Uses of Class
uk.ac.ebi.intact.business.IntactException

Packages that use IntactException

uk.ac.ebi.intact.application.commons.business
uk.ac.ebi.intact.application.commons.search
uk.ac.ebi.intact.application.dataConversion
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.struts.framework.util	This package contains utility methods common for the struts framework.
uk.ac.ebi.intact.application.editor.struts.view.interaction
uk.ac.ebi.intact.application.editor.util
uk.ac.ebi.intact.application.goDensity.business.binaryInteractions
uk.ac.ebi.intact.application.goDensity.business.dag
uk.ac.ebi.intact.application.graph2MIF	The classes of the Graph2MIF application are in this 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.hierarchView.business	Some utility classes and packages.
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.highlightment.source	From what do we select the proteins to highlight.
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.struts.framework	This package contains common classes required for the MVC framework.
uk.ac.ebi.intact.application.predict.business
uk.ac.ebi.intact.application.predict.struts.view
uk.ac.ebi.intact.application.search2.business
uk.ac.ebi.intact.application.statisticView.business.data	Contains the classes holding the statistics data.
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	This package is the implementation of the IntAct data model.
uk.ac.ebi.intact.model.proxy
uk.ac.ebi.intact.persistence	This package provides a persistence capability for intact.
uk.ac.ebi.intact.util	Various utilities and auxiliary scripts.

Uses of IntactException in uk.ac.ebi.intact.application.commons.business

Methods in uk.ac.ebi.intact.application.commons.business that throw IntactException

java.util.Collection

IntactUserI.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue) This method provides a means of searching intact objects, within the constraints provided by the parameters to the method.

Uses of IntactException in uk.ac.ebi.intact.application.commons.search

Methods in uk.ac.ebi.intact.application.commons.search that throw IntactException

java.util.Collection	SearchHelperI.doLookupSimple(java.lang.String searchClass, java.lang.String query, IntactUserI user) Peforms a simple search in the IntAct data for given search class and value.
java.util.Collection	SearchHelperI.doLookup(java.lang.String searchClass, java.lang.String value, IntactUserI user) Search in the IntAct data for a colleciton of object (type=searchClass).
java.util.Collection	SearchHelperI.doLookup(java.util.List searchClasses, java.lang.String value, IntactUserI user) Search in the IntAct data for a colleciton of object (type=searchClass).
java.util.Collection	SearchHelper.doLookupSimple(java.lang.String searchClass, java.lang.String query, IntactUserI user)
java.util.Collection	SearchHelper.doLookup(java.lang.String searchClass, java.lang.String values, IntactUserI user)
java.util.Collection	SearchHelper.doLookup(java.util.List searchClasses, java.lang.String values, IntactUserI user)

Uses of IntactException in uk.ac.ebi.intact.application.dataConversion

Methods in uk.ac.ebi.intact.application.dataConversion that throw IntactException

java.util.Collection	FileGenerator.getDbData(java.lang.String searchPattern) Obtains the data from the dataSource, in preparation for the flat file generation.
static java.util.HashMap	FileGenerator.classifyExperiments(java.lang.String searchPattern) Classify experiments matching searchPattern into a data structure according to species and experiment size.

Uses of IntactException in uk.ac.ebi.intact.application.editor.business

Methods in uk.ac.ebi.intact.application.editor.business that throw IntactException

void	EditUserI.begin()
void	EditUserI.commit()
void	EditUserI.rollback()
void	EditUserI.create(java.lang.Object object)
void	EditUserI.update(java.lang.Object object)
void	EditUserI.delete(java.lang.Object object)
void	EditUserI.persist() Persists the object the user is editing.
void	EditUserI.delete() 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.
void	EditUserI.logoff() Logs off from the application.
java.util.Collection	EditUser.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue)
void	EditUser.begin()
void	EditUser.commit()
void	EditUser.rollback()
void	EditUser.create(java.lang.Object object)
void	EditUser.update(java.lang.Object object)
void	EditUser.delete(java.lang.Object object)
void	EditUser.persist()
void	EditUser.delete()
void	EditUser.logoff()

Constructors in uk.ac.ebi.intact.application.editor.business that throw IntactException

EditUser(java.lang.String mapping, java.lang.String dsClass, java.lang.String user, java.lang.String password)
Constructs an instance of this class with given mapping file and the name of the data source class.

