psidev.psi.mi.xml.model.Participant.getInteractor java code examples

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private void myMethod () {
 SimpleDateFormat s =String pattern;new SimpleDateFormat(pattern)
String template;Locale locale;new SimpleDateFormat(template, locale)
new SimpleDateFormat()
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}

  public int compare(Participant p1, Participant p2) {
    Interactor i1 = p1.getInteractor();
    if( i1 == null ) {
      throw new IllegalArgumentException( "Both participant should hold a valid interactor." );
    }
    Interactor i2 = p2.getInteractor();
    if( i2 == null ) {
      throw new IllegalArgumentException( "Both participant should hold a valid interactor." );
    }
    String name1 = getName( i1 );
    String name2 = getName( i2 );
    int result;
    if ( name1 == null ) {
      result = -1;
    } else if ( name2 == null ) {
      result = 1;
    } else {
      result = name1.compareTo( name2 );
    }
    return result;
  }
} );

  jParticipant.setInteractorRef( mParticipant.getInteractorRef().getRef() );
else
  jParticipant.setInteractorRef( mParticipant.getInteractor().getId() );
jParticipant.setInteractor( interactorConverter.toJaxb( mParticipant.getInteractor() ) );

public static Entry createEntry(Source source, Collection<Interaction> interactions) {
  Entry entry = new Entry();
  entry.setSource(source);
  for (Interaction interaction : interactions) {
    entry.getInteractions().add(interaction);
    for (ExperimentDescription expDesc : interaction.getExperiments()) {
      entry.getExperiments().add(expDesc);
    }
    for (Participant part : interaction.getParticipants()) {
      entry.getInteractors().add(part.getInteractor());
    }
  }
  return entry;
}

private void removeInteractorRedundancy( EntrySet mEntrySet ) {
  if( ConverterContext.getInstance().getConverterConfig().getXmlForm() == PsimiXmlForm.FORM_COMPACT ) {
    for ( Entry entry : mEntrySet.getEntries() ) {
      Map<Interactor, Interactor> uniqueInteractors = new HashMap<Interactor, Interactor>();
      for ( Interaction interaction : entry.getInteractions() ) {
        for ( Participant participant : interaction.getParticipants() ) {
          if( participant.getInteractor() != null ) {
            final Interactor myInteractor = participant.getInteractor();
            if( uniqueInteractors.containsKey( myInteractor ) ) {
              final Interactor uniq = uniqueInteractors.get( myInteractor );
              participant.setInteractor( uniq );
            } else {
              uniqueInteractors.put( myInteractor, myInteractor );
            }
          }
        } // participants
      } // interactions
      // if we had a compact format, we cannot remove interactor redundancy without changing the interactions
      // and update the interactor xref
      if (!uniqueInteractors.isEmpty()){
        entry.getInteractors().clear();
        entry.getInteractors().addAll( uniqueInteractors.keySet() );
      }
    } // entries
  } // model is compact
}

/**
 * @param interaction
 * @return names of these interaction.
 */
private Names getInteractionName(Interaction interaction) {
  Names interactionName = null;
  Collection<Participant> participants = interaction.getParticipants();
  for (Participant participant : participants) {
    if (interactionName != null) {
      String shortLabel = interactionName.getShortLabel().concat("-");
      shortLabel = shortLabel.concat(participant.getInteractor().getNames().getShortLabel().split("_")[0]);
      interactionName.setShortLabel(shortLabel);
    }
    if (interactionName == null) {
      interactionName = new Names();
      interactionName.setShortLabel(participant.getInteractor().getNames().getShortLabel().split("_")[0]);
    }
  }
  if (interactionName == null) {
    log.warn("Interaction don't have a name");
  }
  return interactionName;
}

public static Collection<Object> nonRedundantInteractorsFromPsiEntry(Entry psiEntry) {
  Map<Integer, Object> nonRedundantInteractors = new HashMap<Integer, Object>();
  if( ConverterContext.getInstance().isGenerateExpandedXml() ) {
    // iterate to get the unique experiments/interactors
    for (psidev.psi.mi.xml.model.Interaction interaction : psiEntry.getInteractions()) {
      for (Participant participant : interaction.getParticipants()) {
        if (participant.getInteractor() != null){
          nonRedundantInteractors.put(participant.getInteractor().getId(), participant.getInteractor());
        }
        else if (participant.getInteraction() != null){
          nonRedundantInteractors.put(participant.getInteraction().getId(), participant.getInteraction());
        }
      }
    }
  } else {
    for ( psidev.psi.mi.xml.model.Interactor interactor : psiEntry.getInteractors() ) {
      nonRedundantInteractors.put( interactor.getId(), interactor );
    }
  }
  return nonRedundantInteractors.values();
}

