2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.JalviewLite;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.PDBEntry;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.io.AppletFormatAdapter;
38 import jalview.io.DataSourceType;
39 import jalview.io.FileFormat;
40 import jalview.io.SequenceAnnotationReport;
41 import jalview.schemes.Blosum62ColourScheme;
42 import jalview.schemes.BuriedColourScheme;
43 import jalview.schemes.ClustalxColourScheme;
44 import jalview.schemes.HelixColourScheme;
45 import jalview.schemes.HydrophobicColourScheme;
46 import jalview.schemes.NucleotideColourScheme;
47 import jalview.schemes.PIDColourScheme;
48 import jalview.schemes.PurinePyrimidineColourScheme;
49 import jalview.schemes.StrandColourScheme;
50 import jalview.schemes.TaylorColourScheme;
51 import jalview.schemes.TurnColourScheme;
52 import jalview.schemes.ZappoColourScheme;
53 import jalview.util.MessageManager;
54 import jalview.util.UrlLink;
56 import java.awt.CheckboxMenuItem;
57 import java.awt.Frame;
59 import java.awt.MenuItem;
60 import java.awt.event.ActionEvent;
61 import java.awt.event.ActionListener;
62 import java.awt.event.ItemEvent;
63 import java.awt.event.ItemListener;
64 import java.util.Arrays;
65 import java.util.Collection;
66 import java.util.Collections;
67 import java.util.LinkedHashMap;
68 import java.util.List;
70 import java.util.SortedMap;
71 import java.util.TreeMap;
72 import java.util.Vector;
74 public class APopupMenu extends java.awt.PopupMenu implements
75 ActionListener, ItemListener
77 Menu groupMenu = new Menu();
79 MenuItem editGroupName = new MenuItem();
81 protected MenuItem clustalColour = new MenuItem();
83 protected MenuItem zappoColour = new MenuItem();
85 protected MenuItem taylorColour = new MenuItem();
87 protected MenuItem hydrophobicityColour = new MenuItem();
89 protected MenuItem helixColour = new MenuItem();
91 protected MenuItem strandColour = new MenuItem();
93 protected MenuItem turnColour = new MenuItem();
95 protected MenuItem buriedColour = new MenuItem();
97 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
99 protected MenuItem userDefinedColour = new MenuItem();
101 protected MenuItem PIDColour = new MenuItem();
103 protected MenuItem BLOSUM62Colour = new MenuItem();
105 MenuItem noColourmenuItem = new MenuItem();
107 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
109 final AlignmentPanel ap;
111 MenuItem unGroupMenuItem = new MenuItem();
113 MenuItem createGroupMenuItem = new MenuItem();
115 MenuItem nucleotideMenuItem = new MenuItem();
117 MenuItem purinePyrimidineMenuItem = new MenuItem();
119 Menu colourMenu = new Menu();
121 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
123 CheckboxMenuItem showText = new CheckboxMenuItem();
125 CheckboxMenuItem showColourText = new CheckboxMenuItem();
127 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
129 Menu seqShowAnnotationsMenu = new Menu(
130 MessageManager.getString("label.show_annotations"));
132 Menu seqHideAnnotationsMenu = new Menu(
133 MessageManager.getString("label.hide_annotations"));
135 MenuItem seqAddReferenceAnnotations = new MenuItem(
136 MessageManager.getString("label.add_reference_annotations"));
138 Menu groupShowAnnotationsMenu = new Menu(
139 MessageManager.getString("label.show_annotations"));
141 Menu groupHideAnnotationsMenu = new Menu(
142 MessageManager.getString("label.hide_annotations"));
144 MenuItem groupAddReferenceAnnotations = new MenuItem(
145 MessageManager.getString("label.add_reference_annotations"));
147 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
149 MenuItem copy = new MenuItem(MessageManager.getString("action.copy"));
151 MenuItem cut = new MenuItem(MessageManager.getString("action.cut"));
153 MenuItem toUpper = new MenuItem(
154 MessageManager.getString("label.to_upper_case"));
156 MenuItem toLower = new MenuItem(
157 MessageManager.getString("label.to_lower_case"));
159 MenuItem toggleCase = new MenuItem(
160 MessageManager.getString("label.toggle_case"));
162 Menu outputmenu = new Menu();
164 Menu seqMenu = new Menu();
