Serialized Form

Package uk.ac.ebi.intact.application.commons.exception

Class uk.ac.ebi.intact.application.commons.exception.SessionExpiredException implements Serializable

Package uk.ac.ebi.intact.application.commons.search

Class uk.ac.ebi.intact.application.commons.search.CriteriaBean implements Serializable

Serialized Fields

query

java.lang.String query

The query given by the user

target

java.lang.String target

The property which matches the user's query (could be shortlabel, ac ...). The field is null if the value hasn't given any result.

Package uk.ac.ebi.intact.application.commons.struts.taglibs

Class uk.ac.ebi.intact.application.commons.struts.taglibs.ClearErrorsTag implements Serializable

Class uk.ac.ebi.intact.application.commons.struts.taglibs.DocumentationTag implements Serializable

Serialized Fields

section

java.lang.String section

title

java.lang.String title

The title attribute; defaults to the DEFAULT_TITLE if none specified.

Class uk.ac.ebi.intact.application.commons.struts.taglibs.RestoreErrorsTag implements Serializable

Class uk.ac.ebi.intact.application.commons.struts.taglibs.SaveErrorsTag implements Serializable

Package uk.ac.ebi.intact.application.commons.util

Class uk.ac.ebi.intact.application.commons.util.LoggingInitServlet implements Serializable

Class uk.ac.ebi.intact.application.commons.util.ResetOjbCacheServlet implements Serializable

Package uk.ac.ebi.intact.application.dataConversion

Class uk.ac.ebi.intact.application.dataConversion.DataConversionException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

rootCause

java.lang.Exception rootCause

Package uk.ac.ebi.intact.application.editor.business

Class uk.ac.ebi.intact.application.editor.business.EditUser implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Serialized Fields

myDAOSource

DAOSource myDAOSource

The data source; need this to create a helper.

myEditState

boolean myEditState

Maintains the edit state; it used when inserting the header dynamically. For example, if in the edit state, then append the current object's class type to the header or else display the standard header.

mySelectedTopic

java.lang.String mySelectedTopic

The topic selected by the user.

myEditView

AbstractEditViewBean myEditView

The current view of the user.

mySearchCache

java.util.Collection mySearchCache

Holds the last search results.

myLastQuery

java.lang.String myLastQuery

Stores the last query result.

Package uk.ac.ebi.intact.application.editor.exception

Class uk.ac.ebi.intact.application.editor.exception.BaseException implements Serializable

Serialized Fields

myRootException

java.lang.Throwable myRootException

The root exception.

myMessageKey

java.lang.String myMessageKey

The message key to search in the resource file.

myMessageArgs

java.lang.String[] myMessageArgs

The message arguments.

Class uk.ac.ebi.intact.application.editor.exception.EmptyTopicsException implements Serializable

Class uk.ac.ebi.intact.application.editor.exception.SearchException implements Serializable

Class uk.ac.ebi.intact.application.editor.exception.SessionExpiredException implements Serializable

Package uk.ac.ebi.intact.application.editor.exception.validation

Class uk.ac.ebi.intact.application.editor.exception.validation.ExperimentException implements Serializable

Class uk.ac.ebi.intact.application.editor.exception.validation.InteractionException implements Serializable

Class uk.ac.ebi.intact.application.editor.exception.validation.ShortLabelException implements Serializable

Class uk.ac.ebi.intact.application.editor.exception.validation.ValidationException implements Serializable

Serialized Fields

myFilterKey

java.lang.String myFilterKey

The filter key to filter messages.

Package uk.ac.ebi.intact.application.editor.struts.framework

Class uk.ac.ebi.intact.application.editor.struts.framework.EditorActionServlet implements Serializable

Package uk.ac.ebi.intact.application.editor.struts.framework.util

Class uk.ac.ebi.intact.application.editor.struts.framework.util.AbstractEditViewBean implements Serializable

Serialized Fields

myAnnotObject

AnnotatedObject myAnnotObject

The Annotated object to wrap this bean around.

myEditClass

java.lang.Class myEditClass

The class we are editing.

myShortLabel

java.lang.String myShortLabel

The short label of the current edit object.

myFullName

java.lang.String myFullName

The full name of the current edit object.

myAnnotations

java.util.List myAnnotations

The annotations to display.

myXrefs

java.util.List myXrefs

The Xreferences to display.

myAnnotsToAdd

java.util.List myAnnotsToAdd

List of annotations to add. This collection is cleared once the user commits the transaction.

myAnnotsToDel

java.util.List myAnnotsToDel

List of annotations to del. This collection is cleared once the user commits the transaction.

myAnnotsToUpdate

java.util.List myAnnotsToUpdate

List of annotations to update. This collection is cleared once the user commits the transaction.

myXrefsToAdd

java.util.List myXrefsToAdd

List of xrefs to add. This collection is cleared once the user commits the transaction.

myXrefsToDel

java.util.List myXrefsToDel

List of xrefs to del. This collection is cleared once the user commits the transaction.

myXrefsToUpdate

java.util.List myXrefsToUpdate

List of xrefs to update. This collection is cleared once the user commits the transaction.

