Project

General

Profile

Download (23.7 KB) Statistics
| Branch: | Tag: | Revision:
1
/**
2
 * Copyright (C) 2017 EDIT
3
 * European Distributed Institute of Taxonomy
4
 * http://www.e-taxonomy.eu
5
 *
6
 * The contents of this file are subject to the Mozilla Public License Version 1.1
7
 * See LICENSE.TXT at the top of this package for the full license terms.
8
 */
9
package eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix;
10

    
11
import java.io.File;
12
import java.util.ArrayList;
13
import java.util.Collection;
14
import java.util.HashMap;
15
import java.util.List;
16
import java.util.Map;
17
import java.util.Properties;
18
import java.util.Set;
19
import java.util.UUID;
20
import java.util.stream.Collectors;
21

    
22
import org.apache.commons.collections4.map.LinkedMap;
23
import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
24
import org.eclipse.core.runtime.ICoreRunnable;
25
import org.eclipse.core.runtime.IProgressMonitor;
26
import org.eclipse.core.runtime.jobs.Job;
27
import org.eclipse.jface.layout.GridDataFactory;
28
import org.eclipse.jface.viewers.ComboViewer;
29
import org.eclipse.nebula.widgets.nattable.NatTable;
30
import org.eclipse.nebula.widgets.nattable.config.ConfigRegistry;
31
import org.eclipse.nebula.widgets.nattable.config.DefaultNatTableStyleConfiguration;
32
import org.eclipse.nebula.widgets.nattable.coordinate.PositionCoordinate;
33
import org.eclipse.nebula.widgets.nattable.data.IDataProvider;
34
import org.eclipse.nebula.widgets.nattable.data.ListDataProvider;
35
import org.eclipse.nebula.widgets.nattable.export.command.ExportCommandHandler;
36
import org.eclipse.nebula.widgets.nattable.extension.glazedlists.GlazedListsEventLayer;
37
import org.eclipse.nebula.widgets.nattable.extension.glazedlists.GlazedListsSortModel;
38
import org.eclipse.nebula.widgets.nattable.extension.glazedlists.tree.GlazedListTreeData;
39
import org.eclipse.nebula.widgets.nattable.extension.glazedlists.tree.GlazedListTreeRowModel;
40
import org.eclipse.nebula.widgets.nattable.freeze.CompositeFreezeLayer;
41
import org.eclipse.nebula.widgets.nattable.freeze.FreezeHelper;
42
import org.eclipse.nebula.widgets.nattable.freeze.FreezeLayer;
43
import org.eclipse.nebula.widgets.nattable.grid.GridRegion;
44
import org.eclipse.nebula.widgets.nattable.grid.command.ClientAreaResizeCommand;
45
import org.eclipse.nebula.widgets.nattable.grid.data.DefaultColumnHeaderDataProvider;
46
import org.eclipse.nebula.widgets.nattable.grid.data.DefaultCornerDataProvider;
47
import org.eclipse.nebula.widgets.nattable.grid.data.DefaultRowHeaderDataProvider;
48
import org.eclipse.nebula.widgets.nattable.grid.data.FixedSummaryRowHeaderLayer;
49
import org.eclipse.nebula.widgets.nattable.grid.layer.ColumnHeaderLayer;
50
import org.eclipse.nebula.widgets.nattable.grid.layer.CornerLayer;
51
import org.eclipse.nebula.widgets.nattable.grid.layer.DefaultRowHeaderDataLayer;
52
import org.eclipse.nebula.widgets.nattable.grid.layer.GridLayer;
53
import org.eclipse.nebula.widgets.nattable.layer.AbstractLayer;
54
import org.eclipse.nebula.widgets.nattable.layer.CompositeLayer;
55
import org.eclipse.nebula.widgets.nattable.layer.DataLayer;
56
import org.eclipse.nebula.widgets.nattable.layer.ILayer;
57
import org.eclipse.nebula.widgets.nattable.layer.cell.ColumnOverrideLabelAccumulator;
58
import org.eclipse.nebula.widgets.nattable.layer.stack.DefaultBodyLayerStack;
59
import org.eclipse.nebula.widgets.nattable.selection.SelectionLayer;
60
import org.eclipse.nebula.widgets.nattable.sort.SortHeaderLayer;
61
import org.eclipse.nebula.widgets.nattable.sort.config.SingleClickSortConfiguration;
62
import org.eclipse.nebula.widgets.nattable.style.HorizontalAlignmentEnum;
63
import org.eclipse.nebula.widgets.nattable.style.theme.ModernNatTableThemeConfiguration;
64
import org.eclipse.nebula.widgets.nattable.summaryrow.FixedSummaryRowLayer;
65
import org.eclipse.nebula.widgets.nattable.summaryrow.SummaryRowLayer;
66
import org.eclipse.nebula.widgets.nattable.tree.ITreeRowModel;
67
import org.eclipse.nebula.widgets.nattable.tree.TreeLayer;
68
import org.eclipse.nebula.widgets.nattable.util.GUIHelper;
69
import org.eclipse.swt.SWT;
70
import org.eclipse.swt.layout.GridData;
71
import org.eclipse.swt.layout.GridLayout;
72
import org.eclipse.swt.widgets.Button;
73
import org.eclipse.swt.widgets.Composite;
74

