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
19 package jalview.gui;
\r
23 import jalview.analysis.*;
\r
25 import jalview.datamodel.*;
\r
28 import jalview.schemes.*;
\r
31 import java.awt.event.*;
\r
33 import javax.swing.*;
\r
35 import java.util.Vector;
\r
36 import jalview.io.FormatAdapter;
\r
43 * @version $Revision$
\r
45 public class PopupMenu extends JPopupMenu
\r
47 JMenu groupMenu = new JMenu();
\r
48 JMenuItem groupName = new JMenuItem();
\r
49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
\r
50 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
\r
51 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
\r
52 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
\r
53 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
\r
54 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
\r
55 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
\r
56 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
\r
57 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
\r
58 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
\r
59 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
\r
60 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
\r
61 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
\r
62 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
\r
64 JMenu sequenceMenu = new JMenu();
\r
65 JMenuItem sequenceName = new JMenuItem();
\r
67 JMenuItem unGroupMenuItem = new JMenuItem();
\r
68 JMenuItem outline = new JMenuItem();
\r
69 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
\r
70 JMenu colourMenu = new JMenu();
\r
71 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
\r
72 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
\r
73 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
\r
74 JMenu editMenu = new JMenu();
\r
75 JMenuItem cut = new JMenuItem();
\r
76 JMenuItem copy = new JMenuItem();
\r
77 JMenuItem upperCase = new JMenuItem();
\r
78 JMenuItem lowerCase = new JMenuItem();
\r
79 JMenuItem toggle = new JMenuItem();
\r
80 JMenu pdbMenu = new JMenu();
\r
81 JMenuItem pdbFromFile = new JMenuItem();
\r
82 JMenuItem enterPDB = new JMenuItem();
\r
83 JMenuItem discoverPDB = new JMenuItem();
\r
84 JMenu outputMenu = new JMenu();
\r
87 * Creates a new PopupMenu object.
\r
89 * @param ap DOCUMENT ME!
\r
90 * @param seq DOCUMENT ME!
\r
92 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
\r
94 ///////////////////////////////////////////////////////////
\r
95 // If this is activated from the sequence panel, the user may want to
\r
96 // edit or annotate a particular residue. Therefore display the residue menu
\r
98 // If from the IDPanel, we must display the sequence menu
\r
99 //////////////////////////////////////////////////////////
\r
103 ButtonGroup colours = new ButtonGroup();
\r
104 colours.add(noColourmenuItem);
\r
105 colours.add(clustalColour);
\r
106 colours.add(zappoColour);
\r
107 colours.add(taylorColour);
\r
108 colours.add(hydrophobicityColour);
\r
109 colours.add(helixColour);
\r
110 colours.add(strandColour);
\r
111 colours.add(turnColour);
\r
112 colours.add(buriedColour);
\r
113 colours.add(abovePIDColour);
\r
114 colours.add(userDefinedColour);
\r
115 colours.add(PIDColour);
\r
116 colours.add(BLOSUM62Colour);
\r
118 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
120 JMenuItem item = new JMenuItem( jalview.io.FormatAdapter.WRITEABLE_FORMATS[i] );
\r
122 item.addActionListener(new java.awt.event.ActionListener()
\r
124 public void actionPerformed(ActionEvent e)
\r
126 outputText_actionPerformed(e);
\r
130 outputMenu.add(item);
\r
138 catch (Exception e)
\r
140 e.printStackTrace();
\r
146 int start = Math.max(sequence.getName().length()-15, 0);
\r
147 sequenceMenu.setText(sequence.getName().substring(start));
\r
149 JMenuItem menuItem;
\r
150 if( seq.getDatasetSequence().getPDBId() != null)
\r
152 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
\r
155 while (e.hasMoreElements())
\r
157 final PDBEntry pdb = (PDBEntry) e.nextElement();
\r
159 menuItem = new JMenuItem();
\r
