org.mskcc.psibiopax.converter
Class BioPAXMapperImp

java.lang.Object
  org.mskcc.psibiopax.converter.BioPAXMapperImp

All Implemented Interfaces:

BioPAXMapper

public class BioPAXMapperImp
extends java.lang.Object
implements BioPAXMapper

An base class that creates paxtool models given psi.

Author:

Benjamin Gross

Constructor Summary

BioPAXMapperImp(BioPAXLevel bpLevel)
Constructor.

Method Summary

BioPAXElement	getBioPAXElement(java.lang.String rdfID) Given an RDF ID, returns a matching model element
<T extends BioPAXElement> T	getBioSource(java.lang.String id, BioPAXElement taxonXref, BioPAXElement cellType, BioPAXElement tissue, java.lang.String name) Gets a biosource.
<T extends BioPAXElement> T	getEvidence(java.lang.String id, java.util.Set<? extends BioPAXElement> bpXrefs, java.util.Set<? extends BioPAXElement> evidenceCodes, java.util.Set<? extends BioPAXElement> scoresOrConfidences, java.util.Set<java.lang.String> comments, java.util.Set<? extends BioPAXElement> experimentalForms) Gets an evidence object.
<T extends BioPAXElement> T	getExperimentalForm(java.lang.String id, BioPAXElement formType, BioPAXElement participant) Gets a experimental form object.
<T extends BioPAXElement> T	getFeature(BioPAXElement bpFeature, java.util.Set<? extends BioPAXElement> bpXrefs, java.util.Set<? extends BioPAXElement> featureLocations, BioPAXElement featureType) Used to add feature attributes to given sequence or entity feature.
<T extends BioPAXElement> T	getFeature(java.lang.String id, java.util.Set<? extends BioPAXElement> bpXrefs, java.util.Set<? extends BioPAXElement> featureLocations, BioPAXElement featureType) Gets a sequence or entity feature.
<T extends BioPAXElement> T	getInteraction(java.lang.String id, java.lang.String name, java.lang.String shortName, java.util.Set<java.lang.String> availability, java.util.Set<? extends BioPAXElement> participants, java.util.Set<? extends BioPAXElement> bpEvidence) Gets an interaction.
Model	getModel() Gets the biopax model.
<T extends BioPAXElement> T	getOpenControlledVocabulary(java.lang.String termToSearch) Gets an existing open/controlled vocabulary object.
<T extends BioPAXElement> T	getOpenControlledVocabulary(java.lang.String id, java.lang.String term, java.util.Set<? extends BioPAXElement> bpXrefs) Gets a open/controlled vocabulary object.
<T extends BioPAXElement> T	getParticipant(java.lang.String id, java.util.Set<? extends BioPAXElement> features, BioPAXElement cellularLocation, BioPAXElement bpPhysicalEntity) Gets a participant.
<T extends BioPAXElement> T	getPhysicalEntity(java.lang.String physicalEntityType, java.lang.String id, java.lang.String name, java.lang.String shortName, java.util.Set<java.lang.String> synonyms, java.util.Set<? extends BioPAXElement> bpXrefs, java.lang.String entityRefId, BioPAXElement bioSource, java.lang.String sequence) Gets a physical Entity.
<T extends BioPAXElement> T	getPublicationXref(java.lang.String id) Gets a publication xref.
<T extends BioPAXElement> T	getRelationshipXref(java.lang.String id, java.lang.String refType, java.lang.String refTypeID) Gets a relationship xref.
<T extends BioPAXElement> T	getScoreOrConfidence(java.lang.String id, java.lang.String value, java.util.Set<? extends BioPAXElement> bpXrefs, java.util.Set<java.lang.String> comments) Gets a confidence/score object.
<T extends BioPAXElement> T	getSequenceLocation(java.lang.String seqLocationID, java.lang.String beginSeqSiteID, java.lang.String endSeqSiteID, long beginSequenceInterval, long endSequenceInterval) Gets a sequence location.
<T extends BioPAXElement> T	getUnificationXref(java.lang.String id) Gets a unification xref.
java.lang.String	getXrefID(BioPAXElement bpXref) Given an xref (BioPAXElement) returns its id.
boolean	isGeneticInteraction(java.util.List<java.lang.String> geneticInteractionTerms, java.util.Set<? extends BioPAXElement> bpEvidence) Given a set of evidence objects, determines if interaction (that evidence obj is derived from) is a genetic interaction.
<T extends BioPAXElement> void	setInteractionDataSource(T interaction, java.lang.String id, java.lang.String name, java.util.Set<? extends BioPAXElement> bpXrefs) Creates a data source and adds to given interaction.
void	setModelDataSource(java.lang.String id, java.lang.String name, java.util.Set<? extends BioPAXElement> bpXrefs) Creates a data source on the model.
void	setNamespace(java.lang.String namespace) Sets biopax model namespace.
void	setXrefDBAndID(BioPAXElement bpXref, java.lang.String db, java.lang.String id) Sets given xref's db and id.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BioPAXMapperImp

public BioPAXMapperImp(BioPAXLevel bpLevel)

Constructor.

