2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 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.*;
40 public class PopupMenu
43 JMenu groupMenu = new JMenu();
44 JMenuItem groupName = new JMenuItem();
45 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
46 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
47 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
48 protected JRadioButtonMenuItem hydrophobicityColour = new
49 JRadioButtonMenuItem();
50 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
52 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
54 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
55 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
58 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
59 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
61 JMenu sequenceMenu = new JMenu();
62 JMenuItem sequenceName = new JMenuItem();
64 JMenuItem unGroupMenuItem = new JMenuItem();
65 JMenuItem outline = new JMenuItem();
66 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
67 JMenu colourMenu = new JMenu();
68 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
69 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
70 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
71 JMenu editMenu = new JMenu();
72 JMenuItem cut = new JMenuItem();
73 JMenuItem copy = new JMenuItem();
74 JMenuItem upperCase = new JMenuItem();
75 JMenuItem lowerCase = new JMenuItem();
76 JMenuItem toggle = new JMenuItem();
77 JMenu pdbMenu = new JMenu();
78 JMenuItem pdbFromFile = new JMenuItem();
79 JMenuItem enterPDB = new JMenuItem();
80 JMenuItem discoverPDB = new JMenuItem();
81 JMenu outputMenu = new JMenu();
82 JMenuItem sequenceFeature = new JMenuItem();
83 JMenuItem textColour = new JMenuItem();
84 JMenu jMenu1 = new JMenu();
85 JMenu structureMenu = new JMenu();
86 JMenu viewStructureMenu = new JMenu();
87 // JMenu colStructureMenu = new JMenu();
88 JMenuItem editSequence = new JMenuItem();
89 // JMenuItem annotationMenuItem = new JMenuItem();
92 * Creates a new PopupMenu object.
94 * @param ap DOCUMENT ME!
95 * @param seq DOCUMENT ME!
97 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
99 ///////////////////////////////////////////////////////////
100 // If this is activated from the sequence panel, the user may want to
101 // edit or annotate a particular residue. Therefore display the residue menu
103 // If from the IDPanel, we must display the sequence menu
104 //////////////////////////////////////////////////////////
108 ButtonGroup colours = new ButtonGroup();
109 colours.add(noColourmenuItem);
110 colours.add(clustalColour);
111 colours.add(zappoColour);
112 colours.add(taylorColour);
113 colours.add(hydrophobicityColour);
114 colours.add(helixColour);
115 colours.add(strandColour);
116 colours.add(turnColour);
117 colours.add(buriedColour);
118 colours.add(abovePIDColour);
119 colours.add(userDefinedColour);
120 colours.add(PIDColour);
121 colours.add(BLOSUM62Colour);
123 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
125 JMenuItem item = new JMenuItem(jalview.io.FormatAdapter.WRITEABLE_FORMATS[
128 item.addActionListener(new java.awt.event.ActionListener()
130 public void actionPerformed(ActionEvent e)
132 outputText_actionPerformed(e);
136 outputMenu.add(item);
150 sequenceMenu.setText(sequence.getName());
153 if (seq.getDatasetSequence().getPDBId() != null
154 && seq.getDatasetSequence().getPDBId().size()>0)
156 java.util.Enumeration e = seq.getDatasetSequence().getPDBId().
