import java.util.HashSet;
import java.util.List;
import java.util.Map;
-import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
import eu.etaxonomy.cdm.api.service.IOccurrenceService;
-import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.CdmBase;
-import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
private DerivateLabelProvider labelProvider;
- private Set<SingleRead> multiLinkSingleReads;
-
private DerivateContentProvider contentProvider;
private DerivateSearchCompositeController derivateSearchCompositeController;
* Refreshes the derivate hierarchy tree
*/
public void refreshTree(){
- generateMultiLinkSingleReads();
- labelProvider.setMultiLinkSingleReads(multiLinkSingleReads);
+ //refresh typedesignations
+ labelProvider.refresh();
viewer.refresh();
}
viewer.setInput(rootElements);
}
- private void generateMultiLinkSingleReads() {
- Set<SingleRead> multiLinkSingleReads = new HashSet<SingleRead>();
- for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
- if(entry.getValue().size()>1){
- multiLinkSingleReads.add(entry.getKey());
- }
- }
- this.multiLinkSingleReads = multiLinkSingleReads;
- }
-
/**
* @return a set of {@link SingleRead}s that have multiple parents
*/
public Set<SingleRead> getMultiLinkSingleReads() {
- return this.multiLinkSingleReads;
+ return DerivateLabelProvider.getMultiLinkSingleReads();
}
public Object getSelectionInput() {
*/
package eu.etaxonomy.taxeditor.view.derivateSearch;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
import java.util.Set;
import java.util.UUID;
import org.hibernate.LazyInitializationException;
import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
+import eu.etaxonomy.cdm.api.service.IOccurrenceService;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.DefinedTerm;
import eu.etaxonomy.cdm.model.molecular.DnaSample;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
+import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
+import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
- private Set<SingleRead> multiLinkSingleReads;
+ private static Set<SingleRead> multiLinkSingleReads;
+
+ private static Map<DerivedUnit, List<SpecimenTypeDesignation>> typeDesignations;
private ConversationHolder conversation;
else if(derivate instanceof DerivedUnit){
DerivedUnit derivedUnit = (DerivedUnit)derivate;
if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
+ //check for type designation
+ if(typeDesignations.isEmpty()){
+ for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
+ addTypeDesignation(derivedUnit, specimenTypeDesignation);
+ }
+ }
//java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
//TODO : This is not generic anymore for performance reasons
Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
}
String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
+ //type designation extension
+ List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
+ if(list!=null){
+ for (SpecimenTypeDesignation specimenTypeDesignation : list) {
+ label += "("+specimenTypeDesignation.getTypeStatus()+" of ";
+ for (TaxonNameBase taxonNameBase : specimenTypeDesignation.getTypifiedNames()) {
+ label += taxonNameBase+separator;
+ }
+ if(label.endsWith(separator)){
+ label = label.substring(0, label.length()-separator.length());
+ }
+ label += ")";
+ }
+ }
}
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
//TissueSample should only be created by using it's own class
return label;
}
- /* (non-Javadoc)
- * @see org.eclipse.jface.viewers.ColumnLabelProvider#getImage(java.lang.Object)
- */
@Override
public Image getImage(Object element) {
if(element instanceof TreeNode){
}
/**
- * @param multiLinkSingleReads2
+ * Refreshes cached label extensions
+ * @param multiLinkSingleReads
*/
- public void setMultiLinkSingleReads(Set<SingleRead> multiLinkSingleReads) {
- this.multiLinkSingleReads = multiLinkSingleReads;
+ public void refresh() {
+ this.multiLinkSingleReads = new HashSet<SingleRead>();
+ for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
+ if(entry.getValue().size()>1){
+ multiLinkSingleReads.add(entry.getKey());
+ }
+ }
+ this.typeDesignations = new HashMap<DerivedUnit, List<SpecimenTypeDesignation>>();
+ }
+
+ private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
+ List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
+ if(list==null){
+ list = new ArrayList<SpecimenTypeDesignation>();
+ }
+ list.add(typeDesignation);
+ typeDesignations.put(derivedUnit, list);
+ }
+
+ public static Set<SingleRead> getMultiLinkSingleReads() {
+ return multiLinkSingleReads;
}
}