Parameters:

bpLevel - BioPAXLevel

Method Detail

getModel

public Model getModel()

Gets the biopax model.

Specified by:

getModel in interface BioPAXMapper

Returns:

Model

getUnificationXref

public <T extends BioPAXElement> T getUnificationXref(java.lang.String id)

Gets a unification xref.

Specified by:

getUnificationXref in interface BioPAXMapper

Parameters:

id - String

Returns:

getRelationshipXref

public <T extends BioPAXElement> T getRelationshipXref(java.lang.String id,
                                                       java.lang.String refType,
                                                       java.lang.String refTypeID)

Gets a relationship xref.

Specified by:

getRelationshipXref in interface BioPAXMapper

Parameters:

id - String

refType - String

refTypeID - String

Returns:

getPublicationXref

public <T extends BioPAXElement> T getPublicationXref(java.lang.String id)

Gets a publication xref.

Specified by:

getPublicationXref in interface BioPAXMapper

Parameters:

id - String

Returns:

getEvidence

public <T extends BioPAXElement> T getEvidence(java.lang.String id,
                                               java.util.Set<? extends BioPAXElement> bpXrefs,
                                               java.util.Set<? extends BioPAXElement> evidenceCodes,
                                               java.util.Set<? extends BioPAXElement> scoresOrConfidences,
                                               java.util.Set<java.lang.String> comments,
                                               java.util.Set<? extends BioPAXElement> experimentalForms)

Gets an evidence object.

Specified by:

getEvidence in interface BioPAXMapper

Parameters:

id - String

bpXrefs - Set

evidenceCodes - Set

scoresOrConfidences - Set

comments - Set

experimentalForms - Set

Returns:

getScoreOrConfidence

public <T extends BioPAXElement> T getScoreOrConfidence(java.lang.String id,
                                                        java.lang.String value,
                                                        java.util.Set<? extends BioPAXElement> bpXrefs,
                                                        java.util.Set<java.lang.String> comments)

Gets a confidence/score object.

Specified by:

getScoreOrConfidence in interface BioPAXMapper

Parameters:

id - String

value - String

bpXrefs - Set

comments - Set

Returns:

getExperimentalForm

public <T extends BioPAXElement> T getExperimentalForm(java.lang.String id,
                                                       BioPAXElement formType,
                                                       BioPAXElement participant)

Gets a experimental form object.

Specified by:

getExperimentalForm in interface BioPAXMapper

Parameters:

id - String

formType - BioPAXElement

participant - BioPAXElement

Returns:

getOpenControlledVocabulary

public <T extends BioPAXElement> T getOpenControlledVocabulary(java.lang.String termToSearch)

Gets an existing open/controlled vocabulary object.

Specified by:

getOpenControlledVocabulary in interface BioPAXMapper

Parameters:

termToSearch - String

Returns:

getOpenControlledVocabulary

public <T extends BioPAXElement> T getOpenControlledVocabulary(java.lang.String id,
                                                               java.lang.String term,
                                                               java.util.Set<? extends BioPAXElement> bpXrefs)

Gets a open/controlled vocabulary object.

Specified by:

getOpenControlledVocabulary in interface BioPAXMapper

Parameters:

id - String

term - String

bpXrefs - Set

Returns:

getBioPAXElement

public BioPAXElement getBioPAXElement(java.lang.String rdfID)

Given an RDF ID, returns a matching model element

Specified by:

getBioPAXElement in interface BioPAXMapper

Parameters:

rdfID -

Returns:

BioPAXElement

getInteraction

public <T extends BioPAXElement> T getInteraction(java.lang.String id,
                                                  java.lang.String name,
                                                  java.lang.String shortName,
                                                  java.util.Set<java.lang.String> availability,
                                                  java.util.Set<? extends BioPAXElement> participants,
                                                  java.util.Set<? extends BioPAXElement> bpEvidence)

Gets an interaction.

Specified by:

getInteraction in interface BioPAXMapper

Parameters:

id - String

name - String

shortName - String

availability - Set

participants - Set

bpEvidence - Set

Returns:

getParticipant

public <T extends BioPAXElement> T getParticipant(java.lang.String id,
                                                  java.util.Set<? extends BioPAXElement> features,
                                                  BioPAXElement cellularLocation,
                                                  BioPAXElement bpPhysicalEntity)

Gets a participant.

