Package psidev.psi.mi.jami.xml.cache

Class PsiXmlFileIndexCache

java.lang.Object

psidev.psi.mi.jami.xml.cache.PsiXmlFileIndexCache

All Implemented Interfaces:

PsiXmlIdCache

public class PsiXmlFileIndexCache
extends Object
implements PsiXmlIdCache

Cache using a file and a weak map to cache the objects

Since:

25/06/14

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
PsiXmlFileIndexCache(File file, javax.xml.bind.Unmarshaller unmarshaller, PsiXmlVersion version)	Constructor for PsiXmlFileIndexCache.
PsiXmlFileIndexCache(File file, PsiXmlVersion version, InteractionCategory category)	Constructor for PsiXmlFileIndexCache.

Method Summary

Modifier and Type	Method	Description
void	buildPositionIndex(File f)	Indexes references component of the given file.
void	clear()	Clear all existing records
void	close()	Close cache
boolean	containsAvailability(int id)	To know if it contains a specific id
boolean	containsComplex(int id)	To know if it contains a specific id
boolean	containsComplexFeature(int id)	To know if it contains a specific id
boolean	containsComplexParticipant(int id)	To know if it contains a specific id
boolean	containsExperiment(int id)	To know if it contains a specific id
boolean	containsFeature(int id)	To know if it contains a specific id
boolean	containsInteraction(int id)	To know if it contains a specific id
boolean	containsInteractor(int id)	To know if it contains a specific id
boolean	containsParticipant(int id)	To know if it contains a specific id
boolean	containsVariableParameter(int id)	To know if it contains a specific id
AbstractAvailability	getAvailability(int id)	getAvailability.
Complex	getComplex(int id)	getComplex.
ModelledFeature	getComplexFeature(int id)	getComplexFeature.
ModelledEntity	getComplexParticipant(int id)	getComplexParticipant.
Experiment	getExperiment(int id)	getExperiment.
Feature	getFeature(int id)	getFeature.
Interaction	getInteraction(int id)	getInteraction.
Interactor	getInteractor(int id)	getInteractor.
Entity	getParticipant(int id)	getParticipant.
VariableParameterValue	getVariableParameterValue(int id)	getVariableParameterValue.
void	registerAvailability(int id, AbstractAvailability object)	Register an availability with an id
void	registerComplex(int id, Complex object)	Register a complex with an id
void	registerComplexFeature(int id, ModelledFeature object)	Register a complex feature with an id
Complex	registerComplexLoadedFrom(Interaction f)	registerComplexLoadedFrom.
void	registerComplexParticipant(int id, ModelledEntity object)	Register a participant involved in a complex with an id
void	registerExperiment(int id, Experiment object)	Register an experiment with an id
void	registerFeature(int id, Feature object)	Register a feature with an id
void	registerInteraction(int id, Interaction object)	Register an interaction with an id
void	registerInteractor(int id, Interactor object)	Register an interactor with an id
ModelledFeature	registerModelledFeatureLoadedFrom(Feature f)	registerModelledFeatureLoadedFrom.
ModelledEntity	registerModelledParticipantLoadedFrom(Entity f)	registerModelledParticipantLoadedFrom.
void	registerParticipant(int id, Entity object)	Register a participant with an id
void	registerVariableParameterValue(int id, VariableParameterValue object)	Register a variable parameter value with an id

Methods inherited from class java.lang.Object

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

Constructor Detail

PsiXmlFileIndexCache

public PsiXmlFileIndexCache(File file,
                            javax.xml.bind.Unmarshaller unmarshaller,
                            PsiXmlVersion version)
                     throws IOException

Constructor for PsiXmlFileIndexCache.

Parameters:

file - a File object.

unmarshaller - a Unmarshaller object.

version - a PsiXmlVersion object.

Throws:

IOException - if any.

PsiXmlFileIndexCache

public PsiXmlFileIndexCache(File file,
                            PsiXmlVersion version,
                            InteractionCategory category)
                     throws IOException,
                            javax.xml.bind.JAXBException

Constructor for PsiXmlFileIndexCache.

Parameters:

file - a File object.

version - a PsiXmlVersion object.

category - a InteractionCategory object.

Throws:

IOException - if any.

javax.xml.bind.JAXBException - if any.

Method Detail

registerAvailability

public void registerAvailability(int id,
                                 AbstractAvailability object)

Register an availability with an id

Specified by:

registerAvailability in interface PsiXmlIdCache

Parameters:

id - a int.

object - a AbstractAvailability object.

getAvailability

public AbstractAvailability getAvailability(int id)

getAvailability.

Specified by:

getAvailability in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the availability registered with this id, null if it does not exist

registerExperiment

public void registerExperiment(int id,
                               Experiment object)

Register an experiment with an id

Specified by:

registerExperiment in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Experiment object.

getExperiment

public Experiment getExperiment(int id)

getExperiment.

Specified by:

getExperiment in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the experiment registered with this id, null if it does not exist

registerInteraction

public void registerInteraction(int id,
                                Interaction object)

Register an interaction with an id

Specified by:

registerInteraction in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Interaction object.

getInteraction

public Interaction getInteraction(int id)

getInteraction.