159 while (e.hasMoreElements())
161 final PDBEntry pdb = (PDBEntry) e.nextElement();
163 menuItem = new JMenuItem();
164 menuItem.setText(pdb.getId());
165 menuItem.addActionListener(new java.awt.event.ActionListener()
167 public void actionPerformed(ActionEvent e)
169 Vector seqs = new Vector();
170 for (int i = 0; i < ap.av.alignment.getHeight(); i++)
172 Vector pdbs = ap.av.alignment.getSequenceAt(i).getDatasetSequence().getPDBId();
176 for(int p=0; p<pdbs.size(); p++)
178 PDBEntry p1 = (PDBEntry)pdbs.elementAt(p);
179 if(p1.getId().equals(pdb.getId()))
181 if (!seqs.contains(ap.av.alignment.getSequenceAt(i)))
182 seqs.addElement(ap.av.alignment.getSequenceAt(i));
189 SequenceI [] seqs2 = new SequenceI[seqs.size()];
192 new AppJmol(pdb, seqs2, null, ap);
193 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
196 viewStructureMenu.add(menuItem);
198 /* menuItem = new JMenuItem();
199 menuItem.setText(pdb.getId());
200 menuItem.addActionListener(new java.awt.event.ActionListener()
202 public void actionPerformed(ActionEvent e)
204 colourByStructure(pdb.getId());
207 colStructureMenu.add(menuItem);*/
212 structureMenu.remove(viewStructureMenu);
213 // structureMenu.remove(colStructureMenu);
216 menuItem = new JMenuItem("Hide Sequences");
217 menuItem.addActionListener(new java.awt.event.ActionListener()
219 public void actionPerformed(ActionEvent e)
221 hideSequences(false);
226 if (ap.av.getSelectionGroup() != null
227 && ap.av.getSelectionGroup().getSize() > 1)
229 menuItem = new JMenuItem("Represent Group with " + seq.getName());
230 menuItem.addActionListener(new java.awt.event.ActionListener()
232 public void actionPerformed(ActionEvent e)
237 sequenceMenu.add(menuItem);
240 if (ap.av.hasHiddenRows)
242 final int index = ap.av.alignment.findIndex(seq);
244 if (ap.av.adjustForHiddenSeqs(index) -
245 ap.av.adjustForHiddenSeqs(index - 1) > 1)
247 menuItem = new JMenuItem("Reveal Sequences");
248 menuItem.addActionListener(new ActionListener()
250 public void actionPerformed(ActionEvent e)
252 ap.av.showSequence(index);
253 if (ap.overviewPanel != null)
255 ap.overviewPanel.updateOverviewImage();
262 menuItem = new JMenuItem("Reveal All");
263 menuItem.addActionListener(new ActionListener()
265 public void actionPerformed(ActionEvent e)
267 ap.av.showAllHiddenSeqs();
268 if (ap.overviewPanel != null)
270 ap.overviewPanel.updateOverviewImage();
280 SequenceGroup sg = ap.av.getSelectionGroup();
284 groupName.setText(sg.getName());
286 if (sg.cs instanceof ZappoColourScheme)
288 zappoColour.setSelected(true);
290 else if (sg.cs instanceof TaylorColourScheme)
292 taylorColour.setSelected(true);
294 else if (sg.cs instanceof PIDColourScheme)
296 PIDColour.setSelected(true);
298 else if (sg.cs instanceof Blosum62ColourScheme)
300 BLOSUM62Colour.setSelected(true);
302 else if (sg.cs instanceof UserColourScheme)
304 userDefinedColour.setSelected(true);
306 else if (sg.cs instanceof HydrophobicColourScheme)
308 hydrophobicityColour.setSelected(true);
310 else if (sg.cs instanceof HelixColourScheme)
312 helixColour.setSelected(true);
314 else if (sg.cs instanceof StrandColourScheme)
316 strandColour.setSelected(true);
318 else if (sg.cs instanceof TurnColourScheme)
320 turnColour.setSelected(true);
322 else if (sg.cs instanceof BuriedColourScheme)
324 buriedColour.setSelected(true);
326 else if (sg.cs instanceof ClustalxColourScheme)
328 clustalColour.setSelected(true);
332 noColourmenuItem.setSelected(true);
335 if (sg.cs != null && sg.cs.conservationApplied())
337 conservationMenuItem.setSelected(true);
340 showText.setSelected(sg.getDisplayText());
341 showColourText.setSelected(sg.getColourText());
342 showBoxes.setSelected(sg.getDisplayBoxes());
346 groupMenu.setVisible(false);
347 editMenu.setVisible(false);
350 if (!ap.av.alignment.getGroups().contains(sg))
352 unGroupMenuItem.setVisible(false);
357 sequenceMenu.setVisible(false);
358 structureMenu.setVisible(false);
361 if (links != null && links.size() > 0)
363 JMenu linkMenu = new JMenu("Link");
365 for (int i = 0; i < links.size(); i++)
367 String link = links.elementAt(i).toString();
368 final String label = link.substring(0, link.indexOf("|"));
371 if (link.indexOf("$SEQUENCE_ID$") > -1)
373 // Substitute SEQUENCE_ID string and any matching database reference accessions
374 String url_pref = link.substring(link.indexOf("|") + 1,
375 link.indexOf("$SEQUENCE_ID$"));
377 String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
379 // collect matching db-refs
380 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new String[]{label});
381 // collect id string too
382 String id = seq.getName();
383 if (id.indexOf("|") > -1)
385 id = id.substring(id.lastIndexOf("|") + 1);
390 for (int r=0;r<dbr.length; r++)
392 if (dbr[r].getAccessionId().equals(id))
394 // suppress duplicate link creation for the bare sequence ID string with this link
397 addshowLink(linkMenu, dbr[r].getSource()+"|"+dbr[r].getAccessionId(),
398 url_pref+dbr[r].getAccessionId()+url_suff);
403 // create Bare ID link for this RUL
404 addshowLink(linkMenu, label, url_pref + id + url_suff);
409 // Add a non-dynamic link
410 addshowLink(linkMenu, label, link.substring(link.lastIndexOf("|") + 1));
413 if (sequence != null)
415 sequenceMenu.add(linkMenu);
425 * add a show URL menu item to the given linkMenu
427 * @param label - menu label string
428 * @param url - url to open
430 private void addshowLink(JMenu linkMenu, String label, final String url)
432 JMenuItem item = new JMenuItem(label);
433 item.addActionListener(new java.awt.event.ActionListener()
435 public void actionPerformed(ActionEvent e)
437 new Thread(new Runnable() {
454 * @throws Exception DOCUMENT ME!
456 private void jbInit()
459 groupMenu.setText("Group");
460 groupMenu.setText("Selection");
461 groupName.setText("Name");
462 groupName.addActionListener(new java.awt.event.ActionListener()
464 public void actionPerformed(ActionEvent e)
466 groupName_actionPerformed();
469 sequenceMenu.setText("Sequence");
470 sequenceName.setText("Edit Name/Description");
471 sequenceName.addActionListener(new java.awt.event.ActionListener()
473 public void actionPerformed(ActionEvent e)
475 sequenceName_actionPerformed();
478 PIDColour.setFocusPainted(false);
479 unGroupMenuItem.setText("Remove Group");
480 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
482 public void actionPerformed(ActionEvent e)
484 unGroupMenuItem_actionPerformed();
488 outline.setText("Border colour");
489 outline.addActionListener(new java.awt.event.ActionListener()
491 public void actionPerformed(ActionEvent e)
493 outline_actionPerformed();
496 nucleotideMenuItem.setText("Nucleotide");
497 nucleotideMenuItem.addActionListener(new ActionListener()
499 public void actionPerformed(ActionEvent e)
501 nucleotideMenuItem_actionPerformed();
504 colourMenu.setText("Group Colour");
505 showBoxes.setText("Boxes");
506 showBoxes.setState(true);
507 showBoxes.addActionListener(new ActionListener()
509 public void actionPerformed(ActionEvent e)
511 showBoxes_actionPerformed();
514 showText.setText("Text");
515 showText.setState(true);
516 showText.addActionListener(new ActionListener()
518 public void actionPerformed(ActionEvent e)
520 showText_actionPerformed();
523 showColourText.setText("Colour Text");
524 showColourText.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 showColourText_actionPerformed();
531 editMenu.setText("Edit");
533 cut.addActionListener(new ActionListener()
535 public void actionPerformed(ActionEvent e)
537 cut_actionPerformed();
540 upperCase.setText("To Upper Case");
541 upperCase.addActionListener(new ActionListener()
543 public void actionPerformed(ActionEvent e)
548 copy.setText("Copy");
549 copy.addActionListener(new ActionListener()
551 public void actionPerformed(ActionEvent e)
553 copy_actionPerformed();
556 lowerCase.setText("To Lower Case");
557 lowerCase.addActionListener(new ActionListener()
559 public void actionPerformed(ActionEvent e)
564 toggle.setText("Toggle Case");
565 toggle.addActionListener(new ActionListener()
567 public void actionPerformed(ActionEvent e)
572 pdbMenu.setText("Associate Structure with Sequence");
573 pdbFromFile.setText("From File");
574 pdbFromFile.addActionListener(new ActionListener()
576 public void actionPerformed(ActionEvent e)
578 pdbFromFile_actionPerformed();
581 enterPDB.setText("Enter PDB Id");
582 enterPDB.addActionListener(new ActionListener()
584 public void actionPerformed(ActionEvent e)
586 enterPDB_actionPerformed();
589 discoverPDB.setText("Discover PDB ids");
590 discoverPDB.addActionListener(new ActionListener()
592 public void actionPerformed(ActionEvent e)
594 discoverPDB_actionPerformed();
597 outputMenu.setText("Output to Textbox...");
598 sequenceFeature.setText("Create Sequence Feature");
599 sequenceFeature.addActionListener(new ActionListener()
601 public void actionPerformed(ActionEvent e)
603 sequenceFeature_actionPerformed();
606 textColour.setText("Text Colour");
607 textColour.addActionListener(new ActionListener()
609 public void actionPerformed(ActionEvent e)
611 textColour_actionPerformed();
614 jMenu1.setText("Group");
615 structureMenu.setText("Structure");
616 viewStructureMenu.setText("View Structure");
617 // colStructureMenu.setText("Colour By Structure");
618 editSequence.setText("Edit Sequence...");
619 editSequence.addActionListener(new ActionListener()
621 public void actionPerformed(ActionEvent actionEvent)
623 editSequence_actionPerformed(actionEvent);
626 /* annotationMenuItem.setText("By Annotation");
627 annotationMenuItem.addActionListener(new ActionListener()
629 public void actionPerformed(ActionEvent actionEvent)
631 annotationMenuItem_actionPerformed(actionEvent);
638 this.add(structureMenu);
639 groupMenu.add(editMenu);
640 groupMenu.add(outputMenu);
641 groupMenu.add(sequenceFeature);
642 groupMenu.add(jMenu1);
643 sequenceMenu.add(sequenceName);
644 colourMenu.add(textColour);
645 colourMenu.add(noColourmenuItem);
646 colourMenu.add(clustalColour);
647 colourMenu.add(BLOSUM62Colour);
648 colourMenu.add(PIDColour);
649 colourMenu.add(zappoColour);
650 colourMenu.add(taylorColour);
651 colourMenu.add(hydrophobicityColour);
652 colourMenu.add(helixColour);
653 colourMenu.add(strandColour);
654 colourMenu.add(turnColour);
655 colourMenu.add(buriedColour);
656 colourMenu.add(nucleotideMenuItem);
657 colourMenu.add(userDefinedColour);
659 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
661 java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
662 getUserColourSchemes().keys();
664 while (userColours.hasMoreElements())
666 JMenuItem item = new JMenuItem(userColours.
667 nextElement().toString());
668 item.addActionListener(new ActionListener()
670 public void actionPerformed(ActionEvent evt)
672 userDefinedColour_actionPerformed(evt);
675 colourMenu.add(item);
679 colourMenu.addSeparator();
680 colourMenu.add(abovePIDColour);
681 colourMenu.add(conservationMenuItem);
682 //colourMenu.add(annotationMenuItem);
685 editMenu.add(editSequence);
686 editMenu.add(upperCase);
687 editMenu.add(lowerCase);
688 editMenu.add(toggle);
689 pdbMenu.add(pdbFromFile);
690 pdbMenu.add(enterPDB);
691 pdbMenu.add(discoverPDB);
692 jMenu1.add(groupName);
693 jMenu1.add(unGroupMenuItem);
694 jMenu1.add(colourMenu);
695 jMenu1.add(showBoxes);
696 jMenu1.add(showText);
697 jMenu1.add(showColourText);
699 structureMenu.add(pdbMenu);
700 structureMenu.add(viewStructureMenu);
701 // structureMenu.add(colStructureMenu);
702 noColourmenuItem.setText("None");
703 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
705 public void actionPerformed(ActionEvent e)
707 noColourmenuItem_actionPerformed();
711 clustalColour.setText("Clustalx colours");
712 clustalColour.addActionListener(new java.awt.event.ActionListener()
714 public void actionPerformed(ActionEvent e)
716 clustalColour_actionPerformed();
719 zappoColour.setText("Zappo");
720 zappoColour.addActionListener(new java.awt.event.ActionListener()
722 public void actionPerformed(ActionEvent e)
724 zappoColour_actionPerformed();
727 taylorColour.setText("Taylor");
728 taylorColour.addActionListener(new java.awt.event.ActionListener()
730 public void actionPerformed(ActionEvent e)
732 taylorColour_actionPerformed();
735 hydrophobicityColour.setText("Hydrophobicity");
736 hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()
738 public void actionPerformed(ActionEvent e)
740 hydrophobicityColour_actionPerformed();
743 helixColour.setText("Helix propensity");
744 helixColour.addActionListener(new java.awt.event.ActionListener()
746 public void actionPerformed(ActionEvent e)
748 helixColour_actionPerformed();
751 strandColour.setText("Strand propensity");
752 strandColour.addActionListener(new java.awt.event.ActionListener()
754 public void actionPerformed(ActionEvent e)
756 strandColour_actionPerformed();
759 turnColour.setText("Turn propensity");
760 turnColour.addActionListener(new java.awt.event.ActionListener()
762 public void actionPerformed(ActionEvent e)
764 turnColour_actionPerformed();
767 buriedColour.setText("Buried Index");
768 buriedColour.addActionListener(new java.awt.event.ActionListener()
770 public void actionPerformed(ActionEvent e)
772 buriedColour_actionPerformed();
775 abovePIDColour.setText("Above % Identity");
776 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
778 public void actionPerformed(ActionEvent e)
780 abovePIDColour_actionPerformed();
783 userDefinedColour.setText("User Defined...");
784 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
786 public void actionPerformed(ActionEvent e)
788 userDefinedColour_actionPerformed(e);
791 PIDColour.setText("Percentage Identity");
792 PIDColour.addActionListener(new java.awt.event.ActionListener()
794 public void actionPerformed(ActionEvent e)
796 PIDColour_actionPerformed();
799 BLOSUM62Colour.setText("BLOSUM62");
800 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
802 public void actionPerformed(ActionEvent e)
804 BLOSUM62Colour_actionPerformed();
807 conservationMenuItem.setText("Conservation");
808 conservationMenuItem.addActionListener(new java.awt.event.ActionListener()
810 public void actionPerformed(ActionEvent e)
812 conservationMenuItem_actionPerformed();
822 ap.paintAlignment(true);
824 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
830 * @param e DOCUMENT ME!
832 protected void clustalColour_actionPerformed()
834 SequenceGroup sg = getGroup();
835 sg.cs = new ClustalxColourScheme(sg.getSequences(ap.av.hiddenRepSequences),
836 ap.av.alignment.getWidth());
843 * @param e DOCUMENT ME!
845 protected void zappoColour_actionPerformed()
847 getGroup().cs = new ZappoColourScheme();
854 * @param e DOCUMENT ME!
856 protected void taylorColour_actionPerformed()
858 getGroup().cs = new TaylorColourScheme();
865 * @param e DOCUMENT ME!
867 protected void hydrophobicityColour_actionPerformed()
869 getGroup().cs = new HydrophobicColourScheme();
876 * @param e DOCUMENT ME!
878 protected void helixColour_actionPerformed()
880 getGroup().cs = new HelixColourScheme();
887 * @param e DOCUMENT ME!
889 protected void strandColour_actionPerformed()
891 getGroup().cs = new StrandColourScheme();
898 * @param e DOCUMENT ME!
900 protected void turnColour_actionPerformed()
902 getGroup().cs = new TurnColourScheme();
909 * @param e DOCUMENT ME!
911 protected void buriedColour_actionPerformed()
913 getGroup().cs = new BuriedColourScheme();
920 * @param e DOCUMENT ME!
922 public void nucleotideMenuItem_actionPerformed()
924 getGroup().cs = new NucleotideColourScheme();
931 * @param e DOCUMENT ME!
933 protected void abovePIDColour_actionPerformed()
935 SequenceGroup sg = getGroup();
941 if (abovePIDColour.isSelected())
943 sg.cs.setConsensus(AAFrequency.calculate(
944 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
945 sg.getEndRes() + 1));
947 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs,
948 getGroup().getName());
950 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
952 SliderPanel.showPIDSlider();
954 else // remove PIDColouring
956 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
965 * @param e DOCUMENT ME!
967 protected void userDefinedColour_actionPerformed(ActionEvent e)
969 SequenceGroup sg = getGroup();
971 if (e.getActionCommand().equals("User Defined..."))
973 new UserDefinedColours(ap, sg);
977 UserColourScheme udc = (UserColourScheme) UserDefinedColours.
978 getUserColourSchemes().get(e.getActionCommand());
988 * @param e DOCUMENT ME!
990 protected void PIDColour_actionPerformed()
992 SequenceGroup sg = getGroup();
993 sg.cs = new PIDColourScheme();
994 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
997 sg.getEndRes() + 1));
1004 * @param e DOCUMENT ME!
1006 protected void BLOSUM62Colour_actionPerformed()
1008 SequenceGroup sg = getGroup();
1010 sg.cs = new Blosum62ColourScheme();
1012 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av.
1013 hiddenRepSequences),
1015 sg.getEndRes() + 1));
1023 * @param e DOCUMENT ME!
1025 protected void noColourmenuItem_actionPerformed()
1027 getGroup().cs = null;
1034 * @param e DOCUMENT ME!
1036 protected void conservationMenuItem_actionPerformed()
1038 SequenceGroup sg = getGroup();
1044 if (conservationMenuItem.isSelected())
1046 Conservation c = new Conservation("Group",
1047 ResidueProperties.propHash, 3,
1048 sg.getSequences(ap.av.
1049 hiddenRepSequences),
1051 sg.getEndRes() + 1);
1054 c.verdict(false, ap.av.ConsPercGaps);
1056 sg.cs.setConservation(c);
1058 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1059 SliderPanel.showConservationSlider();
1061 else // remove ConservationColouring
1063 sg.cs.setConservation(null);
1069 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1071 SequenceGroup sg = getGroup();
1077 AnnotationColourGradient acg = new AnnotationColourGradient(
1078 sequence.getAnnotation()[0], null, AnnotationColourGradient.NO_THRESHOLD);
1080 acg.predefinedColours = true;
1089 * @param e DOCUMENT ME!
1091 protected void groupName_actionPerformed()
1094 SequenceGroup sg = getGroup();
1095 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1096 sg.getDescription(),
1098 "Group Description ",
1099 "Edit Group Name/Description");
1106 sg.setName(dialog.getName());
1107 sg.setDescription(dialog.getDescription());
1113 * @return DOCUMENT ME!
1115 SequenceGroup getGroup()
1117 SequenceGroup sg = ap.av.getSelectionGroup();
1118 // this method won't add a new group if it already exists
1121 ap.av.alignment.addGroup(sg);
1130 * @param e DOCUMENT ME!
1132 void sequenceName_actionPerformed()
1134 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1135 sequence.getDescription(),
1137 "Sequence Description ",
1138 "Edit Sequence Name/Description");
1145 if (dialog.getName() != null)
1147 if (dialog.getName().indexOf(" ") > -1)
1149 JOptionPane.showMessageDialog(ap,
1150 "Spaces have been converted to \"_\"",
1151 "No spaces allowed in Sequence Name",
1152 JOptionPane.WARNING_MESSAGE);
1155 sequence.setName(dialog.getName().replace(' ', '_'));
1156 ap.paintAlignment(false);
1159 sequence.setDescription(dialog.getDescription());
1161 ap.av.firePropertyChange("alignment", null,
1162 ap.av.getAlignment().getSequences());
1169 * @param e DOCUMENT ME!
