|
1
|
// $Id$
|
|
2
|
/**
|
|
3
|
* Copyright (C) 2013 EDIT
|
|
4
|
* European Distributed Institute of Taxonomy
|
|
5
|
* http://www.e-taxonomy.eu
|
|
6
|
*
|
|
7
|
* The contents of this file are subject to the Mozilla Public License Version 1.1
|
|
8
|
* See LICENSE.TXT at the top of this package for the full license terms.
|
|
9
|
*/
|
|
10
|
package eu.etaxonomy.taxeditor.view.derivateSearch;
|
|
11
|
|
|
12
|
import java.util.ArrayList;
|
|
13
|
import java.util.Collection;
|
|
14
|
import java.util.HashMap;
|
|
15
|
import java.util.HashSet;
|
|
16
|
import java.util.List;
|
|
17
|
import java.util.Map;
|
|
18
|
import java.util.Map.Entry;
|
|
19
|
import java.util.Set;
|
|
20
|
import java.util.UUID;
|
|
21
|
|
|
22
|
import org.eclipse.jface.viewers.ColumnLabelProvider;
|
|
23
|
import org.eclipse.jface.viewers.TreeNode;
|
|
24
|
import org.eclipse.swt.graphics.Image;
|
|
25
|
import org.hibernate.LazyInitializationException;
|
|
26
|
|
|
27
|
import eu.etaxonomy.cdm.api.conversation.ConversationHolder;
|
|
28
|
import eu.etaxonomy.cdm.api.service.IOccurrenceService;
|
|
29
|
import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
|
|
30
|
import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
|
|
31
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
32
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
|
33
|
import eu.etaxonomy.cdm.model.common.Identifier;
|
|
34
|
import eu.etaxonomy.cdm.model.molecular.DnaSample;
|
|
35
|
import eu.etaxonomy.cdm.model.molecular.Sequence;
|
|
36
|
import eu.etaxonomy.cdm.model.molecular.SingleRead;
|
|
37
|
import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
|
|
38
|
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
|
|
39
|
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
|
|
40
|
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
|
|
41
|
import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
|
|
42
|
import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
|
|
43
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
|
|
44
|
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
|
|
45
|
import eu.etaxonomy.taxeditor.model.ImageResources;
|
|
46
|
import eu.etaxonomy.taxeditor.store.CdmStore;
|
|
47
|
|
|
48
|
/**
|
|
49
|
* Label provider for the views to show {@link SpecimenOrObservationBase}s.<br>
|
|
50
|
* <br>
|
|
51
|
* <b>Note:</b> If you use this label provider you need to assure that you
|
|
52
|
* created a {@link ConversationHolder} resp. have an open session because
|
|
53
|
* the labels are generated from various fields of the derivate hierarchy which
|
|
54
|
* are lazy loaded and could therefore throw a {@link LazyInitializationException}.<br>
|
|
55
|
* Use <b>{@link #setConversation(ConversationHolder)}</b> to assign the session to this provider.
