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/**
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* Copyright (C) 2017 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.taxeditor.editor.descriptiveDataSet.matrix;
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import java.io.File;
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import java.util.ArrayList;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.Properties;
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import java.util.Set;
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import java.util.UUID;
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import java.util.stream.Collectors;
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import javax.inject.Inject;
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import org.apache.commons.collections4.map.LinkedMap;
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import org.eclipse.core.runtime.ICoreRunnable;
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import org.eclipse.core.runtime.IProgressMonitor;
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import org.eclipse.core.runtime.SubMonitor;
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import org.eclipse.core.runtime.jobs.IJobChangeEvent;
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import org.eclipse.core.runtime.jobs.Job;
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import org.eclipse.core.runtime.jobs.JobChangeAdapter;
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import org.eclipse.e4.ui.di.UISynchronize;
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import org.eclipse.jface.layout.GridDataFactory;
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import org.eclipse.jface.viewers.ComboViewer;
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import org.eclipse.nebula.widgets.nattable.NatTable;
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import org.eclipse.nebula.widgets.nattable.config.ConfigRegistry;
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import org.eclipse.nebula.widgets.nattable.config.DefaultNatTableStyleConfiguration;
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import org.eclipse.nebula.widgets.nattable.coordinate.PositionCoordinate;
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import org.eclipse.nebula.widgets.nattable.data.IDataProvider;
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import org.eclipse.nebula.widgets.nattable.data.ListDataProvider;
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import org.eclipse.nebula.widgets.nattable.export.command.ExportCommandHandler;
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import org.eclipse.nebula.widgets.nattable.extension.glazedlists.GlazedListsEventLayer;
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import org.eclipse.nebula.widgets.nattable.extension.glazedlists.GlazedListsSortModel;
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import org.eclipse.nebula.widgets.nattable.extension.glazedlists.tree.GlazedListTreeData;
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import org.eclipse.nebula.widgets.nattable.extension.glazedlists.tree.GlazedListTreeRowModel;
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import org.eclipse.nebula.widgets.nattable.freeze.CompositeFreezeLayer;
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import org.eclipse.nebula.widgets.nattable.freeze.FreezeHelper;
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import org.eclipse.nebula.widgets.nattable.freeze.FreezeLayer;
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import org.eclipse.nebula.widgets.nattable.grid.GridRegion;
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import org.eclipse.nebula.widgets.nattable.grid.command.ClientAreaResizeCommand;
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import org.eclipse.nebula.widgets.nattable.grid.data.DefaultColumnHeaderDataProvider;
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import org.eclipse.nebula.widgets.nattable.grid.data.DefaultCornerDataProvider;
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import org.eclipse.nebula.widgets.nattable.grid.data.DefaultRowHeaderDataProvider;
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import org.eclipse.nebula.widgets.nattable.grid.data.FixedSummaryRowHeaderLayer;
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import org.eclipse.nebula.widgets.nattable.grid.layer.ColumnHeaderLayer;
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import org.eclipse.nebula.widgets.nattable.grid.layer.CornerLayer;
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import org.eclipse.nebula.widgets.nattable.grid.layer.DefaultRowHeaderDataLayer;
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import org.eclipse.nebula.widgets.nattable.grid.layer.GridLayer;
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import org.eclipse.nebula.widgets.nattable.layer.AbstractLayer;
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import org.eclipse.nebula.widgets.nattable.layer.CompositeLayer;
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import org.eclipse.nebula.widgets.nattable.layer.DataLayer;
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import org.eclipse.nebula.widgets.nattable.layer.ILayer;
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import org.eclipse.nebula.widgets.nattable.layer.cell.ColumnOverrideLabelAccumulator;
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import org.eclipse.nebula.widgets.nattable.layer.stack.DefaultBodyLayerStack;
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import org.eclipse.nebula.widgets.nattable.selection.SelectionLayer;
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import org.eclipse.nebula.widgets.nattable.sort.SortHeaderLayer;
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import org.eclipse.nebula.widgets.nattable.sort.config.SingleClickSortConfiguration;
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import org.eclipse.nebula.widgets.nattable.style.HorizontalAlignmentEnum;
