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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.workingSet.matrix;
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import java.io.File;
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import java.io.FileInputStream;
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import java.io.FileOutputStream;
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import java.io.IOException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collection;
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import java.util.Collections;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.HashSet;
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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 javax.annotation.PostConstruct;
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import javax.annotation.PreDestroy;
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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.IProgressMonitor;
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import org.eclipse.e4.ui.di.Focus;
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import org.eclipse.e4.ui.di.Persist;
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import org.eclipse.e4.ui.model.application.ui.MDirtyable;
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import org.eclipse.e4.ui.model.application.ui.basic.MPart;
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import org.eclipse.e4.ui.workbench.modeling.ESelectionService;
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import org.eclipse.jface.layout.GridDataFactory;
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import org.eclipse.jface.viewers.ArrayContentProvider;
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import org.eclipse.jface.viewers.ComboViewer;
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import org.eclipse.jface.viewers.LabelProvider;
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import org.eclipse.jface.viewers.StructuredSelection;
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import org.eclipse.jface.window.Window;
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import org.eclipse.nebula.widgets.nattable.NatTable;
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import org.eclipse.nebula.widgets.nattable.config.AbstractRegistryConfiguration;
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import org.eclipse.nebula.widgets.nattable.config.CellConfigAttributes;
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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.config.IConfigRegistry;
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import org.eclipse.nebula.widgets.nattable.config.IEditableRule;
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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.edit.EditConfigAttributes;
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import org.eclipse.nebula.widgets.nattable.edit.editor.IComboBoxDataProvider;
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import org.eclipse.nebula.widgets.nattable.export.command.ExportCommand;
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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.grid.GridRegion;
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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.hideshow.ColumnHideShowLayer;
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import org.eclipse.nebula.widgets.nattable.hideshow.RowHideShowLayer;
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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.ILayerListener;
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import org.eclipse.nebula.widgets.nattable.layer.cell.ColumnOverrideLabelAccumulator;
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import org.eclipse.nebula.widgets.nattable.layer.cell.ILayerCell;
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import org.eclipse.nebula.widgets.nattable.layer.event.ILayerEvent;
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import org.eclipse.nebula.widgets.nattable.persistence.PersistenceHelper;
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import org.eclipse.nebula.widgets.nattable.persistence.command.DisplayPersistenceDialogCommand;
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import org.eclipse.nebula.widgets.nattable.persistence.command.DisplayPersistenceDialogCommandHandler;
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import org.eclipse.nebula.widgets.nattable.persistence.command.IStateChangedListener;
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import org.eclipse.nebula.widgets.nattable.persistence.command.StateChangeEvent;
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import org.eclipse.nebula.widgets.nattable.persistence.gui.PersistenceDialog;
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import org.eclipse.nebula.widgets.nattable.reorder.ColumnReorderLayer;
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import org.eclipse.nebula.widgets.nattable.reorder.RowReorderLayer;
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import org.eclipse.nebula.widgets.nattable.selection.SelectionLayer;
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import org.eclipse.nebula.widgets.nattable.selection.event.CellSelectionEvent;
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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.DisplayMode;
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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.ui.menu.AbstractHeaderMenuConfiguration;
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import org.eclipse.nebula.widgets.nattable.ui.menu.PopupMenuBuilder;
