2 * Jalview - A Sequence Alignment Editor and Viewer
\r
3 * Copyright (C) 2007 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
24 import java.awt.event.*;
\r
25 import javax.swing.*;
\r
28 import jalview.analysis.*;
\r
29 import jalview.commands.*;
\r
30 import jalview.datamodel.*;
\r
31 import jalview.io.*;
\r
32 import jalview.schemes.*;
\r
38 * @version $Revision$
\r
40 public class PopupMenu
\r
43 JMenu groupMenu = new JMenu();
\r
44 JMenuItem groupName = new JMenuItem();
\r
45 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
\r
46 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
\r
47 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
\r
48 protected JRadioButtonMenuItem hydrophobicityColour = new
\r
49 JRadioButtonMenuItem();
\r
50 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
\r
51 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
\r
52 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
\r
53 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
\r
54 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
\r
55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
\r
56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
\r
57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
\r
58 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
\r
59 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
\r
61 JMenu sequenceMenu = new JMenu();
\r
62 JMenuItem sequenceName = new JMenuItem();
\r
64 JMenuItem unGroupMenuItem = new JMenuItem();
\r
65 JMenuItem outline = new JMenuItem();
\r
66 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
\r
67 JMenu colourMenu = new JMenu();
\r
68 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
\r
69 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
\r
70 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
\r
71 JMenu editMenu = new JMenu();
\r
72 JMenuItem cut = new JMenuItem();
\r
73 JMenuItem copy = new JMenuItem();
\r
74 JMenuItem upperCase = new JMenuItem();
\r
75 JMenuItem lowerCase = new JMenuItem();
\r
76 JMenuItem toggle = new JMenuItem();
\r
77 JMenu pdbMenu = new JMenu();
\r
78 JMenuItem pdbFromFile = new JMenuItem();
\r
79 JMenuItem enterPDB = new JMenuItem();
\r
80 JMenuItem discoverPDB = new JMenuItem();
\r
81 JMenu outputMenu = new JMenu();
\r
82 JMenuItem sequenceFeature = new JMenuItem();
\r
83 JMenuItem textColour = new JMenuItem();
\r
84 JMenu jMenu1 = new JMenu();
\r
85 JMenu structureMenu = new JMenu();
\r
86 JMenu viewStructureMenu = new JMenu();
\r
87 // JMenu colStructureMenu = new JMenu();
\r
88 JMenuItem editSequence = new JMenuItem();
\r
89 // JMenuItem annotationMenuItem = new JMenuItem();
\r
92 * Creates a new PopupMenu object.
\r
94 * @param ap DOCUMENT ME!
\r
95 * @param seq DOCUMENT ME!
\r
97 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
\r
99 ///////////////////////////////////////////////////////////
\r
100 // If this is activated from the sequence panel, the user may want to
\r
101 // edit or annotate a particular residue. Therefore display the residue menu
\r
103 // If from the IDPanel, we must display the sequence menu
\r
104 //////////////////////////////////////////////////////////
\r
108 ButtonGroup colours = new ButtonGroup();
\r
109 colours.add(noColourmenuItem);
\r
110 colours.add(clustalColour);
\r
111 colours.add(zappoColour);
\r
112 colours.add(taylorColour);
\r
113 colours.add(hydrophobicityColour);
\r
114 colours.add(helixColour);
\r
115 colours.add(strandColour);
\r
116 colours.add(turnColour);
\r
117 colours.add(buriedColour);
\r
118 colours.add(abovePIDColour);
\r
119 colours.add(userDefinedColour);
\r
120 colours.add(PIDColour);
\r
121 colours.add(BLOSUM62Colour);
\r