160 menuItem.setText("View PDB entry: " + pdb.getId());
\r
161 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
163 public void actionPerformed(ActionEvent e)
\r
165 new PDBViewer(pdb, sequence, ap.seqPanel.seqCanvas);
\r
168 sequenceMenu.add(menuItem);
\r
172 menuItem = new JMenuItem("Hide Sequences");
\r
173 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
175 public void actionPerformed(ActionEvent e)
\r
177 hideSequences(false);
\r
182 if(ap.av.getSelectionGroup() !=null
\r
183 && ap.av.getSelectionGroup().getSize(false)>1)
\r
185 menuItem = new JMenuItem("Represent Group with " + seq.getName());
\r
186 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
188 public void actionPerformed(ActionEvent e)
\r
190 hideSequences(true);
\r
193 sequenceMenu.add(menuItem);
\r
196 if (ap.av.hasHiddenRows)
\r
198 final int index = ap.av.alignment.findIndex(seq);
\r
200 if (ap.av.adjustForHiddenSeqs(index) -
\r
201 ap.av.adjustForHiddenSeqs(index - 1) > 1)
\r
203 menuItem = new JMenuItem("Reveal Sequences");
\r
204 menuItem.addActionListener(new ActionListener()
\r
206 public void actionPerformed(ActionEvent e)
\r
208 ap.av.showSequence(index);
\r
210 if (ap.overviewPanel != null)
\r
211 ap.overviewPanel.updateOverviewImage();
\r
217 menuItem = new JMenuItem("Reveal All");
\r
218 menuItem.addActionListener(new ActionListener()
\r
220 public void actionPerformed(ActionEvent e)
\r
222 ap.av.showAllHiddenSeqs();
\r
224 if (ap.overviewPanel != null)
\r
225 ap.overviewPanel.updateOverviewImage();
\r
237 SequenceGroup sg = ap.av.getSelectionGroup();
\r
241 groupName.setText(sg.getName());
\r
243 if (sg.cs instanceof ZappoColourScheme)
\r
245 zappoColour.setSelected(true);
\r
247 else if (sg.cs instanceof TaylorColourScheme)
\r
249 taylorColour.setSelected(true);
\r
251 else if (sg.cs instanceof PIDColourScheme)
\r
253 PIDColour.setSelected(true);
\r
255 else if (sg.cs instanceof Blosum62ColourScheme)
\r
257 BLOSUM62Colour.setSelected(true);
\r
259 else if (sg.cs instanceof UserColourScheme)
\r
261 userDefinedColour.setSelected(true);
\r
263 else if (sg.cs instanceof HydrophobicColourScheme)
\r
265 hydrophobicityColour.setSelected(true);
\r
267 else if (sg.cs instanceof HelixColourScheme)
\r
269 helixColour.setSelected(true);
\r
271 else if (sg.cs instanceof StrandColourScheme)
\r
273 strandColour.setSelected(true);
\r
275 else if (sg.cs instanceof TurnColourScheme)
\r
277 turnColour.setSelected(true);
\r
279 else if (sg.cs instanceof BuriedColourScheme)
\r
281 buriedColour.setSelected(true);
\r
283 else if (sg.cs instanceof ClustalxColourScheme)
\r
285 clustalColour.setSelected(true);
\r
289 noColourmenuItem.setSelected(true);
\r
292 if (sg.cs!=null && sg.cs.conservationApplied())
\r
294 conservationMenuItem.setSelected(true);
\r
297 showText.setSelected(sg.getDisplayText());
\r
298 showColourText.setSelected(sg.getColourText());
\r
299 showBoxes.setSelected(sg.getDisplayBoxes());
\r
303 groupMenu.setVisible(false);
\r
304 editMenu.setVisible(false);
\r
307 if (!ap.av.alignment.getGroups().contains(sg))
\r
309 unGroupMenuItem.setVisible(false);
\r
315 sequenceMenu.setVisible(false);
\r
316 pdbMenu.setVisible(false);
\r
319 if(links != null && links.size()>0)
\r
321 JMenu linkMenu = new JMenu("Link");
\r
323 for(int i=0; i<links.size(); i++)
\r
325 String link = links.elementAt(i).toString();
\r
326 final String label = link.substring(0, link.indexOf("|"));
\r
327 item = new JMenuItem(label);
\r
330 if (link.indexOf("$SEQUENCE_ID$") > -1)
\r
332 String id = seq.getName();
\r
333 if (id.indexOf("|") > -1)
\r
334 id = id.substring(id.lastIndexOf("|") + 1);
\r
336 url = link.substring(link.indexOf("|") + 1,
\r
337 link.indexOf("$SEQUENCE_ID$"))
\r
339 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
\r
342 url = link.substring(link.lastIndexOf("|")+1);
\r
345 item.addActionListener(new java.awt.event.ActionListener()
\r
347 public void actionPerformed(ActionEvent e)
\r
353 linkMenu.add(item);
\r
356 sequenceMenu.add(linkMenu);
\r
366 * @throws Exception DOCUMENT ME!