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import org.eclipse.nebula.widgets.nattable.viewport.ViewportLayer;
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import org.eclipse.swt.SWT;
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import org.eclipse.swt.events.SelectionAdapter;
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import org.eclipse.swt.events.SelectionEvent;
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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 org.eclipse.swt.widgets.Label;
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import ca.odell.glazedlists.EventList;
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import ca.odell.glazedlists.GlazedLists;
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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.conversation.ConversationHolder;
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import eu.etaxonomy.cdm.api.conversation.IConversationEnabled;
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import eu.etaxonomy.cdm.api.service.IWorkingSetService;
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import eu.etaxonomy.cdm.model.common.TermVocabulary;
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import eu.etaxonomy.cdm.model.description.DescriptionBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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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.model.description.WorkingSet;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.persistence.hibernate.CdmDataChangeMap;
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import eu.etaxonomy.taxeditor.editor.workingSet.matrix.categorical.CategoricalDataCellEditor;
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import eu.etaxonomy.taxeditor.editor.workingSet.matrix.categorical.CategoricalDataDisplayConverter;
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import eu.etaxonomy.taxeditor.editor.workingSet.matrix.quantitative.QuantitativeDataCellEditor;
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import eu.etaxonomy.taxeditor.editor.workingSet.matrix.quantitative.QuantitativeDataDisplayConverter;
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import eu.etaxonomy.taxeditor.editor.workingSet.matrix.supplementalInfo.SupplementalInfoDisplayConverter;
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import eu.etaxonomy.taxeditor.model.DescriptionHelper;
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import eu.etaxonomy.taxeditor.model.IDirtyMarkable;
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import eu.etaxonomy.taxeditor.model.IPartContentHasDetails;
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import eu.etaxonomy.taxeditor.model.ImageResources;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.session.ICdmEntitySession;
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import eu.etaxonomy.taxeditor.session.ICdmEntitySessionEnabled;
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import eu.etaxonomy.taxeditor.store.CdmStore;
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import eu.etaxonomy.taxeditor.workbench.WorkbenchUtility;
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import eu.etaxonomy.taxeditor.workbench.part.IE4SavablePart;
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/**
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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 implements IE4SavablePart, IPartContentHasDetails, IConversationEnabled, IDirtyMarkable,
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ICdmEntitySessionEnabled{
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private static final List<String> WS_PROPERTY_PATH = Arrays.asList(new String[] {
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"descriptions", //$NON-NLS-1$
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"descriptions.descriptionElements", //$NON-NLS-1$
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"descriptions.descriptionElements.inDescription", //$NON-NLS-1$
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"descriptions.descriptionElements.inDescription.descriptionElements", //$NON-NLS-1$
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"descriptions.descriptionElements.feature", //$NON-NLS-1$
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});
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private static final String CHARACTER_MATRIX_STATE_PROPERTIES = "characterMatrixState.properties";
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private static final int LEADING_COLUMN_COUNT = 4;
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private static final String TAXON_COLUMN = "taxon_column";
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private static final String COLLECTOR_COLUMN = "collector_column";
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private static final String IDENTIFIER_COLUMN = "identifier_column";
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private static final String COUNTRY_COLUMN = "country_column";
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private WorkingSet workingSet;
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private Composite parent;
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private ConversationHolder conversation;
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private ICdmEntitySession cdmEntitySession;
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@Inject
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private ESelectionService selService;
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@Inject