|
|
56
|
*/
|
|
57
|
public class DerivateLabelProvider extends ColumnLabelProvider {
|
|
58
|
|
|
59
|
private static final String NO_SAMPLE_DESIGNATION = "[no sample designation]";
|
|
60
|
|
|
61
|
private static Set<SingleRead> multiLinkSingleReads;
|
|
62
|
|
|
63
|
private static Map<DerivedUnit, List<SpecimenTypeDesignation>> typeDesignations;
|
|
64
|
|
|
65
|
private ConversationHolder conversation;
|
|
66
|
|
|
67
|
private static DefinedTerm photoTerm = null;
|
|
68
|
private static DefinedTerm drawingTerm = null;
|
|
69
|
private static DefinedTerm specimenScanTerm = null;
|
|
70
|
private static DefinedTerm detailImageTerm = null;
|
|
71
|
private static DefinedTerm sampleDesignationTerm = null;
|
|
72
|
|
|
73
|
//FIXME: move static term getters to new singleton utility class
|
|
74
|
private static void initializeTerms() {
|
|
75
|
List<DefinedTerm> preferredTerms = CdmStore.getTermManager().getPreferredTerms(DefinedTerm.class);
|
|
76
|
for (DefinedTerm definedTerm : preferredTerms) {
|
|
77
|
if(definedTerm.getUuid().equals(UUID.fromString("c5c59c42-f254-471e-96c6-09f459f7c903"))){
|
|
78
|
photoTerm = definedTerm;
|
|
79
|
}
|
|
80
|
else if(definedTerm.getUuid().equals(UUID.fromString("669b0409-4aa4-4695-aae4-a95ed27bad4c"))){
|
|
81
|
drawingTerm = definedTerm;
|
|
82
|
}
|
|
83
|
else if(definedTerm.getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
|
|
84
|
specimenScanTerm = definedTerm;
|
|
85
|
}
|
|
86
|
else if(definedTerm.getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
|
|
87
|
detailImageTerm = definedTerm;
|
|
88
|
}
|
|
89
|
else if(definedTerm.getUuid().equals(UUID.fromString("fadeba12-1be3-4bc7-9ff5-361b088d86fc"))){
|
|
90
|
sampleDesignationTerm = definedTerm;
|
|
91
|
}
|
|
92
|
}
|
|
93
|
}
|
|
94
|
|
|
95
|
public static DefinedTerm getLivingPlantPhotoTerm(){
|
|
96
|
if(photoTerm==null){
|
|
97
|
initializeTerms();
|
|
98
|
}
|
|
99
|
return photoTerm;
|
|
100
|
}
|
|
101
|
|
|
102
|
public static DefinedTerm getArtworkTerm(){
|
|
103
|
if(drawingTerm==null){
|
|
104
|
initializeTerms();
|
|
105
|
}
|
|
106
|
return drawingTerm;
|
|
107
|
}
|
|
108
|
|
|
109
|
public static DefinedTerm getSpecimenScanTerm(){
|
|
110
|
if(specimenScanTerm==null){
|
|
111
|
initializeTerms();
|
|
112
|
}
|
|
113
|
return specimenScanTerm;
|
|
114
|
}
|
|
115
|
|
|
116
|
public static DefinedTerm getDetailImageTerm(){
|
|
117
|
if(detailImageTerm==null){
|
|
118
|
initializeTerms();
|
|
119
|
}
|
|
120
|
return detailImageTerm;
|
|
121
|
}
|
|
122
|
|
|
123
|
public static DefinedTerm getSampleDesignationTerm(){
|
|
124
|
if(sampleDesignationTerm==null){
|
|
125
|
initializeTerms();
|
|
126
|
}
|
|
127
|
return sampleDesignationTerm;
|
|
128
|
}
|
|
129
|
|
|
130
|
|
|
131
|
/** {@inheritDoc} */
|
|
132
|
@Override
|
|
133
|
public String getText(Object element) {
|
|
134
|
return getDerivateText(element);
|
|
135
|
}
|
|
136
|
|
|
137
|
/** {@inheritDoc} */
|
|
138
|
@Override
|
|
139
|
public String getToolTipText(Object element) {
|
|
140
|
return getDerivateText(element);
|
|
141
|
}
|
|
142
|
|
|
143
|
/**
|
|
144
|
* @param conversation the conversation to set
|
|
145
|
*/
|
|
146
|
public void setConversation(ConversationHolder conversation) {
|
|
147
|
this.conversation = conversation;
|
|
148
|
}
|
|
149
|
|
|
150
|
public String getDerivateText(Object element){
|
|
151
|
return getDerivateText(element, conversation);
|
|
152
|
}
|
|
153
|
|
|
154
|