Package uk.ac.ebi.intact.application.editor.struts.view

Class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditBean implements Serializable

Serialized Fields

myEditState

java.lang.String myEditState

Keeps track of the edit state; default is in view mode.

Class uk.ac.ebi.intact.application.editor.struts.view.AbstractEditKeyBean implements Serializable

Serialized Fields

myKey

long myKey

The unique identifier for this bean.

Class uk.ac.ebi.intact.application.editor.struts.view.CommentBean implements Serializable

Serialized Fields

myTopic

java.lang.String myTopic

The CV topic.

myAnnotatedText

java.lang.String myAnnotatedText

The annotated text.

Class uk.ac.ebi.intact.application.editor.struts.view.XreferenceBean implements Serializable

Serialized Fields

myDatabaseName

java.lang.String myDatabaseName

The database name.

myPrimaryId

java.lang.String myPrimaryId

The primary id. Set to empty; this is a required field.

mySecondaryId

java.lang.String mySecondaryId

The secondary id.

myReleaseNumber

java.lang.String myReleaseNumber

The release number.

myReferenceQualifer

java.lang.String myReferenceQualifer

The reference qualifier.

Package uk.ac.ebi.intact.application.editor.struts.view.biosrc

Class uk.ac.ebi.intact.application.editor.struts.view.biosrc.BioSourceViewBean implements Serializable

Serialized Fields

myTaxId

java.lang.String myTaxId

The tax id.

myCellType

java.lang.String myCellType

myTissue

java.lang.String myTissue

Package uk.ac.ebi.intact.application.editor.struts.view.cv

Class uk.ac.ebi.intact.application.editor.struts.view.cv.CvDynaForm implements Serializable

Class uk.ac.ebi.intact.application.editor.struts.view.cv.CvViewBean implements Serializable

Package uk.ac.ebi.intact.application.editor.struts.view.experiment

Class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentDynaForm implements Serializable

Class uk.ac.ebi.intact.application.editor.struts.view.experiment.ExperimentViewBean implements Serializable

Serialized Fields

myOrganism

java.lang.String myOrganism

The host organism.

myInter

java.lang.String myInter

The interaction with the experiment.

myIdent

java.lang.String myIdent

The experiment identification.

myHasLargeInts

boolean myHasLargeInts

True if the maximum interactions allowed for the experiment has exceeded.

myLargeInts

int myLargeInts

Holds the number of interactions. This value is only set if #myHasLargeInts is true.

Package uk.ac.ebi.intact.application.editor.struts.view.interaction

Class uk.ac.ebi.intact.application.editor.struts.view.interaction.ExperimentBean implements Serializable

Serialized Fields

myExperiment

Experiment myExperiment

Reference to the object this instance is created with.

Class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionDynaForm implements Serializable

Class uk.ac.ebi.intact.application.editor.struts.view.interaction.InteractionViewBean implements Serializable

Serialized Fields

myKD

java.lang.Float myKD

The KD.

myOrganism

java.lang.String myOrganism

The host organism.

myInteractionType

java.lang.String myInteractionType

The interaction with the experiment.

mySourceExperimentAc

java.lang.String mySourceExperimentAc

This holds the AC of the experiment from this bean is construected.

Class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinBean implements Serializable

Serialized Fields

myInteraction

Interaction myInteraction

The interaction this protein belongs to.

myInteractor

Interactor myInteractor

The interactor of the bean.

myComponent

Component myComponent

The object this instance is created with.

mySPAc

java.lang.String mySPAc

Swiss-Prot AC.

myRole

java.lang.String myRole

The role of this Protein.

myStoichiometry

float myStoichiometry

The stoichiometry.

myOrganism

java.lang.String myOrganism

The organism.

myExpressedIn

java.lang.String myExpressedIn

Expressed in as a biosource short label.

Class uk.ac.ebi.intact.application.editor.struts.view.interaction.ProteinSearchDynaForm implements Serializable

Package uk.ac.ebi.intact.application.goDensity.business.data

Class uk.ac.ebi.intact.application.goDensity.business.data.MyHashtable implements Serializable

Package uk.ac.ebi.intact.application.goDensity.business.image

Class uk.ac.ebi.intact.application.goDensity.business.image.DensityImageServlet implements Serializable

Package uk.ac.ebi.intact.application.goDensity.exception

Class uk.ac.ebi.intact.application.goDensity.exception.DatabaseEmptyException implements Serializable

Class uk.ac.ebi.intact.application.goDensity.exception.GoIdNotInDagException implements Serializable

Class uk.ac.ebi.intact.application.goDensity.exception.KeyNotFoundException implements Serializable

Class uk.ac.ebi.intact.application.goDensity.exception.SameGraphPathException implements Serializable

Package uk.ac.ebi.intact.application.goDensity.struts.business

Class uk.ac.ebi.intact.application.goDensity.struts.business.InitFastGoDag implements Serializable

Package uk.ac.ebi.intact.application.goDensity.struts.view

Class uk.ac.ebi.intact.application.goDensity.struts.view.goInputForm implements Serializable

Serialized Fields

goIds

java.lang.String goIds

textfield

Package uk.ac.ebi.intact.application.graph2MIF

Class uk.ac.ebi.intact.application.graph2MIF.Graph2MIFWSServlet implements Serializable

