2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
23 import jalview.api.FeatureColourI;
24 import jalview.datamodel.SearchResults;
25 import jalview.datamodel.SearchResultsI;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.io.FeaturesFile;
29 import jalview.schemes.FeatureColour;
30 import jalview.util.ColorUtils;
31 import jalview.util.MessageManager;
33 import java.awt.BorderLayout;
34 import java.awt.Color;
35 import java.awt.Dimension;
37 import java.awt.GridLayout;
38 import java.awt.event.ActionEvent;
39 import java.awt.event.ActionListener;
40 import java.awt.event.ItemEvent;
41 import java.awt.event.ItemListener;
42 import java.awt.event.MouseAdapter;
43 import java.awt.event.MouseEvent;
44 import java.util.Arrays;
45 import java.util.Comparator;
46 import java.util.HashMap;
47 import java.util.List;
49 import javax.swing.JColorChooser;
50 import javax.swing.JComboBox;
51 import javax.swing.JLabel;
52 import javax.swing.JPanel;
53 import javax.swing.JScrollPane;
54 import javax.swing.JSpinner;
55 import javax.swing.JTextArea;
56 import javax.swing.JTextField;
57 import javax.swing.SwingConstants;
58 import javax.swing.event.DocumentEvent;
59 import javax.swing.event.DocumentListener;
67 public class FeatureRenderer extends
68 jalview.renderer.seqfeatures.FeatureRenderer
71 * defaults for creating a new feature are the last created
72 * feature type and group
74 static String lastFeatureAdded = "feature_1";
76 static String lastFeatureGroupAdded = "Jalview";
83 * Creates a new FeatureRenderer object
87 public FeatureRenderer(AlignmentPanel alignPanel)
91 if (alignPanel.getSeqPanel() != null
92 && alignPanel.getSeqPanel().seqCanvas != null
93 && alignPanel.getSeqPanel().seqCanvas.fr != null)
95 transferSettings(alignPanel.getSeqPanel().seqCanvas.fr);
99 FeatureColourI oldcol, fcol;
101 int featureIndex = 0;
104 * Presents a dialog allowing the user to add new features, or amend or delete
105 * existing features. Currently this can be on
107 * <li>double-click on a sequence - Amend/Delete features at position</li>
108 * <li>Create sequence feature from pop-up menu on selected region</li>
109 * <li>Create features for pattern matches from Find</li>
111 * If the supplied feature type is null, show (and update on confirm) the type
112 * and group of the last new feature created (with initial defaults of
113 * "feature_1" and "Jalview").
116 * the sequences features are to be created on (if creating
117 * features), or a single sequence (if amending features)
119 * the current features at the position (if amending), or template
120 * new feature(s) with start/end position set (if creating)
122 * true to create features, false to amend or delete
126 protected boolean amendFeatures(final List<SequenceI> sequences,
127 final List<SequenceFeature> features, boolean create,
128 final AlignmentPanel alignPanel)
132 final JPanel mainPanel = new JPanel(new BorderLayout());
134 final JTextField name = new JTextField(25);
135 name.getDocument().addDocumentListener(new DocumentListener()
138 public void insertUpdate(DocumentEvent e)
140 warnIfTypeHidden(mainPanel, name.getText());
144 public void removeUpdate(DocumentEvent e)
146 warnIfTypeHidden(mainPanel, name.getText());
150 public void changedUpdate(DocumentEvent e)
152 warnIfTypeHidden(mainPanel, name.getText());
156 final JTextField group = new JTextField(25);
157 group.getDocument().addDocumentListener(new DocumentListener()
160 public void insertUpdate(DocumentEvent e)
162 warnIfGroupHidden(mainPanel, group.getText());
166 public void removeUpdate(DocumentEvent e)
168 warnIfGroupHidden(mainPanel, group.getText());
172 public void changedUpdate(DocumentEvent e)
174 warnIfGroupHidden(mainPanel, group.getText());
178 final JTextArea description = new JTextArea(3, 25);
179 final JSpinner start = new JSpinner();
180 final JSpinner end = new JSpinner();
181 start.setPreferredSize(new Dimension(80, 20));
182 end.setPreferredSize(new Dimension(80, 20));
183 final FeatureRenderer me = this;
184 final JLabel colour = new JLabel();
185 colour.setOpaque(true);
186 // colour.setBorder(BorderFactory.createEtchedBorder());
187 colour.setMaximumSize(new Dimension(30, 16));
188 colour.addMouseListener(new MouseAdapter()
190 FeatureColourChooser fcc = null;
193 public void mousePressed(MouseEvent evt)
195 if (fcol.isSimpleColour())
197 Color col = JColorChooser.showDialog(Desktop.desktop,
198 MessageManager.getString("label.select_feature_colour"),
202 fcol = new FeatureColour(col);
203 updateColourButton(mainPanel, colour, new FeatureColour(col));
