Clover icon

Coverage Report

  1. Project Clover database Tue Nov 4 2025 11:21:43 GMT
  2. Package jalview.gui

File AnnotationExporter.java

 

Coverage histogram

../../img/srcFileCovDistChart6.png
37% of files have more coverage

Code metrics

26
124
19
1
451
296
36
0.29
6.53
19
1.89

Classes

Class Line # Actions
AnnotationExporter 60 124 36
0.550295855%
 

Contributing tests

This file is covered by 1 test. .

Source view

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 java.awt.Color;
24    import java.awt.Dimension;
25    import java.awt.event.ActionEvent;
26    import java.awt.event.ActionListener;
27    import java.io.FileWriter;
28    import java.io.PrintWriter;
29    import java.util.Locale;
30   
31    import javax.swing.BoxLayout;
32    import javax.swing.ButtonGroup;
33    import javax.swing.JButton;
34    import javax.swing.JCheckBox;
35    import javax.swing.JInternalFrame;
36    import javax.swing.JLabel;
37    import javax.swing.JLayeredPane;
38    import javax.swing.JPanel;
39    import javax.swing.JRadioButton;
40    import javax.swing.SwingConstants;
41   
42    import jalview.api.FeatureRenderer;
43    import jalview.bin.Cache;
44    import jalview.datamodel.AlignmentAnnotation;
45    import jalview.datamodel.SequenceI;
46    import jalview.io.AnnotationFile;
47    import jalview.io.FeaturesFile;
48    import jalview.io.JalviewFileChooser;
49    import jalview.io.JalviewFileView;
50    import jalview.util.MessageManager;
51   
52    /**
53    *
54    * GUI dialog for exporting features or alignment annotations depending upon
55    * which method is called.
56    *
57    * @author AMW
58    *
59    */
 
60    public class AnnotationExporter extends JPanel
61    {
62    private JInternalFrame frame;
63   
64    private AlignmentPanel ap;
65   
66    /*
67    * true if exporting features, false if exporting annotations
68    */
69    private boolean exportFeatures = true;
70   
71    private AlignmentAnnotation[] annotations;
72   
73    private boolean wholeView;
74   
75    /*
76    * option to export linked (CDS/peptide) features when shown
77    * on the alignment, converted to this alignment's coordinates
78    */
79    private JCheckBox includeLinkedFeatures;
80   
81    /*
82    * output format option shown for feature export
83    */
84    JRadioButton GFFFormat = new JRadioButton();
85   
86    /*
87    * output format option shown for annotation export
88    */
89    JRadioButton CSVFormat = new JRadioButton();
90   
91    private JPanel linkedFeaturesPanel;
92   
93    /**
94    * Constructor
95    *
96    * @param panel
97    */
 
98  1 toggle public AnnotationExporter(AlignmentPanel panel)
99    {
100  1 this.ap = panel;
101  1 try
102    {
103  1 jbInit();
104    } catch (Exception ex)
105    {
106  0 ex.printStackTrace();
107    }
108   
109  1 frame = new JInternalFrame();
110  1 frame.setFrameIcon(null);
111  1 frame.setContentPane(this);
112  1 frame.setLayer(JLayeredPane.PALETTE_LAYER);
113  1 Dimension preferredSize = frame.getPreferredSize();
114  1 Desktop.addInternalFrame(frame, "", true, preferredSize.width,
115    preferredSize.height, true, true);
116    }
117   
118    /**
119    * Configures the dialog for options to export visible features. If from a
120    * split frame panel showing linked features, make the option to include these
121    * in the export visible.
122    */
 
123  0 toggle public void exportFeatures()
124    {
125  0 exportFeatures = true;
126  0 CSVFormat.setVisible(false);
127  0 if (ap.av.isShowComplementFeatures())
128    {
129  0 linkedFeaturesPanel.setVisible(true);
130  0 frame.pack();
131    }
132  0 frame.setTitle(MessageManager.getString("label.export_features"));
133    }
134   
135    /**
136    * Configures the dialog for options to export all visible annotations
137    */
 
138  1 toggle public void exportAnnotations()
139    {
140  1 boolean showAnnotation = ap.av.isShowAnnotation();
141  1 exportAnnotation(showAnnotation ? null
142    : ap.av.getAlignment().getAlignmentAnnotation(), true);
143    }
144   
145    /**
146    * Configures the dialog for options to export the given annotation row
147    *
148    * @param toExport
149    */
 
150  1 toggle public void exportAnnotation(AlignmentAnnotation toExport)
151    {
152  1 exportAnnotation(new AlignmentAnnotation[] { toExport }, false);
153    }
154   
 
155  2 toggle private void exportAnnotation(AlignmentAnnotation[] toExport,
156    boolean forWholeView)
157    {
158  2 wholeView = forWholeView;
159  2 annotations = toExport;
160  2 exportFeatures = false;
161  2 GFFFormat.setVisible(false);
162  2 CSVFormat.setVisible(true);
163  2 frame.setTitle(MessageManager.getString("label.export_annotations"));
164    }
165   
 
