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.
21 package jalview.appletgui;
23 import jalview.api.FeatureColourI;
24 import jalview.datamodel.SearchResults;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.datamodel.SequenceI;
27 import jalview.io.FeaturesFile;
28 import jalview.schemes.FeatureColour;
29 import jalview.schemes.UserColourScheme;
30 import jalview.util.MessageManager;
31 import jalview.viewmodel.AlignmentViewport;
33 import java.awt.BorderLayout;
34 import java.awt.Button;
35 import java.awt.Choice;
36 import java.awt.Color;
37 import java.awt.Dimension;
39 import java.awt.Graphics;
40 import java.awt.GridLayout;
41 import java.awt.Label;
42 import java.awt.Panel;
43 import java.awt.ScrollPane;
44 import java.awt.TextArea;
45 import java.awt.TextField;
46 import java.awt.event.ActionEvent;
47 import java.awt.event.ActionListener;
48 import java.awt.event.MouseAdapter;
49 import java.awt.event.MouseEvent;
50 import java.util.Hashtable;
58 public class FeatureRenderer extends
59 jalview.renderer.seqfeatures.FeatureRenderer
62 // Holds web links for feature groups and feature types
63 // in the form label|link
64 Hashtable featureLinks = null;
67 * Creates a new FeatureRenderer object.
71 public FeatureRenderer(AlignmentViewport av)
77 static String lastFeatureAdded;
79 static String lastFeatureGroupAdded;
81 static String lastDescriptionAdded;
85 boolean deleteFeature = false;
87 FeatureColourPanel colourPanel;
89 class FeatureColourPanel extends Panel
95 private boolean isColourByLabel, isGcol;
98 * render a feature style in the amend feature dialog box
100 public void updateColor(FeatureColourI newcol)
104 if (newcol.isSimpleColour())
106 bg = newcol.getColour();
111 if (newcol.isAboveThreshold())
115 else if (newcol.isBelowThreshold())
120 if (isColourByLabel = newcol.isColourByLabel())
122 setBackground(bg = Color.white);
123 vlabel += " (by Label)";
127 setBackground(bg = newcol.getMinColour());
128 maxCol = newcol.getMaxColour();
142 public void paint(Graphics g)
144 Dimension d = getSize();
149 g.setColor(Color.white);
150 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
151 g.setColor(Color.black);
152 Font f = new Font("Verdana", Font.PLAIN, 10);
154 g.drawString(MessageManager.getString("label.label"), 0, 0);
159 g.fillRect(d.width / 2, 0, d.width / 2, d.height);
167 boolean amendFeatures(final SequenceI[] sequences,
168 final SequenceFeature[] features, boolean newFeatures,
169 final AlignmentPanel ap)
171 Panel bigPanel = new Panel(new BorderLayout());
172 final TextField name = new TextField(16);
173 final TextField source = new TextField(16);
174 final TextArea description = new TextArea(3, 35);
175 final TextField start = new TextField(8);
176 final TextField end = new TextField(8);
177 final Choice overlaps;
178 Button deleteButton = new Button("Delete");
179 deleteFeature = false;
181 colourPanel = new FeatureColourPanel();
182 colourPanel.setSize(110, 15);
183 final FeatureRenderer fr = this;
185 Panel panel = new Panel(new GridLayout(3, 1));
187 featureIndex = 0; // feature to be amended.
190 // /////////////////////////////////////
191 // /MULTIPLE FEATURES AT SELECTED RESIDUE
192 if (!newFeatures && features.length > 1)
194 panel = new Panel(new GridLayout(4, 1));
196 tmp.add(new Label("Select Feature: "));
197 overlaps = new Choice();
198 for (int i = 0; i < features.length; i++)
200 String item = features[i].getType() + "/" + features[i].getBegin()
201 + "-" + features[i].getEnd();
203 if (features[i].getFeatureGroup() != null)
205 item += " (" + features[i].getFeatureGroup() + ")";
208 overlaps.addItem(item);
213 overlaps.addItemListener(new java.awt.event.ItemListener()
216 public void itemStateChanged(java.awt.event.ItemEvent e)
218 int index = overlaps.getSelectedIndex();
221 featureIndex = index;
222 name.setText(features[index].getType());
223 description.setText(features[index].getDescription());
224 source.setText(features[index].getFeatureGroup());
225 start.setText(features[index].getBegin() + "");
226 end.setText(features[index].getEnd() + "");
228 SearchResults highlight = new SearchResults();
229 highlight.addResult(sequences[0], features[index].getBegin(),
230 features[index].getEnd());
232 ap.seqPanel.seqCanvas.highlightSearchResults(highlight);
235 FeatureColourI col = getFeatureStyle(name.getText());
238 Color generatedColour = UserColourScheme
239 .createColourFromName(name.getText());
240 col = new FeatureColour(generatedColour);