123 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
\r
125 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
\r
128 item.addActionListener(new java.awt.event.ActionListener()
\r
130 public void actionPerformed(ActionEvent e)
\r
132 outputText_actionPerformed(e);
\r
136 outputMenu.add(item);
\r
143 catch (Exception e)
\r
145 e.printStackTrace();
\r
150 sequenceMenu.setText(sequence.getName());
\r
152 JMenuItem menuItem;
\r
153 if (seq.getDatasetSequence().getPDBId() != null
\r
154 && seq.getDatasetSequence().getPDBId().size()>0)
\r
156 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
\r
159 while (e.hasMoreElements())
\r
161 final PDBEntry pdb = (PDBEntry) e.nextElement();
\r
163 menuItem = new JMenuItem();
\r
164 menuItem.setText(pdb.getId());
\r
165 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
167 public void actionPerformed(ActionEvent e)
\r
169 Vector seqs = new Vector();
\r
170 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
\r
172 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
\r
176 for(int p=0; p<pdbs.size(); p++)
\r
178 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
\r
179 if(p1.getId().equals(pdb.getId()))
\r
181 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
\r
182 seqs.addElement(ap.av.alignment.getSequenceAt(i));
\r
189 SequenceI [] seqs2 = new SequenceI[seqs.size()];
\r
190 seqs.toArray(seqs2);
\r
192 new AppJmol(pdb, seqs2, null, ap);
\r
193 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
\r
196 viewStructureMenu.add(menuItem);
\r
198 /* menuItem = new JMenuItem();
\r
199 menuItem.setText(pdb.getId());
\r
200 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
202 public void actionPerformed(ActionEvent e)
\r
204 colourByStructure(pdb.getId());
\r
207 colStructureMenu.add(menuItem);*/
\r
212 structureMenu.remove(viewStructureMenu);
\r
213 // structureMenu.remove(colStructureMenu);
\r
216 menuItem = new JMenuItem("Hide Sequences");
\r
217 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
219 public void actionPerformed(ActionEvent e)
\r
221 hideSequences(false);
\r
226 if (ap.av.getSelectionGroup() != null
\r
227 && ap.av.getSelectionGroup().getSize() > 1)
\r
229 menuItem = new JMenuItem("Represent Group with " + seq.getName());
\r
230 menuItem.addActionListener(new java.awt.event.ActionListener()
\r
232 public void actionPerformed(ActionEvent e)
\r
234 hideSequences(true);
\r
237 sequenceMenu.add(menuItem);
\r
240 if (ap.av.hasHiddenRows)
\r
242 final int index = ap.av.alignment.findIndex(seq);
\r
244 if (ap.av.adjustForHiddenSeqs(index) -
\r
245 ap.av.adjustForHiddenSeqs(index - 1) > 1)
\r
247 menuItem = new JMenuItem("Reveal Sequences");
\r
248 menuItem.addActionListener(new ActionListener()
\r
250 public void actionPerformed(ActionEvent e)
\r
252 ap.av.showSequence(index);
\r
253 if (ap.overviewPanel != null)
\r
255 ap.overviewPanel.updateOverviewImage();
\r
262 menuItem = new JMenuItem("Reveal All");
\r
263 menuItem.addActionListener(new ActionListener()
\r
265 public void actionPerformed(ActionEvent e)
\r
267 ap.av.showAllHiddenSeqs();
\r
268 if (ap.overviewPanel != null)
\r
270 ap.overviewPanel.updateOverviewImage();
\r
280 SequenceGroup sg = ap.av.getSelectionGroup();
\r
284 groupName.setText(sg.getName());
\r
286 if (sg.cs instanceof ZappoColourScheme)
\r
288 zappoColour.setSelected(true);
\r
290 else if (sg.cs instanceof TaylorColourScheme)
\r
292 taylorColour.setSelected(true);
\r
294 else if (sg.cs instanceof PIDColourScheme)
\r
296 PIDColour.setSelected(true);
\r
298 else if (sg.cs instanceof Blosum62ColourScheme)
\r
300 BLOSUM62Colour.setSelected(true);
\r
302 else if (sg.cs instanceof UserColourScheme)
\r