public static String getDerivateText(Object element, ConversationHolder conversation){
|
|
155
|
//TODO: use list of strings to assemble labels to avoid adding the separator every time and to allow null values
|
|
156
|
TreeNode parentNode = null;
|
|
157
|
TreeNode node = null;
|
|
158
|
Object derivate = element;
|
|
159
|
if(element instanceof TreeNode){
|
|
160
|
node = (TreeNode) element;
|
|
161
|
parentNode = node.getParent();
|
|
162
|
//unwrap specimen from TreeNode
|
|
163
|
derivate = node.getValue();
|
|
164
|
}
|
|
165
|
|
|
166
|
if(conversation!=null){
|
|
167
|
conversation.bind();
|
|
168
|
}
|
|
169
|
|
|
170
|
final String emptyString = "";
|
|
171
|
final String separator = " ";
|
|
172
|
|
|
173
|
String label = emptyString;
|
|
174
|
|
|
175
|
//Field Unit
|
|
176
|
if(derivate instanceof FieldUnit){
|
|
177
|
FieldUnit fieldUnit = (FieldUnit)derivate;
|
|
178
|
if(fieldUnit.getGatheringEvent()!=null){
|
|
179
|
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
|
|
180
|
label += gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getLabel()+separator:emptyString;
|
|
181
|
label += gatheringEvent.getLocality()!=null?gatheringEvent.getLocality().getText()+separator:emptyString;
|
|
182
|
label += gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate()+separator:emptyString;
|
|
183
|
label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
|
|
184
|
}
|
|
185
|
label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():emptyString;
|
|
186
|
}
|
|
187
|
//MediaSpecimen
|
|
188
|
else if(derivate instanceof MediaSpecimen){
|
|
189
|
MediaSpecimen mediaSpecimen = (MediaSpecimen)derivate;
|
|
190
|
if(mediaSpecimen.getMediaSpecimen()!=null){
|
|
191
|
label += mediaSpecimen.getMediaSpecimen().getTitle()!=null?mediaSpecimen.getMediaSpecimen().getTitle().getText()+separator:"[no motif]";
|
|
192
|
label += mediaSpecimen.getMediaSpecimen().getArtist()!=null?mediaSpecimen.getMediaSpecimen().getArtist()+separator:emptyString;
|
|
193
|
}
|
|
194
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = mediaSpecimen.getCollection();
|
|
195
|
if(collection!=null){
|
|
196
|
label += collection.getName()!=null?collection.getName()+" ":emptyString;
|
|
197
|
label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
|
|
198
|
}
|
|
199
|
label += mediaSpecimen.getAccessionNumber()!=null?mediaSpecimen.getAccessionNumber()+separator:emptyString;
|
|
200
|
label += mediaSpecimen.getBarcode()!=null?mediaSpecimen.getBarcode()+separator:emptyString;
|
|
201
|
}
|
|
202
|
//TissueSample + DnaSample
|
|
203
|
else if(derivate instanceof DnaSample){
|
|
204
|
DnaSample dnaSample = (DnaSample)derivate;
|
|
205
|
if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.DnaSample){
|
|
206
|
Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
|
|
207
|
if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
|
|
208
|
label += currentSampleDesignation.getIdentifier()+separator;
|
|
209
|
}
|
|
210
|
else{
|
|
211
|
label += NO_SAMPLE_DESIGNATION+separator;
|
|
212
|
}
|
|
213
|
}
|
|
214
|
else if(((DnaSample) derivate).getRecordBasis()==SpecimenOrObservationType.TissueSample){
|
|
215
|
if(dnaSample.getKindOfUnit()!=null){
|
|
216
|
label += dnaSample.getKindOfUnit()+separator;
|
|
217
|
}
|
|
218
|
Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(dnaSample);
|
|
219
|
if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
|
|
220
|
label += currentSampleDesignation.getIdentifier()+separator;
|
|
221
|
}
|
|
222
|
else{
|
|
223
|
label += NO_SAMPLE_DESIGNATION+separator;