EditUser(java.lang.String mapping, java.lang.String dsClass)
This constructor for Seralization test class.

Uses of IntactException in uk.ac.ebi.intact.application.editor.struts.framework.util

Methods in uk.ac.ebi.intact.application.editor.struts.framework.util that throw IntactException

void	AbstractEditViewBean.persist(EditUserI user) Persists the current state to the persistent system.
void	AbstractEditViewBean.persistOthers(EditUserI user) Persist any sub objects of the edited object.

Uses of IntactException in uk.ac.ebi.intact.application.editor.struts.view.interaction

Methods in uk.ac.ebi.intact.application.editor.struts.view.interaction that throw IntactException

void	InteractionViewBean.persistOthers(EditUserI user)

Uses of IntactException in uk.ac.ebi.intact.application.editor.util

Methods in uk.ac.ebi.intact.application.editor.util that throw IntactException

java.util.List

MenuManager.getMenuList(java.lang.Class targetClass, IntactHelper helper) Return a Vector of all shortLabels of the class, e.g.

Uses of IntactException in uk.ac.ebi.intact.application.goDensity.business.binaryInteractions

Methods in uk.ac.ebi.intact.application.goDensity.business.binaryInteractions that throw IntactException

void	CalcBinInteractionData.dbPopulate(boolean addIfProteinNoGoId) populate database with binary interaction data - but only if bait and prey are annotated by go.

Constructors in uk.ac.ebi.intact.application.goDensity.business.binaryInteractions that throw IntactException

CalcBinInteractionData(IntactHelper helper, boolean ifABait, boolean ifNoBait, boolean baitBait)
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.

Uses of IntactException in uk.ac.ebi.intact.application.goDensity.business.dag

Constructors in uk.ac.ebi.intact.application.goDensity.business.dag that throw IntactException

CvGoDag()
Constructor retrieve the root element of GO hierarchy (of typ CvGoNode) from the database.

Uses of IntactException in uk.ac.ebi.intact.application.graph2MIF

Methods in uk.ac.ebi.intact.application.graph2MIF that throw IntactException

static Graph	GraphFactory.getGraph(java.lang.String queryString, java.lang.Integer depth) getInteractionNetwork retrieves a interactionnetwork (graph) from a given queryString and depth.
java.lang.String	Graph2MIFWSService.getMIF(java.lang.String ac, java.lang.Integer depth, java.lang.Boolean strictmif) getMIF is the only method which is necessary for access.
java.lang.String	Graph2MIFWS.getMIF(java.lang.String ac, java.lang.Integer depth, java.lang.Boolean strictmif) getMIF is the only method which is necessary.

Uses of IntactException in uk.ac.ebi.intact.application.graph2MIF.client

Constructors in uk.ac.ebi.intact.application.graph2MIF.client that throw IntactException

Graph2MIFConsole()

Uses of IntactException in uk.ac.ebi.intact.application.hierarchView.business

Methods in uk.ac.ebi.intact.application.hierarchView.business that throw IntactException

InteractionNetwork	IntactUserI.subGraph(InteractionNetwork in, int graphDepth, java.util.Collection experiments, int complexExpansion) Returns a subgraph centered on startNode.
InteractionNetwork	IntactUser.subGraph(InteractionNetwork in, int graphDepth, java.util.Collection experiments, int complexExpansion) Returns a subgraph centered on startNode (stored in the interaction network).
java.util.Collection	IntactUser.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue)

Constructors in uk.ac.ebi.intact.application.hierarchView.business that throw IntactException

IntactUser(java.lang.String applicationPath)
Constructs an instance of this class with given mapping file and the name of the data source class.

Uses of IntactException in uk.ac.ebi.intact.application.hierarchView.business.graph

Methods in uk.ac.ebi.intact.application.hierarchView.business.graph that throw IntactException

InteractionNetwork

GraphHelper.addInteractionNetwork(InteractionNetwork in, Interactor interactor, int depth) Create or extend an interaction network by using the given Interactor as a central node.