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private MDirtyable dirty;
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@Inject
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private MPart thisPart;
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private NatTable natTable;
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private Map<Integer, Feature> indexToFeatureMap = new HashMap<>();
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private LinkedMap<String, String> propertyToLabelMap = new LinkedMap<>();
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private Properties natTableState;
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private EventList<Object> descriptions;
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private Collection<SpecimenOrObservationBase> specimenCache = null;
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@PostConstruct
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public void create(Composite parent) {
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if(CdmStore.isActive() && conversation==null){
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conversation = CdmStore.createConversation();
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}
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if(cdmEntitySession == null){
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cdmEntitySession = CdmStore.getCurrentSessionManager().newSession(this, true);
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}
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else{
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return;
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}
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parent.setLayout(new GridLayout());
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this.parent = parent;
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}
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public void init(UUID workingSetUuid) {
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this.workingSet = CdmStore.getService(IWorkingSetService.class).load(workingSetUuid, WS_PROPERTY_PATH);
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if(workingSet.getDescriptiveSystem()==null){
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MessagingUtils.informationDialog("Editor could not be opened", "The working set has no feature tree selected.");
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return;
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}
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thisPart.setLabel(workingSet.getLabel());
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Composite toolbarComposite = new Composite(parent, SWT.NONE);
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toolbarComposite.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
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toolbarComposite.setLayout(new GridLayout(4, false));
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//get features/columns stored in working set
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FeatureTree tree = workingSet.getDescriptiveSystem();
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List<Feature> features = new ArrayList<>(tree.getDistinctFeatures());
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Collections.sort(features);
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descriptions = GlazedLists.eventList(getDescriptions(workingSet));
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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, null);
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// wrap the SortedList with the TreeList
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TreeList treeList = new TreeList(sortedList, new DescriptionTreeFormat(), TreeList.NODES_START_EXPANDED);
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ConfigRegistry configRegistry = new ConfigRegistry();
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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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IDataProvider bodyDataProvider = new ListDataProvider<Object>(treeList, columnPropertyAccessor);
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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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SelectionLayer
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^
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RowHideShowLayer
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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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RowReorderLayer
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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 for columns
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ColumnOverrideLabelAccumulator bodyColumnLabelAccumulator =new ColumnOverrideLabelAccumulator(bodyDataLayer);
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bodyDataLayer.setConfigLabelAccumulator(bodyColumnLabelAccumulator);
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propertyToLabelMap.put(TAXON_COLUMN, "Taxon");
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bodyColumnLabelAccumulator.registerColumnOverrides(0, TAXON_COLUMN);
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propertyToLabelMap.put(COLLECTOR_COLUMN, "Collector + No");
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bodyColumnLabelAccumulator.registerColumnOverrides(1, COLLECTOR_COLUMN);
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propertyToLabelMap.put(IDENTIFIER_COLUMN, "Identifier");
