2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2006 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
61 MenuItem toggleCase = new MenuItem("Toggle Case");
\r
62 Menu outputmenu = new Menu();
\r
63 Menu seqMenu = new Menu();
\r
64 MenuItem pdb = new MenuItem();
\r
65 MenuItem hideSeqs = new MenuItem();
\r
66 MenuItem repGroup = new MenuItem();
\r
69 MenuItem revealAll = new MenuItem();
\r
71 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
\r
73 ///////////////////////////////////////////////////////////
\r
74 // If this is activated from the sequence panel, the user may want to
\r
75 // edit or annotate a particular residue. Therefore display the residue menu
\r
77 // If from the IDPanel, we must display the sequence menu
\r
78 //////////////////////////////////////////////////////////
\r
89 e.printStackTrace();
\r
92 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
94 MenuItem item = new MenuItem( jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i] );
\r
96 item.addActionListener(this);
\r
97 outputmenu.add(item);
\r
100 SequenceGroup sg = ap.av.getSelectionGroup();
\r
102 if (sg != null && sg.getSize(false)>0)
\r
104 showText.setState(sg.getDisplayText());
\r
105 showColourText.setState(sg.getColourText());
\r
106 showBoxes.setState(sg.getDisplayBoxes());
\r
107 if (!ap.av.alignment.getGroups().contains(sg))
\r
109 groupMenu.remove(unGroupMenuItem);
\r
121 Menu linkMenu = new Menu("Link");
\r
124 for(int i=0; i<links.size(); i++)
\r
126 link = links.elementAt(i).toString();
\r
127 final String target = link.substring(0, link.indexOf("|"));
\r
128 item = new MenuItem(target);
\r
132 if (link.indexOf("$SEQUENCE_ID$") > -1)
\r
134 String id = seq.getName();
\r
135 if (id.indexOf("|") > -1)
\r
136 id = id.substring(id.lastIndexOf("|") + 1);
\r
138 url = link.substring(link.indexOf("|") + 1,
\r
139 link.indexOf("$SEQUENCE_ID$"))
\r
141 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
\r
144 url = link.substring(link.lastIndexOf("|")+1);
\r
146 System.out.println("add "+url +" "+target);
\r
147 item.addActionListener(new java.awt.event.ActionListener()
\r
149 public void actionPerformed(ActionEvent e)
\r
151 ap.alignFrame.showURL(url, target);
\r
154 linkMenu.add(item);
\r
157 seqMenu.add(linkMenu);
\r
163 seqMenu.setLabel(seq.getName());
\r
164 repGroup.setLabel("Represent Group with " + seq.getName());
\r
169 if(!ap.av.hasHiddenRows)
\r
173 public void itemStateChanged(ItemEvent evt)
\r
175 if(evt.getSource()==abovePIDColour)
\r
176 abovePIDColour_itemStateChanged();
\r
177 else if(evt.getSource()==showColourText)
\r
178 showColourText_itemStateChanged();
\r
179 else if(evt.getSource()==showText)
\r
180 showText_itemStateChanged();
\r
181 else if(evt.getSource()==showBoxes)
\r
182 showBoxes_itemStateChanged() ;
\r
185 public void actionPerformed(ActionEvent evt)
\r
187 Object source = evt.getSource();
\r
188 if(source==clustalColour)
\r
189 clustalColour_actionPerformed();
\r
190 else if(source==zappoColour)
\r
191 zappoColour_actionPerformed();
\r
192 else if(source==taylorColour)
\r
193 taylorColour_actionPerformed();
\r
194 else if(source==hydrophobicityColour)
\r
195 hydrophobicityColour_actionPerformed();
\r
196 else if(source==helixColour)
\r
197 helixColour_actionPerformed();
\r
198 else if(source==strandColour)
\r
199 strandColour_actionPerformed();
\r
200 else if(source==turnColour)
\r
201 turnColour_actionPerformed();
\r
202 else if(source==buriedColour)
\r
203 buriedColour_actionPerformed();
\r
204 else if(source==nucleotideMenuItem)
\r
205 nucleotideMenuItem_actionPerformed();
\r
207 else if (source == userDefinedColour)
\r
208 userDefinedColour_actionPerformed();
\r
209 else if (source == PIDColour)
\r
210 PIDColour_actionPerformed();
\r
211 else if (source == BLOSUM62Colour)
\r
212 BLOSUM62Colour_actionPerformed();
\r
213 else if (source == noColourmenuItem)
\r
214 noColourmenuItem_actionPerformed();
\r
215 else if (source == conservationMenuItem)
\r
216 conservationMenuItem_itemStateChanged();
\r
217 else if (source == unGroupMenuItem)
\r
218 unGroupMenuItem_actionPerformed();
\r
220 else if(source == pdb)
\r
222 else if(source == hideSeqs)
\r
223 hideSequences(false);
\r
224 else if(source == repGroup)
\r
225 hideSequences(true);
\r
226 else if(source == revealAll)
\r
228 ap.av.showAllHiddenSeqs();
\r
231 else if(source==copy)
\r
232 ap.alignFrame.copy_actionPerformed();
\r
233 else if(source==cut)
\r
234 ap.alignFrame.cut_actionPerformed();
\r
235 else if(source==toUpper || source==toLower || source==toggleCase)
\r
237 SequenceGroup sg = ap.av.getSelectionGroup();
\r
240 for (int g = 0; g < sg.getSize(true); g++)
\r
242 int start = sg.getStartRes();
\r
243 int end = sg.getEndRes() + 1;
\r
247 if (ap.av.hasHiddenColumns)
\r
249 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
251 end = sg.getEndRes() + 1;
\r
252 if (end > sg.getEndRes())
\r
253 end = sg.getEndRes() + 1;
\r
256 if (source == toggleCase)
\r
257 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
258 .toggleCase(start, end);
\r
260 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
261 .changeCase(source == toUpper, start, end);
\r
263 if (ap.av.hasHiddenColumns)
\r
265 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
266 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
270 while (end < sg.getEndRes());
\r
272 ap.seqPanel.seqCanvas.repaint();
\r
280 void outputText(ActionEvent e)
\r
282 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
\r
283 Vector vseqs = new Vector();
\r
285 String [] selection = ap.av.getViewAsString(true);
\r
286 SequenceI [] seqs = ap.av.getSelectionAsNewSequence();
\r
287 if (selection != null)
\r
289 for (int i = 0; i < selection.length; i++)
\r
291 Sequence seq = new Sequence(
\r
294 seqs[i].getStart(), seqs[i].getEnd());
\r
295 seq.setDescription(seqs[i].getDescription());
\r
296 vseqs.addElement( seq );
\r
300 Frame frame = new Frame();
\r
302 jalview.bin.JalviewLite.addFrame(frame,
\r
303 "Selection output - " + e.getActionCommand(),
\r
306 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
\r
307 e.getActionCommand(),
\r
309 ap.av.showJVSuffix));
\r
315 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
\r
316 cap.setText("Paste your PDB file here.");
\r
317 cap.setPDBImport(seq);
\r
318 Frame frame = new Frame();
\r
320 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
\r
323 private void jbInit()
\r
326 groupMenu.setLabel("Group");
\r
327 groupMenu.setLabel("Selection");
\r
329 unGroupMenuItem.setLabel("Remove Group");
\r
330 unGroupMenuItem.addActionListener(this);
\r
332 nucleotideMenuItem.setLabel("Nucleotide");
\r
333 nucleotideMenuItem.addActionListener(this);
\r
334 conservationMenuItem.addItemListener(this);
\r
335 abovePIDColour.addItemListener(this);
\r
336 colourMenu.setLabel("Group Colour");
\r
337 showBoxes.setLabel("Boxes");
\r
338 showBoxes.setState(true);
\r
339 showBoxes.addItemListener(this);
\r
341 showText.setLabel("Text");
\r
342 showText.addItemListener(this);
\r
343 showColourText.setLabel("Colour Text");
\r
344 showColourText.addItemListener(this);
\r