Package uk.ac.ebi.intact.application.graph2MIF.conversion

Class uk.ac.ebi.intact.application.graph2MIF.conversion.FusionableGraph implements Serializable

Package uk.ac.ebi.intact.application.graph2MIF.exception

Class uk.ac.ebi.intact.application.graph2MIF.exception.ElementNotParseableException implements Serializable

Class uk.ac.ebi.intact.application.graph2MIF.exception.GraphNotConvertableException implements Serializable

Class uk.ac.ebi.intact.application.graph2MIF.exception.MIFSerializeException implements Serializable

Class uk.ac.ebi.intact.application.graph2MIF.exception.NoGraphRetrievedException implements Serializable

Class uk.ac.ebi.intact.application.graph2MIF.exception.NoInteractorFoundException implements Serializable

Package uk.ac.ebi.intact.application.hierarchView.business

Class uk.ac.ebi.intact.application.hierarchView.business.IntactUser implements Serializable

Serialized Fields

intactHelper

IntactHelper intactHelper

datasource entry point

interactionNetwork

InteractionNetwork interactionNetwork

The current network with which the user is working

clickBehaviour

ClickBehaviourForm clickBehaviour

The current click behaviour

highlightOptions

java.util.Map highlightOptions

Set of highlight options (key/value) given by the user via the web interface

imageBean

ImageBean imageBean

data relatives to the image producing (Image byte code, SVG DOM, HTML MAP)

keys

java.util.Collection keys

Collection of keys received from the current source. The highlightment of the current interaction network is done according to these keys. keys contains a set of keys to take into account in the highlight process selectedKey is the one which has been selected by the user

selectedKey

java.lang.String selectedKey

sourceURL

java.lang.String sourceURL

URL describes the link to the highlight source in the case the user has selected one of those available for the current protein. The URL is encoded in the UTF-8 format.

queryString

java.lang.String queryString

currentDepth

int currentDepth

defaultDepth

int defaultDepth

minimalDepth

int minimalDepth

maximalDepth

int maximalDepth

methodLabel

java.lang.String methodLabel

methodClass

java.lang.String methodClass

behaviour

java.lang.String behaviour

applicationPath

java.lang.String applicationPath

Package uk.ac.ebi.intact.application.hierarchView.business.graph

Class uk.ac.ebi.intact.application.hierarchView.business.graph.InteractionNetwork implements Serializable

Serialized Fields

nodeList

java.util.ArrayList nodeList

Allow to record nodes and keep their order

isInitialized

boolean isInitialized

dimension

ImageDimension dimension

Properties of the final image (size ...)

centralProtein

Interactor centralProtein

Protein from which has been created the interaction network.

centralProteinAC

java.lang.String centralProteinAC

centralNodes

java.util.ArrayList centralNodes

Stores a set of central nodes and interactor. There is one by fusioned interaction network We need to store both because in the case of an interaction, no node are stored.

centralInteractors

java.util.ArrayList centralInteractors

criteriaList

java.util.ArrayList criteriaList

Describe how the interaction network has been built, from which query strings and what is the associated target e.g. the [ShortLabel ABC] and [Xref DEF] That collection contains String[2] (0:queryString, 1:target)

Package uk.ac.ebi.intact.application.hierarchView.business.image

Class uk.ac.ebi.intact.application.hierarchView.business.image.ImageBean implements Serializable

Serialized Fields

mapCode

java.lang.String mapCode

HTML MAP code.

imageHeight

int imageHeight

Size of the image

imageWidth

int imageWidth

Class uk.ac.ebi.intact.application.hierarchView.business.image.ImageDimension implements Serializable

Serialized Fields

xmin

float xmin

xmax

float xmax

ymin

float ymin

ymax

float ymax

Package uk.ac.ebi.intact.application.hierarchView.business.servlet

Class uk.ac.ebi.intact.application.hierarchView.business.servlet.GenerateImage implements Serializable

Package uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated

Class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.ProteinCoordinate implements Serializable

Serialized Fields

id

int id

x

float x

y

float y

__equalsCalc

java.lang.Object __equalsCalc

__hashCodeCalc

boolean __hashCodeCalc

Class uk.ac.ebi.intact.application.hierarchView.business.tulip.client.generated.TulipAccessServiceLocator implements Serializable

Serialized Fields

Tulip_address

java.lang.String Tulip_address

See Also:

Constant Field Values

Package uk.ac.ebi.intact.application.hierarchView.business.tulip.webService

Class uk.ac.ebi.intact.application.hierarchView.business.tulip.webService.ProteinCoordinate implements Serializable

Serialized Fields

id

int id

the protein's id

x

float x

protein's coordinates

y

float y

Package uk.ac.ebi.intact.application.hierarchView.exception

Class uk.ac.ebi.intact.application.hierarchView.exception.MultipleResultException implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.exception.ProteinNotFoundException implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.exception.SessionExpiredException implements Serializable

Package uk.ac.ebi.intact.application.hierarchView.struts.framework

Class uk.ac.ebi.intact.application.hierarchView.struts.framework.IntactBaseForm implements Serializable