Specified by:

getInteraction in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the interaction registered with this id, null if it does not exist

registerInteractor

public void registerInteractor(int id,
                               Interactor object)

Register an interactor with an id

Specified by:

registerInteractor in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Interactor object.

getInteractor

public Interactor getInteractor(int id)

getInteractor.

Specified by:

getInteractor in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the interactor registered with this id, null if it does not exist

registerParticipant

public void registerParticipant(int id,
                                Entity object)

Register a participant with an id

Specified by:

registerParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Entity object.

getParticipant

public Entity getParticipant(int id)

getParticipant.

Specified by:

getParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the participant registered with this id, null if it does not exist

registerFeature

public void registerFeature(int id,
                            Feature object)

Register a feature with an id

Specified by:

registerFeature in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Feature object.

getFeature

public Feature getFeature(int id)

getFeature.

Specified by:

getFeature in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the feature registered with this id, null if it does not exist

registerComplexParticipant

public void registerComplexParticipant(int id,
                                       ModelledEntity object)

Register a participant involved in a complex with an id

Specified by:

registerComplexParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

object - a ModelledEntity object.

getComplexParticipant

public ModelledEntity getComplexParticipant(int id)

getComplexParticipant.

Specified by:

getComplexParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the participant registered with this id, null if it does not exist

registerComplexFeature

public void registerComplexFeature(int id,
                                   ModelledFeature object)

Register a complex feature with an id

Specified by:

registerComplexFeature in interface PsiXmlIdCache

Parameters:

id - a int.

object - a ModelledFeature object.

getComplexFeature

public ModelledFeature getComplexFeature(int id)

getComplexFeature.

Specified by:

getComplexFeature in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the feature registered with this id, null if it does not exist

registerComplex

public void registerComplex(int id,
                            Complex object)

Register a complex with an id

Specified by:

registerComplex in interface PsiXmlIdCache

Parameters:

id - a int.

object - a Complex object.

getComplex

public Complex getComplex(int id)

getComplex.

Specified by:

getComplex in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the complex registered with this id, null if it does not exist

registerVariableParameterValue

public void registerVariableParameterValue(int id,
                                           VariableParameterValue object)

Register a variable parameter value with an id

Specified by:

registerVariableParameterValue in interface PsiXmlIdCache

Parameters:

id - a int.

object - a VariableParameterValue object.

getVariableParameterValue

public VariableParameterValue getVariableParameterValue(int id)

getVariableParameterValue.

Specified by:

getVariableParameterValue in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

the variable parameter value registered with this id, null if it does not exist

clear

public void clear()

Clear all existing records

Specified by:

clear in interface PsiXmlIdCache

close

public void close()

Close cache

Specified by:

close in interface PsiXmlIdCache

containsExperiment

public boolean containsExperiment(int id)

To know if it contains a specific id

Specified by:

containsExperiment in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsAvailability

public boolean containsAvailability(int id)

To know if it contains a specific id

Specified by:

containsAvailability in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsInteraction

public boolean containsInteraction(int id)

To know if it contains a specific id

Specified by:

containsInteraction in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsInteractor

public boolean containsInteractor(int id)

To know if it contains a specific id

Specified by:

containsInteractor in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsParticipant

public boolean containsParticipant(int id)

To know if it contains a specific id

Specified by:

containsParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsFeature

public boolean containsFeature(int id)

To know if it contains a specific id

Specified by:

containsFeature in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsVariableParameter

public boolean containsVariableParameter(int id)

To know if it contains a specific id

Specified by:

containsVariableParameter in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsComplex

public boolean containsComplex(int id)

To know if it contains a specific id

Specified by:

containsComplex in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsComplexParticipant

public boolean containsComplexParticipant(int id)

To know if it contains a specific id

Specified by:

containsComplexParticipant in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

containsComplexFeature

public boolean containsComplexFeature(int id)

To know if it contains a specific id

Specified by:

containsComplexFeature in interface PsiXmlIdCache

Parameters:

id - a int.

Returns:

a boolean.

registerModelledFeatureLoadedFrom

public ModelledFeature registerModelledFeatureLoadedFrom(Feature f)

registerModelledFeatureLoadedFrom.

Specified by:

registerModelledFeatureLoadedFrom in interface PsiXmlIdCache

Parameters:

f - : the loaded feature

Returns:

the converted and registered modelled feature

registerModelledParticipantLoadedFrom

public ModelledEntity registerModelledParticipantLoadedFrom(Entity f)

registerModelledParticipantLoadedFrom.

Specified by:

registerModelledParticipantLoadedFrom in interface PsiXmlIdCache

Parameters:

f - : the loaded participant

Returns:

the converted and registered modelled participant

registerComplexLoadedFrom

public Complex registerComplexLoadedFrom(Interaction f)

registerComplexLoadedFrom.

Specified by:

registerComplexLoadedFrom in interface PsiXmlIdCache

Parameters:

f - : the loaded interaction

Returns:

the converted and registered complex

buildPositionIndex

public void buildPositionIndex(File f)
                        throws IOException

Indexes references component of the given file. that is experiments, interaction, interactor, feature and participant so that we know where they are in the file and we can jump in the right position should we want to extract one of them.

Parameters:

f - the file to index.

Throws:

IOException - if any.