304 userDefinedColour.setSelected(true);
\r
306 else if (sg.cs instanceof HydrophobicColourScheme)
\r
308 hydrophobicityColour.setSelected(true);
\r
310 else if (sg.cs instanceof HelixColourScheme)
\r
312 helixColour.setSelected(true);
\r
314 else if (sg.cs instanceof StrandColourScheme)
\r
316 strandColour.setSelected(true);
\r
318 else if (sg.cs instanceof TurnColourScheme)
\r
320 turnColour.setSelected(true);
\r
322 else if (sg.cs instanceof BuriedColourScheme)
\r
324 buriedColour.setSelected(true);
\r
326 else if (sg.cs instanceof ClustalxColourScheme)
\r
328 clustalColour.setSelected(true);
\r
332 noColourmenuItem.setSelected(true);
\r
335 if (sg.cs != null && sg.cs.conservationApplied())
\r
337 conservationMenuItem.setSelected(true);
\r
340 showText.setSelected(sg.getDisplayText());
\r
341 showColourText.setSelected(sg.getColourText());
\r
342 showBoxes.setSelected(sg.getDisplayBoxes());
\r
346 groupMenu.setVisible(false);
\r
347 editMenu.setVisible(false);
\r
350 if (!ap.av.alignment.getGroups().contains(sg))
\r
352 unGroupMenuItem.setVisible(false);
\r
357 sequenceMenu.setVisible(false);
\r
358 structureMenu.setVisible(false);
\r
361 if (links != null && links.size() > 0)
\r
363 JMenu linkMenu = new JMenu("Link");
\r
365 for (int i = 0; i < links.size(); i++)
\r
367 String link = links.elementAt(i).toString();
\r
368 final String label = link.substring(0, link.indexOf("|"));
\r
369 item = new JMenuItem(label);
\r
372 if (link.indexOf("$SEQUENCE_ID$") > -1)
\r
374 String id = seq.getName();
\r
375 if (id.indexOf("|") > -1)
\r
377 id = id.substring(id.lastIndexOf("|") + 1);
\r
380 url = link.substring(link.indexOf("|") + 1,
\r
381 link.indexOf("$SEQUENCE_ID$"))
\r
383 link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
\r
387 url = link.substring(link.lastIndexOf("|") + 1);
\r
390 item.addActionListener(new java.awt.event.ActionListener()
\r
392 public void actionPerformed(ActionEvent e)
\r
398 linkMenu.add(item);
\r
400 if (sequence != null)
\r
402 sequenceMenu.add(linkMenu);
\r
414 * @throws Exception DOCUMENT ME!
\r
416 private void jbInit()
\r
419 groupMenu.setText("Group");
\r
420 groupMenu.setText("Selection");
\r
421 groupName.setText("Name");
\r
422 groupName.addActionListener(new java.awt.event.ActionListener()
\r
424 public void actionPerformed(ActionEvent e)
\r
426 groupName_actionPerformed();
\r
429 sequenceMenu.setText("Sequence");
\r
430 sequenceName.setText("Edit Name/Description");
\r
431 sequenceName.addActionListener(new java.awt.event.ActionListener()
\r
433 public void actionPerformed(ActionEvent e)
\r
435 sequenceName_actionPerformed();
\r
438 PIDColour.setFocusPainted(false);
\r
439 unGroupMenuItem.setText("Remove Group");
\r
440 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
442 public void actionPerformed(ActionEvent e)
\r
444 unGroupMenuItem_actionPerformed();
\r
448 outline.setText("Border colour");
\r
449 outline.addActionListener(new java.awt.event.ActionListener()
\r
451 public void actionPerformed(ActionEvent e)
\r
453 outline_actionPerformed();
\r
456 nucleotideMenuItem.setText("Nucleotide");
\r
457 nucleotideMenuItem.addActionListener(new ActionListener()
\r
459 public void actionPerformed(ActionEvent e)
\r
461 nucleotideMenuItem_actionPerformed();
\r
464 colourMenu.setText("Group Colour");
\r
465 showBoxes.setText("Boxes");
\r
466 showBoxes.setState(true);
\r
467 showBoxes.addActionListener(new ActionListener()
\r
469 public void actionPerformed(ActionEvent e)
\r
471 showBoxes_actionPerformed();
\r
474 showText.setText("Text");
\r
475 showText.setState(true);
\r
476 showText.addActionListener(new ActionListener()
\r
478 public void actionPerformed(ActionEvent e)
\r
480 showText_actionPerformed();
\r
483 showColourText.setText("Colour Text");
\r
484 showColourText.addActionListener(new ActionListener()
\r
486 public void actionPerformed(ActionEvent e)
\r
488 showColourText_actionPerformed();
\r
491 editMenu.setText("Edit");
\r
492 cut.setText("Cut");
\r
493 cut.addActionListener(new ActionListener()
\r
495 public void actionPerformed(ActionEvent e)
\r
497 cut_actionPerformed();
\r
500 upperCase.setText("To Upper Case");
\r
501 upperCase.addActionListener(new ActionListener()
\r
503 public void actionPerformed(ActionEvent e)
\r
508 copy.setText("Copy");
\r
509 copy.addActionListener(new ActionListener()
\r
511 public void actionPerformed(ActionEvent e)
\r
513 copy_actionPerformed();
\r
516 lowerCase.setText("To Lower Case");
\r
517 lowerCase.addActionListener(new ActionListener()
\r
519 public void actionPerformed(ActionEvent e)
\r
524 toggle.setText("Toggle Case");
\r
525 toggle.addActionListener(new ActionListener()
\r
527 public void actionPerformed(ActionEvent e)
\r
532 pdbMenu.setText("Associate Structure with Sequence");
\r
533 pdbFromFile.setText("From File");
\r
534 pdbFromFile.addActionListener(new ActionListener()
\r
536 public void actionPerformed(ActionEvent e)
\r
538 pdbFromFile_actionPerformed();
\r
541 enterPDB.setText("Enter PDB Id");
\r
542 enterPDB.addActionListener(new ActionListener()
\r
544 public void actionPerformed(ActionEvent e)
\r
546 enterPDB_actionPerformed();
\r
549 discoverPDB.setText("Discover PDB ids");
\r
550 discoverPDB.addActionListener(new ActionListener()
\r
552 public void actionPerformed(ActionEvent e)
\r
554 discoverPDB_actionPerformed();
\r
557 outputMenu.setText("Output to Textbox...");
\r
558 sequenceFeature.setText("Create Sequence Feature");
\r
559 sequenceFeature.addActionListener(new ActionListener()
\r
561 public void actionPerformed(ActionEvent e)
\r
563 sequenceFeature_actionPerformed();
\r
566 textColour.setText("Text Colour");
\r
567 textColour.addActionListener(new ActionListener()
\r
569 public void actionPerformed(ActionEvent e)
\r
571 textColour_actionPerformed();
\r
574 jMenu1.setText("Group");
\r
575 structureMenu.setText("Structure");
\r
576 viewStructureMenu.setText("View Structure");
\r
577 // colStructureMenu.setText("Colour By Structure");
\r
578 editSequence.setText("Edit Sequence...");
\r
579 editSequence.addActionListener(new ActionListener()
\r
581 public void actionPerformed(ActionEvent actionEvent)
\r
583 editSequence_actionPerformed(actionEvent);
\r
586 /* annotationMenuItem.setText("By Annotation");
\r
587 annotationMenuItem.addActionListener(new ActionListener()
\r
589 public void actionPerformed(ActionEvent actionEvent)
\r
591 annotationMenuItem_actionPerformed(actionEvent);
\r
598 this.add(structureMenu);
\r
599 groupMenu.add(editMenu);
\r
600 groupMenu.add(outputMenu);
\r
601 groupMenu.add(sequenceFeature);
\r
602 groupMenu.add(jMenu1);
\r
603 sequenceMenu.add(sequenceName);
\r
604 colourMenu.add(textColour);
\r
605 colourMenu.add(noColourmenuItem);
\r
606 colourMenu.add(clustalColour);
\r
607 colourMenu.add(BLOSUM62Colour);
\r
608 colourMenu.add(PIDColour);
\r
609 colourMenu.add(zappoColour);
\r
610 colourMenu.add(taylorColour);
\r
611 colourMenu.add(hydrophobicityColour);
\r
612 colourMenu.add(helixColour);
\r
613 colourMenu.add(strandColour);
\r
614 colourMenu.add(turnColour);
\r
615 colourMenu.add(buriedColour);
\r
616 colourMenu.add(nucleotideMenuItem);
\r
617 colourMenu.add(userDefinedColour);
\r
619 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
\r
621 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
\r
622 getUserColourSchemes().keys();
\r
624 while (userColours.hasMoreElements())
