2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
\r
3 * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
\r
5 * This file is part of Jalview.
\r
7 * Jalview is free software: you can redistribute it and/or
\r
8 * modify it under the terms of the GNU General Public License
\r
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
\r
11 * Jalview is distributed in the hope that it will be useful, but
\r
12 * WITHOUT ANY WARRANTY; without even the implied warranty
\r
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
\r
14 * PURPOSE. See the GNU General Public License for more details.
\r
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
\r
18 package jalview.gui;
\r
23 import java.awt.event.*;
\r
24 import javax.swing.*;
\r
26 import jalview.datamodel.*;
\r
27 import jalview.io.*;
\r
31 * GUI dialog for exporting features or alignment annotations depending upon
\r
32 * which method is called.
\r
37 public class AnnotationExporter extends JPanel
\r
39 JInternalFrame frame;
\r
43 boolean features = true;
\r
45 AlignmentAnnotation[] annotations;
\r
47 Vector sequenceGroups;
\r
49 Hashtable alignmentProperties;
\r
51 public AnnotationExporter()
\r
56 } catch (Exception ex)
\r
58 ex.printStackTrace();
\r
61 frame = new JInternalFrame();
\r
62 frame.setContentPane(this);
\r
63 frame.setLayer(JLayeredPane.PALETTE_LAYER);
\r
64 Desktop.addInternalFrame(frame, "", 260, 125);
\r
67 public void exportFeatures(AlignmentPanel ap)
\r
71 CSVFormat.setVisible(false);
\r
72 frame.setTitle("Export Features");
\r
75 public void exportAnnotations(AlignmentPanel ap,
\r
76 AlignmentAnnotation[] annotations, Vector sequenceGroups,
\r
77 Hashtable alProperties)
\r
81 GFFFormat.setVisible(false);
\r
82 CSVFormat.setVisible(true);
\r
83 this.annotations = annotations;
\r
84 this.sequenceGroups = sequenceGroups;
\r
85 this.alignmentProperties = alProperties;
\r
86 frame.setTitle("Export Annotations");
\r
89 public void toFile_actionPerformed(ActionEvent e)
\r
91 JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache
\r
92 .getProperty("LAST_DIRECTORY"));
\r
94 chooser.setFileView(new JalviewFileView());
\r
95 chooser.setDialogTitle(features ? "Save Features to File"
\r
96 : "Save Annotation to File");
\r
97 chooser.setToolTipText("Save");
\r
99 int value = chooser.showSaveDialog(this);
\r
101 if (value == JalviewFileChooser.APPROVE_OPTION)
\r
103 String text = "No features found on alignment";
\r
106 if (GFFFormat.isSelected())
\r
108 text = new FeaturesFile().printGFFFormat(ap.av.alignment
\r
109 .getDataset().getSequencesArray(),
\r
110 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());// ap.av.featuresDisplayed//);
\r
114 text = new FeaturesFile().printJalviewFormat(ap.av.alignment
\r
115 .getDataset().getSequencesArray(),
\r
116 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats()); // ap.av.featuresDisplayed);
\r
121 if (CSVFormat.isSelected())
\r
123 text = new AnnotationFile().printCSVAnnotations(annotations);
\r
127 text = new AnnotationFile().printAnnotations(annotations,
\r
128 sequenceGroups, alignmentProperties);
\r
134 java.io.PrintWriter out = new java.io.PrintWriter(
\r
135 new java.io.FileWriter(chooser.getSelectedFile()));
\r
139 } catch (Exception ex)
\r
141 ex.printStackTrace();
\r
145 close_actionPerformed(null);
\r
148 public void toTextbox_actionPerformed(ActionEvent e)
\r
150 String text = "No features found on alignment";