345 outputmenu.setLabel("Output to Textbox...");
\r
346 seqMenu.setLabel("Sequence");
\r
347 pdb.setLabel("View PDB Structure");
\r
348 hideSeqs.setLabel("Hide Sequences");
\r
349 repGroup.setLabel("Represent Group with");
\r
350 revealAll.setLabel("Reveal All");
\r
354 this.add(hideSeqs);
\r
355 this.add(revealAll);
\r
356 groupMenu.add(editMenu);
\r
357 groupMenu.add(outputmenu);
\r
358 groupMenu.addSeparator();
\r
359 groupMenu.add(unGroupMenuItem);
\r
360 groupMenu.add(colourMenu);
\r
361 groupMenu.add(showBoxes);
\r
362 groupMenu.add(showText);
\r
363 groupMenu.add(showColourText);
\r
364 colourMenu.add(noColourmenuItem);
\r
365 colourMenu.add(clustalColour);
\r
366 colourMenu.add(BLOSUM62Colour);
\r
367 colourMenu.add(PIDColour);
\r
368 colourMenu.add(zappoColour);
\r
369 colourMenu.add(taylorColour);
\r
370 colourMenu.add(hydrophobicityColour);
\r
371 colourMenu.add(helixColour);
\r
372 colourMenu.add(strandColour);
\r
373 colourMenu.add(turnColour);
\r
374 colourMenu.add(buriedColour);
\r
375 colourMenu.add(nucleotideMenuItem);
\r
376 colourMenu.add(userDefinedColour);
\r
377 colourMenu.addSeparator();
\r
378 colourMenu.add(abovePIDColour);
\r
379 colourMenu.add(conservationMenuItem);
\r
381 noColourmenuItem.setLabel("None");
\r
382 noColourmenuItem.addActionListener(this);
\r
384 clustalColour.setLabel("Clustalx colours");
\r
385 clustalColour.addActionListener(this);
\r
386 zappoColour.setLabel("Zappo");
\r
387 zappoColour.addActionListener(this);
\r
388 taylorColour.setLabel("Taylor");
\r
389 taylorColour.addActionListener(this);
\r
390 hydrophobicityColour.setLabel("Hydrophobicity");
\r
391 hydrophobicityColour.addActionListener(this);
\r
392 helixColour.setLabel("Helix propensity");
\r
393 helixColour.addActionListener(this);
\r
394 strandColour.setLabel("Strand propensity");
\r
395 strandColour.addActionListener(this);
\r
396 turnColour.setLabel("Turn propensity");
\r
397 turnColour.addActionListener(this);
\r
398 buriedColour.setLabel("Buried Index");
\r
399 buriedColour.addActionListener(this);
\r
400 abovePIDColour.setLabel("Above % Identity");
\r
402 userDefinedColour.setLabel("User Defined");
\r
403 userDefinedColour.addActionListener(this);
\r
404 PIDColour.setLabel("Percentage Identity");
\r
405 PIDColour.addActionListener(this);
\r
406 BLOSUM62Colour.setLabel("BLOSUM62");
\r
407 BLOSUM62Colour.addActionListener(this);
\r
408 conservationMenuItem.setLabel("Conservation");
\r
410 editMenu.add(copy);
\r
411 copy.addActionListener(this);
\r
413 cut.addActionListener(this);
\r
414 editMenu.add(toUpper);
\r
415 toUpper.addActionListener(this);
\r
416 editMenu.add(toLower);
\r
417 toLower.addActionListener(this);
\r
418 editMenu.add(toggleCase);
\r
420 seqMenu.add(repGroup);
\r
421 toggleCase.addActionListener(this);
\r
422 pdb.addActionListener(this);
\r
423 hideSeqs.addActionListener(this);
\r
424 repGroup.addActionListener(this);
\r
425 revealAll.addActionListener(this);
\r
431 ap.seqPanel.seqCanvas.repaint();
\r
432 if(ap.overviewPanel!=null)
\r
433 ap.overviewPanel.updateOverviewImage();
\r
436 protected void clustalColour_actionPerformed()
\r
438 SequenceGroup sg = getGroup();
\r
439 sg.cs = new ClustalxColourScheme(sg.getSequences(true), ap.av.alignment.getWidth());
\r
443 protected void zappoColour_actionPerformed()
\r
445 getGroup().cs = new ZappoColourScheme();
\r
449 protected void taylorColour_actionPerformed()
\r
451 getGroup().cs = new TaylorColourScheme();
\r
455 protected void hydrophobicityColour_actionPerformed()
\r
457 getGroup().cs = new HydrophobicColourScheme();
\r