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import org.eclipse.nebula.widgets.nattable.style.theme.ModernNatTableThemeConfiguration;
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import org.eclipse.nebula.widgets.nattable.summaryrow.FixedSummaryRowLayer;
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import org.eclipse.nebula.widgets.nattable.summaryrow.SummaryRowLayer;
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import org.eclipse.nebula.widgets.nattable.tree.ITreeRowModel;
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import org.eclipse.nebula.widgets.nattable.tree.TreeLayer;
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import org.eclipse.nebula.widgets.nattable.util.GUIHelper;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.layout.GridData;
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import org.eclipse.swt.layout.GridLayout;
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import org.eclipse.swt.widgets.Button;
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import org.eclipse.swt.widgets.Composite;
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import ca.odell.glazedlists.BasicEventList;
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import ca.odell.glazedlists.EventList;
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import ca.odell.glazedlists.SortedList;
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import ca.odell.glazedlists.TreeList;
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import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService;
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import eu.etaxonomy.cdm.api.service.UpdateResult;
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import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
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import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.FeatureNode;
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import eu.etaxonomy.cdm.model.description.FeatureTree;
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import eu.etaxonomy.cdm.model.description.MeasurementUnit;
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import eu.etaxonomy.cdm.model.description.SpecimenDescription;
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import eu.etaxonomy.cdm.model.description.State;
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import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
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import eu.etaxonomy.taxeditor.editor.l10n.Messages;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.workbench.WorkbenchUtility;
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/**
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* Character matrix editor for editing specimen/taxon descriptions in a table
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* @author pplitzner
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* @since Nov 26, 2017
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*
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*/
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public class CharacterMatrix extends Composite {
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private static final String CHARACTER_MATRIX_STATE_PROPERTIES = "characterMatrixState.properties"; //$NON-NLS-1$
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static final int LEADING_COLUMN_COUNT = 4;
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static final String TAXON_COLUMN = "taxon_column"; //$NON-NLS-1$
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static final String COLLECTOR_COLUMN = "collector_column"; //$NON-NLS-1$
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static final String IDENTIFIER_COLUMN = "identifier_column"; //$NON-NLS-1$
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static final String COUNTRY_COLUMN = "country_column"; //$NON-NLS-1$
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static final String LABEL_TAXON_ROW = "TAXON_ROW"; //$NON-NLS-1$
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@Inject
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private UISynchronize sync;
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private DescriptiveDataSet descriptiveDataSet;
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private NatTable natTable;
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private Map<Integer, Feature> indexToFeatureMap = new HashMap<>();
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private Map<Feature, List<State>> categoricalFeatureToStateMap = new HashMap<>();
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private LinkedMap<String, String> propertyToLabelMap = new LinkedMap<>();
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//FIXME use more concrete generic
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private EventList<Object> descriptions;
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private Collection<SpecimenNodeWrapper> specimenCache = null;
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private Map<Feature, CategoricalDataHistogram> featureToHistogramMap = new HashMap<>();
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private Map<Feature, QuantitativeDataStatistics> featureToQuantDataStatisticsMap = new HashMap<>();
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private ListDataProvider<Object> bodyDataProvider;
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private FreezeLayer freezeLayer;
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private List<Feature> features;
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private CharacterMatrixPart part;
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private AbstractLayer topMostLayer;
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private FixedSummaryRowLayer summaryRowLayer;
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private ConfigRegistry configRegistry;
