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.datamodel.SearchResults;
24 import jalview.datamodel.SequenceFeature;
25 import jalview.datamodel.SequenceI;
26 import jalview.schemes.GraduatedColor;
27 import jalview.util.MessageManager;
29 import java.awt.BorderLayout;
30 import java.awt.Color;
31 import java.awt.Dimension;
33 import java.awt.GridLayout;
34 import java.awt.event.ActionEvent;
35 import java.awt.event.ActionListener;
36 import java.awt.event.ItemEvent;
37 import java.awt.event.ItemListener;
38 import java.awt.event.MouseAdapter;
39 import java.awt.event.MouseEvent;
40 import java.util.Arrays;
41 import java.util.Comparator;
43 import javax.swing.JColorChooser;
44 import javax.swing.JComboBox;
45 import javax.swing.JLabel;
46 import javax.swing.JOptionPane;
47 import javax.swing.JPanel;
48 import javax.swing.JScrollPane;
49 import javax.swing.JSpinner;
50 import javax.swing.JTextArea;
51 import javax.swing.JTextField;
52 import javax.swing.SwingConstants;
60 public class FeatureRenderer extends
61 jalview.renderer.seqfeatures.FeatureRenderer implements
62 jalview.api.FeatureRenderer
69 * Creates a new FeatureRenderer object.
74 public FeatureRenderer(AlignmentPanel ap)
79 if (ap != null && ap.getSeqPanel() != null
80 && ap.getSeqPanel().seqCanvas != null
81 && ap.getSeqPanel().seqCanvas.fr != null)
83 transferSettings(ap.getSeqPanel().seqCanvas.fr);
88 // // Feature Editing Dialog
89 // // Will be refactored in next release.
91 static String lastFeatureAdded;
93 static String lastFeatureGroupAdded;
95 static String lastDescriptionAdded;
101 boolean amendFeatures(final SequenceI[] sequences,
102 final SequenceFeature[] features, boolean newFeatures,
103 final AlignmentPanel ap)
108 final JPanel bigPanel = new JPanel(new BorderLayout());
109 final JComboBox overlaps;
110 final JTextField name = new JTextField(25);
111 final JTextField source = new JTextField(25);
112 final JTextArea description = new JTextArea(3, 25);
113 final JSpinner start = new JSpinner();
114 final JSpinner end = new JSpinner();
115 start.setPreferredSize(new Dimension(80, 20));
116 end.setPreferredSize(new Dimension(80, 20));
117 final FeatureRenderer me = this;
118 final JLabel colour = new JLabel();
119 colour.setOpaque(true);
120 // colour.setBorder(BorderFactory.createEtchedBorder());
121 colour.setMaximumSize(new Dimension(30, 16));
122 colour.addMouseListener(new MouseAdapter()
124 FeatureColourChooser fcc = null;
127 public void mousePressed(MouseEvent evt)
129 if (fcol instanceof Color)
131 Color col = JColorChooser.showDialog(Desktop.desktop,
132 MessageManager.getString("label.select_feature_colour"),
137 updateColourButton(bigPanel, colour, col);
145 final String type = features[featureIndex].getType();
146 fcc = new FeatureColourChooser(me, type);
147 fcc.setRequestFocusEnabled(true);
150 fcc.addActionListener(new ActionListener()
154 public void actionPerformed(ActionEvent e)
156 fcol = fcc.getLastColour();
158 setColour(type, fcol);
159 updateColourButton(bigPanel, colour, fcol);
167 JPanel tmp = new JPanel();
168 JPanel panel = new JPanel(new GridLayout(3, 1));
170 // /////////////////////////////////////
171 // /MULTIPLE FEATURES AT SELECTED RESIDUE
172 if (!newFeatures && features.length > 1)
174 panel = new JPanel(new GridLayout(4, 1));
176 tmp.add(new JLabel(MessageManager.getString("label.select_feature")));
177 overlaps = new JComboBox();
178 for (int i = 0; i < features.length; i++)
180 overlaps.addItem(features[i].getType() + "/"
181 + features[i].getBegin() + "-" + features[i].getEnd()
182 + " (" + features[i].getFeatureGroup() + ")");
187 overlaps.addItemListener(new ItemListener()
190 public void itemStateChanged(ItemEvent e)
192 int index = overlaps.getSelectedIndex();
195 featureIndex = index;
196 name.setText(features[index].getType());
197 description.setText(features[index].getDescription());
198 source.setText(features[index].getFeatureGroup());
199 start.setValue(new Integer(features[index].getBegin()));
200 end.setValue(new Integer(features[index].getEnd()));
202 SearchResults highlight = new SearchResults();
203 highlight.addResult(sequences[0], features[index].getBegin(),
204 features[index].getEnd());
206 ap.getSeqPanel().seqCanvas.highlightSearchResults(highlight);
209 Object col = getFeatureStyle(name.getText());
212 col = new jalview.schemes.UserColourScheme()
213 .createColourFromName(name.getText());
216 updateColourButton(bigPanel, colour, col);
223 // ////////////////////////////////////
227 tmp.add(new JLabel(MessageManager.getString("label.name"), JLabel.RIGHT));
232 tmp.add(new JLabel(MessageManager.getString("label.group") + ":",
238 tmp.add(new JLabel(MessageManager.getString("label.colour"),
