
uk.ac.ebi.intact.application.intSeq.struts.controller - package uk.ac.ebi.intact.application.intSeq.struts.controller
This package contains classes related to the Controller component of the MVC framework.
uk.ac.ebi.intact.application.intSeq.struts.framework - package uk.ac.ebi.intact.application.intSeq.struts.framework
This package contains common classes required for the MVC framework.
uk.ac.ebi.intact.application.intSeq.struts.view - package uk.ac.ebi.intact.application.intSeq.struts.view
This package contains classes belonging to the View component of the MVC
framework.
uk.ac.ebi.intact.application.intSeq.struts.view.utils - package uk.ac.ebi.intact.application.intSeq.struts.view.utils
This package contains classes indirectly belonging to the View component of the MVC
framework.
It contains beans classes which make results objects for each line of the display table.

It contains also Decorator classes which imply to include the Design Pattern technology.
uk.ac.ebi.intact.application.predict.business - package uk.ac.ebi.intact.application.predict.business
 
uk.ac.ebi.intact.application.predict.struts.action - package uk.ac.ebi.intact.application.predict.struts.action
 
uk.ac.ebi.intact.application.predict.struts.framework - package uk.ac.ebi.intact.application.predict.struts.framework
 
uk.ac.ebi.intact.application.predict.struts.view - package uk.ac.ebi.intact.application.predict.struts.view
 
uk.ac.ebi.intact.application.predict.util - package uk.ac.ebi.intact.application.predict.util
 
uk.ac.ebi.intact.application.search2.business - package uk.ac.ebi.intact.application.search2.business
 
uk.ac.ebi.intact.application.search2.struts.controller - package uk.ac.ebi.intact.application.search2.struts.controller
 
uk.ac.ebi.intact.application.search2.struts.framework - package uk.ac.ebi.intact.application.search2.struts.framework
 
uk.ac.ebi.intact.application.search2.struts.framework.util - package uk.ac.ebi.intact.application.search2.struts.framework.util
 
uk.ac.ebi.intact.application.search2.struts.view - package uk.ac.ebi.intact.application.search2.struts.view
 
uk.ac.ebi.intact.application.search2.struts.view.details - package uk.ac.ebi.intact.application.search2.struts.view.details
 
uk.ac.ebi.intact.application.search2.struts.view.html - package uk.ac.ebi.intact.application.search2.struts.view.html
 
uk.ac.ebi.intact.application.search2.struts.view.single - package uk.ac.ebi.intact.application.search2.struts.view.single
 
uk.ac.ebi.intact.application.search2.struts.view.single.chunked - package uk.ac.ebi.intact.application.search2.struts.view.single.chunked
 
uk.ac.ebi.intact.application.statisticView.business - package uk.ac.ebi.intact.application.statisticView.business
Classes which implement the business logic of the StatisticView application are
in this package.
uk.ac.ebi.intact.application.statisticView.business.data - package uk.ac.ebi.intact.application.statisticView.business.data
Contains the classes holding the statistics data.
uk.ac.ebi.intact.application.statisticView.business.graphic - package uk.ac.ebi.intact.application.statisticView.business.graphic
Chart drawing package.
uk.ac.ebi.intact.application.statisticView.struts.controller - package uk.ac.ebi.intact.application.statisticView.struts.controller
 
uk.ac.ebi.intact.application.statisticView.struts.view - package uk.ac.ebi.intact.application.statisticView.struts.view
 
uk.ac.ebi.intact.application.synchron - package uk.ac.ebi.intact.application.synchron
This package provides a capability for different IntAct servers (nodes) to exchange data entries.
uk.ac.ebi.intact.business - package uk.ac.ebi.intact.business
This package contains the helper class which allows clients to access the business tier
for intact.
uk.ac.ebi.intact.model - package uk.ac.ebi.intact.model
This package is the implementation of the IntAct data model.
uk.ac.ebi.intact.model.proxy - package uk.ac.ebi.intact.model.proxy
 
uk.ac.ebi.intact.persistence - package uk.ac.ebi.intact.persistence
This package provides a persistence capability for intact.
uk.ac.ebi.intact.simpleGraph - package uk.ac.ebi.intact.simpleGraph
A simple graph package for temporary processing, for example to prepare output for graph analysis packages.
uk.ac.ebi.intact.util - package uk.ac.ebi.intact.util
Various utilities and auxiliary scripts.
uk.ac.ebi.intact.util.fileParsing - package uk.ac.ebi.intact.util.fileParsing
 
