2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
3 * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 import java.awt.event.*;
28 import jalview.analysis.*;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
33 import jalview.util.UrlLink;
41 public class PopupMenu
44 JMenu groupMenu = new JMenu();
45 JMenuItem groupName = new JMenuItem();
46 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
47 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
48 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
49 protected JRadioButtonMenuItem hydrophobicityColour = new
50 JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
55 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
56 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
59 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
60 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
62 JMenu sequenceMenu = new JMenu();
63 JMenuItem sequenceName = new JMenuItem();
65 JMenuItem unGroupMenuItem = new JMenuItem();
66 JMenuItem outline = new JMenuItem();
67 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
68 JMenu colourMenu = new JMenu();
69 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
70 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
71 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
72 JMenu editMenu = new JMenu();
73 JMenuItem cut = new JMenuItem();
74 JMenuItem copy = new JMenuItem();
75 JMenuItem upperCase = new JMenuItem();
76 JMenuItem lowerCase = new JMenuItem();
77 JMenuItem toggle = new JMenuItem();
78 JMenu pdbMenu = new JMenu();
79 JMenuItem pdbFromFile = new JMenuItem();
80 JMenuItem enterPDB = new JMenuItem();
81 JMenuItem discoverPDB = new JMenuItem();
82 JMenu outputMenu = new JMenu();
83 JMenuItem sequenceFeature = new JMenuItem();
84 JMenuItem textColour = new JMenuItem();
85 JMenu jMenu1 = new JMenu();
86 JMenu structureMenu = new JMenu();
87 JMenu viewStructureMenu = new JMenu();
88 // JMenu colStructureMenu = new JMenu();
89 JMenuItem editSequence = new JMenuItem();
90 // JMenuItem annotationMenuItem = new JMenuItem();
93 * Creates a new PopupMenu object.
95 * @param ap DOCUMENT ME!
96 * @param seq DOCUMENT ME!
98 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
100 ///////////////////////////////////////////////////////////
101 // If this is activated from the sequence panel, the user may want to
102 // edit or annotate a particular residue. Therefore display the residue menu
104 // If from the IDPanel, we must display the sequence menu
105 //////////////////////////////////////////////////////////
109 ButtonGroup colours = new ButtonGroup();
110 colours.add(noColourmenuItem);
111 colours.add(clustalColour);
112 colours.add(zappoColour);
113 colours.add(taylorColour);
114 colours.add(hydrophobicityColour);
115 colours.add(helixColour);
116 colours.add(strandColour);
117 colours.add(turnColour);
118 colours.add(buriedColour);
119 colours.add(abovePIDColour);
120 colours.add(userDefinedColour);
121 colours.add(PIDColour);
122 colours.add(BLOSUM62Colour);
124 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
126 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
129 item.addActionListener(new java.awt.event.ActionListener()
131 public void actionPerformed(ActionEvent e)
133 outputText_actionPerformed(e);
137 outputMenu.add(item);
151 sequenceMenu.setText(sequence.getName());
154 if (seq.getDatasetSequence().getPDBId() != null
155 && seq.getDatasetSequence().getPDBId().size()>0)
157 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
