2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
\r
5 * This program is free software; you can redistribute it and/or
\r
6 * modify it under the terms of the GNU General Public License
\r
7 * as published by the Free Software Foundation; either version 2
\r
8 * of the License, or (at your option) any later version.
\r
10 * This program is distributed in the hope that it will be useful,
\r
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
\r
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
\r
13 * GNU General Public License for more details.
\r
15 * You should have received a copy of the GNU General Public License
\r
16 * along with this program; if not, write to the Free Software
\r
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
\r
20 package jalview.appletgui;
\r
23 import java.awt.event.*;
\r
24 import java.util.Vector;
\r
26 import jalview.analysis.*;
\r
27 import jalview.datamodel.*;
\r
28 import jalview.schemes.*;
\r
30 public class APopupMenu
\r
31 extends java.awt.PopupMenu implements ActionListener, ItemListener
\r
33 Menu groupMenu = new Menu();
\r
34 protected MenuItem clustalColour = new MenuItem();
\r
35 protected MenuItem zappoColour = new MenuItem();
\r
36 protected MenuItem taylorColour = new MenuItem();
\r
37 protected MenuItem hydrophobicityColour = new MenuItem();
\r
38 protected MenuItem helixColour = new MenuItem();
\r
39 protected MenuItem strandColour = new MenuItem();
\r
40 protected MenuItem turnColour = new MenuItem();
\r
41 protected MenuItem buriedColour = new MenuItem();
\r
42 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
\r
43 protected MenuItem userDefinedColour = new MenuItem();
\r
44 protected MenuItem PIDColour = new MenuItem();
\r
45 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
46 MenuItem noColourmenuItem = new MenuItem();
\r
47 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
49 final AlignmentPanel ap;
\r
50 MenuItem unGroupMenuItem = new MenuItem();
\r
51 MenuItem nucleotideMenuItem = new MenuItem();
\r
52 Menu colourMenu = new Menu();
\r
53 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
\r
54 CheckboxMenuItem showText = new CheckboxMenuItem();
\r
55 CheckboxMenuItem showColourText = new CheckboxMenuItem();
\r
56 Menu editMenu = new Menu("Edit");
\r
57 MenuItem copy = new MenuItem("Copy (Jalview Only)");
\r
58 MenuItem cut = new MenuItem("Cut (Jalview Only)");
\r
59 MenuItem toUpper = new MenuItem("To Upper Case");
\r
60 MenuItem toLower = new MenuItem("To Lower Case");
\r
62 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
\r
64 ///////////////////////////////////////////////////////////
\r
65 // If this is activated from the sequence panel, the user may want to
\r
66 // edit or annotate a particular residue. Therefore display the residue menu
\r
68 // If from the IDPanel, we must display the sequence menu
\r
69 //////////////////////////////////////////////////////////
\r
79 e.printStackTrace();
\r
82 SequenceGroup sg = ap.av.getSelectionGroup();
\r
84 if (sg != null && sg.getSize()>0)
\r
86 showText.setState(sg.getDisplayText());
\r
87 showColourText.setState(sg.getColourText());
\r
88 showBoxes.setState(sg.getDisplayBoxes());
\r
96 if (!ap.av.alignment.getGroups().contains(sg))
\r
98 groupMenu.remove(unGroupMenuItem);
\r
101 if (seq != null && links!=null)
\r
103 Menu linkMenu = new Menu("Link");
\r
106 for(int i=0; i<links.size(); i++)
\r
108 link = links.elementAt(i).toString();
\r
109 final String target = link.substring(0, link.indexOf("|"));
\r
110 item = new MenuItem(target);
\r
111 String id = seq.getName();
\r
112 if(id.indexOf("|")>-1)
\r
113 id = id.substring(id.lastIndexOf("|")+1);
\r
115 final String url = link.substring(link.indexOf("|")+1, link.indexOf("$SEQUENCE_ID$"))
\r
117 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
\r
119 item.addActionListener(new java.awt.event.ActionListener()
\r
121 public void actionPerformed(ActionEvent e)
\r
123 ap.alignFrame.showURL(url, target);
\r
126 linkMenu.add(item);
\r
130 item = new MenuItem("Show PDB Structure");
\r
131 item.addActionListener(new java.awt.event.ActionListener()
\r
133 public void actionPerformed(ActionEvent e)
\r
145 public void itemStateChanged(ItemEvent evt)
\r
147 if(evt.getSource()==abovePIDColour)
\r
148 abovePIDColour_itemStateChanged();
\r
149 else if(evt.getSource()==showColourText)
\r
150 showColourText_itemStateChanged();
\r
151 else if(evt.getSource()==showText)