166 MenuItem pdb = new MenuItem();
168 MenuItem hideSeqs = new MenuItem();
170 MenuItem repGroup = new MenuItem();
172 MenuItem sequenceName = new MenuItem(
173 MessageManager.getString("label.edit_name_description"));
175 MenuItem sequenceFeature = new MenuItem(
176 MessageManager.getString("label.create_sequence_feature"));
178 MenuItem editSequence = new MenuItem(
179 MessageManager.getString("label.edit_sequence"));
181 MenuItem sequenceDetails = new MenuItem(
182 MessageManager.getString("label.sequence_details"));
184 MenuItem selSeqDetails = new MenuItem(
185 MessageManager.getString("label.sequence_details"));
187 MenuItem makeReferenceSeq = new MenuItem();
191 MenuItem revealAll = new MenuItem();
193 MenuItem revealSeq = new MenuItem();
196 * index of sequence to be revealed
198 int revealSeq_index = -1;
200 Menu menu1 = new Menu();
202 public APopupMenu(AlignmentPanel apanel, final SequenceI seq,
203 Vector<String> links)
205 // /////////////////////////////////////////////////////////
206 // If this is activated from the sequence panel, the user may want to
207 // edit or annotate a particular residue. Therefore display the residue menu
209 // If from the IDPanel, we must display the sequence menu
210 // ////////////////////////////////////////////////////////
218 } catch (Exception e)
223 for (String ff : FileFormat.getWritableFormats(true))
225 MenuItem item = new MenuItem(ff);
227 item.addActionListener(this);
228 outputmenu.add(item);
231 buildAnnotationSubmenus();
233 SequenceGroup sg = ap.av.getSelectionGroup();
234 if (sg != null && sg.getSize() > 0)
236 editGroupName.setLabel(MessageManager.formatMessage(
237 "label.name_param", new Object[] { sg.getName() }));
238 showText.setState(sg.getDisplayText());
239 showColourText.setState(sg.getColourText());
240 showBoxes.setState(sg.getDisplayBoxes());
241 displayNonconserved.setState(sg.getShowNonconserved());
242 if (!ap.av.getAlignment().getGroups().contains(sg))
244 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
245 groupMenu.remove(unGroupMenuItem);
249 menu1.setLabel(MessageManager.getString("action.edit_group"));
250 groupMenu.remove(createGroupMenuItem);
260 if (links != null && links.size() > 0)
262 addFeatureLinks(seq, links);
265 // TODO: add group link menu entry here
268 seqMenu.setLabel(seq.getName());
269 if (seq == ap.av.getAlignment().getSeqrep())
271 makeReferenceSeq.setLabel(MessageManager
272 .getString("action.unmark_as_reference"));// Unmark
277 makeReferenceSeq.setLabel(MessageManager
278 .getString("action.set_as_reference")); // );
280 repGroup.setLabel(MessageManager.formatMessage(
281 "label.represent_group_with", new Object[] { seq.getName() }));
288 if (!ap.av.hasHiddenRows())
295 final int index = ap.av.getAlignment().findIndex(seq);
297 if (ap.av.adjustForHiddenSeqs(index)
298 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
300 revealSeq_index = index;
310 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
315 void addFeatureLinks(final SequenceI seq, List<String> links)
317 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
318 Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
320 for (String link : links)
322 UrlLink urlLink = null;
325 urlLink = new UrlLink(link);
326 } catch (Exception foo)
328 System.err.println("Exception for URLLink '" + link + "': "
333 if (!urlLink.isValid())
335 System.err.println(urlLink.getInvalidMessage());
339 urlLink.createLinksFromSeq(seq, linkset);
342 addshowLinks(linkMenu, linkset.values());
344 // disable link menu if there are no valid entries
345 if (linkMenu.getItemCount() > 0)
347 linkMenu.setEnabled(true);
351 linkMenu.setEnabled(false);
356 seqMenu.add(linkMenu);
365 private void addshowLinks(Menu linkMenu, Collection<List<String>> linkset)
367 for (List<String> linkstrset : linkset)
369 // split linkstr into label and url
370 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
375 * Build menus for annotation types that may be shown or hidden, and for
376 * 'reference annotations' that may be added to the alignment.
