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Interactor.getShortName
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How to use
getShortName
method
in
psidev.psi.mi.jami.model.Interactor

Best Java code snippets using psidev.psi.mi.jami.model.Interactor.getShortName (Showing top 13 results out of 315)

origin: psidev.psi.mi.jami/jami-core

public void onShortNameUpdate(T protein, String oldShortName) {
  interactorChangeLogger.log(Level.INFO, "The short name " + oldShortName + " has been updated with " + protein.getShortName() + " in the interactor " + protein.toString());
}
origin: psidev.psi.mi/psimi-schema-validator

@Override
public Collection<ValidatorMessage> check(Interactor interactor) throws ValidatorException {
  if (interactor.getShortName() == null ||
      interactor.getShortName().length() == 0 ||
      PsiXmlUtils.UNSPECIFIED.equals(interactor.getShortName()) ||
      MitabUtils.UNKNOWN_NAME.equals(interactor.getShortName())){
    // list of messages to return
    MiContext experimentContext = RuleUtils.buildContext(interactor, "interactor");
    return Collections.singletonList(new ValidatorMessage( "Interactors must have a valid short name (or alias in MITAB).'",
        MessageLevel.ERROR,
        experimentContext,
        this ) );
  }
  return Collections.EMPTY_LIST;
}
origin: psidev.psi.mi.jami/jami-core

String firstName = firstShortNameAlphabeticalOrder.getInteractor().getShortName().trim().toLowerCase();
String secondName = p.getInteractor().getShortName().trim().toLowerCase();
origin: psidev.psi.mi.jami/jami-core

String firstName = firstShortNameAlphabeticalOrder.getInteractor().getShortName().trim().toLowerCase();
String secondName = p.getInteractor().getShortName().trim().toLowerCase();
origin: psidev.psi.mi.jami/jami-mitab

escapeAndWriteString(interactor.getShortName());
writer.write("(");
writer.write(MitabUtils.DISPLAY_SHORT);
origin: uk.ac.ebi.intact.dataexchange/structured-abstract

protected void buildInteractionkey(I interaction) {
  this.stringBuilder.setLength(0);
  this.interactorAcs.clear();
  // read ordered set of interactor acs
  for (Object obj : interaction.getParticipants()) {
    Participant component = (Participant)obj;
    interactorAcs.add(component.getInteractor() instanceof IntactInteractor ?
        ((IntactInteractor) component.getInteractor()).getAc() : component.getInteractor().getShortName());
  }
  for (String prL : interactorAcs) {
    stringBuilder.append("    ");
    stringBuilder.append(prL);
  }
  // interaction type
  stringBuilder.append(interaction.getInteractionType().getMIIdentifier());
  // experiment
  CvTerm method = extractInteractionDetectionMethodFrom(interaction);
  if (method != null) {
    stringBuilder.append("    ");
    stringBuilder.append(method.getMIIdentifier());
  }
}
origin: psidev.psi.mi.jami/jami-core

String shortName1 = interactor1.getShortName();
String shortName2 = interactor2.getShortName();
if (shortName1.equals(shortName2)){
  return true;
origin: psidev.psi.mi.jami/jami-core

hashcode = 31*hashcode + interactor.getShortName().hashCode();
hashcode = 31*hashcode + (interactor.getFullName() != null ? interactor.getFullName().hashCode() : 0);
origin: psidev.psi.mi.jami/jami-core

/***
 * This method will copy properties of interactor source in interactor target and will override all the other properties of Target interactor.
 * @param source
 * @param target
 */
public static void copyAndOverrideBasicInteractorProperties(Interactor source, Interactor target){
  if (source != null && target != null){
    target.setShortName(source.getShortName());
    target.setFullName(source.getFullName());
    target.setInteractorType(source.getInteractorType());
    target.setOrganism(source.getOrganism());
    // copy collections
    target.getAnnotations().clear();
    target.getAnnotations().addAll(source.getAnnotations());
    target.getIdentifiers().clear();
    target.getIdentifiers().addAll(source.getIdentifiers());
    target.getAliases().clear();
    target.getAliases().addAll(source.getAliases());
    target.getXrefs().clear();
    target.getXrefs().addAll(source.getXrefs());
    target.getChecksums().clear();
    target.getChecksums().addAll(source.getChecksums());
  }
}
origin: psidev.psi.mi.jami/jami-core

String shortName1 = interactor1.getShortName();
String shortName2 = interactor2.getShortName();
int comp = shortName1.compareTo(shortName2);
origin: uk.ac.ebi.intact.dataexchange/structured-abstract

this.ac = (interactor instanceof IntactInteractor) ? ((IntactInteractor)interactor).getAc() : interactor.getShortName();
this.shortName = interactor.getShortName();
origin: psidev.psi.mi.jami/jami-interactionviewer-json

MIJsonUtils.writeProperty("label", JSONValue.escape(object.getShortName()), writer);
MIJsonUtils.writeEndObject(writer);
origin: psidev.psi.mi.jami/jami-interactionviewer-json

private void writeInteractorComponent(Interactor object) throws IOException {
  MIJsonUtils.writeStartObject(writer);
  MIJsonUtils.writeProperty("label", JSONValue.escape(object.getShortName()), writer);
psidev.psi.mi.jami.modelInteractorgetShortName

Javadoc

The short name of the interactor. It cannot be null or empty. Ex: brca2

Popular methods of Interactor

  • getAliases
    Collection of aliases for an interactor The Collection cannot be null and if the interactor does not
  • getAnnotations
    Collection of annotations for an interactor. The set cannot be null and if the interactor does not h
  • getIdentifiers
    Set of identifiers for this interactor. The identifiers can be from different databases, can be prim
  • getInteractorType
    The molecule type of this interactor. It is a controlled vocabulary term and cannot be null. Ex: pro
  • getOrganism
    The original source organism for this interactor. It can be null in case of chemical compounds/synth
  • getChecksums
    Set of checksums computed for this interactor. The Collection cannot be null so when an interactor d
  • getXrefs
    Collection of other xrefs that give more information about the interactor. Ex: GO references to give
  • getFullName
    The full name of the interactor. It can be null Ex: Breast cancer type 2 susceptibility protein
  • getPreferredIdentifier
    The identifier in the list of identifiers which is the preferred identifier. If no identifiers is pr
  • setFullName
    Sets the full name of the interactor
  • setOrganism
    Sets the source organism of this interactor
  • setInteractorType
    Sets the molecule type for this interactor If the given type is null, this method automatically sets
  • setOrganism,
  • setInteractorType,
  • setShortName

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