Package psidev.psi.mi.jami.utils.clone

Class InteractionCloner

java.lang.Object

psidev.psi.mi.jami.utils.clone.InteractionCloner

public class InteractionCloner
extends Object

Utility class to clone and copy interaction properties

Since:

13/02/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Constructor	Description
InteractionCloner()

Method Summary

Modifier and Type	Method	Description
static void	copyAndOverrideBasicInteractionProperties(Interaction source, Interaction target, boolean createNewParticipant, boolean ignoreParticipants)	This method will copy basic properties of interaction source in interaction target and will override all the other properties of Target interaction.
static void	copyAndOverrideBasicParticipantsToBinary(Interaction source, BinaryInteraction target, boolean createNewParticipant, boolean self)	This method will copy participants of interaction source in binary target.
static void	copyAndOverrideInteractionEvidenceProperties(InteractionEvidence source, InteractionEvidence target, boolean createNewParticipant, boolean ignoreParticipants)	This method will copy properties of interaction source in interaction target and will override all the other properties of Target interaction.
static void	copyAndOverrideModelledInteractionProperties(ModelledInteraction source, ModelledInteraction target, boolean createNewParticipant, boolean ignoreParticipants)	This method will copy properties of interaction source in interaction target and will override all the other properties of Target interaction.
static void	copyAndOverrideModelledParticipantsToBinary(ModelledInteraction source, ModelledBinaryInteraction target, boolean createNewParticipant, boolean self)	This method will copy participants of modelled interaction source in binary target.
static void	copyAndOverrideParticipantsEvidencesToBinary(InteractionEvidence source, BinaryInteractionEvidence target, boolean createNewParticipant, boolean self)	This method will copy participants of interaction evidence source in binary target.

Methods inherited from class java.lang.Object

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

Constructor Detail

InteractionCloner

public InteractionCloner()

Method Detail

copyAndOverrideInteractionEvidenceProperties

public static void copyAndOverrideInteractionEvidenceProperties(InteractionEvidence source,
                                                                InteractionEvidence target,
                                                                boolean createNewParticipant,
                                                                boolean ignoreParticipants)

This method will copy properties of interaction source in interaction target and will override all the other properties of Target interaction. This method will set the experiment of this interaction evidence but it will not add this interaction to the list of interactionEvidences This method will add all the participant evidences of the source but will not set their interactionEvidence to the target

Parameters:

source - a InteractionEvidence object.

target - a InteractionEvidence object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source. It will then set the interactionEvidence of the cloned participants to target

ignoreParticipants - If true, this method will clone the interaction properties and ignore the participants of the source

copyAndOverrideModelledInteractionProperties

public static void copyAndOverrideModelledInteractionProperties(ModelledInteraction source,
                                                                ModelledInteraction target,
                                                                boolean createNewParticipant,
                                                                boolean ignoreParticipants)

This method will copy properties of interaction source in interaction target and will override all the other properties of Target interaction. This method will add all the participant of the source but will not set their modelledInteraction to the target

Parameters:

source - a ModelledInteraction object.

target - a ModelledInteraction object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source. It will then set the modelledInteraction of the cloned participants to target

ignoreParticipants - If true, this method will clone the interaction properties and ignore the participants of the source

copyAndOverrideBasicInteractionProperties

public static void copyAndOverrideBasicInteractionProperties(Interaction source,
                                                             Interaction target,
                                                             boolean createNewParticipant,
                                                             boolean ignoreParticipants)

This method will copy basic properties of interaction source in interaction target and will override all the other properties of Target interaction.

Parameters:

source - a Interaction object.

target - a Interaction object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source.

ignoreParticipants - If true, this method will clone the interaction properties and ignore the participants of the source

copyAndOverrideParticipantsEvidencesToBinary

public static void copyAndOverrideParticipantsEvidencesToBinary(InteractionEvidence source,
                                                                BinaryInteractionEvidence target,
                                                                boolean createNewParticipant,
                                                                boolean self)

This method will copy participants of interaction evidence source in binary target.

Parameters:

source - a InteractionEvidence object.

target - a BinaryInteractionEvidence object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source. It will then set the interactionEvidence of the cloned participants to target

self - If true, it will only look at the first participant and duplicate this participant with stoichiometry 0

Throws:

IllegalArgumentException - if the number of participants in source is superior to 2 or superior to 1 with self = true

copyAndOverrideModelledParticipantsToBinary

public static void copyAndOverrideModelledParticipantsToBinary(ModelledInteraction source,
                                                               ModelledBinaryInteraction target,
                                                               boolean createNewParticipant,
                                                               boolean self)

This method will copy participants of modelled interaction source in binary target.

Parameters:

source - a ModelledInteraction object.

target - a ModelledBinaryInteraction object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source. It will then set the modelledInteraction of the cloned participants to target

self - if true, we only take the first participant and duplicate it in the Binary interaction. We then set the stoichiometry to 0 for the second interactor

Throws:

IllegalArgumentException - if the source has more than two participants or more than one participant when self is true

copyAndOverrideBasicParticipantsToBinary

public static void copyAndOverrideBasicParticipantsToBinary(Interaction source,
                                                            BinaryInteraction target,
                                                            boolean createNewParticipant,
                                                            boolean self)

This method will copy participants of interaction source in binary target.

Parameters:

source - a Interaction object.

target - a BinaryInteraction object.

createNewParticipant - If true, this method will clone each participant from source instead of reusing the participant instances from source.

self - if true, we only take the first participant and duplicate it in the Binary interaction. We then set the stoichiometry to 0 for the second interactor

Throws:

IllegalArgumentException - if the source has more than two participants or more than one participant when self is true