org.biopax.paxtools.persistence.level2
Class PathwaySearch

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

public class PathwaySearch
extends BaseSearch

pathway search class

Constructor Summary

PathwaySearch(HiRDBSession session)
construct

Method Summary

protected void	fetchAllNEXT_STEPOfPathway(pathwayComponent p, java.util.HashSet<pathwayStep> result)
protected void	fetchAllPreviousStepOfPathway(javax.persistence.EntityManager em, pathwayComponent p, java.util.HashSet<pathwayStep> result)
protected void	fetchAllSubPathway(pathwayComponent p, java.util.HashSet<pathway> result)
protected void	fetchAllSuperPathway(javax.persistence.EntityManager em, pathway p, java.util.HashSet<pathway> result)
protected java.util.Set<pathwayStep>	fetchBackStep(javax.persistence.EntityManager em, pathwayStep inElem)
protected java.util.Set<pathwayComponent>	fetchChildPathwayComponentOrProcess(pathwayComponent inElem)
protected void	fetchEC_NUMBERInPathwayComponent(pathwayComponent pc, java.util.HashSet<java.lang.String> result)
protected void	fetchEvidence(pathwayComponent pc, java.util.HashSet<evidence> result)
protected void	fetchInteraction(pathwayComponent pc, java.util.HashSet<interaction> result)
protected java.util.Set<pathwayStep>	fetchNEXT_STEPOfPathway(pathway p)
protected java.util.Set<openControlledVocabulary>	fetchOpenControlledVocabularyByTerm(javax.persistence.EntityManager em, java.lang.String term)
protected java.util.Set<pathway>	fetchPathwayByPathwayComonent(javax.persistence.EntityManager em, pathwayComponent inPC)
protected java.util.Set<pathwayStep>	fetchPathwayStepByProcess(javax.persistence.EntityManager em, process inProcess)
protected void	fetchPhysicalEntity(BioPAXElement e, java.util.HashSet<physicalEntity> result)
protected java.util.Set<pathwayStep>	fetchPreviousStepOfPathway(javax.persistence.EntityManager em, pathway p)
protected java.util.Set<pathwayComponent>	fetchSubPathwayComponent(pathwayComponent inElem)
protected java.util.Set<pathway>	fetchSuperPathway(javax.persistence.EntityManager em, pathwayComponent inPC)
protected void	fetchXref(BioPAXElement e, java.util.HashSet<xref> result)
java.util.Set<evidence>	getAllEvidenceListInPathway(pathway p) get all evidence in pathway
java.util.Set<pathwayStep>	getAllNEXT_STEPListOfPathway(pathway p) get all NEXT_STEP of pathway
java.util.Set<pathwayStep>	getAllPreviousStepListOfPathway(pathway p) get all previous steps of pathway
java.util.Set<pathway>	getAllSubPathwayList(pathway p) get all sub pathway
java.util.Set<pathway>	getAllSuperPathwayList(pathway p) get all super pathway
java.util.Set<java.lang.String>	getEC_NUMBERListInPathway(pathway p) get EC_NUMBER in pathway
java.util.Set<interaction>	getInteractionListInPathway(pathway p) get interaction in pathway
java.util.Set<pathwayStep>	getNEXT_STEPListOfPathway(pathway p) get NEXT_STEP of pathway
java.util.Set<pathway>	getPathwayList() get all pathway
java.util.Set<pathway>	getPathwayListByNAME(java.lang.String regex, boolean bIncludeSynonyms) get pathway by NAME
java.util.Set<pathway>	getPathwayListByORGANISM(java.lang.String regex) get pathway by ORGANISM
java.util.Set<pathway>	getPathwayListByTERMOfEVIDENCE_CODE(java.lang.String regex) get pathway by TERM of EVIDENCE_CODE
java.util.Set<physicalEntity>	getPhysicalEntityListInPathway(pathway p) get physicalEntity in pathway
java.util.Set<pathwayStep>	getPreviousStepListOfPathway(pathway p) get previous steps of pathway
java.util.Set<pathway>	getSuperPathwayList(pathway p) get super pathway
pathway	getTopLevelPathway(pathway p) get top level pathway

Methods inherited from class java.lang.Object

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

Constructor Detail

PathwaySearch

public PathwaySearch(HiRDBSession session)

construct

Parameters:

session -

Method Detail

getPathwayList

public java.util.Set<pathway> getPathwayList()

get all pathway

Returns:

all pathway

getPathwayListByNAME

public java.util.Set<pathway> getPathwayListByNAME(java.lang.String regex,
                                                   boolean bIncludeSynonyms)

get pathway by NAME

Parameters:

regex -

bIncludeSynonyms -

Returns:

pathway

getPathwayListByORGANISM

public java.util.Set<pathway> getPathwayListByORGANISM(java.lang.String regex)

get pathway by ORGANISM

Parameters:

regex -

Returns:

pathway

getSuperPathwayList

public java.util.Set<pathway> getSuperPathwayList(pathway p)

get super pathway

Parameters:

pathway - sub pathway

Returns:

super pathway

fetchSuperPathway

protected java.util.Set<pathway> fetchSuperPathway(javax.persistence.EntityManager em,
                                                   pathwayComponent inPC)

