3 import jalview.datamodel.*;
\r
4 import jalview.analysis.*;
\r
5 import jalview.schemes.*;
\r
6 import javax.swing.*;
\r
7 import java.awt.event.*;
\r
10 public class PopupMenu extends JPopupMenu
\r
12 JMenu groupMenu = new JMenu();
\r
13 JMenuItem copyGroup = new JMenuItem();
\r
14 JMenuItem moveGroup = new JMenuItem();
\r
15 JMenuItem deleteSequences = new JMenuItem();
\r
16 JMenuItem analyze = new JMenuItem();
\r
17 JMenu defineMenu = new JMenu();
\r
18 JMenuItem groupName = new JMenuItem();
\r
19 JMenuItem groupAnnotation = new JMenuItem();
\r
20 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
\r
21 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
\r
22 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
\r
23 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
\r
24 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
\r
25 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
\r
26 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
\r
27 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
\r
28 protected JRadioButtonMenuItem abovePIDColour = new JRadioButtonMenuItem();
\r
29 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
\r
30 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
\r
31 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
\r
32 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
\r
33 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
\r
37 JMenu sequenceMenu = new JMenu();
\r
38 JMenuItem sequenceName = new JMenuItem();
\r
39 JMenu residueMenu = new JMenu();
\r
40 JMenuItem annotateResidue = new JMenuItem();
\r
44 public PopupMenu(AlignmentPanel ap, SequenceI seq)
\r
46 ///////////////////////////////////////////////////////////
\r
47 // If this is activated from the sequence panel, the user may want to
\r
48 // edit or annotate a particular residue. Therefore display the residue menu
\r
50 // If from the IDPanel, we must display the sequence menu
\r
51 //////////////////////////////////////////////////////////
\r
56 ButtonGroup colours = new ButtonGroup();
\r
57 colours.add(noColourmenuItem);
\r
58 colours.add(clustalColour);
\r
59 colours.add(zappoColour);
\r
60 colours.add(taylorColour);
\r
61 colours.add(hydrophobicityColour);
\r
62 colours.add(helixColour);
\r
63 colours.add(strandColour);
\r
64 colours.add(turnColour);
\r
65 colours.add(buriedColour);
\r
66 colours.add(abovePIDColour);
\r
67 colours.add(userDefinedColour);
\r
68 colours.add(PIDColour);
\r
69 colours.add(BLOSUM62Colour);
\r
74 { e.printStackTrace(); }
\r
76 SequenceGroup sg = ap.av.getRubberbandGroup();
\r
78 groupName.setText( sg.getName() );
\r
82 residueMenu.setVisible(false);
\r
83 sequenceName.setText( sequence.getName() );
\r
86 sequenceMenu.setVisible(false);
\r
89 private void jbInit() throws Exception
\r
91 groupMenu.setText("Group");
\r
92 copyGroup.setText("Copy region to new Alignment");
\r
93 copyGroup.addActionListener(new java.awt.event.ActionListener()
\r
95 public void actionPerformed(ActionEvent e)
\r
97 copyGroup_actionPerformed(e);
\r
100 moveGroup.setText("Move sequences to new Alignment");
\r
101 moveGroup.addActionListener(new java.awt.event.ActionListener()
\r
103 public void actionPerformed(ActionEvent e)
\r
105 moveGroup_actionPerformed(e);
\r
108 deleteSequences.setText("Delete sequences");
\r
109 deleteSequences.addActionListener(new java.awt.event.ActionListener()
\r
111 public void actionPerformed(ActionEvent e)
\r
113 deleteSequences_actionPerformed(e);
\r
116 analyze.setText("Analyze");
\r
117 analyze.addActionListener(new java.awt.event.ActionListener()
\r
119 public void actionPerformed(ActionEvent e)
\r
121 analyze_actionPerformed(e);
\r
124 defineMenu.setText("Define");
\r
125 groupName.setText("Name");
\r
126 groupName.addActionListener(new java.awt.event.ActionListener()
\r
128 public void actionPerformed(ActionEvent e)
\r
130 groupName_actionPerformed(e);
\r
133 groupAnnotation.setText("Annotation");
\r
134 groupAnnotation.addActionListener(new java.awt.event.ActionListener()
\r
136 public void actionPerformed(ActionEvent e)
\r
138 groupAnnotation_actionPerformed(e);
\r
141 sequenceMenu.setText("Sequence");
\r
142 sequenceName.setText("sequenceName");
\r
143 sequenceName.addActionListener(new java.awt.event.ActionListener()
\r
145 public void actionPerformed(ActionEvent e)
\r
147 sequenceName_actionPerformed(e);
\r
150 residueMenu.setText("Residue");
\r
151 annotateResidue.setText("annotate residue???");
\r
152 PIDColour.setFocusPainted(false);
\r
154 this.add(sequenceMenu);
