public Element createEndCertainStatus( UserSessionDownload session, Element parent ) { return createCertainStatus( session, parent, END_STATUS ); } }
public Element createStartStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType ) { return createStatus( session, parent, fuzzyType, START_STATUS ); }
CvObject2xmlPSI2.getInstance().createStartStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createStartCertainStatus( session, locationElement ); CvObject2xmlPSI2.getInstance().createEndStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createEndCertainStatus( session, locationElement );
Element element = getXmlFromCache( session, parent, cvObject ); createNames( session, element, cvObject ); createCvObjectXrefs( session, xrefElement, cvObject ); updateCache( session, parent, cvObject, element );
if ( hasPsiXref( cvObject, CvComponentRole.BAIT_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.PREY_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.NEUTRAL_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.SELF_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_TARGET_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else if ( hasPsiXref( cvObject, CvComponentRole.UNSPECIFIED_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else { createNames( session, element, newCvObject ); createCvObjectXrefs( session, xrefElement, newCvObject ); element.appendChild( xrefElement );
private Element createStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType, String tagName ) { Element element = session.createElement( tagName ); // 1. Generating names... createNames( session, element, fuzzyType ); // 2. generating xref... Element xrefElement = session.createElement( "xref" ); createCvObjectXrefs( session, xrefElement, fuzzyType ); if ( xrefElement.hasChildNodes() ) { element.appendChild( xrefElement ); } 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 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() ); } } }
CvObject2xmlPSI2.getInstance().createStartStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createStartCertainStatus( session, locationElement ); CvObject2xmlPSI2.getInstance().createEndStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createEndCertainStatus( session, locationElement );
Element element = getXmlFromCache( session, parent, cvObject ); createNames( session, element, cvObject ); createCvObjectXrefs( session, xrefElement, cvObject ); updateCache( session, parent, cvObject, element );
if ( hasPsiXref( cvObject, CvComponentRole.BAIT_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.PREY_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.NEUTRAL_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.SELF_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_TARGET_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else if ( hasPsiXref( cvObject, CvComponentRole.UNSPECIFIED_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getNeutral(); } else { createNames( session, element, newCvObject ); createCvObjectXrefs( session, xrefElement, newCvObject ); element.appendChild( xrefElement );
private Element createStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType, String tagName ) { Element element = session.createElement( tagName ); // 1. Generating names... createNames( session, element, fuzzyType ); // 2. generating xref... Element xrefElement = session.createElement( "xref" ); createCvObjectXrefs( session, xrefElement, fuzzyType ); if ( xrefElement.hasChildNodes() ) { element.appendChild( xrefElement ); } 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 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() ); } } }
CvObject2xmlPSI2.getInstance().createStartStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createStartCertainStatus( session, locationElement ); CvObject2xmlPSI2.getInstance().createEndStatus( session, locationElement, range.getFromCvFuzzyType() ); } else { CvObject2xmlPSI2.getInstance().createEndCertainStatus( session, locationElement );
Element element = getXmlFromCache( session, parent, cvObject ); createNames( session, element, cvObject ); createCvObjectXrefs( session, xrefElement, cvObject ); updateCache( session, parent, cvObject, element );
if ( hasPsiXref( cvObject, CvComponentRole.BAIT_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.PREY_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.NEUTRAL_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.SELF_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_TARGET_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.UNSPECIFIED_PSI_REF ) ) { newCvObject = cvObject; } else { createNames( session, element, newCvObject ); createCvObjectXrefs( session, xrefElement, newCvObject ); element.appendChild( xrefElement );
private Element createStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType, String tagName ) { Element element = session.createElement( tagName ); // 1. Generating names... createNames( session, element, fuzzyType ); // 2. generating xref... Element xrefElement = session.createElement( "xref" ); createCvObjectXrefs( session, xrefElement, fuzzyType ); if ( xrefElement.hasChildNodes() ) { element.appendChild( xrefElement ); } parent.appendChild( element ); return element; }
public Element createEndCertainStatus( UserSessionDownload session, Element parent ) { return createCertainStatus( session, parent, END_STATUS ); } }
public Element createStartStatus( UserSessionDownload session, Element parent, CvFuzzyType fuzzyType ) { return createStatus( session, parent, fuzzyType, START_STATUS ); }
/** * 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() ); } } }
if ( hasPsiXref( cvObject, CvComponentRole.BAIT_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.PREY_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.NEUTRAL_PSI_REF ) ) { newCvObject = IntactContext.getCurrentInstance().getCvContext().getUnspecified(); } else if ( hasPsiXref( cvObject, CvComponentRole.SELF_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.ENZYME_TARGET_PSI_REF ) ) { newCvObject = cvObject; } else if ( hasPsiXref( cvObject, CvComponentRole.UNSPECIFIED_PSI_REF ) ) { newCvObject = cvObject; } else { createNames( session, element, newCvObject ); createCvObjectXrefs( session, xrefElement, newCvObject ); element.appendChild( xrefElement );