378 private void buildAnnotationSubmenus()
381 * First for the currently selected sequence (if there is one):
383 final List<SequenceI> selectedSequence = (seq == null ? Collections
384 .<SequenceI> emptyList() : Arrays.asList(seq));
385 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
386 seqHideAnnotationsMenu, selectedSequence);
387 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
391 * and repeat for the current selection group (if there is one):
393 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
394 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
396 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
397 groupHideAnnotationsMenu, selectedGroup);
398 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
403 * Determine whether or not to enable 'add reference annotations' menu item.
404 * It is enable if there are any annotations, on any of the selected
405 * sequences, which are not yet on the alignment (visible or not).
408 * @param forSequences
410 private void configureReferenceAnnotationsMenu(MenuItem menuItem,
411 List<SequenceI> forSequences)
413 menuItem.setEnabled(false);
416 * Temporary store to hold distinct calcId / type pairs for the tooltip.
417 * Using TreeMap means calcIds are shown in alphabetical order.
419 SortedMap<String, String> tipEntries = new TreeMap<String, String>();
420 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
421 AlignmentI al = this.ap.av.getAlignment();
422 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
423 tipEntries, candidates, al);
424 if (!candidates.isEmpty())
426 StringBuilder tooltip = new StringBuilder(64);
427 tooltip.append(MessageManager.getString("label.add_annotations_for"));
430 * Found annotations that could be added. Enable the menu item, and
431 * configure its action.
433 menuItem.setEnabled(true);
435 menuItem.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent e)
440 addReferenceAnnotations_actionPerformed(candidates);
447 * Add annotations to the sequences and to the alignment.
450 * a map whose keys are sequences on the alignment, and values a list
451 * of annotations to add to each sequence
453 protected void addReferenceAnnotations_actionPerformed(
454 Map<SequenceI, List<AlignmentAnnotation>> candidates)
456 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
457 final AlignmentI alignment = this.ap.getAlignment();
458 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
464 * add a show URL menu item to the given linkMenu
468 * - menu label string
472 private void addshowLink(Menu linkMenu, final String target,
475 addshowLink(linkMenu, target, target, url);
479 * add a show URL menu item to the given linkMenu
483 * - URL target window
485 * - menu label string
489 private void addshowLink(Menu linkMenu, final String target,
490 final String label, final String url)
492 MenuItem item = new MenuItem(label);
493 item.addActionListener(new java.awt.event.ActionListener()
496 public void actionPerformed(ActionEvent e)
498 ap.alignFrame.showURL(url, target);
505 public void itemStateChanged(ItemEvent evt)
507 if (evt.getSource() == abovePIDColour)
509 abovePIDColour_itemStateChanged();
511 else if (evt.getSource() == showColourText)
513 showColourText_itemStateChanged();
515 else if (evt.getSource() == showText)
517 showText_itemStateChanged();
519 else if (evt.getSource() == showBoxes)
521 showBoxes_itemStateChanged();
523 else if (evt.getSource() == displayNonconserved)
525 this.showNonconserved_itemStateChanged();
530 public void actionPerformed(ActionEvent evt)
532 Object source = evt.getSource();
533 if (source == clustalColour)
535 clustalColour_actionPerformed();
537 else if (source == zappoColour)
539 zappoColour_actionPerformed();
541 else if (source == taylorColour)
543 taylorColour_actionPerformed();
545 else if (source == hydrophobicityColour)
547 hydrophobicityColour_actionPerformed();
549 else if (source == helixColour)
551 helixColour_actionPerformed();
553 else if (source == strandColour)
