org.biopax.paxtools.persistence.level2
Class InteractionSearch

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

public class InteractionSearch
extends BaseSearch

interaction search class

Constructor Summary

InteractionSearch(HiRDBSession session)
construct

Method Summary

protected java.util.Set<control>	fetchControlByCONTROLLED(javax.persistence.EntityManager em, java.lang.String regex, boolean bIncludeSynonyms)
protected java.util.Set<physicalInteraction>	fetchPhysicalInteractionByINTERACTION_TYPE(javax.persistence.EntityManager em, java.lang.String regex)
java.util.Set<biochemicalReaction>	getBiochemicalReactionList() get all biochemicalReaction
java.util.Set<biochemicalReaction>	getBiochemicalReactionListByEC_NUMBER(java.lang.String regex) get biochemicalReaction by EC_NUMBER
java.util.Set<catalysis>	getCatalysisList() get all catalysis
java.util.Set<complexAssembly>	getComplexAssemblyList() get all complexAssembly
java.util.Set<physicalEntityParticipant>	getCONTROLLERListByCONTROLLED(java.lang.String regex, boolean bIncludeSynonyms) get CONTROLLER By CONTROLLED
java.util.Set<control>	getControlList() get all control
java.util.Set<control>	getControlListByCONTROLLED(java.lang.String regex, boolean bIncludeSynonyms) get control by CONTROLLED
java.util.Set<conversion>	getConversionList() get all conversion
java.util.Set<interaction>	getInteractionList() get all interaction
java.util.Set<interaction>	getInteractionListByINTERACTION_TYPE(java.lang.String regex) get interaction by INTERACTION_TYPE
java.util.Set<interaction>	getInteractionListByNAME(java.lang.String regex, boolean bIncludeSynonyms) get interaction by NAME
java.util.Set<modulation>	getModulationList() get all modulation
java.util.Set<transport>	getTransportList() get all transport
java.util.Set<transportWithBiochemicalReaction>	getTransportWithBiochemicalReactionList() get all transportWithBiochemicalReaction

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionSearch

public InteractionSearch(HiRDBSession session)

construct

Parameters:

session -

Method Detail

getInteractionList

public java.util.Set<interaction> getInteractionList()

get all interaction

Returns:

all interaction

getControlList

public java.util.Set<control> getControlList()

get all control

Returns:

all control

getCatalysisList

public java.util.Set<catalysis> getCatalysisList()

get all catalysis

Returns:

all catalysis

getModulationList

public java.util.Set<modulation> getModulationList()

get all modulation

Returns:

all modulation

getConversionList

public java.util.Set<conversion> getConversionList()

get all conversion

Returns:

all conversion

getBiochemicalReactionList

public java.util.Set<biochemicalReaction> getBiochemicalReactionList()

get all biochemicalReaction

Returns:

all biochemicalReaction

getTransportWithBiochemicalReactionList

public java.util.Set<transportWithBiochemicalReaction> getTransportWithBiochemicalReactionList()

get all transportWithBiochemicalReaction

Returns:

all transportWithBiochemicalReaction

getComplexAssemblyList

public java.util.Set<complexAssembly> getComplexAssemblyList()

get all complexAssembly

Returns:

all complexAssembly

getTransportList

public java.util.Set<transport> getTransportList()

get all transport

Returns:

all transport

getInteractionListByNAME

public java.util.Set<interaction> getInteractionListByNAME(java.lang.String regex,
                                                           boolean bIncludeSynonyms)

get interaction by NAME

Parameters:

regex -

bIncludeSynonyms -

Returns:

interaction

getInteractionListByINTERACTION_TYPE

public java.util.Set<interaction> getInteractionListByINTERACTION_TYPE(java.lang.String regex)

get interaction by INTERACTION_TYPE

Parameters:

regex -

Returns:

interaction

fetchPhysicalInteractionByINTERACTION_TYPE

protected java.util.Set<physicalInteraction> fetchPhysicalInteractionByINTERACTION_TYPE(javax.persistence.EntityManager em,
                                                                                        java.lang.String regex)

getBiochemicalReactionListByEC_NUMBER

public java.util.Set<biochemicalReaction> getBiochemicalReactionListByEC_NUMBER(java.lang.String regex)

get biochemicalReaction by EC_NUMBER

Parameters:

regex -

Returns:

biochemicalReaction

getControlListByCONTROLLED

public java.util.Set<control> getControlListByCONTROLLED(java.lang.String regex,
                                                         boolean bIncludeSynonyms)

get control by CONTROLLED

Parameters:

regex -

bIncludeSynonyms -

Returns:

control

fetchControlByCONTROLLED

protected java.util.Set<control> fetchControlByCONTROLLED(javax.persistence.EntityManager em,
                                                          java.lang.String regex,
                                                          boolean bIncludeSynonyms)

getCONTROLLERListByCONTROLLED

public java.util.Set<physicalEntityParticipant> getCONTROLLERListByCONTROLLED(java.lang.String regex,
                                                                              boolean bIncludeSynonyms)

get CONTROLLER By CONTROLLED

Parameters:

regex -

bIncludeSynonyms -

Returns:

physicalEntityParticipant