2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.Conservation;
25 import jalview.commands.ChangeCaseCommand;
26 import jalview.commands.EditCommand;
27 import jalview.commands.EditCommand.Action;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.Sequence;
31 import jalview.datamodel.SequenceFeature;
32 import jalview.datamodel.SequenceGroup;
33 import jalview.datamodel.SequenceI;
34 import jalview.io.AppletFormatAdapter;
35 import jalview.io.SequenceAnnotationReport;
36 import jalview.schemes.Blosum62ColourScheme;
37 import jalview.schemes.BuriedColourScheme;
38 import jalview.schemes.ClustalxColourScheme;
39 import jalview.schemes.HelixColourScheme;
40 import jalview.schemes.HydrophobicColourScheme;
41 import jalview.schemes.NucleotideColourScheme;
42 import jalview.schemes.PIDColourScheme;
43 import jalview.schemes.ResidueProperties;
44 import jalview.schemes.StrandColourScheme;
45 import jalview.schemes.TaylorColourScheme;
46 import jalview.schemes.TurnColourScheme;
47 import jalview.schemes.ZappoColourScheme;
48 import jalview.util.MessageManager;
49 import jalview.util.UrlLink;
51 import java.awt.CheckboxMenuItem;
52 import java.awt.Frame;
54 import java.awt.MenuItem;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.awt.event.ItemEvent;
58 import java.awt.event.ItemListener;
59 import java.util.List;
60 import java.util.Vector;
62 public class APopupMenu extends java.awt.PopupMenu implements
63 ActionListener, ItemListener
65 Menu groupMenu = new Menu();
67 MenuItem editGroupName = new MenuItem();
69 protected MenuItem clustalColour = new MenuItem();
71 protected MenuItem zappoColour = new MenuItem();
73 protected MenuItem taylorColour = new MenuItem();
75 protected MenuItem hydrophobicityColour = new MenuItem();
77 protected MenuItem helixColour = new MenuItem();
79 protected MenuItem strandColour = new MenuItem();
81 protected MenuItem turnColour = new MenuItem();
83 protected MenuItem buriedColour = new MenuItem();
85 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
87 protected MenuItem userDefinedColour = new MenuItem();
89 protected MenuItem PIDColour = new MenuItem();
91 protected MenuItem BLOSUM62Colour = new MenuItem();
93 MenuItem noColourmenuItem = new MenuItem();
95 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
97 final AlignmentPanel ap;
99 MenuItem unGroupMenuItem = new MenuItem();
101 MenuItem createGroupMenuItem = new MenuItem();
103 MenuItem nucleotideMenuItem = new MenuItem();
105 Menu colourMenu = new Menu();
107 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
109 CheckboxMenuItem showText = new CheckboxMenuItem();
111 CheckboxMenuItem showColourText = new CheckboxMenuItem();
113 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
115 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
117 MenuItem copy = new MenuItem(
118 MessageManager.getString("label.jalview_copy"));
120 MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
122 MenuItem toUpper = new MenuItem(
123 MessageManager.getString("label.to_upper_case"));
125 MenuItem toLower = new MenuItem(
126 MessageManager.getString("label.to_lower_case"));
128 MenuItem toggleCase = new MenuItem(
129 MessageManager.getString("label.toggle_case"));
131 Menu outputmenu = new Menu();
133 Menu seqMenu = new Menu();
135 MenuItem pdb = new MenuItem();
137 MenuItem hideSeqs = new MenuItem();
139 MenuItem repGroup = new MenuItem();
141 MenuItem sequenceName = new MenuItem(
142 MessageManager.getString("label.edit_name_description"));
144 MenuItem sequenceFeature = new MenuItem(
145 MessageManager.getString("label.create_sequence_feature"));
147 MenuItem editSequence = new MenuItem(
148 MessageManager.getString("label.edit_sequence"));
150 MenuItem sequenceDetails = new MenuItem(
151 MessageManager.getString("label.sequence_details") + "...");
153 MenuItem selSeqDetails = new MenuItem(
154 MessageManager.getString("label.sequence_details") + "...");
156 MenuItem makeReferenceSeq = new MenuItem();
160 MenuItem revealAll = new MenuItem();
162 MenuItem revealSeq = new MenuItem();
165 * index of sequence to be revealed
167 int revealSeq_index = -1;
169 Menu menu1 = new Menu();
171 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
173 // /////////////////////////////////////////////////////////
174 // If this is activated from the sequence panel, the user may want to
175 // edit or annotate a particular residue. Therefore display the residue menu