\r
626 JMenuItem item = new JMenuItem(userColours.
\r
627 nextElement().toString());
\r
628 item.addActionListener(new ActionListener()
\r
630 public void actionPerformed(ActionEvent evt)
\r
632 userDefinedColour_actionPerformed(evt);
\r
635 colourMenu.add(item);
\r
639 colourMenu.addSeparator();
\r
640 colourMenu.add(abovePIDColour);
\r
641 colourMenu.add(conservationMenuItem);
\r
642 //colourMenu.add(annotationMenuItem);
\r
643 editMenu.add(copy);
\r
645 editMenu.add(editSequence);
\r
646 editMenu.add(upperCase);
\r
647 editMenu.add(lowerCase);
\r
648 editMenu.add(toggle);
\r
649 pdbMenu.add(pdbFromFile);
\r
650 pdbMenu.add(enterPDB);
\r
651 pdbMenu.add(discoverPDB);
\r
652 jMenu1.add(groupName);
\r
653 jMenu1.add(unGroupMenuItem);
\r
654 jMenu1.add(colourMenu);
\r
655 jMenu1.add(showBoxes);
\r
656 jMenu1.add(showText);
\r
657 jMenu1.add(showColourText);
\r
658 jMenu1.add(outline);
\r
659 structureMenu.add(pdbMenu);
\r
660 structureMenu.add(viewStructureMenu);
\r
661 // structureMenu.add(colStructureMenu);
\r
662 noColourmenuItem.setText("None");
\r
663 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
\r
665 public void actionPerformed(ActionEvent e)
\r
667 noColourmenuItem_actionPerformed();
\r
671 clustalColour.setText("Clustalx colours");
\r
672 clustalColour.addActionListener(new java.awt.event.ActionListener()
\r
674 public void actionPerformed(ActionEvent e)
\r
676 clustalColour_actionPerformed();
\r
679 zappoColour.setText("Zappo");
\r
680 zappoColour.addActionListener(new java.awt.event.ActionListener()
\r
682 public void actionPerformed(ActionEvent e)
\r
684 zappoColour_actionPerformed();
\r
687 taylorColour.setText("Taylor");
\r
688 taylorColour.addActionListener(new java.awt.event.ActionListener()
\r
690 public void actionPerformed(ActionEvent e)
\r
692 taylorColour_actionPerformed();
\r
695 hydrophobicityColour.setText("Hydrophobicity");
\r
696 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
\r
698 public void actionPerformed(ActionEvent e)
\r
700 hydrophobicityColour_actionPerformed();
\r
703 helixColour.setText("Helix propensity");
\r
704 helixColour.addActionListener(new java.awt.event.ActionListener()
\r
706 public void actionPerformed(ActionEvent e)
\r
708 helixColour_actionPerformed();
\r
711 strandColour.setText("Strand propensity");
\r
712 strandColour.addActionListener(new java.awt.event.ActionListener()
\r
714 public void actionPerformed(ActionEvent e)
\r
716 strandColour_actionPerformed();
\r
719 turnColour.setText("Turn propensity");
\r
720 turnColour.addActionListener(new java.awt.event.ActionListener()
\r
722 public void actionPerformed(ActionEvent e)
\r
724 turnColour_actionPerformed();
\r
727 buriedColour.setText("Buried Index");
\r
728 buriedColour.addActionListener(new java.awt.event.ActionListener()
\r
730 public void actionPerformed(ActionEvent e)
\r
732 buriedColour_actionPerformed();
\r
735 abovePIDColour.setText("Above % Identity");
\r
736 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
\r
738 public void actionPerformed(ActionEvent e)
\r
740 abovePIDColour_actionPerformed();
\r
743 userDefinedColour.setText("User Defined...");
\r
744 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
\r
746 public void actionPerformed(ActionEvent e)
\r
748 userDefinedColour_actionPerformed(e);
\r
751 PIDColour.setText("Percentage Identity");
\r
752 PIDColour.addActionListener(new java.awt.event.ActionListener()
\r
754 public void actionPerformed(ActionEvent e)
\r
756 PIDColour_actionPerformed();
\r
759 BLOSUM62Colour.setText("BLOSUM62");
\r
760 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
\r
762 public void actionPerformed(ActionEvent e)
\r
764 BLOSUM62Colour_actionPerformed();
\r
767 conservationMenuItem.setText("Conservation");
\r
768 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
\r
770 public void actionPerformed(ActionEvent e)
\r
772 conservationMenuItem_actionPerformed();
\r
782 ap.paintAlignment(true);
\r
784 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
\r
790 * @param e DOCUMENT ME!
\r
792 protected void clustalColour_actionPerformed()
\r
794 SequenceGroup sg = getGroup();
\r
795 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
\r
796 ap.av.alignment.getWidth());
\r
803 * @param e DOCUMENT ME!
\r
805 protected void zappoColour_actionPerformed()
\r
807 getGroup().cs = new ZappoColourScheme();
\r
814 * @param e DOCUMENT ME!
\r
816 protected void taylorColour_actionPerformed()
\r
818 getGroup().cs = new TaylorColourScheme();
\r
825 * @param e DOCUMENT ME!
\r
827 protected void hydrophobicityColour_actionPerformed()
\r
829 getGroup().cs = new HydrophobicColourScheme();
\r
836 * @param e DOCUMENT ME!
\r
838 protected void helixColour_actionPerformed()
\r
840 getGroup().cs = new HelixColourScheme();
\r
847 * @param e DOCUMENT ME!
\r
849 protected void strandColour_actionPerformed()
\r
851 getGroup().cs = new StrandColourScheme();
\r
858 * @param e DOCUMENT ME!
\r
860 protected void turnColour_actionPerformed()
\r
862 getGroup().cs = new TurnColourScheme();
\r
869 * @param e DOCUMENT ME!