\r
368 private void jbInit() throws Exception
\r
370 groupMenu.setText("Group");
\r
371 groupMenu.setText("Selection");
\r
372 groupName.setText("Name");
\r
373 groupName.addActionListener(new java.awt.event.ActionListener()
\r
375 public void actionPerformed(ActionEvent e)
\r
377 groupName_actionPerformed(e);
\r
380 sequenceMenu.setText("Sequence");
\r
381 sequenceName.setText("Edit Name/Description");
\r
382 sequenceName.addActionListener(new java.awt.event.ActionListener()
\r
384 public void actionPerformed(ActionEvent e)
\r
386 sequenceName_actionPerformed(e);
\r
389 PIDColour.setFocusPainted(false);
\r
390 unGroupMenuItem.setText("Remove Group");
\r
391 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
393 public void actionPerformed(ActionEvent e)
\r
395 unGroupMenuItem_actionPerformed(e);
\r
399 outline.setText("Border colour");
\r
400 outline.addActionListener(new java.awt.event.ActionListener()
\r
402 public void actionPerformed(ActionEvent e)
\r
404 outline_actionPerformed(e);
\r
407 nucleotideMenuItem.setText("Nucleotide");
\r
408 nucleotideMenuItem.addActionListener(new ActionListener()
\r
410 public void actionPerformed(ActionEvent e)
\r
412 nucleotideMenuItem_actionPerformed(e);
\r
415 colourMenu.setText("Group Colour");
\r
416 showBoxes.setText("Boxes");
\r
417 showBoxes.setState(true);
\r
418 showBoxes.addActionListener(new ActionListener()
\r
420 public void actionPerformed(ActionEvent e)
\r
422 showBoxes_actionPerformed(e);
\r
425 showText.setText("Text");
\r
426 showText.setState(true);
\r
427 showText.addActionListener(new ActionListener()
\r
429 public void actionPerformed(ActionEvent e)
\r
431 showText_actionPerformed(e);
\r
434 showColourText.setText("Colour Text");
\r
435 showColourText.addActionListener(new ActionListener()
\r
437 public void actionPerformed(ActionEvent e)
\r
439 showColourText_actionPerformed(e);
\r
442 editMenu.setText("Edit");
\r
443 cut.setText("Cut");
\r
444 cut.addActionListener(new ActionListener()
\r
446 public void actionPerformed(ActionEvent e)
\r
448 cut_actionPerformed(e);
\r
451 upperCase.setText("To Upper Case");
\r
452 upperCase.addActionListener(new ActionListener()
\r
454 public void actionPerformed(ActionEvent e)
\r
456 upperCase_actionPerformed(e);
\r
459 copy.setText("Copy");
\r
460 copy.addActionListener(new ActionListener()
\r
462 public void actionPerformed(ActionEvent e)
\r
464 copy_actionPerformed(e);
\r
467 lowerCase.setText("To Lower Case");
\r
468 lowerCase.addActionListener(new ActionListener()
\r
470 public void actionPerformed(ActionEvent e)
\r
472 lowerCase_actionPerformed(e);
\r
475 toggle.setText("Toggle Case");
\r
476 toggle.addActionListener(new ActionListener()
\r
478 public void actionPerformed(ActionEvent e)
\r
480 toggle_actionPerformed(e);
\r
483 pdbMenu.setText("Associate Structure with Sequence");
\r
484 pdbFromFile.setText("From File");
\r
485 pdbFromFile.addActionListener(new ActionListener()
\r
487 public void actionPerformed(ActionEvent e)
\r
489 pdbFromFile_actionPerformed(e);
\r
492 enterPDB.setText("Enter PDB Id");
\r
493 enterPDB.addActionListener(new ActionListener()
\r
495 public void actionPerformed(ActionEvent e)
\r
497 enterPDB_actionPerformed(e);
\r
500 discoverPDB.setText("Discover PDB ids");
\r
501 discoverPDB.addActionListener(new ActionListener()
\r
503 public void actionPerformed(ActionEvent e)
\r
505 discoverPDB_actionPerformed(e);
\r
508 outputMenu.setText("Output to Textbox...");
\r
512 groupMenu.add(editMenu);
\r
513 groupMenu.add(outputMenu);
\r
514 groupMenu.addSeparator();
\r
515 groupMenu.add(groupName);
\r
516 groupMenu.add(unGroupMenuItem);
\r
517 groupMenu.add(colourMenu);
\r
518 groupMenu.add(showBoxes);
\r
519 groupMenu.add(showText);
\r
520 groupMenu.add(showColourText);
\r
521 groupMenu.add(outline);
\r
522 sequenceMenu.add(sequenceName);
\r
523 sequenceMenu.add(pdbMenu);
\r
524 colourMenu.add(noColourmenuItem);
\r
525 colourMenu.add(clustalColour);
\r
526 colourMenu.add(BLOSUM62Colour);
\r
527 colourMenu.add(PIDColour);
\r
