/** * Generate the confidence for the given annotatedObject according to the PSI version specified in the session. * * @param session * @param parent the parent Element to which we will attach the generated element. * @param object the object from which we will get the confidence values. * * @return the generated Element or null if none could be generated. */ protected Element createConfidence( UserSessionDownload session, Element parent, AnnotatedObject object ) { Confidence2xmlI confidence = Confidence2xmlFactory.getInstance( session ); return confidence.create( session, parent, object ); }
/** * Generate the xref tag of the given protein. That content is attached to the given parent Element. * * @param session * @param parent the proteinInteractor Element to which we will attach the Xref Element and its content. * @param protein the protein from which we get the Xref that will be used to generate the PSI XML. * * @return the xref tag and its attached content. */ private Element createProteinXrefs( UserSessionDownload session, Element parent, Protein protein ) { return Protein2xmlCommons.getInstance().createProteinXrefs( session, parent, protein ); }
/** * Generate an filled attributeList based upon the annotation of the given AnnotatedObject. * * @param session * @param parent the Element to which we will attach the newly generated AttributeList. * @param object the Annotated object from which we generate the attributes. * * @return a newly created attributeList or null if none were created. */ protected Element createAttributeList( UserSessionDownload session, Element parent, AnnotatedObject object ) { return createAttributeList( session, parent, object, null ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * get the value what will be used as ID of the smallMolecule. * * @param smallMolecule the protein for which we need an ID. * * @return the ID of the protein. */ private String getSmallMoleculeId( SmallMolecule smallMolecule ) { return SmallMolecule2xmlCommons.getInstance().getSmallMoleculeId( smallMolecule ); }
/** * Create PSI Xrefs from an IntAct cvObject. <br> Put Xref(psi-mi, identity) as primaryRef, any other as * secondaryRef. <br> If not psi-mi available, take randomly an other one. * * @param session * @param parent the DOM element to which we will add the newly generated PSI Xref. * @param cvObject the cvObject from which we get the Xref to generate. */ private void createCvObjectXrefs( UserSessionDownload session, Element parent, CvObject cvObject ) { CvObject2xmlCommons.getInstance().createCvObjectXrefs( session, parent, cvObject ); }
/** * Generate the xref tag of the given smallMolecule. That content is attached to the given parent Element. * * @param session * @param parent the proteinInteractor Element to which we will attach the Xref Element and its content. * @param smallMolecule the smallMolecule from which we get the Xref that will be used to generate the PSI XML. * * @return the xref tag and its attached content. */ private Element createSmallMoleculeXrefs( UserSessionDownload session, Element parent, SmallMolecule smallMolecule ) { return SmallMolecule2xmlCommons.getInstance().createSmallMoleculeXrefs( session, parent, smallMolecule ); }
/** * 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( Experiment experiment ) { return Experiment2xmlCommons.getInstance().getExperimentId( experiment ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * Generate the confidence for the given annotatedObject according to the PSI version specified in the session. * * @param session * @param parent the parent Element to which we will attach the generated element. * @param object the object from which we will get the confidence values. * * @return the generated Element or null if none could be generated. */ protected Element createConfidence( UserSessionDownload session, Element parent, AnnotatedObject object ) { Confidence2xmlI confidence = Confidence2xmlFactory.getInstance( session ); return confidence.create( session, parent, object ); }
/** * Generate the xref tag of the given protein. That content is attached to the given parent Element. * * @param session * @param parent the proteinInteractor Element to which we will attach the Xref Element and its content. * @param protein the protein from which we get the Xref that will be used to generate the PSI XML. * * @return the xref tag and its attached content. */ private Element createProteinXrefs( UserSessionDownload session, Element parent, Protein protein ) { return Protein2xmlCommons.getInstance().createProteinXrefs( session, parent, protein ); }
/** * get the value what will be used as ID of the smallMolecule. * * @param smallMolecule the protein for which we need an ID. * * @return the ID of the protein. */ private String getSmallMoleculeId( SmallMolecule smallMolecule ) { return SmallMolecule2xmlCommons.getInstance().getSmallMoleculeId( smallMolecule ); }
/** * Generate an filled attributeList based upon the annotation of the given AnnotatedObject. * * @param session * @param parent the Element to which we will attach the newly generated AttributeList. * @param object the Annotated object from which we generate the attributes. * * @return a newly created attributeList or null if none were created. */ protected Element createAttributeList( UserSessionDownload session, Element parent, AnnotatedObject object ) { return createAttributeList( session, parent, object, null ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * Generate the confidence for the given annotatedObject according to the PSI version specified in the session. * * @param session * @param parent the parent Element to which we will attach the generated element. * @param object the object from which we will get the confidence values. * * @return the generated Element or null if none could be generated. */ protected Element createConfidence( UserSessionDownload session, Element parent, AnnotatedObject object ) { Confidence2xmlI confidence = Confidence2xmlFactory.getInstance( session ); return confidence.create( session, parent, object ); }
/** * Generate the xref tag of the given protein. That content is attached to the given parent Element. * * @param session * @param parent the proteinInteractor Element to which we will attach the Xref Element and its content. * @param protein the protein from which we get the Xref that will be used to generate the PSI XML. * * @return the xref tag and its attached content. */ private Element createProteinXrefs( UserSessionDownload session, Element parent, Protein protein ) { return Protein2xmlCommons.getInstance().createProteinXrefs( session, parent, protein ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }
/** * Generate and add to the given element the Xrefs of the feature. * * @param session * @param parent The element to which we add the xref tag and its content. * @param feature the IntAct feature from which we get the Xrefs. */ private static void createFeatureXrefs( UserSessionDownload session, Element parent, Feature feature ) { Feature2xmlCommons.getInstance().createFeatureXrefs( session, parent, feature ); }