\r
155 this.add(residueMenu);
\r
156 groupMenu.add(defineMenu);
\r
157 groupMenu.addSeparator();
\r
158 groupMenu.add(copyGroup);
\r
159 groupMenu.add(moveGroup);
\r
160 groupMenu.add(deleteSequences);
\r
161 groupMenu.addSeparator();
\r
162 groupMenu.add(analyze);
\r
163 defineMenu.add(groupName);
\r
164 defineMenu.add(groupAnnotation);
\r
165 defineMenu.addSeparator();
\r
166 defineMenu.add(noColourmenuItem);
\r
167 defineMenu.add(clustalColour);
\r
168 defineMenu.add(zappoColour);
\r
169 defineMenu.add(taylorColour);
\r
170 defineMenu.add(hydrophobicityColour);
\r
171 defineMenu.add(helixColour);
\r
172 defineMenu.add(strandColour);
\r
173 defineMenu.add(turnColour);
\r
174 defineMenu.add(buriedColour);
\r
175 defineMenu.add(userDefinedColour);
\r
176 defineMenu.add(PIDColour);
\r
177 defineMenu.add(BLOSUM62Colour);
\r
178 defineMenu.addSeparator();
\r
179 defineMenu.add(abovePIDColour);
\r
180 defineMenu.add(conservationMenuItem);
\r
182 sequenceMenu.add(sequenceName);
\r
183 residueMenu.add(annotateResidue);
\r
185 noColourmenuItem.setText("None");
\r
186 noColourmenuItem.setSelected(true);
\r
187 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
189 public void actionPerformed(ActionEvent e)
\r
191 noColourmenuItem_actionPerformed(e);
\r
195 clustalColour.setSelected(false);
\r
196 clustalColour.setText("Clustalx colours");
\r
197 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
199 public void actionPerformed(ActionEvent e)
\r
201 clustalColour_actionPerformed(e);
\r
204 zappoColour.setText("Zappo colour scheme");
\r
205 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
207 public void actionPerformed(ActionEvent e)
\r
209 zappoColour_actionPerformed(e);
\r
212 taylorColour.setText("Taylor colour scheme");
\r
213 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
215 public void actionPerformed(ActionEvent e)
\r
217 taylorColour_actionPerformed(e);
\r
220 hydrophobicityColour.setText("By hydrophobicity");
\r
221 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
\r
223 public void actionPerformed(ActionEvent e)
\r
225 hydrophobicityColour_actionPerformed(e);
\r
228 helixColour.setText("Helix propensity");
\r
229 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
231 public void actionPerformed(ActionEvent e)
\r
233 helixColour_actionPerformed(e);
\r
236 strandColour.setText("Strand propensity");
\r
237 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
239 public void actionPerformed(ActionEvent e)
\r
241 strandColour_actionPerformed(e);
\r
244 turnColour.setText("Turn propensity");
\r
245 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
247 public void actionPerformed(ActionEvent e)
\r
249 turnColour_actionPerformed(e);
\r
252 buriedColour.setText("Buried index");
\r
253 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
255 public void actionPerformed(ActionEvent e)
\r
257 buriedColour_actionPerformed(e);
\r
260 abovePIDColour.setText("Above PID threshold only");
\r
261 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
\r
263 public void actionPerformed(ActionEvent e)
\r
265 abovePIDColour_actionPerformed(e);
\r
268 userDefinedColour.setText("User defined colours");
\r
269 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
271 public void actionPerformed(ActionEvent e)
\r
273 userDefinedColour_actionPerformed(e);
\r
276 PIDColour.setText("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.setText("BLOSUM62 score");
\r
285 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
287 public void actionPerformed(ActionEvent e)
\r
289 BLOSUM62Colour_actionPerformed(e);
\r
292 conservationMenuItem.setText("By conservation");
\r
293 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
295 public void actionPerformed(ActionEvent e)
\r
297 conservationMenuItem_actionPerformed(e);
\r
307 ap.seqPanel.seqCanvas.paintFlag=true;
\r
308 ap.seqPanel.repaint();
\r
311 protected void clustalColour_actionPerformed(ActionEvent e)
\r
313 getGroup().cs = new ClustalxColourScheme();
\r
317 protected void zappoColour_actionPerformed(ActionEvent e)
\r
319 getGroup().cs = new ZappoColourScheme();
\r
323 protected void taylorColour_actionPerformed(ActionEvent e)
\r
325 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
362 public void conservationColourIncMenuItem_actionPerformed(ActionEvent e)
\r
364 ConservationIncrementPanel cip = new ConservationIncrementPanel(viewport, alignPanel);
\r
365 JInternalFrame frame = new JInternalFrame();
\r
366 frame.setContentPane(cip);
\r
367 Desktop.addInternalFrame(frame, "Conservation Colour Increment", 400,90);