\r
153 if (GFFFormat.isSelected())
\r
155 text = new FeaturesFile().printGFFFormat(ap.av.alignment
\r
156 .getDataset().getSequencesArray(),
\r
157 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
161 text = new FeaturesFile().printJalviewFormat(ap.av.alignment
\r
162 .getDataset().getSequencesArray(),
\r
163 getDisplayedFeatureCols(), true, ap.av.isShowNpFeats());
\r
166 else if (!features)
\r
168 if (CSVFormat.isSelected())
\r
170 text = new AnnotationFile().printCSVAnnotations(annotations);
\r
174 text = new AnnotationFile().printAnnotations(annotations,
\r
175 sequenceGroups, alignmentProperties);
\r
179 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
181 Desktop.addInternalFrame(cap, (features ? "Features for - "
\r
182 : "Annotations for - ")
\r
183 + ap.alignFrame.getTitle(), 600, 500);
\r
185 close_actionPerformed(null);
\r
188 private Hashtable getDisplayedFeatureCols()
\r
190 Hashtable fcols = new Hashtable();
\r
191 Enumeration en = ap.av.featuresDisplayed.keys();
\r
192 FeatureRenderer fr = ap.seqPanel.seqCanvas.getFeatureRenderer(); // consider
\r
196 while (en.hasMoreElements())
\r
198 Object col = en.nextElement();
\r
199 fcols.put(col, fr.featureColours.get(col));
\r
204 public void close_actionPerformed(ActionEvent e)
\r
208 frame.setClosed(true);
\r
209 } catch (java.beans.PropertyVetoException ex)
\r
214 private void jbInit() throws Exception
\r
216 this.setLayout(flowLayout1);
\r
217 toFile.setText("to File");
\r
218 toFile.addActionListener(new ActionListener()
\r
220 public void actionPerformed(ActionEvent e)
\r
222 toFile_actionPerformed(e);
\r
225 toTextbox.setText("to Textbox");
\r
226 toTextbox.addActionListener(new ActionListener()
\r
228 public void actionPerformed(ActionEvent e)
\r
230 toTextbox_actionPerformed(e);
\r
233 close.setText("Close");
\r
234 close.addActionListener(new ActionListener()
\r
236 public void actionPerformed(ActionEvent e)
\r
238 close_actionPerformed(e);
\r
241 jalviewFormat.setOpaque(false);
\r
242 jalviewFormat.setSelected(true);
\r
243 jalviewFormat.setText("Jalview");
\r
244 GFFFormat.setOpaque(false);
\r
245 GFFFormat.setText("GFF");
\r
246 CSVFormat.setOpaque(false);
\r
247 CSVFormat.setText("CSV(Spreadsheet)");
\r
248 jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
\r
249 jLabel1.setText("Format: ");
\r
250 this.setBackground(Color.white);
\r
251 jPanel3.setBorder(BorderFactory.createEtchedBorder());
\r
252 jPanel3.setOpaque(false);
\r
253 jPanel1.setOpaque(false);
\r
254 jPanel1.add(toFile);
\r
255 jPanel1.add(toTextbox);
\r
256 jPanel1.add(close);
\r
257 jPanel3.add(jLabel1);
\r
258 jPanel3.add(jalviewFormat);
\r
259 jPanel3.add(GFFFormat);
\r
260 jPanel3.add(CSVFormat);
\r
261 buttonGroup.add(jalviewFormat);
\r
262 buttonGroup.add(GFFFormat);
\r
263 buttonGroup.add(CSVFormat);
\r
264 this.add(jPanel3, null);
\r
265 this.add(jPanel1, null);
\r
268 JPanel jPanel1 = new JPanel();
\r
270 JButton toFile = new JButton();
\r
272 JButton toTextbox = new JButton();
\r
274 JButton close = new JButton();
\r
276 ButtonGroup buttonGroup = new ButtonGroup();
\r
278 JRadioButton jalviewFormat = new JRadioButton();
\r
280 JRadioButton GFFFormat = new JRadioButton();
\r
282 JRadioButton CSVFormat = new JRadioButton();
\r
284 JLabel jLabel1 = new JLabel();
\r
286 JPanel jPanel3 = new JPanel();
\r
288 FlowLayout flowLayout1 = new FlowLayout();
\r