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.Vector;
61 public class APopupMenu extends java.awt.PopupMenu implements
62 ActionListener, ItemListener
64 Menu groupMenu = new Menu();
66 MenuItem editGroupName = new MenuItem();
68 protected MenuItem clustalColour = new MenuItem();
70 protected MenuItem zappoColour = new MenuItem();
72 protected MenuItem taylorColour = new MenuItem();
74 protected MenuItem hydrophobicityColour = new MenuItem();
76 protected MenuItem helixColour = new MenuItem();
78 protected MenuItem strandColour = new MenuItem();
80 protected MenuItem turnColour = new MenuItem();
82 protected MenuItem buriedColour = new MenuItem();
84 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
86 protected MenuItem userDefinedColour = new MenuItem();
88 protected MenuItem PIDColour = new MenuItem();
90 protected MenuItem BLOSUM62Colour = new MenuItem();
92 MenuItem noColourmenuItem = new MenuItem();
94 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
96 final AlignmentPanel ap;
98 MenuItem unGroupMenuItem = new MenuItem();
100 MenuItem createGroupMenuItem = new MenuItem();
102 MenuItem nucleotideMenuItem = new MenuItem();
104 Menu colourMenu = new Menu();
106 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
108 CheckboxMenuItem showText = new CheckboxMenuItem();
110 CheckboxMenuItem showColourText = new CheckboxMenuItem();
112 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
114 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
116 MenuItem copy = new MenuItem(
117 MessageManager.getString("label.jalview_copy"));
119 MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
121 MenuItem toUpper = new MenuItem(
122 MessageManager.getString("label.to_upper_case"));
124 MenuItem toLower = new MenuItem(
125 MessageManager.getString("label.to_lower_case"));
127 MenuItem toggleCase = new MenuItem(
128 MessageManager.getString("label.toggle_case"));
130 Menu outputmenu = new Menu();
132 Menu seqMenu = new Menu();
134 MenuItem pdb = new MenuItem();
136 MenuItem hideSeqs = new MenuItem();
138 MenuItem repGroup = new MenuItem();
140 MenuItem sequenceName = new MenuItem(
141 MessageManager.getString("label.edit_name_description"));
143 MenuItem sequenceFeature = new MenuItem(
144 MessageManager.getString("label.create_sequence_feature"));
146 MenuItem editSequence = new MenuItem(
147 MessageManager.getString("label.edit_sequence"));
149 MenuItem sequenceDetails = new MenuItem(
150 MessageManager.getString("label.sequence_details") + "...");
152 MenuItem selSeqDetails = new MenuItem(
153 MessageManager.getString("label.sequence_details") + "...");
155 MenuItem makeReferenceSeq = new MenuItem();
159 MenuItem revealAll = new MenuItem();
161 MenuItem revealSeq = new MenuItem();
164 * index of sequence to be revealed
166 int revealSeq_index = -1;
168 Menu menu1 = new Menu();
170 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
172 // /////////////////////////////////////////////////////////
173 // If this is activated from the sequence panel, the user may want to
174 // edit or annotate a particular residue. Therefore display the residue menu
176 // If from the IDPanel, we must display the sequence menu
177 // ////////////////////////////////////////////////////////
185 } catch (Exception e)
190 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
192 MenuItem item = new MenuItem(
193 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
195 item.addActionListener(this);
196 outputmenu.add(item);
199 SequenceGroup sg = ap.av.getSelectionGroup();
201 if (sg != null && sg.getSize() > 0)
203 editGroupName.setLabel(MessageManager.formatMessage(
204 "label.name_param", new String[]
206 showText.setState(sg.getDisplayText());
207 showColourText.setState(sg.getColourText());
208 showBoxes.setState(sg.getDisplayBoxes());
209 displayNonconserved.setState(sg.getShowNonconserved());
210 if (!ap.av.getAlignment().getGroups().contains(sg))
212 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
213 groupMenu.remove(unGroupMenuItem);
217 menu1.setLabel(MessageManager.getString("action.edit_group"));
218 groupMenu.remove(createGroupMenuItem);
228 if (links != null && links.size() > 0)
230 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
232 for (int i = 0; i < links.size(); i++)
234 link = links.elementAt(i).toString();
235 UrlLink urlLink = new UrlLink(link);
236 if (!urlLink.isValid())
238 System.err.println(urlLink.getInvalidMessage());
241 final String target = urlLink.getTarget(); // link.substring(0,
242 // link.indexOf("|"));
243 final String label = urlLink.getLabel();
244 if (seq != null && urlLink.isDynamic())
247 // collect matching db-refs
248 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
249 seq.getDBRef(), new String[]
251 // collect id string too
252 String id = seq.getName();
253 String descr = seq.getDescription();
254 if (descr != null && descr.length() < 1)
260 for (int r = 0; r < dbr.length; r++)
262 if (id != null && dbr[r].getAccessionId().equals(id))
264 // suppress duplicate link creation for the bare sequence ID
265 // string with this link
268 // create Bare ID link for this RUL
269 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
273 for (int u = 0; u < urls.length; u += 2)
275 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
282 // create Bare ID link for this RUL
283 String[] urls = urlLink.makeUrls(id, true);
286 for (int u = 0; u < urls.length; u += 2)
288 addshowLink(linkMenu, label, urls[u + 1]);
291 // addshowLink(linkMenu, target, url_pref + id + url_suff);
293 // Now construct URLs from description but only try to do it for regex
295 if (descr != null && urlLink.getRegexReplace() != null)
297 // create link for this URL from description only if regex matches
298 String[] urls = urlLink.makeUrls(descr, true);
301 for (int u = 0; u < urls.length; u += 2)
303 addshowLink(linkMenu, label, urls[u + 1]);
310 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
315 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
316 * string and any matching database reference accessions String url_pref
317 * = link.substring(link.indexOf("|") + 1,
318 * link.indexOf("$SEQUENCE_ID$"));
320 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
321 * // collect matching db-refs DBRefEntry[] dbr =
322 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
323 * String[]{target}); // collect id string too String id =
324 * seq.getName(); if (id.indexOf("|") > -1) { id =
325 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
326 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
327 * suppress duplicate link creation for the bare sequence ID string with
328 * this link id = null; } addshowLink(linkMenu,
329 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
330 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
331 * create Bare ID link for this RUL addshowLink(linkMenu, target,
332 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
333 * link.substring(link.lastIndexOf("|")+1)); }
336 if (linkMenu.getItemCount() > 0)
340 seqMenu.add(linkMenu);
348 // TODO: add group link menu entry here
351 seqMenu.setLabel(seq.getName());
352 if (seq == ap.av.getAlignment().getSeqrep())
354 makeReferenceSeq.setLabel(MessageManager
355 .getString("action.unmark_as_reference"));// Unmark
360 makeReferenceSeq.setLabel(MessageManager
361 .getString("action.set_as_reference")); // );
363 repGroup.setLabel(MessageManager.formatMessage(
364 "label.represent_group_with", new String[]
372 if (!ap.av.hasHiddenRows())
379 final int index = ap.av.getAlignment().findIndex(seq);
381 if (ap.av.adjustForHiddenSeqs(index)
382 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
384 revealSeq_index = index;
394 * add a show URL menu item to the given linkMenu
398 * - menu label string
402 private void addshowLink(Menu linkMenu, final String target,
405 addshowLink(linkMenu, target, target, url);
409 * add a show URL menu item to the given linkMenu
413 * - URL target window
415 * - menu label string
419 private void addshowLink(Menu linkMenu, final String target,
420 final String label, final String url)
422 MenuItem item = new MenuItem(label);
423 item.addActionListener(new java.awt.event.ActionListener()
425 public void actionPerformed(ActionEvent e)
427 ap.alignFrame.showURL(url, target);
433 public void itemStateChanged(ItemEvent evt)
435 if (evt.getSource() == abovePIDColour)
437 abovePIDColour_itemStateChanged();
439 else if (evt.getSource() == showColourText)
441 showColourText_itemStateChanged();
443 else if (evt.getSource() == showText)
445 showText_itemStateChanged();
447 else if (evt.getSource() == showBoxes)
449 showBoxes_itemStateChanged();
451 else if (evt.getSource() == displayNonconserved)
453 this.showNonconserved_itemStateChanged();
457 public void actionPerformed(ActionEvent evt)
459 Object source = evt.getSource();
460 if (source == clustalColour)
462 clustalColour_actionPerformed();
464 else if (source == zappoColour)
466 zappoColour_actionPerformed();
468 else if (source == taylorColour)
470 taylorColour_actionPerformed();
472 else if (source == hydrophobicityColour)
474 hydrophobicityColour_actionPerformed();
476 else if (source == helixColour)
478 helixColour_actionPerformed();
480 else if (source == strandColour)
482 strandColour_actionPerformed();
484 else if (source == turnColour)
486 turnColour_actionPerformed();
488 else if (source == buriedColour)
490 buriedColour_actionPerformed();
492 else if (source == nucleotideMenuItem)
494 nucleotideMenuItem_actionPerformed();
497 else if (source == userDefinedColour)
499 userDefinedColour_actionPerformed();
501 else if (source == PIDColour)
503 PIDColour_actionPerformed();
505 else if (source == BLOSUM62Colour)
507 BLOSUM62Colour_actionPerformed();
509 else if (source == noColourmenuItem)
511 noColourmenuItem_actionPerformed();
513 else if (source == conservationMenuItem)
515 conservationMenuItem_itemStateChanged();
517 else if (source == unGroupMenuItem)
519 unGroupMenuItem_actionPerformed();
522 else if (source == createGroupMenuItem)
524 createGroupMenuItem_actionPerformed();
527 else if (source == sequenceName)
531 else if (source == makeReferenceSeq)
533 makeReferenceSeq_actionPerformed();
535 else if (source == sequenceDetails)
537 showSequenceDetails();
539 else if (source == selSeqDetails)
541 showSequenceSelectionDetails();
543 else if (source == pdb)
547 else if (source == hideSeqs)
549 hideSequences(false);
551 else if (source == repGroup)
555 else if (source == revealSeq)
557 ap.av.showSequence(revealSeq_index);
559 else if (source == revealAll)
561 ap.av.showAllHiddenSeqs();
564 else if (source == editGroupName)
566 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
567 getGroup().getDescription(), " Group Name",
568 "Group Description", ap.alignFrame,
569 "Edit Group Name / Description", 500, 100, true);
573 getGroup().setName(dialog.getName().replace(' ', '_'));
574 getGroup().setDescription(dialog.getDescription());
578 else if (source == copy)
580 ap.alignFrame.copy_actionPerformed();
582 else if (source == cut)
584 ap.alignFrame.cut_actionPerformed();
586 else if (source == editSequence)
588 SequenceGroup sg = ap.av.getSelectionGroup();
594 seq = (Sequence) sg.getSequenceAt(0);
597 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
598 sg.getStartRes(), sg.getEndRes() + 1), null,
599 "Edit Sequence ", null,
601 ap.alignFrame, "Edit Sequence", 500, 100, true);
605 EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
606 Action.REPLACE, dialog.getName().replace(' ',
607 ap.av.getGapCharacter()),
608 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
609 sg.getStartRes(), sg.getEndRes() + 1,
610 ap.av.getAlignment());
612 ap.alignFrame.addHistoryItem(editCommand);
614 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
619 else if (source == toUpper || source == toLower || source == toggleCase)
621 SequenceGroup sg = ap.av.getSelectionGroup();
622 Vector regions = new Vector();
625 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(),
719 ap.av.showJVSuffix, ap.av, true));
723 protected void showSequenceSelectionDetails()
725 createSequenceDetailsReport(ap.av.getSequenceSelection());
728 protected void showSequenceDetails()
730 createSequenceDetailsReport(new SequenceI[]
734 public void createSequenceDetailsReport(SequenceI[] sequences)
737 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
739 StringBuffer contents = new StringBuffer();
740 for (SequenceI seq : sequences)
742 contents.append(MessageManager.formatMessage(
743 "label.annotation_for_displayid", new String[]
744 { seq.getDisplayId(true) }));
745 new SequenceAnnotationReport(null)
746 .createSequenceAnnotationReport(
752 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
754 contents.append("</p>");
756 Frame frame = new Frame();
758 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
759 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
760 : "Selection"), 600, 500);
761 cap.setText(MessageManager.formatMessage("label.html_content",
763 { contents.toString() }));
768 EditNameDialog dialog = new EditNameDialog(seq.getName(),
769 seq.getDescription(), " Sequence Name",
770 "Sequence Description", ap.alignFrame,
771 "Edit Sequence Name / Description", 500, 100, true);
775 seq.setName(dialog.getName());
776 seq.setDescription(dialog.getDescription());
777 ap.paintAlignment(false);
783 if (seq.getPDBId() != null)
785 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
787 if (ap.av.applet.jmolAvailable)
789 new jalview.appletgui.AppletJmol(entry, new Sequence[]
790 { seq }, null, ap, AppletFormatAdapter.URL);
794 new MCview.AppletPDBViewer(entry, new Sequence[]
795 { seq }, null, ap, AppletFormatAdapter.URL);
801 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
802 cap.setText(MessageManager.getString("label.paste_pdb_file"));
803 cap.setPDBImport(seq);
804 Frame frame = new Frame();
806 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
807 "label.paste_pdb_file_for_sequence", new String[]
808 { seq.getName() }), 400, 300);
812 private void jbInit() throws Exception
814 groupMenu.setLabel(MessageManager.getString("label.selection"));
815 sequenceFeature.addActionListener(this);
817 editGroupName.addActionListener(this);
818 unGroupMenuItem.setLabel(MessageManager
819 .getString("action.remove_group"));
820 unGroupMenuItem.addActionListener(this);
822 createGroupMenuItem.setLabel(MessageManager
823 .getString("action.create_group"));
824 createGroupMenuItem.addActionListener(this);
826 nucleotideMenuItem.setLabel(MessageManager
827 .getString("label.nucleotide"));
828 nucleotideMenuItem.addActionListener(this);
829 conservationMenuItem.addItemListener(this);
830 abovePIDColour.addItemListener(this);
831 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
832 showBoxes.setLabel(MessageManager.getString("action.boxes"));
833 showBoxes.setState(true);
834 showBoxes.addItemListener(this);
835 sequenceName.addActionListener(this);
836 sequenceDetails.addActionListener(this);
837 selSeqDetails.addActionListener(this);
838 displayNonconserved.setLabel(MessageManager
839 .getString("label.show_non_conversed"));
840 displayNonconserved.setState(false);
841 displayNonconserved.addItemListener(this);
842 showText.setLabel(MessageManager.getString("action.text"));
843 showText.addItemListener(this);
844 showColourText.setLabel(MessageManager.getString("label.colour_text"));
845 showColourText.addItemListener(this);
846 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
847 seqMenu.setLabel(MessageManager.getString("label.sequence"));
848 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
849 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
850 repGroup.setLabel(MessageManager.formatMessage(
851 "label.represent_group_with", new String[]
853 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
854 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
855 menu1.setLabel(MessageManager.getString("label.group") + ":");
861 // groupMenu.add(selSeqDetails);
862 groupMenu.add(editMenu);
863 groupMenu.add(outputmenu);
864 groupMenu.add(sequenceFeature);
865 groupMenu.add(createGroupMenuItem);
866 groupMenu.add(unGroupMenuItem);
867 groupMenu.add(menu1);
869 colourMenu.add(noColourmenuItem);
870 colourMenu.add(clustalColour);
871 colourMenu.add(BLOSUM62Colour);
872 colourMenu.add(PIDColour);
873 colourMenu.add(zappoColour);
874 colourMenu.add(taylorColour);
875 colourMenu.add(hydrophobicityColour);
876 colourMenu.add(helixColour);
877 colourMenu.add(strandColour);
878 colourMenu.add(turnColour);
879 colourMenu.add(buriedColour);
880 colourMenu.add(nucleotideMenuItem);
881 colourMenu.add(userDefinedColour);
882 colourMenu.addSeparator();
883 colourMenu.add(abovePIDColour);
884 colourMenu.add(conservationMenuItem);
886 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
887 noColourmenuItem.addActionListener(this);
889 clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
890 clustalColour.addActionListener(this);
891 zappoColour.setLabel(MessageManager.getString("label.zappo"));
892 zappoColour.addActionListener(this);
893 taylorColour.setLabel(MessageManager.getString("label.taylor"));
894 taylorColour.addActionListener(this);
895 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
896 hydrophobicityColour.addActionListener(this);
897 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
898 helixColour.addActionListener(this);
899 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
900 strandColour.addActionListener(this);
901 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
902 turnColour.addActionListener(this);
903 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
904 buriedColour.addActionListener(this);
905 abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
907 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
908 userDefinedColour.addActionListener(this);
909 PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
910 PIDColour.addActionListener(this);
911 BLOSUM62Colour.setLabel("BLOSUM62");
912 BLOSUM62Colour.addActionListener(this);
913 conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
916 copy.addActionListener(this);
918 cut.addActionListener(this);
920 editMenu.add(editSequence);
921 editSequence.addActionListener(this);
923 editMenu.add(toUpper);
924 toUpper.addActionListener(this);
925 editMenu.add(toLower);
926 toLower.addActionListener(this);
927 editMenu.add(toggleCase);
928 seqMenu.add(sequenceName);
929 seqMenu.add(makeReferenceSeq);
930 // seqMenu.add(sequenceDetails);
932 if (!ap.av.applet.useXtrnalSviewer)
936 seqMenu.add(repGroup);
937 menu1.add(editGroupName);
938 menu1.add(colourMenu);
939 menu1.add(showBoxes);
941 menu1.add(showColourText);
942 menu1.add(displayNonconserved);
943 toggleCase.addActionListener(this);
944 pdb.addActionListener(this);
945 hideSeqs.addActionListener(this);
946 repGroup.addActionListener(this);
947 revealAll.addActionListener(this);
948 revealSeq.addActionListener(this);
949 makeReferenceSeq.addActionListener(this);
954 ap.paintAlignment(true);
957 protected void clustalColour_actionPerformed()
959 SequenceGroup sg = getGroup();
960 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
964 protected void zappoColour_actionPerformed()
966 getGroup().cs = new ZappoColourScheme();
970 protected void taylorColour_actionPerformed()
972 getGroup().cs = new TaylorColourScheme();
976 protected void hydrophobicityColour_actionPerformed()
978 getGroup().cs = new HydrophobicColourScheme();
982 protected void helixColour_actionPerformed()
984 getGroup().cs = new HelixColourScheme();
988 protected void strandColour_actionPerformed()
990 getGroup().cs = new StrandColourScheme();
994 protected void turnColour_actionPerformed()
996 getGroup().cs = new TurnColourScheme();
1000 protected void buriedColour_actionPerformed()
1002 getGroup().cs = new BuriedColourScheme();
1006 public void nucleotideMenuItem_actionPerformed()
1008 getGroup().cs = new NucleotideColourScheme();
1012 protected void abovePIDColour_itemStateChanged()
1014 SequenceGroup sg = getGroup();
1020 if (abovePIDColour.getState())
1022 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1023 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1024 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1027 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1029 SliderPanel.showPIDSlider();
1033 // remove PIDColouring
1035 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1042 protected void userDefinedColour_actionPerformed()
1044 new UserDefinedColours(ap, getGroup());
1047 protected void PIDColour_actionPerformed()
1049 SequenceGroup sg = getGroup();
1050 sg.cs = new PIDColourScheme();
1051 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1052 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1056 protected void BLOSUM62Colour_actionPerformed()
1058 SequenceGroup sg = getGroup();
1060 sg.cs = new Blosum62ColourScheme();
1062 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1063 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1068 protected void noColourmenuItem_actionPerformed()
1070 getGroup().cs = null;
1074 protected void conservationMenuItem_itemStateChanged()
1076 SequenceGroup sg = getGroup();
1082 if (conservationMenuItem.getState())
1085 sg.cs.setConservation(Conservation.calculateConservation("Group",
1086 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1087 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1088 .getWidth(), false, ap.av.getConsPercGaps(), false));
1089 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1090 SliderPanel.showConservationSlider();
1093 // remove ConservationColouring
1095 sg.cs.setConservation(null);
1101 SequenceGroup getGroup()
1103 SequenceGroup sg = ap.av.getSelectionGroup();
1105 // this method won't add a new group if it already exists
1108 ap.av.getAlignment().addGroup(sg);
1114 void unGroupMenuItem_actionPerformed()
1116 SequenceGroup sg = ap.av.getSelectionGroup();
1117 ap.av.getAlignment().deleteGroup(sg);
1118 ap.av.setSelectionGroup(null);
1119 ap.paintAlignment(true);
1122 void createGroupMenuItem_actionPerformed()
1124 getGroup(); // implicitly create group
1128 public void showColourText_itemStateChanged()
1130 getGroup().setColourText(showColourText.getState());
1134 public void showText_itemStateChanged()
1136 getGroup().setDisplayText(showText.getState());
1139 public void makeReferenceSeq_actionPerformed()
1141 if (!ap.av.getAlignment().hasSeqrep())
1143 // initialise the display flags so the user sees something happen
1144 ap.av.setDisplayReferenceSeq(true);
1145 ap.av.setColourByReferenceSeq(true);
1146 ap.av.getAlignment().setSeqrep(seq);
1150 if (ap.av.getAlignment().getSeqrep() == seq)
1152 ap.av.getAlignment().setSeqrep(null);
1156 ap.av.getAlignment().setSeqrep(seq);
1162 public void showNonconserved_itemStateChanged()
1164 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1168 public void showBoxes_itemStateChanged()
1170 getGroup().setDisplayBoxes(showBoxes.getState());
1174 void hideSequences(boolean representGroup)
1176 SequenceGroup sg = ap.av.getSelectionGroup();
1177 if (sg == null || sg.getSize() < 1)
1179 ap.av.hideSequence(new SequenceI[]
1184 ap.av.setSelectionGroup(null);
1188 ap.av.hideRepSequences(seq, sg);
1193 int gsize = sg.getSize();
1196 hseqs = new SequenceI[gsize];
1199 for (int i = 0; i < gsize; i++)
1201 hseqs[index++] = sg.getSequenceAt(i);
1204 ap.av.hideSequence(hseqs);
1205 ap.av.sendSelection();