A B C E G I O P R S

A

addModel(Model) - Method in interface org.mskcc.psibiopax.converter.BioPAXMarshaller

Method called when BioPAX data is ready to be marshalled

addModel(Model) - Method in class org.mskcc.psibiopax.converter.BioPAXMarshallerImp

Our implementation of BioPAXMarshaller interface.

B

BioPAXMapper - Interface in org.mskcc.psibiopax.converter

An interface which provides methods to query a Paxtools model.

BioPAXMapperImp - Class in org.mskcc.psibiopax.converter

An base class that creates paxtool models given psi.

BioPAXMapperImp(BioPAXLevel) - Constructor for class org.mskcc.psibiopax.converter.BioPAXMapperImp

Constructor.

BioPAXMarshaller - Interface in org.mskcc.psibiopax.converter

Definition of the BioPAXMarshaller interface.

BioPAXMarshallerImp - Class in org.mskcc.psibiopax.converter

This class waits for each EntryProcessor thread to finish.

BioPAXMarshallerImp(PSIMIBioPAXConverter, BioPAXLevel, OutputStream, int) - Constructor for class org.mskcc.psibiopax.converter.BioPAXMarshallerImp

C

conversionIsComplete - Variable in class org.mskcc.psibiopax.converter.PSIMIBioPAXConverter

Ref to boolean which indicates conversion is complete.

convert(InputStream, OutputStream) - Method in class org.mskcc.psibiopax.converter.PSIMIBioPAXConverter

Converts the psi data in inputStream and places into outputStream.

convert(EntrySet, OutputStream) - Method in class org.mskcc.psibiopax.converter.PSIMIBioPAXConverter

Converts the psi data in the EntrySet and places into outputstream.

convert(InputStream, OutputStream) - Method in interface org.mskcc.psibiopax.converter.PSIMIConverter

Converts the psi data in inputStream and places into outputStream.

convert(EntrySet, OutputStream) - Method in interface org.mskcc.psibiopax.converter.PSIMIConverter

Converts the psi data in the EntrySet and places into outputstream.

E

EntryMapper - Class in org.mskcc.psibiopax.converter

A thread class which processes an entry in a psi xml doc.

EntryMapper(BioPAXMapper, BioPAXMarshaller, Entry) - Constructor for class org.mskcc.psibiopax.converter.EntryMapper

Constructor.

EntryMapper(BioPAXMapper, BioPAXMarshaller, Entry, long) - Constructor for class org.mskcc.psibiopax.converter.EntryMapper

Constructor.

G

getBioPAXElement(String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Given an RDF ID, returns a matching model element

getBioPAXElement(String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Given an RDF ID, returns a matching model element

getBioSource(String, BioPAXElement, BioPAXElement, BioPAXElement, String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a biosource.

getBioSource(String, BioPAXElement, BioPAXElement, BioPAXElement, String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a biosource.

getEvidence(String, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, Set<String>, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets an evidence object.

getEvidence(String, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, Set<String>, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets an evidence object.

getExperimentalForm(String, BioPAXElement, BioPAXElement) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a experimental form object.

getExperimentalForm(String, BioPAXElement, BioPAXElement) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a experimental form object.

getFeature(BioPAXElement, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, BioPAXElement) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Used to add feature attributes to given sequence or entity feature.

getFeature(String, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, BioPAXElement) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a sequence or entity feature.

getFeature(BioPAXElement, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, BioPAXElement) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Used to add feature attributes to given sequence or entity feature.

getFeature(String, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>, BioPAXElement) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a sequence or entity feature.

getInteraction(String, String, String, Set<String>, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets an interaction.

getInteraction(String, String, String, Set<String>, Set<? extends BioPAXElement>, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets an interaction.

getModel() - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets the biopax model.

getModel() - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets the biopax model.

getOpenControlledVocabulary(String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets an existing open/controlled vocabulary object.

getOpenControlledVocabulary(String, String, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a open/controlled vocabulary object.

getOpenControlledVocabulary(String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets an existing open/controlled vocabulary object.

getOpenControlledVocabulary(String, String, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a open/controlled vocabulary object.

getParticipant(String, Set<? extends BioPAXElement>, BioPAXElement, BioPAXElement) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a participant.

getParticipant(String, Set<? extends BioPAXElement>, BioPAXElement, BioPAXElement) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a participant.

getPhysicalEntity(String, String, String, String, Set<String>, Set<? extends BioPAXElement>, String, BioPAXElement, String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a physical Entity.

getPhysicalEntity(String, String, String, String, Set<String>, Set<? extends BioPAXElement>, String, BioPAXElement, String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a physical Entity.

getPublicationXref(String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a publication xref.

getPublicationXref(String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a publication xref.

getRelationshipXref(String, String, String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a relationship xref.

getRelationshipXref(String, String, String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a relationship xref.

getScoreOrConfidence(String, String, Set<? extends BioPAXElement>, Set<String>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a confidence/score object.

getScoreOrConfidence(String, String, Set<? extends BioPAXElement>, Set<String>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a confidence/score object.

getSequenceLocation(String, String, String, long, long) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a sequence location.

getSequenceLocation(String, String, String, long, long) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a sequence location.

getUnificationXref(String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Gets a unification xref.

getUnificationXref(String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Gets a unification xref.

getXrefID(BioPAXElement) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Given an xref (BioPAXElement) returns its id.

getXrefID(BioPAXElement) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Given an xref (BioPAXElement) returns its id.

I

isGeneticInteraction(List<String>, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Given a set of evidence objects, determines if interaction (that evidence obj is derived from) is a genetic interaction.

isGeneticInteraction(List<String>, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Given a set of evidence objects, determines if interaction (that evidence obj is derived from) is a genetic interaction.

O

org.mskcc.psibiopax.converter - package org.mskcc.psibiopax.converter

P

PSIMIBioPAXConverter - Class in org.mskcc.psibiopax.converter

The converter class.

PSIMIBioPAXConverter(BioPAXLevel) - Constructor for class org.mskcc.psibiopax.converter.PSIMIBioPAXConverter

Constructor.

PSIMIConverter - Interface in org.mskcc.psibiopax.converter

An interface which provides methods to convert a PSI-MI file.

R

RDF_ID_PREFIX - Static variable in class org.mskcc.psibiopax.converter.EntryMapper

rdf id prefix.

run() - Method in class org.mskcc.psibiopax.converter.BioPAXMarshallerImp

Our implementation of run.

run() - Method in class org.mskcc.psibiopax.converter.EntryMapper

Our implementation of run.

S

setInteractionDataSource(T, String, String, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Creates a data source and adds to given interaction.

setInteractionDataSource(T, String, String, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Creates a data source and adds to given interaction.

setModelDataSource(String, String, Set<? extends BioPAXElement>) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Creates a data source on the model.

setModelDataSource(String, String, Set<? extends BioPAXElement>) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Creates a data source on the model.

setNamespace(String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Sets biopax model namespace.

setNamespace(String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Sets biopax model namespace.

setXrefDBAndID(BioPAXElement, String, String) - Method in interface org.mskcc.psibiopax.converter.BioPAXMapper

Sets given xref's db and id.

setXrefDBAndID(BioPAXElement, String, String) - Method in class org.mskcc.psibiopax.converter.BioPAXMapperImp

Sets given xref's db and id.

A B C E G I O P R S