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bodyColumnLabelAccumulator.registerColumnOverrides(2, IDENTIFIER_COLUMN);
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propertyToLabelMap.put(COUNTRY_COLUMN, "Country");
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bodyColumnLabelAccumulator.registerColumnOverrides(3, COUNTRY_COLUMN);
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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(bodyColumnLabelAccumulator, 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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RowReorderLayer rowReorderLayer = new RowReorderLayer(eventLayer);
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ColumnReorderLayer columnReorderLayer = new ColumnReorderLayer(rowReorderLayer);
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ColumnHideShowLayer columnHideShowLayer = new ColumnHideShowLayer(columnReorderLayer);
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RowHideShowLayer rowHideShowLayer = new RowHideShowLayer(columnHideShowLayer);
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SelectionLayer selectionLayer = new SelectionLayer(rowHideShowLayer);
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TreeLayer treeLayer = new TreeLayer(selectionLayer, treeRowModel);
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ViewportLayer viewportLayer = new ViewportLayer(treeLayer);
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// create a standalone FixedSummaryRowLayer
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// since the summary row should be fixed at the top of the body
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// region the horizontal dependency of the FixedSummaryRowLayer
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// is the ViewportLayer
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FixedSummaryRowLayer summaryRowLayer =
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new FixedSummaryRowLayer(bodyDataLayer, viewportLayer, 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);
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composite.setChildLayer(GridRegion.BODY, viewportLayer, 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, viewportLayer, 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,
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composite, selectionLayer);
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365
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fixedSummaryRowHeaderLayer.setSummaryRowLabel("\u2211");
|
366
|
|
367
|
|
368
|
/**
|
369
|
* corner layer
|
370
|
*/
|
371
|
ILayer cornerLayer = new CornerLayer(
|
372
|
new DataLayer(new DefaultCornerDataProvider(columnHeaderDataProvider, rowHeaderDataProvider)),
|
373
|
fixedSummaryRowHeaderLayer, sortHeaderLayer);
|
374
|
|
375
|
|
376
|
/**
|
377
|
* GRID layer (composition of all other layers)
|
378
|
*/
|
379
|
GridLayer gridLayer = new GridLayer(composite, sortHeaderLayer, fixedSummaryRowHeaderLayer, cornerLayer);
|
380
|
|
381
|
|
382
|
|
383
|
natTable = new NatTable(parent, gridLayer, false);
|
384
|
|
385
|
|
386
|
/**
|
387
|
* CONFIGURATION
|
388
|
*/
|
389
|
natTable.setConfigRegistry(configRegistry);
|
390
|
|
391
|
|
392
|
//add default configuration because autoconfigure is set to false in constructor
|
393
|
natTable.addConfiguration(new DefaultNatTableStyleConfiguration());
|
394
|
|
395
|
//FIXME: this is for DEBUG ONLY
|
396
|
// natTable.addConfiguration(new DebugMenuConfiguration(natTable));
|
397
|
|
398
|
// override the default sort configuration and change the mouse bindings
|
399
|
// to sort on a single click
|
400
|
natTable.addConfiguration(new SingleClickSortConfiguration());
|
401
|
|
402
|
|
403
|
// add the header menu configuration for adding the column header menu
|
404
|
// with hide/show actions
|
405
|
natTable.addConfiguration(new AbstractHeaderMenuConfiguration(natTable) {
|
406
|
|
407
|
@Override
|
408
|
protected PopupMenuBuilder createColumnHeaderMenu(NatTable natTable) {
|
409
|
return super.createColumnHeaderMenu(natTable)
|
410
|
.withHideColumnMenuItem()
|
411
|
.withShowAllColumnsMenuItem();
|
412
|
}
|
413
|
|
414
|
@Override
|
415
|
protected PopupMenuBuilder createRowHeaderMenu(NatTable natTable) {
|
416
|
return super.createRowHeaderMenu(natTable)
|
417
|
.withHideRowMenuItem()
|
418
|
.withShowAllRowsMenuItem();
|
419
|
}
|
420
|
|
421
|
@Override
|
422
|
protected PopupMenuBuilder createCornerMenu(NatTable natTable) {
|
423
|
return super.createCornerMenu(natTable)
|
424
|
.withShowAllColumnsMenuItem()
|
425
|
.withShowAllRowsMenuItem();
|
426
|
}
|
427
|
});
|
428
|
|
429
|
// add custom configuration for data conversion and add column labels to viewport layer
|
430
|
viewportLayer.addConfiguration(new AbstractRegistryConfiguration() {
|
431
|
@Override
|
432
|
public void configureRegistry(IConfigRegistry configRegistry) {
|
433
|
//add display converter for string representation
|
434
|
configRegistry.registerConfigAttribute(
|
435
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
436
|
new SupplementalInfoDisplayConverter(),
|
437
|
DisplayMode.NORMAL,
|
438
|
TAXON_COLUMN);
|
439
|
configRegistry.registerConfigAttribute(
|
440
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
441
|
new SupplementalInfoDisplayConverter(),
|
442
|
DisplayMode.NORMAL,
|
443
|
COLLECTOR_COLUMN);
|
444
|
configRegistry.registerConfigAttribute(
|
445
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
446
|
new SupplementalInfoDisplayConverter(),
|
447
|
DisplayMode.NORMAL,
|
448
|
IDENTIFIER_COLUMN);
|
449
|
configRegistry.registerConfigAttribute(
|
450
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
451
|
new SupplementalInfoDisplayConverter(),
|
452
|