555 strandColour_actionPerformed();
557 else if (source == turnColour)
559 turnColour_actionPerformed();
561 else if (source == buriedColour)
563 buriedColour_actionPerformed();
565 else if (source == nucleotideMenuItem)
567 nucleotideMenuItem_actionPerformed();
569 else if (source == purinePyrimidineMenuItem)
571 purinePyrimidineColour_actionPerformed();
574 else if (source == userDefinedColour)
576 userDefinedColour_actionPerformed();
578 else if (source == PIDColour)
580 PIDColour_actionPerformed();
582 else if (source == BLOSUM62Colour)
584 BLOSUM62Colour_actionPerformed();
586 else if (source == noColourmenuItem)
588 noColourmenuItem_actionPerformed();
590 else if (source == conservationMenuItem)
592 conservationMenuItem_itemStateChanged();
594 else if (source == unGroupMenuItem)
596 unGroupMenuItem_actionPerformed();
599 else if (source == createGroupMenuItem)
601 createGroupMenuItem_actionPerformed();
604 else if (source == sequenceName)
608 else if (source == makeReferenceSeq)
610 makeReferenceSeq_actionPerformed();
612 else if (source == sequenceDetails)
614 showSequenceDetails();
616 else if (source == selSeqDetails)
618 showSequenceSelectionDetails();
620 else if (source == pdb)
624 else if (source == hideSeqs)
626 hideSequences(false);
628 else if (source == repGroup)
632 else if (source == revealSeq)
634 ap.av.showSequence(revealSeq_index);
636 else if (source == revealAll)
638 ap.av.showAllHiddenSeqs();
641 else if (source == editGroupName)
643 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
644 getGroup().getDescription(), " Group Name",
645 "Group Description", ap.alignFrame,
646 "Edit Group Name / Description", 500, 100, true);
650 getGroup().setName(dialog.getName().replace(' ', '_'));
651 getGroup().setDescription(dialog.getDescription());
655 else if (source == copy)
657 ap.alignFrame.copy_actionPerformed();
659 else if (source == cut)
661 ap.alignFrame.cut_actionPerformed();
663 else if (source == editSequence)
665 SequenceGroup sg = ap.av.getSelectionGroup();
671 seq = sg.getSequenceAt(0);
674 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
675 sg.getStartRes(), sg.getEndRes() + 1), null,
676 "Edit Sequence ", null,
678 ap.alignFrame, "Edit Sequence", 500, 100, true);
682 EditCommand editCommand = new EditCommand(
683 MessageManager.getString("label.edit_sequences"),
684 Action.REPLACE, dialog.getName().replace(' ',
685 ap.av.getGapCharacter()),
686 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
687 sg.getStartRes(), sg.getEndRes() + 1,
688 ap.av.getAlignment());
690 ap.alignFrame.addHistoryItem(editCommand);
692 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
697 else if (source == toUpper || source == toLower || source == toggleCase)
699 SequenceGroup sg = ap.av.getSelectionGroup();
702 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
703 sg.getStartRes(), sg.getEndRes() + 1);
708 if (source == toggleCase)
710 description = "Toggle Case";
711 caseChange = ChangeCaseCommand.TOGGLE_CASE;
713 else if (source == toUpper)
715 description = "To Upper Case";
716 caseChange = ChangeCaseCommand.TO_UPPER;
720 description = "To Lower Case";
721 caseChange = ChangeCaseCommand.TO_LOWER;
724 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
725 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
726 startEnd, caseChange);
728 ap.alignFrame.addHistoryItem(caseCommand);
730 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
735 else if (source == sequenceFeature)
737 SequenceGroup sg = ap.av.getSelectionGroup();
743 int rsize = 0, gSize = sg.getSize();
744 SequenceI[] rseqs, seqs = new SequenceI[gSize];
745 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
747 for (int i = 0; i < gSize; i++)
749 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
750 int end = sg.findEndRes(sg.getSequenceAt(i));
753 seqs[rsize] = sg.getSequenceAt(i);
754 features[rsize] = new SequenceFeature(null, null, null, start,
759 rseqs = new SequenceI[rsize];