    
75
import ca.odell.glazedlists.BasicEventList;
76
import ca.odell.glazedlists.EventList;
77
import ca.odell.glazedlists.SortedList;
78
import ca.odell.glazedlists.TreeList;
79
import eu.etaxonomy.cdm.api.application.CdmApplicationState;
80
import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
81
import eu.etaxonomy.cdm.api.service.IProgressMonitorService;
82
import eu.etaxonomy.cdm.api.service.UpdateResult;
83
import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
84
import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
85
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
86
import eu.etaxonomy.cdm.model.description.Feature;
87
import eu.etaxonomy.cdm.model.description.FeatureNode;
88
import eu.etaxonomy.cdm.model.description.FeatureTree;
89
import eu.etaxonomy.cdm.model.description.MeasurementUnit;
90
import eu.etaxonomy.cdm.model.description.SpecimenDescription;
91
import eu.etaxonomy.cdm.model.description.State;
92
import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
93
import eu.etaxonomy.taxeditor.editor.l10n.Messages;
94
import eu.etaxonomy.taxeditor.model.MessagingUtils;
95
import eu.etaxonomy.taxeditor.store.CdmStore;
96
import eu.etaxonomy.taxeditor.workbench.WorkbenchUtility;
97

    
98
/**
99
 * Character matrix editor for editing specimen/taxon descriptions in a table
100
 * @author pplitzner
101
 * @since Nov 26, 2017
102
 *
103
 */
104
public class CharacterMatrix extends Composite {
105

    
106
    private static final String CHARACTER_MATRIX_STATE_PROPERTIES = "characterMatrixState.properties"; //$NON-NLS-1$
107

    
108
    static final int LEADING_COLUMN_COUNT = 4;
109
    static final String TAXON_COLUMN = "taxon_column"; //$NON-NLS-1$
110
    static final String COLLECTOR_COLUMN = "collector_column"; //$NON-NLS-1$
111
    static final String IDENTIFIER_COLUMN = "identifier_column"; //$NON-NLS-1$
112
    static final String COUNTRY_COLUMN = "country_column"; //$NON-NLS-1$
113

    
114
    static final String LABEL_TAXON_ROW = "TAXON_ROW"; //$NON-NLS-1$
115

    
116
    private DescriptiveDataSet descriptiveDataSet;
117

    
118
    private NatTable natTable;
119

    
120
    private Map<Integer, Feature> indexToFeatureMap = new HashMap<>();
121

    
122
    private Map<Feature, List<State>> categoricalFeatureToStateMap = new HashMap<>();
123

    
124
    private LinkedMap<String, String> propertyToLabelMap = new LinkedMap<>();
125

    
126
    //FIXME use more concrete generic
127
    private EventList<Object> descriptions;
128

    
129
    private Collection<SpecimenNodeWrapper> specimenCache = null;
130

    
131
    private Map<Feature, CategoricalDataHistogram> featureToHistogramMap = new HashMap<>();
132

    
133
    private Map<Feature, DescriptiveStatistics> featureToQuantStatisticsMap = new HashMap<>();
134

