ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );
ProteinHolder holder = getProtein( psiComponent ); final Protein psiProtein; if ( holder.isSpliceVariantExisting() ) { if ( featureAreEquals( intactComponent, psiComponent ) ) {
createShortlabel( interactionTag, experiments ); Annotation annotation = searchIntactAnnotation( annotationTag );
String intactMI = getPsiID( intactFeature.getCvFeatureType() ); if ( intactFeature.getCvFeatureIdentification() != null ) { intactMI = getPsiID( intactFeature.getCvFeatureIdentification() ); if ( areRangeEquals( range, location ) ) {
alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
ProteinHolder holder = getProtein( psiComponent ); final Protein psiProtein; if ( holder.isSpliceVariantExisting() ) { if ( featureAreEquals( intactComponent, psiComponent ) ) {
createShortlabel( interactionTag, experiments ); Annotation annotation = searchIntactAnnotation( annotationTag );
String intactMI = getPsiID( intactFeature.getCvFeatureType() ); if ( intactFeature.getCvFeatureIdentification() != null ) { intactMI = getPsiID( intactFeature.getCvFeatureIdentification() ); if ( areRangeEquals( range, location ) ) {
alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
ProteinHolder holder = getProtein( psiComponent ); final Protein psiProtein; if ( holder.isSpliceVariantExisting() ) { if ( featureAreEquals( intactComponent, psiComponent ) ) {
createShortlabel( interactionTag, experiments ); Annotation annotation = searchIntactAnnotation( annotationTag );
String intactMI = getPsiID( intactFeature.getCvFeatureType() ); if ( intactFeature.getCvFeatureIdentification() != null ) { intactMI = getPsiID( intactFeature.getCvFeatureIdentification() ); if ( areRangeEquals( range, location ) ) {
final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );
alreadyExistsInIntact( psiInteraction, experiments, intactInteraction ); // update experiments !
ProteinParticipantTag proteinParticipant = (ProteinParticipantTag) iterator.next(); final String role = proteinParticipant.getRole(); final ProteinHolder proteinHolder = getProtein( proteinParticipant ); final String geneName = getGeneName( proteinHolder ); baitShortlabel = getLabelFromCollection( baits, true ); // fail on error preyShortlabel = getLabelFromCollection( preys, false ); // don't fail on error if ( preyShortlabel == null ) { preyShortlabel = getLabelFromCollection( neutrals, true ); // fail on error createInteractionShortLabels( interaction, experiments, baitShortlabel, preyShortlabel );
final InteractionTag interaction = (InteractionTag) iterator.next(); try { Collection createdInteractions = InteractionPersister.persist( interaction );