528 colourMenu.add(zappoColour);
\r
529 colourMenu.add(taylorColour);
\r
530 colourMenu.add(hydrophobicityColour);
\r
531 colourMenu.add(helixColour);
\r
532 colourMenu.add(strandColour);
\r
533 colourMenu.add(turnColour);
\r
534 colourMenu.add(buriedColour);
\r
535 colourMenu.add(nucleotideMenuItem);
\r
536 colourMenu.add(userDefinedColour);
\r
538 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
\r
540 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
541 getUserColourSchemes().keys();
\r
543 while (userColours.hasMoreElements())
\r
545 JMenuItem item = new JMenuItem(userColours.
\r
546 nextElement().toString());
\r
547 item.addActionListener(new ActionListener()
\r
549 public void actionPerformed(ActionEvent evt)
\r
551 userDefinedColour_actionPerformed(evt);
\r
554 colourMenu.add(item);
\r
559 colourMenu.addSeparator();
\r
560 colourMenu.add(abovePIDColour);
\r
561 colourMenu.add(conservationMenuItem);
\r
562 editMenu.add(copy);
\r
564 editMenu.add(upperCase);
\r
565 editMenu.add(lowerCase);
\r
566 editMenu.add(toggle);
\r
567 pdbMenu.add(pdbFromFile);
\r
568 pdbMenu.add(enterPDB);
\r
569 pdbMenu.add(discoverPDB);
\r
570 noColourmenuItem.setText("None");
\r
571 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
573 public void actionPerformed(ActionEvent e)
\r
575 noColourmenuItem_actionPerformed(e);
\r
579 clustalColour.setText("Clustalx colours");
\r
580 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
582 public void actionPerformed(ActionEvent e)
\r
584 clustalColour_actionPerformed(e);
\r
587 zappoColour.setText("Zappo");
\r
588 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
590 public void actionPerformed(ActionEvent e)
\r
592 zappoColour_actionPerformed(e);
\r
595 taylorColour.setText("Taylor");
\r
596 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
598 public void actionPerformed(ActionEvent e)
\r
600 taylorColour_actionPerformed(e);
\r
603 hydrophobicityColour.setText("Hydrophobicity");
\r
604 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
\r
606 public void actionPerformed(ActionEvent e)
\r
608 hydrophobicityColour_actionPerformed(e);
\r
611 helixColour.setText("Helix propensity");
\r
612 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
614 public void actionPerformed(ActionEvent e)
\r
616 helixColour_actionPerformed(e);
\r
619 strandColour.setText("Strand propensity");
\r
620 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
622 public void actionPerformed(ActionEvent e)
\r
624 strandColour_actionPerformed(e);
\r
627 turnColour.setText("Turn propensity");
\r
628 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
630 public void actionPerformed(ActionEvent e)
\r
632 turnColour_actionPerformed(e);
\r
635 buriedColour.setText("Buried Index");
\r
636 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
638 public void actionPerformed(ActionEvent e)
\r
640 buriedColour_actionPerformed(e);
\r
643 abovePIDColour.setText("Above % Identity");
\r
644 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
\r
646 public void actionPerformed(ActionEvent e)
\r
648 abovePIDColour_actionPerformed(e);
\r
651 userDefinedColour.setText("User Defined...");
\r
652 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
654 public void actionPerformed(ActionEvent e)
\r
656 userDefinedColour_actionPerformed(e);
\r
659 PIDColour.setText("Percentage Identity");
\r
660 PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
662 public void actionPerformed(ActionEvent e)
\r
664 PIDColour_actionPerformed(e);
\r
667 BLOSUM62Colour.setText("BLOSUM62");
\r
668 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
670 public void actionPerformed(ActionEvent e)
\r
672 BLOSUM62Colour_actionPerformed(e);
\r
675 conservationMenuItem.setText("Conservation");
\r
676 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
678 public void actionPerformed(ActionEvent e)
\r
680 conservationMenuItem_actionPerformed(e);
\r
690 if (ap.overviewPanel != null)
\r
691 ap.overviewPanel.updateOverviewImage();
\r
693 ap.seqPanel.repaint();
\r
699 * @param e DOCUMENT ME!
