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uk.ac.ebi.intact.application.dataConversion.psiDownload
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How to use uk.ac.ebi.intact.application.dataConversion.psiDownload

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiDownload (Showing top 20 results out of 315)

origin: uk.ac.ebi.intact.app/data-conversion

/**
 * Builds an empty PSI document of the specified version.
 *
 * @param session The user session that contains the requested PSI version.
 *
 * @return a XML Document representing an empty PSI document.
 */
public static Document buildPsiDocument( UserSessionDownload session ) {
  return buildPsiDocument( session, null );
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param component the component for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getParticipantId( UserSessionDownload session, Component component ) {
  long id = session.getParticipantIdentifier( component );
  return "" + id;
}
origin: uk.ac.ebi.intact.app/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getExperimentId( UserSessionDownload session, Experiment experiment ) {
  long id = session.getExperimentIdentifier( experiment );
  return "" + id;
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

/**
 * get the value what will be used as ID of the protein.
 *
 * @param interactor the interactor for which we need an ID.
 *
 * @return the ID of the protein.
 */
private String getInteractorId( UserSessionDownload session, Interactor interactor ) {
  long id = session.getInteractorIdentifier( interactor );
  return "" + id;
}
origin: uk.ac.ebi.intact.app/data-conversion

/**
 * Return the entry element of the PSI document. If the element doesn't exist, it is created.
 *
 * @return the source Element.
 */
public Element getEntryElement() {
  return getEntryElement( false );
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

public UserSessionDownload( PsiVersion psiVersion, Institution source ) {
  this.psiVersion = psiVersion;
  this.source = source;
  psiDocument = PsiDocumentFactory.buildPsiDocument( this, source );
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getParticipantId( UserSessionDownload session, Component component ) {
  long id = session.getParticipantIdentifier( component );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getExperimentId( UserSessionDownload session, Experiment experiment ) {
  long id = session.getExperimentIdentifier( experiment );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * get the value what will be used as ID of the protein.
 *
 * @param protein the protein for which we need an ID.
 *
 * @return the ID of the protein.
 */
private String getProteinId( UserSessionDownload session, Protein protein ) {
  long id = session.getInteractorIdentifier( protein );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * Return the entry element of the PSI document. If the element doesn't exist, it is created.
 *
 * @return the source Element.
 */
public Element getEntryElement() {
  return getEntryElement( false );
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

/**
 * Builds an empty PSI document of the specified version.
 *
 * @param session The user session that contains the requested PSI version.
 *
 * @return a XML Document representing an empty PSI document.
 */
public static Document buildPsiDocument(UserSessionDownload session) {
  return buildPsiDocument(session, null);
}
origin: uk.ac.ebi.intact.app/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getParticipantId( UserSessionDownload session, Component component ) {
  long id = session.getParticipantIdentifier( component );
  return "" + id;
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getExperimentId( UserSessionDownload session, Experiment experiment ) {
  long id = session.getExperimentIdentifier( experiment );
  return "" + id;
}
origin: uk.ac.ebi.intact.app/data-conversion

/**
 * get the value what will be used as ID of the protein.
 *
 * @param interactor the interactor for which we need an ID.
 *
 * @return the ID of the protein.
 */
private String getInteractorId( UserSessionDownload session, Interactor interactor ) {
  long id = session.getInteractorIdentifier( interactor );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * Builds an empty PSI document of the specified version.
 *
 * @param session The user session that contains the requested PSI version.
 *
 * @return a XML Document representing an empty PSI document.
 */
public static Document buildPsiDocument( UserSessionDownload session ) {
  return buildPsiDocument( session, null );
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getParticipantId( UserSessionDownload session, Component component ) {
  long id = session.getParticipantIdentifier( component );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getExperimentId( UserSessionDownload session, Experiment experiment ) {
  long id = session.getExperimentIdentifier( experiment );
  return "" + id;
}
origin: uk.ac.ebi.intact.util/data-conversion

public UserSessionDownload( PsiVersion psiVersion, Institution source ) {
  this.psiVersion = psiVersion;
  this.source = source;
  psiDocument = PsiDocumentFactory.buildPsiDocument( this, source );
}
origin: uk.ac.ebi.intact.app/data-conversion

/**
 * get the value what will be used as ID of the experiment.
 *
 * @param experiment the experiment for which we need an ID.
 *
 * @return the ID of the experiment.
 */
private String getParticipantId( UserSessionDownload session, Component component ) {
  long id = session.getParticipantIdentifier( component );
  return "" + id;
}
origin: uk.ac.ebi.intact.dataexchange.psimi.legacy/data-conversion

/**
 * Return a PSI document. Create a new wmpty one if it doesn't exists yet.
 *
 * @return a PSI document.
 */
public Document getPsiDocument() {
  if ( psiDocument == null ) {
    psiDocument = PsiDocumentFactory.buildPsiDocument( this );
  }
  return psiDocument;
}
uk.ac.ebi.intact.application.dataConversion.psiDownload

Most used classes

  • CvMapping
    Holds a Controlled Vocabulary Mapping. The mapping is loaded from a file and the CvMapping is then q
  • ExperimentDownload
    That class is not meant to be used in production but rather as a playground for PSI file generation.
  • PsiDocumentFactory
    TODO document this ;o)
  • UserSessionDownload
    User session for a PSI Download. Are stored here, everything we need to build efficiently a PSI doc
  • AbstractAnnotatedObject2xml
    Process common attributes of all AnnotatedObject. eg. shortlabel, fullname, Annotations, Xrefs
  • Annotation2xml,
  • BioSource2xmlCommons,
  • BioSource2xmlFactory,
  • BioSource2xmlI,
  • Component2xmlFactory,
  • Component2xmlI,
  • Confidence2xmlFactory,
  • Confidence2xmlI,
  • Cv2Source,
  • CvClass2Source,
  • CvObject2xmlCommons,
  • CvObject2xmlFactory,
  • CvObject2xmlI,
  • Experiment2xmlCommons
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