Serialized Fields

myErrors

org.apache.struts.action.ActionErrors myErrors

Error container

myMessages

org.apache.struts.action.ActionMessages myMessages

Message container

Package uk.ac.ebi.intact.application.hierarchView.struts.taglibs

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHighlightOptions implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayHttpContentTag implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplayInteractionNetworkTag implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.DisplaySourceTag implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.RestoreContextFromCookieTag implements Serializable

Class uk.ac.ebi.intact.application.hierarchView.struts.taglibs.SaveContextInCookieTag implements Serializable

Package uk.ac.ebi.intact.application.hierarchView.struts.view

Class uk.ac.ebi.intact.application.hierarchView.struts.view.ClickBehaviourForm implements Serializable

Serialized Fields

myAction

int myAction

Saves the user action.

actionName

java.lang.String actionName

Class uk.ac.ebi.intact.application.hierarchView.struts.view.HighlightmentForm implements Serializable

Serialized Fields

behaviour

java.lang.String behaviour

behaviour.

Class uk.ac.ebi.intact.application.hierarchView.struts.view.InitForm implements Serializable

Serialized Fields

host

java.lang.String host

protocol

java.lang.String protocol

Class uk.ac.ebi.intact.application.hierarchView.struts.view.InteractionNetworkForm implements Serializable

Serialized Fields

myAction

int myAction

Saves the user action.

actionName

java.lang.String actionName

Class uk.ac.ebi.intact.application.hierarchView.struts.view.SearchForm implements Serializable

Serialized Fields

queryString

java.lang.String queryString

method

java.lang.String method

The highlight method That attribute can be null because in case only one method is available, the form dont show the choice to make easier the user interface.

myAction

int myAction

Saves the user action.

actionName

java.lang.String actionName

Package uk.ac.ebi.intact.application.intSeq.exception

Class uk.ac.ebi.intact.application.intSeq.exception.BlastException implements Serializable

Serialized Fields

commandMessage

java.lang.String commandMessage

Class uk.ac.ebi.intact.application.intSeq.exception.IntactSrsException implements Serializable

Serialized Fields

commandMessage

java.lang.String commandMessage

Package uk.ac.ebi.intact.application.intSeq.struts.view

Class uk.ac.ebi.intact.application.intSeq.struts.view.ProteinSearchForm implements Serializable

Serialized Fields

searchString

java.lang.String searchString

The protein topic captured by the user in the provided text field in srsSearch.jsp

Class uk.ac.ebi.intact.application.intSeq.struts.view.SequenceSimilarityForm implements Serializable

Serialized Fields

sequence

java.lang.String sequence

The protein sequence captured by the user in the provided textarea of similaritySearch.jsp This sequence must be in Fasta format.

Package uk.ac.ebi.intact.application.predict.business

Class uk.ac.ebi.intact.application.predict.business.PredictUser implements Serializable

Serialized Fields

myHelper

IntactHelper myHelper

The intact helper to access the database.

mySpecie

java.lang.String mySpecie

The current specie (as a link).

myResources

java.util.ResourceBundle myResources

The resource bundle for the application.

Class uk.ac.ebi.intact.application.predict.business.PredictUserOra implements Serializable

Class uk.ac.ebi.intact.application.predict.business.PredictUserPg implements Serializable

Package uk.ac.ebi.intact.application.predict.struts.framework

Class uk.ac.ebi.intact.application.predict.struts.framework.PredictActionServlet implements Serializable

Package uk.ac.ebi.intact.application.search2.struts.framework

Class uk.ac.ebi.intact.application.search2.struts.framework.IntactActionServlet implements Serializable

Package uk.ac.ebi.intact.application.search2.struts.view

Class uk.ac.ebi.intact.application.search2.struts.view.AbstractViewBean implements Serializable

Serialized Fields

helpLink

java.lang.String helpLink

The default link to help pages (to localhost). Typically used in stylesheets.

contextPath

java.lang.String contextPath

Context path of the current application.

highlightMap

java.util.Set highlightMap

A collection of short labels to highlight.

Class uk.ac.ebi.intact.application.search2.struts.view.WelcomeForm implements Serializable

Package uk.ac.ebi.intact.application.search2.struts.view.details

Class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean implements Serializable

Class uk.ac.ebi.intact.application.search2.struts.view.details.BinaryDetailsViewBean.BinaryData implements Serializable

Serialized Fields

data

java.util.HashMap data

Class uk.ac.ebi.intact.application.search2.struts.view.details.DetailsViewBean implements Serializable

Serialized Fields

wrappedObjects

java.util.Collection wrappedObjects

Stores the object being wrapped. Mainly used for alternative display options by other views. This should be overriden by subclasses wishing to use alternative objects (eg BasicObject).

