org.mskcc.psibiopax.converter
Interface BioPAXMapper

All Known Implementing Classes:

BioPAXMapperImp

public interface BioPAXMapper

An interface which provides methods to query a Paxtools model.

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> scoresOrConfidence, 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> xrefs) 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.

Method Detail

getModel

Model getModel()

Gets the biopax model.

Returns:

Model

getUnificationXref

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

Gets a unification xref.

Parameters:

id - String

Returns:

getRelationshipXref

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

Gets a relationship xref.

Parameters:

id - String

refType - String

refTypeID - String

Returns:

getPublicationXref

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

Gets a publication xref.

Parameters:

id - String

Returns:

getEvidence

<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> scoresOrConfidence,
                                        java.util.Set<java.lang.String> comments,
                                        java.util.Set<? extends BioPAXElement> experimentalForms)

Gets an evidence object.

Parameters:

id - String

bpXrefs - Set

evidenceCodes - Set

scoresOrConfidences - Set

comments - Set

experimentalForms - Set

Returns:

getScoreOrConfidence

<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.

Parameters:

id - String

value - String

bpXrefs - Set

comments - Set

Returns:

getExperimentalForm

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

Gets a experimental form object.

Parameters:

id - String

formType - BioPAXElement

participant - BioPAXElement

Returns:

getOpenControlledVocabulary

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

Gets an existing open/controlled vocabulary object.

Parameters:

termToSearch - String

Returns:

getOpenControlledVocabulary

<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.

Parameters:

id - String

term - String

bpXrefs - Set

Returns:

getBioPAXElement

BioPAXElement getBioPAXElement(java.lang.String rdfID)

Given an RDF ID, returns a matching model element

Parameters:

rdfID -

Returns:

BioPAXElement

getInteraction

<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.

Parameters:

id - String

name - String

shortName - String

availability - Set

participants - Set

bpEvidence - Set

Returns:

getParticipant

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

Gets a participant.

Parameters:

id - String

features -

cellularLocation - BioPAXElement

bpPhysicalEntity - BioPAXElement

Returns:

getPhysicalEntity

<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.

Parameters:

physicalEntityType - String

id - String

name - String

shortName - String

synonyms - Set

bpXrefs - Set

bioSource - BioPAXElement

sequence - String

Returns:

getBioSource

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

Gets a biosource.

Parameters:

id - String

taxonXref - BioPAXElement

cellType - BioPAXElement

tissue - BioPAXElement

name - String

Returns:

getFeature

<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.

Parameters:

bpSequenceFeature - BioPAXElement

bpXrefs - Set

featureLocations - Set

featureType - BioPAXElement

Returns:

getFeature

<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.

Parameters:

id - String

bpXrefs - Set

featureLocations - Set

featureType - BioPAXElement

Returns:

getSequenceLocation

<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.

Parameters:

seqLocationID - String

beginSeqSiteID - String

beginSequenceInterval - long

endSequenceInterval - long

Returns:

getXrefID

java.lang.String getXrefID(BioPAXElement bpXref)

Given an xref (BioPAXElement) returns its id.

Parameters:

bpXref - BioPAXElement

Returns:

String

setXrefDBAndID

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

Sets given xref's db and id.

Parameters:

xrefType - BioPAXElement

db - String

id - String

setNamespace

void setNamespace(java.lang.String namespace)

Sets biopax model namespace.

Parameters:

namespace - String

setModelDataSource

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

Creates a data source on the model.

Parameters:

id - String

name - String

xrefs - Set

setInteractionDataSource

<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.

Parameters:

id - String

name - String

bpXrefs - Set

isGeneticInteraction

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.

Parameters:

geneticInteractionTerms - List

bpEvidence - Set

Returns:

boolean