Uses of IntactException in uk.ac.ebi.intact.application.hierarchView.highlightment.source

Methods in uk.ac.ebi.intact.application.hierarchView.highlightment.source that throw IntactException

abstract java.util.List	HighlightmentSource.getSourceUrls(java.util.Collection xRefs, java.util.Collection selectedXRefs, java.lang.String applicationPath) Return a collection of URL corresponding to the selected protein and source eg.
java.util.List	GoHighlightmentSource.getSourceUrls(java.util.Collection xRefs, java.util.Collection selectedXRefs, java.lang.String applicationPath)

Uses of IntactException in uk.ac.ebi.intact.application.intSeq.business

Methods in uk.ac.ebi.intact.application.intSeq.business that throw IntactException

java.util.ArrayList	RunSimilaritySearchIF.RetrieveParseResult() return the file which contains all Blast results from the user's request.
java.util.ArrayList	RunSimilaritySearch.RetrieveParseResult() In case of a good blast execution, the output blast file would be parsed.
protected boolean	RunSimilaritySearch.ExecBlast() FillSeqFileConcatCommand 1) creates and full the input file, and also complete the command line.
protected void	RunSimilaritySearch.FillSeqFileConcatCommand(java.lang.String inputDir, boolean input) This method creates a random file name in the good directory: input files and output files are managed in two different directories.
java.util.ArrayList	ManagerFilesBlast.ResultParsing(java.util.ArrayList patterns, int jWhichGroup) 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.
void	ManagerFiles.PutInFile(java.lang.String sequence) This method allows to write a string, more or less long, in a file which has been created before.
void	ManagerFiles.CreateWriter() if the PutInFile method needs to be managed in a loop, the FileWriter has to be created only once.
java.lang.String	ManagerFiles.ReadingFile() This method allows to recover the file content in a String.
java.util.ArrayList	ManagerFiles.ResultParsing(java.util.ArrayList patternList, int jWhichGroup) This method parses a file with only one item requiered and returns the list of this item possibly retrieved in several lines.
java.util.ArrayList	ManagerFiles.ResultParsingTableFile(java.lang.String pattern) This method parses a file from one Regular Expression given.
protected void	ManagerFiles.PrepareBufferedReader() This method prepares the buffered reader, to put the file managed in a buffer, which allow to work on its content and parse it.
boolean	CallingSrsIF.GetBooleanIntactId() check if the protein topic still corresponds to an Intact entry.
java.util.ArrayList	CallingSrsIF.RetrieveAccDes() request result: return a list of accession numbers and its own description.
java.lang.String	CallingSrsIF.GetSequenceFasta() return the sequence, which allows to run a multi-alignment algorithm (like Fasta or Blast).
java.util.ArrayList	CallingSrs.RetrieveAccDes() Wgetz execution + parsing of the WGETZ output file
java.lang.String	CallingSrs.GetSequenceFasta() 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)
protected void	CallingSrs.ExecFinalCommand(boolean acOrSeqRequest) 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.
protected void	CallingSrs.WebSrs(java.lang.String path) This method manages the execution of the Wgetz URL.

Uses of IntactException in uk.ac.ebi.intact.application.intSeq.struts.framework

Methods in uk.ac.ebi.intact.application.intSeq.struts.framework that throw IntactException

protected java.util.ArrayList

IntactBaseAction.ManageBlastResult(java.lang.String sequence, java.lang.String commLine, java.lang.String perc_base, java.lang.String param) 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.

Uses of IntactException in uk.ac.ebi.intact.application.predict.business

Methods in uk.ac.ebi.intact.application.predict.business that throw IntactException

static PredictUser	PredictUser.create(java.lang.String mapping, java.lang.String dsClass) Factory method to create different instances of Predict user instances depending on the JDBC subprotocol.
java.util.Collection	PredictUser.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue)
java.util.List	PredictUser.getSpecies() Returns a list of tax ids for species from the database.
java.util.List	PredictUser.getDbInfo(java.lang.String specie) Returns a list of beans created from ia_payg database.

Uses of IntactException in uk.ac.ebi.intact.application.predict.struts.view

Constructors in uk.ac.ebi.intact.application.predict.struts.view that throw IntactException

ResultBean(Protein protein, int rank)

Uses of IntactException in uk.ac.ebi.intact.application.search2.business

Methods in uk.ac.ebi.intact.application.search2.business that throw IntactException

java.util.Collection

IntactUserImpl.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue)

Constructors in uk.ac.ebi.intact.application.search2.business that throw IntactException

IntactUserImpl(java.lang.String mapping, java.lang.String dsClass)
Constructs an instance of this class with given mapping file and the name of the data source class.

Uses of IntactException in uk.ac.ebi.intact.application.statisticView.business.data

Methods in uk.ac.ebi.intact.application.statisticView.business.data that throw IntactException

java.lang.String

StatisticsBean.getMoreRecentStatisticsDate()

Uses of IntactException in uk.ac.ebi.intact.business

Subclasses of IntactException in uk.ac.ebi.intact.business

class

DuplicateLabelException Exception class to provide more meaningful error messages.

Methods in uk.ac.ebi.intact.business that throw IntactException

java.util.Collection	SearchI.paramSearch(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue, boolean includeSubClass, boolean matchSubString) This method provides a means of searching intact objects, within the constraints provided by the parameters to the method.
java.util.List	SearchI.stringSearch(java.lang.String objectType, java.lang.String searchString, boolean includeSubClass, boolean matchSubString) Searches objects by searchString in all "relevant" fields.
Graph	SearchI.subGraph(Interactor startNode, int graphDepth, java.util.Collection experiments, int complexExpansion, Graph graph) Returns a subgraph centered on startNode.
void	IntactHelper.closeStore() close the data source.
void	IntactHelper.startTransaction(int transactionType) starts a business level transaction.
void	IntactHelper.finishTransaction() ends a busines transaction.
void	IntactHelper.undoTransaction() unwraps a transaction.
void	IntactHelper.create(java.util.Collection objects) This method provides a create operation for intact objects.
void	IntactHelper.delete(java.lang.Object obj) This method provides a delete operation.
void	IntactHelper.create(java.lang.Object obj) Convenience method to create a single object in persistent store.
void	IntactHelper.update(java.lang.Object obj) This method provides an update operation.
java.util.Collection	IntactHelper.paramSearch(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue, boolean includeSubClass, boolean matchSubString)
java.util.List	IntactHelper.stringSearch(java.lang.String objectType, java.lang.String searchString, boolean includeSubClass, boolean matchSubString) Not Yet Fully Implemented.
java.util.Iterator	IntactHelper.iterSearch(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue) Search which provides an Iterator rather than a Collection.
java.util.Iterator	IntactHelper.getColumnData(java.lang.String type, java.lang.String[] cols) Allows access to column data rather than whole objects.
java.util.Collection	IntactHelper.searchBySQL(java.lang.String type, java.lang.String sqlString) Allows search by raw SQL String.
