uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag.getOrganism java code examples

Common ways to obtain ProteinInteractorTag

private void myMethod () {
 ProteinInteractorTag p =Conversion.psiUpload.model.ProteinParticipantTag proteinParticipant;proteinParticipant.getProteinInteractor()
Map map;Object key;(ProteinInteractorTag) map.get(key)
Conversion.psiUpload.parser.ParticipantListParser participantListParser;Object key;(ProteinInteractorTag) participantListParser.getInteractors().get(key)
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}

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}

  /**
   * Get an Intact Protein out of a ProteinInteractorTag.
   *
   * @param proteinParticipant
   *
   * @return the IntAct Protein correcponding to the given ProteinParticipantTag.
   */
  private static ProteinHolder getProtein( final ProteinParticipantTag proteinParticipant ) {

    final ProteinInteractorTag proteinInteractor = proteinParticipant.getProteinInteractor();

    OrganismTag organism = proteinInteractor.getOrganism();
    BioSource bioSource = null;
    if ( organism != null ) {
      bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
    }

    String proteinId = proteinInteractor.getPrimaryXref().getId();
    String db = proteinInteractor.getPrimaryXref().getDb();

//        System.out.println( "Search interactor (" + proteinInteractor.getShortlabel() + ") from cache(" +
//                            proteinId + ", " + db + ", " + bioSource.getShortLabel() + ")" );

    return ProteinInteractorChecker.getProtein( proteinId, db, bioSource );
  }
}

  uniprotID = proteinInteractor.getPrimaryXref().getId();
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();

  uniprotID = proteinInteractor.getPrimaryXref().getId();
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();

  uniprotID = proteinInteractor.getPrimaryXref().getId();
if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();

if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();
} else {
  taxid = "taxid not specified";

if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();
} else {
  taxid = "taxid not specified";

if ( proteinInteractor != null && proteinInteractor.getOrganism() != null ) {
  taxid = proteinInteractor.getOrganism().getTaxId();
} else {
  taxid = "taxid not specified";

           final BioSourceFactory bioSourceFactory ) {
final OrganismTag organism = proteinInteractor.getOrganism();
String taxId = null;
if ( organism != null ) {

           final BioSourceFactory bioSourceFactory ) {
final OrganismTag organism = proteinInteractor.getOrganism();
String taxId = null;
if ( organism != null ) {

           final BioSourceFactory bioSourceFactory ) {
final OrganismTag organism = proteinInteractor.getOrganism();
String taxId = null;
if ( organism != null ) {

    if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) {
               proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
               proteinId + "):";
  BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
  if ( bioSource == null ) {
    String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
         proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
         proteinId + "). Reason: " + ie.getMessage();
ie.printStackTrace();

    if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) {
               proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
               proteinId + "):";
  BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
  if ( bioSource == null ) {
    String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
         proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
         proteinId + "). Reason: " + ie.getMessage();
ie.printStackTrace();

    if ( protein1.getBioSource().getTaxId().equals( proteinInteractor.getOrganism().getTaxId() ) ) {
               proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
               proteinId + "):";
  BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
  if ( bioSource == null ) {
    String message = "Could not find a BioSource using the definition: " + proteinInteractor.getOrganism();
         proteinInteractor.getOrganism().getTaxId() + ") and Xref: " + db + "(" +
         proteinId + "). Reason: " + ie.getMessage();
ie.printStackTrace();

final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();

final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();

final BioSource bioSource = OrganismChecker.getBioSource( proteinInteractor.getOrganism() );
final String proteinId = proteinInteractor.getPrimaryXref().getId();
final String db = proteinInteractor.getPrimaryXref().getDb();

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How to use getOrganismmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag.getOrganism (Showing top 18 results out of 315)

How to use
getOrganism
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag