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.ArrayList;
45 import java.util.Arrays;
46 import java.util.Comparator;
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
68 extends 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 JLabel colour = new JLabel();
184 colour.setOpaque(true);
185 // colour.setBorder(BorderFactory.createEtchedBorder());
186 colour.setMaximumSize(new Dimension(30, 16));
187 colour.addMouseListener(new MouseAdapter()
190 * open colour chooser on click in colour panel
193 public void mousePressed(MouseEvent evt)
195 if (fcol.isSimpleColour())
197 // BH 2018 JavaScript-compatible color dialog
198 Desktop.desktop.dialogData = new Object[] {
199 "label.select_feature_colour", this, mainPanel, colour };
201 .onDialogReturn(JColorChooser.showDialog(Desktop.desktop,
202 MessageManager.getString("label.select_feature_colour"),
208 * variable colour dialog - on OK, refetch the updated
209 * feature colour and update this display
211 final String ft = features.get(featureIndex).getType();
212 final String type = ft == null ? lastFeatureAdded : ft;
213 FeatureTypeSettings fcc = new FeatureTypeSettings(
214 FeatureRenderer.this, type);
215 fcc.setRequestFocusEnabled(true);
217 fcc.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent e)
222 fcol = FeatureRenderer.this.getFeatureStyle(ft);
223 setColour(type, fcol);
224 updateColourButton(mainPanel, colour, fcol);
230 JPanel gridPanel = new JPanel(new GridLayout(3, 1));
232 if (!create && features.size() > 1)
235 * more than one feature at selected position -
236 * add a drop-down to choose the feature to amend
237 * space pad text if necessary to make entries distinct
239 gridPanel = new JPanel(new GridLayout(4, 1));
240 JPanel choosePanel = new JPanel();
241 choosePanel.add(new JLabel(
242 MessageManager.getString("label.select_feature") + ":"));
243 final JComboBox<String> overlaps = new JComboBox<>();
244 List<String> added = new ArrayList<>();
245 for (SequenceFeature sf : features)
247 String text = String.format("%s/%d-%d (%s)", sf.getType(),
248 sf.getBegin(), sf.getEnd(), sf.getFeatureGroup());
249 while (added.contains(text))
253 overlaps.addItem(text);
256 choosePanel.add(overlaps);
258 overlaps.addItemListener(new ItemListener()
261 public void itemStateChanged(ItemEvent e)
263 int index = overlaps.getSelectedIndex();
266 featureIndex = index;
267 SequenceFeature sf = features.get(index);
268 name.setText(sf.getType());
269 description.setText(sf.getDescription());
270 group.setText(sf.getFeatureGroup());
271 start.setValue(new Integer(sf.getBegin()));
272 end.setValue(new Integer(sf.getEnd()));
274 SearchResultsI highlight = new SearchResults();
275 highlight.addResult(sequences.get(0), sf.getBegin(),
278 alignPanel.getSeqPanel().seqCanvas.highlightSearchResults(
281 FeatureColourI col = getFeatureStyle(name.getText());
284 col = new FeatureColour(
285 ColorUtils.createColourFromName(name.getText()));
288 updateColourButton(mainPanel, colour, col);
292 gridPanel.add(choosePanel);
295 JPanel namePanel = new JPanel();
296 gridPanel.add(namePanel);
297 namePanel.add(new JLabel(MessageManager.getString("label.name:"),
301 JPanel groupPanel = new JPanel();
302 gridPanel.add(groupPanel);
303 groupPanel.add(new JLabel(MessageManager.getString("label.group:"),
305 groupPanel.add(group);
307 JPanel colourPanel = new JPanel();
308 gridPanel.add(colourPanel);
309 colourPanel.add(new JLabel(MessageManager.getString("label.colour"),
311 colourPanel.add(colour);
312 colour.setPreferredSize(new Dimension(150, 15));
313 colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
314 colour.setForeground(Color.black);
315 colour.setHorizontalAlignment(SwingConstants.CENTER);
316 colour.setVerticalAlignment(SwingConstants.CENTER);
317 colour.setHorizontalTextPosition(SwingConstants.CENTER);
318 colour.setVerticalTextPosition(SwingConstants.CENTER);
319 mainPanel.add(gridPanel, BorderLayout.NORTH);
321 JPanel descriptionPanel = new JPanel();
322 descriptionPanel.add(new JLabel(
323 MessageManager.getString("label.description:"), JLabel.RIGHT));
324 description.setFont(JvSwingUtils.getTextAreaFont());
325 description.setLineWrap(true);
326 descriptionPanel.add(new JScrollPane(description));
330 mainPanel.add(descriptionPanel, BorderLayout.SOUTH);
332 JPanel startEndPanel = new JPanel();
333 startEndPanel.add(new JLabel(MessageManager.getString("label.start"),
335 startEndPanel.add(start);
336 startEndPanel.add(new JLabel(MessageManager.getString("label.end"),
338 startEndPanel.add(end);
339 mainPanel.add(startEndPanel, BorderLayout.CENTER);
343 mainPanel.add(descriptionPanel, BorderLayout.CENTER);
347 * default feature type and group to that of the first feature supplied,
348 * or to the last feature created if not supplied (null value)
350 SequenceFeature firstFeature = features.get(0);
351 boolean useLastDefaults = firstFeature.getType() == null;
352 final String featureType = useLastDefaults ? lastFeatureAdded
353 : firstFeature.getType();
354 final String featureGroup = useLastDefaults ? lastFeatureGroupAdded
355 : firstFeature.getFeatureGroup();
356 name.setText(featureType);
357 group.setText(featureGroup);