uk.ac.ebi.intact.util.fileParsing.beans - package uk.ac.ebi.intact.util.fileParsing.beans
 
uk.ac.ebi.intact.util.logging - package uk.ac.ebi.intact.util.logging
Contains IntAct dedicated Appender for log4J.
undeploy() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
Undeploy the web service according to collected data
 (ie undeployment file name).
undoTransaction() - 
Method in class uk.ac.ebi.intact.business.IntactHelper
unwraps a transaction.
uniprotDatabase - 
Static variable in class uk.ac.ebi.intact.util.UpdateProteinsI
Xref databases
UPDATE_INTERACTION_NETWORK - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
 
update(IntactHelper) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
update(IntactHelper) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
Update an annotated object in the database.
update(IntactHelper) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
update(Object) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
 
update(Object) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
update(Object) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
This method provides an update operation.
update(Object) - 
Method in class uk.ac.ebi.intact.persistence.ObjectBridgeDAO
 
update(Object) - 
Method in interface uk.ac.ebi.intact.persistence.DAO
updates a given object which was oroginally obtained in
 another transaction.
updateAnnotatedObject(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Gathers values in the view bean and updates the existing AnnotatedObject
 if it exists or create a new annotated object for the view and sets the
 annotated object.
updateAnnotatedObject(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
updateAnnotatedObject(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.cv.CvViewBean
 
updateAnnotatedObject(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
updateAnnotatedObject(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
updateCon() - 
Method in class uk.ac.ebi.intact.application.goDensity.business.data.DbTools
if connection to db is closed, the connection will be established again
UpdateException - exception uk.ac.ebi.intact.persistence.UpdateException.
Exception class to provide more meaningful error messages.
UpdateException() - 
Constructor for class uk.ac.ebi.intact.persistence.UpdateException
The default construstor with a default error message.
UpdateException(String) - 
Constructor for class uk.ac.ebi.intact.persistence.UpdateException
 
UpdateException(String, Exception) - 
Constructor for class uk.ac.ebi.intact.persistence.UpdateException
this constructor is used typically to pass on extra failure
 information from excpetions thrown elsewhere, eg from within other APIs
updateFromForm(DynaActionForm) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Updates the internal data from given form.
updateFromForm(DynaActionForm) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean
 
updateFromForm(DynaActionForm) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
updateFromForm(DynaActionForm) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
updateInteractionNetwork(IntactUserI, int) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseAction
Update the interaction network according to the specified action type:
 
       StrutsConstants.CREATE_INTERACTION_NETWORK : create a new interaction network 
       StrutsConstants.ADD_INTERACTION_NETWORK : add a new interaction network to the existing's one
       StrutsConstants.UPDATE_INTERACTION_NETWORK : rebuild the current interaction network by taking into account any depth change 
 
 Any errors are stored in the ActionErrors object.
updateProtein(String, String, String, String, String) - 
Method in class uk.ac.ebi.intact.util.InsertGo
Insert or update a protein object.
UpdateProteins - class uk.ac.ebi.intact.util.UpdateProteins.
Parse an URL and update the IntAct database.
UpdateProteins(IntactHelper) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteins
 
UpdateProteins(IntactHelper, boolean) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteins
 
UpdateProteinsI - class uk.ac.ebi.intact.util.UpdateProteinsI.
Defines the functionality of protein import utilities.
UpdateProteinsI.UpdateException - exception uk.ac.ebi.intact.util.UpdateProteinsI.UpdateException.
 
UpdateProteinsI.UpdateException(String) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteinsI.UpdateException
 
UpdateProteinsI(boolean) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteinsI
 
UpdateProteinsI(IntactHelper) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteinsI
Default constructor which initialize the bioSource cache to default.
UpdateProteinsI(IntactHelper, boolean) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteinsI
Default constructor which initialize the bioSource cache to default.
UpdateProteinsI(IntactHelper, int) - 
Constructor for class uk.ac.ebi.intact.util.UpdateProteinsI
 
updateSearchCache(AnnotatedObject) - 
Method in interface uk.ac.ebi.intact.application.editor.business.EditUserI
Clears existing search cache and replace it with given bean.
updateSearchCache(AnnotatedObject) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
 
updateUniqueAnnotation(CvTopic, String, Institution) - 
Method in interface uk.ac.ebi.intact.model.AnnotatedObject
 
updateUniqueAnnotation(CvTopic, String, Institution) - 
Method in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
Create or update an annotation.
updateUniqueAnnotation(CvTopic, String, Institution) - 
Method in class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy
 
url - 
Variable in class uk.ac.ebi.intact.application.intSeq.struts.view.utils.SrsResultBean
 
url - 
Variable in class uk.ac.ebi.intact.model.Institution
TODO comments
USeONLyPRECALCULATIOnDATA - 
Static variable in class uk.ac.ebi.intact.application.goDensity.setupGoDensity.Config