210 final String ft = features.get(featureIndex).getType();
211 final String type = ft == null ? lastFeatureAdded : ft;
212 fcc = new FeatureColourChooser(me, type);
213 fcc.setRequestFocusEnabled(true);
216 fcc.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent e)
222 fcol = fcc.getLastColour();
224 setColour(type, fcol);
225 updateColourButton(mainPanel, colour, fcol);
233 JPanel gridPanel = new JPanel(new GridLayout(3, 1));
235 if (!create && features.size() > 1)
238 * more than one feature at selected position - add a drop-down
239 * to choose the feature to amend
241 gridPanel = new JPanel(new GridLayout(4, 1));
242 JPanel choosePanel = new JPanel();
243 choosePanel.add(new JLabel(MessageManager
244 .getString("label.select_feature")
246 final JComboBox<String> overlaps = new JComboBox<String>();
247 for (SequenceFeature sf : features)
249 String text = sf.getType() + "/" + sf.getBegin() + "-"
250 + sf.getEnd() + " (" + sf.getFeatureGroup() + ")";
251 overlaps.addItem(text);
253 choosePanel.add(overlaps);
255 overlaps.addItemListener(new ItemListener()
258 public void itemStateChanged(ItemEvent e)
260 int index = overlaps.getSelectedIndex();
263 featureIndex = index;
264 SequenceFeature sf = features.get(index);
265 name.setText(sf.getType());
266 description.setText(sf.getDescription());
267 group.setText(sf.getFeatureGroup());
268 start.setValue(new Integer(sf.getBegin()));
269 end.setValue(new Integer(sf.getEnd()));
271 SearchResultsI highlight = new SearchResults();
272 highlight.addResult(sequences.get(0), sf.getBegin(),
275 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
278 FeatureColourI col = getFeatureStyle(name.getText());
281 col = new FeatureColour(ColorUtils
282 .createColourFromName(name.getText()));
285 updateColourButton(mainPanel, colour, col);
289 gridPanel.add(choosePanel);
292 JPanel namePanel = new JPanel();
293 gridPanel.add(namePanel);
294 namePanel.add(new JLabel(MessageManager.getString("label.name:"),
298 JPanel groupPanel = new JPanel();
299 gridPanel.add(groupPanel);
300 groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
302 groupPanel.add(group);
304 JPanel colourPanel = new JPanel();
305 gridPanel.add(colourPanel);
306 colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
308 colourPanel.add(colour);
309 colour.setPreferredSize(new Dimension(150, 15));
310 colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
311 colour.setForeground(Color.black);
312 colour.setHorizontalAlignment(SwingConstants.CENTER);
313 colour.setVerticalAlignment(SwingConstants.CENTER);
314 colour.setHorizontalTextPosition(SwingConstants.CENTER);
315 colour.setVerticalTextPosition(SwingConstants.CENTER);
316 mainPanel.add(gridPanel, BorderLayout.NORTH);
318 JPanel descriptionPanel = new JPanel();
319 descriptionPanel.add(new JLabel(MessageManager
320 .getString("label.description:"),
322 description.setFont(JvSwingUtils.getTextAreaFont());
323 description.setLineWrap(true);
324 descriptionPanel.add(new JScrollPane(description));
328 mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
330 JPanel startEndPanel = new JPanel();
331 startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
333 startEndPanel.add(start);
334 startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
336 startEndPanel.add(end);
337 mainPanel.add(startEndPanel, BorderLayout.CENTER);
341 mainPanel.add(descriptionPanel, BorderLayout.CENTER);
345 * default feature type and group to that of the first feature supplied,
346 * or to the last feature created if not supplied (null value)
348 SequenceFeature firstFeature = features.get(0);
349 boolean useLastDefaults = firstFeature.getType() == null;
350 final String featureType = useLastDefaults ? lastFeatureAdded
351 : firstFeature.getType();
352 final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
353 : firstFeature.getFeatureGroup();
354 name.setText(featureType);
355 group.setText(featureGroup);
357 start.setValue(new Integer(firstFeature.getBegin()));
358 end.setValue(new Integer(firstFeature.getEnd()));
359 description.setText(firstFeature.getDescription());
360 updateColourButton(mainPanel, colour,
361 (oldcol = fcol = getFeatureStyle(name.getText())));
365 options = new Object[] { MessageManager.getString("label.amend"),
366 MessageManager.getString("action.delete"),
367 MessageManager.getString("action.cancel") };
371 options = new Object[] { MessageManager.getString("action.ok"),
372 MessageManager.getString("action.cancel") };
375 String title = create ? MessageManager
376 .getString("label.create_new_sequence_features")
