org.biopax.paxtools.persistence.level2
Class PhysicalEntitySearch

java.lang.Object
  org.biopax.paxtools.persistence.level2.BaseSearch
      org.biopax.paxtools.persistence.level2.PhysicalEntitySearch

public class PhysicalEntitySearch
extends BaseSearch

physicalEntity search class

Constructor Summary

PhysicalEntitySearch(HiRDBSession session)
construct

Method Summary

java.util.Set<complex>	getComplexList() get all complex
java.util.Set<dna>	getDnaList() get all dna
java.util.Set<physicalEntity>	getPhysicalEntityList() get all physical entity
java.util.Set<physicalEntity>	getPhysicalEntityListByNAME(java.lang.String regex, boolean bIncludeSynonyms) get physicalEntity by NAME
java.util.Set<physicalEntity>	getPhysicalEntityListByORGANISM(java.lang.String regex) get physicalEntity by ORGANISM
java.util.Set<protein>	getProteinList() get all protein
java.util.Set<rna>	getRnaList() get all rna
java.util.Set<sequenceEntity>	getSequenceEntityListBySEQUENCE(java.lang.String sequence, boolean bExactMatch) get sequenceEntity by SEQUENCE
java.util.Set<smallMolecule>	getSmallMoleculeList() get all smallMolecule

Methods inherited from class java.lang.Object

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

Constructor Detail

PhysicalEntitySearch

public PhysicalEntitySearch(HiRDBSession session)

construct

Parameters:

session -

Method Detail

getPhysicalEntityList

public java.util.Set<physicalEntity> getPhysicalEntityList()

get all physical entity

Returns:

all physical entity

getComplexList

public java.util.Set<complex> getComplexList()

get all complex

Returns:

all complex

getDnaList

public java.util.Set<dna> getDnaList()

get all dna

Returns:

all dna

getProteinList

public java.util.Set<protein> getProteinList()

get all protein

Returns:

all protein

getRnaList

public java.util.Set<rna> getRnaList()

get all rna

Returns:

all rna

getSmallMoleculeList

public java.util.Set<smallMolecule> getSmallMoleculeList()

get all smallMolecule

Returns:

all smallMolecule

getPhysicalEntityListByNAME

public java.util.Set<physicalEntity> getPhysicalEntityListByNAME(java.lang.String regex,
                                                                 boolean bIncludeSynonyms)

get physicalEntity by NAME

Returns:

physicalEntity

getPhysicalEntityListByORGANISM

public java.util.Set<physicalEntity> getPhysicalEntityListByORGANISM(java.lang.String regex)

get physicalEntity by ORGANISM

Returns:

physicalEntity

getSequenceEntityListBySEQUENCE

public java.util.Set<sequenceEntity> getSequenceEntityListBySEQUENCE(java.lang.String sequence,
                                                                     boolean bExactMatch)

get sequenceEntity by SEQUENCE

Returns:

sequenceEntity