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
25 import jalview.analysis.*;
\r
26 import jalview.datamodel.*;
\r
27 import jalview.schemes.*;
\r
29 public class APopupMenu
\r
30 extends java.awt.PopupMenu
\r
32 Menu groupMenu = new Menu();
\r
33 protected MenuItem clustalColour = new MenuItem();
\r
34 protected MenuItem zappoColour = new MenuItem();
\r
35 protected MenuItem taylorColour = new MenuItem();
\r
36 protected MenuItem hydrophobicityColour = new MenuItem();
\r
37 protected MenuItem helixColour = new MenuItem();
\r
38 protected MenuItem strandColour = new MenuItem();
\r
39 protected MenuItem turnColour = new MenuItem();
\r
40 protected MenuItem buriedColour = new MenuItem();
\r
41 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
\r
42 protected MenuItem userDefinedColour = new MenuItem();
\r
43 protected MenuItem PIDColour = new MenuItem();
\r
44 protected MenuItem BLOSUM62Colour = new MenuItem();
\r
45 MenuItem noColourmenuItem = new MenuItem();
\r
46 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
\r
49 Menu sequenceMenu = new Menu();
\r
50 MenuItem sequenceName = new MenuItem();
\r
52 MenuItem unGroupMenuItem = new MenuItem();
\r
53 MenuItem nucleotideMenuItem = new MenuItem();
\r
54 Menu colourMenu = new Menu();
\r
55 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
\r
56 CheckboxMenuItem showText = new CheckboxMenuItem();
\r
57 CheckboxMenuItem showColourText = new CheckboxMenuItem();
\r
59 public APopupMenu(AlignmentPanel ap, Sequence seq)
\r
61 ///////////////////////////////////////////////////////////
\r
62 // If this is activated from the sequence panel, the user may want to
\r
63 // edit or annotate a particular residue. Therefore display the residue menu
\r
65 // If from the IDPanel, we must display the sequence menu
\r
66 //////////////////////////////////////////////////////////
\r
77 e.printStackTrace();
\r
80 SequenceGroup sg = ap.av.getSelectionGroup();
\r
83 showText.setState(sg.getDisplayText());
\r
84 showColourText.setState(sg.getColourText());
\r
85 showBoxes.setState(sg.getDisplayBoxes());
\r
88 if (!ap.av.alignment.getGroups().contains(sg))
\r
90 groupMenu.remove(unGroupMenuItem);
\r
95 remove(sequenceMenu);
\r
100 private void jbInit()
\r
103 groupMenu.setLabel("Group");
\r
104 groupMenu.setLabel("Define");
\r
106 sequenceMenu.setLabel("Sequence");
\r
107 sequenceName.setLabel("Edit name");
\r
108 unGroupMenuItem.setLabel("Remove Group");
\r
109 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
111 public void actionPerformed(ActionEvent e)
\r
113 unGroupMenuItem_actionPerformed(e);
\r
117 nucleotideMenuItem.setLabel("Nucleotide");
\r
118 nucleotideMenuItem.addActionListener(new ActionListener()
\r
120 public void actionPerformed(ActionEvent e)
\r
122 nucleotideMenuItem_actionPerformed(e);
\r
125 conservationMenuItem.addItemListener(new ItemListener()
\r
127 public void itemStateChanged(ItemEvent itemEvent)
\r
129 conservationMenuItem_itemStateChanged(itemEvent);
\r
132 abovePIDColour.addItemListener(new ItemListener()
\r
134 public void itemStateChanged(ItemEvent itemEvent)
\r
136 abovePIDColour_itemStateChanged(itemEvent);
\r
139 colourMenu.setLabel("Group Colour");
\r
140 showBoxes.setLabel("Boxes");
\r
141 showBoxes.setState(true);
\r
142 showBoxes.addItemListener(new ItemListener()
\r
144 public void itemStateChanged(ItemEvent itemEvent)
\r
146 showBoxes_itemStateChanged(itemEvent);
\r
150 showText.setLabel("Text");
\r
151 showText.addItemListener(new ItemListener()
\r
153 public void itemStateChanged(ItemEvent itemEvent)
\r
155 showText_itemStateChanged(itemEvent);
\r
158 showColourText.setLabel("Colour Text");
\r
159 showColourText.addItemListener(new ItemListener()
\r
161 public void itemStateChanged(ItemEvent itemEvent)
\r
163 showColourText_itemStateChanged(itemEvent);
\r
168 this.add(sequenceMenu);
\r
169 groupMenu.add(unGroupMenuItem);
\r
170 groupMenu.add(colourMenu);
\r
171 groupMenu.addSeparator();