Specified by:

getParticipant in interface BioPAXMapper

Parameters:

id - String

features -

cellularLocation - BioPAXElement

bpPhysicalEntity - BioPAXElement

Returns:

getPhysicalEntity

public <T extends BioPAXElement> T getPhysicalEntity(java.lang.String physicalEntityType,
                                                     java.lang.String id,
                                                     java.lang.String name,
                                                     java.lang.String shortName,
                                                     java.util.Set<java.lang.String> synonyms,
                                                     java.util.Set<? extends BioPAXElement> bpXrefs,
                                                     java.lang.String entityRefId,
                                                     BioPAXElement bioSource,
                                                     java.lang.String sequence)

Gets a physical Entity.

Specified by:

getPhysicalEntity in interface BioPAXMapper

Parameters:

physicalEntityType - String

id - String

name - String

shortName - String

synonyms - Set

bpXrefs - Set

bioSource - BioPAXElement

sequence - String

Returns:

getBioSource

public <T extends BioPAXElement> T getBioSource(java.lang.String id,
                                                BioPAXElement taxonXref,
                                                BioPAXElement cellType,
                                                BioPAXElement tissue,
                                                java.lang.String name)

Gets a biosource.

Specified by:

getBioSource in interface BioPAXMapper

Parameters:

id - String

taxonXref - BioPAXElement

cellType - BioPAXElement

tissue - BioPAXElement

name - String

Returns:

getFeature

public <T extends BioPAXElement> T getFeature(BioPAXElement bpFeature,
                                              java.util.Set<? extends BioPAXElement> bpXrefs,
                                              java.util.Set<? extends BioPAXElement> featureLocations,
                                              BioPAXElement featureType)

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

Specified by:

getFeature in interface BioPAXMapper

Parameters:

bpFeature - BioPAXElement

bpXrefs - Set

featureLocations - Set

featureType - BioPAXElement

Returns:

getFeature

public <T extends BioPAXElement> T getFeature(java.lang.String id,
                                              java.util.Set<? extends BioPAXElement> bpXrefs,
                                              java.util.Set<? extends BioPAXElement> featureLocations,
                                              BioPAXElement featureType)

Gets a sequence or entity feature.

Specified by:

getFeature in interface BioPAXMapper

Parameters:

id - String

bpXrefs - Set

featureLocations - Set

featureType - BioPAXElement

Returns:

getSequenceLocation

public <T extends BioPAXElement> T getSequenceLocation(java.lang.String seqLocationID,
                                                       java.lang.String beginSeqSiteID,
                                                       java.lang.String endSeqSiteID,
                                                       long beginSequenceInterval,
                                                       long endSequenceInterval)

Gets a sequence location.

Specified by:

getSequenceLocation in interface BioPAXMapper

Parameters:

seqLocationID - String

beginSeqSiteID - String

endSeqSiteID - String

beginSequenceInterval - long

endSequenceInterval - long

Returns:

getXrefID

public java.lang.String getXrefID(BioPAXElement bpXref)

Given an xref (BioPAXElement) returns its id.

Specified by:

getXrefID in interface BioPAXMapper

Parameters:

bpXref - BioPAXElement

Returns:

String

setXrefDBAndID

public void setXrefDBAndID(BioPAXElement bpXref,
                           java.lang.String db,
                           java.lang.String id)

Sets given xref's db and id.

Specified by:

setXrefDBAndID in interface BioPAXMapper

Parameters:

bpXref - BioPAXElement

db - String

id - String

setNamespace

public void setNamespace(java.lang.String namespace)

Sets biopax model namespace.

Specified by:

setNamespace in interface BioPAXMapper

Parameters:

namespace - String

setModelDataSource

public void setModelDataSource(java.lang.String id,
                               java.lang.String name,
                               java.util.Set<? extends BioPAXElement> bpXrefs)

Creates a data source on the model.

Specified by:

setModelDataSource in interface BioPAXMapper

Parameters:

id - String

name - String

bpXrefs - Set

setInteractionDataSource

public <T extends BioPAXElement> void setInteractionDataSource(T interaction,
                                                               java.lang.String id,
                                                               java.lang.String name,
                                                               java.util.Set<? extends BioPAXElement> bpXrefs)

Creates a data source and adds to given interaction.

Specified by:

setInteractionDataSource in interface BioPAXMapper

Parameters:

id - String

bpXrefs - Set

name - String

isGeneticInteraction

public boolean isGeneticInteraction(java.util.List<java.lang.String> geneticInteractionTerms,
                                    java.util.Set<? extends BioPAXElement> bpEvidence)

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

Specified by:

isGeneticInteraction in interface BioPAXMapper

Parameters:

geneticInteractionTerms - List

bpEvidence - Set

Returns:

boolean