How to use uk.ac.ebi.intact.application.dataConversion.psiDownload.xmlGenerator.psi25

/**
 * Convert an annotatedObject annotations in to confidence value in PSI.
 *
 * @param session
 * @param parent          the Element to which we will attach the generated confidence.
 * @param annotatedObject the object from which we get the annotations.
 *
 * @return the generated confidence or null if none could be generated.
 */
public Element create( UserSessionDownload session, Element parent, AnnotatedObject annotatedObject ) {
  Element element = null;
  if ( annotatedObject instanceof Interaction ) {
    element = create( session, parent, annotatedObject, CvTopic.AUTHOR_CONFIDENCE );
  } else if ( annotatedObject instanceof Experiment ) {
    element = create( session, parent, annotatedObject, CvTopic.CONFIDENCE_MAPPING );
  } else {
    // error, type not supported.
    throw new UnsupportedOperationException( "a confidence can only be generated for an interaction or an experiemnt." );
  }
  return element;
}

public Element createHostOrganism( UserSessionDownload session,
                  Element parent,
                  BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + HOST_ORGANISM_TAG_NAME + "." );
  } else {
    if ( !HOST_ORGANISM_PARENT_NODE.equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( parent.getNodeName() + " found, you must give a " +
                        HOST_ORGANISM_PARENT_NODE + " to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  Element element = getHostOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, HOST_ORGANISM_TAG_NAME );
    updateHostOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

public Element createOrganism( UserSessionDownload session,
                Element parent,
                BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + ORGANISM_TAG_NAME + "." );
  } else {
    if ( !"interactor".equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( "You must give a interactor parent to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null session." );
  }
  Element element = getOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, ORGANISM_TAG_NAME );
    updateOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

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

  private Element createParticipant( UserSessionDownload session, Element parent, Interactor interactor, Feature feature ) {

    Element participantElement = session.createElement( "participant" );

    Feature2xmlPSI25 f2xml = (Feature2xmlPSI25) Feature2xmlFactory.getInstance( session );
    f2xml.createReference( session, participantElement, feature );

    parent.appendChild( participantElement );

    return participantElement;
  }
}

  /**
   * 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 AbstractXref2Xml getInstance( UserSessionDownload session ) {

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI2.getInstance();

    } else {

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

  private Element createConfidenceElement(UserSessionDownload session, CvObject unit, Object value) {
    Element confidenceElement = session.createElement(CONFIDENCE_TAG_NAME);

    // 2. Generating Unit...
    Element unitElement = session.createElement(CONFIDENCE_UNIT_TAG_NAME);
    createNames(session, unitElement, unit);
    confidenceElement.appendChild(unitElement);

    // TODO check if it has MI reference, if so export them as xref of the confidence.unit.

    // 3. Generating value...
    Element valueElement = session.createElement(CONFIDENCE_VALUE_TAG_NAME);
    Text valueTextElement = session.createTextNode((String)value);
    valueElement.appendChild(valueTextElement);
    confidenceElement.appendChild(valueElement);
    return confidenceElement;
  }
}

public Element createHostOrganism( UserSessionDownload session,
                  Element parent,
                  BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + HOST_ORGANISM_TAG_NAME + "." );
  } else {
    if ( !HOST_ORGANISM_PARENT_NODE.equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( parent.getNodeName() + " found, you must give a " +
                        HOST_ORGANISM_PARENT_NODE + " to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  Element element = getHostOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, HOST_ORGANISM_TAG_NAME );
    updateHostOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

public Element createOrganism( UserSessionDownload session,
                Element parent,
                BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + ORGANISM_TAG_NAME + "." );
  } else {
    if ( !"interactor".equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( "You must give a interactor parent to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null session." );
  }
  Element element = getOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, ORGANISM_TAG_NAME );
    updateOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

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

/**
 * Convert an annotatedObject annotations in to confidence value in PSI.
 *
 * @param session
 * @param parent          the Element to which we will attach the generated confidence.
 * @param annotatedObject the object from which we get the annotations.
 *
 * @return the generated confidence or null if none could be generated.
 */
public Element create( UserSessionDownload session, Element parent, AnnotatedObject annotatedObject ) {
  Element element = null;
  if ( annotatedObject instanceof Interaction ) {
    element = create( session, parent, annotatedObject, CvTopic.AUTHOR_CONFIDENCE );
  } else if ( annotatedObject instanceof Experiment ) {
    element = create( session, parent, annotatedObject, CvTopic.CONFIDENCE_MAPPING );
  } else {
    // error, type not supported.
    throw new UnsupportedOperationException( "a confidence can only be generated for an interaction or an experiemnt." );
  }
  return element;
}

  private Element createParticipant( UserSessionDownload session, Element parent, Interactor interactor, Feature feature ) {