160 while (e.hasMoreElements())
162 final PDBEntry pdb = (PDBEntry) e.nextElement();
164 menuItem = new JMenuItem();
165 menuItem.setText(pdb.getId());
166 menuItem.addActionListener(new java.awt.event.ActionListener()
168 public void actionPerformed(ActionEvent e)
170 Vector seqs = new Vector();
171 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
173 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
177 for(int p=0; p<pdbs.size(); p++)
179 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
180 if(p1.getId().equals(pdb.getId()))
182 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
183 seqs.addElement(ap.av.alignment.getSequenceAt(i));
190 SequenceI [] seqs2 = new SequenceI[seqs.size()];
193 new AppJmol(pdb, seqs2, null, ap);
194 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
197 viewStructureMenu.add(menuItem);
199 /* menuItem = new JMenuItem();
200 menuItem.setText(pdb.getId());
201 menuItem.addActionListener(new java.awt.event.ActionListener()
203 public void actionPerformed(ActionEvent e)
205 colourByStructure(pdb.getId());
208 colStructureMenu.add(menuItem);*/
213 structureMenu.remove(viewStructureMenu);
214 // structureMenu.remove(colStructureMenu);
217 menuItem = new JMenuItem("Hide Sequences");
218 menuItem.addActionListener(new java.awt.event.ActionListener()
220 public void actionPerformed(ActionEvent e)
222 hideSequences(false);
227 if (ap.av.getSelectionGroup() != null
228 && ap.av.getSelectionGroup().getSize() > 1)
230 menuItem = new JMenuItem("Represent Group with " + seq.getName());
231 menuItem.addActionListener(new java.awt.event.ActionListener()
233 public void actionPerformed(ActionEvent e)
238 sequenceMenu.add(menuItem);
241 if (ap.av.hasHiddenRows)
243 final int index = ap.av.alignment.findIndex(seq);
245 if (ap.av.adjustForHiddenSeqs(index) -
246 ap.av.adjustForHiddenSeqs(index - 1) > 1)
248 menuItem = new JMenuItem("Reveal Sequences");
249 menuItem.addActionListener(new ActionListener()
251 public void actionPerformed(ActionEvent e)
253 ap.av.showSequence(index);
254 if (ap.overviewPanel != null)
256 ap.overviewPanel.updateOverviewImage();
263 menuItem = new JMenuItem("Reveal All");
264 menuItem.addActionListener(new ActionListener()
266 public void actionPerformed(ActionEvent e)
268 ap.av.showAllHiddenSeqs();
269 if (ap.overviewPanel != null)
271 ap.overviewPanel.updateOverviewImage();
281 SequenceGroup sg = ap.av.getSelectionGroup();
285 groupName.setText(sg.getName());
287 if (sg.cs instanceof ZappoColourScheme)
289 zappoColour.setSelected(true);
291 else if (sg.cs instanceof TaylorColourScheme)
293 taylorColour.setSelected(true);
295 else if (sg.cs instanceof PIDColourScheme)
297 PIDColour.setSelected(true);
299 else if (sg.cs instanceof Blosum62ColourScheme)
301 BLOSUM62Colour.setSelected(true);
303 else if (sg.cs instanceof UserColourScheme)
305 userDefinedColour.setSelected(true);
307 else if (sg.cs instanceof HydrophobicColourScheme)
309 hydrophobicityColour.setSelected(true);
311 else if (sg.cs instanceof HelixColourScheme)
313 helixColour.setSelected(true);
315 else if (sg.cs instanceof StrandColourScheme)
317 strandColour.setSelected(true);
319 else if (sg.cs instanceof TurnColourScheme)
321 turnColour.setSelected(true);
323 else if (sg.cs instanceof BuriedColourScheme)
325 buriedColour.setSelected(true);
327 else if (sg.cs instanceof ClustalxColourScheme)
329 clustalColour.setSelected(true);
333 noColourmenuItem.setSelected(true);
336 if (sg.cs != null && sg.cs.conservationApplied())
338 conservationMenuItem.setSelected(true);