Class uk.ac.ebi.intact.application.search2.struts.view.details.InteractionDetailsViewBean implements Serializable

Class uk.ac.ebi.intact.application.search2.struts.view.details.ProteinDetailsViewBean implements Serializable

Package uk.ac.ebi.intact.application.search2.struts.view.single

Class uk.ac.ebi.intact.application.search2.struts.view.single.ExperimentSingleViewBean implements Serializable

Class uk.ac.ebi.intact.application.search2.struts.view.single.InteractionSingleViewBean implements Serializable

Class uk.ac.ebi.intact.application.search2.struts.view.single.ProteinSingleViewBean implements Serializable

Class uk.ac.ebi.intact.application.search2.struts.view.single.SingleViewBean implements Serializable

Serialized Fields

wrappedObject

AnnotatedObject wrappedObject

Stores the object being wrapped. Mainly used for alternative display options by other views. This should be overriden by subclasses wishing to use alternative objects (eg BasicObject).

Package uk.ac.ebi.intact.application.search2.struts.view.single.chunked

Class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ChunkedSingleViewBean implements Serializable

Serialized Fields

maxChunk

int maxChunk

Max count of chunk we can display out of the wrapped object

selectedChunk

int selectedChunk

The chunk we will wisplay

Class uk.ac.ebi.intact.application.search2.struts.view.single.chunked.ExperimentChunkedSingleViewBean implements Serializable

Package uk.ac.ebi.intact.application.statisticView.business.data

Class uk.ac.ebi.intact.application.statisticView.business.data.NoDataException implements Serializable

Package uk.ac.ebi.intact.application.statisticView.struts.view

Class uk.ac.ebi.intact.application.statisticView.struts.view.FilterForm implements Serializable

Serialized Fields

start

java.lang.String start

stop

java.lang.String stop

Package uk.ac.ebi.intact.business

Class uk.ac.ebi.intact.business.DuplicateLabelException implements Serializable

Class uk.ac.ebi.intact.business.IntactException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

rootCause

java.lang.Exception rootCause

Class uk.ac.ebi.intact.business.IntactHelper implements Serializable

Serialization Methods

readExternal

public void readExternal(java.io.ObjectInput in)
                  throws java.io.IOException,
                         java.lang.ClassNotFoundException

Used for serialization via Externalizable. Needed because basic serialization does not work with the Log4J logger.

Throws:

java.io.IOException - Thrwon if there were problems reading from disk.

java.lang.ClassNotFoundException - thrown if the class definition needed to create an instance is not available.

writeExternal

public void writeExternal(java.io.ObjectOutput out)
                   throws java.io.IOException

Method required for writing to disk via Serializable. Needed because basic serialization does not work due to the use of the Log4J logger.

Throws:

java.io.IOException - thrown if there were problems writing to disk.

Package uk.ac.ebi.intact.model

Class uk.ac.ebi.intact.model.Alias implements Serializable

Serialized Fields

name

java.lang.String name

Alternative name for the object.

cvAliasType

CvAliasType cvAliasType

the type of that alias.

cvAliasTypeAc

java.lang.String cvAliasTypeAc

parentAc

java.lang.String parentAc

Accession id to the Object to which refers that alias.

Class uk.ac.ebi.intact.model.AnnotatedObjectImpl implements Serializable

Serialized Fields

curatorAc

java.lang.String curatorAc

shortLabel

java.lang.String shortLabel

Short name for the object, not necessarily unique. To be used for example in minimised displays of the object.

fullName

java.lang.String fullName

The full name or a minimal description of the object.

annotations

java.util.Collection annotations

curator

Person curator

The curator who has last edited the object.

xrefs

java.util.Collection xrefs

aliases

java.util.Collection aliases

Hold aliases of an Annotated object. ie. alternative name for the current object.

references

java.util.Collection references

Class uk.ac.ebi.intact.model.Annotation implements Serializable

Serialized Fields

cvTopicAc

java.lang.String cvTopicAc

topicAc

java.lang.String topicAc

annotationText

java.lang.String annotationText

Text describing one aspect of the annotation of an object.

cvTopic

CvTopic cvTopic

TODO comments

Class uk.ac.ebi.intact.model.BasicObjectImpl implements Serializable

Serialized Fields

ownerAc

java.lang.String ownerAc

evidences

java.util.Collection evidences

TODO comments + plural name

owner

Institution owner

TODO comments

Class uk.ac.ebi.intact.model.BioSource implements Serializable

Serialized Fields

cvCellCycleAc

java.lang.String cvCellCycleAc

cvDevelopmentalStageAc

java.lang.String cvDevelopmentalStageAc

cvTissueAc

java.lang.String cvTissueAc

cvCellTypeAc

java.lang.String cvCellTypeAc

cvCompartmentAc

java.lang.String cvCompartmentAc

taxId

java.lang.String taxId

The NCBI tax id.

cvCellCycle

CvCellCycle cvCellCycle

TODO comments

cvDevelopmentalStage

CvDevelopmentalStage cvDevelopmentalStage

TODO comments

cvTissue

CvTissue cvTissue

TODO comments

cvCellType

CvCellType cvCellType

TODO comments

cvCompartment

CvCompartment cvCompartment

TODO comments

Class uk.ac.ebi.intact.model.Complex implements Serializable

Serialized Fields

mw

float mw

Molecular weight of the complex in kilodalton.