\r
701 protected void clustalColour_actionPerformed(ActionEvent e)
\r
703 SequenceGroup sg = getGroup();
\r
704 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
\r
705 ap.av.alignment.getWidth());
\r
712 * @param e DOCUMENT ME!
\r
714 protected void zappoColour_actionPerformed(ActionEvent e)
\r
716 getGroup().cs = new ZappoColourScheme();
\r
723 * @param e DOCUMENT ME!
\r
725 protected void taylorColour_actionPerformed(ActionEvent e)
\r
727 getGroup().cs = new TaylorColourScheme();
\r
734 * @param e DOCUMENT ME!
\r
736 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
738 getGroup().cs = new HydrophobicColourScheme();
\r
745 * @param e DOCUMENT ME!
\r
747 protected void helixColour_actionPerformed(ActionEvent e)
\r
749 getGroup().cs = new HelixColourScheme();
\r
756 * @param e DOCUMENT ME!
\r
758 protected void strandColour_actionPerformed(ActionEvent e)
\r
760 getGroup().cs = new StrandColourScheme();
\r
767 * @param e DOCUMENT ME!
\r
769 protected void turnColour_actionPerformed(ActionEvent e)
\r
771 getGroup().cs = new TurnColourScheme();
\r
778 * @param e DOCUMENT ME!
\r
780 protected void buriedColour_actionPerformed(ActionEvent e)
\r
782 getGroup().cs = new BuriedColourScheme();
\r
789 * @param e DOCUMENT ME!
\r
791 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
\r
793 getGroup().cs = new NucleotideColourScheme();
\r
800 * @param e DOCUMENT ME!
\r
802 protected void abovePIDColour_actionPerformed(ActionEvent e)
\r
804 SequenceGroup sg = getGroup();
\r
808 if (abovePIDColour.isSelected())
\r
810 sg.cs.setConsensus(AAFrequency.calculate(
\r
811 sg.getSequences(true), 0,
\r
812 ap.av.alignment.getWidth()));
\r
814 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
815 getGroup().getName());
\r
817 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
819 SliderPanel.showPIDSlider();
\r
821 else // remove PIDColouring
\r
823 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
832 * @param e DOCUMENT ME!
\r
834 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
836 SequenceGroup sg = getGroup();
\r
838 if (e.getActionCommand().equals("User Defined..."))
\r
839 new UserDefinedColours(ap, sg);
\r
842 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
843 getUserColourSchemes().get(e.getActionCommand());
\r
851 * @param e DOCUMENT ME!
\r
853 protected void PIDColour_actionPerformed(ActionEvent e)
\r
855 SequenceGroup sg = getGroup();
\r
856 sg.cs = new PIDColourScheme();
\r
857 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
858 ap.av.alignment.getWidth()));
\r
865 * @param e DOCUMENT ME!
\r
867 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
869 SequenceGroup sg = getGroup();
\r
871 sg.cs = new Blosum62ColourScheme();
\r
873 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
874 ap.av.alignment.getWidth()));
\r
882 * @param e DOCUMENT ME!
\r
884 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
886 getGroup().cs = null;
\r
893 * @param e DOCUMENT ME!
\r
895 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
897 SequenceGroup sg = getGroup();
\r
901 if (conservationMenuItem.isSelected())
\r
903 Conservation c = new Conservation("Group",
\r
904 ResidueProperties.propHash, 3,
\r
905 sg.getSequences(true), 0,
\r
906 ap.av.alignment.getWidth());
\r
909 c.verdict(false, ap.av.ConsPercGaps);
\r
911 sg.cs.setConservation(c);
\r
913 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
914 SliderPanel.showConservationSlider();
\r
916 else // remove ConservationColouring
\r
918 sg.cs.setConservation(null);
\r
927 * @param e DOCUMENT ME!