341 showText.setSelected(sg.getDisplayText());
342 showColourText.setSelected(sg.getColourText());
343 showBoxes.setSelected(sg.getDisplayBoxes());
347 groupMenu.setVisible(false);
348 editMenu.setVisible(false);
351 if (!ap.av.alignment.getGroups().contains(sg))
353 unGroupMenuItem.setVisible(false);
358 sequenceMenu.setVisible(false);
359 structureMenu.setVisible(false);
362 if (links != null && links.size() > 0)
364 JMenu linkMenu = new JMenu("Link");
366 for (int i = 0; i < links.size(); i++)
368 String link = links.elementAt(i).toString();
369 UrlLink urlLink = null;
371 urlLink = new UrlLink(link);
372 } catch (Exception foo) {
373 jalview.bin.Cache.log.error("Exception for URLLink '"+link+"'",foo);
376 if (!urlLink.isValid())
378 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
381 final String label = urlLink.getLabel();
382 if (urlLink.isDynamic())
385 // collect matching db-refs
386 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{urlLink.getTarget()});
387 // collect id string too
388 String id = seq.getName();
391 for (int r=0;r<dbr.length; r++)
393 if (id!=null && dbr[r].getAccessionId().equals(id))
395 // suppress duplicate link creation for the bare sequence ID string with this link
398 // create Bare ID link for this RUL
399 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
402 for (int u=0; u<urls.length; u+=2)
404 addshowLink(linkMenu, label+"|"+urls[u],urls[u+1]);
411 // create Bare ID link for this RUL
412 String[] urls = urlLink.makeUrls(id, true);
415 for (int u=0; u<urls.length; u+=2)
417 addshowLink(linkMenu, label, urls[u+1]);
423 // Add a non-dynamic link
424 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
427 if (sequence != null)
429 sequenceMenu.add(linkMenu);
439 * add a show URL menu item to the given linkMenu
441 * @param label - menu label string
442 * @param url - url to open
444 private void addshowLink(JMenu linkMenu, String label, final String url)
446 JMenuItem item = new JMenuItem(label);
447 item.setToolTipText("open URL: "+url);
448 item.addActionListener(new java.awt.event.ActionListener()
450 public void actionPerformed(ActionEvent e)
452 new Thread(new Runnable() {
469 * @throws Exception DOCUMENT ME!
471 private void jbInit()
474 groupMenu.setText("Group");
475 groupMenu.setText("Selection");
476 groupName.setText("Name");
477 groupName.addActionListener(new java.awt.event.ActionListener()
479 public void actionPerformed(ActionEvent e)
481 groupName_actionPerformed();
484 sequenceMenu.setText("Sequence");
485 sequenceName.setText("Edit Name/Description");
486 sequenceName.addActionListener(new java.awt.event.ActionListener()
488 public void actionPerformed(ActionEvent e)
490 sequenceName_actionPerformed();
493 PIDColour.setFocusPainted(false);
494 unGroupMenuItem.setText("Remove Group");
495 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
497 public void actionPerformed(ActionEvent e)
499 unGroupMenuItem_actionPerformed();
503 outline.setText("Border colour");
504 outline.addActionListener(new java.awt.event.ActionListener()
506 public void actionPerformed(ActionEvent e)
508 outline_actionPerformed();
511 nucleotideMenuItem.setText("Nucleotide");
512 nucleotideMenuItem.addActionListener(new ActionListener()
514 public void actionPerformed(ActionEvent e)
516 nucleotideMenuItem_actionPerformed();
519 colourMenu.setText("Group Colour");
520 showBoxes.setText("Boxes");
521 showBoxes.setState(true);
522 showBoxes.addActionListener(new ActionListener()
524 public void actionPerformed(ActionEvent e)
526 showBoxes_actionPerformed();
529 showText.setText("Text");
530 showText.setState(true);
531 showText.addActionListener(new ActionListener()
533 public void actionPerformed(ActionEvent e)
535 showText_actionPerformed();
538 showColourText.setText("Colour Text");
539 showColourText.addActionListener(new ActionListener()
541 public void actionPerformed(ActionEvent e)
543 showColourText_actionPerformed();
546 editMenu.setText("Edit");
548 cut.addActionListener(new ActionListener()
550 public void actionPerformed(ActionEvent e)
552 cut_actionPerformed();
555 upperCase.setText("To Upper Case");
556 upperCase.addActionListener(new ActionListener()
558 public void actionPerformed(ActionEvent e)
563 copy.setText("Copy");
564 copy.addActionListener(new ActionListener()
566 public void actionPerformed(ActionEvent e)
568 copy_actionPerformed();
571 lowerCase.setText("To Lower Case");
572 lowerCase.addActionListener(new ActionListener()
574 public void actionPerformed(ActionEvent e)
579 toggle.setText("Toggle Case");
580 toggle.addActionListener(new ActionListener()
582 public void actionPerformed(ActionEvent e)
587 pdbMenu.setText("Associate Structure with Sequence");
588 pdbFromFile.setText("From File");
589 pdbFromFile.addActionListener(new ActionListener()
591 public void actionPerformed(ActionEvent e)
593 pdbFromFile_actionPerformed();
596 enterPDB.setText("Enter PDB Id");
597 enterPDB.addActionListener(new ActionListener()
599 public void actionPerformed(ActionEvent e)
601 enterPDB_actionPerformed();
604 discoverPDB.setText("Discover PDB ids");
605 discoverPDB.addActionListener(new ActionListener()
607 public void actionPerformed(ActionEvent e)
609 discoverPDB_actionPerformed();
612 outputMenu.setText("Output to Textbox...");
613 sequenceFeature.setText("Create Sequence Feature");
614 sequenceFeature.addActionListener(new ActionListener()
616 public void actionPerformed(ActionEvent e)
618 sequenceFeature_actionPerformed();
621 textColour.setText("Text Colour");
622 textColour.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 textColour_actionPerformed();
629 jMenu1.setText("Group");
630 structureMenu.setText("Structure");
631 viewStructureMenu.setText("View Structure");
632 // colStructureMenu.setText("Colour By Structure");
633 editSequence.setText("Edit Sequence...");
634 editSequence.addActionListener(new ActionListener()
636 public void actionPerformed(ActionEvent actionEvent)
638 editSequence_actionPerformed(actionEvent);
641 /* annotationMenuItem.setText("By Annotation");
642 annotationMenuItem.addActionListener(new ActionListener()
644 public void actionPerformed(ActionEvent actionEvent)
646 annotationMenuItem_actionPerformed(actionEvent);
653 this.add(structureMenu);
654 groupMenu.add(editMenu);
655 groupMenu.add(outputMenu);
656 groupMenu.add(sequenceFeature);
657 groupMenu.add(jMenu1);
658 sequenceMenu.add(sequenceName);
659 colourMenu.add(textColour);
660 colourMenu.add(noColourmenuItem);
661 colourMenu.add(clustalColour);
662 colourMenu.add(BLOSUM62Colour);
663 colourMenu.add(PIDColour);
664 colourMenu.add(zappoColour);
665 colourMenu.add(taylorColour);
666 colourMenu.add(hydrophobicityColour);
667 colourMenu.add(helixColour);
668 colourMenu.add(strandColour);
669 colourMenu.add(turnColour);
670 colourMenu.add(buriedColour);
671 colourMenu.add(nucleotideMenuItem);
672 colourMenu.add(userDefinedColour);
674 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
676 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
677 getUserColourSchemes().keys();
679 while (userColours.hasMoreElements())