Class uk.ac.ebi.intact.model.Component implements Serializable

Serialized Fields

interactorAc

java.lang.String interactorAc

interactionAc

java.lang.String interactionAc

cvComponentRoleAc

java.lang.String cvComponentRoleAc

expressedInAc

java.lang.String expressedInAc

stoichiometry

float stoichiometry

Represents the relative quantitity of the interactor participating in the interaction. Default is one. To describe for example a homodimer, an interaction might have only one substrate, but the relative quantity would be 2.

expressedIn

BioSource expressedIn

TODO Represents ...

interactor

Interactor interactor

TODO comments

interaction

Interaction interaction

TODO comments

bindingDomains

java.util.Collection bindingDomains

The domain a Substrate binds by.

cvComponentRole

CvComponentRole cvComponentRole

TODO comments

Class uk.ac.ebi.intact.model.CvAliasType implements Serializable

Class uk.ac.ebi.intact.model.CvCellCycle implements Serializable

Class uk.ac.ebi.intact.model.CvCellType implements Serializable

Class uk.ac.ebi.intact.model.CvCompartment implements Serializable

Class uk.ac.ebi.intact.model.CvComponentRole implements Serializable

Class uk.ac.ebi.intact.model.CvDagObject implements Serializable

Serialized Fields

children

java.util.Collection children

TODO comments Children are unique

parents

java.util.Collection parents

TODO comments Parents are unique

Class uk.ac.ebi.intact.model.CvDatabase implements Serializable

Class uk.ac.ebi.intact.model.CvDevelopmentalStage implements Serializable

Class uk.ac.ebi.intact.model.CvEvidenceType implements Serializable

Class uk.ac.ebi.intact.model.CvFeatureIdentification implements Serializable

Class uk.ac.ebi.intact.model.CvFeatureType implements Serializable

Class uk.ac.ebi.intact.model.CvGoNode implements Serializable

Serialized Fields

visited

java.util.HashSet visited

record nodes that have been visited during graph exploration.
Used by "getAllChilds"

level

int level

level of hierarchy in dag. Level 0 is the original node (this).

Class uk.ac.ebi.intact.model.CvIdentification implements Serializable

Class uk.ac.ebi.intact.model.CvInteraction implements Serializable

Class uk.ac.ebi.intact.model.CvInteractionType implements Serializable

Class uk.ac.ebi.intact.model.CvJournal implements Serializable

Class uk.ac.ebi.intact.model.CvModificationType implements Serializable

Class uk.ac.ebi.intact.model.CvObject implements Serializable

Class uk.ac.ebi.intact.model.CvProductRole implements Serializable

Class uk.ac.ebi.intact.model.CvProteinForm implements Serializable

Class uk.ac.ebi.intact.model.CvReferenceQualifier implements Serializable

Class uk.ac.ebi.intact.model.CvTissue implements Serializable

Class uk.ac.ebi.intact.model.CvTopic implements Serializable

Class uk.ac.ebi.intact.model.CvXrefQualifier implements Serializable

Class uk.ac.ebi.intact.model.Experiment implements Serializable

Serialized Fields

detectionMethodAc

java.lang.String detectionMethodAc

identMethodAc

java.lang.String identMethodAc

relatedExperimentAc

java.lang.String relatedExperimentAc

cvIdentificationAc

java.lang.String cvIdentificationAc

cvInteractionAc

java.lang.String cvInteractionAc

bioSourceAc

java.lang.String bioSourceAc

interactions

java.util.Collection interactions

TODO comments TODO would be easier/meaningful to have plural

relatedExperiment

Experiment relatedExperiment

One experiment should group all interactions from a publication which have been performed under the same conditions. However, one experiment might explicitely involve different conditions, for example a time series, or before and after a stimulus. This association can establish this relation. This might be extended into an association class which could state the type of relationship.

cvIdentification

CvIdentification cvIdentification

TODO comments

cvInteraction

CvInteraction cvInteraction

TODO comments

bioSource

BioSource bioSource

TODO comments

Class uk.ac.ebi.intact.model.Feature implements Serializable

Serialized Fields

xrefAc

java.lang.String xrefAc

proteinAc

java.lang.String proteinAc

componentAc

java.lang.String componentAc

boundDomainAc

java.lang.String boundDomainAc

cvFeatureIdentificationAc

java.lang.String cvFeatureIdentificationAc

xref

Xref xref

References a description of a domain in an external database.

cvFeatureType

CvFeatureType cvFeatureType

TODO comments

protein

Protein protein

TODO comments

component

Component component

The Substrate a domain belongs to.

boundDomain

Feature boundDomain

The domain the current domain binds to.

ranges

java.util.Collection ranges

TODO comments

cvFeatureIdentification

CvFeatureIdentification cvFeatureIdentification

TODO comments

Class uk.ac.ebi.intact.model.Institution implements Serializable

Serialized Fields

shortLabel

java.lang.String shortLabel

The name of the institution.

postalAddress

java.lang.String postalAddress

Postal address. Format: One string with line breaks.