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());
      }
    }
  }
}

protected String displayParticipant(Participant p) {
  // fetch role
  String role = "";
  for (ExperimentalRole aRole : p.getExperimentalRoles()) {
    if (role.length() > 0) {
      role += "&";
    }
    if (aRole.hasNames()) {
      role += aRole.getNames().getShortLabel();
    } else {
      role += "?";
    }
  }
  // fetch interactor
  String interactor = p.getInteractor().getNames().getShortLabel();
  return interactor + ":" + role;
}

private String displayParticipant( Participant p ) {
  // fetch role
  String role = "";
  for ( ExperimentalRole aRole : p.getExperimentalRoles() ) {
    if ( role.length() > 0 ) {
      role += "&";
    }
    if ( aRole.hasNames() ) {
      role += aRole.getNames().getShortLabel();
    } else {
      role += "?";
    }
  }
  // fetch interactor
  String interactor = p.getInteractor().getNames().getShortLabel();
  return interactor + ":" + role;
}

if (participant.getInteractor() == null && participant.getInteraction() == null) {
  throw new PsiConversionException("Participant without interactor found: "+participant+" in interaction: "+interaction);

Interactor interactor = participant.getInteractor();
String name = interactor.getNames().getShortLabel();
String type = interactor.getInteractorType().getNames().getShortLabel();

for(Participant p : interaction.getParticipants()) {
  if(p.hasInteractor()) {
    String type = getName(p.getInteractor().getInteractorType().getNames());
    if(type==null) type = "protein"; //default type (if unspecified)
    participantTypes.add(type.toLowerCase());
      + "; so we'll replace 'gene' with 'dna' (a quick fix)");
  for(Participant p : interaction.getParticipants()) {
    if(p.hasInteractor() && p.getInteractor().getInteractorType().hasNames()) {
      String type = getName(p.getInteractor().getInteractorType().getNames());
      if("gene".equalsIgnoreCase(type)) {
        p.getInteractor().getInteractorType().getNames().setShortLabel("dna");

mEntry.getInteractors().add(mParticipant.getInteractor());
participantIds.add(mParticipant.getInteractor().getId());

private void processEdge(final Participant source, final Participant target, final Interaction interaction,
    final Collection<Participant> nodes, CyTable nodeTable, CyTable edgeTable) {
  Interactor sourceInteractor = source.getInteractor();
  Interactor targetInteractor = target.getInteractor();
  
  if (sourceInteractor == null || targetInteractor == null) {
    return;
  }
  
  final CyNode sourceCyNode = id2NodeMap.get(sourceInteractor.getId());
  final CyNode targetCyNode = id2NodeMap.get(targetInteractor.getId());
  
  // PPI does not have directinarity
  final CyEdge edge = network.addEdge(sourceCyNode, targetCyNode, false);
  // TODO: what's the best value for interaction?
  edgeTable.getRow(edge.getSUID()).set(CyEdge.INTERACTION, "pp");
  final String sourceName = nodeTable.getRow(sourceCyNode.getSUID()).get(CyNetwork.NAME, String.class);
  final String targetName = nodeTable.getRow(targetCyNode.getSUID()).get(CyNetwork.NAME, String.class);
  edgeTable.getRow(edge.getSUID()).set(CyNetwork.NAME, sourceName + " (pp) " + targetName);
  mapNames(edgeTable, edge.getSUID(), interaction.getNames(), null);
  mapAttributes(interaction.getAttributes(), edgeTable, edge.getSUID());
  final Collection<InteractionType> types = interaction.getInteractionTypes();
  mapInteractionType(types, edgeTable, edge.getSUID());
}

for (psidev.psi.mi.xml.model.Interaction mInteraction : mEntry.getInteractions()) {
  for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) {
    mEntry.getInteractors().add(mParticipant.getInteractor());

if (participant.getInteractor() != null){
  interactor = this.interactorConverter.psiToIntact(participant.getInteractor());

for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) {
  if (!participantIds.contains(mParticipant.getId())) {
    jEntry.getInteractorList().getInteractors().add(interactorConverter.toJaxb(mParticipant.getInteractor()));
    participantIds.add(mParticipant.getId());

for (psidev.psi.mi.xml.model.Participant mParticipant : mInteraction.getParticipants()) {
  if (!participantIds.contains(mParticipant.getId())) {
    jEntry.getInteractorList().getInteractors().add( interactorConverter.toJaxb(mParticipant.getInteractor()));
    participantIds.add(mParticipant.getId());

public static Component newComponent(Institution institution, Participant participant, uk.ac.ebi.intact.model.Interaction interaction) {
  Interactor interactor = new InteractorConverter(institution).psiToIntact(participant.getInteractor());

  entity = createParticipant(participant, participant.getInteractor(), avail, pro, false);
} else if(participant.hasInteraction()) {

Javadoc

Gets the value of the interactor property.

Popular methods of Participant

getExperimentalRoles
Gets the value of the experimentalRoleList property.
getFeatures
Gets the value of the featureList property.
getAttributes
Gets the value of the attributeList property.
getBiologicalRole
Gets the value of the biologicalRole property.
getExperimentalInteractors
Gets the value of the experimentalInteractorList property.
getId
Gets the value of the id property.
getInteraction
getParticipantIdentificationMethods
Gets the value of the participantIdentificationMethodList property.
hasExperimentalRoles
Check if the optional experimentalRoles is defined.
setBiologicalRole
Sets the value of the biologicalRole property.
setInteractor
Sets the value of the interactor property.
<init>

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How to use getInteractormethodin psidev.psi.mi.xml.model.Participant

Best Java code snippets using psidev.psi.mi.xml.model.Participant.getInteractor (Showing top 20 results out of 315)

How to use
getInteractor
method
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psidev.psi.mi.xml.model.Participant