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") + "...");
157 MenuItem revealAll = new MenuItem();
159 MenuItem revealSeq = new MenuItem();
162 * index of sequence to be revealed
164 int revealSeq_index = -1;
166 Menu menu1 = new Menu();
168 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
170 // /////////////////////////////////////////////////////////
171 // If this is activated from the sequence panel, the user may want to
172 // edit or annotate a particular residue. Therefore display the residue menu
174 // If from the IDPanel, we must display the sequence menu
175 // ////////////////////////////////////////////////////////
183 } catch (Exception e)
188 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
190 MenuItem item = new MenuItem(
191 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
193 item.addActionListener(this);
194 outputmenu.add(item);
197 SequenceGroup sg = ap.av.getSelectionGroup();
199 if (sg != null && sg.getSize() > 0)
201 editGroupName.setLabel(MessageManager.formatMessage(
202 "label.name_param", new String[]
204 showText.setState(sg.getDisplayText());
205 showColourText.setState(sg.getColourText());
206 showBoxes.setState(sg.getDisplayBoxes());
207 displayNonconserved.setState(sg.getShowNonconserved());
208 if (!ap.av.getAlignment().getGroups().contains(sg))
210 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
211 groupMenu.remove(unGroupMenuItem);
215 menu1.setLabel(MessageManager.getString("action.edit_group"));
216 groupMenu.remove(createGroupMenuItem);
226 if (links != null && links.size() > 0)
228 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
230 for (int i = 0; i < links.size(); i++)
232 link = links.elementAt(i).toString();
233 UrlLink urlLink = new UrlLink(link);
234 if (!urlLink.isValid())
236 System.err.println(urlLink.getInvalidMessage());
239 final String target = urlLink.getTarget(); // link.substring(0,
240 // link.indexOf("|"));
241 final String label = urlLink.getLabel();
242 if (seq != null && urlLink.isDynamic())
245 // collect matching db-refs
246 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
247 seq.getDBRef(), new String[]
249 // collect id string too
250 String id = seq.getName();
251 String descr = seq.getDescription();
252 if (descr != null && descr.length() < 1)
258 for (int r = 0; r < dbr.length; r++)
260 if (id != null && dbr[r].getAccessionId().equals(id))
262 // suppress duplicate link creation for the bare sequence ID
263 // string with this link
266 // create Bare ID link for this RUL
267 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
271 for (int u = 0; u < urls.length; u += 2)
273 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
280 // create Bare ID link for this RUL
281 String[] urls = urlLink.makeUrls(id, true);
284 for (int u = 0; u < urls.length; u += 2)
286 addshowLink(linkMenu, label, urls[u + 1]);
289 // addshowLink(linkMenu, target, url_pref + id + url_suff);
291 // Now construct URLs from description but only try to do it for regex
293 if (descr != null && urlLink.getRegexReplace() != null)
295 // create link for this URL from description only if regex matches
296 String[] urls = urlLink.makeUrls(descr, true);
299 for (int u = 0; u < urls.length; u += 2)
301 addshowLink(linkMenu, label, urls[u + 1]);
308 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
313 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
314 * string and any matching database reference accessions String url_pref
315 * = link.substring(link.indexOf("|") + 1,
316 * link.indexOf("$SEQUENCE_ID$"));
318 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
319 * // collect matching db-refs DBRefEntry[] dbr =
320 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
321 * String[]{target}); // collect id string too String id =
322 * seq.getName(); if (id.indexOf("|") > -1) { id =
323 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
324 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
325 * suppress duplicate link creation for the bare sequence ID string with
326 * this link id = null; } addshowLink(linkMenu,
327 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
328 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
329 * create Bare ID link for this RUL addshowLink(linkMenu, target,
330 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
331 * link.substring(link.lastIndexOf("|")+1)); }
334 if (linkMenu.getItemCount() > 0)