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private DefaultBodyLayerStack bodyLayer;
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private boolean isTreeView = true;
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private CharacterMatrixToolbar toolbar;
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private boolean isShowTooltips = true;
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public CharacterMatrix(Composite parent, CharacterMatrixPart part) {
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super(parent, SWT.NONE);
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this.part = part;
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this.setLayout(new GridLayout());
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createToolBar();
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natTable = new NatTable(this, false);
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createBottomToolbar();
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}
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private void createToolBar(){
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toolbar = new CharacterMatrixToolbar(this, SWT.NONE);
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}
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@SuppressWarnings("unused")
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private void createBottomToolbar() {
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new CharacterMatrixBottomToolbar(this, SWT.NONE);
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}
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private void applyStyles(){
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ModernNatTableThemeConfiguration configuration = new ModernNatTableThemeConfiguration();
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configuration.summaryRowHAlign = HorizontalAlignmentEnum.CENTER;
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// NOTE: Getting the colors and fonts from the GUIHelper ensures that
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// they are disposed properly (required by SWT)
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configuration.summaryRowBgColor = GUIHelper.getColor(255, 255, 153);
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configuration.cHeaderBgColor = GUIHelper.getColor(211, 211, 211);
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configuration.rHeaderBgColor = GUIHelper.getColor(211, 211, 211);
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natTable.addConfiguration(configuration);
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}
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void toggleTreeFlat(boolean isTree, Button btnToggleFlat, Button btnToggleTree, Button btnCollapseAll, Button btnExpandAll, Button btnFreezeSuppInfo) {
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isTreeView = isTree;
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createTable(isTree, freezeLayer.isFrozen());
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btnToggleFlat.setEnabled(isTree);
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btnToggleTree.setEnabled(!isTree);
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btnCollapseAll.setEnabled(isTree);
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btnExpandAll.setEnabled(isTree);
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}
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public boolean isTreeView() {
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return isTreeView;
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}
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public void createTable(boolean treeView, boolean freezeSupplementalColumns){
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/**
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* layers
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*/
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createLayers(treeView);
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/**
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* configuration
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*/
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configureNatTable(treeView, configRegistry, topMostLayer, summaryRowLayer);
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/**
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* handlers and listeners
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*/
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registerHandlersAndListeners(topMostLayer);
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//grab all space
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GridDataFactory.fillDefaults().grab(true, true).applyTo(natTable);
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//update label to current data set
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toolbar.getWsLabel().setText(descriptiveDataSet.getLabel());
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toolbar.getWsLabel().setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
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toolbar.getWsLabel().getParent().layout();
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//initial freeze of supplemental columns
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freezeSupplementalColumns(freezeSupplementalColumns);
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//add tooltip to table
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new CategoricalChartTooltip(this);
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new QuantitativeChartTooltip(this);
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this.layout();
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natTable.doCommand(new ClientAreaResizeCommand(natTable));
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}
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private List<Feature> initFeatureList(FeatureNode node){