\r
871 protected void buriedColour_actionPerformed()
\r
873 getGroup().cs = new BuriedColourScheme();
\r
880 * @param e DOCUMENT ME!
\r
882 public void nucleotideMenuItem_actionPerformed()
\r
884 getGroup().cs = new NucleotideColourScheme();
\r
891 * @param e DOCUMENT ME!
\r
893 protected void abovePIDColour_actionPerformed()
\r
895 SequenceGroup sg = getGroup();
\r
901 if (abovePIDColour.isSelected())
\r
903 sg.cs.setConsensus(AAFrequency.calculate(
\r
904 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
\r
905 sg.getEndRes() + 1));
\r
907 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
\r
908 getGroup().getName());
\r
910 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
\r
912 SliderPanel.showPIDSlider();
\r
914 else // remove PIDColouring
\r
916 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
\r
925 * @param e DOCUMENT ME!
\r
927 protected void userDefinedColour_actionPerformed(ActionEvent e)
\r
929 SequenceGroup sg = getGroup();
\r
931 if (e.getActionCommand().equals("User Defined..."))
\r
933 new UserDefinedColours(ap, sg);
\r
937 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
\r
938 getUserColourSchemes().get(e.getActionCommand());
\r
948 * @param e DOCUMENT ME!
\r
950 protected void PIDColour_actionPerformed()
\r
952 SequenceGroup sg = getGroup();
\r
953 sg.cs = new PIDColourScheme();
\r
954 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
955 hiddenRepSequences),
\r
957 sg.getEndRes() + 1));
\r
964 * @param e DOCUMENT ME!
\r
966 protected void BLOSUM62Colour_actionPerformed()
\r
968 SequenceGroup sg = getGroup();
\r
970 sg.cs = new Blosum62ColourScheme();
\r
972 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
\r
973 hiddenRepSequences),
\r
975 sg.getEndRes() + 1));
\r
983 * @param e DOCUMENT ME!
\r
985 protected void noColourmenuItem_actionPerformed()
\r
987 getGroup().cs = null;
\r
994 * @param e DOCUMENT ME!
\r
996 protected void conservationMenuItem_actionPerformed()
\r
998 SequenceGroup sg = getGroup();
\r
1004 if (conservationMenuItem.isSelected())
\r
1006 Conservation c = new Conservation("Group",
\r
1007 ResidueProperties.propHash, 3,
\r
1008 sg.getSequences(ap.av.
\r
1009 hiddenRepSequences),
\r
1011 sg.getEndRes() + 1);
\r
1014 c.verdict(false, ap.av.ConsPercGaps);
\r
1016 sg.cs.setConservation(c);
\r
1018 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
\r
1019 SliderPanel.showConservationSlider();
\r
1021 else // remove ConservationColouring
\r
1023 sg.cs.setConservation(null);
\r
1029 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
\r
1031 SequenceGroup sg = getGroup();
\r
1037 AnnotationColourGradient acg = new AnnotationColourGradient(
\r
1038 sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
\r
1040 acg.predefinedColours = true;
\r
1049 * @param e DOCUMENT ME!
\r
1051 protected void groupName_actionPerformed()
\r
1054 SequenceGroup sg = getGroup();
\r
1055 EditNameDialog dialog = new EditNameDialog(sg.getName(),
\r
1056 sg.getDescription(),
\r
1058 "Group Description ",
\r
1059 "Edit Group Name/Description");
\r
1061 if (!dialog.accept)
\r
1066 sg.setName(dialog.getName());
\r
1067 sg.setDescription(dialog.getDescription());
\r
1073 * @return DOCUMENT ME!
\r
1075 SequenceGroup getGroup()
\r
1077 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1078 // this method won't add a new group if it already exists
\r
1081 ap.av.alignment.addGroup(sg);
\r
1090 * @param e DOCUMENT ME!
\r
1092 void sequenceName_actionPerformed()
\r
1094 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
\r
1095 sequence.getDescription(),
\r
1096 " Sequence Name ",
\r
1097 "Sequence Description ",
\r
1098 "Edit Sequence Name/Description");
\r
1100 if (!dialog.accept)
\r
1105 if (dialog.getName() != null)
\r
1107 if (dialog.getName().indexOf(" ") > -1)
\r
1109 JOptionPane.showMessageDialog(ap,
\r
1110 "Spaces have been converted to \"_\"",
\r
1111 "No spaces allowed in Sequence Name",
\r
1112 JOptionPane.WARNING_MESSAGE);
\r
1115 sequence.setName(dialog.getName().replace(' ', '_'));
\r
1116 ap.paintAlignment(false);
\r
1119 sequence.setDescription(dialog.getDescription());
\r
1121 ap.av.firePropertyChange("alignment", null,
\r
1122 ap.av.getAlignment().getSequences());
\r
1129 * @param e DOCUMENT ME!