461 protected void helixColour_actionPerformed()
\r
463 getGroup().cs = new HelixColourScheme();
\r
467 protected void strandColour_actionPerformed()
\r
469 getGroup().cs = new StrandColourScheme();
\r
473 protected void turnColour_actionPerformed()
\r
475 getGroup().cs = new TurnColourScheme();
\r
479 protected void buriedColour_actionPerformed()
\r
481 getGroup().cs = new BuriedColourScheme();
\r
485 public void nucleotideMenuItem_actionPerformed()
\r
487 getGroup().cs = new NucleotideColourScheme();
\r
491 protected void abovePIDColour_itemStateChanged()
\r
493 SequenceGroup sg = getGroup();
\r
497 if (abovePIDColour.getState())
\r
499 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
500 ap.av.alignment.getWidth()));
\r
501 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
502 getGroup().getName());
\r
504 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
506 SliderPanel.showPIDSlider();
\r
509 else // remove PIDColouring
\r
511 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
518 protected void userDefinedColour_actionPerformed()
\r
520 new UserDefinedColours(ap, getGroup());
\r
523 protected void PIDColour_actionPerformed()
\r
525 SequenceGroup sg = getGroup();
\r
526 sg.cs = new PIDColourScheme();
\r
527 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
528 ap.av.alignment.getWidth()));
\r
532 protected void BLOSUM62Colour_actionPerformed()
\r
534 SequenceGroup sg = getGroup();
\r
536 sg.cs = new Blosum62ColourScheme();
\r
538 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
539 ap.av.alignment.getWidth()));
\r
544 protected void noColourmenuItem_actionPerformed()
\r
546 getGroup().cs = null;
\r
550 protected void conservationMenuItem_itemStateChanged()
\r
552 SequenceGroup sg = getGroup();
\r
556 if (conservationMenuItem.getState())
\r
559 Conservation c = new Conservation("Group",
\r
560 ResidueProperties.propHash, 3,
\r
561 sg.getSequences(true), 0,
\r
562 ap.av.alignment.getWidth());
\r
565 c.verdict(false, ap.av.ConsPercGaps);
\r
567 sg.cs.setConservation(c);
\r
569 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
570 SliderPanel.showConservationSlider();
\r
572 else // remove ConservationColouring
\r
574 sg.cs.setConservation(null);
\r
581 SequenceGroup getGroup()
\r
583 SequenceGroup sg = ap.av.getSelectionGroup();
\r
585 // this method won't add a new group if it already exists
\r
587 ap.av.alignment.addGroup(sg);
\r
592 void unGroupMenuItem_actionPerformed()
\r
594 SequenceGroup sg = ap.av.getSelectionGroup();
\r
595 ap.av.alignment.deleteGroup(sg);
\r
596 ap.av.setSelectionGroup(null);
\r
600 public void showColourText_itemStateChanged()
\r
602 getGroup().setColourText(showColourText.getState());
\r
606 public void showText_itemStateChanged()
\r
608 getGroup().setDisplayText(showText.getState());
\r
612 public void showBoxes_itemStateChanged()
\r
614 getGroup().setDisplayBoxes(showBoxes.getState());
\r
618 void hideSequences(boolean representGroup)
\r
620 SequenceGroup sg = ap.av.getSelectionGroup();
\r
621 if(sg==null || sg.getSize(false)<1)
\r
623 ap.av.hideSequence(new SequenceI[]{seq});
\r
627 int gsize = sg.getSize(false);
\r
628 SequenceI [] hseqs;
\r
630 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
633 while(index < gsize)
\r
635 if(representGroup && sg.getSequenceAt(index)!=seq)
\r
637 seq.addHiddenSequence(sg.getSequenceAt(index));
\r
638 hseqs[index] = sg.getSequenceAt(index);
\r
640 else if(!representGroup)
\r
642 hseqs[index] = sg.getSequenceAt(index);
\r
647 ap.av.hideSequence(hseqs);
\r
649 ap.av.setSelectionGroup(null);
\r