    
135
    private ListDataProvider<Object> bodyDataProvider;
136

    
137
    private FreezeLayer freezeLayer;
138

    
139
    private List<Feature> features;
140

    
141
    private CharacterMatrixPart part;
142

    
143
    private AbstractLayer topMostLayer;
144

    
145
    private FixedSummaryRowLayer summaryRowLayer;
146

    
147
    private ConfigRegistry configRegistry;
148

    
149
    private DefaultBodyLayerStack bodyLayer;
150

    
151
    private boolean isTreeView = true;
152

    
153
    private CharacterMatrixToolbar toolbar;
154

    
155
    private boolean isShowTooltips = true;
156

    
157
    public CharacterMatrix(Composite parent, CharacterMatrixPart part) {
158
        super(parent, SWT.NONE);
159
        this.part = part;
160
        this.setLayout(new GridLayout());
161

    
162
        createToolBar();
163

    
164
        natTable = new NatTable(this, false);
165

    
166
        createBottomToolbar();
167

    
168
    }
169

    
170
    private void createToolBar(){
171
        toolbar = new CharacterMatrixToolbar(this, SWT.NONE);
172
    }
173

    
174
    @SuppressWarnings("unused")
175
    private void createBottomToolbar() {
176
        new CharacterMatrixBottomToolbar(this, SWT.NONE);
177
    }
178

    
179

    
180
    private void applyStyles(){
181
        ModernNatTableThemeConfiguration configuration = new ModernNatTableThemeConfiguration();
182
        configuration.summaryRowHAlign = HorizontalAlignmentEnum.CENTER;
183
        // NOTE: Getting the colors and fonts from the GUIHelper ensures that
184
        // they are disposed properly (required by SWT)
185
        configuration.summaryRowBgColor = GUIHelper.getColor(255, 255, 153);
186
        configuration.cHeaderBgColor = GUIHelper.getColor(211, 211, 211);
187
        configuration.rHeaderBgColor = GUIHelper.getColor(211, 211, 211);
188
        natTable.addConfiguration(configuration);
189

    
190
    }
191

    
192
    void toggleTreeFlat(boolean isTree, Button btnToggleFlat, Button btnToggleTree, Button btnCollapseAll, Button btnExpandAll, Button btnFreezeSuppInfo) {
193
        isTreeView = isTree;
194
        createTable(isTree);
195
        btnToggleFlat.setEnabled(isTree);
196
        btnToggleTree.setEnabled(!isTree);
197
        btnCollapseAll.setEnabled(isTree);
198
        btnExpandAll.setEnabled(isTree);
199
    }
200

    
201
    public boolean isTreeView() {
202
        return isTreeView;
203
    }
204

    
205
    public void createTable(boolean treeView){
206
        /**
207
         * layers
208
         */
209
        createLayers(treeView);
210

    
211
        /**
212
         * configuration
213
         */
214
        configureNatTable(treeView, configRegistry, topMostLayer, summaryRowLayer);
215

    
216
        /**
217
         * handlers and listeners
218
         */
219
        registerHandlersAndListeners(topMostLayer);
220

    
221
        //grab all space
222
        GridDataFactory.fillDefaults().grab(true, true).applyTo(natTable);
223

    
224
        //update label to current data set
225
        toolbar.getWsLabel().setText(descriptiveDataSet.getLabel());
226
        toolbar.getWsLabel().setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
227
        toolbar.getWsLabel().getParent().layout();
228

    
229
        //initial freeze of supplemental columns
230
        freezeSupplementalColumns(true);
231

    
232

    
233
        //add tooltip to table
234
        new ChartTooltip(this);
235

    
236
        this.layout();
237
        natTable.doCommand(new ClientAreaResizeCommand(natTable));
238
    }
239

    
240
    private List<Feature> initFeatureList(FeatureNode node){
241
        List<Feature> features = new ArrayList<>();
242
        node.getChildNodes().forEach(childNode->
243
                {
244
                    features.add(childNode.getFeature());
245
                    features.addAll(initFeatureList(childNode));
246
                });
247
        return features;
248
    }
249