\r
368 frame.setMaximizable(false);
\r
373 protected void abovePIDColour_actionPerformed(ActionEvent e)
\r
375 SliderPanel sp = new SliderPanel(ap, 70, false, getGroup().cs );
\r
376 JInternalFrame frame = new JInternalFrame();
\r
377 frame.setContentPane(sp);
\r
378 Desktop.addInternalFrame(frame, "Percentage Identity Threshold", 400,90);
\r
379 frame.setMaximizable(false);
\r
384 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
386 JInternalFrame frame = new JInternalFrame();
\r
387 UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());
\r
388 frame.setContentPane(chooser);
\r
389 Desktop.addInternalFrame(frame,"User defined colours", 450,540 );
\r
390 frame.setResizable(false);
\r
391 frame.setIconifiable(false);
\r
392 frame.setMaximizable(false);
\r
396 protected void PIDColour_actionPerformed(ActionEvent e)
\r
401 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
403 getGroup().cs = new Blosum62ColourScheme(ap.av);
\r
408 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
410 getGroup().cs = null;
\r
414 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
416 SequenceGroup sg = getGroup();
\r
418 Conservation c = new Conservation("Group",
\r
419 ResidueProperties.propHash, 3, sg.sequences, sg.getStartRes(),
\r
423 c.verdict(false, 100);
\r
424 ConservationColourScheme ccs = new ConservationColourScheme(c, sg.cs);
\r
431 protected void groupAnnotation_actionPerformed(ActionEvent e)
\r
436 protected void groupName_actionPerformed(ActionEvent e)
\r
438 SequenceGroup sg = getGroup();
\r
439 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop, "Enter new group name", "Edit group name", JOptionPane.QUESTION_MESSAGE);
\r
444 groupName.setText(reply);
\r
447 protected void copyGroup_actionPerformed(ActionEvent e)
\r
449 SequenceGroup sg = ap.av.getRubberbandGroup();
\r
451 SequenceI[] s = new Sequence[sg.sequences.size()];
\r
452 for (int i=0; i < sg.sequences.size(); i++)
\r
454 s[i] = new Sequence( sg.getSequenceAt(i));
\r
455 s[i].setSequence( s[i].getSequence(sg.getStartRes(), sg.getEndRes()+1) );
\r
457 AlignFrame af = new AlignFrame(new Alignment(s));
\r
458 int newHeight = s.length * af.viewport.getCharHeight() + 200;
\r
459 if (newHeight > 500)
\r
461 Desktop.addInternalFrame(af, "Copied sequences", 700, newHeight);
\r
464 protected void moveGroup_actionPerformed(ActionEvent e)
\r
466 SequenceGroup sg = ap.av.getRubberbandGroup();
\r
468 SequenceI[] s = new Sequence[sg.sequences.size()];
\r
470 for (int i=0; i < sg.sequences.size(); i++)
\r
471 s[i] = new Sequence( sg.getSequenceAt(i));
\r
473 AlignFrame af = new AlignFrame(new Alignment(s));
\r
474 int newHeight = s.length * af.viewport.getCharHeight() + 200;
\r
477 Desktop.addInternalFrame(af, "Copied sequences", 700,newHeight);
\r
480 for (int i=0; i < sg.sequences.size(); i++)
\r
481 ap.av.alignment.deleteSequence(sg.getSequenceAt(i));
\r
484 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
\r
485 ap.RefreshPanels();
\r
490 protected void deleteSequences_actionPerformed(ActionEvent e)
\r
492 SequenceGroup sg = ap.av.getRubberbandGroup();
\r
493 for (int i=0;i < sg.sequences.size(); i++)
\r
494 ap.av.getAlignment().deleteSequence(sg.getSequenceAt(i));
\r
496 ap.av.alignment.deleteGroup(sg);
\r
497 ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());
\r
498 ap.seqPanel.parent.RefreshPanels();
\r
502 protected void analyze_actionPerformed(ActionEvent e)
\r
504 CutAndPasteTransfer cap = new CutAndPasteTransfer(false);
\r
505 JInternalFrame frame = new JInternalFrame();
\r
506 cap.formatForOutput();
\r
507 frame.setContentPane(cap);
\r
508 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
509 SequenceGroup sg = getGroup();
\r
510 StringBuffer sb = new StringBuffer();
\r
512 for(int i=0; i<sg.sequences.size(); i++)
\r
514 Sequence tmp = (Sequence)sg.sequences.get(i);
\r
515 sb.append( tmp.getSequence(sg.getStartRes(), sg.getEndRes()+1));
\r
519 sb.append("Something amazing will happen soon");
\r
520 cap.setText( sb.toString() );
\r
524 SequenceGroup getGroup()
\r
526 SequenceGroup sg = ap.av.getRubberbandGroup();
\r
528 // this method won't add a new group if it already exists
\r
529 ap.av.alignment.addGroup(sg);
\r
533 void sequenceName_actionPerformed(ActionEvent e)
\r
535 String id = sequence.getName();
\r
536 String s = (String)JOptionPane.showInternalInputDialog(
\r
538 "Edit sequence name",
\r
539 "Edit sequence name",
\r
540 JOptionPane.PLAIN_MESSAGE,
\r
547 sequence.setName(s);
\r
548 ap.RefreshPanels();
\r