760 tfeatures = new SequenceFeature[rsize];
761 System.arraycopy(seqs, 0, rseqs, 0, rsize);
762 System.arraycopy(features, 0, tfeatures, 0, rsize);
763 features = tfeatures;
766 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
769 ap.alignFrame.sequenceFeatures.setState(true);
770 ap.av.setShowSequenceFeatures(true);
772 ap.highlightSearchResults(null);
782 void outputText(ActionEvent e)
784 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
786 Frame frame = new Frame();
788 JalviewLite.addFrame(frame, MessageManager.formatMessage(
789 "label.selection_output_command",
790 new Object[] { e.getActionCommand() }), 600, 500);
791 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
792 // now returns a full copy of sequence data
793 // TODO consider using getSequenceSelection instead here
795 FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
796 cap.setText(new AppletFormatAdapter().formatSequences(fileFormat,
797 ap.av.getShowJVSuffix(), ap, true));
801 protected void showSequenceSelectionDetails()
803 createSequenceDetailsReport(ap.av.getSequenceSelection());
806 protected void showSequenceDetails()
808 createSequenceDetailsReport(new SequenceI[] { seq });
811 public void createSequenceDetailsReport(SequenceI[] sequences)
814 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
816 StringBuilder contents = new StringBuilder(128);
817 for (SequenceI seq : sequences)
819 contents.append(MessageManager.formatMessage(
820 "label.annotation_for_displayid",
821 new Object[] { seq.getDisplayId(true) }));
822 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
827 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr
828 .getMinMax() : null);
829 contents.append("</p>");
831 Frame frame = new Frame();
833 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
834 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
835 : "Selection"), 600, 500);
836 cap.setText(MessageManager.formatMessage("label.html_content",
837 new Object[] { contents.toString() }));
842 EditNameDialog dialog = new EditNameDialog(seq.getName(),
843 seq.getDescription(), " Sequence Name",
844 "Sequence Description", ap.alignFrame,
845 "Edit Sequence Name / Description", 500, 100, true);
849 seq.setName(dialog.getName());
850 seq.setDescription(dialog.getDescription());
851 ap.paintAlignment(false);
857 Vector<PDBEntry> pdbs = seq.getAllPDBEntries();
858 if (pdbs != null&& !pdbs.isEmpty())
860 PDBEntry entry = pdbs.firstElement();
862 if (ap.av.applet.jmolAvailable)
864 new jalview.appletgui.AppletJmol(entry, new SequenceI[] { seq },
865 null, ap, DataSourceType.URL);
869 new MCview.AppletPDBViewer(entry, new SequenceI[] { seq }, null,
870 ap, DataSourceType.URL);
876 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
877 cap.setText(MessageManager.getString("label.paste_pdb_file"));
878 cap.setPDBImport(seq);
879 Frame frame = new Frame();
881 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
882 "label.paste_pdb_file_for_sequence",
883 new Object[] { seq.getName() }), 400, 300);
887 private void jbInit() throws Exception
889 groupMenu.setLabel(MessageManager.getString("label.selection"));
890 sequenceFeature.addActionListener(this);
892 editGroupName.addActionListener(this);
893 unGroupMenuItem.setLabel(MessageManager
894 .getString("action.remove_group"));
895 unGroupMenuItem.addActionListener(this);
897 createGroupMenuItem.setLabel(MessageManager
898 .getString("action.create_group"));
899 createGroupMenuItem.addActionListener(this);
901 nucleotideMenuItem.setLabel(MessageManager
902 .getString("label.nucleotide"));
903 nucleotideMenuItem.addActionListener(this);
904 purinePyrimidineMenuItem.setLabel(MessageManager
905 .getString("label.purine_pyrimidine"));
906 purinePyrimidineMenuItem.addActionListener(this);
907 conservationMenuItem.addItemListener(this);
908 abovePIDColour.addItemListener(this);
909 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
910 showBoxes.setLabel(MessageManager.getString("action.boxes"));