 - true -> only precalculated go-go-densities will be displayed.
USER - 
Static variable in interface uk.ac.ebi.intact.application.predict.struts.framework.PredictConstants
The key to access a user session object.
USER_KEY - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.business.Constants
Key name of the user in the session
USER_KEY - 
Static variable in class uk.ac.ebi.intact.model.Constants
The session scope attribute under which the User object
 for the currently logged in user is stored.
Utilities - class uk.ac.ebi.intact.application.hierarchView.business.image.Utilities.
This class give some usefull methods
Utilities - class uk.ac.ebi.intact.util.Utilities.
Various IntAct related utilities.
Utilities() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.image.Utilities
 
Utilities() - 
Constructor for class uk.ac.ebi.intact.util.Utilities
 



V

validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.cv.CvDynaForm
Validate the properties that have been set from the HTTP request.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentDynaForm
Validate the properties that have been set from the HTTP request.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinSearchDynaForm
Validates the search input values.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionDynaForm
Validates Interaction info page.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm
Validate the properties that have been set from this HTTP request,
 and return an ActionErrors object that encapsulates any
 validation errors that have been found.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm
Validate the properties that have been set from this HTTP request,
 and return an ActionErrors object that encapsulates any
 validation errors that have been found.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm
Validate the properties that have been set from this HTTP request,
 and return an ActionErrors object that encapsulates any
 validation errors that have been found.
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm
 
validate(ActionMapping, HttpServletRequest) - 
Method in class uk.ac.ebi.intact.application.search2.struts.view.WelcomeForm
Validate the properties that have been set from the HTTP request.
validate(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean
Validates the data in the view bean.
validate(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean
 
validate(EditUserI) - 
Method in class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean
 
ValidationException - exception uk.ac.ebi.intact.application.editor.exception.validation.ValidationException.
Super exception class for all the validation exceptions.
ValidationException(String, String) - 
Constructor for class uk.ac.ebi.intact.application.editor.exception.validation.ValidationException
Constructs with message and filter keys.
value - 
Variable in class uk.ac.ebi.intact.application.hierarchView.struts.view.utils.LabelValueBean
The value to be returned to the server.
valueBound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
Will call this method when an object is bound to a session.
valueBound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Will call this method when an object is bound to a session.
valueBound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
Will call this method when an object is bound to a session.
valueBound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
Will call this method when an object is bound to a session.
valueUnbound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.editor.business.EditUser
Will call this method when an object is unbound from a session.
valueUnbound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.IntactUser
Will call this method when an object is unbound from a session.
valueUnbound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.predict.business.PredictUser
Will call this method when an object is unbound from a session.
valueUnbound(HttpSessionBindingEvent) - 
Method in class uk.ac.ebi.intact.application.search2.business.IntactUserImpl
Will call this method when an object is unbound from a session.
VerifProtSeq(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm
 
VIEW - 
Static variable in class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean
The editing state.
VIEW_BEAN - 
Static variable in interface uk.ac.ebi.intact.application.search2.struts.framework.util.SearchConstants
The view bean for a single CvObject.
ViewBeanFactory - class uk.ac.ebi.intact.application.search2.struts.view.ViewBeanFactory.
 
VisibleHighlightmentBehaviour - class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.VisibleHighlightmentBehaviour.
Behaviour allowing to display only highlighted protein and hide all others.
VisibleHighlightmentBehaviour() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.highlightment.behaviour.VisibleHighlightmentBehaviour
 



W

WEB_SERVICE_PROPERTIES - 
Static variable in interface uk.ac.ebi.intact.application.hierarchView.business.IntactUserI
 
WEB_SERVICE_PROPERTY_FILE - 
Static variable in class uk.ac.ebi.intact.application.hierarchView.struts.StrutsConstants
Where to find the properties file
WebServiceManager - class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager.
Allows to deploy and undeploy the web service.
WebServiceManager() - 
Constructor for class uk.ac.ebi.intact.application.hierarchView.business.tulip.WebServiceManager
 
