org.sigpath.datamodel.models
Class BasePathway

java.lang.Object
  org.sigpath.datamodel.lset.CollectableImpl
      org.sigpath.datamodel.SigPathEntityImpl
          org.sigpath.datamodel.models.BasePathway

All Implemented Interfaces:

InstanceCallbacks, Collectable, SigPathEntity

Direct Known Subclasses:

Model, Pathway

public class BasePathway
extends SigPathEntityImpl

Represents a Pathway setup. The setup defines the chemicals and reactions which are included in the Pathway.

Field Summary

protected Collection<Interaction>	interactions
protected Collection	moleculeSet

Fields inherited from class org.sigpath.datamodel.SigPathEntityImpl

forwardReferences

Constructor Summary

BasePathway()
Default constructor.

BasePathway(SigPathFactory factory)

BasePathway(SigPathFactory factory, String spid)

Method Summary

protected void	addChemical(SigPathFactory factory, Chemical chemical)
void	addEReaction(SigPathFactory factory, EnzymaticReaction eRxn)
void	addInteraction(SigPathFactory factory, Interaction reaction)
void	addMoleculeToSet(Molecule mol)
void	addReaction(SigPathFactory factory, Reaction reaction)
Chemical	getChemicalBySpid(String spid)
Collection	getEReactions()
Set	getForwardReferences() Forward references are reactions, and chemicals involved in the the pahtway.
Collection<Interaction>	getInteractions()
Molecule	getMoleculeBySpid(String spid)
Iterator	getMolecules() Returns all molecules used by this Pathway.
Collection	getMoleculeSet()
Collection	getReactions()

Methods inherited from class org.sigpath.datamodel.SigPathEntityImpl

addAlias, addAliases, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, isIndexed, jdoPostLoad, jdoPreClear, jdoPreDelete, jdoPreStore, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setForwardReferences, setIndexed, setName, setSpid

Methods inherited from class org.sigpath.datamodel.lset.CollectableImpl

createCollectionsSet, getCollections

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sigpath.datamodel.lset.Collectable

getCollections

Field Detail

moleculeSet

protected Collection moleculeSet

interactions

protected Collection<Interaction> interactions

Constructor Detail

BasePathway

public BasePathway()

Default constructor.

BasePathway

public BasePathway(SigPathFactory factory)

BasePathway

public BasePathway(SigPathFactory factory,
                   String spid)

Method Detail

getInteractions

public Collection<Interaction> getInteractions()

addReaction

public void addReaction(SigPathFactory factory,
                        Reaction reaction)

addInteraction

public void addInteraction(SigPathFactory factory,
                           Interaction reaction)

getReactions

public Collection getReactions()

addEReaction

public void addEReaction(SigPathFactory factory,
                         EnzymaticReaction eRxn)

getEReactions

public Collection getEReactions()

addChemical

protected void addChemical(SigPathFactory factory,
                           Chemical chemical)

addMoleculeToSet

public void addMoleculeToSet(Molecule mol)

getMolecules

public Iterator getMolecules()

Returns all molecules used by this Pathway.

Returns:

An iterator that traverses the set of molecules.

See Also:

Molecule

getChemicalBySpid

public Chemical getChemicalBySpid(String spid)

getMoleculeBySpid

public Molecule getMoleculeBySpid(String spid)

getMoleculeSet

public Collection getMoleculeSet()

getForwardReferences

public Set getForwardReferences()

Forward references are reactions, and chemicals involved in the the pahtway.

Returns: