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
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
209 if (ap.overviewPanel != null)
\r
210 ap.overviewPanel.updateOverviewImage();
\r
216 menuItem = new JMenuItem("Reveal All");
\r
217 menuItem.addActionListener(new ActionListener()
\r
219 public void actionPerformed(ActionEvent e)
\r
221 ap.av.showAllHiddenSeqs();
\r
222 if (ap.overviewPanel != null)
\r
223 ap.overviewPanel.updateOverviewImage();
\r
235 SequenceGroup sg = ap.av.getSelectionGroup();
\r
239 groupName.setText(sg.getName());
\r
241 if (sg.cs instanceof ZappoColourScheme)
\r
243 zappoColour.setSelected(true);
\r
245 else if (sg.cs instanceof TaylorColourScheme)
\r
247 taylorColour.setSelected(true);
\r
249 else if (sg.cs instanceof PIDColourScheme)
\r
251 PIDColour.setSelected(true);
\r
253 else if (sg.cs instanceof Blosum62ColourScheme)
\r
255 BLOSUM62Colour.setSelected(true);
\r
257 else if (sg.cs instanceof UserColourScheme)
\r
259 userDefinedColour.setSelected(true);
\r
261 else if (sg.cs instanceof HydrophobicColourScheme)
\r
263 hydrophobicityColour.setSelected(true);
\r
265 else if (sg.cs instanceof HelixColourScheme)
\r
267 helixColour.setSelected(true);
\r
269 else if (sg.cs instanceof StrandColourScheme)
\r
271 strandColour.setSelected(true);
\r
273 else if (sg.cs instanceof TurnColourScheme)
\r
275 turnColour.setSelected(true);
\r
277 else if (sg.cs instanceof BuriedColourScheme)
\r
279 buriedColour.setSelected(true);
\r
281 else if (sg.cs instanceof ClustalxColourScheme)
\r
283 clustalColour.setSelected(true);
\r
287 noColourmenuItem.setSelected(true);
\r
290 if (sg.cs!=null && sg.cs.conservationApplied())
\r
292 conservationMenuItem.setSelected(true);
\r
295 showText.setSelected(sg.getDisplayText());
\r
296 showColourText.setSelected(sg.getColourText());
\r
297 showBoxes.setSelected(sg.getDisplayBoxes());
\r
301 groupMenu.setVisible(false);
\r
302 editMenu.setVisible(false);
\r
305 if (!ap.av.alignment.getGroups().contains(sg))
\r
307 unGroupMenuItem.setVisible(false);
\r
313 sequenceMenu.setVisible(false);
\r
314 pdbMenu.setVisible(false);
\r
317 if(links != null && links.size()>0)
\r
319 JMenu linkMenu = new JMenu("Link");
\r
321 for(int i=0; i<links.size(); i++)
\r
323 String link = links.elementAt(i).toString();
\r
324 final String label = link.substring(0, link.indexOf("|"));
\r
325 item = new JMenuItem(label);
\r
328 if (link.indexOf("$SEQUENCE_ID$") > -1)
\r
330 String id = seq.getName();
\r
331 if (id.indexOf("|") > -1)
\r
332 id = id.substring(id.lastIndexOf("|") + 1);
\r
334 url = link.substring(link.indexOf("|") + 1,
\r
335 link.indexOf("$SEQUENCE_ID$"))
\r
337 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
\r
340 url = link.substring(link.lastIndexOf("|")+1);
\r
343 item.addActionListener(new java.awt.event.ActionListener()
\r
345 public void actionPerformed(ActionEvent e)
\r
351 linkMenu.add(item);
\r
354 sequenceMenu.add(linkMenu);
\r
364 * @throws Exception DOCUMENT ME!