|
|
224
|
}
|
|
225
|
}
|
|
226
|
|
|
227
|
}
|
|
228
|
//DerivedUnit + TissueSample
|
|
229
|
else if(derivate instanceof DerivedUnit){
|
|
230
|
DerivedUnit derivedUnit = (DerivedUnit)derivate;
|
|
231
|
if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
|
|
232
|
//check for type designation
|
|
233
|
if(typeDesignations.get(derivedUnit)==null){
|
|
234
|
for (SpecimenTypeDesignation specimenTypeDesignation : CdmStore.getService(IOccurrenceService.class).listTypeDesignations(derivedUnit, null, null, null, null)) {
|
|
235
|
addTypeDesignation(derivedUnit, specimenTypeDesignation);
|
|
236
|
}
|
|
237
|
}
|
|
238
|
//java.util.Collection<FieldUnit> fieldUnits = CdmStore.getService(IOccurrenceService.class).getFieldUnits(derivedUnit.getUuid());
|
|
239
|
//TODO : This is not generic anymore for performance reasons
|
|
240
|
Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
|
|
241
|
if(originals!=null && originals.size() ==1) {
|
|
242
|
SpecimenOrObservationBase specimen = originals.iterator().next();
|
|
243
|
if(specimen instanceof FieldUnit) {
|
|
244
|
FieldUnit fieldUnit = (FieldUnit)specimen;
|
|
245
|
GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
|
|
246
|
if(gatheringEvent!=null){
|
|
247
|
label += gatheringEvent.getCollector()!=null?gatheringEvent.getCollector()+separator:emptyString;
|
|
248
|
}
|
|
249
|
label += fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber()+separator:emptyString;
|
|
250
|
}
|
|
251
|
}
|
|
252
|
|
|
253
|
eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
|
|
254
|
if(collection!=null){
|
|
255
|
label += collection.getCode()!=null?"("+collection.getCode()+")"+separator:emptyString;
|
|
256
|
}
|
|
257
|
String mostSignificantIdentifier = derivedUnit.getMostSignificantIdentifier();
|
|
258
|
label += mostSignificantIdentifier!=null?mostSignificantIdentifier+separator:emptyString;
|
|
259
|
//type designation extension
|
|
260
|
List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
|
|
261
|
if(list!=null){
|
|
262
|
for (SpecimenTypeDesignation specimenTypeDesignation : list) {
|
|
263
|
label += "("+specimenTypeDesignation.getTypeStatus()+" of ";
|
|
264
|
for (TaxonNameBase taxonNameBase : specimenTypeDesignation.getTypifiedNames()) {
|
|
265
|
label += taxonNameBase+separator;
|
|
266
|
}
|
|
267
|
if(label.endsWith(separator)){
|
|
268
|
label = label.substring(0, label.length()-separator.length());
|
|
269
|
}
|
|
270
|
label += ")";
|
|
271
|
}
|
|
272
|
}
|
|
273
|
}
|
|
274
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
|
|
275
|
//TissueSample should only be created by using it's own class
|
|
276
|
//in future using only one class with different SpecimenOrObservationTypes is desired
|
|
277
|
// label += derivedUnit.getKindOfUnit() + NO_SAMPLE_DESIGNATION;
|
|
278
|
}
|
|
279
|
}
|
|
280
|
//Sequence
|
|
281
|
else if(derivate instanceof Sequence){
|
|
282
|
Sequence sequence = (Sequence)derivate;
|
|
283
|
Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
|
|
284
|
if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
|
|
285
|
label += currentSampleDesignation.getIdentifier()+separator;
|
|
286
|
}
|
|
287
|
else{
|
|
288
|
label += NO_SAMPLE_DESIGNATION+separator;
|
|
289
|
}
|
|
290
|
label += sequence.getDnaMarker()!=null?sequence.getDnaMarker():emptyString;
|
|
291
|
}
|
|
292
|
//SingleRead
|
|
293
|
else if(derivate instanceof SingleRead){
|
|
294
|
SingleRead singleRead = (SingleRead)derivate;
|
|
295
|