DisplayMode.NORMAL,
|
453
|
COUNTRY_COLUMN);
|
454
|
features.forEach(feature->registerColumnConfiguration(feature, configRegistry));
|
455
|
}
|
456
|
|
457
|
});
|
458
|
|
459
|
//register aggregation configuration for each feature
|
460
|
features.forEach(feature->summaryRowLayer.addConfiguration(new AggregationConfiguration(bodyDataProvider, feature)));
|
461
|
|
462
|
// add the ExportCommandHandler to the ViewportLayer in order to make
|
463
|
// exporting work
|
464
|
viewportLayer.registerCommandHandler(new ExportCommandHandler(viewportLayer));
|
465
|
|
466
|
//propagate single cell selection
|
467
|
natTable.addLayerListener(new ILayerListener() {
|
468
|
@Override
|
469
|
public void handleLayerEvent(ILayerEvent event) {
|
470
|
if(event instanceof CellSelectionEvent){
|
471
|
CellSelectionEvent cellSelectionEvent = (CellSelectionEvent)event;
|
472
|
Collection<ILayerCell> selectedCells = cellSelectionEvent.getSelectionLayer().getSelectedCells();
|
473
|
StructuredSelection selection = new StructuredSelection();
|
474
|
if(selectedCells.size()==1){
|
475
|
ILayerCell cell = selectedCells.iterator().next();
|
476
|
Object dataValue = cell.getDataValue();
|
477
|
if(dataValue!=null){
|
478
|
selection = new StructuredSelection(dataValue);
|
479
|
}
|
480
|
}
|
481
|
selService.setSelection(selection);
|
482
|
}
|
483
|
}
|
484
|
});
|
485
|
|
486
|
natTable.configure();
|
487
|
|
488
|
GridDataFactory.fillDefaults().grab(true, true).applyTo(natTable);
|
489
|
|
490
|
/**
|
491
|
* Info label
|
492
|
*/
|
493
|
Label wsLabel = new Label(toolbarComposite, SWT.NONE);
|
494
|
wsLabel.setText(workingSet.getLabel());
|
495
|
wsLabel.setLayoutData(new GridData(SWT.FILL, SWT.CENTER, true, false));
|
496
|
|
497
|
/**
|
498
|
* Table state persistence
|
499
|
*/
|
500
|
natTableState = new Properties();
|
501
|
//load persisted state
|
502
|
File statePropertiesFile = getStatePropertiesFile();
|
503
|
FileInputStream inputStream;
|
504
|
try {
|
505
|
inputStream = new FileInputStream(statePropertiesFile);
|
506
|
natTableState.load(inputStream);
|
507
|
} catch (IOException e) {
|
508
|
MessagingUtils.info("No initial state properties file found for character matrix");
|
509
|
}
|
510
|
|
511
|
DisplayPersistenceDialogCommandHandler handler =
|
512
|
new DisplayPersistenceDialogCommandHandler(natTableState, natTable);
|
513
|
gridLayer.registerCommandHandler(handler);
|
514
|
// create a combobox for showing the available view states
|
515
|
ComboViewer comboStates= new ComboViewer(toolbarComposite, SWT.DROP_DOWN) ;
|
516
|
Collection<String> availableStates = PersistenceHelper.getAvailableStates(natTableState);
|
517
|
comboStates.setLabelProvider(new LabelProvider(){
|
518
|
@Override
|
519
|
public String getText(Object element) {
|
520
|
if(element instanceof String && ((String) element).isEmpty()){
|
521
|
return "-default-";
|
522
|
}
|
523
|
return super.getText(element);
|
524
|
}
|
525
|
});
|
526
|
comboStates.setContentProvider(new ArrayContentProvider());
|
527
|
comboStates.addSelectionChangedListener(e->
|
528
|
{
|
529
|
int index = comboStates.getCombo().getSelectionIndex();
|
530
|
if (index >= 0) {
|
531
|
String selected = comboStates.getCombo().getItem(index);
|
532
|
// load the state
|
533
|
natTable.loadState(selected, natTableState);
|
534
|
natTableState.setProperty(PersistenceDialog.ACTIVE_VIEW_CONFIGURATION_KEY, selected);
|
535
|
}
|
536
|
});
|
537
|
comboStates.setInput(availableStates);
|
538
|
if(comboStates.getCombo().getItemCount()>0){
|
539
|
comboStates.getCombo().select(0);
|
540
|
}
|
541
|
|
542
|
// add listener to update the combo on view state management changes
|
543
|
handler.addStateChangeListener(new IStateChangedListener() {
|
544
|
@Override
|
545
|
public void handleStateChange(StateChangeEvent event) {
|
546
|
comboStates.setInput(PersistenceHelper.getAvailableStates(natTableState));
|
547
|
selectStateItem(comboStates, event.getViewConfigName());
|
548
|
}
|
549
|
});
|
550
|
|
551
|
// add button to show dialog
|
552
|
Button btnManageState = new Button(toolbarComposite, SWT.PUSH);
|
553
|
btnManageState.setImage(ImageResources.getImage(ImageResources.SETTINGS));
|
554
|
btnManageState.addSelectionListener(new SelectionAdapter() {
|
555
|
@Override
|
556
|
public void widgetSelected(SelectionEvent e) {
|
557
|
natTable.doCommand(new DisplayPersistenceDialogCommand(natTable));
|
558
|
selectStateItem(comboStates, natTableState.get(PersistenceDialog.ACTIVE_VIEW_CONFIGURATION_KEY).toString());
|
559
|
}
|
560
|
});
|
561
|
|
562
|
/**
|
563
|
* excel export
|
564
|
*/
|
565
|
Button btnExcelExport = new Button(toolbarComposite, SWT.PUSH);
|
566
|
btnExcelExport.setToolTipText("Export to Excel");
|
567
|
btnExcelExport.setImage(ImageResources.getImage(ImageResources.EXPORT));
|
568
|
btnExcelExport.addSelectionListener(new SelectionAdapter() {
|
569
|
@Override
|
570
|
public void widgetSelected(SelectionEvent e) {
|
571
|
natTable.doCommand(
|
572
|
new ExportCommand(
|
573
|
natTable.getConfigRegistry(),
|
574
|
natTable.getShell()));
|
575
|
}
|
576
|
});
|
577
|
|
578
|
/**
|
579
|
* Add description button
|
580
|
*/
|
581
|
Button btnAddDescription = new Button(parent, SWT.PUSH);
|
582
|
btnAddDescription.setImage(ImageResources.getImage(ImageResources.ADD_ICON));
|
583
|
btnAddDescription.addSelectionListener(new SelectionAdapter() {
|
584
|
@Override
|
585
|
public void widgetSelected(SelectionEvent e) {
|
586
|
SpecimenSelectionDialog dialog = new SpecimenSelectionDialog(natTable.getShell(), CharacterMatrix.this);
|
587
|
if(dialog.open()==Window.OK){
|
588
|
Collection<SpecimenOrObservationBase> specimens = dialog.getSpecimen();
|
589
|
boolean hasAdded = false;
|
590
|
for (SpecimenOrObservationBase specimen : specimens) {
|
591
|
SpecimenDescription description = getDescriptionForWorkingSet(specimen);
|
592
|
if(!workingSet.getDescriptions().contains(description)){
|
593
|
CharacterMatrix.this.descriptions.add(new RowWrapper(description));
|
594
|
workingSet.addDescription(description);
|
595
|
hasAdded = true;
|
596
|
}
|
597
|
}
|
598
|
if(hasAdded){
|
599
|
setDirty();
|
600
|
}
|
601
|
}
|
602
|
}
|
603
|
});
|
604
|
parent.layout();
|
605
|
}
|
606
|
|
607
|
private void selectStateItem(ComboViewer comboStates, String stateName){
|
608
|
String[] items = comboStates.getCombo().getItems();
|
609
|
for(int i=0;i<items.length;i++){
|
610
|
if(items[i].equals(stateName)){
|
611
|
comboStates.getCombo().select(i);
|
612
|
break;
|
613
|
}
|
614
|
}
|
615
|
}
|
616
|
|
617
|
private SpecimenDescription getDescriptionForWorkingSet(SpecimenOrObservationBase specimen){
|
618
|
Set<Feature> wsFeatures = workingSet.getDescriptiveSystem().getDistinctFeatures();
|
619
|
List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
|
620
|
|
621
|
for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
|
622
|
Set<Feature> specimenDescriptionFeatures = new HashSet<>();
|
623
|
//gather specimen description features and check for match with WS features
|
624
|
for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
|
625
|
Feature feature = specimenDescriptionElement.getFeature();
|
626
|
specimenDescriptionFeatures.add(feature);
|
627
|
if(wsFeatures.contains(feature)){
|
628
|
matchingDescriptionElements.add(specimenDescriptionElement);
|
629
|
}
|
630
|
}
|
631
|
//if description with the exact same features is found return the description
|
632
|
if(specimenDescriptionFeatures.equals(wsFeatures)){
|
633
|
return specimenDescription;
|
634
|
}
|
635
|
}
|
636
|
//Create new specimen description if no match was found
|
637
|
setDirty();
|
638
|
SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
|
639
|
newDesription.setTitleCache("WorkingSet "+workingSet.getLabel()+": "+newDesription.generateTitle(), true);
|
640
|
|
641
|
//check for equals description element (same feature and same values)
|
642
|
Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
|
643
|
for(DescriptionElementBase element:matchingDescriptionElements){
|
644
|
List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
|
645
|
if(list==null){
|
646
|
list = new ArrayList<>();
|
647
|
}
|
648
|
list.add(element);
|
649
|
featureToElementMap.put(element.getFeature(), list);
|
650
|
}
|
651
|
Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
|
652
|
for(Feature feature:featureToElementMap.keySet()){
|
653
|
List<DescriptionElementBase> elements = featureToElementMap.get(feature);
|
654
|
//no duplicate description elements found for this feature
|
655
|
if(elements.size()==1){
|
656
|
descriptionElementsToClone.add(elements.get(0));
|
657
|
}
|
658
|
//duplicates found -> check if all are equal
|
659
|
else{
|
660
|
DescriptionElementBase match = null;
|
661
|
for (DescriptionElementBase descriptionElementBase : elements) {
|
662
|
if(match==null){
|
663
|
match = descriptionElementBase;
|
664
|
}
|
665
|
else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
|
666
|
match = null;
|
667
|
MessagingUtils.informationDialog("Multiple data found",
|
668
|
String.format("Multiple description elements with different values "
|
669
|
+ "found for feature '%s'.\nData will not be copied to new specimen description.", feature.getLabel()));
|
670
|
break;
|
671
|
}
|
672
|
}
|
673
|
if(match!=null){
|
674
|
descriptionElementsToClone.add(match);
|
675
|
}
|
676
|
}
|
677
|
}
|
678
|
//clone matching descriptionElements
|
679
|
for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
|
680
|
DescriptionElementBase clone;
|
681
|
try {
|
682
|
clone = descriptionElementBase.clone(newDesription);
|
683
|
clone.getSources().forEach(source -> source.setOriginalNameString(DescriptionHelper.getLabel(descriptionElementBase)));
|
684
|
} catch (CloneNotSupportedException e) {
|
685
|
MessagingUtils.error(CharacterMatrix.class, e);
|
686
|
}
|
687
|
}
|
688
|
return newDesription;
|
689
|
|
690
|
}
|
691
|
|
692
|
private void initLabels(final ColumnOverrideLabelAccumulator columnLabelAccumulator,
|
693
|
int index, Feature feature) {
|
694
|
|
695
|
columnLabelAccumulator.registerColumnOverrides(index+LEADING_COLUMN_COUNT, MatrixUtility.getProperty(feature));
|
696
|
indexToFeatureMap.put(index+LEADING_COLUMN_COUNT, feature);
|
697
|
|
698
|
String featureLabel = feature.getLabel();
|
699
|
String property = featureLabel;
|
700
|
//show unit for quantitative data
|
701
|
if(feature.isSupportsQuantitativeData()){
|
702
|
Set<MeasurementUnit> recommendedMeasurementUnits = feature.getRecommendedMeasurementUnits();
|
703
|
if(recommendedMeasurementUnits.size()!=1){
|
704
|
MessagingUtils.warningDialog("Column initialization problem", CharacterMatrix.class,
|
705
|
String.format("Only one unit is allowed for quantitative data: %s", feature.getLabel()));
|
706
|
return;
|
707
|
}
|
708
|
MeasurementUnit unit = recommendedMeasurementUnits.iterator().next();
|
709
|
featureLabel += " ["+unit.getLabel()+"]";
|
710
|
}
|
711
|
propertyToLabelMap.put(property, featureLabel);
|
712
|
}
|
713
|
|
714
|
private void registerColumnConfiguration(Feature feature, IConfigRegistry configRegistry) {
|
715
|
//make cell editable
|
716
|
configRegistry.registerConfigAttribute(
|
717
|
EditConfigAttributes.CELL_EDITABLE_RULE,
|
718
|
IEditableRule.ALWAYS_EDITABLE,
|
719
|
DisplayMode.EDIT,
|
720
|
MatrixUtility.getProperty(feature)
|
721
|
);
|
722
|
if(feature.isSupportsQuantitativeData()){
|
723
|
//add display converter for string representation
|
724
|
configRegistry.registerConfigAttribute(
|
725
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
726
|
new QuantitativeDataDisplayConverter(),
|
727
|
DisplayMode.NORMAL,
|
728
|
MatrixUtility.getProperty(feature));
|
729
|
//register quantitative editor
|
730
|
configRegistry.registerConfigAttribute(
|
731
|
EditConfigAttributes.CELL_EDITOR,
|
732
|
new QuantitativeDataCellEditor(feature.getRecommendedStatisticalMeasures(), this),
|
733
|
DisplayMode.EDIT,
|
734
|
MatrixUtility.getProperty(feature));
|
735
|
}
|
736
|
else if(feature.isSupportsCategoricalData()){
|
737
|
//add display converter for string representation
|
738
|
configRegistry.registerConfigAttribute(
|
739
|
CellConfigAttributes.DISPLAY_CONVERTER,
|
740
|
new CategoricalDataDisplayConverter(),
|
741
|
DisplayMode.NORMAL,
|
742
|
MatrixUtility.getProperty(feature));
|
743
|
|
744
|
//add combo box cell editor
|
745
|
CategoricalDataCellEditor comboBoxCellEditor = new CategoricalDataCellEditor(new IComboBoxDataProvider() {
|
746
|
|
747
|
@Override
|
748
|
public List<?> getValues(int columnIndex, int rowIndex) {
|
749
|
List<State> states = new ArrayList<>();
|
750
|
Feature feature = indexToFeatureMap.get(columnIndex);
|
751
|
if(feature.isSupportsCategoricalData()){
|
752
|
Set<TermVocabulary<State>> stateVocs = feature.getSupportedCategoricalEnumerations();
|
753
|
for (TermVocabulary<State> voc : stateVocs) {
|
754
|
states.addAll(voc.getTerms());
|
755
|
}
|
756
|
}
|
757
|
return states;
|
758
|
}
|
759
|
}, 5, this);
|
760
|
//register editor
|
761
|
configRegistry.registerConfigAttribute(EditConfigAttributes.CELL_EDITOR,
|
762
|
comboBoxCellEditor,
|
763
|
DisplayMode.EDIT,
|
764
|
MatrixUtility.getProperty(feature));
|
765
|
|
766
|
}
|
767
|
|
768
|
}
|
769
|
|
770
|
private List<RowWrapper> getDescriptions(WorkingSet workingSet) {
|
771
|
List<RowWrapper> rowWrappers = new ArrayList<>();
|
772
|
Set<DescriptionBase> wsDescriptions = workingSet.getDescriptions();
|
773
|
for (DescriptionBase descriptionBase : wsDescriptions) {
|
774
|
if(descriptionBase instanceof SpecimenDescription){
|
775
|
rowWrappers.add(new RowWrapper((SpecimenDescription) descriptionBase));
|
776
|
}
|
777
|
}
|
778
|
return rowWrappers;
|
779
|
}
|
780
|
|
781
|
public Map<Integer, Feature> getIndexToFeatureMap() {
|
782
|
return indexToFeatureMap;
|
783
|
}
|
784
|
|
785
|
public LinkedMap<String, String> getPropertyToLabelMap() {
|
786
|
return propertyToLabelMap;
|
787
|
}
|
788
|
|
789
|
public void setDirty() {
|
790
|
this.dirty.setDirty(true);
|
791
|
}
|
792
|
|
793
|
public NatTable getNatTable() {
|
794
|
return natTable;
|
795
|
}
|
796
|
|
797
|
public WorkingSet getWorkingSet() {
|
798
|
return workingSet;
|
799
|
}
|
800
|
|
801
|
public Collection<SpecimenOrObservationBase> getSpecimenCache() {
|
802
|
return specimenCache;
|
803
|
}
|
804
|
|
805
|
public void setSpecimenCache(Collection<SpecimenOrObservationBase> specimenCache) {
|
806
|
this.specimenCache = specimenCache;
|
807
|
}
|
808
|
|
809
|
@Persist
|
810
|
@Override
|
811
|
public void save(IProgressMonitor monitor) {
|
812
|
CdmStore.getService(IWorkingSetService.class).merge(workingSet, true);
|
813
|
conversation.commit();
|
814
|
dirty.setDirty(false);
|
815
|
}
|
816
|
|
817
|
@Focus
|
818
|
public void setFocus(){
|
819
|
if(conversation!=null){
|
820
|
conversation.bind();
|
821
|
}
|
822
|
if(cdmEntitySession != null) {
|
823
|
cdmEntitySession.bind();
|
824
|
}
|
825
|
}
|
826
|
|
827
|
@PreDestroy
|
828
|
public void dispose(){
|
829
|
if (conversation != null) {
|
830
|
conversation.close();
|
831
|
conversation = null;
|
832
|
}
|
833
|
if(cdmEntitySession != null) {
|
834
|
cdmEntitySession.dispose();
|
835
|
cdmEntitySession = null;
|
836
|
}
|
837
|
dirty.setDirty(false);
|
838
|
if(natTableState!=null){
|
839
|
try (FileOutputStream tableStateStream =
|
840
|
new FileOutputStream(getStatePropertiesFile())) {
|
841
|
natTableState.store(tableStateStream, null);
|
842
|
} catch (IOException ioe) {
|
843
|
ioe.printStackTrace();
|
844
|
}
|
845
|
}
|
846
|
}
|
847
|
|
848
|
private File getStatePropertiesFile() {
|
849
|
return new File(WorkbenchUtility.getBaseLocation(), CHARACTER_MATRIX_STATE_PROPERTIES);
|
850
|
}
|
851
|
|
852
|
/**
|
853
|
* {@inheritDoc}
|
854
|
*/
|
855
|
@Override
|
856
|
public void update(CdmDataChangeMap arg0) {
|
857
|
}
|
858
|
|
859
|
/**
|
860
|
* {@inheritDoc}
|
861
|
*/
|
862
|
@Override
|
863
|
public ConversationHolder getConversationHolder() {
|
864
|
return conversation;
|
865
|
}
|
866
|
|
867
|
/**
|
868
|
* {@inheritDoc}
|
869
|
*/
|
870
|
@Override
|
871
|
public void changed(Object element) {
|
872
|
setDirty();
|
873
|
natTable.refresh();
|
874
|
}
|
875
|
|
876
|
/**
|
877
|
* {@inheritDoc}
|
878
|
*/
|
879
|
@Override
|
880
|
public void forceDirty() {
|
881
|
setDirty();
|
882
|
}
|
883
|
|
884
|
|
885
|
/**
|
886
|
* {@inheritDoc}
|
887
|
*/
|
888
|
@Override
|
889
|
public ICdmEntitySession getCdmEntitySession() {
|
890
|
return cdmEntitySession;
|
891
|
}
|
892
|
|
893
|
|
894
|
/**
|
895
|
* {@inheritDoc}
|
896
|
*/
|
897
|
@Override
|
898
|
public Collection<WorkingSet> getRootEntities() {
|
899
|
return Collections.singleton(this.workingSet);
|
900
|
}
|
901
|
|
902
|
|
903
|
/**
|
904
|
* {@inheritDoc}
|
905
|
*/
|
906
|
@Override
|
907
|
public Map<Object, List<String>> getPropertyPathsMap() {
|
908
|
Map<Object, List<String>> propertyMap = new HashMap<>();
|
909
|
propertyMap.put(SpecimenOrObservationBase.class,WS_PROPERTY_PATH);
|
910
|
return propertyMap;
|
911
|
}
|
912
|
|
913
|
/*
|
914
|
* Using a String directly as the tree item has the possible disadvantage of
|
915
|
* haven non-unique items in the tree within subtrees.