WebSrs(String) - 
Method in class uk.ac.ebi.intact.application.intSeq.business.CallingSrs
This method manages the execution of the Wgetz URL.
WelcomeAction - class uk.ac.ebi.intact.application.predict.struts.action.WelcomeAction.
Performs the required initialisations for a user search session when
 they have been through the welcome page.
WelcomeAction - class uk.ac.ebi.intact.application.search2.struts.controller.WelcomeAction.
Performs the required initialisations for a user search session when
 they have been through the welcome page.
WelcomeAction() - 
Constructor for class uk.ac.ebi.intact.application.predict.struts.action.WelcomeAction
 
WelcomeAction() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.controller.WelcomeAction
 
WelcomeForm - class uk.ac.ebi.intact.application.search2.struts.view.WelcomeForm.
Dummy form bean for the welcome page.
WelcomeForm() - 
Constructor for class uk.ac.ebi.intact.application.search2.struts.view.WelcomeForm
 
writeData(String, Document) - 
Method in class uk.ac.ebi.intact.application.dataConversion.PsiDataBuilder
 
writeData(String, Document) - 
Method in interface uk.ac.ebi.intact.application.dataConversion.DataBuilder
This method dumps the data created to the specified file destination.
writeExperimentsClassification(HashMap) - 
Static method in class uk.ac.ebi.intact.application.dataConversion.FileGenerator
Output the experiment classification, suitable for scripting
writeExternal(ObjectOutput) - 
Method in class uk.ac.ebi.intact.business.IntactHelper
Method required for writing to disk via Serializable.
writeGoDefinitions(Class, IntactHelper, String, String) - 
Static method in class uk.ac.ebi.intact.util.GoTools
Write a Controlled vocabulary in GO definition format flat file.



X

xmin() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
 
XmlBuilder - class uk.ac.ebi.intact.util.XmlBuilder.
This utility class provides operations for generating XML, typically
 in the form of Document or Element objects.
XmlBuilder() - 
Constructor for class uk.ac.ebi.intact.util.XmlBuilder
Note that this default constructor will build a default IntactHelper object with
 default configuration settings.
XmlBuilder(IntactHelper) - 
Constructor for class uk.ac.ebi.intact.util.XmlBuilder
Sets up an XML builder with suitable persistent store access.
XmlDumper - class uk.ac.ebi.intact.application.synchron.XmlDumper.
Dump all data to XML in a normalised XML format.
XmlDumper() - 
Constructor for class uk.ac.ebi.intact.application.synchron.XmlDumper
 
XmlLoader - class uk.ac.ebi.intact.application.synchron.XmlLoader.
Purpose : extracts data objects from an XML file, inserts
 new data entries in the local database and update already
 existing data entries.
XmlLoader() - 
Constructor for class uk.ac.ebi.intact.application.synchron.XmlLoader
 
XmlLoader(PersistenceBroker) - 
Constructor for class uk.ac.ebi.intact.application.synchron.XmlLoader
 
Xref - class uk.ac.ebi.intact.model.Xref.
Represents a crossreference to another database.
Xref(Institution, CvDatabase, String, String, String, CvXrefQualifier) - 
Constructor for class uk.ac.ebi.intact.model.Xref
Creates a valid Xref instance.
xrefAc - 
Variable in class uk.ac.ebi.intact.model.Feature
 
xrefAc - 
Variable in class uk.ac.ebi.intact.model.Reference
 
XrefDispatchAction - class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction.
Dispatcher action which dispatches according to 'dispatch' parameter.
XrefDispatchAction() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.action.XrefDispatchAction
 
XreferenceBean - class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean.
Bean to store data for x'references.
XreferenceBean() - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Default constructor.
XreferenceBean(Xref) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Instantiate an object of this class from a Xref object.
XreferenceBean(Xref, long) - 
Constructor for class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean
Instantiates with given xref and key.
XrefHelper - class uk.ac.ebi.intact.application.commons.util.XrefHelper.
This class contains various useful utilities related to Xref.
xrefs - 
Variable in class uk.ac.ebi.intact.model.AnnotatedObjectImpl
 



Y

ymin() - 
Method in class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension
 



_

_key2HashSet - 
Variable in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
All keys are stored in this Hashtable.
_sitePrefix - 
Static variable in class uk.ac.ebi.intact.persistence.AbstractSequenceManager
The prefix for all ID strings
_stmt - 
Static variable in class uk.ac.ebi.intact.persistence.AbstractSequenceManager
Prepared SQL statement to get a new id from a database sequence object.
_values - 
Variable in class uk.ac.ebi.intact.application.goDensity.business.data.Key2HashSet
Each value within the Hashtable _key2HashSet hast on HashSet - set of unique values


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IntAct Project - EMBL-EBI 2004 - intact-help@ebi.ac.uk