fullName

java.lang.String fullName

TODO comments

url

java.lang.String url

TODO comments

Class uk.ac.ebi.intact.model.IntactNode implements Serializable

Serialized Fields

ftpAddress

java.lang.String ftpAddress

TODO comments

ftpDirectory

java.lang.String ftpDirectory

TODO comments

ftpLogin

java.lang.String ftpLogin

TODO comments

ftpPassword

java.lang.String ftpPassword

TODO comments

lastCheckId

int lastCheckId

TODO comments

lastProvidedId

int lastProvidedId

TODO comments

lastProvidedDate

java.sql.Timestamp lastProvidedDate

TODO comments

rejected

int rejected

TODO comments

ownerPrefix

java.lang.String ownerPrefix

TODO comments

Class uk.ac.ebi.intact.model.IntactObjectImpl implements Serializable

Serialized Fields

NEW_LINE

java.lang.String NEW_LINE

This is used in toString() in order to be platform compatible.

ojbConcreteClass

java.lang.String ojbConcreteClass

TODO: comments

ac

java.lang.String ac

The unique accession number of an object. This is defined as protected to allow concrete subclasses to generate copies if required.

created

java.sql.Timestamp created

Creation date of an object. The type is java.sql.Date, not java.util.Data, for database compatibility.

updated

java.sql.Timestamp updated

The last update of the object. The type is java.sql.Date, not java.util.Data, for database compatibility.

Class uk.ac.ebi.intact.model.InteractionImpl implements Serializable

Serialized Fields

cvInteractionTypeAc

java.lang.String cvInteractionTypeAc

kD

java.lang.Float kD

TODO Represents ...

components

java.util.Collection components

TODO comments

released

java.util.Collection released

TODO comments

experiments

java.util.Collection experiments

TODO comments

cvInteractionType

CvInteractionType cvInteractionType

TODO comments

Class uk.ac.ebi.intact.model.InteractorImpl implements Serializable

Serialized Fields

bioSourceAc

java.lang.String bioSourceAc

bioSource

BioSource bioSource

The biological source of the Interactor.

activeInstances

java.util.Collection activeInstances

TODO comments

products

java.util.Collection products

TODO comments

Class uk.ac.ebi.intact.model.JournalRef implements Serializable

Serialized Fields

cvJournalAc

java.lang.String cvJournalAc

pubmidId

java.lang.Integer pubmidId

TODO Represents ...

firstpage

java.lang.String firstpage

TODO Represents ...

cvJournal

CvJournal cvJournal

TODO comments

Class uk.ac.ebi.intact.model.Modification implements Serializable

Serialized Fields

rangeAc

java.lang.String rangeAc

cvModificationTypeAc

java.lang.String cvModificationTypeAc

range

Range range

TODO comments

cvModificationType

CvModificationType cvModificationType

TODO comments

Class uk.ac.ebi.intact.model.NucleicAcid implements Serializable

Class uk.ac.ebi.intact.model.Person implements Serializable

Serialized Fields

institutionAc

java.lang.String institutionAc

firstNames

java.lang.String firstNames

The first names of a person, as they should be shown in any output.

surName

java.lang.String surName

The surname.

telephone

java.lang.String telephone

The full, international telephone number. Represented as a String, but should contain only digits and blanks, for example 0049 122349 5555.

email

java.lang.String email

The full email address. example: test@nowhere.com

institution

Institution institution

Describes the relationship between a person and his/her institution. A person belongs to zero or one institution, if he/she should have for example more than one employer, one must be chosen.

Class uk.ac.ebi.intact.model.Product implements Serializable

Serialized Fields

interactionAc

java.lang.String interactionAc

interactorAc

java.lang.String interactorAc

cvProductRoleAc

java.lang.String cvProductRoleAc

stoichiometry

float stoichiometry

TODO Represents ...

interaction

Interaction interaction

TODO comments

interactor

Interactor interactor

TODO comments

cvProductRole

CvProductRole cvProductRole

TODO comments

Class uk.ac.ebi.intact.model.ProteinImpl implements Serializable

Serialized Fields

cvProteinFormAc

java.lang.String cvProteinFormAc

formOfAc

java.lang.String formOfAc

TODO comments

crc64

java.lang.String crc64

Represents the CRC64 checksum. This checksum is used to detect potential inconsistencies between the sequence the object refers to and the external sequence object, for example when the external object has been updated.

formOf

Protein formOf

TODO comments

cvProteinForm

CvProteinForm cvProteinForm

TODO comments

features

java.util.Collection features

TODO comments

modifications

java.util.Collection modifications

TODO comments

sequenceChunks

java.util.Collection sequenceChunks

The protein sequence. If the protein is present in a public database, the sequence should not be repeated.

Class uk.ac.ebi.intact.model.Range implements Serializable

Serialized Fields

ModificationAc

java.lang.String ModificationAc

posFrom

int posFrom

TODO Represents ...

posTo

int posTo

TODO Represents ...

modification

Modification modification

TODO comments

Class uk.ac.ebi.intact.model.Reference implements Serializable

Serialized Fields

submissionRefAc

java.lang.String submissionRefAc

xrefAc

java.lang.String xrefAc

title

java.lang.String title

TODO COMMENTS

authors

java.lang.String authors

TODO COMMENTS

annotatedObjects

java.util.Collection annotatedObjects

TODO COMMENTS

submissionRef

SubmissionRef submissionRef

TODO COMMENTS

xref

Xref xref

TODO COMMENTS TODO is it used ?