\r
152 showText_itemStateChanged();
\r
153 else if(evt.getSource()==showBoxes)
\r
154 showBoxes_itemStateChanged() ;
\r
157 public void actionPerformed(ActionEvent evt)
\r
159 Object source = evt.getSource();
\r
160 if(source==clustalColour)
\r
161 clustalColour_actionPerformed();
\r
162 else if(source==zappoColour)
\r
163 zappoColour_actionPerformed();
\r
164 else if(source==taylorColour)
\r
165 taylorColour_actionPerformed();
\r
166 else if(source==hydrophobicityColour)
\r
167 hydrophobicityColour_actionPerformed();
\r
168 else if(source==helixColour)
\r
169 helixColour_actionPerformed();
\r
170 else if(source==strandColour)
\r
171 strandColour_actionPerformed();
\r
172 else if(source==clustalColour)
\r
173 turnColour_actionPerformed();
\r
174 else if(source==buriedColour)
\r
175 buriedColour_actionPerformed();
\r
176 else if(source==nucleotideMenuItem)
\r
177 nucleotideMenuItem_actionPerformed();
\r
179 else if(source==userDefinedColour)
\r
180 userDefinedColour_actionPerformed();
\r
181 else if(source==PIDColour)
\r
182 PIDColour_actionPerformed();
\r
183 else if(source==BLOSUM62Colour)
\r
184 BLOSUM62Colour_actionPerformed();
\r
185 else if(source==noColourmenuItem)
\r
186 noColourmenuItem_actionPerformed();
\r
187 else if(source==conservationMenuItem)
\r
188 conservationMenuItem_itemStateChanged();
\r
189 else if(source==unGroupMenuItem)
\r
190 unGroupMenuItem_actionPerformed();
\r
192 else if(source==copy)
\r
193 ap.alignFrame.copy_actionPerformed();
\r
194 else if(source==cut)
\r
195 ap.alignFrame.cut_actionPerformed();
\r
196 else if(source==toUpper)
\r
198 SequenceGroup sg = ap.av.getSelectionGroup();
\r
201 for (int g = 0; g < sg.getSize(); g++)
\r
203 sg.getSequenceAt(g).changeCase(true, sg.getStartRes(),
\r
204 sg.getEndRes() + 1);
\r
206 ap.seqPanel.seqCanvas.repaint();
\r
209 else if(source==toLower)
\r
211 SequenceGroup sg = ap.av.getSelectionGroup();
\r
214 for (int g = 0; g < sg.getSize(); g++)
\r
216 sg.getSequenceAt(g).changeCase(false, sg.getStartRes(),
\r
217 sg.getEndRes() + 1);
\r
219 ap.seqPanel.seqCanvas.repaint();
\r
225 void addPDB(Sequence seq)
\r
227 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
\r
228 cap.setText("Paste your PDB file here.");
\r
229 cap.setPDBImport(seq);
\r
230 Frame frame = new Frame();
\r
232 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
\r
235 private void jbInit()
\r
238 groupMenu.setLabel("Group");
\r
239 groupMenu.setLabel("Define");
\r
241 unGroupMenuItem.setLabel("Remove Group");
\r
242 unGroupMenuItem.addActionListener(this);
\r
244 nucleotideMenuItem.setLabel("Nucleotide");
\r
245 nucleotideMenuItem.addActionListener(this);
\r
246 conservationMenuItem.addItemListener(this);
\r
247 abovePIDColour.addItemListener(this);
\r
248 colourMenu.setLabel("Group Colour");
\r
249 showBoxes.setLabel("Boxes");
\r
250 showBoxes.setState(true);
\r
251 showBoxes.addItemListener(this);
\r
253 showText.setLabel("Text");
\r
254 showText.addItemListener(this);
\r
255 showColourText.setLabel("Colour Text");
\r
256 showColourText.addItemListener(this);
\r
259 groupMenu.add(unGroupMenuItem);
\r
260 groupMenu.add(colourMenu);
\r
261 groupMenu.addSeparator();
\r
262 groupMenu.add(showBoxes);
\r
263 groupMenu.add(showText);
\r
264 groupMenu.add(showColourText);
\r
265 colourMenu.add(noColourmenuItem);
\r
266 colourMenu.add(clustalColour);
\r
267 colourMenu.add(BLOSUM62Colour);
\r
268 colourMenu.add(PIDColour);
\r
269 colourMenu.add(zappoColour);
\r
270 colourMenu.add(taylorColour);
\r
271 colourMenu.add(hydrophobicityColour);
\r
272 colourMenu.add(helixColour);
\r
273 colourMenu.add(strandColour);
\r
274 colourMenu.add(turnColour);
\r
275 colourMenu.add(buriedColour);
\r
276 colourMenu.add(nucleotideMenuItem);
\r
277 colourMenu.add(userDefinedColour);
\r
278 colourMenu.addSeparator();
\r
279 colourMenu.add(abovePIDColour);
\r
280 colourMenu.add(conservationMenuItem);
\r
282 noColourmenuItem.setLabel("None");
\r
283 noColourmenuItem.addActionListener(this);
\r
285 clustalColour.setLabel("Clustalx colours");
\r
286 clustalColour.addActionListener(this);
\r
287 zappoColour.setLabel("Zappo");
\r
288 zappoColour.addActionListener(this);
\r
289 taylorColour.setLabel("Taylor");
\r
290 taylorColour.addActionListener(this);
\r
291 hydrophobicityColour.setLabel("Hydrophobicity");
\r
292 hydrophobicityColour.addActionListener(this);
\r
293 helixColour.setLabel("Helix propensity");
