uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi2.Protein2xmlPSI2 java code examples

/**
 * Generates an proteinInteractorRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinInteractorRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinInteractorRef Element.
 */
public Element createProteinInteracorReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_INTERACTOR_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

element.setAttribute( "id", getProteinId( session, protein ) );
createNames( session, element, protein );
createProteinXrefs( session, element, protein );
createAttributeList( session, element, protein );

  /**
   * Gives the right version of the Psi XML generator according to the user's session
   *
   * @param session the user session that will indicate which version of the Psi generator is required
   *
   * @return
   */
  public static Protein2xmlI getInstance( UserSessionDownload session ) {

    if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) {

      return Protein2xmlPSI1.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) {

      return Protein2xmlPSI2.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() +
                       ". Please use Interactor2xmlPSI25 instead." );

    } else {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() );
    }
  }
}

element.setAttribute( "id", getProteinId( session, protein ) );
createNames( session, element, protein );
createProteinXrefs( session, element, protein );
createAttributeList( session, element, protein );

  /**
   * Gives the right version of the Psi XML generator according to the user's session
   *
   * @param session the user session that will indicate which version of the Psi generator is required
   *
   * @return
   */
  public static Protein2xmlI getInstance( UserSessionDownload session ) {

    if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) {

      return Protein2xmlPSI1.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) {

      return Protein2xmlPSI2.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() +
                       ". Please use Interactor2xmlPSI25 instead." );

    } else {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() );
    }
  }
}

element.setAttribute( "id", getProteinId( session, protein ) );
createNames( session, element, protein );
createProteinXrefs( session, element, protein );
createAttributeList( session, element, protein );

/**
 * Generates an proteinInteractorRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinInteractorRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinInteractorRef Element.
 */
public Element createProteinInteracorReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_INTERACTOR_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

  /**
   * Gives the right version of the Psi XML generator according to the user's session
   *
   * @param session the user session that will indicate which version of the Psi generator is required
   *
   * @return
   */
  public static Protein2xmlI getInstance( UserSessionDownload session ) {

    if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) {

      return Protein2xmlPSI1.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) {

      return Protein2xmlPSI2.getInstance();

    } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() +
                       ". Please use Interactor2xmlPSI25 instead." );

    } else {

      throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() );
    }
  }
}

/**
 * Generates an proteinParticipantRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinParticipantRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinParticipantRef Element.
 */
public Element createParticipantReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_PARTICIPANT_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Generates an proteinParticipantRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinParticipantRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinParticipantRef Element.
 */
public Element createParticipantReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_PARTICIPANT_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Generates an proteinParticipantRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinParticipantRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinParticipantRef Element.
 */
public Element createParticipantReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_PARTICIPANT_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_PARTICIPANT_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

/**
 * Generates an proteinInteractorRef out of an IntAct Protein.
 *
 * @param session
 * @param parent  the Element to which we will add the proteinInteractorRef.
 * @param protein the IntAct Protein that we convert to PSI.
 *
 * @return the generated proteinInteractorRef Element.
 */
public Element createProteinInteracorReference( UserSessionDownload session, Element parent, Protein protein ) {
  // TODO test that.
  // 1. Checking...
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null UserSessionDownload." );
  }
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null parent to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( protein == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + PROTEIN_INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( PROTEIN_INTERACTOR_REF_TAG_NAME );
  element.setAttribute( "ref", getProteinId( session, protein ) );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}

Javadoc

Process the common behaviour of an IntAct Protein when exporting PSI version 2.

Most used methods

createAttributeList
createNames
createProteinXrefs
Generate the xref tag of the given protein. That content is attached to the given parent Element.
getInstance
getProteinId
get the value what will be used as ID of the protein.

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How to useProtein2xmlPSI2 in uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi2

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