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List<Feature> features = new ArrayList<>();
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node.getChildNodes().forEach(childNode->
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{
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features.add(childNode.getFeature());
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features.addAll(initFeatureList(childNode));
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});
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return features;
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}
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public void initDescriptiveDataSet(DescriptiveDataSet descriptiveDataSet){
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this.descriptiveDataSet = descriptiveDataSet;
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//get features/columns stored in descriptive data set
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FeatureTree tree = descriptiveDataSet.getDescriptiveSystem();
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features = initFeatureList(tree.getRoot());
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//init state data for categorical features
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features.forEach(feature->
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{
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if(feature.isSupportsCategoricalData()){
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List<State> supportedStates = new ArrayList<>();
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feature.getSupportedCategoricalEnumerations().forEach(voc->supportedStates.addAll(voc.getTerms()));
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categoricalFeatureToStateMap.put(feature, supportedStates);
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}
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});
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descriptions = new BasicEventList<>();
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}
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private void createLayers(boolean treeView) {
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// use the SortedList constructor with 'null' for the Comparator
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// because the Comparator will be set by configuration
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SortedList<Object> sortedList = new SortedList<>(descriptions, new MatrixRowComparator());
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// wrap the SortedList with the TreeList
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TreeList<Object> treeList = new TreeList(sortedList, new DescriptionTreeFormat(descriptiveDataSet), TreeList.NODES_START_EXPANDED);
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/**
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* data provider
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*/
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SpecimenColumnPropertyAccessor columnPropertyAccessor = new SpecimenColumnPropertyAccessor(this);
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bodyDataProvider = treeView?new ListDataProvider<>(treeList, columnPropertyAccessor):new ListDataProvider<>(sortedList, columnPropertyAccessor);
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configRegistry = new ConfigRegistry();
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/**
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* BODY layer
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*
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*
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CompositeLayer
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- (top) SummaryRowLayer
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- (bottom) ViewportLayer
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^
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ViewportLayer
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^
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TreeLayer (default visible)
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^
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CompositeFreezeLayer
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- viewportLayer
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- selectionLayer
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- freezeLayer
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^
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FreezeLayer
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^
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SelectionLayer
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^
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ColumnHideShowLayer
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^
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ColumnReorderLayer
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^
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DataLayer
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*
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*/
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DataLayer bodyDataLayer = new DataLayer(bodyDataProvider);
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//register labels
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CharacterMatrixConfigLabelAccumulator labelAccumulator = new CharacterMatrixConfigLabelAccumulator(this);
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bodyDataLayer.setConfigLabelAccumulator(labelAccumulator);
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propertyToLabelMap.put(TAXON_COLUMN, Messages.CharacterMatrix_TAXON);
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propertyToLabelMap.put(COLLECTOR_COLUMN, Messages.CharacterMatrix_COLLECTOR_NO);
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propertyToLabelMap.put(IDENTIFIER_COLUMN, Messages.CharacterMatrix_IDENTIFIER);