681 JMenuItem item = new JMenuItem(userColours.
682 nextElement().toString());
683 item.addActionListener(new ActionListener()
685 public void actionPerformed(ActionEvent evt)
687 userDefinedColour_actionPerformed(evt);
690 colourMenu.add(item);
694 colourMenu.addSeparator();
695 colourMenu.add(abovePIDColour);
696 colourMenu.add(conservationMenuItem);
697 //colourMenu.add(annotationMenuItem);
700 editMenu.add(editSequence);
701 editMenu.add(upperCase);
702 editMenu.add(lowerCase);
703 editMenu.add(toggle);
704 pdbMenu.add(pdbFromFile);
705 pdbMenu.add(enterPDB);
706 pdbMenu.add(discoverPDB);
707 jMenu1.add(groupName);
708 jMenu1.add(unGroupMenuItem);
709 jMenu1.add(colourMenu);
710 jMenu1.add(showBoxes);
711 jMenu1.add(showText);
712 jMenu1.add(showColourText);
714 structureMenu.add(pdbMenu);
715 structureMenu.add(viewStructureMenu);
716 // structureMenu.add(colStructureMenu);
717 noColourmenuItem.setText("None");
718 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
720 public void actionPerformed(ActionEvent e)
722 noColourmenuItem_actionPerformed();
726 clustalColour.setText("Clustalx colours");
727 clustalColour.addActionListener(new java.awt.event.ActionListener()
729 public void actionPerformed(ActionEvent e)
731 clustalColour_actionPerformed();
734 zappoColour.setText("Zappo");
735 zappoColour.addActionListener(new java.awt.event.ActionListener()
737 public void actionPerformed(ActionEvent e)
739 zappoColour_actionPerformed();
742 taylorColour.setText("Taylor");
743 taylorColour.addActionListener(new java.awt.event.ActionListener()
745 public void actionPerformed(ActionEvent e)
747 taylorColour_actionPerformed();
750 hydrophobicityColour.setText("Hydrophobicity");
751 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
753 public void actionPerformed(ActionEvent e)
755 hydrophobicityColour_actionPerformed();
758 helixColour.setText("Helix propensity");
759 helixColour.addActionListener(new java.awt.event.ActionListener()
761 public void actionPerformed(ActionEvent e)
763 helixColour_actionPerformed();
766 strandColour.setText("Strand propensity");
767 strandColour.addActionListener(new java.awt.event.ActionListener()
769 public void actionPerformed(ActionEvent e)
771 strandColour_actionPerformed();
774 turnColour.setText("Turn propensity");
775 turnColour.addActionListener(new java.awt.event.ActionListener()
777 public void actionPerformed(ActionEvent e)
779 turnColour_actionPerformed();
782 buriedColour.setText("Buried Index");
783 buriedColour.addActionListener(new java.awt.event.ActionListener()
785 public void actionPerformed(ActionEvent e)
787 buriedColour_actionPerformed();
790 abovePIDColour.setText("Above % Identity");
791 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
793 public void actionPerformed(ActionEvent e)
795 abovePIDColour_actionPerformed();
798 userDefinedColour.setText("User Defined...");
799 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
801 public void actionPerformed(ActionEvent e)
803 userDefinedColour_actionPerformed(e);
806 PIDColour.setText("Percentage Identity");
807 PIDColour.addActionListener(new java.awt.event.ActionListener()
809 public void actionPerformed(ActionEvent e)
811 PIDColour_actionPerformed();
814 BLOSUM62Colour.setText("BLOSUM62");
815 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
817 public void actionPerformed(ActionEvent e)
819 BLOSUM62Colour_actionPerformed();
822 conservationMenuItem.setText("Conservation");
823 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
825 public void actionPerformed(ActionEvent e)
827 conservationMenuItem_actionPerformed();
837 ap.paintAlignment(true);
839 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
845 * @param e DOCUMENT ME!
847 protected void clustalColour_actionPerformed()
849 SequenceGroup sg = getGroup();
850 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
851 ap.av.alignment.getWidth());
858 * @param e DOCUMENT ME!
860 protected void zappoColour_actionPerformed()
862 getGroup().cs = new ZappoColourScheme();
869 * @param e DOCUMENT ME!
871 protected void taylorColour_actionPerformed()
873 getGroup().cs = new TaylorColourScheme();
880 * @param e DOCUMENT ME!
882 protected void hydrophobicityColour_actionPerformed()
884 getGroup().cs = new HydrophobicColourScheme();
891 * @param e DOCUMENT ME!
893 protected void helixColour_actionPerformed()
895 getGroup().cs = new HelixColourScheme();
902 * @param e DOCUMENT ME!
904 protected void strandColour_actionPerformed()
906 getGroup().cs = new StrandColourScheme();
913 * @param e DOCUMENT ME!
