org.sigpath.datamodel
Class BioPolymerImpl

java.lang.Object
  org.sigpath.datamodel.lset.CollectableImpl
      org.sigpath.datamodel.SigPathEntityImpl
          org.sigpath.datamodel.ChemicalImpl
              org.sigpath.datamodel.BioPolymerImpl

All Implemented Interfaces:

InstanceCallbacks, BioPolymer, Chemical, Collectable, MacroMolecule, SigPathEntity

Direct Known Subclasses:

ProteinImpl

public class BioPolymerImpl
extends ChemicalImpl
implements BioPolymer

Protein implementation. This is a read-write implementation. Access policy, if any is enforced through the ChemicalManager.

Version:

$Revision: 5731 $

Author:

Fabien Campagne

Field Summary

Fields inherited from class org.sigpath.datamodel.SigPathEntityImpl

forwardReferences

Constructor Summary

	BioPolymerImpl() Default constructor.
protected	BioPolymerImpl(SigPathFactory factory)
protected	BioPolymerImpl(SigPathFactory factory, String spid)

Method Summary

long	getLength() Returns the length of the sequence of this biopolymer.
String	getResidueCodes() Gets the residue codes for this biopolymer.
String	getResidueCodes(long start, long end) Gets a segment of the residue codes for this biopolymer.
void	setResidueCodes(String residueCodes) Sets the residue codes for this biopolymer.

Methods inherited from class org.sigpath.datamodel.ChemicalImpl

addBecomesInfo, addComesFromInfo, contains, getBecomes, getComesFrom, getForwardReferences, getOrganism, involvedIn, isBackgroundInformation, jdoPreDelete, setInvolvedIn, setInvolvedIn, setInvolvedIn, setInvolvedIn, setInvolvedIn, setOrganism

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, 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.Chemical

contains, getBecomes, getComesFrom, getOrganism, involvedIn, isBackgroundInformation, setInvolvedIn, setInvolvedIn, setInvolvedIn, setOrganism

Methods inherited from interface org.sigpath.datamodel.SigPathEntity

addAlias, addAliases, addReview, addUserComment, changeAlias, getAliases, getAliasesCollection, getAliasesIterator, getChangeLog, getCombinedStringLength, getComments, getDescription, getExternalReferences, getForwardReferences, getLiteratureReferences, getName, getReviews, getSpid, getUserComments, isExportable, removeAlias, removeAliases, removeReviews, setAliases, setAliasesCollection, setChangeLog, setComments, setDescription, setExportable, setName, setSpid

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

getCollections

Constructor Detail

BioPolymerImpl

public BioPolymerImpl()

Default constructor.

BioPolymerImpl

protected BioPolymerImpl(SigPathFactory factory)

BioPolymerImpl

protected BioPolymerImpl(SigPathFactory factory,
                         String spid)

Method Detail

setResidueCodes

public void setResidueCodes(String residueCodes)

Description copied from interface: BioPolymer

Sets the residue codes for this biopolymer. Non IUB/IUPAC amino acid and nucleic acid codes are filtered from residue_codes and are not stored.

Specified by:

setResidueCodes in interface BioPolymer

getResidueCodes

public String getResidueCodes()

Description copied from interface: BioPolymer

Gets the residue codes for this biopolymer. Residue codes are encoded with IUB/IUPAC amino acid and nucleic acid codes.

Specified by:

getResidueCodes in interface BioPolymer

getResidueCodes

public String getResidueCodes(long start,
                              long end)

Description copied from interface: BioPolymer

Gets a segment of the residue codes for this biopolymer. Residue codes are encoded with IUB/IUPAC amino acid and nucleic acid codes.

Specified by:

getResidueCodes in interface BioPolymer

Parameters:

start - Start offset within the total sequence for the segment to be returned. (Inclusive.)

end - End offset within the total sequence for the segment to be returned. (Inclusive.)

getLength

public long getLength()

Returns the length of the sequence of this biopolymer. The length is cached in this implementation so that this operation is quick.

Specified by:

getLength in interface BioPolymer