177 // If from the IDPanel, we must display the sequence menu
178 // ////////////////////////////////////////////////////////
186 } catch (Exception e)
191 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
193 MenuItem item = new MenuItem(
194 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
196 item.addActionListener(this);
197 outputmenu.add(item);
200 SequenceGroup sg = ap.av.getSelectionGroup();
202 if (sg != null && sg.getSize() > 0)
204 editGroupName.setLabel(MessageManager.formatMessage(
205 "label.name_param", new String[]
207 showText.setState(sg.getDisplayText());
208 showColourText.setState(sg.getColourText());
209 showBoxes.setState(sg.getDisplayBoxes());
210 displayNonconserved.setState(sg.getShowNonconserved());
211 if (!ap.av.getAlignment().getGroups().contains(sg))
213 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
214 groupMenu.remove(unGroupMenuItem);
218 menu1.setLabel(MessageManager.getString("action.edit_group"));
219 groupMenu.remove(createGroupMenuItem);
229 if (links != null && links.size() > 0)
231 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
233 for (int i = 0; i < links.size(); i++)
235 link = links.elementAt(i).toString();
236 UrlLink urlLink = new UrlLink(link);
237 if (!urlLink.isValid())
239 System.err.println(urlLink.getInvalidMessage());
242 final String target = urlLink.getTarget(); // link.substring(0,
243 // link.indexOf("|"));
244 final String label = urlLink.getLabel();
245 if (seq != null && urlLink.isDynamic())
248 // collect matching db-refs
249 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
250 seq.getDBRef(), new String[]
252 // collect id string too
253 String id = seq.getName();
254 String descr = seq.getDescription();
255 if (descr != null && descr.length() < 1)
261 for (int r = 0; r < dbr.length; r++)
263 if (id != null && dbr[r].getAccessionId().equals(id))
265 // suppress duplicate link creation for the bare sequence ID
266 // string with this link
269 // create Bare ID link for this RUL
270 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
274 for (int u = 0; u < urls.length; u += 2)
276 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
283 // create Bare ID link for this RUL
284 String[] urls = urlLink.makeUrls(id, true);
287 for (int u = 0; u < urls.length; u += 2)
289 addshowLink(linkMenu, label, urls[u + 1]);
292 // addshowLink(linkMenu, target, url_pref + id + url_suff);
294 // Now construct URLs from description but only try to do it for regex
296 if (descr != null && urlLink.getRegexReplace() != null)
298 // create link for this URL from description only if regex matches
299 String[] urls = urlLink.makeUrls(descr, true);
302 for (int u = 0; u < urls.length; u += 2)
304 addshowLink(linkMenu, label, urls[u + 1]);
311 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
316 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
317 * string and any matching database reference accessions String url_pref
318 * = link.substring(link.indexOf("|") + 1,
319 * link.indexOf("$SEQUENCE_ID$"));
321 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
322 * // collect matching db-refs DBRefEntry[] dbr =
323 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
324 * String[]{target}); // collect id string too String id =
325 * seq.getName(); if (id.indexOf("|") > -1) { id =
326 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
327 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
328 * suppress duplicate link creation for the bare sequence ID string with
329 * this link id = null; } addshowLink(linkMenu,
330 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
331 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
332 * create Bare ID link for this RUL addshowLink(linkMenu, target,
333 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
334 * link.substring(link.lastIndexOf("|")+1)); }
337 if (linkMenu.getItemCount() > 0)
341 seqMenu.add(linkMenu);
349 // TODO: add group link menu entry here
352 seqMenu.setLabel(seq.getName());
353 if (seq == ap.av.getAlignment().getSeqrep())
355 makeReferenceSeq.setLabel(MessageManager
356 .getString("action.unmark_as_reference"));// Unmark
361 makeReferenceSeq.setLabel(MessageManager
362 .getString("action.set_as_reference")); // );
364 repGroup.setLabel(MessageManager.formatMessage(
365 "label.represent_group_with", new String[]
373 if (!ap.av.hasHiddenRows())
380 final int index = ap.av.getAlignment().findIndex(seq);
382 if (ap.av.adjustForHiddenSeqs(index)