    
250
    public void initDescriptiveDataSet(DescriptiveDataSet descriptiveDataSet){
251
        this.descriptiveDataSet = descriptiveDataSet;
252
        //get features/columns stored in descriptive data set
253
        FeatureTree tree = descriptiveDataSet.getDescriptiveSystem();
254
        features = initFeatureList(tree.getRoot());
255

    
256
        //init state data for categorical features
257
        features.forEach(feature->
258
        {
259
            if(feature.isSupportsCategoricalData()){
260
                List<State> supportedStates = new ArrayList<>();
261
                feature.getSupportedCategoricalEnumerations().forEach(voc->supportedStates.addAll(voc.getTerms()));
262
                categoricalFeatureToStateMap.put(feature, supportedStates);
263
            }
264
        });
265
        descriptions = new BasicEventList<>();
266

    
267
    }
268

    
269
    private void createLayers(boolean treeView) {
270
        // use the SortedList constructor with 'null' for the Comparator
271
        // because the Comparator will be set by configuration
272
        SortedList<Object> sortedList = new SortedList<>(descriptions, new MatrixRowComparator());
273
        // wrap the SortedList with the TreeList
274
        TreeList<Object> treeList = new TreeList(sortedList, new DescriptionTreeFormat(descriptiveDataSet), TreeList.NODES_START_EXPANDED);
275
        /**
276
         * data provider
277
         */
278
        SpecimenColumnPropertyAccessor columnPropertyAccessor = new SpecimenColumnPropertyAccessor(this);
279
        bodyDataProvider = treeView?new ListDataProvider<>(treeList, columnPropertyAccessor):new ListDataProvider<>(sortedList, columnPropertyAccessor);
280

    
281
        configRegistry = new ConfigRegistry();
282

    
283

    
284
        /**
285
         * BODY layer
286
         *
287
         *
288

    
289
        CompositeLayer
290
         - (top) SummaryRowLayer
291
         - (bottom) ViewportLayer
292

    
293
             ^
294
        ViewportLayer
295

    
296
             ^
297
        TreeLayer (default visible)
298

    
299
             ^
300
        CompositeFreezeLayer
301
         - viewportLayer
302
         - selectionLayer
303
         - freezeLayer
304

    
305
             ^
306
        FreezeLayer
307

    
308
             ^
309
        SelectionLayer
310

    
311
             ^
312
        ColumnHideShowLayer
313

    
314
             ^
315
        ColumnReorderLayer
316

    
317
             ^
318
        DataLayer
319

    
320
         *
321

    
322
         */
323
        DataLayer bodyDataLayer = new DataLayer(bodyDataProvider);
324

    
325
        //register labels
326
        CharacterMatrixConfigLabelAccumulator labelAccumulator = new CharacterMatrixConfigLabelAccumulator(this);
327
        bodyDataLayer.setConfigLabelAccumulator(labelAccumulator);
328

    
329

    
330
        propertyToLabelMap.put(TAXON_COLUMN, Messages.CharacterMatrix_TAXON);
331
        propertyToLabelMap.put(COLLECTOR_COLUMN, Messages.CharacterMatrix_COLLECTOR_NO);
332
        propertyToLabelMap.put(IDENTIFIER_COLUMN, Messages.CharacterMatrix_IDENTIFIER);
333
        propertyToLabelMap.put(COUNTRY_COLUMN, Messages.CharacterMatrix_COUNTRY);
334
        for(int i=0;i<features.size();i++){
335
            Feature feature = features.get(i);
336
            initLabels(i, feature);
337
        }
338

    
339
        // layer for event handling of GlazedLists and PropertyChanges
340
        GlazedListsEventLayer eventLayer = new GlazedListsEventLayer<>(bodyDataLayer, treeList);
341
        GlazedListTreeData treeData = new GlazedListTreeData<>(treeList);
342
        ITreeRowModel treeRowModel = new GlazedListTreeRowModel<>(treeData);
343