\r
172 groupMenu.add(showBoxes);
\r
173 groupMenu.add(showText);
\r
174 groupMenu.add(showColourText);
\r
175 sequenceMenu.add(sequenceName);
\r
176 colourMenu.add(noColourmenuItem);
\r
177 colourMenu.add(clustalColour);
\r
178 colourMenu.add(BLOSUM62Colour);
\r
179 colourMenu.add(PIDColour);
\r
180 colourMenu.add(zappoColour);
\r
181 colourMenu.add(taylorColour);
\r
182 colourMenu.add(hydrophobicityColour);
\r
183 colourMenu.add(helixColour);
\r
184 colourMenu.add(strandColour);
\r
185 colourMenu.add(turnColour);
\r
186 colourMenu.add(buriedColour);
\r
187 colourMenu.add(nucleotideMenuItem);
\r
188 colourMenu.add(userDefinedColour);
\r
189 colourMenu.addSeparator();
\r
190 colourMenu.add(abovePIDColour);
\r
191 colourMenu.add(conservationMenuItem);
\r
193 noColourmenuItem.setLabel("None");
\r
194 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
196 public void actionPerformed(ActionEvent e)
\r
198 noColourmenuItem_actionPerformed(e);
\r
202 clustalColour.setLabel("Clustalx colours");
\r
203 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
205 public void actionPerformed(ActionEvent e)
\r
207 clustalColour_actionPerformed(e);
\r
210 zappoColour.setLabel("Zappo");
\r
211 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
213 public void actionPerformed(ActionEvent e)
\r
215 zappoColour_actionPerformed(e);
\r
218 taylorColour.setLabel("Taylor");
\r
219 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
221 public void actionPerformed(ActionEvent e)
\r
223 taylorColour_actionPerformed(e);
\r
226 hydrophobicityColour.setLabel("Hydrophobicity");
\r
227 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
\r
229 public void actionPerformed(ActionEvent e)
\r
231 hydrophobicityColour_actionPerformed(e);
\r
234 helixColour.setLabel("Helix propensity");
\r
235 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
237 public void actionPerformed(ActionEvent e)
\r
239 helixColour_actionPerformed(e);
\r
242 strandColour.setLabel("Strand propensity");
\r
243 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
245 public void actionPerformed(ActionEvent e)
\r
247 strandColour_actionPerformed(e);
\r
250 turnColour.setLabel("Turn propensity");
\r
251 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
253 public void actionPerformed(ActionEvent e)
\r
255 turnColour_actionPerformed(e);
\r
258 buriedColour.setLabel("Buried Index");
\r
259 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
261 public void actionPerformed(ActionEvent e)
\r
263 buriedColour_actionPerformed(e);
\r
266 abovePIDColour.setLabel("Above % Identity");
\r
268 userDefinedColour.setLabel("User Defined");
\r
269 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
271 public void actionPerformed(ActionEvent e)
\r
273 userDefinedColour_actionPerformed(e);
\r
276 PIDColour.setLabel("Percentage Identity");
\r
277 PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
279 public void actionPerformed(ActionEvent e)
\r
281 PIDColour_actionPerformed(e);
\r
284 BLOSUM62Colour.setLabel("BLOSUM62");
\r
285 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
287 public void actionPerformed(ActionEvent e)
\r
289 BLOSUM62Colour_actionPerformed(e);
\r
292 conservationMenuItem.setLabel("Conservation");
\r
298 SequenceGroup sg = getGroup();
\r
301 SuperGroup superG = ap.av.alignment.getSuperGroup(sg);
\r
303 if (superG != null)
\r
305 superG.setSuperGroupProperties(sg);
\r
308 ap.seqPanel.seqCanvas.repaint();
\r
311 protected void clustalColour_actionPerformed(ActionEvent e)
\r
313 SequenceGroup sg = getGroup();
\r
314 sg.cs = new ClustalxColourScheme(sg.sequences, ap.av.alignment.getWidth());
\r
318 protected void zappoColour_actionPerformed(ActionEvent e)
\r
320 getGroup().cs = new ZappoColourScheme();
\r
324 protected void taylorColour_actionPerformed(ActionEvent e)
\r
326 getGroup().cs = new TaylorColourScheme();
\r
330 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
