/** * 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 ( !"experimentDescription".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a experimentDescription 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 ( !"proteinInteractor".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a proteinInteractorparent 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; }
ckeckParentName( parent ); createShortlabel( session, names, object ); createFullname( session, names, object );
/** * 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() ); } } }
/** * 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 CvObject2xmlI getInstance( UserSessionDownload session ) { if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) { return CvObject2xmlPSI1.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) { return CvObject2xmlPSI2.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) { // WE USE HERE THE PSI2 IMPLEMENTATION return CvObject2xmlPSI2.getInstance(); } else { throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() ); } } }
/** * 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 Experiment2xmlI getInstance( UserSessionDownload session ) { if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) { return Experiment2xmlPSI1.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) { return Experiment2xmlPSI2.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) { return Experiment2xmlPSI25.getInstance(); } else { throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() ); } } }
/** * 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 Confidence2xmlI getInstance( UserSessionDownload session ) { if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) { return Confidence2xmlPSI1.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) { return Confidence2xmlPSI2.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) { return Confidence2xmlPSI25.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 ( !"experimentDescription".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a experimentDescription 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 ( !"proteinInteractor".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a proteinInteractorparent 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; }
ckeckParentName( parent ); createShortlabel( session, names, object ); createFullname( session, names, object );
/** * 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; }
/** * 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() ); } } }
/** * 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 CvObject2xmlI getInstance( UserSessionDownload session ) { if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) { return CvObject2xmlPSI1.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) { return CvObject2xmlPSI2.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) { // WE USE HERE THE PSI2 IMPLEMENTATION return CvObject2xmlPSI2.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 ( !"experimentDescription".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a experimentDescription 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 ( !"proteinInteractor".equals( parent.getNodeName() ) ) { throw new IllegalArgumentException( "You must give a proteinInteractorparent 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; }
ckeckParentName( parent ); createShortlabel( session, names, object ); createFullname( session, names, object );
/** * 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; }
/** * 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() ); } } }
/** * 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 CvObject2xmlI getInstance( UserSessionDownload session ) { if ( session.getPsiVersion().equals( PsiVersion.VERSION_1 ) ) { return CvObject2xmlPSI1.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_2 ) ) { return CvObject2xmlPSI2.getInstance(); } else if ( session.getPsiVersion().equals( PsiVersion.VERSION_25 ) ) { // WE USE HERE THE PSI2 IMPLEMENTATION return CvObject2xmlPSI2.getInstance(); } else { throw new IllegalStateException( "We do not support PSI version " + session.getPsiVersion() ); } } }