    
344
        bodyLayer = new DefaultBodyLayerStack(eventLayer);
345
        final SelectionLayer selectionLayer = bodyLayer.getSelectionLayer();
346
        freezeLayer = new FreezeLayer(selectionLayer);
347
        final CompositeFreezeLayer compositeFreezeLayer = new CompositeFreezeLayer(
348
                freezeLayer, bodyLayer.getViewportLayer(), selectionLayer);
349
        TreeLayer treeLayer = new TreeLayer(compositeFreezeLayer, treeRowModel);
350

    
351
        topMostLayer = treeView?treeLayer:compositeFreezeLayer;
352

    
353
        summaryRowLayer = new FixedSummaryRowLayer(bodyDataLayer, topMostLayer, configRegistry, false);
354
        //regoster labels with summary prefix for summary layer
355
        ColumnOverrideLabelAccumulator summaryColumnLabelAccumulator =new ColumnOverrideLabelAccumulator(bodyDataLayer);
356
        summaryRowLayer.setConfigLabelAccumulator(summaryColumnLabelAccumulator);
357
        for(int i=0;i<features.size();i++){
358
            Feature feature = features.get(i);
359
            summaryColumnLabelAccumulator.registerColumnOverrides(
360
                    i+LEADING_COLUMN_COUNT,
361
                    SummaryRowLayer.DEFAULT_SUMMARY_COLUMN_CONFIG_LABEL_PREFIX+MatrixUtility.getProperty(feature));
362
        }
363
        // because the horizontal dependency is the ViewportLayer
364
        // we need to set the composite dependency to false
365
        summaryRowLayer.setHorizontalCompositeDependency(false);
366

    
367
        CompositeLayer composite = new CompositeLayer(1, 2);
368
        composite.setChildLayer("SUMMARY", summaryRowLayer, 0, 0); //$NON-NLS-1$
369
        composite.setChildLayer(GridRegion.BODY, topMostLayer, 0, 1);
370

    
371

    
372
        /**
373
         * column header layer
374
         */
375
        IDataProvider columnHeaderDataProvider = new DefaultColumnHeaderDataProvider(
376
                propertyToLabelMap.values().toArray(new String[] {}), propertyToLabelMap);
377
        DataLayer columnHeaderDataLayer = new DataLayer(columnHeaderDataProvider);
378
        ColumnHeaderLayer columnHeaderLayer = new ColumnHeaderLayer(columnHeaderDataLayer, topMostLayer, selectionLayer);
379

    
380
        // add the SortHeaderLayer to the column header layer stack
381
        // as we use GlazedLists, we use the GlazedListsSortModel which
382
        // delegates the sorting to the SortedList
383
        final SortHeaderLayer<SpecimenDescription> sortHeaderLayer = new SortHeaderLayer<>(
384
                columnHeaderLayer,
385
                new GlazedListsSortModel<>(
386
                        sortedList,
387
                        columnPropertyAccessor,
388
                        configRegistry,
389
                        columnHeaderDataLayer));
390

    
391

    
392
        /**
393
         * row header layer
394
         */
395
        IDataProvider rowHeaderDataProvider = new DefaultRowHeaderDataProvider(bodyDataProvider);
396
        DefaultRowHeaderDataLayer rowHeaderDataLayer = new DefaultRowHeaderDataLayer(rowHeaderDataProvider);
397
        FixedSummaryRowHeaderLayer fixedSummaryRowHeaderLayer = new FixedSummaryRowHeaderLayer(rowHeaderDataLayer,
398
                composite, selectionLayer);
399
        fixedSummaryRowHeaderLayer.setSummaryRowLabel("\u2211"); //$NON-NLS-1$
400

    
401

    
402
        /**
403
         * corner layer
404
         */
405
        ILayer cornerLayer = new CornerLayer(
406
                new DataLayer(new DefaultCornerDataProvider(columnHeaderDataProvider, rowHeaderDataProvider)),
407
                fixedSummaryRowHeaderLayer, sortHeaderLayer);
408

    
409

    
410
        /**
411
         * GRID layer (composition of all other layers)
412
         */
413
        GridLayer gridLayer = new GridLayer(composite, sortHeaderLayer, fixedSummaryRowHeaderLayer, cornerLayer);
414