359 start.setValue(new Integer(firstFeature.getBegin()));
360 end.setValue(new Integer(firstFeature.getEnd()));
361 description.setText(firstFeature.getDescription());
362 updateColourButton(mainPanel, colour,
363 (oldcol = fcol = getFeatureStyle(featureType)));
367 options = new Object[] { MessageManager.getString("label.amend"),
368 MessageManager.getString("action.delete"),
369 MessageManager.getString("action.cancel") };
373 options = new Object[] { MessageManager.getString("action.ok"),
374 MessageManager.getString("action.cancel") };
377 String title = create
378 ? MessageManager.getString("label.create_new_sequence_features")
379 : MessageManager.formatMessage("label.amend_delete_features",
381 { sequences.get(0).getName() });
386 int reply = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
387 mainPanel, title, JvOptionPane.YES_NO_CANCEL_OPTION,
388 JvOptionPane.QUESTION_MESSAGE, null, options,
389 MessageManager.getString("action.ok"));
391 FeaturesFile ffile = new FeaturesFile();
393 final String enteredType = name.getText().trim();
394 final String enteredGroup = group.getText().trim();
395 final String enteredDescription = description.getText().replaceAll("\n", " ");
397 if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
400 * update default values only if creating using default values
404 lastFeatureAdded = enteredType;
405 lastFeatureGroupAdded = enteredGroup;
406 // TODO: determine if the null feature group is valid
407 if (lastFeatureGroupAdded.length() < 1)
409 lastFeatureGroupAdded = null;
416 SequenceFeature sf = features.get(featureIndex);
418 if (reply == JvOptionPane.NO_OPTION)
421 * NO_OPTION corresponds to the Delete button
423 sequences.get(0).getDatasetSequence().deleteFeature(sf);
424 // update Feature Settings for removal of feature / group
427 else if (reply == JvOptionPane.YES_OPTION)
430 * YES_OPTION corresponds to the Amend button
431 * need to refresh Feature Settings if type, group or colour changed;
432 * note we don't force the feature to be visible - the user has been
433 * warned if a hidden feature type or group was entered
435 boolean refreshSettings = (!featureType.equals(enteredType) || !featureGroup
436 .equals(enteredGroup));
437 refreshSettings |= (fcol != oldcol);
438 setColour(enteredType, fcol);
439 int newBegin = sf.begin;
443 newBegin = ((Integer) start.getValue()).intValue();
444 newEnd = ((Integer) end.getValue()).intValue();
445 } catch (NumberFormatException ex)
447 // JSpinner doesn't accept invalid format data :-)
451 * replace the feature by deleting it and adding a new one
452 * (to ensure integrity of SequenceFeatures data store)
454 sequences.get(0).deleteFeature(sf);
455 SequenceFeature newSf = new SequenceFeature(sf, enteredType,
456 newBegin, newEnd, enteredGroup, sf.getScore());
457 newSf.setDescription(enteredDescription);
458 ffile.parseDescriptionHTML(newSf, false);
459 // amend features dialog only updates one sequence at a time
460 sequences.get(0).addSequenceFeature(newSf);
469 // NEW FEATURES ADDED
471 if (reply == JvOptionPane.OK_OPTION && enteredType.length() > 0)
473 for (int i = 0; i < sequences.size(); i++)
475 SequenceFeature sf = features.get(i);
476 SequenceFeature sf2 = new SequenceFeature(enteredType,
477 enteredDescription, sf.getBegin(), sf.getEnd(),
479 ffile.parseDescriptionHTML(sf2, false);
480 sequences.get(i).addSequenceFeature(sf2);
483 setColour(enteredType, fcol);
487 alignPanel.paintAlignment(true, true);
497 alignPanel.paintAlignment(true, true);
502 void processColorDialog(Color col)
504 JPanel mainPanel = (JPanel) Desktop.desktop.dialogData[2];
505 JLabel colour = (JLabel) Desktop.desktop.dialogData[3];
508 fcol = new FeatureColour(col);
509 updateColourButton(mainPanel, colour, fcol);
514 * Show a warning message if the entered type is one that is currently hidden
519 protected void warnIfTypeHidden(JPanel panel, String type)
521 if (getRenderOrder().contains(type))
523 if (!showFeatureOfType(type))
525 String msg = MessageManager.formatMessage("label.warning_hidden",
526 MessageManager.getString("label.feature_type"), type);
527 JvOptionPane.showMessageDialog(panel, msg, "",
528 JvOptionPane.OK_OPTION);
534 * Show a warning message if the entered group is one that is currently hidden
539 protected void warnIfGroupHidden(JPanel panel, String group)
541 if (featureGroups.containsKey(group) && !featureGroups.get(group))
543 String msg = MessageManager.formatMessage("label.warning_hidden",
544 MessageManager.getString("label.group"), group);
545 JvOptionPane.showMessageDialog(panel, msg, "",
546 JvOptionPane.OK_OPTION);
551 * update the amend feature button dependent on the given style
557 protected void updateColourButton(JPanel bigPanel, JLabel colour,
561 colour.setIcon(null);
562 colour.setToolTipText(null);
565 if (col.isSimpleColour())
567 colour.setBackground(col.getColour());
571 colour.setBackground(bigPanel.getBackground());
572 colour.setForeground(Color.black);
573 FeatureSettings.renderGraduatedColor(colour, col);
578 * Orders features in render precedence (last in order is last to render, so
579 * displayed on top of other features)
583 public void orderFeatures(Comparator<String> order)
585 Arrays.sort(renderOrder, order);