\r
1131 void unGroupMenuItem_actionPerformed()
\r
1133 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1134 ap.av.alignment.deleteGroup(sg);
\r
1135 ap.av.setSelectionGroup(null);
\r
1142 * @param e DOCUMENT ME!
\r
1144 protected void outline_actionPerformed()
\r
1146 SequenceGroup sg = getGroup();
\r
1147 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
\r
1152 sg.setOutlineColour(col);
\r
1161 * @param e DOCUMENT ME!
\r
1163 public void showBoxes_actionPerformed()
\r
1165 getGroup().setDisplayBoxes(showBoxes.isSelected());
\r
1172 * @param e DOCUMENT ME!
\r
1174 public void showText_actionPerformed()
\r
1176 getGroup().setDisplayText(showText.isSelected());
\r
1183 * @param e DOCUMENT ME!
\r
1185 public void showColourText_actionPerformed()
\r
1187 getGroup().setColourText(showColourText.isSelected());
\r
1191 public void showLink(String url)
\r
1195 jalview.util.BrowserLauncher.openURL(url);
\r
1197 catch (Exception ex)
\r
1199 JOptionPane.showInternalMessageDialog(Desktop.desktop,
\r
1200 "Unixers: Couldn't find default web browser."
\r
1202 "\nAdd the full path to your browser in Preferences.",
\r
1203 "Web browser not found",
\r
1204 JOptionPane.WARNING_MESSAGE);
\r
1206 ex.printStackTrace();
\r
1210 void hideSequences(boolean representGroup)
\r
1212 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1213 if (sg == null || sg.getSize() < 1)
\r
1215 ap.av.hideSequence(new SequenceI[]
\r
1220 ap.av.setSelectionGroup(null);
\r
1222 if (representGroup)
\r
1224 ap.av.hideRepSequences(sequence, sg);
\r
1229 int gsize = sg.getSize();
\r
1230 SequenceI[] hseqs;
\r
1232 hseqs = new SequenceI[gsize];
\r
1235 for (int i = 0; i < gsize; i++)
\r
1237 hseqs[index++] = sg.getSequenceAt(i);
\r
1240 ap.av.hideSequence(hseqs);
\r
1243 public void copy_actionPerformed()
\r
1245 ap.alignFrame.copy_actionPerformed(null);
\r
1248 public void cut_actionPerformed()
\r
1250 ap.alignFrame.cut_actionPerformed(null);
\r
1253 void changeCase(ActionEvent e)
\r
1255 Object source = e.getSource();
\r
1256 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1260 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
\r
1261 sg.getStartRes(), sg.getEndRes() + 1);
\r
1263 String description;
\r
1266 if (source == toggle)
\r
1268 description = "Toggle Case";
\r
1269 caseChange = ChangeCaseCommand.TOGGLE_CASE;
\r
1271 else if (source == upperCase)
\r
1273 description = "To Upper Case";
\r
1274 caseChange = ChangeCaseCommand.TO_UPPER;
\r
1278 description = "To Lower Case";
\r
1279 caseChange = ChangeCaseCommand.TO_LOWER;
\r
1282 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
\r
1283 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1284 startEnd, caseChange
\r
1287 ap.alignFrame.addHistoryItem(caseCommand);
\r
1289 ap.av.firePropertyChange("alignment", null,
\r
1290 ap.av.getAlignment().getSequences());
\r
1295 public void outputText_actionPerformed(ActionEvent e)
\r
1297 CutAndPasteTransfer cap = new CutAndPasteTransfer();
\r
1298 cap.setForInput(null);
\r
1299 Desktop.addInternalFrame(cap,
\r
1300 "Alignment output - " + e.getActionCommand(), 600,
\r
1303 String[] omitHidden = null;
\r
1305 if (ap.av.hasHiddenColumns)
\r
1307 System.out.println("PROMPT USER HERE");
\r
1308 omitHidden = ap.av.getViewAsString(true);
\r
1311 cap.setText(new FormatAdapter().formatSequences(
\r
1312 e.getActionCommand(),
\r
1313 ap.av.getSelectionAsNewSequence(),
\r
1317 public void pdbFromFile_actionPerformed()
\r
1319 jalview.io.JalviewFileChooser chooser
\r
1320 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
\r
1322 "LAST_DIRECTORY"));
\r
1323 chooser.setFileView(new jalview.io.JalviewFileView());
\r
1324 chooser.setDialogTitle("Select a PDB file");
\r
1325 chooser.setToolTipText("Load a PDB file");
\r
1327 int value = chooser.showOpenDialog(null);
\r
1329 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
\r
1331 PDBEntry entry = new PDBEntry();
\r
1332 String choice = chooser.getSelectedFile().getPath();
\r
1333 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
\r
1336 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
\r
1337 jalview.io.AppletFormatAdapter.FILE);
\r
1339 if (pdbfile.id == null)
\r
1341 String reply = JOptionPane.showInternalInputDialog(
\r
1343 "Couldn't find a PDB id in the file supplied."