if(parentNode!=null && parentNode.getValue() instanceof Sequence){
|
|
296
|
Sequence sequence = (Sequence) parentNode.getValue();
|
|
297
|
Identifier<DnaSample> currentSampleDesignation = getCurrentSampleDesignation(sequence);
|
|
298
|
if(currentSampleDesignation!=null && currentSampleDesignation.getIdentifier()!=null){
|
|
299
|
label = currentSampleDesignation.getIdentifier()+separator;
|
|
300
|
}
|
|
301
|
else{
|
|
302
|
label += NO_SAMPLE_DESIGNATION+separator;
|
|
303
|
}
|
|
304
|
label += singleRead.getPrimer()!=null?singleRead.getPrimer().getLabel()+separator:emptyString;
|
|
305
|
if(sequence!=null && sequence.getDnaMarker()!=null){
|
|
306
|
label += sequence.getDnaMarker()+separator;
|
|
307
|
}
|
|
308
|
if(singleRead.getAmplificationResult()!=null && singleRead.getAmplificationResult().getAmplification()!=null){
|
|
309
|
label += singleRead.getAmplificationResult().getAmplification().getLabelCache()+separator;
|
|
310
|
}
|
|
311
|
}
|
|
312
|
}
|
|
313
|
//SOOB
|
|
314
|
else if(derivate instanceof SpecimenOrObservationBase){
|
|
315
|
SpecimenOrObservationBase<?> specimen = (SpecimenOrObservationBase<?>) derivate;
|
|
316
|
SpecimenOrObservationType type = specimen.getRecordBasis();
|
|
317
|
return specimen.getTitleCache() + (type!=null?" ["+type.toString()+"]":emptyString);
|
|
318
|
}
|
|
319
|
if(label.isEmpty()){
|
|
320
|
label = derivate.toString();
|
|
321
|
}
|
|
322
|
//remove last comma
|
|
323
|
else if(label.endsWith(separator)){
|
|
324
|
label = label.substring(0, label.length()-separator.length());
|
|
325
|
}
|
|
326
|
return label;
|
|
327
|
}
|
|
328
|
|
|
329
|
@Override
|
|
330
|
public Image getImage(Object element) {
|
|
331
|
if(element instanceof TreeNode){
|
|
332
|
element = ((TreeNode) element).getValue();
|
|
333
|
}
|
|
334
|
if(element instanceof CdmBase){
|
|
335
|
CdmBase cdmBase = (CdmBase)element;
|
|
336
|
boolean hasCharacterData = false;
|
|
337
|
if(cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
|
|
338
|
SpecimenOrObservationBase<?> specimen = HibernateProxyHelper.deproxy(cdmBase, SpecimenOrObservationBase.class);
|
|
339
|
if(specimen.hasCharacterData()){
|
|
340
|
hasCharacterData = true;
|
|
341
|
}
|
|
342
|
}
|
|
343
|
if(cdmBase.isInstanceOf(FieldUnit.class)){
|
|
344
|
return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
|
|
345
|
}
|
|
346
|
else if(cdmBase.isInstanceOf(DerivedUnit.class)){
|
|
347
|
DerivedUnit derivedUnit = HibernateProxyHelper.deproxy(element, DerivedUnit.class);
|
|
348
|
if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.FieldUnit){
|
|
349
|
return hasCharacterData?ImageResources.getImage(ImageResources.FIELD_UNIT_CHARACTER_DATA):ImageResources.getImage(ImageResources.FIELD_UNIT);
|
|
350
|
}
|
|
351
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.DnaSample){
|
|
352
|
return hasCharacterData?ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DNA_SAMPLE_DERIVATE);
|
|
353
|
}
|
|
354
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.TissueSample){
|
|
355
|
return hasCharacterData?ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.TISSUE_SAMPLE_DERIVATE);
|
|
356
|
}
|
|
357
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
|
|
358
|
return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_DERIVATE);
|
|
359
|
}
|
|
360
|
else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.Media){
|
|
361
|
if(derivedUnit.getKindOfUnit()!=null){
|
|
362
|
if(derivedUnit.getKindOfUnit().equals(getArtworkTerm())){
|
|