\r
366 private void jbInit() throws Exception
\r
368 groupMenu.setText("Group");
\r
369 groupMenu.setText("Selection");
\r
370 groupName.setText("Name");
\r
371 groupName.addActionListener(new java.awt.event.ActionListener()
\r
373 public void actionPerformed(ActionEvent e)
\r
375 groupName_actionPerformed(e);
\r
378 sequenceMenu.setText("Sequence");
\r
379 sequenceName.setText("Edit Name/Description");
\r
380 sequenceName.addActionListener(new java.awt.event.ActionListener()
\r
382 public void actionPerformed(ActionEvent e)
\r
384 sequenceName_actionPerformed(e);
\r
387 PIDColour.setFocusPainted(false);
\r
388 unGroupMenuItem.setText("Remove Group");
\r
389 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
391 public void actionPerformed(ActionEvent e)
\r
393 unGroupMenuItem_actionPerformed(e);
\r
397 outline.setText("Border colour");
\r
398 outline.addActionListener(new java.awt.event.ActionListener()
\r
400 public void actionPerformed(ActionEvent e)
\r
402 outline_actionPerformed(e);
\r
405 nucleotideMenuItem.setText("Nucleotide");
\r
406 nucleotideMenuItem.addActionListener(new ActionListener()
\r
408 public void actionPerformed(ActionEvent e)
\r
410 nucleotideMenuItem_actionPerformed(e);
\r
413 colourMenu.setText("Group Colour");
\r
414 showBoxes.setText("Boxes");
\r
415 showBoxes.setState(true);
\r
416 showBoxes.addActionListener(new ActionListener()
\r
418 public void actionPerformed(ActionEvent e)
\r
420 showBoxes_actionPerformed(e);
\r
423 showText.setText("Text");
\r
424 showText.setState(true);
\r
425 showText.addActionListener(new ActionListener()
\r
427 public void actionPerformed(ActionEvent e)
\r
429 showText_actionPerformed(e);
\r
432 showColourText.setText("Colour Text");
\r
433 showColourText.addActionListener(new ActionListener()
\r
435 public void actionPerformed(ActionEvent e)
\r
437 showColourText_actionPerformed(e);
\r
440 editMenu.setText("Edit");
\r
441 cut.setText("Cut");
\r
442 cut.addActionListener(new ActionListener()
\r
444 public void actionPerformed(ActionEvent e)
\r
446 cut_actionPerformed(e);
\r
449 upperCase.setText("To Upper Case");
\r
450 upperCase.addActionListener(new ActionListener()
\r
452 public void actionPerformed(ActionEvent e)
\r
454 upperCase_actionPerformed(e);
\r
457 copy.setText("Copy");
\r
458 copy.addActionListener(new ActionListener()
\r
460 public void actionPerformed(ActionEvent e)
\r
462 copy_actionPerformed(e);
\r
465 lowerCase.setText("To Lower Case");
\r
466 lowerCase.addActionListener(new ActionListener()
\r
468 public void actionPerformed(ActionEvent e)
\r
470 lowerCase_actionPerformed(e);
\r
473 toggle.setText("Toggle Case");
\r
474 toggle.addActionListener(new ActionListener()
\r
476 public void actionPerformed(ActionEvent e)
\r
478 toggle_actionPerformed(e);
\r
481 pdbMenu.setText("Associate Structure with Sequence");
\r
482 pdbFromFile.setText("From File");
\r
483 pdbFromFile.addActionListener(new ActionListener()
\r
485 public void actionPerformed(ActionEvent e)
\r
487 pdbFromFile_actionPerformed(e);
\r
490 enterPDB.setText("Enter PDB Id");
\r
491 enterPDB.addActionListener(new ActionListener()
\r
493 public void actionPerformed(ActionEvent e)
\r
495 enterPDB_actionPerformed(e);
\r
498 discoverPDB.setText("Discover PDB ids");
\r
499 discoverPDB.addActionListener(new ActionListener()
\r
501 public void actionPerformed(ActionEvent e)
\r
503 discoverPDB_actionPerformed(e);
\r
506 outputMenu.setText("Output to Textbox...");
\r
510 groupMenu.add(editMenu);
\r
511 groupMenu.add(outputMenu);
\r
512 groupMenu.addSeparator();
\r
513 groupMenu.add(groupName);
\r
514 groupMenu.add(unGroupMenuItem);
\r
515 groupMenu.add(colourMenu);
\r
516 groupMenu.add(showBoxes);
\r
517 groupMenu.add(showText);
\r
518 groupMenu.add(showColourText);
\r
519 groupMenu.add(outline);
\r
520 sequenceMenu.add(sequenceName);
\r
521 sequenceMenu.add(pdbMenu);
\r
522 colourMenu.add(noColourmenuItem);
\r
523 colourMenu.add(clustalColour);
\r
524 colourMenu.add(BLOSUM62Colour);
\r
525 colourMenu.add(PIDColour);
\r
526 colourMenu.add(zappoColour);
\r
527 colourMenu.add(taylorColour);
\r
528 colourMenu.add(hydrophobicityColour);
\r
529 colourMenu.add(helixColour);
\r
530 colourMenu.add(strandColour);
\r
531 colourMenu.add(turnColour);
\r
532 colourMenu.add(buriedColour);
\r
533 colourMenu.add(nucleotideMenuItem);
\r
534 colourMenu.add(userDefinedColour);
\r
536 if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
\r
538 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
539 getUserColourSchemes().keys();
\r
541 while (userColours.hasMoreElements())
