JAL-2416 allow space in score matrix name
[jalview.git] / src / jalview / gui / AnnotationExporter.java
1 /*
2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
4  * 
5  * This file is part of Jalview.
6  * 
7  * Jalview is free software: you can redistribute it and/or
8  * modify it under the terms of the GNU General Public License 
9  * as published by the Free Software Foundation, either version 3
10  * of the License, or (at your option) any later version.
11  *  
12  * Jalview is distributed in the hope that it will be useful, but 
13  * WITHOUT ANY WARRANTY; without even the implied warranty 
14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
15  * PURPOSE.  See the GNU General Public License for more details.
16  * 
17  * You should have received a copy of the GNU General Public License
18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
19  * The Jalview Authors are detailed in the 'AUTHORS' file.
20  */
21 package jalview.gui;
22
23 import jalview.api.FeatureColourI;
24 import jalview.datamodel.AlignmentAnnotation;
25 import jalview.datamodel.SequenceI;
26 import jalview.io.AnnotationFile;
27 import jalview.io.FeaturesFile;
28 import jalview.io.JalviewFileChooser;
29 import jalview.io.JalviewFileView;
30 import jalview.util.MessageManager;
31
32 import java.awt.BorderLayout;
33 import java.awt.Color;
34 import java.awt.FlowLayout;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.util.Map;
38
39 import javax.swing.BorderFactory;
40 import javax.swing.ButtonGroup;
41 import javax.swing.JButton;
42 import javax.swing.JInternalFrame;
43 import javax.swing.JLabel;
44 import javax.swing.JLayeredPane;
45 import javax.swing.JPanel;
46 import javax.swing.JRadioButton;
47 import javax.swing.SwingConstants;
48
49 /**
50  * 
51  * GUI dialog for exporting features or alignment annotations depending upon
52  * which method is called.
53  * 
54  * @author AMW
55  * 
56  */
57 public class AnnotationExporter extends JPanel
58 {
59   JInternalFrame frame;
60
61   AlignmentPanel ap;
62
63   boolean features = true;
64
65   private AlignmentAnnotation[] annotations;
66
67   private boolean wholeView;
68
69   public AnnotationExporter()
70   {
71     try
72     {
73       jbInit();
74     } catch (Exception ex)
75     {
76       ex.printStackTrace();
77     }
78
79     frame = new JInternalFrame();
80     frame.setContentPane(this);
81     frame.setLayer(JLayeredPane.PALETTE_LAYER);
82     Desktop.addInternalFrame(frame, "", frame.getPreferredSize().width,
83             frame.getPreferredSize().height);
84   }
85
86   public void exportFeatures(AlignmentPanel ap)
87   {
88     this.ap = ap;
89     features = true;
90     CSVFormat.setVisible(false);
91     frame.setTitle(MessageManager.getString("label.export_features"));
92   }
93
94   public void exportAnnotations(AlignmentPanel ap)
95   {
96     this.ap = ap;
97     annotations = ap.av.isShowAnnotation() ? null : ap.av.getAlignment()
98             .getAlignmentAnnotation();
99     wholeView = true;
100     startExportAnnotation();
101   }
102
103   public void exportAnnotations(AlignmentPanel alp,
104           AlignmentAnnotation[] toExport)
105   {
106     ap = alp;
107     annotations = toExport;
108     wholeView = false;
109     startExportAnnotation();
110   }
111
112   private void startExportAnnotation()
113   {
114     features = false;
115     GFFFormat.setVisible(false);
116     CSVFormat.setVisible(true);
117     frame.setTitle(MessageManager.getString("label.export_annotations"));
118   }
119
120   public void toFile_actionPerformed(ActionEvent e)
121   {
122     JalviewFileChooser chooser = new JalviewFileChooser(
123             jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
124
125     chooser.setFileView(new JalviewFileView());
126     chooser.setDialogTitle(features ? MessageManager
127             .getString("label.save_features_to_file") : MessageManager
128             .getString("label.save_annotation_to_file"));
129     chooser.setToolTipText(MessageManager.getString("action.save"));
130
131     int value = chooser.showSaveDialog(this);
132
133     if (value == JalviewFileChooser.APPROVE_OPTION)
134     {
135       String text = getFileContents();
136
137       try
138       {
139         java.io.PrintWriter out = new java.io.PrintWriter(
140                 new java.io.FileWriter(chooser.getSelectedFile()));
141
142         out.print(text);
143         out.close();
144       } catch (Exception ex)
145       {
146         ex.printStackTrace();
147       }
148     }
149
150     close_actionPerformed(null);
151   }
152
153   private String getFileContents()
154   {
155     String text = MessageManager
156             .getString("label.no_features_on_alignment");
157     if (features)
158     {
159       Map<String, FeatureColourI> displayedFeatureColours = ap
160               .getFeatureRenderer().getDisplayedFeatureCols();
161       FeaturesFile formatter = new FeaturesFile();
162       SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
163       Map<String, FeatureColourI> featureColours = ap.getFeatureRenderer()
164               .getDisplayedFeatureCols();
165       boolean includeNonPositional = ap.av.isShowNPFeats();
166       if (GFFFormat.isSelected())
