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/**
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* Copyright (C) 2007 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.molecular.handler;
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import java.io.File;
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import java.io.IOException;
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import org.biojava.bio.chromatogram.UnsupportedChromatogramFormatException;
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import org.eclipse.core.commands.AbstractHandler;
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import org.eclipse.core.commands.ExecutionEvent;
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import org.eclipse.core.commands.ExecutionException;
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import org.eclipse.swt.widgets.FileDialog;
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import org.eclipse.ui.IEditorPart;
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import eu.etaxonomy.taxeditor.model.AbstractUtility;
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import eu.etaxonomy.taxeditor.model.MessagingUtils;
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import eu.etaxonomy.taxeditor.molecular.TaxeditorMolecularPlugin;
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import eu.etaxonomy.taxeditor.molecular.editor.AlignmentEditor;
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/**
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* Handler that loads an additional read into the contig alignment displayed by an instance of {@link AlignmentEditor}.
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*
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* @author Ben Stöver
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* @author pplitzner
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*/
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public class LoadPherogramHandler extends AbstractHandler {
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//TODO Change so that also URIs which do not point to files can be specified.
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/* (non-Javadoc)
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* @see org.eclipse.core.commands.IHandler#execute(org.eclipse.core.commands.ExecutionEvent)
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*/
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@Override
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public Object execute(ExecutionEvent event) throws ExecutionException {
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IEditorPart activeEditor = AbstractUtility.getActiveEditor();
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if (activeEditor instanceof AlignmentEditor) {
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AlignmentEditor alignmentEditor = (AlignmentEditor)activeEditor;
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FileDialog fileDialog = new FileDialog(alignmentEditor.getSite().getShell());
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fileDialog.setText("Import pherogram into contig alignment");
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fileDialog.setFilterNames(new String[]{"All supported formats", "AB1 pherogram files", "SCF pherogram files", "All files"});
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fileDialog.setFilterExtensions(new String[]{"*.ab1;*.scf", "*.ab1", "*.scf", "*.*"});
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String path = fileDialog.open();
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if (path != null) {
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try {
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alignmentEditor.addRead(new File(path).toURI(), false);
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}
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catch (UnsupportedChromatogramFormatException e) {
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MessagingUtils.errorDialog("Unsupported format", this, "The format of the pherogram file \"" + path +
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"\" is not supported. (Only AB1 and SCF are supported.)", TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
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}
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catch (IOException e) {
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MessagingUtils.errorDialog("Unsupported format", this,
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"An IO error occurred while trying to read the file \"" + path + "\".",
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TaxeditorMolecularPlugin.PLUGIN_ID, e, false); //TODO set pluginID
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}
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}
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}
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return null;
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}
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}
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