\r
543 JMenuItem item = new JMenuItem(userColours.
\r
544 nextElement().toString());
\r
545 item.addActionListener(new ActionListener()
\r
547 public void actionPerformed(ActionEvent evt)
\r
549 userDefinedColour_actionPerformed(evt);
\r
552 colourMenu.add(item);
\r
557 colourMenu.addSeparator();
\r
558 colourMenu.add(abovePIDColour);
\r
559 colourMenu.add(conservationMenuItem);
\r
560 editMenu.add(copy);
\r
562 editMenu.add(upperCase);
\r
563 editMenu.add(lowerCase);
\r
564 editMenu.add(toggle);
\r
565 pdbMenu.add(pdbFromFile);
\r
566 pdbMenu.add(enterPDB);
\r
567 pdbMenu.add(discoverPDB);
\r
568 noColourmenuItem.setText("None");
\r
569 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
571 public void actionPerformed(ActionEvent e)
\r
573 noColourmenuItem_actionPerformed(e);
\r
577 clustalColour.setText("Clustalx colours");
\r
578 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
580 public void actionPerformed(ActionEvent e)
\r
582 clustalColour_actionPerformed(e);
\r
585 zappoColour.setText("Zappo");
\r
586 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
588 public void actionPerformed(ActionEvent e)
\r
590 zappoColour_actionPerformed(e);
\r
593 taylorColour.setText("Taylor");
\r
594 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
596 public void actionPerformed(ActionEvent e)
\r
598 taylorColour_actionPerformed(e);
\r
601 hydrophobicityColour.setText("Hydrophobicity");
\r
602 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
\r
604 public void actionPerformed(ActionEvent e)
\r
606 hydrophobicityColour_actionPerformed(e);
\r
609 helixColour.setText("Helix propensity");
\r
610 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
612 public void actionPerformed(ActionEvent e)
\r
614 helixColour_actionPerformed(e);
\r
617 strandColour.setText("Strand propensity");
\r
618 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
620 public void actionPerformed(ActionEvent e)
\r
622 strandColour_actionPerformed(e);
\r
625 turnColour.setText("Turn propensity");
\r
626 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
628 public void actionPerformed(ActionEvent e)
\r
630 turnColour_actionPerformed(e);
\r
633 buriedColour.setText("Buried Index");
\r
634 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
636 public void actionPerformed(ActionEvent e)
\r
638 buriedColour_actionPerformed(e);
\r
641 abovePIDColour.setText("Above % Identity");
\r
642 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
\r
644 public void actionPerformed(ActionEvent e)
\r
646 abovePIDColour_actionPerformed(e);
\r
649 userDefinedColour.setText("User Defined...");
\r
650 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
652 public void actionPerformed(ActionEvent e)
\r
654 userDefinedColour_actionPerformed(e);
\r
657 PIDColour.setText("Percentage Identity");
\r
658 PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
660 public void actionPerformed(ActionEvent e)
\r
662 PIDColour_actionPerformed(e);
\r
665 BLOSUM62Colour.setText("BLOSUM62");
\r
666 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
668 public void actionPerformed(ActionEvent e)
\r
670 BLOSUM62Colour_actionPerformed(e);
\r
673 conservationMenuItem.setText("Conservation");
\r
674 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
676 public void actionPerformed(ActionEvent e)
\r
678 conservationMenuItem_actionPerformed(e);
\r
688 if (ap.overviewPanel != null)
\r
689 ap.overviewPanel.updateOverviewImage();
\r
691 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
697 * @param e DOCUMENT ME!
\r
699 protected void clustalColour_actionPerformed(ActionEvent e)
\r
701 SequenceGroup sg = getGroup();
\r
702 sg.cs = new ClustalxColourScheme(sg.getSequences(true),
\r
703 ap.av.alignment.getWidth());
\r
710 * @param e DOCUMENT ME!
\r
712 protected void zappoColour_actionPerformed(ActionEvent e)
\r
714 getGroup().cs = new ZappoColourScheme();
\r
721 * @param e DOCUMENT ME!
\r
723 protected void taylorColour_actionPerformed(ActionEvent e)
\r
725 getGroup().cs = new TaylorColourScheme();
\r
732 * @param e DOCUMENT ME!
\r
734 protected void hydrophobicityColour_actionPerformed(ActionEvent e)
\r
736 getGroup().cs = new HydrophobicColourScheme();
\r
743 * @param e DOCUMENT ME!
\r
745 protected void helixColour_actionPerformed(ActionEvent e)
\r
747 getGroup().cs = new HelixColourScheme();
\r
754 * @param e DOCUMENT ME!
\r
756 protected void strandColour_actionPerformed(ActionEvent e)
\r
758 getGroup().cs = new StrandColourScheme();
\r
765 * @param e DOCUMENT ME!
\r
767 protected void turnColour_actionPerformed(ActionEvent e)
\r
769 getGroup().cs = new TurnColourScheme();
\r
776 * @param e DOCUMENT ME!
\r
778 protected void buriedColour_actionPerformed(ActionEvent e)
\r
780 getGroup().cs = new BuriedColourScheme();
\r
787 * @param e DOCUMENT ME!
\r
789 public void nucleotideMenuItem_actionPerformed(ActionEvent e)
\r
791 getGroup().cs = new NucleotideColourScheme();
\r
798 * @param e DOCUMENT ME!
\r
800 protected void abovePIDColour_actionPerformed(ActionEvent e)
\r
802 SequenceGroup sg = getGroup();
\r
806 if (abovePIDColour.isSelected())
\r
808 sg.cs.setConsensus(AAFrequency.calculate(
\r
809 sg.getSequences(true), 0,
\r
810 ap.av.alignment.getWidth()));
\r
812 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
813 getGroup().getName());
\r
815 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
817 SliderPanel.showPIDSlider();
\r
819 else // remove PIDColouring
\r
821 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
830 * @param e DOCUMENT ME!
\r
832 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
834 SequenceGroup sg = getGroup();
\r
836 if (e.getActionCommand().equals("User Defined..."))
\r
837 new UserDefinedColours(ap, sg);
\r
840 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
841 getUserColourSchemes().get(e.getActionCommand());
\r
849 * @param e DOCUMENT ME!
\r
851 protected void PIDColour_actionPerformed(ActionEvent e)
\r
853 SequenceGroup sg = getGroup();
\r
854 sg.cs = new PIDColourScheme();
\r
855 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
856 ap.av.alignment.getWidth()));
\r
863 * @param e DOCUMENT ME!
\r
865 protected void BLOSUM62Colour_actionPerformed(ActionEvent e)
\r
867 SequenceGroup sg = getGroup();
\r
869 sg.cs = new Blosum62ColourScheme();
\r
871 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(true), 0,
\r
872 ap.av.alignment.getWidth()));
\r
880 * @param e DOCUMENT ME!
\r
882 protected void noColourmenuItem_actionPerformed(ActionEvent e)
\r
884 getGroup().cs = null;
\r
891 * @param e DOCUMENT ME!
\r
893 protected void conservationMenuItem_actionPerformed(ActionEvent e)
\r
895 SequenceGroup sg = getGroup();
\r
899 if (conservationMenuItem.isSelected())
\r
901 Conservation c = new Conservation("Group",
\r
902 ResidueProperties.propHash, 3,
\r
903 sg.getSequences(true), 0,
\r
904 ap.av.alignment.getWidth());
\r
907 c.verdict(false, ap.av.ConsPercGaps);
\r
909 sg.cs.setConservation(c);
\r
911 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
912 SliderPanel.showConservationSlider();
\r
914 else // remove ConservationColouring
\r
916 sg.cs.setConservation(null);
\r
925 * @param e DOCUMENT ME!
\r
927 protected void groupName_actionPerformed(ActionEvent e)
\r
929 SequenceGroup sg = getGroup();
\r
930 String reply = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
931 "Enter new group name", "Edit group name",
\r
932 JOptionPane.QUESTION_MESSAGE);
\r
940 groupName.setText(reply);
\r
946 * @param e DOCUMENT ME!
\r
948 protected void analyze_actionPerformed(ActionEvent e)
\r
950 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
951 JInternalFrame frame = new JInternalFrame();
\r
952 frame.setContentPane(cap);
\r
953 Desktop.addInternalFrame(frame, "Analyze this - ", 400, 300);
\r
955 SequenceGroup sg = getGroup();
\r
956 StringBuffer sb = new StringBuffer();
\r
958 for (int i = 0; i < sg.getSize(false); i++)
\r
960 Sequence tmp = (Sequence) sg.getSequences(false).elementAt(i);
\r
961 sb.append(tmp.getSequence(sg.getStartRes(), sg.getEndRes() + 1));
\r
965 sb.append("Something amazing will happen soon");
\r
966 cap.setText(sb.toString());
\r
972 * @return DOCUMENT ME!
\r
974 SequenceGroup getGroup()
\r
976 SequenceGroup sg = ap.av.getSelectionGroup();
\r
977 // this method won't add a new group if it already exists
\r
979 ap.av.alignment.addGroup(sg);
\r
987 * @param e DOCUMENT ME!
\r
989 void sequenceName_actionPerformed(ActionEvent e)
\r
991 JLabel idlabel = new JLabel( " Sequence Name ");
\r
992 JLabel desclabel = new JLabel("Sequence Description ");
\r
993 idlabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
994 desclabel.setFont(new Font("Courier", Font.PLAIN, 12));
\r
995 JTextField id = new JTextField(sequence.getName(), 40);
\r
996 JTextField description = new JTextField(sequence.getDescription(), 40);
\r
997 JPanel panel = new JPanel(new BorderLayout());
\r
998 JPanel panel2 = new JPanel(new BorderLayout());
\r
999 panel2.add(idlabel, BorderLayout.WEST);
\r
1000 panel2.add(id, BorderLayout.CENTER);
\r
1001 panel.add(panel2, BorderLayout.NORTH);
\r
1002 panel2 = new JPanel(new BorderLayout());
\r
1003 panel2.add(desclabel, BorderLayout.WEST);
\r
1004 panel2.add(description, BorderLayout.CENTER);
\r
1005 panel.add(panel2, BorderLayout.SOUTH);
\r
1008 int reply = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
\r
1009 panel, "Edit Sequence Name/Description",
\r
1010 JOptionPane.OK_CANCEL_OPTION );
\r
1013 if (reply != JOptionPane.OK_OPTION )
\r
1018 String s = id.getText();
\r
1022 if (s.indexOf(" ") > -1)
\r
1024 JOptionPane.showMessageDialog(ap,
\r
1025 "Spaces have been converted to \"_\"",
\r
1026 "No spaces allowed in Sequence Name",
\r
1027 JOptionPane.WARNING_MESSAGE);
\r
1030 s = s.replace(' ', '_');
\r
1031 sequence.getDatasetSequence().setName(s);
\r
1032 sequence.setName(s);
\r
1036 sequence.getDatasetSequence().setDescription(description.getText());
\r
1037 sequence.setDescription(description.getText());
\r
1043 * @param e DOCUMENT ME!
\r
1045 void unGroupMenuItem_actionPerformed(ActionEvent e)
\r
1047 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1048 ap.av.alignment.deleteGroup(sg);
\r
1049 ap.av.setSelectionGroup(null);
\r
1057 * @param e DOCUMENT ME!
\r
1059 protected void outline_actionPerformed(ActionEvent e)
\r
1061 SequenceGroup sg = getGroup();
\r
1062 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1067 sg.setOutlineColour(col);
\r
1076 * @param e DOCUMENT ME!
\r
1078 public void showBoxes_actionPerformed(ActionEvent e)
\r
1080 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1087 * @param e DOCUMENT ME!
\r
1089 public void showText_actionPerformed(ActionEvent e)
\r
1091 getGroup().setDisplayText(showText.isSelected());
\r
1098 * @param e DOCUMENT ME!
\r
1100 public void showColourText_actionPerformed(ActionEvent e)
\r
1102 getGroup().setColourText(showColourText.isSelected());
\r
1106 public void showLink(String url)
\r
1110 jalview.util.BrowserLauncher.openURL(url);
\r
1112 catch (Exception ex)
\r
1114 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1115 "Unixers: Couldn't find default web browser."
