Examples with Identifiable org.vcell.util.document.Identifiable used on opensource projects

Example 11 with Identifiable

use of org.vcell.util.document.Identifiable in project vcell by virtualcell.

the class MIRIAMAnnotationViewer method printResourceMappings.

public static String printResourceMappings(VCMetaData metaData) {
    StringBuffer strBuffer = new StringBuffer();
    strBuffer.append("\n\n ResourceMappings : \n");
    Set<Registry.Entry> entrySet = metaData.getRegistry().getAllEntries();
    for (Registry.Entry entry : entrySet) {
        Resource resource = entry.getResource();
        if (resource != null) {
            strBuffer.append(resource.stringValue());
            Identifiable identifiable = entry.getIdentifiable();
            strBuffer.append(" ============= " + metaData.getIdentifiableProvider().getVCID(identifiable).toASCIIString());
            strBuffer.append("\n");
        }
    }
    return strBuffer.toString();
}

Example 12 with Identifiable

use of org.vcell.util.document.Identifiable in project vcell by virtualcell.

the class MiriamTreeModel method annotationChanged.

public void annotationChanged(AnnotationEvent annotationEvent) {
    Identifiable identifiable = annotationEvent.getIdentifiable();
    // if identifiable is not null, then we can repair just the subtree for that identifiable
    createTree();
    fireTreeStructureChanged(this, getPathToRoot(((DefaultMutableTreeNode) getRoot())), null, null);
}

Example 13 with Identifiable

use of org.vcell.util.document.Identifiable in project vcell by virtualcell.

the class VCMetaDataMiriamManager method getDublinCoreDateMap.

// this is not yet cached.
public Map<Identifiable, Map<DateQualifier, Set<DublinCoreDate>>> getDublinCoreDateMap() {
    Map<Identifiable, Map<DateQualifier, Set<DublinCoreDate>>> map = new HashMap<Identifiable, Map<DateQualifier, Set<DublinCoreDate>>>();
    Set<Entry> allEntries = vcMetaData.getRegistry().getAllEntries();
    Graph rdfData = vcMetaData.getRdfData();
    for (Entry entry : allEntries) {
        Resource resource = entry.getResource();
        if (resource != null) {
            Identifiable identifiable = entry.getIdentifiable();
            Map<DateQualifier, Set<DublinCoreDate>> qualifierDateMap = new HashMap<DateQualifier, Set<DublinCoreDate>>();
            for (DublinCoreQualifier.DateQualifier dateQualifier : AnnotationQualifiers.DC_date_all) {
                Set<DublinCoreDate> dateStrings = new HashSet<DublinCoreDate>();
                Iterator<Statement> stmtIter = rdfData.match(resource, dateQualifier.getProperty(), null);
                while (stmtIter.hasNext()) {
                    Statement statement = stmtIter.next();
                    Value dateObject = statement.getObject();
                    if (dateObject instanceof Literal) {
                        Literal dateLiteral = (Literal) dateObject;
                        String dateString = dateLiteral.stringValue();
                        dateStrings.add(new DublinCoreDate(dateString));
                    }
                }
                if (!dateStrings.isEmpty()) {
                    qualifierDateMap.put(dateQualifier, dateStrings);
                }
            }
            if (!qualifierDateMap.isEmpty()) {
                map.put(identifiable, qualifierDateMap);
            }
        }
    }
    return map;
}

Example 14 with Identifiable

use of org.vcell.util.document.Identifiable in project vcell by virtualcell.

the class AnnotationMapping method getRefInfo.

private HashMap<String, String> getRefInfo(BioModel bioModel, Identifiable identifiable) {
    HashMap<String, String> info = new HashMap<String, String>();
    VCMetaData vcMetaData = bioModel.getVCMetaData();
    MiriamManager miriamManager = vcMetaData.getMiriamManager();
    TreeMap<Identifiable, Map<MiriamRefGroup, MIRIAMQualifier>> miriamDescrHeir = miriamManager.getMiriamTreeMap();
    Map<MiriamRefGroup, MIRIAMQualifier> refGroupMap = miriamDescrHeir.get(identifiable);
    if (refGroupMap != null) {
        for (MiriamRefGroup refGroup : refGroupMap.keySet()) {
            MIRIAMQualifier qualifier = refGroupMap.get(refGroup);
            String[] quaTemp = qualifier.toString().split("/");
            String bioQualifier = quaTemp[quaTemp.length - 1];
            bioQualifier = bioQualifier.substring(0, bioQualifier.length() - 1);
            for (MiriamResource miriamResource : refGroup.getMiriamRefs()) {
                String refSource = miriamResource.getMiriamURN();
                String[] temp = refSource.split(":");
                String sourceInfo = temp[2] + ":" + bioQualifier;
                String refId = miriamResource.getIdentifier();
                info.put(refId, sourceInfo);
            // System.out.println(refId + "*********" + sourceInfo);
            }
        }
    }
    return info;
}