    
415
        natTable.setLayer(gridLayer);
416

    
417
    }
418

    
419
    private void registerHandlersAndListeners(AbstractLayer topMostLayer) {
420
        // add the ExportCommandHandler to the ViewportLayer in order to make
421
        // exporting work
422
        topMostLayer.registerCommandHandler(new ExportCommandHandler(topMostLayer));
423

    
424
        //propagate single cell selection
425
        natTable.addLayerListener(new CellSelectionListener(part));
426

    
427
        //register handler for view configuration menu
428
        natTable.registerCommandHandler(toolbar.getDisplayPersistenceDialogCommandHandler());
429
    }
430

    
431
    private void configureNatTable(boolean treeView,
432
            ConfigRegistry configRegistry,
433
            AbstractLayer topMostLayer,
434
            FixedSummaryRowLayer summaryRowLayer) {
435
        /**
436
         * CONFIGURATION
437
         */
438
        natTable.setConfigRegistry(configRegistry);
439

    
440
        applyStyles();
441

    
442
        //add default configuration because autoconfigure is set to false in constructor
443
        natTable.addConfiguration(new DefaultNatTableStyleConfiguration());
444

    
445
        //FIXME: this is for DEBUG ONLY
446
        //        natTable.addConfiguration(new DebugMenuConfiguration(natTable));
447

    
448
        // override the default sort configuration and change the mouse bindings
449
        // to sort on a single click
450
        if(!treeView){
451
            natTable.addConfiguration(new SingleClickSortConfiguration());
452
        }
453

    
454
        natTable.addConfiguration(new CharacterMatrixLabelStyleConfiguration());
455

    
456
        // add the header menu configuration for adding the column header menu
457
        // with hide/show actions
458
        natTable.addConfiguration(new CharacterMatrixHeaderMenuConfiguration(natTable));
459

    
460
        // add custom configuration for data conversion and add column labels to viewport layer
461
        topMostLayer.addConfiguration(new DataConversionConfiguration(this));
462

    
463
        //register aggregation configuration
464
        summaryRowLayer.addConfiguration(new AggregationConfiguration(this));
465

    
466
        natTable.configure();
467
    }
468

    
469
    void freezeSupplementalColumns(boolean freeze){
470
        if(freeze){
471
            FreezeHelper.freeze(freezeLayer, bodyLayer.getViewportLayer(),
472
                    new PositionCoordinate(bodyLayer.getViewportLayer(), 0, 0),
473
                    new PositionCoordinate(bodyLayer.getViewportLayer(), LEADING_COLUMN_COUNT-1, -1));
474
        }
475
        else{
476
            FreezeHelper.unfreeze(freezeLayer, bodyLayer.getViewportLayer());
477
        }
478
    }
479

    
480
    void selectStateItem(ComboViewer comboStates, String stateName){
481
        String[] items = comboStates.getCombo().getItems();
482
        for(int i=0;i<items.length;i++){
483
            if(items[i].equals(stateName)){
484
                comboStates.getCombo().select(i);
485
                break;
486
            }
487
        }
488
    }
489

    
490
    private void initLabels(int index, Feature feature) {
491
        indexToFeatureMap.put(index+LEADING_COLUMN_COUNT, feature);
492

    
493
        String featureLabel = feature.getLabel();
494
        String property = featureLabel;
495
        //show unit for quantitative data
496
        if(feature.isSupportsQuantitativeData()){
497
            Set<MeasurementUnit> recommendedMeasurementUnits = feature.getRecommendedMeasurementUnits();
498
            if(recommendedMeasurementUnits.size()>1){
499
                MessagingUtils.warningDialog(Messages.CharacterMatrix_INIT_PROBLEM, CharacterMatrix.class,
500
                        String.format(Messages.CharacterMatrix_INIT_PROBLEM_MESSAGE, feature.getLabel()));
501
            }
502
            if(recommendedMeasurementUnits.size()==1){
503
                MeasurementUnit unit = recommendedMeasurementUnits.iterator().next();
504
                featureLabel += " ["+unit.getIdInVocabulary()+"]"; //$NON-NLS-1$ //$NON-NLS-2$
505
            }
506
        }
507
        propertyToLabelMap.put(property, featureLabel);
508
    }
509

