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

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

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}
origin: psidev.psi.mi/psi25-xml

public static Range createRangeCertain(long startPosition, long endPosition) {
  Position start = new Position(startPosition);
  Position end = new Position(endPosition);
  return new Range(createRangeStatusCertain(), start, createRangeStatusCertain(), end);
}
origin: psidev.psi.mi/psi25-xml

public static Bibref createBibref(String publicationId, String dbAc, String dbName) {
  DbReference dbReference = createDbReference(publicationId, dbAc, dbName, "MI:0358", "primary-reference");
  Xref xref = new Xref(dbReference);
  return new Bibref(xref);
}
origin: psidev.psi.mi/psi25-xml

public static <C extends CvType> C createCvType(Class<C> cvTypeClass, String miRef, String label) {
  C cv = createCvType(cvTypeClass, label);
  cv.setXref(createXrefPsiMi(miRef));
  return cv;
}
origin: uk.ac.ebi.intact.dataexchange.psimi/intact-psixml-converters

  protected Object psiElementKey(Source psiObject) {
    String key;

    if (psiObject.getNames() != null) {
      key = "source:"+psiObject.getNames().getShortLabel();
    } else if (psiObject.getXref() != null) {
      key = "source:xref:"+psiObject.getXref().getPrimaryRef().getId();
    } else if (psiObject.getBibref() != null) {
      key = "source:bibref:"+psiObject.getBibref().getXref().getPrimaryRef().getId();
    } else {
      throw new PsiConversionException("Could not create key to cache the source: "+psiObject);
    }

    return key;

  }
}
origin: psidev.psi.mi/psi25-xml

public static Interactor createInteractor(String primaryId, String dbMi, InteractorType interactorType, Organism organism) {
  Interactor interactor = new Interactor();
  assignNextId(interactor);
  interactor.setNames(createNames(primaryId, null));
  interactor.setInteractorType(interactorType);
  interactor.setOrganism(organism);
  interactor.setXref(createXrefIdentity(primaryId, dbMi, dbMi));
  return interactor;
}
origin: psidev.psi.mi/psimitab

  /**
   * Get the interactor's shortlabel.
   * @param interactor
   * @return the name of null of no shortlabel available.
   */
  private String getName(Interactor interactor) {
    if( interactor.getNames() != null ) {
      if ( interactor.getNames().hasShortLabel() ) {
        return interactor.getNames().getShortLabel();
      }
    }

    return null;
  }
}
origin: psidev.psi.mi/psi25-xml

public Range( RangeStatus startStatus, Position begin, RangeStatus endStatus, Position end ) {
  setStartStatus( startStatus );
  setBegin( begin );
  setEndStatus( endStatus );
  setEnd( end );
}
origin: psidev.psi.mi/psi25-xml

public static Source createSource(String name, String description, String sourcePublicationId, String miId) {
  Source source = new Source();
  Names names = createNames(name, description);
  source.setNames(names);
  if (miId != null) {
    Xref miRef = createXrefPsiMi(miId);
    source.setXref(miRef);
  }
  if (sourcePublicationId != null) {
    source.setBibref(createBibrefPubmed(sourcePublicationId));
  }
  return source;
}
origin: psidev.psi.mi/psi25-xml

public static Organism createOrganism(int taxid, String name) {
  Organism organism = new Organism();
  organism.setNames(createNames(name, null));
  organism.setNcbiTaxId(taxid);
  return organism;
}
origin: psidev.psi.mi/psi25-xml

/**
 * 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;
}
origin: psidev.psi.mi/psi25-xml

public static Xref createXrefIdentity(String primaryId, String dbMi, String dbName) {
  Xref xref = new Xref();
  xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, "MI:0356", "identity"));
  return xref;
}
origin: psidev.psi.mi/psi25-xml

public static Range createRange(RangeStatus startStatus, RangeStatus endStatus, long startPosition, long endPosition) {
  Position start = new Position(startPosition);
  Position end = new Position(endPosition);
  return new Range(startStatus, start, endStatus, end);
}
origin: psidev.psi.mi/psi25-xml

public static DbReference createDbReferencePsiMi(String psiMiRef) {
  DbReference ref = createDbReferenceIdentity(psiMiRef, "MI:0488", "psi-mi");
  ref.setId(psiMiRef);
  return ref;
}
origin: psidev.psi.mi/psi25-xml

public static InteractorType createInteractorType(String mi, String name) {
  InteractorType intType = createCvType(InteractorType.class, name);
  intType.setXref(createXrefPsiMi(mi));
  return intType;
}
origin: psidev.psi.mi/psi25-xml

public static Confidence createConfidence(String value, String unitMi, String unitName){
  Unit unit = createCvType( Unit.class, unitMi, unitName);
  return new Confidence(unit, value);
}
origin: psidev.psi.mi/psi25-xml

  @Override
  public int hashCode() {
    int result = 31;
    //result = (names != null ? names.hashCode() : 0);
    result = 31 * result + ( xref != null ? xref.hashCode() : 0 );
    result = 31 * result + ( interactorType != null ? interactorType.hashCode() : 0 );
    result = 31 * result + ( organism != null ? organism.hashCode() : 0 );
    result = 31 * result + ( sequence != null ? sequence.hashCode() : 0 );
    return result;
  }
}
origin: psidev.psi.mi/psi25-xml

  @Override
  public int hashCode() {
    int result;
    result = ( names != null ? names.hashCode() : 0 );
    result = 29 * result + ( xref != null ? xref.hashCode() : 0 );
    return result;
  }
}
origin: psidev.psi.mi/psi25-xml

  @Override
  public int hashCode() {
    int result;
    result = id;
    result = 29 * result + ( bibref != null ? bibref.hashCode() : 0 );
    result = 29 * result + ( interactionDetectionMethod != null ? interactionDetectionMethod.hashCode() : 0 );
    return result;
  }
}
origin: psidev.psi.mi/psi25-xml

  @Override
  public int hashCode() {
    int result;
    result = ( participant != null ? participant.hashCode() : 0 );
    result = 29 * result + ( feature != null ? feature.hashCode() : 0 );
    return result;
  }
}
origin: psidev.psi.mi/psi25-xml

public static Xref createXref(String primaryId, String dbMi, String dbName, String qualifierMi, String qualifierName) {
  Xref xref = new Xref();
  xref.setPrimaryRef(createDbReference(primaryId, dbMi, dbName, qualifierMi, qualifierName));
  return xref;
}
psidev.psi.mi.xml.model

Most used classes

  • Entry
    Java class for anonymous complex type. The following schema fragment specifies the expected conte
  • EntrySet
    Root element of the Molecular Interaction Format Java class for entrySet element declaration. Th
  • ExperimentDescription
    Describes one set of experimental parameters. Java class for experimentType complex type. The fo
  • Interaction
  • Participant
    A molecule participating in an interaction. Java class for participantType complex type. The fol
  • Alias,
  • Attribute,
  • Bibref,
  • DbReference,
  • Interactor,
  • InteractorType,
  • Names,
  • Organism,
  • Xref,
  • Confidence,
  • CvType,
  • Feature,
  • Interval,
  • Range
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