1171 void unGroupMenuItem_actionPerformed()
1173 SequenceGroup sg = ap.av.getSelectionGroup();
1174 ap.av.alignment.deleteGroup(sg);
1175 ap.av.setSelectionGroup(null);
1182 * @param e DOCUMENT ME!
1184 protected void outline_actionPerformed()
1186 SequenceGroup sg = getGroup();
1187 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1192 sg.setOutlineColour(col);
1201 * @param e DOCUMENT ME!
1203 public void showBoxes_actionPerformed()
1205 getGroup().setDisplayBoxes(showBoxes.isSelected());
1212 * @param e DOCUMENT ME!
1214 public void showText_actionPerformed()
1216 getGroup().setDisplayText(showText.isSelected());
1223 * @param e DOCUMENT ME!
1225 public void showColourText_actionPerformed()
1227 getGroup().setColourText(showColourText.isSelected());
1231 public void showLink(String url)
1235 jalview.util.BrowserLauncher.openURL(url);
1237 catch (Exception ex)
1239 JOptionPane.showInternalMessageDialog(Desktop.desktop,
1240 "Unixers: Couldn't find default web browser."
1242 "\nAdd the full path to your browser in Preferences.",
1243 "Web browser not found",
1244 JOptionPane.WARNING_MESSAGE);
1246 ex.printStackTrace();
1250 void hideSequences(boolean representGroup)
1252 SequenceGroup sg = ap.av.getSelectionGroup();
1253 if (sg == null || sg.getSize() < 1)
1255 ap.av.hideSequence(new SequenceI[]
1260 ap.av.setSelectionGroup(null);
1264 ap.av.hideRepSequences(sequence, sg);
1269 int gsize = sg.getSize();
1272 hseqs = new SequenceI[gsize];
1275 for (int i = 0; i < gsize; i++)
1277 hseqs[index++] = sg.getSequenceAt(i);
1280 ap.av.hideSequence(hseqs);
1283 public void copy_actionPerformed()
1285 ap.alignFrame.copy_actionPerformed(null);
1288 public void cut_actionPerformed()
1290 ap.alignFrame.cut_actionPerformed(null);
1293 void changeCase(ActionEvent e)
1295 Object source = e.getSource();
1296 SequenceGroup sg = ap.av.getSelectionGroup();
1300 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
1301 sg.getStartRes(), sg.getEndRes() + 1);
1306 if (source == toggle)
1308 description = "Toggle Case";
1309 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1311 else if (source == upperCase)
1313 description = "To Upper Case";
1314 caseChange = ChangeCaseCommand.TO_UPPER;
1318 description = "To Lower Case";
1319 caseChange = ChangeCaseCommand.TO_LOWER;
1322 ChangeCaseCommand caseCommand = new ChangeCaseCommand(
1323 description, sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1324 startEnd, caseChange
1327 ap.alignFrame.addHistoryItem(caseCommand);
1329 ap.av.firePropertyChange("alignment", null,
1330 ap.av.getAlignment().getSequences());
1335 public void outputText_actionPerformed(ActionEvent e)
1337 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1338 cap.setForInput(null);
1339 Desktop.addInternalFrame(cap,
1340 "Alignment output - " + e.getActionCommand(), 600,
1343 String[] omitHidden = null;
1345 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens or we simply trust the user wants wysiwig behaviour
1346 SequenceGroup sg = ap.av.getSelectionGroup();
1347 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1348 omitHidden = ap.av.getViewAsString(true);
1349 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1350 AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1351 for (int i=0; i<nala.length; i++)
1353 AlignmentAnnotation na =nala[i];
1354 oal.addAnnotation(na);
1356 cap.setText(new FormatAdapter().formatSequences(
1357 e.getActionCommand(),
1359 omitHidden, csel, sg));
1363 public void pdbFromFile_actionPerformed()
1365 jalview.io.JalviewFileChooser chooser
1366 = new jalview.io.JalviewFileChooser(jalview.bin.Cache.