    
510
    public void loadDescriptions(DescriptiveDataSet descriptiveDataSet) {
511
        UUID monitorUuid = CdmStore.getService(IDescriptiveDataSetService.class).monitGetRowWrapper(descriptiveDataSet);
512
        IProgressMonitorService progressMonitorService = CdmApplicationState.getCurrentAppConfig().getProgressMonitorService();
513

    
514

    
515
        String jobLabel = "Load character data";
516
        Job job = Job.create(jobLabel, (ICoreRunnable) monitor -> {
517
            monitor.beginTask(jobLabel, IProgressMonitor.UNKNOWN);
518
            while(progressMonitorService.isMonitorThreadRunning(monitorUuid)){
519
                if(monitor.isCanceled()){
520
                    progressMonitorService.interrupt(monitorUuid);
521
                }
522
            }
523
            IRemotingProgressMonitor remotingMonitor = progressMonitorService.getRemotingMonitor(monitorUuid);
524
            Object result = remotingMonitor.getResult();
525
            if(result instanceof Collection){
526
                Collection<RowWrapperDTO> wrappers = (Collection<RowWrapperDTO>) result;
527
                wrappers.forEach(wrapper->CharacterMatrix.this.descriptions.add(wrapper));
528
            }
529
            monitor.done();
530
        });
531
        job.schedule(1000);
532
    }
533

    
534
    public List<State> getSupportedStatesForCategoricalFeature(Feature feature){
535
        return categoricalFeatureToStateMap.get(feature);
536
    }
537

    
538
    public Map<Integer, Feature> getIndexToFeatureMap() {
539
        return indexToFeatureMap;
540
    }
541

    
542
    public LinkedMap<String, String> getPropertyToLabelMap() {
543
        return propertyToLabelMap;
544
    }
545

    
546
    public void setDirty() {
547
        part.setDirty();
548
    }
549

    
550
    public NatTable getNatTable() {
551
        return natTable;
552
    }
553

    
554
    public EventList<Object> getDescriptions() {
555
        return descriptions;
556
    }
557

    
558
    public DescriptiveDataSet getDescriptiveDataSet() {
559
        return descriptiveDataSet;
560
    }
561

    
562
    public Collection<SpecimenNodeWrapper> getSpecimenCache() {
563
        return specimenCache;
564
    }
565

    
566
    public void setSpecimenCache(Collection<SpecimenNodeWrapper> specimenCache) {
567
        this.specimenCache = specimenCache.stream()
568
                .filter(wrapper ->
569
        //map descriptions on a list of uuids of the described specimen
570
        !this.descriptions.stream()
571
        .map(o->((RowWrapperDTO)o).getSpecimen().getUuid())
572
        .collect(Collectors.toList())
573
        //an check if the specimen to add is already contained
574
        .contains(wrapper.getUuidAndTitleCache().getUuid())
575
        )
576
        .collect(Collectors.toList());
577
    }
578

    
579
    public Properties getNatTableState() {
580
        return toolbar.getNatTableState();
581
    }
582

    
583
    public ListDataProvider<Object> getBodyDataProvider() {
584
        return bodyDataProvider;
585
    }
586

    
587
    DefaultBodyLayerStack getBodyLayer() {
588
        return bodyLayer;
589
    }
590

    
591
    File getStatePropertiesFile() {
592
        return new File(WorkbenchUtility.getBaseLocation(), CHARACTER_MATRIX_STATE_PROPERTIES);
593
    }
594

    
595
    public List<Feature> getFeatures() {
596
        return features;
597
    }
598

    
599
    public void addUpdateResult(UpdateResult result){
600
        part.addUpdateResult(result);
601
    }
602

    
603
    public Map<Feature, CategoricalDataHistogram> getFeatureToHistogramMap() {
604
        return featureToHistogramMap;
605
    }
606

    
607
    public Map<Feature, DescriptiveStatistics> getFeatureToQuantStatisticsMap() {
608
        return featureToQuantStatisticsMap;
609
    }
610

    
611
    public void toogleIsShowTooltips() {
612
        this.isShowTooltips = !this.isShowTooltips;
613
    }
614

    
615
    public boolean isShowTooltips() {
616
        return isShowTooltips;
617
    }
618

    
619
}
(4-4/18)