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propertyToLabelMap.put(COUNTRY_COLUMN, Messages.CharacterMatrix_COUNTRY);
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for(int i=0;i<features.size();i++){
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Feature feature = features.get(i);
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initLabels(i, feature);
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}
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// layer for event handling of GlazedLists and PropertyChanges
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GlazedListsEventLayer eventLayer = new GlazedListsEventLayer<>(bodyDataLayer, treeList);
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GlazedListTreeData treeData = new GlazedListTreeData<>(treeList);
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ITreeRowModel treeRowModel = new GlazedListTreeRowModel<>(treeData);
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bodyLayer = new DefaultBodyLayerStack(eventLayer);
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final SelectionLayer selectionLayer = bodyLayer.getSelectionLayer();
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freezeLayer = new FreezeLayer(selectionLayer);
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final CompositeFreezeLayer compositeFreezeLayer = new CompositeFreezeLayer(
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freezeLayer, bodyLayer.getViewportLayer(), selectionLayer);
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TreeLayer treeLayer = new TreeLayer(compositeFreezeLayer, treeRowModel);
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topMostLayer = treeView?treeLayer:compositeFreezeLayer;
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summaryRowLayer = new FixedSummaryRowLayer(bodyDataLayer, topMostLayer, configRegistry, false);
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//regoster labels with summary prefix for summary layer
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ColumnOverrideLabelAccumulator summaryColumnLabelAccumulator =new ColumnOverrideLabelAccumulator(bodyDataLayer);
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summaryRowLayer.setConfigLabelAccumulator(summaryColumnLabelAccumulator);
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for(int i=0;i<features.size();i++){
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Feature feature = features.get(i);
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summaryColumnLabelAccumulator.registerColumnOverrides(
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i+LEADING_COLUMN_COUNT,
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SummaryRowLayer.DEFAULT_SUMMARY_COLUMN_CONFIG_LABEL_PREFIX+MatrixUtility.getProperty(feature));
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}
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// because the horizontal dependency is the ViewportLayer
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// we need to set the composite dependency to false
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summaryRowLayer.setHorizontalCompositeDependency(false);
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CompositeLayer composite = new CompositeLayer(1, 2);
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composite.setChildLayer("SUMMARY", summaryRowLayer, 0, 0); //$NON-NLS-1$
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composite.setChildLayer(GridRegion.BODY, topMostLayer, 0, 1);
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/**
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* column header layer
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*/
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IDataProvider columnHeaderDataProvider = new DefaultColumnHeaderDataProvider(
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propertyToLabelMap.values().toArray(new String[] {}), propertyToLabelMap);
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DataLayer columnHeaderDataLayer = new DataLayer(columnHeaderDataProvider);
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ColumnHeaderLayer columnHeaderLayer = new ColumnHeaderLayer(columnHeaderDataLayer, topMostLayer, selectionLayer);
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// add the SortHeaderLayer to the column header layer stack
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// as we use GlazedLists, we use the GlazedListsSortModel which
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// delegates the sorting to the SortedList
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final SortHeaderLayer<SpecimenDescription> sortHeaderLayer = new SortHeaderLayer<>(
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columnHeaderLayer,
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new GlazedListsSortModel<>(
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sortedList,
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columnPropertyAccessor,
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configRegistry,
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columnHeaderDataLayer));
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/**
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* row header layer
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*/
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IDataProvider rowHeaderDataProvider = new DefaultRowHeaderDataProvider(bodyDataProvider);
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DefaultRowHeaderDataLayer rowHeaderDataLayer = new DefaultRowHeaderDataLayer(rowHeaderDataProvider);
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FixedSummaryRowHeaderLayer fixedSummaryRowHeaderLayer = new FixedSummaryRowHeaderLayer(rowHeaderDataLayer,
|
405
|
composite, selectionLayer);
|
406
|
fixedSummaryRowHeaderLayer.setSummaryRowLabel("\u2211"); //$NON-NLS-1$
|
407
|
|
408
|
|
409
|
/**
|
410
|
* corner layer
|
411
|
*/
|
412
|