    Element participantElement = session.createElement( "participant" );

    Feature2xmlPSI25 f2xml = (Feature2xmlPSI25) Feature2xmlFactory.getInstance( session );
    f2xml.createReference( session, participantElement, feature );

    parent.appendChild( participantElement );

    return participantElement;
  }
}

  /**
   * 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 AbstractXref2Xml getInstance( UserSessionDownload session ) {

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI2.getInstance();

    } else {

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

public Element createHostOrganism( UserSessionDownload session,
                  Element parent,
                  BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + HOST_ORGANISM_TAG_NAME + "." );
  } else {
    if ( !HOST_ORGANISM_PARENT_NODE.equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( parent.getNodeName() + " found, you must give a " +
                        HOST_ORGANISM_PARENT_NODE + " to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  Element element = getHostOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, HOST_ORGANISM_TAG_NAME );
    updateHostOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

public Element createOrganism( UserSessionDownload session,
                Element parent,
                BioSource bioSource ) {
  if ( parent == null ) {
    throw new IllegalArgumentException( "You must give a non null BioSource to build a " + ORGANISM_TAG_NAME + "." );
  } else {
    if ( !"interactor".equals( parent.getNodeName() ) ) {
      throw new IllegalArgumentException( "You must give a interactor parent to build a " + ORGANISM_TAG_NAME + "." );
    }
  }
  if ( session == null ) {
    throw new IllegalArgumentException( "You must give a non null session." );
  }
  Element element = getOrganismFromCache( session, bioSource );
  if ( element == null ) {
    element = create( session, parent, bioSource, ORGANISM_TAG_NAME );
    updateOrganismCache( session, bioSource, element );
  } else {
    parent.appendChild( element );
  }
  return element;
}

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

/**
 * Convert an annotatedObject annotations in to confidence value in PSI.
 *
 * @param session
 * @param parent          the Element to which we will attach the generated confidence.
 * @param annotatedObject the object from which we get the annotations.
 *
 * @return the generated confidence or null if none could be generated.
 */
public Element create( UserSessionDownload session, Element parent, AnnotatedObject annotatedObject ) {
  Element element = null;
  if ( annotatedObject instanceof Interaction ) {
    element = create( session, parent, annotatedObject, CvTopic.AUTHOR_CONFIDENCE );
  } else if ( annotatedObject instanceof Experiment ) {
    element = create( session, parent, annotatedObject, CvTopic.CONFIDENCE_MAPPING );
  } else {
    // error, type not supported.
    throw new UnsupportedOperationException( "a confidence can only be generated for an interaction or an experiemnt." );
  }
  return element;
}

  private Element createParticipant( UserSessionDownload session, Element parent, Interactor interactor, Feature feature ) {

    Element participantElement = session.createElement( "participant" );

    Feature2xmlPSI25 f2xml = (Feature2xmlPSI25) Feature2xmlFactory.getInstance( session );
    f2xml.createReference( session, participantElement, feature );

    parent.appendChild( participantElement );

    return participantElement;
  }
}

  /**
   * 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 AbstractXref2Xml getInstance( UserSessionDownload session ) {

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI1.getInstance();

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

      return Xref2xmlPSI2.getInstance();

    } else {

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

/**
 * Generates an interactorRef out of an IntAct interactor.
 *
 * @param session
 * @param parent     the Element to which we will add the interactorRef.
 * @param interactor the IntAct interactor that we convert to PSI.
 *
 * @return the generated interactorRef Element.
 */
public Element createInteractorReference( UserSessionDownload session, Element parent, Interactor interactor ) {
  // 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 " + INTERACTOR_REF_TAG_NAME + "." );
  }
  if ( interactor == null ) {
    throw new IllegalArgumentException( "You must give a non null protein to build an " + INTERACTOR_REF_TAG_NAME + "." );
  }
  // 2. Initialising the element...
  Element element = session.createElement( INTERACTOR_REF_TAG_NAME );
  Text refText = session.createTextNode( getInteractorId( session, interactor ) );
  element.appendChild( refText );
  // 3. Attaching the newly created element to the parent...
  parent.appendChild( element );
  return element;
}