383 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
385 revealSeq_index = index;
395 * add a show URL menu item to the given linkMenu
399 * - menu label string
403 private void addshowLink(Menu linkMenu, final String target,
406 addshowLink(linkMenu, target, target, url);
410 * add a show URL menu item to the given linkMenu
414 * - URL target window
416 * - menu label string
420 private void addshowLink(Menu linkMenu, final String target,
421 final String label, final String url)
423 MenuItem item = new MenuItem(label);
424 item.addActionListener(new java.awt.event.ActionListener()
426 public void actionPerformed(ActionEvent e)
428 ap.alignFrame.showURL(url, target);
434 public void itemStateChanged(ItemEvent evt)
436 if (evt.getSource() == abovePIDColour)
438 abovePIDColour_itemStateChanged();
440 else if (evt.getSource() == showColourText)
442 showColourText_itemStateChanged();
444 else if (evt.getSource() == showText)
446 showText_itemStateChanged();
448 else if (evt.getSource() == showBoxes)
450 showBoxes_itemStateChanged();
452 else if (evt.getSource() == displayNonconserved)
454 this.showNonconserved_itemStateChanged();
458 public void actionPerformed(ActionEvent evt)
460 Object source = evt.getSource();
461 if (source == clustalColour)
463 clustalColour_actionPerformed();
465 else if (source == zappoColour)
467 zappoColour_actionPerformed();
469 else if (source == taylorColour)
471 taylorColour_actionPerformed();
473 else if (source == hydrophobicityColour)
475 hydrophobicityColour_actionPerformed();
477 else if (source == helixColour)
479 helixColour_actionPerformed();
481 else if (source == strandColour)
483 strandColour_actionPerformed();
485 else if (source == turnColour)
487 turnColour_actionPerformed();
489 else if (source == buriedColour)
491 buriedColour_actionPerformed();
493 else if (source == nucleotideMenuItem)
495 nucleotideMenuItem_actionPerformed();
498 else if (source == userDefinedColour)
500 userDefinedColour_actionPerformed();
502 else if (source == PIDColour)
504 PIDColour_actionPerformed();
506 else if (source == BLOSUM62Colour)
508 BLOSUM62Colour_actionPerformed();
510 else if (source == noColourmenuItem)
512 noColourmenuItem_actionPerformed();
514 else if (source == conservationMenuItem)
516 conservationMenuItem_itemStateChanged();
518 else if (source == unGroupMenuItem)
520 unGroupMenuItem_actionPerformed();
523 else if (source == createGroupMenuItem)
525 createGroupMenuItem_actionPerformed();
528 else if (source == sequenceName)
532 else if (source == makeReferenceSeq)
534 makeReferenceSeq_actionPerformed();
536 else if (source == sequenceDetails)
538 showSequenceDetails();
540 else if (source == selSeqDetails)
542 showSequenceSelectionDetails();
544 else if (source == pdb)
548 else if (source == hideSeqs)
550 hideSequences(false);
552 else if (source == repGroup)
556 else if (source == revealSeq)
558 ap.av.showSequence(revealSeq_index);
560 else if (source == revealAll)
562 ap.av.showAllHiddenSeqs();
565 else if (source == editGroupName)
567 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
568 getGroup().getDescription(), " Group Name",
569 "Group Description", ap.alignFrame,
570 "Edit Group Name / Description", 500, 100, true);
574 getGroup().setName(dialog.getName().replace(' ', '_'));
575 getGroup().setDescription(dialog.getDescription());
579 else if (source == copy)
581 ap.alignFrame.copy_actionPerformed();
583 else if (source == cut)
585 ap.alignFrame.cut_actionPerformed();
587 else if (source == editSequence)
589 SequenceGroup sg = ap.av.getSelectionGroup();
595 seq = (Sequence) sg.getSequenceAt(0);
598 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
599 sg.getStartRes(), sg.getEndRes() + 1), null,
600 "Edit Sequence ", null,
602 ap.alignFrame, "Edit Sequence", 500, 100, true);
606 EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
607 Action.REPLACE, dialog.getName().replace(' ',
608 ap.av.getGapCharacter()),
609 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
610 sg.getStartRes(), sg.getEndRes() + 1,
611 ap.av.getAlignment());
613 ap.alignFrame.addHistoryItem(editCommand);
615 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
620 else if (source == toUpper || source == toLower || source == toggleCase)
622 SequenceGroup sg = ap.av.getSelectionGroup();
625 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
626 sg.getStartRes(), sg.getEndRes() + 1);
631 if (source == toggleCase)