\r
929 protected void groupName_actionPerformed(ActionEvent e)
\r
931 SequenceGroup sg = getGroup();
\r
932 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
933 "Enter new group name", "Edit group name",
\r
934 JOptionPane.QUESTION_MESSAGE);
\r
942 groupName.setText(reply);
\r
948 * @param e DOCUMENT ME!
\r
950 protected void analyze_actionPerformed(ActionEvent e)
\r
952 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
953 JInternalFrame frame = new JInternalFrame();
\r
954 frame.setContentPane(cap);
\r
955 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
957 SequenceGroup sg = getGroup();
\r
958 StringBuffer sb = new StringBuffer();
\r
960 for (int i = 0; i < sg.getSize(false); i++)
\r
962 Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
\r
963 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
967 sb.append("Something amazing will happen soon");
\r
968 cap.setText(sb.toString());
\r
974 * @return DOCUMENT ME!
\r
976 SequenceGroup getGroup()
\r
978 SequenceGroup sg = ap.av.getSelectionGroup();
\r
979 // this method won't add a new group if it already exists
\r
981 ap.av.alignment.addGroup(sg);
\r
989 * @param e DOCUMENT ME!
\r
991 void sequenceName_actionPerformed(ActionEvent e)
\r
993 JLabel idlabel = new JLabel( " Sequence Name ");
\r
994 JLabel desclabel = new JLabel("Sequence Description ");
\r
995 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
996 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
997 JTextField id = new JTextField(sequence.getName(), 40);
\r
998 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
999 JPanel panel = new JPanel(new BorderLayout());
\r
1000 JPanel panel2 = new JPanel(new BorderLayout());
\r
1001 panel2.add(idlabel, BorderLayout.WEST);
\r
1002 panel2.add(id, BorderLayout.CENTER);
\r
1003 panel.add(panel2, BorderLayout.NORTH);
\r
1004 panel2 = new JPanel(new BorderLayout());
\r
1005 panel2.add(desclabel, BorderLayout.WEST);
\r
1006 panel2.add(description, BorderLayout.CENTER);
\r
1007 panel.add(panel2, BorderLayout.SOUTH);
\r
1010 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1011 panel, "Edit Sequence Name/Description",
\r
1012 JOptionPane.OK_CANCEL_OPTION );
\r
1015 if (reply != JOptionPane.OK_OPTION )
\r
1020 String s = id.getText();
\r
1024 if (s.indexOf(" ") > -1)
\r
1026 JOptionPane.showMessageDialog(ap,
\r
1027 "Spaces have been converted to \"_\"",
\r
1028 "No spaces allowed in Sequence Name",
\r
1029 JOptionPane.WARNING_MESSAGE);
\r
1032 s = s.replace(' ', '_');
\r
1033 sequence.getDatasetSequence().setName(s);
\r
1034 sequence.setName(s);
\r
1038 sequence.getDatasetSequence().setDescription(description.getText());
\r
1039 sequence.setDescription(description.getText());
\r
1045 * @param e DOCUMENT ME!
\r
1047 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1049 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1050 ap.av.alignment.deleteGroup(sg);
\r
1051 ap.av.setSelectionGroup(null);
\r
1059 * @param e DOCUMENT ME!
\r
1061 protected void outline_actionPerformed(ActionEvent e)
\r
1063 SequenceGroup sg = getGroup();
\r
1064 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1069 sg.setOutlineColour(col);
\r
1078 * @param e DOCUMENT ME!
\r
1080 public void showBoxes_actionPerformed(ActionEvent e)
\r
1082 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1089 * @param e DOCUMENT ME!
\r
1091 public void showText_actionPerformed(ActionEvent e)
\r
1093 getGroup().setDisplayText(showText.isSelected());
\r
1100 * @param e DOCUMENT ME!
\r
1102 public void showColourText_actionPerformed(ActionEvent e)
\r
1104 getGroup().setColourText(showColourText.isSelected());
\r
1108 public void showLink(String url)
\r
1112 jalview.util.BrowserLauncher.openURL(url);
\r
1114 catch (Exception ex)
\r
1116 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1117 "Unixers: Couldn't find default web browser."