ILayer cornerLayer = new CornerLayer(
|
413
|
new DataLayer(new DefaultCornerDataProvider(columnHeaderDataProvider, rowHeaderDataProvider)),
|
414
|
fixedSummaryRowHeaderLayer, sortHeaderLayer);
|
415
|
|
416
|
|
417
|
/**
|
418
|
* GRID layer (composition of all other layers)
|
419
|
*/
|
420
|
GridLayer gridLayer = new GridLayer(composite, sortHeaderLayer, fixedSummaryRowHeaderLayer, cornerLayer);
|
421
|
|
422
|
natTable.setLayer(gridLayer);
|
423
|
|
424
|
}
|
425
|
|
426
|
private void registerHandlersAndListeners(AbstractLayer topMostLayer) {
|
427
|
// add the ExportCommandHandler to the ViewportLayer in order to make
|
428
|
// exporting work
|
429
|
topMostLayer.registerCommandHandler(new ExportCommandHandler(topMostLayer));
|
430
|
|
431
|
//propagate single cell selection
|
432
|
natTable.addLayerListener(new CellSelectionListener(part));
|
433
|
|
434
|
//register handler for view configuration menu
|
435
|
natTable.registerCommandHandler(toolbar.getDisplayPersistenceDialogCommandHandler());
|
436
|
}
|
437
|
|
438
|
private void configureNatTable(boolean treeView,
|
439
|
ConfigRegistry configRegistry,
|
440
|
AbstractLayer topMostLayer,
|
441
|
FixedSummaryRowLayer summaryRowLayer) {
|
442
|
/**
|
443
|
* CONFIGURATION
|
444
|
*/
|
445
|
natTable.setConfigRegistry(configRegistry);
|
446
|
|
447
|
applyStyles();
|
448
|
|
449
|
//add default configuration because autoconfigure is set to false in constructor
|
450
|
natTable.addConfiguration(new DefaultNatTableStyleConfiguration());
|
451
|
|
452
|
//FIXME: this is for DEBUG ONLY
|
453
|
// natTable.addConfiguration(new DebugMenuConfiguration(natTable));
|
454
|
|
455
|
// override the default sort configuration and change the mouse bindings
|
456
|
// to sort on a single click
|
457
|
if(!treeView){
|
458
|
natTable.addConfiguration(new SingleClickSortConfiguration());
|
459
|
}
|
460
|
|
461
|
natTable.addConfiguration(new CharacterMatrixLabelStyleConfiguration());
|
462
|
|
463
|
// add the header menu configuration for adding the column header menu
|
464
|
// with hide/show actions
|
465
|
natTable.addConfiguration(new CharacterMatrixHeaderMenuConfiguration(natTable));
|
466
|
|
467
|
// add custom configuration for data conversion and add column labels to viewport layer
|
468
|
topMostLayer.addConfiguration(new CellEditorDataConversionConfiguration(this));
|
469
|
|
470
|
//register aggregation configuration
|
471
|
summaryRowLayer.addConfiguration(new AggregationConfiguration(this));
|
472
|
|
473
|
natTable.configure();
|
474
|
}
|
475
|
|
476
|
void freezeSupplementalColumns(boolean freeze){
|
477
|
if(freeze){
|
478
|
FreezeHelper.freeze(freezeLayer, bodyLayer.getViewportLayer(),
|
479
|
new PositionCoordinate(bodyLayer.getViewportLayer(), 0, 0),
|
480
|
new PositionCoordinate(bodyLayer.getViewportLayer(), LEADING_COLUMN_COUNT-1, -1));
|
481
|
}
|
482
|
else{
|
483
|
FreezeHelper.unfreeze(freezeLayer, bodyLayer.getViewportLayer());
|
484
|
}
|
485
|
}
|
486
|
|
487
|
void selectStateItem(ComboViewer comboStates, String stateName){
|
488
|
String[] items = comboStates.getCombo().getItems();
|
489
|
for(int i=0;i<items.length;i++){
|
490
|
if(items[i].equals(stateName)){
|
491
|
comboStates.getCombo().select(i);
|
492
|
break;
|
493
|
}
|
494
|
}
|
495
|
}
|
496
|
|
497
|
private void initLabels(int index, Feature feature) {
|
498
|
indexToFeatureMap.put(index+LEADING_COLUMN_COUNT, feature);
|
499
|
|
500
|
String featureLabel = feature.getLabel();
|
501
|
String property = featureLabel;
|
502
|
//show unit for quantitative data
|
503
|
if(feature.isSupportsQuantitativeData()){
|
504
|
Set<MeasurementUnit> recommendedMeasurementUnits = feature.getRecommendedMeasurementUnits();
|
505
|
if(recommendedMeasurementUnits.size()>1){
|
506
|
MessagingUtils.warningDialog(Messages.CharacterMatrix_INIT_PROBLEM, CharacterMatrix.class,
|
507
|
String.format(Messages.CharacterMatrix_INIT_PROBLEM_MESSAGE, feature.getLabel()));
|
508
|
}
|
509
|
if(recommendedMeasurementUnits.size()==1){
|
510
|
MeasurementUnit unit = recommendedMeasurementUnits.iterator().next();
|
511
|
featureLabel += " ["+unit.getIdInVocabulary()+"]"; //$NON-NLS-1$ //$NON-NLS-2$
|
512
|
}
|
513
|
}
|
514
|
propertyToLabelMap.put(property, featureLabel);
|
515
|
}
|
516
|
|
517
|
public void loadDescriptions(DescriptiveDataSet descriptiveDataSet) {
|
518
|
UUID monitorUuid = CdmStore.getService(IDescriptiveDataSetService.class).monitGetRowWrapper(descriptiveDataSet);
|
519
|
|
520
|
final Collection<RowWrapperDTO> wrappers = new ArrayList<>();
|
521
|
String jobLabel = Messages.CharacterMatrix_LOAD_CHARACTER_DATA;
|
522
|
Job job = Job.create(jobLabel, (ICoreRunnable) monitor -> {
|
523
|
SubMonitor subMonitor = SubMonitor.convert(monitor);
|
524
|
subMonitor.beginTask(jobLabel, IProgressMonitor.UNKNOWN);
|
525
|
IRemotingProgressMonitor remotingMonitor;
|
526
|
try {
|
527
|
remotingMonitor = CdmStore.getProgressMonitorClientManager()
|
528
|
.pollMonitor(jobLabel,
|
529
|
monitorUuid,
|
530
|
50,
|
531
|
null,
|
532
|
(List)null,
|
533
|
subMonitor);
|
534
|
} catch (InterruptedException e) {
|
535
|
MessagingUtils.informationDialog(Messages.CharacterMatrix_LOADING_FAILED_TITLE,
|
536
|
Messages.CharacterMatrix_LOADING_FAILED_MESSAGE);
|
537
|
return;
|
538
|
}
|
539
|
Object result = remotingMonitor.getResult();
|
540
|
if(result instanceof Collection){
|
541
|
wrappers.addAll((Collection<RowWrapperDTO>) result);
|
542
|
}
|
543
|
if(wrappers.isEmpty()){
|
544
|
MessagingUtils.informationDialog(Messages.CharacterMatrix_NO_DESCRIPTION_TITLE,
|
545
|
Messages.CharacterMatrix_NO_DESCRIPTION_MESSAGE);
|
546
|
}
|
547
|
monitor.done();
|
548
|
});
|
549
|
job.addJobChangeListener(new JobChangeAdapter(){
|
550
|
@Override
|
551
|
public void done(IJobChangeEvent event) {
|
552
|
sync.syncExec(()->{
|
553
|
List<RowWrapperDTO> rowsWithoutTaxonNode = wrappers.stream().filter(row->row.getTaxonNode()==null).collect(Collectors.toList());
|
554
|
if(!rowsWithoutTaxonNode.isEmpty()){
|
555
|
String collect = rowsWithoutTaxonNode.stream().
