org.biopax.paxtools.impl.level2
Class ModelImpl

java.lang.Object
  org.biopax.paxtools.impl.level2.ModelImpl

All Implemented Interfaces:

Model

public class ModelImpl
extends java.lang.Object
implements Model

Main container class to access BioPAX objects.

Field Summary

Fields inherited from interface org.biopax.paxtools.model.level2.Model

BP_PREFIX

Constructor Summary

ModelImpl()

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) This method removes the element without dependency checking.
void	setFactory(BioPAXFactory factory)

Methods inherited from class java.lang.Object

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

Constructor Detail

ModelImpl

public ModelImpl()

Method Detail

getIdMap

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

Specified by:

getIdMap in interface Model

getNameSpacePrefixMap

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

Specified by:

getNameSpacePrefixMap in interface Model

setFactory

public void setFactory(BioPAXFactory factory)

Specified by:

setFactory in interface Model

getObjects

public java.util.Set<BioPAXElement> getObjects()

Specified by:

getObjects in interface Model

getObjects

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

Specified by:

getObjects in interface Model

remove

public void remove(BioPAXElement aBioPAXElement)

This method removes the element without dependency checking.

Specified by:

remove in interface Model

Parameters:

aBioPAXElement - to be removed

contains

public boolean contains(BioPAXElement aBioPAXElement)

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

Specified by:

contains in interface Model

Parameters:

aBioPAXElement - to be checked

Returns:

true if the parameter is in the object set

containsEquivalent

public boolean containsEquivalent(BioPAXElement aBioPAXElement)

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

Specified by:

containsEquivalent in interface Model

Parameters:

aBioPAXElement - to be checked

Returns:

true is an equivalent object exists in the level2.

addBioSource

public bioSource addBioSource(java.lang.String id)

Specified by:

addBioSource in interface Model

addBiochemicalReaction

public biochemicalReaction addBiochemicalReaction(java.lang.String id)

Specified by:

addBiochemicalReaction in interface Model

addCatalysis

public catalysis addCatalysis(java.lang.String id)

Specified by:

addCatalysis in interface Model

addChemicalStructure

public chemicalStructure addChemicalStructure(java.lang.String id)

Specified by:

addChemicalStructure in interface Model

addComplex

public complex addComplex(java.lang.String id)

Specified by:

addComplex in interface Model

addComplexAssembly

public complexAssembly addComplexAssembly(java.lang.String id)

Specified by:

addComplexAssembly in interface Model

addInteraction

public interaction addInteraction(java.lang.String id)

Specified by:

addInteraction in interface Model

addPhysicalInteraction

public physicalInteraction addPhysicalInteraction(java.lang.String id)

Specified by:

addPhysicalInteraction in interface Model

addConfidence

public confidence addConfidence(java.lang.String id)

Specified by:

addConfidence in interface Model

addControl

public control addControl(java.lang.String id)

Specified by:

addControl in interface Model

addConversion

public conversion addConversion(java.lang.String id)

Specified by:

addConversion in interface Model

addDataSource

public dataSource addDataSource(java.lang.String id)

Specified by:

addDataSource in interface Model

addDeltaGprimeO

public deltaGprimeO addDeltaGprimeO(java.lang.String id)

Specified by:

addDeltaGprimeO in interface Model

addDna

public dna addDna(java.lang.String id)

Specified by:

addDna in interface Model

addEvidence

public evidence addEvidence(java.lang.String id)

Specified by:

addEvidence in interface Model

addExperimentalForm

public experimentalForm addExperimentalForm(java.lang.String id)

Specified by:

addExperimentalForm in interface Model

addKPrime

public kPrime addKPrime(java.lang.String id)

Specified by:

addKPrime in interface Model

addModulation

public modulation addModulation(java.lang.String id)

Specified by:

addModulation in interface Model

addOpenControlledVocabulary

public openControlledVocabulary addOpenControlledVocabulary(java.lang.String id)

Specified by:

addOpenControlledVocabulary in interface Model

addPathway

public pathway addPathway(java.lang.String id)

Specified by:

addPathway in interface Model

addPathwayStep

public pathwayStep addPathwayStep(java.lang.String id)

Specified by:

addPathwayStep in interface Model

addPhysicalEntity

public physicalEntity addPhysicalEntity(java.lang.String id)

Specified by:

addPhysicalEntity in interface Model

addPhysicalEntityParticipant

public physicalEntityParticipant addPhysicalEntityParticipant(java.lang.String id)

Specified by:

addPhysicalEntityParticipant in interface Model

addProtein

public protein addProtein(java.lang.String id)

Specified by:

addProtein in interface Model

addPublicationXref

public publicationXref addPublicationXref(java.lang.String id)

Specified by:

addPublicationXref in interface Model

addRelationshipXref

public relationshipXref addRelationshipXref(java.lang.String id)

Specified by:

addRelationshipXref in interface Model

addRna

public rna addRna(java.lang.String id)

Specified by:

addRna in interface Model

addSequenceFeature

public sequenceFeature addSequenceFeature(java.lang.String id)

Specified by:

addSequenceFeature in interface Model

addSequenceParticipant

public sequenceParticipant addSequenceParticipant(java.lang.String id)

Specified by:

addSequenceParticipant in interface Model

addSequenceSite

public sequenceSite addSequenceSite(java.lang.String id)

Specified by:

addSequenceSite in interface Model

addSequenceInterval

public sequenceInterval addSequenceInterval(java.lang.String id)

Specified by:

addSequenceInterval in interface Model

addSmallMolecule

public smallMolecule addSmallMolecule(java.lang.String id)

Specified by:

addSmallMolecule in interface Model

addTransport

public transport addTransport(java.lang.String id)

Specified by:

addTransport in interface Model

addTransportWithBiochemicalReaction

public transportWithBiochemicalReaction addTransportWithBiochemicalReaction(java.lang.String id)

Specified by:

addTransportWithBiochemicalReaction in interface Model

addUnificationXref

public unificationXref addUnificationXref(java.lang.String id)

Specified by:

addUnificationXref in interface Model

add

public void add(BioPAXElement aBioPAXElement)

Specified by:

add in interface Model