fetchPathwayStepByProcess

protected java.util.Set<pathwayStep> fetchPathwayStepByProcess(javax.persistence.EntityManager em,
                                                               process inProcess)

fetchPathwayByPathwayComonent

protected java.util.Set<pathway> fetchPathwayByPathwayComonent(javax.persistence.EntityManager em,
                                                               pathwayComponent inPC)

getAllSuperPathwayList

public java.util.Set<pathway> getAllSuperPathwayList(pathway p)

get all super pathway

Parameters:

pathway - sub pathway

Returns:

all super pathway

fetchAllSuperPathway

protected void fetchAllSuperPathway(javax.persistence.EntityManager em,
                                    pathway p,
                                    java.util.HashSet<pathway> result)

getAllSubPathwayList

public java.util.Set<pathway> getAllSubPathwayList(pathway p)

get all sub pathway

Parameters:

p - pathway

Returns:

all sub pathway

fetchSubPathwayComponent

protected java.util.Set<pathwayComponent> fetchSubPathwayComponent(pathwayComponent inElem)

fetchChildPathwayComponentOrProcess

protected java.util.Set<pathwayComponent> fetchChildPathwayComponentOrProcess(pathwayComponent inElem)

fetchAllSubPathway

protected void fetchAllSubPathway(pathwayComponent p,
                                  java.util.HashSet<pathway> result)

getTopLevelPathway

public pathway getTopLevelPathway(pathway p)

get top level pathway

Parameters:

p - pathway

Returns:

top level pathway

getNEXT_STEPListOfPathway

public java.util.Set<pathwayStep> getNEXT_STEPListOfPathway(pathway p)

get NEXT_STEP of pathway

Parameters:

p - pathway

Returns:

pathwayStep

fetchNEXT_STEPOfPathway

protected java.util.Set<pathwayStep> fetchNEXT_STEPOfPathway(pathway p)

getAllNEXT_STEPListOfPathway

public java.util.Set<pathwayStep> getAllNEXT_STEPListOfPathway(pathway p)

get all NEXT_STEP of pathway

Parameters:

p - pathway

Returns:

pathwayStep

fetchAllNEXT_STEPOfPathway

protected void fetchAllNEXT_STEPOfPathway(pathwayComponent p,
                                          java.util.HashSet<pathwayStep> result)

getPreviousStepListOfPathway

public java.util.Set<pathwayStep> getPreviousStepListOfPathway(pathway p)

get previous steps of pathway

Parameters:

p - pathway

Returns:

pathwayStep

fetchPreviousStepOfPathway

protected java.util.Set<pathwayStep> fetchPreviousStepOfPathway(javax.persistence.EntityManager em,
                                                                pathway p)

fetchBackStep

protected java.util.Set<pathwayStep> fetchBackStep(javax.persistence.EntityManager em,
                                                   pathwayStep inElem)

getAllPreviousStepListOfPathway

public java.util.Set<pathwayStep> getAllPreviousStepListOfPathway(pathway p)

get all previous steps of pathway

Parameters:

p - pathway

Returns:

pathwayStep

fetchAllPreviousStepOfPathway

protected void fetchAllPreviousStepOfPathway(javax.persistence.EntityManager em,
                                             pathwayComponent p,
                                             java.util.HashSet<pathwayStep> result)

getEC_NUMBERListInPathway

public java.util.Set<java.lang.String> getEC_NUMBERListInPathway(pathway p)

get EC_NUMBER in pathway

Parameters:

p - pathway

Returns:

EC_NUMBER

fetchEC_NUMBERInPathwayComponent

protected void fetchEC_NUMBERInPathwayComponent(pathwayComponent pc,
                                                java.util.HashSet<java.lang.String> result)

getPhysicalEntityListInPathway

public java.util.Set<physicalEntity> getPhysicalEntityListInPathway(pathway p)

get physicalEntity in pathway

Parameters:

p - pathway

Returns:

physicalEntity

fetchPhysicalEntity

protected void fetchPhysicalEntity(BioPAXElement e,
                                   java.util.HashSet<physicalEntity> result)

getInteractionListInPathway

public java.util.Set<interaction> getInteractionListInPathway(pathway p)

get interaction in pathway

Parameters:

p - pathway

Returns:

interaction

fetchInteraction

protected void fetchInteraction(pathwayComponent pc,
                                java.util.HashSet<interaction> result)

getAllEvidenceListInPathway

public java.util.Set<evidence> getAllEvidenceListInPathway(pathway p)

get all evidence in pathway

Parameters:

p - pathway

Returns:

evidence

fetchEvidence

protected void fetchEvidence(pathwayComponent pc,
                             java.util.HashSet<evidence> result)

fetchXref

protected void fetchXref(BioPAXElement e,
                         java.util.HashSet<xref> result)

getPathwayListByTERMOfEVIDENCE_CODE

public java.util.Set<pathway> getPathwayListByTERMOfEVIDENCE_CODE(java.lang.String regex)

get pathway by TERM of EVIDENCE_CODE

Parameters:

regex -

Returns:

pathway

fetchOpenControlledVocabularyByTerm

protected java.util.Set<openControlledVocabulary> fetchOpenControlledVocabularyByTerm(javax.persistence.EntityManager em,
                                                                                      java.lang.String term)