911 showBoxes.setState(true);
912 showBoxes.addItemListener(this);
913 sequenceName.addActionListener(this);
914 sequenceDetails.addActionListener(this);
915 selSeqDetails.addActionListener(this);
916 displayNonconserved.setLabel(MessageManager
917 .getString("label.show_non_conserved"));
918 displayNonconserved.setState(false);
919 displayNonconserved.addItemListener(this);
920 showText.setLabel(MessageManager.getString("action.text"));
921 showText.addItemListener(this);
922 showColourText.setLabel(MessageManager.getString("label.colour_text"));
923 showColourText.addItemListener(this);
924 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
925 seqMenu.setLabel(MessageManager.getString("label.sequence"));
926 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
927 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
928 repGroup.setLabel(MessageManager.formatMessage(
929 "label.represent_group_with", new Object[] { "" }));
930 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
931 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
932 menu1.setLabel(MessageManager.getString("label.group:"));
938 // groupMenu.add(selSeqDetails);
939 groupMenu.add(groupShowAnnotationsMenu);
940 groupMenu.add(groupHideAnnotationsMenu);
941 groupMenu.add(groupAddReferenceAnnotations);
942 groupMenu.add(editMenu);
943 groupMenu.add(outputmenu);
944 groupMenu.add(sequenceFeature);
945 groupMenu.add(createGroupMenuItem);
946 groupMenu.add(unGroupMenuItem);
947 groupMenu.add(menu1);
949 colourMenu.add(noColourmenuItem);
950 colourMenu.add(clustalColour);
951 colourMenu.add(BLOSUM62Colour);
952 colourMenu.add(PIDColour);
953 colourMenu.add(zappoColour);
954 colourMenu.add(taylorColour);
955 colourMenu.add(hydrophobicityColour);
956 colourMenu.add(helixColour);
957 colourMenu.add(strandColour);
958 colourMenu.add(turnColour);
959 colourMenu.add(buriedColour);
960 colourMenu.add(nucleotideMenuItem);
961 colourMenu.add(purinePyrimidineMenuItem);
962 colourMenu.add(userDefinedColour);
963 colourMenu.addSeparator();
964 colourMenu.add(abovePIDColour);
965 colourMenu.add(conservationMenuItem);
967 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
968 noColourmenuItem.addActionListener(this);
970 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
971 clustalColour.addActionListener(this);
972 zappoColour.setLabel(MessageManager.getString("label.zappo"));
973 zappoColour.addActionListener(this);
974 taylorColour.setLabel(MessageManager.getString("label.taylor"));
975 taylorColour.addActionListener(this);
976 hydrophobicityColour.setLabel(MessageManager
977 .getString("label.hydrophobicity"));
978 hydrophobicityColour.addActionListener(this);
980 .setLabel(MessageManager.getString("label.helix_propensity"));
981 helixColour.addActionListener(this);
982 strandColour.setLabel(MessageManager
983 .getString("label.strand_propensity"));
984 strandColour.addActionListener(this);
985 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
986 turnColour.addActionListener(this);
987 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
988 buriedColour.addActionListener(this);
989 abovePIDColour.setLabel(MessageManager
990 .getString("label.above_identity_threshold"));
992 userDefinedColour.setLabel(MessageManager
993 .getString("action.user_defined"));
994 userDefinedColour.addActionListener(this);
995 PIDColour.setLabel(MessageManager
996 .getString("label.percentage_identity"));
997 PIDColour.addActionListener(this);
998 BLOSUM62Colour.setLabel(MessageManager
999 .getString("label.blosum62_score"));
1000 BLOSUM62Colour.addActionListener(this);
1001 conservationMenuItem.setLabel(MessageManager
1002 .getString("label.conservation"));
1005 copy.addActionListener(this);
1007 cut.addActionListener(this);
1009 editMenu.add(editSequence);
1010 editSequence.addActionListener(this);
1012 editMenu.add(toUpper);
1013 toUpper.addActionListener(this);
1014 editMenu.add(toLower);
1015 toLower.addActionListener(this);
1016 editMenu.add(toggleCase);
1017 seqMenu.add(seqShowAnnotationsMenu);
1018 seqMenu.add(seqHideAnnotationsMenu);
1019 seqMenu.add(seqAddReferenceAnnotations);
1020 seqMenu.add(sequenceName);
1021 seqMenu.add(makeReferenceSeq);
1022 // seqMenu.add(sequenceDetails);
1024 if (!ap.av.applet.useXtrnalSviewer)
1028 seqMenu.add(repGroup);
1029 menu1.add(editGroupName);
1030 menu1.add(colourMenu);
1031 menu1.add(showBoxes);
1032 menu1.add(showText);
1033 menu1.add(showColourText);
1034 menu1.add(displayNonconserved);
1035 toggleCase.addActionListener(this);
1036 pdb.addActionListener(this);
1037 hideSeqs.addActionListener(this);
1038 repGroup.addActionListener(this);
1039 revealAll.addActionListener(this);
1040 revealSeq.addActionListener(this);
1041 makeReferenceSeq.addActionListener(this);
1046 ap.paintAlignment(true);
1049 protected void clustalColour_actionPerformed()
1051 SequenceGroup sg = getGroup();
1052 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1056 protected void zappoColour_actionPerformed()
1058 getGroup().cs = new ZappoColourScheme();
1062 protected void taylorColour_actionPerformed()
1064 getGroup().cs = new TaylorColourScheme();
1068 protected void hydrophobicityColour_actionPerformed()
1070 getGroup().cs = new HydrophobicColourScheme();
1074 protected void helixColour_actionPerformed()
1076 getGroup().cs = new HelixColourScheme();
1080 protected void strandColour_actionPerformed()
1082 getGroup().cs = new StrandColourScheme();
1086 protected void turnColour_actionPerformed()
1088 getGroup().cs = new TurnColourScheme();
1092 protected void buriedColour_actionPerformed()
1094 getGroup().cs = new BuriedColourScheme();
1098 public void nucleotideMenuItem_actionPerformed()
1100 getGroup().cs = new NucleotideColourScheme();
1104 public void purinePyrimidineColour_actionPerformed()
1106 getGroup().cs = new PurinePyrimidineColourScheme();
1110 protected void abovePIDColour_itemStateChanged()
1112 SequenceGroup sg = getGroup();
1118 if (abovePIDColour.getState())
1120 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1121 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1122 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1125 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1127 SliderPanel.showPIDSlider();
1131 // remove PIDColouring
1133 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1140 protected void userDefinedColour_actionPerformed()
1142 new UserDefinedColours(ap, getGroup());
1145 protected void PIDColour_actionPerformed()
1147 SequenceGroup sg = getGroup();
1148 sg.cs = new PIDColourScheme();
1149 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1150 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1154 protected void BLOSUM62Colour_actionPerformed()
1156 SequenceGroup sg = getGroup();
1158 sg.cs = new Blosum62ColourScheme();
1160 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
1161 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
1166 protected void noColourmenuItem_actionPerformed()
1168 getGroup().cs = null;
1172 protected void conservationMenuItem_itemStateChanged()
1174 SequenceGroup sg = getGroup();
1180 if (conservationMenuItem.getState())
1182 sg.cs.setConservation(Conservation.calculateConservation("Group", sg
1183 .getSequences(ap.av.getHiddenRepSequences()), 0, ap.av
1184 .getAlignment().getWidth(), false, ap.av.getConsPercGaps(),
1186 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1187 SliderPanel.showConservationSlider();
1190 // remove ConservationColouring
1192 sg.cs.setConservation(null);
1198 SequenceGroup getGroup()
1200 SequenceGroup sg = ap.av.getSelectionGroup();
1202 // this method won't add a new group if it already exists
1205 ap.av.getAlignment().addGroup(sg);
1211 void unGroupMenuItem_actionPerformed()
1213 SequenceGroup sg = ap.av.getSelectionGroup();
1214 ap.av.getAlignment().deleteGroup(sg);
1215 ap.av.setSelectionGroup(null);
1216 ap.paintAlignment(true);
1219 void createGroupMenuItem_actionPerformed()
1221 getGroup(); // implicitly create group