243 colourPanel.updateColor(col);
250 // ////////////////////////////////////
254 tmp.add(new Label("Name: ", Label.RIGHT));
259 tmp.add(new Label("Group: ", Label.RIGHT));
264 tmp.add(new Label("Colour: ", Label.RIGHT));
265 tmp.add(colourPanel);
267 bigPanel.add(panel, BorderLayout.NORTH);
270 panel.add(new Label("Description: ", Label.RIGHT));
271 panel.add(new ScrollPane().add(description));
275 bigPanel.add(panel, BorderLayout.SOUTH);
278 panel.add(new Label(" Start:", Label.RIGHT));
280 panel.add(new Label(" End:", Label.RIGHT));
282 bigPanel.add(panel, BorderLayout.CENTER);
286 bigPanel.add(panel, BorderLayout.CENTER);
289 if (lastFeatureAdded == null)
291 if (features[0].type != null)
293 lastFeatureAdded = features[0].type;
297 lastFeatureAdded = "feature_1";
301 if (lastFeatureGroupAdded == null)
303 if (features[0].featureGroup != null)
305 lastFeatureGroupAdded = features[0].featureGroup;
309 lastFeatureAdded = "Jalview";
313 String title = newFeatures ? MessageManager
314 .getString("label.create_new_sequence_features")
315 : MessageManager.formatMessage("label.amend_delete_features",
316 new String[] { sequences[0].getName() });
318 final JVDialog dialog = new JVDialog(ap.alignFrame, title, true, 385,
321 dialog.setMainPanel(bigPanel);
325 name.setText(lastFeatureAdded);
326 source.setText(lastFeatureGroupAdded);
330 dialog.ok.setLabel(MessageManager.getString("label.amend"));
331 dialog.buttonPanel.add(deleteButton, 1);
332 deleteButton.addActionListener(new ActionListener()
335 public void actionPerformed(ActionEvent evt)
337 deleteFeature = true;
338 dialog.setVisible(false);
341 name.setText(features[0].getType());
342 source.setText(features[0].getFeatureGroup());
345 start.setText(features[0].getBegin() + "");
346 end.setText(features[0].getEnd() + "");
347 description.setText(features[0].getDescription());
348 // lookup (or generate) the feature colour
349 FeatureColourI fcol = getFeatureStyle(name.getText());
350 // simply display the feature color in a box
351 colourPanel.updateColor(fcol);
352 dialog.setResizable(true);
353 // TODO: render the graduated color in the box.
354 colourPanel.addMouseListener(new MouseAdapter()
357 public void mousePressed(MouseEvent evt)
359 if (!colourPanel.isGcol)
361 new UserDefinedColours(fr, ap.alignFrame);
365 new FeatureColourChooser(ap.alignFrame, name.getText());
366 dialog.transferFocus();
370 dialog.setVisible(true);
372 FeaturesFile ffile = new FeaturesFile();
376 // This ensures that the last sequence
377 // is refreshed and new features are rendered
379 lastFeatureAdded = name.getText().trim();
380 lastFeatureGroupAdded = source.getText().trim();
381 lastDescriptionAdded = description.getText().replace('\n', ' ');
384 if (lastFeatureGroupAdded != null && lastFeatureGroupAdded.length() < 1)
386 lastFeatureGroupAdded = null;
392 SequenceFeature sf = features[featureIndex];
395 sf.type = lastFeatureAdded;
396 sf.featureGroup = lastFeatureGroupAdded;
397 sf.description = lastDescriptionAdded;
398 if (!colourPanel.isGcol)
400 // update colour - otherwise its already done.
401 setColour(sf.type, new FeatureColour(colourPanel.getBackground()));
405 sf.begin = Integer.parseInt(start.getText());
406 sf.end = Integer.parseInt(end.getText());
407 } catch (NumberFormatException ex)
411 ffile.parseDescriptionHTML(sf, false);
412 setVisible(lastFeatureAdded); // if user edited name then make sure new
417 sequences[0].deleteFeature(sf);
423 if (dialog.accept && name.getText().length() > 0)
425 for (int i = 0; i < sequences.length; i++)
427 features[i].type = lastFeatureAdded;
428 features[i].featureGroup = lastFeatureGroupAdded;
429 features[i].description = lastDescriptionAdded;
430 sequences[i].addSequenceFeature(features[i]);
431 ffile.parseDescriptionHTML(features[i], false);
434 Color newColour = colourPanel.getBackground();
435 // setColour(lastFeatureAdded, fcol);
437 if (lastFeatureGroupAdded != null)
439 setGroupVisibility(lastFeatureGroupAdded, true);
441 setColour(lastFeatureAdded, new FeatureColour(newColour)); // was fcol
442 setVisible(lastFeatureAdded);
443 findAllFeatures(false); // different to original applet behaviour ?
444 // findAllFeatures();
448 // no update to the alignment
452 // refresh the alignment and the feature settings dialog
453 if (((jalview.appletgui.AlignViewport) av).featureSettings != null)
455 ((jalview.appletgui.AlignViewport) av).featureSettings.refreshTable();
457 // findAllFeatures();
459 ap.paintAlignment(true);