377 : MessageManager.formatMessage("label.amend_delete_features",
378 new String[] { sequences.get(0).getName() });
383 int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
384 mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
385 JvOptionPane.QUESTION_MESSAGE, null, options,
386 MessageManager.getString("action.ok"));
388 FeaturesFile ffile = new FeaturesFile();
390 if (reply == JvOptionPane.OK_OPTION && name.getText().length() > 0)
393 * update default values only if creating using default values
397 lastFeatureAdded = name.getText().trim();
398 lastFeatureGroupAdded = group.getText().trim();
399 // TODO: determine if the null feature group is valid
400 if (lastFeatureGroupAdded.length() < 1)
402 lastFeatureGroupAdded = null;
409 SequenceFeature sf = features.get(featureIndex);
411 if (reply == JvOptionPane.NO_OPTION)
414 * NO_OPTION corresponds to the Delete button
416 sequences.get(0).getDatasetSequence().deleteFeature(sf);
417 // update Feature Settings for removal of feature / group
420 else if (reply == JvOptionPane.YES_OPTION)
423 * YES_OPTION corresponds to the Amend button
424 * need to refresh Feature Settings if type, group or colour changed
426 String newType = name.getText().trim();
427 String newFeatureGroup = group.getText().trim();
428 String newDescription = description.getText().replaceAll("\n", " ");
429 boolean refreshSettings = (!featureType.equals(sf.type) || !featureGroup
430 .equals(sf.featureGroup));
431 refreshSettings |= (fcol != oldcol);
432 setColour(newType, fcol);
433 /*?*/ getFeaturesDisplayed().setVisible(newType);
434 int newBegin = sf.begin;
438 newBegin = ((Integer) start.getValue()).intValue();
439 newEnd = ((Integer) end.getValue()).intValue();
440 } catch (NumberFormatException ex)
442 // JSpinner doesn't accept invalid format data :-)
446 * replace the feature by deleting it and adding a new one
447 * (to ensure integrity of SequenceFeatures data store)
449 sequences.get(0).deleteFeature(sf);
450 SequenceFeature newSf = new SequenceFeature(newType,
451 newDescription, newBegin, newEnd, sf.getScore(),
453 // ensure any additional properties are copied
454 if (sf.otherDetails != null)
456 newSf.otherDetails = new HashMap<String, Object>(sf.otherDetails);
458 ffile.parseDescriptionHTML(newSf, false);
459 // add any additional links not parsed from description
460 if (sf.links != null)
462 for (String link : sf.links)
467 // amend features only gets one sequence to act on
468 sequences.get(0).addSequenceFeature(newSf);
477 // NEW FEATURES ADDED
479 if (reply == JvOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
481 for (int i = 0; i < sequences.size(); i++)
483 SequenceFeature sf = features.get(i);
484 sf.type = name.getText().trim();
485 // fix for JAL-1538 - always set feature group here
486 sf.featureGroup = group.getText().trim();
487 sf.description = description.getText().replaceAll("\n", " ");
488 sequences.get(i).addSequenceFeature(sf);
489 ffile.parseDescriptionHTML(sf, false);
492 setColour(lastFeatureAdded, fcol);
496 alignPanel.paintAlignment(true);
506 alignPanel.paintAlignment(true);
512 * Show a warning message if the entered type is one that is currently hidden
517 protected void warnIfTypeHidden(JPanel panel, String type)
519 if (getRenderOrder().contains(type))
521 if (!showFeatureOfType(type))
523 String msg = MessageManager.formatMessage("label.warning_hidden",
524 MessageManager.getString("label.feature_type"), type);
525 JvOptionPane.showMessageDialog(panel, msg, "",
526 JvOptionPane.OK_OPTION);
532 * Show a warning message if the entered group is one that is currently hidden
537 protected void warnIfGroupHidden(JPanel panel, String group)
539 if (featureGroups.containsKey(group) && !featureGroups.get(group))
541 String msg = MessageManager.formatMessage("label.warning_hidden",
542 MessageManager.getString("label.group"), group);
543 JvOptionPane.showMessageDialog(panel, msg, "", JvOptionPane.OK_OPTION);
548 * update the amend feature button dependent on the given style
554 protected void updateColourButton(JPanel bigPanel, JLabel colour,
558 colour.setIcon(null);
559 colour.setToolTipText(null);
562 if (col.isSimpleColour())
564 colour.setBackground(col.getColour());
568 colour.setBackground(bigPanel.getBackground());
569 colour.setForeground(Color.black);
570 FeatureSettings.renderGraduatedColor(colour, col);
575 * Orders features in render precedence (last in order is last to render, so
576 * displayed on top of other features)
580 public void orderFeatures(Comparator<String> order)
582 Arrays.sort(renderOrder, order);