338 seqMenu.add(linkMenu);
346 // TODO: add group link menu entry here
349 seqMenu.setLabel(seq.getName());
350 repGroup.setLabel(MessageManager.formatMessage(
351 "label.represent_group_with", new String[]
359 if (!ap.av.hasHiddenRows())
366 final int index = ap.av.getAlignment().findIndex(seq);
368 if (ap.av.adjustForHiddenSeqs(index)
369 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
371 revealSeq_index = index;
381 * add a show URL menu item to the given linkMenu
385 * - menu label string
389 private void addshowLink(Menu linkMenu, final String target,
392 addshowLink(linkMenu, target, target, url);
396 * add a show URL menu item to the given linkMenu
400 * - URL target window
402 * - menu label string
406 private void addshowLink(Menu linkMenu, final String target,
407 final String label, final String url)
409 MenuItem item = new MenuItem(label);
410 item.addActionListener(new java.awt.event.ActionListener()
412 public void actionPerformed(ActionEvent e)
414 ap.alignFrame.showURL(url, target);
420 public void itemStateChanged(ItemEvent evt)
422 if (evt.getSource() == abovePIDColour)
424 abovePIDColour_itemStateChanged();
426 else if (evt.getSource() == showColourText)
428 showColourText_itemStateChanged();
430 else if (evt.getSource() == showText)
432 showText_itemStateChanged();
434 else if (evt.getSource() == showBoxes)
436 showBoxes_itemStateChanged();
438 else if (evt.getSource() == displayNonconserved)
440 this.showNonconserved_itemStateChanged();
444 public void actionPerformed(ActionEvent evt)
446 Object source = evt.getSource();
447 if (source == clustalColour)
449 clustalColour_actionPerformed();
451 else if (source == zappoColour)
453 zappoColour_actionPerformed();
455 else if (source == taylorColour)
457 taylorColour_actionPerformed();
459 else if (source == hydrophobicityColour)
461 hydrophobicityColour_actionPerformed();
463 else if (source == helixColour)
465 helixColour_actionPerformed();
467 else if (source == strandColour)
469 strandColour_actionPerformed();
471 else if (source == turnColour)
473 turnColour_actionPerformed();
475 else if (source == buriedColour)
477 buriedColour_actionPerformed();
479 else if (source == nucleotideMenuItem)
481 nucleotideMenuItem_actionPerformed();
484 else if (source == userDefinedColour)
486 userDefinedColour_actionPerformed();
488 else if (source == PIDColour)
490 PIDColour_actionPerformed();
492 else if (source == BLOSUM62Colour)
494 BLOSUM62Colour_actionPerformed();
496 else if (source == noColourmenuItem)
498 noColourmenuItem_actionPerformed();
500 else if (source == conservationMenuItem)
502 conservationMenuItem_itemStateChanged();
504 else if (source == unGroupMenuItem)
506 unGroupMenuItem_actionPerformed();
509 else if (source == createGroupMenuItem)
511 createGroupMenuItem_actionPerformed();
514 else if (source == sequenceName)
518 else if (source == sequenceDetails)
520 showSequenceDetails();
522 else if (source == selSeqDetails)
524 showSequenceSelectionDetails();
526 else if (source == pdb)
530 else if (source == hideSeqs)
532 hideSequences(false);
534 else if (source == repGroup)
538 else if (source == revealSeq)
540 ap.av.showSequence(revealSeq_index);
542 else if (source == revealAll)
544 ap.av.showAllHiddenSeqs();
547 else if (source == editGroupName)
549 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
550 getGroup().getDescription(), " Group Name",
551 "Group Description", ap.alignFrame,
552 "Edit Group Name / Description", 500, 100, true);
556 getGroup().setName(dialog.getName().replace(' ', '_'));
557 getGroup().setDescription(dialog.getDescription());
561 else if (source == copy)
563 ap.alignFrame.copy_actionPerformed();
565 else if (source == cut)
567 ap.alignFrame.cut_actionPerformed();
569 else if (source == editSequence)
571 SequenceGroup sg = ap.av.getSelectionGroup();
577 seq = (Sequence) sg.getSequenceAt(0);
580 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
581 sg.getStartRes(), sg.getEndRes() + 1), null,
582 "Edit Sequence ", null,
584 ap.alignFrame, "Edit Sequence", 500, 100, true);
588 EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
589 Action.REPLACE, dialog.getName().replace(' ',
590 ap.av.getGapCharacter()),
591 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
592 sg.getStartRes(), sg.getEndRes() + 1,
593 ap.av.getAlignment());
595 ap.alignFrame.addHistoryItem(editCommand);
597 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