|
556
|
map(row->row.getSpecimenDescription().toString())
|
557
|
.collect(Collectors.joining("\n\n - ")); //$NON-NLS-1$
|
558
|
MessagingUtils.warningDialog(
|
559
|
Messages.CharacterMatrix_NO_NODE_FOUND_TITLE,
|
560
|
this.getClass(),
|
561
|
String.format(Messages.CharacterMatrix_NO_NODE_FOUND_MESSAGE, collect)
|
562
|
);
|
563
|
}
|
564
|
wrappers.stream().filter(row->row.getTaxonNode()!=null).forEach(wrapper->CharacterMatrix.this.descriptions.add(wrapper));
|
565
|
loadingDone();
|
566
|
});
|
567
|
}
|
568
|
});
|
569
|
job.schedule();
|
570
|
}
|
571
|
|
572
|
private void loadingDone() {
|
573
|
this.part.loadingDone();
|
574
|
}
|
575
|
|
576
|
public List<State> getSupportedStatesForCategoricalFeature(Feature feature){
|
577
|
return categoricalFeatureToStateMap.get(feature);
|
578
|
}
|
579
|
|
580
|
public Map<Integer, Feature> getIndexToFeatureMap() {
|
581
|
return indexToFeatureMap;
|
582
|
}
|
583
|
|
584
|
public LinkedMap<String, String> getPropertyToLabelMap() {
|
585
|
return propertyToLabelMap;
|
586
|
}
|
587
|
|
588
|
public void setDirty() {
|
589
|
part.setDirty();
|
590
|
}
|
591
|
|
592
|
public NatTable getNatTable() {
|
593
|
return natTable;
|
594
|
}
|
595
|
|
596
|
public EventList<Object> getDescriptions() {
|
597
|
return descriptions;
|
598
|
}
|
599
|
|
600
|
public DescriptiveDataSet getDescriptiveDataSet() {
|
601
|
return descriptiveDataSet;
|
602
|
}
|
603
|
|
604
|
public Collection<SpecimenNodeWrapper> getSpecimenCache() {
|
605
|
return specimenCache;
|
606
|
}
|
607
|
|
608
|
public void setSpecimenCache(Collection<SpecimenNodeWrapper> specimenCache) {
|
609
|
this.specimenCache = specimenCache.stream()
|
610
|
.filter(wrapper ->
|
611
|
//map descriptions on a list of uuids of the described specimen
|
612
|
!this.descriptions.stream()
|
613
|
.map(o->((RowWrapperDTO)o).getSpecimen().getUuid())
|
614
|
.collect(Collectors.toList())
|
615
|
//an check if the specimen to add is already contained
|
616
|
.contains(wrapper.getUuidAndTitleCache().getUuid())
|
617
|
)
|
618
|
.collect(Collectors.toList());
|
619
|
}
|
620
|
|
621
|
public Properties getNatTableState() {
|
622
|
return toolbar.getNatTableState();
|
623
|
}
|
624
|
|
625
|
public ListDataProvider<Object> getBodyDataProvider() {
|
626
|
return bodyDataProvider;
|
627
|
}
|
628
|
|
629
|
DefaultBodyLayerStack getBodyLayer() {
|
630
|
return bodyLayer;
|
631
|
}
|
632
|
|
633
|
File getStatePropertiesFile() {
|
634
|
return new File(WorkbenchUtility.getBaseLocation(), CHARACTER_MATRIX_STATE_PROPERTIES);
|
635
|
}
|
636
|
|
637
|
public List<Feature> getFeatures() {
|
638
|
return features;
|
639
|
}
|
640
|
|
641
|
public void addUpdateResult(UpdateResult result){
|
642
|
part.addUpdateResult(result);
|
643
|
}
|
644
|
|
645
|
public Map<Feature, CategoricalDataHistogram> getFeatureToHistogramMap() {
|
646
|
return featureToHistogramMap;
|
647
|
}
|
648
|
|
649
|
public Map<Feature, QuantitativeDataStatistics> getFeatureToQuantDataStatisticsMap() {
|
650
|
return featureToQuantDataStatisticsMap;
|
651
|
}
|
652
|
|
653
|
public void toogleIsShowTooltips() {
|
654
|
this.isShowTooltips = !this.isShowTooltips;
|
655
|
}
|
656
|
|
657
|
public boolean isShowTooltips() {
|
658
|
return isShowTooltips;
|
659
|
}
|
660
|
|
661
|
}
|