363
|
return hasCharacterData?ImageResources.getImage(ImageResources.ARTWORK_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.ARTWORK_DERIVATE);
|
|
364
|
}
|
|
365
|
else if(derivedUnit.getKindOfUnit().equals(getLivingPlantPhotoTerm())){
|
|
366
|
return hasCharacterData?ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.LIVING_PLANT_PHOTO_DERIVATE);
|
|
367
|
}
|
|
368
|
else if(derivedUnit.getKindOfUnit().equals(getSpecimenScanTerm())){
|
|
369
|
return hasCharacterData?ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.SPECIMEN_SCAN_DERIVATE);
|
|
370
|
}
|
|
371
|
else if(derivedUnit.getKindOfUnit().equals(getDetailImageTerm())){
|
|
372
|
return hasCharacterData?ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE_CHARACTER_DATA):ImageResources.getImage(ImageResources.DETAIL_IMAGE_DERIVATE);
|
|
373
|
}
|
|
374
|
}
|
|
375
|
}
|
|
376
|
}
|
|
377
|
else if(cdmBase.isInstanceOf(Sequence.class)){
|
|
378
|
return ImageResources.getImage(ImageResources.SEQUENCE_DERIVATE);
|
|
379
|
}
|
|
380
|
|
|
381
|
else if(cdmBase.isInstanceOf(SingleRead.class)){
|
|
382
|
if(multiLinkSingleReads!=null && multiLinkSingleReads.contains(element)){
|
|
383
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE_MULTILINK);
|
|
384
|
}
|
|
385
|
else{
|
|
386
|
return ImageResources.getImage(ImageResources.SINGLE_READ_DERIVATE);
|
|
387
|
}
|
|
388
|
}
|
|
389
|
}
|
|
390
|
return super.getImage(element);
|
|
391
|
}
|
|
392
|
|
|
393
|
public static Identifier<DnaSample> getCurrentSampleDesignation(CdmBase entity) {
|
|
394
|
if(entity.isInstanceOf(DnaSample.class)){
|
|
395
|
DnaSample dnaSample = HibernateProxyHelper.deproxy(entity, DnaSample.class);
|
|
396
|
for (Identifier<DnaSample> identifier : dnaSample.getIdentifiers()) {
|
|
397
|
if(identifier.getType()!=null && identifier.getType().equals(DerivateLabelProvider.getSampleDesignationTerm())){
|
|
398
|
//first sample designation is the current
|
|
399
|
return identifier;
|
|
400
|
}
|
|
401
|
}
|
|
402
|
}
|
|
403
|
else if(entity.isInstanceOf(Sequence.class)){
|
|
404
|
Sequence sequence = HibernateProxyHelper.deproxy(entity, Sequence.class);
|
|
405
|
if(sequence.getDnaSample()!=null){
|
|
406
|
return getCurrentSampleDesignation(sequence.getDnaSample());
|
|
407
|
}
|
|
408
|
}
|
|
409
|
return null;
|
|
410
|
}
|
|
411
|
|
|
412
|
/**
|
|
413
|
* Refreshes cached label extensions
|
|
414
|
* @param multiLinkSingleReads
|
|
415
|
*/
|
|
416
|
public void refresh() {
|
|
417
|
DerivateLabelProvider.multiLinkSingleReads = new HashSet<SingleRead>();
|
|
418
|
for(Entry<SingleRead, Collection<Sequence>> entry:CdmStore.getService(ISequenceService.class).getSingleReadSequencesMap().entrySet()){
|
|
419
|
if(entry.getValue().size()>1){
|
|
420
|
multiLinkSingleReads.add(entry.getKey());
|
|
421
|
}
|
|
422
|
}
|
|
423
|
DerivateLabelProvider.typeDesignations = new HashMap<DerivedUnit, List<SpecimenTypeDesignation>>();
|
|
424
|
}
|
|
425
|
|
|
426
|
private static void addTypeDesignation(DerivedUnit derivedUnit, SpecimenTypeDesignation typeDesignation){
|
|
427
|
List<SpecimenTypeDesignation> list = typeDesignations.get(derivedUnit);
|
|
428
|
if(list==null){
|
|
429
|
list = new ArrayList<SpecimenTypeDesignation>();
|
|
430
|
}
|
|
431
|
list.add(typeDesignation);
|
|
432
|
typeDesignations.put(derivedUnit, list);
|
|
433
|
}
|
|
434
|
|
|
435
|
public static Set<SingleRead> getMultiLinkSingleReads() {
|
|
436
|
return multiLinkSingleReads;
|
|
437
|
}
|
|
438
|
|
|
439
|
}
|