\r
1116 +"\nAdd the full path to your browser in Preferences.",
\r
1117 "Web browser not found", JOptionPane.WARNING_MESSAGE );
\r
1120 ex.printStackTrace();
\r
1124 void hideSequences(boolean representGroup)
\r
1126 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1127 if(sg==null || sg.getSize(false)<1)
\r
1129 ap.av.hideSequence(new SequenceI[]{sequence});
\r
1133 int gsize = sg.getSize(false);
\r
1134 SequenceI [] hseqs;
\r
1136 hseqs = new SequenceI[ representGroup ? gsize-1 : gsize ];
\r
1139 while(index < gsize)
\r
1141 if(representGroup && sg.getSequenceAt(index)!=sequence)
\r
1143 sequence.addHiddenSequence(sg.getSequenceAt(index));
\r
1144 hseqs[index] = sg.getSequenceAt(index);
\r
1146 else if(!representGroup)
\r
1148 hseqs[index] = sg.getSequenceAt(index);
\r
1153 ap.av.hideSequence(hseqs);
\r
1155 ap.av.setSelectionGroup(null);
\r
1158 public void copy_actionPerformed(ActionEvent e)
\r
1160 ap.alignFrame.copy_actionPerformed(null);
\r
1163 public void cut_actionPerformed(ActionEvent e)
\r
1165 ap.alignFrame.cut_actionPerformed(null);
\r
1168 public void upperCase_actionPerformed(ActionEvent e)
\r
1170 changeCase(e.getSource());
\r
1173 public void lowerCase_actionPerformed(ActionEvent e)
\r
1175 changeCase(e.getSource());
\r
1178 public void toggle_actionPerformed(ActionEvent e)
\r
1180 changeCase(e.getSource());
\r
1183 void changeCase(Object source)
\r
1185 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1188 for (int g = 0; g < sg.getSize(true); g++)
\r
1190 int start = sg.getStartRes();
\r
1191 int end = sg.getEndRes() + 1;
\r
1195 if (ap.av.hasHiddenColumns)
\r
1197 end = ap.av.colSel.getHiddenBoundaryRight(start);
\r
1199 end = sg.getEndRes() + 1;
\r
1200 if (end > sg.getEndRes())
\r
1201 end = sg.getEndRes() + 1;
\r
1204 if (source == toggle)
\r
1205 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
1206 .toggleCase(start, end);
\r
1208 ( (SequenceI) sg.getSequences(true).elementAt(g))
\r
1209 .changeCase(source == upperCase, start, end);
\r
1211 if (ap.av.hasHiddenColumns)
\r
1213 start = ap.av.colSel.adjustForHiddenColumns(end);
\r
1214 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
\r
1218 while (end < sg.getEndRes());
\r
1220 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
1224 public void outputText_actionPerformed(ActionEvent e)
\r
1226 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1227 Desktop.addInternalFrame(cap,
\r
1228 "Alignment output - " + e.getActionCommand(), 600,
\r
1231 String [] omitHidden = null;
\r
1233 if(ap.av.hasHiddenColumns)
\r
1235 System.out.println("PROMPT USER HERE");
\r
1236 omitHidden = ap.av.getViewAsString(true);
\r
1239 cap.setText(new FormatAdapter().formatSequences(
\r
1240 e.getActionCommand(),
\r
1241 ap.av.getSelectionAsNewSequence(),
\r
1246 public void pdbFromFile_actionPerformed(ActionEvent e)
\r
1248 jalview.io.JalviewFileChooser chooser
\r
1249 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1251 "LAST_DIRECTORY"));
\r
1252 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1253 chooser.setDialogTitle("Select a PDB file");
\r
1254 chooser.setToolTipText("Load a PDB file");
\r
1256 int value = chooser.showOpenDialog(null);
\r
1258 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1260 PDBEntry entry = new PDBEntry();
\r
1261 String choice = chooser.getSelectedFile().getPath();
\r
1262 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1265 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1266 jalview.io.AppletFormatAdapter.FILE);
\r
1268 if (pdbfile.id == null)
\r
1270 String reply = JOptionPane.showInternalInputDialog(
\r
1272 "Couldn't find a PDB id in the file supplied."
\r
1273 + "Please enter an Id to identify this structure.",
\r
1274 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1275 if (reply == null)
\r
1278 entry.setId(reply);
\r
1281 entry.setId(pdbfile.id);
\r
1283 catch (java.io.IOException ex)
\r
1285 ex.printStackTrace();
\r
1288 entry.setFile(choice);
\r
1289 sequence.getDatasetSequence().addPDBId(entry);
\r
1294 public void enterPDB_actionPerformed(ActionEvent e)
\r
1296 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1297 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1299 if (id != null && id.length() > 0)
\r
1301 PDBEntry entry = new PDBEntry();
\r
1303 sequence.getDatasetSequence()
\r
1308 public void discoverPDB_actionPerformed(ActionEvent e)
\r
1310 new jalview.io.DBRefFetcher(
\r
1311 ap.av.getAlignment(), ap.alignFrame).fetchDBRefs(false);
\r