166  1 toggle public void setExportAsCSV()
167    {
168  1 if (CSVFormat != null)
169    {
170  1 CSVFormat.setSelected(true);
171    }
172    }
173   
 
174  0 toggle private void toFile_actionPerformed()
175    {
176    // TODO: JAL-3048 JalviewFileChooser - Save option
177  0 JalviewFileChooser chooser = new JalviewFileChooser(
178    Cache.getProperty("LAST_DIRECTORY"));
179   
180  0 chooser.setFileView(new JalviewFileView());
181  0 chooser.setDialogTitle(exportFeatures
182    ? MessageManager.getString("label.save_features_to_file")
183    : MessageManager.getString("label.save_annotation_to_file"));
184  0 chooser.setToolTipText(MessageManager.getString("action.save"));
185   
186  0 int value = chooser.showSaveDialog(this);
187   
188  0 if (value == JalviewFileChooser.APPROVE_OPTION)
189    {
190  0 String text = getText();
191   
192  0 try
193    {
194  0 PrintWriter out = new PrintWriter(
195    new FileWriter(chooser.getSelectedFile()));
196  0 out.print(text);
197  0 out.close();
198    } catch (Exception ex)
199    {
200  0 ex.printStackTrace();
201    }
202    }
203   
204  0 close_actionPerformed();
205    }
206   
207    /**
208    * Answers the text to output for either Features (in GFF or Jalview format)
209    * or Annotations (in CSV or Jalview format)
210    *
211    * @return
212    */
 
213  0 toggle public String getText()
214    {
215  0 return exportFeatures ? getFeaturesText() : getAnnotationsText();
216    }
217   
218    /**
219    * Returns the text contents for output of annotations in either CSV or
220    * Jalview format
221    *
222    * @return
223    */
 
224  2 toggle public String getAnnotationsText()
225    {
226  2 String text;
227  2 if (CSVFormat.isSelected())
228    {
229  2 text = new AnnotationFile().printCSVAnnotations(
230  2 wholeView ? ap.av.getAlignment().getAlignmentAnnotation()
231    : annotations);
232    }
233    else
234    {
235  0 if (wholeView)
236    {
237  0 text = new AnnotationFile().printAnnotationsForView(ap.av);
238    }
239    else
240    {
241  0 text = new AnnotationFile().printAnnotations(annotations, null,
242    null);
243    }
244    }
245  2 return text;
246    }
247   
248    /**
249    * Returns the text contents for output of features in either GFF or Jalview
250    * format
251    *
252    * @return
253    */
 
254  0 toggle public String getFeaturesText()
255    {
256  0 String text;
257  0 SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
258  0 boolean includeNonPositional = ap.av.isShowNPFeats();
259   
260  0 FeaturesFile formatter = new FeaturesFile();
261  0 final FeatureRenderer fr = ap.getFeatureRenderer();
262  0 boolean includeComplement = includeLinkedFeatures.isSelected();
263   
264  0 if (GFFFormat.isSelected())
265    {
266  0 text = formatter.printGffFormat(sequences, fr, includeNonPositional,
267    includeComplement);
268    }
269    else
270    {
271  0 text = formatter.printJalviewFormat(sequences, fr,
272    includeNonPositional, includeComplement);
273    }
274  0 return text;
275    }
276   
 
277  0 toggle private void toTextbox_actionPerformed()
278    {
279  0 CutAndPasteTransfer cap = new CutAndPasteTransfer();
280   
281  0 try
282    {
283  0 String text = getText();
284  0 cap.setText(text);
285  0 Desktop.addInternalFrame(cap, (exportFeatures ? MessageManager
286    .formatMessage("label.features_for_params", new String[]
287    { ap.alignFrame.getTitle() })
288    : MessageManager.formatMessage("label.annotations_for_params",
289    new String[]
290    { ap.alignFrame.getTitle() })),
291    600, 500);
292    } catch (OutOfMemoryError oom)
293    {
294  0 new OOMWarning((exportFeatures ? MessageManager.formatMessage(
295    "label.generating_features_for_params", new String[]
296    { ap.alignFrame.getTitle() })
297    : MessageManager.formatMessage(
298    "label.generating_annotations_for_params",
299    new String[]
300    { ap.alignFrame.getTitle() })),
301    oom);
302  0 cap.dispose();
303    }
304   
305  0 close_actionPerformed();
306    }
307   
 
308  0 toggle private void close_actionPerformed()
309    {
310  0 try
311    {
312  0 frame.setClosed(true);
313    } catch (java.beans.PropertyVetoException ex)
314    {
315    }
316    }
317   
318    /**
319    * Adds widgets to the panel
320    *
321    * @throws Exception
322    */
 