\r
1118 +"\nAdd the full path to your browser in Preferences.",
\r
1119 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1122 ex.printStackTrace();
\r
1126 void hideSequences(boolean representGroup)
\r
1128 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1129 if(sg==null || sg.getSize(false)<1)
\r
1131 ap.av.hideSequence(sequence);
\r
1136 while(index < sg.getSize(false))
\r
1138 if(representGroup && sg.getSequenceAt(index)!=sequence)
\r
1140 sequence.addHiddenSequence(sg.getSequenceAt(index));
\r
1141 ap.av.hideSequence(sg.getSequenceAt(index));
\r
1143 else if(!representGroup)
\r
1145 ap.av.hideSequence(sg.getSequenceAt(index));
\r
1150 ap.av.setSelectionGroup(null);
\r
1155 public void copy_actionPerformed(ActionEvent e)
\r
1157 ap.alignFrame.copy_actionPerformed(null);
\r
1160 public void cut_actionPerformed(ActionEvent e)
\r
1162 ap.alignFrame.cut_actionPerformed(null);
\r
1165 public void upperCase_actionPerformed(ActionEvent e)
\r
1167 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1171 for(int g=0; g<sg.getSize(true); g++)
\r
1173 ( (SequenceI)sg.getSequences(true).elementAt(g))
\r
1174 .changeCase(true, sg.getStartRes(), sg.getEndRes()+1);
\r
1179 public void lowerCase_actionPerformed(ActionEvent e)
\r
1181 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1185 for(int g=0; g<sg.getSize(true); g++)
\r
1187 ( (SequenceI)sg.getSequences(true).elementAt(g))
\r
1188 .changeCase(false, sg.getStartRes(), sg.getEndRes()+1);
\r
1193 public void toggle_actionPerformed(ActionEvent e)
\r
1195 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1199 for (int g = 0; g < sg.getSize(true); g++)
\r
1201 ( (SequenceI)sg.getSequences(true).elementAt(g))
\r
1202 .toggleCase(sg.getStartRes(), sg.getEndRes() + 1);
\r
1208 public void outputText_actionPerformed(ActionEvent e)
\r
1210 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1211 Desktop.addInternalFrame(cap,
\r
1212 "Alignment output - " + e.getActionCommand(), 600,
\r
1215 String [] omitHidden = null;
\r
1217 if(ap.av.hasHiddenColumns)
\r
1219 System.out.println("PROMPT USER HERE");
\r
1220 omitHidden = ap.av.getViewAsString(true);
\r
1223 cap.setText(new FormatAdapter().formatSequences(
\r
1224 e.getActionCommand(),
\r
1225 ap.av.getSelectionAsNewSequence(),
\r
1230 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1232 jalview.io.JalviewFileChooser chooser
\r
1233 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1235 "LAST_DIRECTORY"));
\r
1236 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1237 chooser.setDialogTitle("Select a PDB file");
\r
1238 chooser.setToolTipText("Load a PDB file");
\r
1240 int value = chooser.showOpenDialog(null);
\r
1242 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1244 PDBEntry entry = new PDBEntry();
\r
1245 String choice = chooser.getSelectedFile().getPath();
\r
1246 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1249 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1250 jalview.io.AppletFormatAdapter.FILE);
\r
1252 if (pdbfile.id == null)
\r
1254 String reply = JOptionPane.showInternalInputDialog(
\r
1256 "Couldn't find a PDB id in the file supplied."
\r
1257 + "Please enter an Id to identify this structure.",
\r
1258 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1259 if (reply == null)
\r
1262 entry.setId(reply);
\r
1265 entry.setId(pdbfile.id);
\r
1267 catch (java.io.IOException ex)
\r
1269 ex.printStackTrace();
\r
1272 entry.setFile(choice);
\r
1273 sequence.getDatasetSequence().addPDBId(entry);
\r
1278 public void enterPDB_actionPerformed(ActionEvent e)
\r
1280 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1281 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1283 if (id != null && id.length() > 0)
\r
1285 PDBEntry entry = new PDBEntry();
\r
1287 sequence.getDatasetSequence()
\r
1292 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1294 new jalview.io.DBRefFetcher(
\r
1295 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r