\r
1344 + "Please enter an Id to identify this structure.",
\r
1345 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
\r
1346 if (reply == null)
\r
1351 entry.setId(reply);
\r
1355 entry.setId(pdbfile.id);
\r
1358 catch (java.io.IOException ex)
\r
1360 ex.printStackTrace();
\r
1363 entry.setFile(choice);
\r
1364 sequence.getDatasetSequence().addPDBId(entry);
\r
1369 public void enterPDB_actionPerformed()
\r
1371 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
\r
1372 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
\r
1374 if (id != null && id.length() > 0)
\r
1376 PDBEntry entry = new PDBEntry();
\r
1377 entry.setId(id.toUpperCase());
\r
1378 sequence.getDatasetSequence()
\r
1383 public void discoverPDB_actionPerformed()
\r
1385 SequenceI[] sequences =
\r
1386 ap.av.selectionGroup == null ?
\r
1387 new Sequence[]{sequence}
\r
1388 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
\r
1390 new jalview.io.DBRefFetcher(sequences,
\r
1391 ap.alignFrame).fetchDBRefs(false);
\r
1394 public void sequenceFeature_actionPerformed()
\r
1396 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1402 int gSize = sg.getSize();
\r
1403 SequenceI[] seqs = new SequenceI[gSize];
\r
1404 SequenceFeature[] features = new SequenceFeature[gSize];
\r
1406 for (int i = 0; i < gSize; i++)
\r
1408 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
\r
1409 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
\r
1410 int end = sg.findEndRes(sg.getSequenceAt(i));
\r
1411 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
\r
1414 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
\r
1415 .amendFeatures(seqs, features, true, ap))
\r
1417 ap.alignFrame.showSeqFeatures.setSelected(true);
\r
1418 ap.av.setShowSequenceFeatures(true);
\r
1419 ap.highlightSearchResults(null);
\r
1423 public void textColour_actionPerformed()
\r
1425 SequenceGroup sg = getGroup();
\r
1428 new TextColourChooser().chooseColour(ap, sg);
\r
1432 public void colourByStructure(String pdbid)
\r
1434 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
\r
1435 .colourSequenceFromStructure(sequence, pdbid);
\r
1437 AlignmentAnnotation an = new AlignmentAnnotation(
\r
1438 "Structure", "Coloured by "+pdbid, anots);
\r
1440 ap.av.alignment.addAnnotation(an);
\r
1441 an.createSequenceMapping(sequence, 0, true);
\r
1442 //an.adjustForAlignment();
\r
1443 ap.av.alignment.setAnnotationIndex(an,0);
\r
1445 ap.adjustAnnotationHeight();
\r
1447 sequence.addAlignmentAnnotation(an);
\r
1451 public void editSequence_actionPerformed(ActionEvent actionEvent)
\r
1453 SequenceGroup sg = ap.av.getSelectionGroup();
\r
1457 if (sequence == null)
\r
1458 sequence = (Sequence) sg.getSequenceAt(0);
\r
1460 EditNameDialog dialog = new EditNameDialog(
\r
1461 sequence.getSequenceAsString(
\r
1463 sg.getEndRes() + 1),
\r
1469 if (dialog.accept)
\r
1471 EditCommand editCommand = new EditCommand(
\r
1472 "Edit Sequences", EditCommand.REPLACE,
\r
1473 dialog.getName().replace(' ', ap.av.getGapCharacter()),
\r
1474 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
\r
1475 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
\r
1478 ap.alignFrame.addHistoryItem(editCommand);
\r
1480 ap.av.firePropertyChange("alignment", null,
\r
1481 ap.av.getAlignment().getSequences());
\r