org.biopax.paxtools.model.level2
Interface Model

All Known Implementing Classes:

ModelImpl

public interface Model

This is the interface for container classes for BioPAX models.

Field Summary

static java.lang.String

BP_PREFIX

Method Summary

void	add(BioPAXElement aBioPAXElement)
biochemicalReaction	addBiochemicalReaction(java.lang.String id)
bioSource	addBioSource(java.lang.String id)
catalysis	addCatalysis(java.lang.String id)
chemicalStructure	addChemicalStructure(java.lang.String id)
complex	addComplex(java.lang.String id)
complexAssembly	addComplexAssembly(java.lang.String id)
confidence	addConfidence(java.lang.String id)
control	addControl(java.lang.String id)
conversion	addConversion(java.lang.String id)
dataSource	addDataSource(java.lang.String id)
deltaGprimeO	addDeltaGprimeO(java.lang.String id)
dna	addDna(java.lang.String id)
evidence	addEvidence(java.lang.String id)
experimentalForm	addExperimentalForm(java.lang.String id)
interaction	addInteraction(java.lang.String id)
kPrime	addKPrime(java.lang.String id)
modulation	addModulation(java.lang.String id)
openControlledVocabulary	addOpenControlledVocabulary(java.lang.String id)
pathway	addPathway(java.lang.String id)
pathwayStep	addPathwayStep(java.lang.String id)
physicalEntity	addPhysicalEntity(java.lang.String id)
physicalEntityParticipant	addPhysicalEntityParticipant(java.lang.String id)
physicalInteraction	addPhysicalInteraction(java.lang.String id)
protein	addProtein(java.lang.String id)
publicationXref	addPublicationXref(java.lang.String id)
relationshipXref	addRelationshipXref(java.lang.String id)
rna	addRna(java.lang.String id)
sequenceFeature	addSequenceFeature(java.lang.String id)
sequenceInterval	addSequenceInterval(java.lang.String id)
sequenceParticipant	addSequenceParticipant(java.lang.String id)
sequenceSite	addSequenceSite(java.lang.String id)
smallMolecule	addSmallMolecule(java.lang.String id)
transport	addTransport(java.lang.String id)
transportWithBiochemicalReaction	addTransportWithBiochemicalReaction(java.lang.String id)
unificationXref	addUnificationXref(java.lang.String id)
boolean	contains(BioPAXElement aBioPAXElement) This method returns true if only the parameter is actually contained within this level2
boolean	containsEquivalent(BioPAXElement aBioPAXElement) THis method returns true if the paramter or an equalivant object as defined by the method exists in the level2.
java.util.Map<java.lang.String,BioPAXElement>	getIdMap()
java.util.Map<java.lang.String,java.lang.String>	getNameSpacePrefixMap()
java.util.Set<BioPAXElement>	getObjects()
java.util.Set<BioPAXElement>	getObjects(java.lang.Class filterBy)
void	remove(BioPAXElement aBioPAXElement)
void	setFactory(BioPAXFactory factory)

Field Detail

BP_PREFIX

static final java.lang.String BP_PREFIX

See Also:

Constant Field Values

Method Detail

add

void add(BioPAXElement aBioPAXElement)

addBioSource

bioSource addBioSource(java.lang.String id)

addBiochemicalReaction

biochemicalReaction addBiochemicalReaction(java.lang.String id)

addCatalysis

catalysis addCatalysis(java.lang.String id)

addChemicalStructure

chemicalStructure addChemicalStructure(java.lang.String id)

addComplex

complex addComplex(java.lang.String id)

addComplexAssembly

complexAssembly addComplexAssembly(java.lang.String id)

addConfidence

confidence addConfidence(java.lang.String id)

addControl

control addControl(java.lang.String id)

addConversion

conversion addConversion(java.lang.String id)

addDataSource

dataSource addDataSource(java.lang.String id)

addDeltaGprimeO

deltaGprimeO addDeltaGprimeO(java.lang.String id)

addDna

dna addDna(java.lang.String id)

addEvidence

evidence addEvidence(java.lang.String id)

addExperimentalForm

experimentalForm addExperimentalForm(java.lang.String id)

addInteraction

interaction addInteraction(java.lang.String id)

addKPrime

kPrime addKPrime(java.lang.String id)

addModulation

modulation addModulation(java.lang.String id)

addOpenControlledVocabulary

openControlledVocabulary addOpenControlledVocabulary(java.lang.String id)

addPathway

pathway addPathway(java.lang.String id)

addPathwayStep

pathwayStep addPathwayStep(java.lang.String id)

addPhysicalEntity

physicalEntity addPhysicalEntity(java.lang.String id)

addPhysicalEntityParticipant

physicalEntityParticipant addPhysicalEntityParticipant(java.lang.String id)

addPhysicalInteraction

physicalInteraction addPhysicalInteraction(java.lang.String id)

addProtein

protein addProtein(java.lang.String id)

addPublicationXref

publicationXref addPublicationXref(java.lang.String id)

addRelationshipXref

relationshipXref addRelationshipXref(java.lang.String id)

addRna

rna addRna(java.lang.String id)

addSequenceFeature

sequenceFeature addSequenceFeature(java.lang.String id)

addSequenceInterval

sequenceInterval addSequenceInterval(java.lang.String id)

addSequenceParticipant

sequenceParticipant addSequenceParticipant(java.lang.String id)

addSequenceSite

sequenceSite addSequenceSite(java.lang.String id)

addSmallMolecule

smallMolecule addSmallMolecule(java.lang.String id)

addTransport

transport addTransport(java.lang.String id)

addTransportWithBiochemicalReaction

transportWithBiochemicalReaction addTransportWithBiochemicalReaction(java.lang.String id)

addUnificationXref

unificationXref addUnificationXref(java.lang.String id)

contains

boolean contains(BioPAXElement aBioPAXElement)

This method returns true if only the parameter is actually contained within this level2

Parameters:

aBioPAXElement - to be checked

Returns:

true if the parameter is in the object set

containsEquivalent

boolean containsEquivalent(BioPAXElement aBioPAXElement)

THis method returns true if the paramter or an equalivant object as defined by the method exists in the level2.

Parameters:

aBioPAXElement - to be checked

Returns:

true is an equivalent object exists in the level2.

getIdMap

java.util.Map<java.lang.String,BioPAXElement> getIdMap()

getNameSpacePrefixMap

java.util.Map<java.lang.String,java.lang.String> getNameSpacePrefixMap()

getObjects

java.util.Set<BioPAXElement> getObjects()

getObjects

java.util.Set<BioPAXElement> getObjects(java.lang.Class filterBy)

remove

void remove(BioPAXElement aBioPAXElement)

setFactory

void setFactory(BioPAXFactory factory)