|
916
|
*/
|
917
|
private class DescriptionTreeFormat implements TreeList.Format<Object> {
|
918
|
|
919
|
private Map parentMapping = new HashMap<>();
|
920
|
|
921
|
/**
|
922
|
* Populate path with a list describing the path from a root node to
|
923
|
* this element. Upon returning, the list must have size >= 1, where the
|
924
|
* provided element identical to the list's last element. This
|
925
|
* implementation will use the first object found for a last name as
|
926
|
* root node by storing it within a map. If there is already an object
|
927
|
* stored for the lastname of the given element, it will be used as root
|
928
|
* for the path.
|
929
|
*/
|
930
|
@Override
|
931
|
public void getPath(List path, Object element) {
|
932
|
if(element instanceof RowWrapper){
|
933
|
//TODO: check for multiple taxon nodes in multiple classifications
|
934
|
Taxon taxon = (Taxon) ((RowWrapper) element).getAssociatedTaxa().iterator().next();
|
935
|
Set<TaxonNode> taxonNodes = taxon.getTaxonNodes();
|
936
|
if(taxonNodes!=null){
|
937
|
TaxonNode node = taxonNodes.iterator().next();
|
938
|
addPathRecursive(path, node);
|
939
|
// Object rowWrapperParentNode = parentMapping.get(node);
|
940
|
// if(rowWrapperParentNode!=null){
|
941
|
// path.add(rowWrapperParentNode);
|
942
|
// }
|
943
|
// else{
|
944
|
// TaxonNode parentNode = HibernateProxyHelper.deproxy(node.getParent(), TaxonNode.class);
|
945
|
// while(parentNode!=null){
|
946
|
// path.add(parentNode);
|
947
|
// parentMapping.put(node, parentNode);
|
948
|
// if(parentNode instanceof TaxonNode){
|
949
|
// if(parentMapping.get(parentNode)!=null){
|
950
|
// path.add(parentMapping).get(parentNode);
|
951
|
// }
|
952
|
// else{
|
953
|
// parentNode = HibernateProxyHelper.deproxy(parentNode.getParent(), TaxonNode.class);
|
954
|
// }
|
955
|
// }
|
956
|
// }
|
957
|
// }
|
958
|
}
|
959
|
}
|
960
|
path.add(element);
|
961
|
}
|
962
|
|
963
|
private void addPathRecursive(List path, TaxonNode node){
|
964
|
if(node.getParent()!=null){
|
965
|
addPathRecursive(path, node.getParent());
|
966
|
path.add(node);
|
967
|
}
|
968
|
}
|
969
|
|
970
|
/**
|
971
|
* Simply always return true.
|
972
|
*
|
973
|
* @return true if this element can have child elements, or
|
974
|
* false if it is always a leaf node.
|
975
|
*/
|
976
|
@Override
|
977
|
public boolean allowsChildren(Object element) {
|
978
|
return true;
|
979
|
}
|
980
|
|
981
|
/**
|
982
|
* Returns the comparator used to order path elements of the specified
|
983
|
* depth. If enforcing order at this level is not intended, this method
|
984
|
* should return null. We do a simple sorting of the last
|
985
|
* names of the persons to show so the tree nodes are sorted in
|
986
|
* alphabetical order.
|
987
|
*/
|
988
|
@Override
|
989
|
public Comparator<Object> getComparator(int depth) {
|
990
|
return new Comparator<Object>() {
|
991
|
|
992
|
@Override
|
993
|
public int compare(Object o1, Object o2) {
|
994
|
// if(o1 instanceof RowWrapper && o2 instanceof RowWrapper){
|
995
|
// return ((RowWrapper) o1).getSpecimenDescription().getId()-(((RowWrapper) o2).getSpecimenDescription().getId());
|
996
|
// }
|
997
|
// else
|
998
|
if(o1 instanceof TaxonNode && o2 instanceof TaxonNode){
|
999
|
return ((TaxonNode) o1).getTaxon().getName().getNameCache().compareTo(((TaxonNode) o2).getTaxon().getName().getNameCache());
|
1000
|
}
|
1001
|
return 0;
|
1002
|
}
|
1003
|
|
1004
|
};
|
1005
|
}
|
1006
|
}
|
1007
|
|
1008
|
|
1009
|
}
|