241 colour.setPreferredSize(new Dimension(150, 15));
242 colour.setFont(new java.awt.Font("Verdana", Font.PLAIN, 9));
243 colour.setForeground(Color.black);
244 colour.setHorizontalAlignment(SwingConstants.CENTER);
245 colour.setVerticalAlignment(SwingConstants.CENTER);
246 colour.setHorizontalTextPosition(SwingConstants.CENTER);
247 colour.setVerticalTextPosition(SwingConstants.CENTER);
248 bigPanel.add(panel, BorderLayout.NORTH);
250 panel = new JPanel();
251 panel.add(new JLabel(MessageManager.getString("label.description"),
253 description.setFont(JvSwingUtils.getTextAreaFont());
254 description.setLineWrap(true);
255 panel.add(new JScrollPane(description));
259 bigPanel.add(panel, BorderLayout.SOUTH);
261 panel = new JPanel();
262 panel.add(new JLabel(MessageManager.getString("label.start"),
265 panel.add(new JLabel(MessageManager.getString("label.end"),
268 bigPanel.add(panel, BorderLayout.CENTER);
272 bigPanel.add(panel, BorderLayout.CENTER);
275 if (lastFeatureAdded == null)
277 if (features[0].type != null)
279 lastFeatureAdded = features[0].type;
283 lastFeatureAdded = "feature_1";
287 if (lastFeatureGroupAdded == null)
289 if (features[0].featureGroup != null)
291 lastFeatureGroupAdded = features[0].featureGroup;
295 lastFeatureGroupAdded = "Jalview";
301 name.setText(lastFeatureAdded);
302 source.setText(lastFeatureGroupAdded);
306 name.setText(features[0].getType());
307 source.setText(features[0].getFeatureGroup());
310 start.setValue(new Integer(features[0].getBegin()));
311 end.setValue(new Integer(features[0].getEnd()));
312 description.setText(features[0].getDescription());
313 updateColourButton(bigPanel, colour,
314 (oldcol = fcol = getFeatureStyle(name.getText())));
318 options = new Object[] { "Amend", "Delete", "Cancel" };
322 options = new Object[] { "OK", "Cancel" };
325 String title = newFeatures ? MessageManager
326 .getString("label.create_new_sequence_features")
327 : MessageManager.formatMessage("label.amend_delete_features",
328 new String[] { sequences[0].getName() });
330 int reply = JOptionPane.showInternalOptionDialog(Desktop.desktop,
331 bigPanel, title, JOptionPane.YES_NO_CANCEL_OPTION,
332 JOptionPane.QUESTION_MESSAGE, null, options,
333 MessageManager.getString("action.ok"));
335 jalview.io.FeaturesFile ffile = new jalview.io.FeaturesFile();
337 if (reply == JOptionPane.OK_OPTION && name.getText().length() > 0)
339 // This ensures that the last sequence
340 // is refreshed and new features are rendered
342 lastFeatureAdded = name.getText().trim();
343 lastFeatureGroupAdded = source.getText().trim();
344 lastDescriptionAdded = description.getText().replaceAll("\n", " ");
345 // TODO: determine if the null feature group is valid
346 if (lastFeatureGroupAdded.length() < 1)
348 lastFeatureGroupAdded = null;
354 SequenceFeature sf = features[featureIndex];
356 if (reply == JOptionPane.NO_OPTION)
358 sequences[0].getDatasetSequence().deleteFeature(sf);
360 else if (reply == JOptionPane.YES_OPTION)
362 sf.type = lastFeatureAdded;
363 sf.featureGroup = lastFeatureGroupAdded;
364 sf.description = lastDescriptionAdded;
366 setColour(sf.type, fcol);
367 getFeaturesDisplayed().setVisible(sf.type);
371 sf.begin = ((Integer) start.getValue()).intValue();
372 sf.end = ((Integer) end.getValue()).intValue();
373 } catch (NumberFormatException ex)
377 ffile.parseDescriptionHTML(sf, false);
381 // NEW FEATURES ADDED
383 if (reply == JOptionPane.OK_OPTION && lastFeatureAdded.length() > 0)
385 for (int i = 0; i < sequences.length; i++)
387 features[i].type = lastFeatureAdded;
388 // fix for JAL-1538 - always set feature group here
389 features[i].featureGroup = lastFeatureGroupAdded;
390 features[i].description = lastDescriptionAdded;
391 sequences[i].addSequenceFeature(features[i]);
392 ffile.parseDescriptionHTML(features[i], false);
395 if (lastFeatureGroupAdded != null)
397 setGroupVisibility(lastFeatureGroupAdded, true);
399 setColour(lastFeatureAdded, fcol);
400 setVisible(lastFeatureAdded);
402 findAllFeatures(false);
404 ap.paintAlignment(true);
414 ap.paintAlignment(true);
420 * update the amend feature button dependent on the given style
426 protected void updateColourButton(JPanel bigPanel, JLabel colour,
430 colour.setIcon(null);
431 colour.setToolTipText(null);
434 if (col2 instanceof Color)
436 colour.setBackground((Color) col2);
440 colour.setBackground(bigPanel.getBackground());
441 colour.setForeground(Color.black);
442 FeatureSettings.renderGraduatedColor(colour, (GraduatedColor) col2);
443 // colour.setForeground(colour.getBackground());
448 * Orders features in render precedence (last in order is last to render, so
449 * displayed on top of other features)
453 public void orderFeatures(Comparator<String> order)
455 Arrays.sort(renderOrder, order);