915 protected void turnColour_actionPerformed()
917 getGroup().cs = new TurnColourScheme();
924 * @param e DOCUMENT ME!
926 protected void buriedColour_actionPerformed()
928 getGroup().cs = new BuriedColourScheme();
935 * @param e DOCUMENT ME!
937 public void nucleotideMenuItem_actionPerformed()
939 getGroup().cs = new NucleotideColourScheme();
946 * @param e DOCUMENT ME!
948 protected void abovePIDColour_actionPerformed()
950 SequenceGroup sg = getGroup();
956 if (abovePIDColour.isSelected())
958 sg.cs.setConsensus(AAFrequency.calculate(
959 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
960 sg.getEndRes() + 1));
962 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
963 getGroup().getName());
965 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
967 SliderPanel.showPIDSlider();
969 else // remove PIDColouring
971 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
980 * @param e DOCUMENT ME!
982 protected void userDefinedColour_actionPerformed(ActionEvent e)
984 SequenceGroup sg = getGroup();
986 if (e.getActionCommand().equals("User Defined..."))
988 new UserDefinedColours(ap, sg);
992 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
993 getUserColourSchemes().get(e.getActionCommand());
1003 * @param e DOCUMENT ME!
1005 protected void PIDColour_actionPerformed()
1007 SequenceGroup sg = getGroup();
1008 sg.cs = new PIDColourScheme();
1009 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1010 hiddenRepSequences),
1012 sg.getEndRes() + 1));
1019 * @param e DOCUMENT ME!
1021 protected void BLOSUM62Colour_actionPerformed()
1023 SequenceGroup sg = getGroup();
1025 sg.cs = new Blosum62ColourScheme();
1027 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1028 hiddenRepSequences),
1030 sg.getEndRes() + 1));
1038 * @param e DOCUMENT ME!
1040 protected void noColourmenuItem_actionPerformed()
1042 getGroup().cs = null;
1049 * @param e DOCUMENT ME!
1051 protected void conservationMenuItem_actionPerformed()
1053 SequenceGroup sg = getGroup();
1059 if (conservationMenuItem.isSelected())
1061 Conservation c = new Conservation("Group",
1062 ResidueProperties.propHash, 3,
1063 sg.getSequences(ap.av.
1064 hiddenRepSequences),
1066 sg.getEndRes() + 1);
1069 c.verdict(false, ap.av.ConsPercGaps);
1071 sg.cs.setConservation(c);
1073 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1074 SliderPanel.showConservationSlider();
1076 else // remove ConservationColouring
1078 sg.cs.setConservation(null);
1084 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1086 SequenceGroup sg = getGroup();
1092 AnnotationColourGradient acg = new AnnotationColourGradient(
1093 sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
1095 acg.predefinedColours = true;
1104 * @param e DOCUMENT ME!
1106 protected void groupName_actionPerformed()
1109 SequenceGroup sg = getGroup();
1110 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1111 sg.getDescription(),
1113 "Group Description ",
1114 "Edit Group Name/Description");
1121 sg.setName(dialog.getName());
1122 sg.setDescription(dialog.getDescription());
1128 * @return DOCUMENT ME!
1130 SequenceGroup getGroup()
1132 SequenceGroup sg = ap.av.getSelectionGroup();
1133 // this method won't add a new group if it already exists
1136 ap.av.alignment.addGroup(sg);
1145 * @param e DOCUMENT ME!
1147 void sequenceName_actionPerformed()
1149 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1150 sequence.getDescription(),
1152 "Sequence Description ",
1153 "Edit Sequence Name/Description");
1160 if (dialog.getName() != null)
1162 if (dialog.getName().indexOf(" ") > -1)
1164 JOptionPane.showMessageDialog(ap,
1165 "Spaces have been converted to \"_\"",
1166 "No spaces allowed in Sequence Name",
1167 JOptionPane.WARNING_MESSAGE);
1170 sequence.setName(dialog.getName().replace(' ', '_'));
1171 ap.paintAlignment(false);
1174 sequence.setDescription(dialog.getDescription());
1176 ap.av.firePropertyChange("alignment", null,
1177 ap.av.getAlignment().getSequences());
1184 * @param e DOCUMENT ME!