\r
294 helixColour.addActionListener(this);
\r
295 strandColour.setLabel("Strand propensity");
\r
296 strandColour.addActionListener(this);
\r
297 turnColour.setLabel("Turn propensity");
\r
298 turnColour.addActionListener(this);
\r
299 buriedColour.setLabel("Buried Index");
\r
300 buriedColour.addActionListener(this);
\r
301 abovePIDColour.setLabel("Above % Identity");
\r
303 userDefinedColour.setLabel("User Defined");
\r
304 userDefinedColour.addActionListener(this);
\r
305 PIDColour.setLabel("Percentage Identity");
\r
306 PIDColour.addActionListener(this);
\r
307 BLOSUM62Colour.setLabel("BLOSUM62");
\r
308 BLOSUM62Colour.addActionListener(this);
\r
309 conservationMenuItem.setLabel("Conservation");
\r
312 editMenu.add(copy);
\r
313 copy.addActionListener(this);
\r
315 cut.addActionListener(this);
\r
316 editMenu.add(toUpper);
\r
317 toUpper.addActionListener(this);
\r
318 editMenu.add(toLower);
\r
319 toLower.addActionListener(this);
\r
325 ap.seqPanel.seqCanvas.repaint();
\r
326 if(ap.overviewPanel!=null)
\r
327 ap.overviewPanel.updateOverviewImage();
\r
330 protected void clustalColour_actionPerformed()
\r
332 SequenceGroup sg = getGroup();
\r
333 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
\r
337 protected void zappoColour_actionPerformed()
\r
339 getGroup().cs = new ZappoColourScheme();
\r
343 protected void taylorColour_actionPerformed()
\r
345 getGroup().cs = new TaylorColourScheme();
\r
349 protected void hydrophobicityColour_actionPerformed()
\r
351 getGroup().cs = new HydrophobicColourScheme();
\r
355 protected void helixColour_actionPerformed()
\r
357 getGroup().cs = new HelixColourScheme();
\r
361 protected void strandColour_actionPerformed()
\r
363 getGroup().cs = new StrandColourScheme();
\r
367 protected void turnColour_actionPerformed()
\r
369 getGroup().cs = new TurnColourScheme();
\r
373 protected void buriedColour_actionPerformed()
\r
375 getGroup().cs = new BuriedColourScheme();
\r
379 public void nucleotideMenuItem_actionPerformed()
\r
381 getGroup().cs = new NucleotideColourScheme();
\r
385 protected void abovePIDColour_itemStateChanged()
\r
387 SequenceGroup sg = getGroup();
\r
391 if (abovePIDColour.getState())
\r
393 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
394 ap.av.alignment.getWidth()));
\r
395 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
396 getGroup().getName());
\r
398 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
400 SliderPanel.showPIDSlider();
\r
403 else // remove PIDColouring
\r
405 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
412 protected void userDefinedColour_actionPerformed()
\r
414 new UserDefinedColours(ap, getGroup());
\r
417 protected void PIDColour_actionPerformed()
\r
419 SequenceGroup sg = getGroup();
\r
420 sg.cs = new PIDColourScheme();
\r
421 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
422 ap.av.alignment.getWidth()));
\r
426 protected void BLOSUM62Colour_actionPerformed()
\r
428 SequenceGroup sg = getGroup();
\r
430 sg.cs = new Blosum62ColourScheme();
\r
432 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
433 ap.av.alignment.getWidth()));
\r
438 protected void noColourmenuItem_actionPerformed()
\r
440 getGroup().cs = null;
\r
444 protected void conservationMenuItem_itemStateChanged()
\r
446 SequenceGroup sg = getGroup();
\r
450 if (conservationMenuItem.getState())
\r
453 Conservation c = new Conservation("Group",
\r
454 ResidueProperties.propHash, 3,
\r
456 ap.av.alignment.getWidth());
\r
459 c.verdict(false, ap.av.ConsPercGaps);
\r
461 sg.cs.setConservation(c);
\r
463 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
464 SliderPanel.showConservationSlider();
\r
466 else // remove ConservationColouring
\r
468 sg.cs.setConservation(null);
\r
475 SequenceGroup getGroup()
\r
477 SequenceGroup sg = ap.av.getSelectionGroup();
\r
479 // this method won't add a new group if it already exists
\r
481 ap.av.alignment.addGroup(sg);
\r
486 void unGroupMenuItem_actionPerformed()
\r
488 SequenceGroup sg = ap.av.getSelectionGroup();
\r
489 ap.av.alignment.deleteGroup(sg);
\r
490 ap.av.setSelectionGroup(null);
\r
494 public void showColourText_itemStateChanged()
\r
496 getGroup().setColourText(showColourText.getState());
\r
500 public void showText_itemStateChanged()
\r
502 getGroup().setDisplayText(showText.getState());
\r
506 public void showBoxes_itemStateChanged()
\r
508 getGroup().setDisplayBoxes(showBoxes.getState());
\r