332 getGroup().cs = new HydrophobicColourScheme();
\r
336 protected void helixColour_actionPerformed(ActionEvent e)
\r
338 getGroup().cs = new HelixColourScheme();
\r
342 protected void strandColour_actionPerformed(ActionEvent e)
\r
344 getGroup().cs = new StrandColourScheme();
\r
348 protected void turnColour_actionPerformed(ActionEvent e)
\r
350 getGroup().cs = new TurnColourScheme();
\r
354 protected void buriedColour_actionPerformed(ActionEvent e)
\r
356 getGroup().cs = new BuriedColourScheme();
\r
360 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
\r
362 getGroup().cs = new NucleotideColourScheme();
\r
366 protected void abovePIDColour_itemStateChanged(ItemEvent ie)
\r
368 SequenceGroup sg = getGroup();
\r
369 if (abovePIDColour.getState())
\r
371 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
372 ap.av.alignment.getWidth()));
\r
373 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
374 getGroup().getName());
\r
375 if (sg.cs instanceof ResidueColourScheme)
\r
377 ( (ResidueColourScheme) sg.cs).setThreshold(threshold);
\r
379 else if (sg.cs instanceof ScoreColourScheme)
\r
381 ( (ScoreColourScheme) sg.cs).setThreshold(threshold);
\r
384 SliderPanel.showPIDSlider();
\r
387 else // remove PIDColouring
\r
389 ResidueColourScheme rcs = (ResidueColourScheme) sg.cs;
\r
390 rcs.setThreshold(0);
\r
398 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
400 new UserDefinedColours(ap, getGroup());
\r
403 protected void PIDColour_actionPerformed(ActionEvent e)
\r
405 SequenceGroup sg = getGroup();
\r
406 sg.cs = new PIDColourScheme();
\r
407 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
408 ap.av.alignment.getWidth()));
\r
412 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
414 SequenceGroup sg = getGroup();
\r
416 sg.cs = new Blosum62ColourScheme();
\r
418 sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0,
\r
419 ap.av.alignment.getWidth()));
\r
424 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
426 getGroup().cs = null;
\r
430 protected void conservationMenuItem_itemStateChanged(ItemEvent ie)
\r
432 SequenceGroup sg = getGroup();
\r
434 if (conservationMenuItem.getState())
\r
437 Conservation c = new Conservation("Group",
\r
438 ResidueProperties.propHash, 3,
\r
440 ap.av.alignment.getWidth());
\r
443 c.verdict(false, ap.av.ConsPercGaps);
\r
444 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
448 SliderPanel.setConservationSlider(ap, ccs, sg.getName());
\r
449 SliderPanel.showConservationSlider();
\r
451 else // remove ConservationColouring
\r
453 ConservationColourScheme ccs = (ConservationColourScheme) sg.cs;
\r
460 protected void analyze_actionPerformed(ActionEvent e)
\r
462 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
\r
463 Frame frame = new Frame();
\r
465 jalview.bin.JalviewLite.addFrame(frame, "Analyze this - ", 400, 300);
\r
466 SequenceGroup sg = getGroup();
\r
467 StringBuffer sb = new StringBuffer();
\r
469 for (int i = 0; i < sg.sequences.size(); i++)
\r
471 Sequence tmp = (Sequence) sg.sequences.elementAt(i);
\r
472 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
476 sb.append("Something amazing will happen soon");
\r
477 cap.setText(sb.toString());
\r
481 SequenceGroup getGroup()
\r
483 SequenceGroup sg = ap.av.getSelectionGroup();
\r
485 // this method won't add a new group if it already exists
\r
487 ap.av.alignment.addGroup(sg);
\r
492 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
494 SequenceGroup sg = ap.av.getSelectionGroup();
\r
495 ap.av.alignment.deleteGroup(sg);
\r
496 ap.av.setSelectionGroup(null);
\r
500 public void showColourText_itemStateChanged(ItemEvent itemEvent)
\r
502 getGroup().setColourText(showColourText.getState());
\r
506 public void showText_itemStateChanged(ItemEvent itemEvent)
\r
508 getGroup().setDisplayText(showText.getState());
\r
512 public void showBoxes_itemStateChanged(ItemEvent itemEvent)
\r
514 getGroup().setDisplayBoxes(showBoxes.getState());
\r