1186 void unGroupMenuItem_actionPerformed()
1188 SequenceGroup sg = ap.av.getSelectionGroup();
1189 ap.av.alignment.deleteGroup(sg);
1190 ap.av.setSelectionGroup(null);
1197 * @param e DOCUMENT ME!
1199 protected void outline_actionPerformed()
1201 SequenceGroup sg = getGroup();
1202 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1207 sg.setOutlineColour(col);
1216 * @param e DOCUMENT ME!
1218 public void showBoxes_actionPerformed()
1220 getGroup().setDisplayBoxes(showBoxes.isSelected());
1227 * @param e DOCUMENT ME!
1229 public void showText_actionPerformed()
1231 getGroup().setDisplayText(showText.isSelected());
1238 * @param e DOCUMENT ME!
1240 public void showColourText_actionPerformed()
1242 getGroup().setColourText(showColourText.isSelected());
1246 public void showLink(String url)
1250 jalview.util.BrowserLauncher.openURL(url);
1252 catch (Exception ex)
1254 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1255 "Unixers: Couldn't find default web browser."
1257 "\nAdd the full path to your browser in Preferences.",
1258 "Web browser not found",
1259 JOptionPane.WARNING_MESSAGE);
1261 ex.printStackTrace();
1265 void hideSequences(boolean representGroup)
1267 SequenceGroup sg = ap.av.getSelectionGroup();
1268 if (sg == null || sg.getSize() < 1)
1270 ap.av.hideSequence(new SequenceI[]
1275 ap.av.setSelectionGroup(null);
1279 ap.av.hideRepSequences(sequence, sg);
1284 int gsize = sg.getSize();
1287 hseqs = new SequenceI[gsize];
1290 for (int i = 0; i < gsize; i++)
1292 hseqs[index++] = sg.getSequenceAt(i);
1295 ap.av.hideSequence(hseqs);
1298 public void copy_actionPerformed()
1300 ap.alignFrame.copy_actionPerformed(null);
1303 public void cut_actionPerformed()
1305 ap.alignFrame.cut_actionPerformed(null);
1308 void changeCase(ActionEvent e)
1310 Object source = e.getSource();
1311 SequenceGroup sg = ap.av.getSelectionGroup();
1315 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
1316 sg.getStartRes(), sg.getEndRes() + 1);
1321 if (source == toggle)
1323 description = "Toggle Case";
1324 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1326 else if (source == upperCase)
1328 description = "To Upper Case";
1329 caseChange = ChangeCaseCommand.TO_UPPER;
1333 description = "To Lower Case";
1334 caseChange = ChangeCaseCommand.TO_LOWER;
1337 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
1338 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1339 startEnd, caseChange
1342 ap.alignFrame.addHistoryItem(caseCommand);
1344 ap.av.firePropertyChange("alignment", null,
1345 ap.av.getAlignment().getSequences());
1350 public void outputText_actionPerformed(ActionEvent e)
1352 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1353 cap.setForInput(null);
1354 Desktop.addInternalFrame(cap,
1355 "Alignment output - " + e.getActionCommand(), 600,
1358 String[] omitHidden = null;
1360 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
1361 SequenceGroup sg = ap.av.getSelectionGroup();
1362 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1363 omitHidden = ap.av.getViewAsString(true);
1364 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1365 AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1366 for (int i=0; i<nala.length; i++)
1368 AlignmentAnnotation na =nala[i];
1369 oal.addAnnotation(na);
1371 cap.setText(new FormatAdapter().formatSequences(
1372 e.getActionCommand(),
1374 omitHidden, csel, sg));
1378 public void pdbFromFile_actionPerformed()
1380 jalview.io.JalviewFileChooser chooser
1381 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1384 chooser.setFileView(new jalview.io.JalviewFileView());
1385 chooser.setDialogTitle("Select a PDB file");
1386 chooser.setToolTipText("Load a PDB file");
1388 int value = chooser.showOpenDialog(null);
1390 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1392 PDBEntry entry = new PDBEntry();
1393 String choice = chooser.getSelectedFile().getPath();
1394 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1397 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1398 jalview.io.AppletFormatAdapter.FILE);
1400 if (pdbfile.id == null)
1402 String reply = JOptionPane.showInternalInputDialog(
1404 "Couldn't find a PDB id in the file supplied."