Class uk.ac.ebi.intact.model.SmallMolecule implements Serializable

Class uk.ac.ebi.intact.model.SubmissionRef implements Serializable

Serialized Fields

referenceAc

java.lang.String referenceAc

holdDate

java.util.Date holdDate

todo Represents ...

reference

Reference reference

TODO comments

Class uk.ac.ebi.intact.model.Xref implements Serializable

Serialized Fields

parentAc

java.lang.String parentAc

Ac of the object which holds that Xref

cvXrefQualifierAc

java.lang.String cvXrefQualifierAc

cvDatabaseAc

java.lang.String cvDatabaseAc

primaryId

java.lang.String primaryId

Primary identifier of the database referred to.

secondaryId

java.lang.String secondaryId

Secondary identifier of the database. This will usually be a meaningful name, for example a domain name.

dbRelease

java.lang.String dbRelease

The release number of the external database from which the object has been updated.

cvXrefQualifier

CvXrefQualifier cvXrefQualifier

TODO comments

cvDatabase

CvDatabase cvDatabase

TODO comments

Package uk.ac.ebi.intact.model.proxy

Class uk.ac.ebi.intact.model.proxy.AnnotatedObjectProxy implements Serializable

Class uk.ac.ebi.intact.model.proxy.BasicObjectProxy implements Serializable

Class uk.ac.ebi.intact.model.proxy.IntactObjectProxy implements Serializable

Class uk.ac.ebi.intact.model.proxy.InteractionProxy implements Serializable

Class uk.ac.ebi.intact.model.proxy.InteractorProxy implements Serializable

Class uk.ac.ebi.intact.model.proxy.ProteinProxy implements Serializable

Package uk.ac.ebi.intact.persistence

Class uk.ac.ebi.intact.persistence.CreateException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

Class uk.ac.ebi.intact.persistence.DataSourceException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

Class uk.ac.ebi.intact.persistence.IntactRowReaderImpl implements Serializable

Class uk.ac.ebi.intact.persistence.ObjectBridgeDAO implements Serializable

Serialized Fields

logger

org.apache.log4j.Logger logger

A log utility, used if required

cache

java.util.HashMap cache

cache to be used for caching by unique search parameters. The parameter is the key, and the value is the key used by the OJB cache.

cachedClasses

java.util.HashSet cachedClasses

determines which classes are to be cached.

repositoryFile

java.lang.String repositoryFile

OJB repository file (contains mappings).

user

java.lang.String user

The user name to access the database.

password

java.lang.String password

The password to access the database.

transactionType

int transactionType

defines the current transaction type - defaults to JDBC in begin unless object level specified. Initialised to an 'unknown' value

connectionDetails

java.lang.String connectionDetails

Class uk.ac.ebi.intact.persistence.ObjectBridgeDAOSource implements Serializable

Serialization Methods

readObject

private void readObject(java.io.ObjectInputStream in)
                 throws java.io.IOException,
                        java.lang.ClassNotFoundException

Logger is set in this method as it is declared as transient.

Throws:

java.io.IOException - for errors in reading from the stream (required by the method signature)

java.lang.ClassNotFoundException - required by the method signature.

Serialized Fields

repositoryFile

java.lang.String repositoryFile

user

java.lang.String user

password

java.lang.String password

Class uk.ac.ebi.intact.persistence.SearchException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

rootCause

java.lang.Exception rootCause

Class uk.ac.ebi.intact.persistence.TransactionException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

Class uk.ac.ebi.intact.persistence.UpdateException implements Serializable

Serialized Fields

nestedMessage

java.lang.String nestedMessage

rootCause

java.lang.Exception rootCause

Package uk.ac.ebi.intact.simpleGraph

Class uk.ac.ebi.intact.simpleGraph.BasicGraph implements Serializable

Serialized Fields

id

java.lang.String id

label

java.lang.String label

Class uk.ac.ebi.intact.simpleGraph.Edge implements Serializable

Serialized Fields

node1

NodeI node1

node2

NodeI node2

Component1

Component Component1

Component2

Component Component2

Class uk.ac.ebi.intact.simpleGraph.Graph implements Serializable

Serialized Fields

nodes

java.util.HashMap nodes

edges

java.util.ArrayList edges

visited

java.util.HashSet visited

Class uk.ac.ebi.intact.simpleGraph.Node implements Serializable

Serialized Fields

interactor

Interactor interactor

Package uk.ac.ebi.intact.util

Class uk.ac.ebi.intact.util.GoServerProxy.GoIdNotFoundException implements Serializable

Class uk.ac.ebi.intact.util.HttpProxyManager.ProxyConfigurationNotFound implements Serializable

Class uk.ac.ebi.intact.util.NewtServerProxy.TaxIdNotFoundException implements Serializable

Class uk.ac.ebi.intact.util.UpdateProteinsI.UpdateException implements Serializable

Class uk.ac.ebi.intact.util.XmlBuilder implements Serializable

Serialized Fields

helper

IntactHelper helper

expandedCache

java.util.HashMap expandedCache

compactCache

java.util.HashMap compactCache