java.util.Collection	IntactHelper.search(java.lang.String objectType, java.lang.String searchParam, java.lang.String searchValue) This method provides a means of searching intact objects, within the constraints provided by the parameters to the method.
java.util.Collection	IntactHelper.search(java.lang.Object obj) Deprecated. This should not be used with the new model, as applications should not use no-arg constructors.
java.util.Collection	IntactHelper.getRelations(BasicObject base) This method obtains the nearest neighbours (ie the next level of related objects) to a given intact object.
java.util.Collection	IntactHelper.getObjectsByXref(java.lang.Class clazz, java.lang.String aPrimaryId) Searches for objects by classname and Xref.
java.util.Collection	IntactHelper.getSpliceProteinsByXref(java.lang.String primaryId) Searches for splice objects by primaryId.
java.lang.Object	IntactHelper.getObjectByXref(java.lang.Class clazz, java.lang.String aPrimaryId) Searches for a unique Object by classname and Xref.
java.util.Collection	IntactHelper.getObjectsByAlias(java.lang.Class clazz, java.lang.String aliasName) Search for objects by any alias with the specified name.
java.util.Collection	IntactHelper.getObjectsByAlias(java.lang.Class clazz, java.lang.String aliasName, java.lang.String aliasTypeShortLabel) Search for objects by any alias with the specified name.
java.util.Collection	IntactHelper.getObjectsByAlias(java.lang.Class clazz, java.lang.String aliasName, CvAliasType cvAliasType) Search for objects by any alias with the specified name.
java.lang.Object	IntactHelper.getObjectByLabel(java.lang.Class clazz, java.lang.String label) Return an Object by classname and shortLabel.
java.lang.Object	IntactHelper.getObjectByAc(java.lang.Class clazz, java.lang.String ac) Return an Object by classname and ac.
java.lang.Object	IntactHelper.getObjectByName(java.lang.Class clazz, java.lang.String name) This method retrieves an intact object, given a class and the object's full name (provided that name is unique).
BioSource	IntactHelper.getBioSourceByName(java.lang.String name) This method is used for searching by scientific name (provided that name is unique).
BioSource	IntactHelper.getBioSourceByTaxId(java.lang.String taxId) Searches for a BioSource given a tax ID.
java.util.Collection	IntactHelper.getInteractorBySource(java.lang.Class clazz, BioSource source) This method is used for obtaining an interactor given a specific BioSource and the subclass of Interactor that is to be searched for.
Experiment	IntactHelper.getExperimentBySource(BioSource source) Search for an experiment given a specific BioSource.
java.util.Collection	IntactHelper.getComponentsByRole(CvComponentRole role) Search for components given a role.
java.util.Collection	IntactHelper.getInteractionsByType(CvInteractionType type) Search for interactions given a type.
java.util.Collection	IntactHelper.getExperimentsByInstitution(Institution institution) Search for Experiments given an Institution.
Protein	IntactHelper.getProteinByXref(Xref xref) Search for Protein given a cross reference.
void	IntactHelper.deleteAllElements(java.util.Collection aCollection) Delete all elements in a collection.
Graph	IntactHelper.subGraph(Interactor startNode, int graphDepth, java.util.Collection experiments, int complexExpansion, Graph graph) Returns a subgraph centered on startNode.
java.sql.Connection	IntactHelper.getJDBCConnection() Gets the underlying JDBC connection.
Institution	IntactHelper.getInstitution() 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.

