org.biopax.paxtools.persistence.level2
Class MiscSearch

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

public class MiscSearch
extends BaseSearch

misc search class

Constructor Summary

MiscSearch(HiRDBSession session)
construct

Method Summary

java.util.Set<java.lang.String>	getDataSourceList() get data source
java.util.Set<entity>	getEntityListByAVAIRABILITY(java.lang.String regex) get entity by AVAIRABILITY
java.util.Set<entity>	getEntityListByCOMMENT(java.lang.String regex) get entity by COMMENT
java.util.Set<entity>	getEntityListByDATA_SOURCE(java.lang.String regex) get entity by DATA_SOURCE
java.util.Set<entity>	getEntityListByDBAndIDOfXREF(java.lang.String regexDB, java.lang.String id) get entity by DB and ID of xref
java.util.Set<entity>	getEntityListByNAME(java.lang.String regex, boolean bIncludeSynonyms) get entity by NAME
complex	isCOMPONENTSof(physicalEntityParticipant pep) get back pointer of COMPONENTS
java.util.Set<pathwayStep>	isNEXT_STEPof(pathwayStep ps) get back pointer of NEXT_STEP
java.util.Set<interaction>	isPARTICIPANTSof(InteractionParticipant ip)
java.util.Set<pathway>	isPATHWAY_COMPONENTSof(pathwayComponent pc) get back pointer of PATHWAY_COMPONENT
java.util.Set<physicalEntityParticipant>	isPHYSICAL_ENTITYof(physicalEntity pe) get back pointer of PHYSICAL_ENTITY
java.util.Set<pathwayStep>	isSTEP_INTERACTIONSof(process p) get back pointer of STEP_INTERACTIONS
java.util.Set<XReferrable>	isXREFof(xref x) get back pointer of XREF

Methods inherited from class java.lang.Object

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

Constructor Detail

MiscSearch

public MiscSearch(HiRDBSession session)

construct

Parameters:

session -

Method Detail

isNEXT_STEPof

public java.util.Set<pathwayStep> isNEXT_STEPof(pathwayStep ps)

get back pointer of NEXT_STEP

Parameters:

pathwayStep -

Returns:

back pointer of NEXT_STEP

isPATHWAY_COMPONENTSof

public java.util.Set<pathway> isPATHWAY_COMPONENTSof(pathwayComponent pc)

get back pointer of PATHWAY_COMPONENT

Parameters:

pathwayComponent -

Returns:

back pointer of PATHWAY_COMPONENT

isSTEP_INTERACTIONSof

public java.util.Set<pathwayStep> isSTEP_INTERACTIONSof(process p)

get back pointer of STEP_INTERACTIONS

Parameters:

process -

Returns:

back pointer of STEP_INTERACTIONS

isXREFof

public java.util.Set<XReferrable> isXREFof(xref x)

get back pointer of XREF

Parameters:

XReferrable -

Returns:

back pointer of XREF

isPARTICIPANTSof

public java.util.Set<interaction> isPARTICIPANTSof(InteractionParticipant ip)

isCOMPONENTSof

public complex isCOMPONENTSof(physicalEntityParticipant pep)

get back pointer of COMPONENTS

Parameters:

physicalEntityParticipant -

Returns:

back pointer of COMPONENTS

isPHYSICAL_ENTITYof

public java.util.Set<physicalEntityParticipant> isPHYSICAL_ENTITYof(physicalEntity pe)

get back pointer of PHYSICAL_ENTITY

Parameters:

physicalEntity -

Returns:

back pointer of PHYSICAL_ENTITY

getEntityListByDATA_SOURCE

public java.util.Set<entity> getEntityListByDATA_SOURCE(java.lang.String regex)

get entity by DATA_SOURCE

Parameters:

regex -

Returns:

entities

getEntityListByDBAndIDOfXREF

public java.util.Set<entity> getEntityListByDBAndIDOfXREF(java.lang.String regexDB,
                                                          java.lang.String id)

get entity by DB and ID of xref

Parameters:

regexDB -

id -

Returns:

entities

getEntityListByNAME

public java.util.Set<entity> getEntityListByNAME(java.lang.String regex,
                                                 boolean bIncludeSynonyms)

get entity by NAME

Parameters:

regex -

bIncludeSynonyms -

Returns:

entities

getDataSourceList

public java.util.Set<java.lang.String> getDataSourceList()

get data source

Returns:

data source names

getEntityListByAVAIRABILITY

public java.util.Set<entity> getEntityListByAVAIRABILITY(java.lang.String regex)

get entity by AVAIRABILITY

Parameters:

regex -

Returns:

entities

getEntityListByCOMMENT

public java.util.Set<entity> getEntityListByCOMMENT(java.lang.String regex)

get entity by COMMENT

Parameters:

regex -

Returns:

entities