1405 + "Please enter an Id to identify this structure.",
1406 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1416 entry.setId(pdbfile.id);
1419 catch (java.io.IOException ex)
1421 ex.printStackTrace();
1424 entry.setFile(choice);
1425 sequence.getDatasetSequence().addPDBId(entry);
1430 public void enterPDB_actionPerformed()
1432 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1433 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1435 if (id != null && id.length() > 0)
1437 PDBEntry entry = new PDBEntry();
1438 entry.setId(id.toUpperCase());
1439 sequence.getDatasetSequence()
1444 public void discoverPDB_actionPerformed()
1447 final SequenceI[] sequences =
1448 ((ap.av.selectionGroup == null)
1449 ? new Sequence[]{sequence}
1450 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1451 Thread discpdb = new Thread(new Runnable() {
1455 new jalview.ws.DBRefFetcher(sequences,
1456 ap.alignFrame).fetchDBRefs(false);
1463 public void sequenceFeature_actionPerformed()
1465 SequenceGroup sg = ap.av.getSelectionGroup();
1471 int gSize = sg.getSize();
1472 SequenceI[] seqs = new SequenceI[gSize];
1473 SequenceFeature[] features = new SequenceFeature[gSize];
1475 for (int i = 0; i < gSize; i++)
1477 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1478 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1479 int end = sg.findEndRes(sg.getSequenceAt(i));
1480 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
1483 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
1484 .amendFeatures(seqs, features, true, ap))
1486 ap.alignFrame.showSeqFeatures.setSelected(true);
1487 ap.av.setShowSequenceFeatures(true);
1488 ap.highlightSearchResults(null);
1492 public void textColour_actionPerformed()
1494 SequenceGroup sg = getGroup();
1497 new TextColourChooser().chooseColour(ap, sg);
1501 public void colourByStructure(String pdbid)
1503 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
1504 .colourSequenceFromStructure(sequence, pdbid);
1506 AlignmentAnnotation an = new AlignmentAnnotation(
1507 "Structure", "Coloured by "+pdbid, anots);
1509 ap.av.alignment.addAnnotation(an);
1510 an.createSequenceMapping(sequence, 0, true);
1511 //an.adjustForAlignment();
1512 ap.av.alignment.setAnnotationIndex(an,0);
1514 ap.adjustAnnotationHeight();
1516 sequence.addAlignmentAnnotation(an);
1520 public void editSequence_actionPerformed(ActionEvent actionEvent)
1522 SequenceGroup sg = ap.av.getSelectionGroup();
1526 if (sequence == null)
1527 sequence = (Sequence) sg.getSequenceAt(0);
1529 EditNameDialog dialog = new EditNameDialog(
1530 sequence.getSequenceAsString(
1532 sg.getEndRes() + 1),
1540 EditCommand editCommand = new EditCommand(
1541 "Edit Sequences", EditCommand.REPLACE,
1542 dialog.getName().replace(' ', ap.av.getGapCharacter()),
1543 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1544 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
1547 ap.alignFrame.addHistoryItem(editCommand);
1549 ap.av.firePropertyChange("alignment", null,
1550 ap.av.getAlignment().getSequences());