1225 public void showColourText_itemStateChanged()
1227 getGroup().setColourText(showColourText.getState());
1231 public void showText_itemStateChanged()
1233 getGroup().setDisplayText(showText.getState());
1237 public void makeReferenceSeq_actionPerformed()
1239 if (!ap.av.getAlignment().hasSeqrep())
1241 // initialise the display flags so the user sees something happen
1242 ap.av.setDisplayReferenceSeq(true);
1243 ap.av.setColourByReferenceSeq(true);
1244 ap.av.getAlignment().setSeqrep(seq);
1248 if (ap.av.getAlignment().getSeqrep() == seq)
1250 ap.av.getAlignment().setSeqrep(null);
1254 ap.av.getAlignment().setSeqrep(seq);
1260 public void showNonconserved_itemStateChanged()
1262 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1266 public void showBoxes_itemStateChanged()
1268 getGroup().setDisplayBoxes(showBoxes.getState());
1272 void hideSequences(boolean representGroup)
1274 ap.av.hideSequences(seq, representGroup);
1278 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
1279 * "All" is added first, followed by a separator. Then add any annotation
1280 * types associated with the current selection. Separate menus are built for
1281 * the selected sequence group (if any), and the selected sequence.
1283 * Some annotation rows are always rendered together - these can be identified
1284 * by a common graphGroup property > -1. Only one of each group will be marked
1285 * as visible (to avoid duplication of the display). For such groups we add a
1286 * composite type name, e.g.
1288 * IUPredWS (Long), IUPredWS (Short)
1292 protected void buildAnnotationTypesMenus(Menu showMenu, Menu hideMenu,
1293 List<SequenceI> forSequences)
1295 showMenu.removeAll();
1296 hideMenu.removeAll();
1298 final List<String> all = Arrays.asList(new String[] { MessageManager
1299 .getString("label.all") });
1300 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
1301 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
1303 showMenu.addSeparator();
1304 hideMenu.addSeparator();
1306 final AlignmentAnnotation[] annotations = ap.getAlignment()
1307 .getAlignmentAnnotation();
1310 * Find shown/hidden annotations types, distinguished by source (calcId),
1311 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1312 * the insertion order, which is the order of the annotations on the
1315 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
1316 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
1317 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1318 AlignmentAnnotationUtils.asList(annotations), forSequences);
1320 for (String calcId : hiddenTypes.keySet())
1322 for (List<String> type : hiddenTypes.get(calcId))
1324 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1328 // grey out 'show annotations' if none are hidden
1329 showMenu.setEnabled(!hiddenTypes.isEmpty());
1331 for (String calcId : shownTypes.keySet())
1333 for (List<String> type : shownTypes.get(calcId))
1335 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1339 // grey out 'hide annotations' if none are shown
1340 hideMenu.setEnabled(!shownTypes.isEmpty());
1344 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1347 * @param showOrHideMenu
1348 * the menu to add to
1349 * @param forSequences
1350 * the sequences whose annotations may be shown or hidden
1355 * if true this is a special label meaning 'All'
1356 * @param actionIsShow
1357 * if true, the select menu item action is to show the annotation
1360 protected void addAnnotationTypeToShowHide(Menu showOrHideMenu,
1361 final List<SequenceI> forSequences, String calcId,
1362 final List<String> types, final boolean allTypes,
1363 final boolean actionIsShow)
1365 String label = types.toString(); // [a, b, c]
1366 label = label.substring(1, label.length() - 1);
1367 final MenuItem item = new MenuItem(label);
1368 item.addActionListener(new java.awt.event.ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1374 types, forSequences, allTypes, actionIsShow);
1378 showOrHideMenu.add(item);