1369 chooser.setFileView(new jalview.io.JalviewFileView());
1370 chooser.setDialogTitle("Select a PDB file");
1371 chooser.setToolTipText("Load a PDB file");
1373 int value = chooser.showOpenDialog(null);
1375 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1377 PDBEntry entry = new PDBEntry();
1378 String choice = chooser.getSelectedFile().getPath();
1379 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1382 MCview.PDBfile pdbfile = new MCview.PDBfile(choice,
1383 jalview.io.AppletFormatAdapter.FILE);
1385 if (pdbfile.id == null)
1387 String reply = JOptionPane.showInternalInputDialog(
1389 "Couldn't find a PDB id in the file supplied."
1390 + "Please enter an Id to identify this structure.",
1391 "No PDB Id in File", JOptionPane.QUESTION_MESSAGE);
1401 entry.setId(pdbfile.id);
1404 catch (java.io.IOException ex)
1406 ex.printStackTrace();
1409 entry.setFile(choice);
1410 sequence.getDatasetSequence().addPDBId(entry);
1415 public void enterPDB_actionPerformed()
1417 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1418 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1420 if (id != null && id.length() > 0)
1422 PDBEntry entry = new PDBEntry();
1423 entry.setId(id.toUpperCase());
1424 sequence.getDatasetSequence()
1429 public void discoverPDB_actionPerformed()
1431 SequenceI[] sequences =
1432 ap.av.selectionGroup == null ?
1433 new Sequence[]{sequence}
1434 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment);
1436 new jalview.ws.DBRefFetcher(sequences,
1437 ap.alignFrame).fetchDBRefs(false);
1440 public void sequenceFeature_actionPerformed()
1442 SequenceGroup sg = ap.av.getSelectionGroup();
1448 int gSize = sg.getSize();
1449 SequenceI[] seqs = new SequenceI[gSize];
1450 SequenceFeature[] features = new SequenceFeature[gSize];
1452 for (int i = 0; i < gSize; i++)
1454 seqs[i] = sg.getSequenceAt(i).getDatasetSequence();
1455 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1456 int end = sg.findEndRes(sg.getSequenceAt(i));
1457 features[i] = new SequenceFeature(null, null, null, start, end, "Jalview");
1460 if (ap.seqPanel.seqCanvas.getFeatureRenderer()
1461 .amendFeatures(seqs, features, true, ap))
1463 ap.alignFrame.showSeqFeatures.setSelected(true);
1464 ap.av.setShowSequenceFeatures(true);
1465 ap.highlightSearchResults(null);
1469 public void textColour_actionPerformed()
1471 SequenceGroup sg = getGroup();
1474 new TextColourChooser().chooseColour(ap, sg);
1478 public void colourByStructure(String pdbid)
1480 Annotation [] anots = jalview.structure.StructureSelectionManager.getStructureSelectionManager()
1481 .colourSequenceFromStructure(sequence, pdbid);
1483 AlignmentAnnotation an = new AlignmentAnnotation(
1484 "Structure", "Coloured by "+pdbid, anots);
1486 ap.av.alignment.addAnnotation(an);
1487 an.createSequenceMapping(sequence, 0, true);
1488 //an.adjustForAlignment();
1489 ap.av.alignment.setAnnotationIndex(an,0);
1491 ap.adjustAnnotationHeight();
1493 sequence.addAlignmentAnnotation(an);
1497 public void editSequence_actionPerformed(ActionEvent actionEvent)
1499 SequenceGroup sg = ap.av.getSelectionGroup();
1503 if (sequence == null)
1504 sequence = (Sequence) sg.getSequenceAt(0);
1506 EditNameDialog dialog = new EditNameDialog(
1507 sequence.getSequenceAsString(
1509 sg.getEndRes() + 1),
1517 EditCommand editCommand = new EditCommand(
1518 "Edit Sequences", EditCommand.REPLACE,
1519 dialog.getName().replace(' ', ap.av.getGapCharacter()),
1520 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1521 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment
1524 ap.alignFrame.addHistoryItem(editCommand);
1526 ap.av.firePropertyChange("alignment", null,
1527 ap.av.getAlignment().getSequences());