Constructors in uk.ac.ebi.intact.business that throw IntactException

IntactHelper(DAOSource source)
Constructor - requires a datasource to be provided.

IntactHelper()
Shortcut constructor

IntactHelper(DAOSource source, java.lang.String user, java.lang.String password)
Constructor allowing a helper instance to be created with a given username and password.

IntactHelper(java.util.Map classInfo, DAOSource source)
This constructor allows creation of an IntactHelper with a Map of java classnames to PropertyDescriptor information.

Uses of IntactException in uk.ac.ebi.intact.model

Methods in uk.ac.ebi.intact.model that throw IntactException

void	ProteinImpl.setSequence(IntactHelper helper, java.lang.String aSequence, java.lang.String crc64)
void	ProteinImpl.setSequence(IntactHelper helper, java.lang.String aSequence) 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.
java.util.Collection	CvGoNode.getInteractors(IntactHelper helper)
void	Protein.setSequence(IntactHelper helper, java.lang.String aSequence, java.lang.String crc64)
void	Protein.setSequence(IntactHelper helper, java.lang.String aSequence)
AnnotatedObject	AnnotatedObject.update(IntactHelper helper)
AnnotatedObject	AnnotatedObjectImpl.update(IntactHelper helper) Update an annotated object in the database.

Uses of IntactException in uk.ac.ebi.intact.model.proxy

Methods in uk.ac.ebi.intact.model.proxy that throw IntactException

void	ProteinProxy.setSequence(IntactHelper helper, java.lang.String aSequence, java.lang.String crc64)
void	ProteinProxy.setSequence(IntactHelper helper, java.lang.String aSequence)
AnnotatedObject	AnnotatedObjectProxy.update(IntactHelper helper)

Uses of IntactException in uk.ac.ebi.intact.persistence

Constructors in uk.ac.ebi.intact.persistence that throw IntactException

PostgresSequenceManager(org.apache.ojb.broker.PersistenceBroker broker)
Public constructor

OracleSequenceManager(org.apache.ojb.broker.PersistenceBroker broker)

AbstractSequenceManager(org.apache.ojb.broker.PersistenceBroker broker)
Public constructor

Uses of IntactException in uk.ac.ebi.intact.util

Subclasses of IntactException in uk.ac.ebi.intact.util

static class

GoServerProxy.GoIdNotFoundException

Methods in uk.ac.ebi.intact.util that throw IntactException

void	SanityChecker.checkExperiments() Performs checks on Experiments.
void	SanityChecker.checkExperimentsPubmedIds() Performs checks on Experiments.
void	SanityChecker.checkInteractions() Performs Interaction checks.
void	SanityChecker.checkInteractionsBaitAndPrey() Performs Interaction checks.
void	SanityChecker.checkProteins() Performs checks against Proteins.
Protein	InsertGo.updateProtein(java.lang.String shortLabel, java.lang.String spAc, java.lang.String sgdAc, java.lang.String goAc, java.lang.String pubmedAc) Insert or update a protein object.
void	InsertComplexGiot.process(java.lang.String outputFilename)
java.lang.String	InsertComplexGiot.createInteractionShortLabel(java.lang.String bait, java.lang.String prey) Creata an interaction shortlabel.
abstract Protein	UpdateProteinsI.insertSimpleProtein(java.lang.String anAc, CvDatabase aDatabase, java.lang.String aTaxId) Creates a simple Protein object for entries which are not in SPTR.
Protein	UpdateProteins.insertSimpleProtein(java.lang.String anAc, CvDatabase aDatabase, java.lang.String aTaxId) Creates a simple Protein object for entries which are not in SPTR.
void	InsertComplex.insertComponent(Interaction act, java.lang.String spAc, CvComponentRole role) Insert a Component object linking an Interactor to an Interaction.
static java.lang.String	GoTools.getUniqueShortLabel(IntactHelper helper, java.lang.Class targetClass, java.lang.String ac, java.lang.String label, java.lang.String externalAc) Generate a label which is unique in targetClass and resembles label.
static CvObject	GoTools.insertDefinition(java.util.Hashtable definition, IntactHelper helper, java.lang.String goidDatabase, java.lang.Class targetClass, boolean deleteold) Insert a GO term into IntAct.
static void	GoTools.writeGoDefinitions(java.lang.Class aTargetClass, IntactHelper helper, java.lang.String goidDatabase, java.lang.String targetFile) Write a Controlled vocabulary in GO definition format flat file.
static CvObject	GoTools.selectCvObject(IntactHelper helper, java.lang.String goidDatabase, java.lang.String goid, java.lang.String shortLabel, java.lang.Class targetClass) Select an appropriate CvObject for update if it exists.
static CvObject	GoTools.selectCvObject(IntactHelper helper, java.lang.String goidDatabase, java.util.Hashtable definition, java.lang.Class targetClass) Select an appropriate CvObject for update if it exists.
BioSource	BioSourceFactory.getValidBioSource(java.lang.String aTaxId) Create or update a BioSource object from a taxid.
java.lang.String	BioSourceFactory.getUpToDateTaxid(java.lang.String taxid) Gives a valid taxid.

Constructors in uk.ac.ebi.intact.util that throw IntactException

XmlBuilder(IntactHelper helper)
Sets up an XML builder with suitable persistent store access.

XmlBuilder()
Note that this default constructor will build a default IntactHelper object with default configuration settings.

SanityChecker(IntactHelper helper, java.io.PrintWriter writer)

InsertComplexGiot(java.lang.String giotUrl, java.lang.String cgSptrMappingUrl, java.lang.String sptrGeneMappingUrl, IntactHelper helper)

GoaTools(java.lang.String url)

BioSourceFactory(IntactHelper helper)