public static Collection<ExperimentDescription> nonRedundantExperimentsFromPsiEntry(Entry psiEntry) { Map<Integer,ExperimentDescription> nonRedundantExps = new HashMap<Integer,ExperimentDescription>(); if( ConverterContext.getInstance().isGenerateCompactXml() ) { for (ExperimentDescription expDesc : psiEntry.getExperiments()) { nonRedundantExps.put(expDesc.getId(), expDesc); } } else { for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) { for (ExperimentDescription exp : interaction.getExperiments()) { nonRedundantExps.put(exp.getId(), exp); } } } return nonRedundantExps.values(); }
/** * Retrieve an experiment description in an interaction using an experiment ref * @param eref : the experiment reference * @param i : the interaction to look into * @return the experiment which has been found */ private ExperimentDescription findExperimentDescriptionInInteraction(ExperimentRef eref, Interaction i){ for ( ExperimentDescription ed : i.getExperiments() ) { if( ed.getId() == eref.getRef() ) { return ed; } } return null; }
private void normalizeEntry(Entry entry) { if (entry.getExperiments().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { interaction.getExperimentRefs().clear(); for (ExperimentDescription exp : interaction.getExperiments()) { entry.getExperiments().add(exp); interaction.getExperimentRefs().add(new ExperimentRef(exp.getId())); } } } if (entry.getInteractors().isEmpty()) { for (Interaction interaction : entry.getInteractions()) { for(Participant participant : interaction.getParticipants()) { entry.getInteractors().add(participant.getInteractor()); } } } }
public psidev.psi.mi.xml253.jaxb.ParticipantType.ParticipantIdentificationMethodList.ParticipantIdentificationMethod toJaxb( psidev.psi.mi.xml.model.ParticipantIdentificationMethod mParticipantIdentificationMethod ) throws ConverterException { if ( mParticipantIdentificationMethod == null ) { throw new IllegalArgumentException( "You must give a non null model Participant Identification Method." ); } // Initialise the JAXB object reading the model // 1. convert the CvType psidev.psi.mi.xml253.jaxb.ParticipantType.ParticipantIdentificationMethodList.ParticipantIdentificationMethod jParticipantIdentificationMethod = cvTypeConverter.toJaxb( mParticipantIdentificationMethod, psidev.psi.mi.xml253.jaxb.ParticipantType.ParticipantIdentificationMethodList.ParticipantIdentificationMethod.class ); // 2. convert remaining components // experiments if ( mParticipantIdentificationMethod.hasExperiments() ) { for ( ExperimentDescription mExperiment : mParticipantIdentificationMethod.getExperiments() ) { addExperimentRef( jParticipantIdentificationMethod, mExperiment.getId() ); } } else if ( mParticipantIdentificationMethod.hasExperimentRefs() ) { for ( ExperimentRef mExperiment : mParticipantIdentificationMethod.getExperimentRefs() ) { addExperimentRef( jParticipantIdentificationMethod, mExperiment.getRef() ); } } return jParticipantIdentificationMethod; }
public psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethod toJaxb( psidev.psi.mi.xml.model.ParticipantIdentificationMethod mParticipantIdentificationMethod ) throws ConverterException { if ( mParticipantIdentificationMethod == null ) { throw new IllegalArgumentException( "You must give a non null model Participant Identification Method." ); } // Initialise the JAXB object reading the model // 1. convert the CvType psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethod jParticipantIdentificationMethod = cvTypeConverter.toJaxb( mParticipantIdentificationMethod, psidev.psi.mi.xml254.jaxb.ParticipantIdentificationMethod.class ); // 2. convert remaining components // experiments if ( mParticipantIdentificationMethod.hasExperiments() ) { for ( ExperimentDescription mExperiment : mParticipantIdentificationMethod.getExperiments() ) { addExperimentRef( jParticipantIdentificationMethod, mExperiment.getId() ); } } else if ( mParticipantIdentificationMethod.hasExperimentRefs() ) { for ( ExperimentRef mExperiment : mParticipantIdentificationMethod.getExperimentRefs() ) { addExperimentRef( jParticipantIdentificationMethod, mExperiment.getRef() ); } } return jParticipantIdentificationMethod; }
jExperimentalPreparation.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
jExperimentalPreparation.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
jExperimentalRole.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
jExperimentalRole.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
Integer experimentId = mExperiment.getId(); jInferredInteraction.getExperimentRefList().getExperimentReves().add( experimentId );
Integer experimentId = mExperiment.getId(); jInferredInteraction.getExperimentRefList().getExperimentReves().add( experimentId );
jExperimentalInteractor.getExperimentRefList().getExperimentReves().add( experimentDescription.getId() );
jExperimentalInteractor.getExperimentRefList().getExperimentReves().add( experimentDescription.getId() );
jConfidence.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
jConfidence.getExperimentRefList().getExperimentReves().add( mExperiment.getId() );
jParameter.setExperimentRef( mParameter.getExperiment().getId() ); } else if ( mParameter.hasExperimentRef() ) { jParameter.setExperimentRef( mParameter.getExperimentRef().getRef() );
jParameter.setExperimentRef( mParameter.getExperiment().getId() ); } else if ( mParameter.hasExperimentRef() ) { jParameter.setExperimentRef( mParameter.getExperimentRef().getRef() );
jParameter.setExperimentRef( mParameter.getExperiment().getId() ); } else if ( mParameter.hasExperimentRef() ) { jParameter.setExperimentRef( mParameter.getExperimentRef().getRef() );
jParameter.setExperimentRef( mParameter.getExperiment().getId() ); } else if ( mParameter.hasExperimentRef() ) { jParameter.setExperimentRef( mParameter.getExperimentRef().getRef() );
public psidev.psi.mi.xml.model.Parameter intactToPsi( T intactObject ) { psidev.psi.mi.xml.model.Parameter parameter = new psidev.psi.mi.xml.model.Parameter(intactObject.getCvParameterType().getShortLabel(), intactObject.getFactor()); intactStartConversation(parameter); parameter.setTermAc(intactObject.getCvParameterType().getIdentifier()); if (intactObject.getBase() != null) { parameter.setBase(intactObject.getBase()); } if (intactObject.getBase() != null) { parameter.setBase(intactObject.getBase()); } if (intactObject.getExponent() != null) { parameter.setExponent(intactObject.getExponent()); } if (intactObject.getUncertainty() != null) { parameter.setUncertainty(intactObject.getUncertainty()); } if (intactObject.getCvParameterUnit() != null) { parameter.setUnit(intactObject.getCvParameterUnit().getShortLabel()); parameter.setUnitAc(intactObject.getCvParameterUnit().getIdentifier()); } if(intactObject.getExperiment() != null) { parameter.setExperimentRef(new ExperimentRef(experimentConverter.intactToPsi(intactObject.getExperiment()).getId())); } intactEndConversion(intactObject); return parameter; }