602 else if (source == toUpper || source == toLower || source == toggleCase)
604 SequenceGroup sg = ap.av.getSelectionGroup();
605 Vector regions = new Vector();
608 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
609 sg.getStartRes(), sg.getEndRes() + 1);
614 if (source == toggleCase)
616 description = "Toggle Case";
617 caseChange = ChangeCaseCommand.TOGGLE_CASE;
619 else if (source == toUpper)
621 description = "To Upper Case";
622 caseChange = ChangeCaseCommand.TO_UPPER;
626 description = "To Lower Case";
627 caseChange = ChangeCaseCommand.TO_LOWER;
630 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
631 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
632 startEnd, caseChange);
634 ap.alignFrame.addHistoryItem(caseCommand);
636 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
641 else if (source == sequenceFeature)
643 SequenceGroup sg = ap.av.getSelectionGroup();
649 int rsize = 0, gSize = sg.getSize();
650 SequenceI[] rseqs, seqs = new SequenceI[gSize];
651 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
653 for (int i = 0; i < gSize; i++)
655 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
656 int end = sg.findEndRes(sg.getSequenceAt(i));
659 seqs[rsize] = sg.getSequenceAt(i);
660 features[rsize] = new SequenceFeature(null, null, null, start,
665 rseqs = new SequenceI[rsize];
666 tfeatures = new SequenceFeature[rsize];
667 System.arraycopy(seqs, 0, rseqs, 0, rsize);
668 System.arraycopy(features, 0, tfeatures, 0, rsize);
669 features = tfeatures;
672 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
675 ap.alignFrame.sequenceFeatures.setState(true);
676 ap.av.setShowSequenceFeatures(true);;
677 ap.highlightSearchResults(null);
687 void outputText(ActionEvent e)
689 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
691 Frame frame = new Frame();
693 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
694 "label.selection_output_command", new String[]
695 { e.getActionCommand() }), 600, 500);
696 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
697 // now returns a full copy of sequence data
698 // TODO consider using getSequenceSelection instead here
700 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
701 e.getActionCommand(),
702 ap.av.showJVSuffix, ap.av, true));
706 protected void showSequenceSelectionDetails()
708 createSequenceDetailsReport(ap.av.getSequenceSelection());
711 protected void showSequenceDetails()
713 createSequenceDetailsReport(new SequenceI[]
717 public void createSequenceDetailsReport(SequenceI[] sequences)
720 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
722 StringBuffer contents = new StringBuffer();
723 for (SequenceI seq : sequences)
725 contents.append(MessageManager.formatMessage(
726 "label.annotation_for_displayid", new String[]
727 { seq.getDisplayId(true) }));
728 new SequenceAnnotationReport(null)
729 .createSequenceAnnotationReport(
735 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.getMinMax()
737 contents.append("</p>");
739 Frame frame = new Frame();
741 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
742 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
743 : "Selection"), 600, 500);
744 cap.setText(MessageManager.formatMessage("label.html_content",
746 { contents.toString() }));
751 EditNameDialog dialog = new EditNameDialog(seq.getName(),
752 seq.getDescription(), " Sequence Name",
753 "Sequence Description", ap.alignFrame,
754 "Edit Sequence Name / Description", 500, 100, true);
758 seq.setName(dialog.getName());
759 seq.setDescription(dialog.getDescription());
760 ap.paintAlignment(false);
766 if (seq.getPDBId() != null)
768 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
770 if (ap.av.applet.jmolAvailable)
772 new jalview.appletgui.AppletJmol(entry, new Sequence[]
773 { seq }, null, ap, AppletFormatAdapter.URL);
777 new MCview.AppletPDBViewer(entry, new Sequence[]
778 { seq }, null, ap, AppletFormatAdapter.URL);
784 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
785 cap.setText(MessageManager.getString("label.paste_pdb_file"));
786 cap.setPDBImport(seq);
787 Frame frame = new Frame();
789 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
790 "label.paste_pdb_file_for_sequence", new String[]
791 { seq.getName() }), 400, 300);
795 private void jbInit() throws Exception
797 groupMenu.setLabel(MessageManager.getString("label.selection"));
798 sequenceFeature.addActionListener(this);
800 editGroupName.addActionListener(this);
801 unGroupMenuItem.setLabel(MessageManager
802 .getString("action.remove_group"));
803 unGroupMenuItem.addActionListener(this);
805 createGroupMenuItem.setLabel(MessageManager
806 .getString("action.create_group"));
807 createGroupMenuItem.addActionListener(this);
809 nucleotideMenuItem.setLabel(MessageManager
810 .getString("label.nucleotide"));
811 nucleotideMenuItem.addActionListener(this);
812 conservationMenuItem.addItemListener(this);
813 abovePIDColour.addItemListener(this);
814 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
815 showBoxes.setLabel(MessageManager.getString("action.boxes"));
816 showBoxes.setState(true);
817 showBoxes.addItemListener(this);
818 sequenceName.addActionListener(this);
819 sequenceDetails.addActionListener(this);
820 selSeqDetails.addActionListener(this);
821 displayNonconserved.setLabel(MessageManager
822 .getString("label.show_non_conversed"));
823 displayNonconserved.setState(false);
824 displayNonconserved.addItemListener(this);
825 showText.setLabel(MessageManager.getString("action.text"));
826 showText.addItemListener(this);
827 showColourText.setLabel(MessageManager.getString("label.colour_text"));
828 showColourText.addItemListener(this);
829 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
830 seqMenu.setLabel(MessageManager.getString("label.sequence"));
831 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
832 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
833 repGroup.setLabel(MessageManager.formatMessage(
834 "label.represent_group_with", new String[]
836 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
837 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
838 menu1.setLabel(MessageManager.getString("label.group") + ":");
844 // groupMenu.add(selSeqDetails);
845 groupMenu.add(editMenu);
846 groupMenu.add(outputmenu);
847 groupMenu.add(sequenceFeature);
848 groupMenu.add(createGroupMenuItem);
849 groupMenu.add(unGroupMenuItem);
850 groupMenu.add(menu1);
852 colourMenu.add(noColourmenuItem);
853 colourMenu.add(clustalColour);
854 colourMenu.add(BLOSUM62Colour);
855 colourMenu.add(PIDColour);
856 colourMenu.add(zappoColour);
857 colourMenu.add(taylorColour);
858 colourMenu.add(hydrophobicityColour);
859 colourMenu.add(helixColour);
860 colourMenu.add(strandColour);
861 colourMenu.add(turnColour);
862 colourMenu.add(buriedColour);
863 colourMenu.add(nucleotideMenuItem);
864 colourMenu.add(userDefinedColour);
865 colourMenu.addSeparator();
866 colourMenu.add(abovePIDColour);
867 colourMenu.add(conservationMenuItem);
869 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
870 noColourmenuItem.addActionListener(this);
872 clustalColour.setLabel(MessageManager.getString("label.clustalx_colours"));
873 clustalColour.addActionListener(this);
874 zappoColour.setLabel(MessageManager.getString("label.zappo"));
875 zappoColour.addActionListener(this);
876 taylorColour.setLabel(MessageManager.getString("label.taylor"));
877 taylorColour.addActionListener(this);
878 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
879 hydrophobicityColour.addActionListener(this);
880 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
881 helixColour.addActionListener(this);
882 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
883 strandColour.addActionListener(this);
884 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
885 turnColour.addActionListener(this);
886 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
887 buriedColour.addActionListener(this);
888 abovePIDColour.setLabel(MessageManager.getString("label.above_identity_percentage"));
890 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
891 userDefinedColour.addActionListener(this);
892 PIDColour.setLabel(MessageManager.getString("action.percentage_identity"));
893 PIDColour.addActionListener(this);
894 BLOSUM62Colour.setLabel("BLOSUM62");
895 BLOSUM62Colour.addActionListener(this);
896 conservationMenuItem.setLabel(MessageManager.getString("label.conservation"));
899 copy.addActionListener(this);
901 cut.addActionListener(this);
903 editMenu.add(editSequence);
904 editSequence.addActionListener(this);
906 editMenu.add(toUpper);
907 toUpper.addActionListener(this);
908 editMenu.add(toLower);
909 toLower.addActionListener(this);
910 editMenu.add(toggleCase);
911 seqMenu.add(sequenceName);
912 // seqMenu.add(sequenceDetails);
914 if (!ap.av.applet.useXtrnalSviewer)
918 seqMenu.add(repGroup);
919 menu1.add(editGroupName);
920 menu1.add(colourMenu);
921 menu1.add(showBoxes);
923 menu1.add(showColourText);
924 menu1.add(displayNonconserved);
925 toggleCase.addActionListener(this);
926 pdb.addActionListener(this);
927 hideSeqs.addActionListener(this);
928 repGroup.addActionListener(this);
929 revealAll.addActionListener(this);
930 revealSeq.addActionListener(this);
935 ap.paintAlignment(true);
938 protected void clustalColour_actionPerformed()
940 SequenceGroup sg = getGroup();
941 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
945 protected void zappoColour_actionPerformed()
947 getGroup().cs = new ZappoColourScheme();
951 protected void taylorColour_actionPerformed()
953 getGroup().cs = new TaylorColourScheme();
957 protected void hydrophobicityColour_actionPerformed()
959 getGroup().cs = new HydrophobicColourScheme();
963 protected void helixColour_actionPerformed()
965 getGroup().cs = new HelixColourScheme();
969 protected void strandColour_actionPerformed()
971 getGroup().cs = new StrandColourScheme();
975 protected void turnColour_actionPerformed()
977 getGroup().cs = new TurnColourScheme();
981 protected void buriedColour_actionPerformed()
983 getGroup().cs = new BuriedColourScheme();
987 public void nucleotideMenuItem_actionPerformed()
989 getGroup().cs = new NucleotideColourScheme();
993 protected void abovePIDColour_itemStateChanged()
995 SequenceGroup sg = getGroup();
1001 if (abovePIDColour.getState())
1003 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1004 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1005 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1008 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1010 SliderPanel.showPIDSlider();
1014 // remove PIDColouring
1016 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1023 protected void userDefinedColour_actionPerformed()
1025 new UserDefinedColours(ap, getGroup());
1028 protected void PIDColour_actionPerformed()
1030 SequenceGroup sg = getGroup();
1031 sg.cs = new PIDColourScheme();
1032 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1033 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1037 protected void BLOSUM62Colour_actionPerformed()
1039 SequenceGroup sg = getGroup();
1041 sg.cs = new Blosum62ColourScheme();
1043 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1044 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1049 protected void noColourmenuItem_actionPerformed()
1051 getGroup().cs = null;
1055 protected void conservationMenuItem_itemStateChanged()
1057 SequenceGroup sg = getGroup();
1063 if (conservationMenuItem.getState())
1066 sg.cs.setConservation(Conservation.calculateConservation("Group",
1067 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1068 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1069 .getWidth(), false, ap.av.getConsPercGaps(), false));
1070 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1071 SliderPanel.showConservationSlider();
1074 // remove ConservationColouring
1076 sg.cs.setConservation(null);
1082 SequenceGroup getGroup()
1084 SequenceGroup sg = ap.av.getSelectionGroup();
1086 // this method won't add a new group if it already exists
1089 ap.av.getAlignment().addGroup(sg);
1095 void unGroupMenuItem_actionPerformed()
1097 SequenceGroup sg = ap.av.getSelectionGroup();
1098 ap.av.getAlignment().deleteGroup(sg);
1099 ap.av.setSelectionGroup(null);
1100 ap.paintAlignment(true);
1103 void createGroupMenuItem_actionPerformed()
1105 getGroup(); // implicitly create group
1109 public void showColourText_itemStateChanged()
1111 getGroup().setColourText(showColourText.getState());
1115 public void showText_itemStateChanged()
1117 getGroup().setDisplayText(showText.getState());
1121 public void showNonconserved_itemStateChanged()
1123 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1127 public void showBoxes_itemStateChanged()
1129 getGroup().setDisplayBoxes(showBoxes.getState());
1133 void hideSequences(boolean representGroup)
1135 SequenceGroup sg = ap.av.getSelectionGroup();
1136 if (sg == null || sg.getSize() < 1)
1138 ap.av.hideSequence(new SequenceI[]
1143 ap.av.setSelectionGroup(null);
1147 ap.av.hideRepSequences(seq, sg);
1152 int gsize = sg.getSize();
1155 hseqs = new SequenceI[gsize];
1158 for (int i = 0; i < gsize; i++)
1160 hseqs[index++] = sg.getSequenceAt(i);
1163 ap.av.hideSequence(hseqs);
1164 ap.av.sendSelection();