167       {
168         text = new FeaturesFile().printGffFormat(ap.av.getAlignment()
169                 .getDataset().getSequencesArray(), displayedFeatureColours,
170                 true, ap.av.isShowNPFeats());
171         text = formatter.printGffFormat(sequences, featureColours, true,
172                 includeNonPositional);
173       }
174       else
175       {
176         text = new FeaturesFile().printJalviewFormat(ap.av.getAlignment()
177                 .getDataset().getSequencesArray(), displayedFeatureColours,
178                 true, ap.av.isShowNPFeats()); // ap.av.featuresDisplayed);
179         text = formatter.printJalviewFormat(sequences, featureColours,
180                 true, includeNonPositional);
181       }
182     }
183     else
184     {
185       if (CSVFormat.isSelected())
186       {
187         text = new AnnotationFile().printCSVAnnotations(annotations);
188       }
189       else
190       {
191         if (wholeView)
192         {
193           text = new AnnotationFile().printAnnotationsForView(ap.av);
194         }
195         else
196         {
197           text = new AnnotationFile().printAnnotations(annotations, null,
198                   null);
199         }
200       }
201     }
202     return text;
203   }
204
205   public void toTextbox_actionPerformed(ActionEvent e)
206   {
207     CutAndPasteTransfer cap = new CutAndPasteTransfer();
208
209     try
210     {
211       String text = getFileContents();
212       cap.setText(text);
213       Desktop.addInternalFrame(
214               cap,
215               (features ? MessageManager.formatMessage(
216                       "label.features_for_params",
217                       new String[] { ap.alignFrame.getTitle() })
218                       : MessageManager.formatMessage(
219                               "label.annotations_for_params",
220                               new String[] { ap.alignFrame.getTitle() })),
221               600, 500);
222     } catch (OutOfMemoryError oom)
223     {
224       new OOMWarning((features ? MessageManager.formatMessage(
225               "label.generating_features_for_params",
226               new String[] { ap.alignFrame.getTitle() })
227               : MessageManager.formatMessage(
228                       "label.generating_annotations_for_params",
229                       new String[] { ap.alignFrame.getTitle() })), oom);
230       cap.dispose();
231     }
232
233     close_actionPerformed(null);
234   }
235
236   public void close_actionPerformed(ActionEvent e)
237   {
238     try
239     {
240       frame.setClosed(true);
241     } catch (java.beans.PropertyVetoException ex)
242     {
243     }
244   }
245
246   private void jbInit() throws Exception
247   {
248     this.setLayout(new BorderLayout());
249
250     toFile.setText(MessageManager.getString("label.to_file"));
251     toFile.addActionListener(new ActionListener()
252     {
253       @Override
254       public void actionPerformed(ActionEvent e)
255       {
256         toFile_actionPerformed(e);
257       }
258     });
259     toTextbox.setText(MessageManager.getString("label.to_textbox"));
260     toTextbox.addActionListener(new ActionListener()
261     {
262       @Override
263       public void actionPerformed(ActionEvent e)
264       {
265         toTextbox_actionPerformed(e);
266       }
267     });
268     close.setText(MessageManager.getString("action.close"));
269     close.addActionListener(new ActionListener()
270     {
271       @Override
272       public void actionPerformed(ActionEvent e)
273       {
274         close_actionPerformed(e);
275       }
276     });
277     jalviewFormat.setOpaque(false);
278     jalviewFormat.setSelected(true);
279     jalviewFormat.setText("Jalview");
280     GFFFormat.setOpaque(false);
281     GFFFormat.setText("GFF");
282     CSVFormat.setOpaque(false);
283     CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
284     jLabel1.setHorizontalAlignment(SwingConstants.TRAILING);
285     jLabel1.setText(MessageManager.getString("action.format") + " ");
286     this.setBackground(Color.white);
287     jPanel3.setBorder(BorderFactory.createEtchedBorder());
288     jPanel3.setOpaque(false);
289     jPanel1.setOpaque(false);
290     jPanel1.add(toFile);
291     jPanel1.add(toTextbox);
292     jPanel1.add(close);
293     jPanel3.add(jLabel1);
294     jPanel3.add(jalviewFormat);
295     jPanel3.add(GFFFormat);
296     jPanel3.add(CSVFormat);
297     buttonGroup.add(jalviewFormat);
298     buttonGroup.add(GFFFormat);
299     buttonGroup.add(CSVFormat);
300     this.add(jPanel3, BorderLayout.CENTER);
301     this.add(jPanel1, BorderLayout.SOUTH);
302   }
303
304   JPanel jPanel1 = new JPanel();
305
306   JButton toFile = new JButton();
307
308   JButton toTextbox = new JButton();
309
310   JButton close = new JButton();
311
312   ButtonGroup buttonGroup = new ButtonGroup();
313
314   JRadioButton jalviewFormat = new JRadioButton();
315
316   JRadioButton GFFFormat = new JRadioButton();
317
318   JRadioButton CSVFormat = new JRadioButton();
319
320   JLabel jLabel1 = new JLabel();
321
322   JPanel jPanel3 = new JPanel();
323
324   FlowLayout flowLayout1 = new FlowLayout();
325 }