323  1 toggle private void jbInit() throws Exception
324    {
325  1 this.setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
326  1 this.setBackground(Color.white);
327   
328  1 JPanel formatPanel = buildFormatOptionsPanel();
329  1 JPanel linkedFeatures = buildLinkedFeaturesPanel();
330  1 JPanel actionsPanel = buildActionsPanel();
331   
332  1 this.add(formatPanel);
333  1 this.add(linkedFeatures);
334  1 this.add(actionsPanel);
335    }
336   
337    /**
338    * Builds a panel with a checkbox for the option to export linked
339    * (CDS/peptide) features. This is hidden by default, and only made visible if
340    * exporting features from a split frame panel which is configured to show
341    * linked features.
342    *
343    * @return
344    */
 
345  1 toggle private JPanel buildLinkedFeaturesPanel()
346    {
347  1 linkedFeaturesPanel = new JPanel();
348  1 linkedFeaturesPanel.setOpaque(false);
349   
350  1 boolean nucleotide = ap.av.isNucleotide();
351  1 String complement = nucleotide ? MessageManager
352    .getString("label.protein").toLowerCase(Locale.ROOT) : "CDS";
353  1 JLabel label = new JLabel(MessageManager
354    .formatMessage("label.include_linked_features", complement));
355  1 label.setHorizontalAlignment(SwingConstants.TRAILING);
356  1 String tooltip = MessageManager
357    .formatMessage("label.include_linked_tooltip", complement);
358  1 label.setToolTipText(JvSwingUtils.wrapTooltip(true, tooltip));
359   
360  1 includeLinkedFeatures = new JCheckBox();
361  1 linkedFeaturesPanel.add(label);
362  1 linkedFeaturesPanel.add(includeLinkedFeatures);
363  1 linkedFeaturesPanel.setVisible(false);
364   
365  1 return linkedFeaturesPanel;
366    }
367   
368    /**
369    * Builds the panel with to File or Textbox or Close actions
370    *
371    * @return
372    */
 
373  1 toggle JPanel buildActionsPanel()
374    {
375  1 JPanel actionsPanel = new JPanel();
376  1 actionsPanel.setOpaque(false);
377   
378  1 JButton toFile = new JButton(MessageManager.getString("label.to_file"));
379  1 toFile.addActionListener(new ActionListener()
380    {
 
381  0 toggle @Override
382    public void actionPerformed(ActionEvent e)
383    {
384  0 toFile_actionPerformed();
385    }
386    });
387  1 JButton toTextbox = new JButton(
388    MessageManager.getString("label.to_textbox"));
389  1 toTextbox.addActionListener(new ActionListener()
390    {
 
391  0 toggle @Override
392    public void actionPerformed(ActionEvent e)
393    {
394  0 toTextbox_actionPerformed();
395    }
396    });
397  1 JButton close = new JButton(MessageManager.getString("action.close"));
398  1 close.addActionListener(new ActionListener()
399    {
 
400  0 toggle @Override
401    public void actionPerformed(ActionEvent e)
402    {
403  0 close_actionPerformed();
404    }
405    });
406   
407  1 actionsPanel.add(toFile);
408  1 actionsPanel.add(toTextbox);
409  1 actionsPanel.add(close);
410   
411  1 return actionsPanel;
412    }
413   
414    /**
415    * Builds the panel with options to output in Jalview, GFF or CSV format. GFF
416    * is only made visible when exporting features, CSV only when exporting
417    * annotation.
418    *
419    * @return
420    */
 
421  1 toggle JPanel buildFormatOptionsPanel()
422    {
423  1 JPanel formatPanel = new JPanel();
424    // formatPanel.setBorder(BorderFactory.createEtchedBorder());
425  1 formatPanel.setOpaque(false);
426   
427  1 JRadioButton jalviewFormat = new JRadioButton("Jalview");
428  1 jalviewFormat.setOpaque(false);
429  1 jalviewFormat.setSelected(true);
430  1 GFFFormat.setOpaque(false);
431  1 GFFFormat.setText("GFF");
432  1 CSVFormat.setOpaque(false);
433  1 CSVFormat.setText(MessageManager.getString("label.csv_spreadsheet"));
434   
435  1 ButtonGroup buttonGroup = new ButtonGroup();
436  1 buttonGroup.add(jalviewFormat);
437  1 buttonGroup.add(GFFFormat);
438  1 buttonGroup.add(CSVFormat);
439   
440  1 JLabel format = new JLabel(
441    MessageManager.getString("action.format") + " ");
442  1 format.setHorizontalAlignment(SwingConstants.TRAILING);
443   
444  1 formatPanel.add(format);
445  1 formatPanel.add(jalviewFormat);
446  1 formatPanel.add(GFFFormat);
447  1 formatPanel.add(CSVFormat);
448   
449  1 return formatPanel;
450    }
451    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 4 2025 11:32:25 GMT using coverage data from Tue Nov 4 2025 11:32:11 GMT.
  • OpenClover is free and open-source software.