633 description = "Toggle Case";
634 caseChange = ChangeCaseCommand.TOGGLE_CASE;
636 else if (source == toUpper)
638 description = "To Upper Case";
639 caseChange = ChangeCaseCommand.TO_UPPER;
643 description = "To Lower Case";
644 caseChange = ChangeCaseCommand.TO_LOWER;
647 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
648 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
649 startEnd, caseChange);
651 ap.alignFrame.addHistoryItem(caseCommand);
653 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
658 else if (source == sequenceFeature)
660 SequenceGroup sg = ap.av.getSelectionGroup();
666 int rsize = 0, gSize = sg.getSize();
667 SequenceI[] rseqs, seqs = new SequenceI[gSize];
668 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
670 for (int i = 0; i < gSize; i++)
672 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
673 int end = sg.findEndRes(sg.getSequenceAt(i));
676 seqs[rsize] = sg.getSequenceAt(i);
677 features[rsize] = new SequenceFeature(null, null, null, start,
682 rseqs = new SequenceI[rsize];
683 tfeatures = new SequenceFeature[rsize];
684 System.arraycopy(seqs, 0, rseqs, 0, rsize);
685 System.arraycopy(features, 0, tfeatures, 0, rsize);
686 features = tfeatures;
689 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
692 ap.alignFrame.sequenceFeatures.setState(true);
693 ap.av.setShowSequenceFeatures(true);;
694 ap.highlightSearchResults(null);
704 void outputText(ActionEvent e)
706 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
708 Frame frame = new Frame();
710 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
711 "label.selection_output_command", new String[]
712 { e.getActionCommand() }), 600, 500);
713 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
714 // now returns a full copy of sequence data
715 // TODO consider using getSequenceSelection instead here
717 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
718 e.getActionCommand(), ap.av.getShowJVSuffix(), ap.av, true));
722 protected void showSequenceSelectionDetails()
724 createSequenceDetailsReport(ap.av.getSequenceSelection());
727 protected void showSequenceDetails()
729 createSequenceDetailsReport(new SequenceI[]
733 public void createSequenceDetailsReport(SequenceI[] sequences)
736 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
738 StringBuffer contents = new StringBuffer();
739 for (SequenceI seq : sequences)
741 contents.append(MessageManager.formatMessage(
742 "label.annotation_for_displayid", new String[]
743 { seq.getDisplayId(true) }));
744 new SequenceAnnotationReport(null)
745 .createSequenceAnnotationReport(
751 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
753 contents.append("</p>");
755 Frame frame = new Frame();
757 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
758 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
759 : "Selection"), 600, 500);
760 cap.setText(MessageManager.formatMessage("label.html_content",
762 { contents.toString() }));
767 EditNameDialog dialog = new EditNameDialog(seq.getName(),
768 seq.getDescription(), " Sequence Name",
769 "Sequence Description", ap.alignFrame,
770 "Edit Sequence Name / Description", 500, 100, true);
774 seq.setName(dialog.getName());
775 seq.setDescription(dialog.getDescription());
776 ap.paintAlignment(false);
782 if (seq.getPDBId() != null)
784 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
786 if (ap.av.applet.jmolAvailable)
788 new jalview.appletgui.AppletJmol(entry, new Sequence[]
789 { seq }, null, ap, AppletFormatAdapter.URL);
793 new MCview.AppletPDBViewer(entry, new Sequence[]
794 { seq }, null, ap, AppletFormatAdapter.URL);
800 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
801 cap.setText(MessageManager.getString("label.paste_pdb_file"));
802 cap.setPDBImport(seq);
803 Frame frame = new Frame();
805 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
806 "label.paste_pdb_file_for_sequence", new String[]
807 { seq.getName() }), 400, 300);
811 private void jbInit() throws Exception
813 groupMenu.setLabel(MessageManager.getString("label.selection"));
814 sequenceFeature.addActionListener(this);
816 editGroupName.addActionListener(this);
817 unGroupMenuItem.setLabel(MessageManager
818 .getString("action.remove_group"));
819 unGroupMenuItem.addActionListener(this);
821 createGroupMenuItem.setLabel(MessageManager
822 .getString("action.create_group"));
823 createGroupMenuItem.addActionListener(this);
825 nucleotideMenuItem.setLabel(MessageManager
826 .getString("label.nucleotide"));
827 nucleotideMenuItem.addActionListener(this);
828 conservationMenuItem.addItemListener(this);
829 abovePIDColour.addItemListener(this);
830 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
831 showBoxes.setLabel(MessageManager.getString("action.boxes"));
832 showBoxes.setState(true);
833 showBoxes.addItemListener(this);
834 sequenceName.addActionListener(this);
835 sequenceDetails.addActionListener(this);
836 selSeqDetails.addActionListener(this);
837 displayNonconserved.setLabel(MessageManager
838 .getString("label.show_non_conversed"));
839 displayNonconserved.setState(false);
840 displayNonconserved.addItemListener(this);
841 showText.setLabel(MessageManager.getString("action.text"));
842 showText.addItemListener(this);
843 showColourText.setLabel(MessageManager.getString("label.colour_text"));
844 showColourText.addItemListener(this);
845 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
846 seqMenu.setLabel(MessageManager.getString("label.sequence"));
847 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
848 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
849 repGroup.setLabel(MessageManager.formatMessage(
850 "label.represent_group_with", new String[]
852 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
853 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
854 menu1.setLabel(MessageManager.getString("label.group") + ":");
860 // groupMenu.add(selSeqDetails);
861 groupMenu.add(editMenu);
862 groupMenu.add(outputmenu);
863 groupMenu.add(sequenceFeature);
864 groupMenu.add(createGroupMenuItem);
865 groupMenu.add(unGroupMenuItem);
866 groupMenu.add(menu1);
868 colourMenu.add(noColourmenuItem);
869 colourMenu.add(clustalColour);
870 colourMenu.add(BLOSUM62Colour);
871 colourMenu.add(PIDColour);
872 colourMenu.add(zappoColour);
873 colourMenu.add(taylorColour);
874 colourMenu.add(hydrophobicityColour);
875 colourMenu.add(helixColour);
876 colourMenu.add(strandColour);
877 colourMenu.add(turnColour);
878 colourMenu.add(buriedColour);
879 colourMenu.add(nucleotideMenuItem);
880 colourMenu.add(userDefinedColour);
881 colourMenu.addSeparator();
882 colourMenu.add(abovePIDColour);
883 colourMenu.add(conservationMenuItem);
885 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
886 noColourmenuItem.addActionListener(this);
888 clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
889 clustalColour.addActionListener(this);
890 zappoColour.setLabel(MessageManager.getString("label.zappo"));
891 zappoColour.addActionListener(this);
892 taylorColour.setLabel(MessageManager.getString("label.taylor"));
893 taylorColour.addActionListener(this);
894 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
895 hydrophobicityColour.addActionListener(this);
896 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
897 helixColour.addActionListener(this);
898 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
899 strandColour.addActionListener(this);
900 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
901 turnColour.addActionListener(this);
902 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
903 buriedColour.addActionListener(this);
904 abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
906 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
907 userDefinedColour.addActionListener(this);
908 PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
909 PIDColour.addActionListener(this);
910 BLOSUM62Colour.setLabel("BLOSUM62");
911 BLOSUM62Colour.addActionListener(this);
912 conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
915 copy.addActionListener(this);
917 cut.addActionListener(this);
919 editMenu.add(editSequence);
920 editSequence.addActionListener(this);
922 editMenu.add(toUpper);
923 toUpper.addActionListener(this);
924 editMenu.add(toLower);
925 toLower.addActionListener(this);
926 editMenu.add(toggleCase);
927 seqMenu.add(sequenceName);
928 seqMenu.add(makeReferenceSeq);
929 // seqMenu.add(sequenceDetails);
931 if (!ap.av.applet.useXtrnalSviewer)
935 seqMenu.add(repGroup);
936 menu1.add(editGroupName);
937 menu1.add(colourMenu);
938 menu1.add(showBoxes);
940 menu1.add(showColourText);
941 menu1.add(displayNonconserved);
942 toggleCase.addActionListener(this);
943 pdb.addActionListener(this);
944 hideSeqs.addActionListener(this);
945 repGroup.addActionListener(this);
946 revealAll.addActionListener(this);
947 revealSeq.addActionListener(this);
948 makeReferenceSeq.addActionListener(this);
953 ap.paintAlignment(true);
956 protected void clustalColour_actionPerformed()
958 SequenceGroup sg = getGroup();
959 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
963 protected void zappoColour_actionPerformed()
965 getGroup().cs = new ZappoColourScheme();
969 protected void taylorColour_actionPerformed()
971 getGroup().cs = new TaylorColourScheme();
975 protected void hydrophobicityColour_actionPerformed()
977 getGroup().cs = new HydrophobicColourScheme();
981 protected void helixColour_actionPerformed()
983 getGroup().cs = new HelixColourScheme();
987 protected void strandColour_actionPerformed()
989 getGroup().cs = new StrandColourScheme();
993 protected void turnColour_actionPerformed()
995 getGroup().cs = new TurnColourScheme();
999 protected void buriedColour_actionPerformed()
1001 getGroup().cs = new BuriedColourScheme();
1005 public void nucleotideMenuItem_actionPerformed()
1007 getGroup().cs = new NucleotideColourScheme();
1011 protected void abovePIDColour_itemStateChanged()
1013 SequenceGroup sg = getGroup();
1019 if (abovePIDColour.getState())
1021 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1022 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1023 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1026 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1028 SliderPanel.showPIDSlider();
1032 // remove PIDColouring
1034 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1041 protected void userDefinedColour_actionPerformed()
1043 new UserDefinedColours(ap, getGroup());
1046 protected void PIDColour_actionPerformed()
1048 SequenceGroup sg = getGroup();
1049 sg.cs = new PIDColourScheme();
1050 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1051 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1055 protected void BLOSUM62Colour_actionPerformed()
1057 SequenceGroup sg = getGroup();
1059 sg.cs = new Blosum62ColourScheme();
1061 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1062 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1067 protected void noColourmenuItem_actionPerformed()
1069 getGroup().cs = null;
1073 protected void conservationMenuItem_itemStateChanged()
1075 SequenceGroup sg = getGroup();
1081 if (conservationMenuItem.getState())
1084 sg.cs.setConservation(Conservation.calculateConservation("Group",
1085 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1086 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1087 .getWidth(), false, ap.av.getConsPercGaps(), false));
1088 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1089 SliderPanel.showConservationSlider();
1092 // remove ConservationColouring
1094 sg.cs.setConservation(null);
1100 SequenceGroup getGroup()
1102 SequenceGroup sg = ap.av.getSelectionGroup();
1104 // this method won't add a new group if it already exists
1107 ap.av.getAlignment().addGroup(sg);
1113 void unGroupMenuItem_actionPerformed()
1115 SequenceGroup sg = ap.av.getSelectionGroup();
1116 ap.av.getAlignment().deleteGroup(sg);
1117 ap.av.setSelectionGroup(null);
1118 ap.paintAlignment(true);
1121 void createGroupMenuItem_actionPerformed()
1123 getGroup(); // implicitly create group
1127 public void showColourText_itemStateChanged()
1129 getGroup().setColourText(showColourText.getState());
1133 public void showText_itemStateChanged()
1135 getGroup().setDisplayText(showText.getState());
1138 public void makeReferenceSeq_actionPerformed()
1140 if (!ap.av.getAlignment().hasSeqrep())
1142 // initialise the display flags so the user sees something happen
1143 ap.av.setDisplayReferenceSeq(true);
1144 ap.av.setColourByReferenceSeq(true);
1145 ap.av.getAlignment().setSeqrep(seq);
1149 if (ap.av.getAlignment().getSeqrep() == seq)
1151 ap.av.getAlignment().setSeqrep(null);
1155 ap.av.getAlignment().setSeqrep(seq);
1161 public void showNonconserved_itemStateChanged()
1163 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1167 public void showBoxes_itemStateChanged()
1169 getGroup().setDisplayBoxes(showBoxes.getState());
1173 void hideSequences(boolean representGroup)
1175 SequenceGroup sg = ap.av.getSelectionGroup();
1176 if (sg == null || sg.getSize() < 1)
1178 ap.av.hideSequence(new SequenceI[]
1183 ap.av.setSelectionGroup(null);
1187 ap.av.hideRepSequences(seq, sg);
1192 int gsize = sg.getSize();
1195 hseqs = new SequenceI[gsize];
1198 for (int i = 0; i < gsize; i++)
1200 hseqs[index++] = sg.getSequenceAt(i);
1203 ap.av.hideSequence(hseqs);
1204 ap.av.sendSelection();