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.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
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.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.gui.ColourMenuHelper.ColourChangeListener;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileFormats;
44 import jalview.io.FormatAdapter;
45 import jalview.io.SequenceAnnotationReport;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.ColourSchemes;
49 import jalview.schemes.PIDColourScheme;
50 import jalview.util.GroupUrlLink;
51 import jalview.util.GroupUrlLink.UrlStringTooLongException;
52 import jalview.util.MessageManager;
53 import jalview.util.UrlLink;
55 import java.awt.Color;
56 import java.awt.event.ActionEvent;
57 import java.awt.event.ActionListener;
58 import java.util.ArrayList;
59 import java.util.Arrays;
60 import java.util.Collection;
61 import java.util.Collections;
62 import java.util.Hashtable;
63 import java.util.LinkedHashMap;
64 import java.util.List;
66 import java.util.SortedMap;
67 import java.util.TreeMap;
68 import java.util.Vector;
70 import javax.swing.JCheckBoxMenuItem;
71 import javax.swing.JColorChooser;
72 import javax.swing.JMenu;
73 import javax.swing.JMenuItem;
74 import javax.swing.JPopupMenu;
80 * @version $Revision: 1.118 $
82 public class PopupMenu extends JPopupMenu implements ColourChangeListener
84 JMenu groupMenu = new JMenu();
86 JMenuItem groupName = new JMenuItem();
88 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
90 protected JMenuItem modifyPID = new JMenuItem();
92 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
94 protected JMenuItem modifyConservation = new JMenuItem();
98 JMenu sequenceMenu = new JMenu();
100 JMenuItem sequenceName = new JMenuItem();
102 JMenuItem sequenceDetails = new JMenuItem();
104 JMenuItem sequenceSelDetails = new JMenuItem();
106 JMenuItem makeReferenceSeq = new JMenuItem();
108 JMenuItem chooseAnnotations = new JMenuItem();
112 JMenuItem createGroupMenuItem = new JMenuItem();
114 JMenuItem unGroupMenuItem = new JMenuItem();
116 JMenuItem outline = new JMenuItem();
118 JMenu colourMenu = new JMenu();
120 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
122 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
124 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
126 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
128 JMenu editMenu = new JMenu();
130 JMenuItem cut = new JMenuItem();
132 JMenuItem copy = new JMenuItem();
134 JMenuItem upperCase = new JMenuItem();
136 JMenuItem lowerCase = new JMenuItem();
138 JMenuItem toggle = new JMenuItem();
140 JMenu pdbMenu = new JMenu();
142 JMenu outputMenu = new JMenu();
144 JMenu seqShowAnnotationsMenu = new JMenu();
146 JMenu seqHideAnnotationsMenu = new JMenu();
148 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
149 MessageManager.getString("label.add_reference_annotations"));
151 JMenu groupShowAnnotationsMenu = new JMenu();
153 JMenu groupHideAnnotationsMenu = new JMenu();
155 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
156 MessageManager.getString("label.add_reference_annotations"));
158 JMenuItem sequenceFeature = new JMenuItem();
160 JMenuItem textColour = new JMenuItem();
162 JMenu jMenu1 = new JMenu();
164 JMenuItem pdbStructureDialog = new JMenuItem();
166 JMenu rnaStructureMenu = new JMenu();
168 JMenuItem editSequence = new JMenuItem();
170 JMenu groupLinksMenu;
172 JMenuItem hideInsertions = new JMenuItem();
175 * Creates a new PopupMenu object.
182 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
184 this(ap, seq, links, null);
194 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
195 List<String> links, List<String> groupLinks)
197 // /////////////////////////////////////////////////////////
198 // If this is activated from the sequence panel, the user may want to
199 // edit or annotate a particular residue. Therefore display the residue menu
201 // If from the IDPanel, we must display the sequence menu
202 // ////////////////////////////////////////////////////////
206 for (String ff : FileFormats.getInstance().getWritableFormats(true))
208 JMenuItem item = new JMenuItem(ff);
210 item.addActionListener(new ActionListener()
213 public void actionPerformed(ActionEvent e)
215 outputText_actionPerformed(e);
219 outputMenu.add(item);
223 * Build menus for annotation types that may be shown or hidden, and for
224 * 'reference annotations' that may be added to the alignment. First for the
225 * currently selected sequence (if there is one):
227 final List<SequenceI> selectedSequence = (seq == null ? Collections
228 .<SequenceI> emptyList() : Arrays.asList(seq));
229 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
230 seqHideAnnotationsMenu, selectedSequence);
231 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
235 * And repeat for the current selection group (if there is one):
237 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
238 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
240 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
241 groupHideAnnotationsMenu, selectedGroup);
242 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
248 } catch (Exception e)
256 sequenceMenu.setText(sequence.getName());
257 if (seq == ap.av.getAlignment().getSeqrep())
259 makeReferenceSeq.setText(MessageManager
260 .getString("action.unmark_as_reference"));
264 makeReferenceSeq.setText(MessageManager
265 .getString("action.set_as_reference"));
268 if (!ap.av.getAlignment().isNucleotide())
270 remove(rnaStructureMenu);
274 int origCount = rnaStructureMenu.getItemCount();
276 * add menu items to 2D-render any alignment or sequence secondary
277 * structure annotation
279 AlignmentAnnotation[] aas = ap.av.getAlignment()
280 .getAlignmentAnnotation();
283 for (final AlignmentAnnotation aa : aas)
285 if (aa.isValidStruc() && aa.sequenceRef == null)
288 * valid alignment RNA secondary structure annotation
290 menuItem = new JMenuItem();
291 menuItem.setText(MessageManager.formatMessage(
292 "label.2d_rna_structure_line",
293 new Object[] { aa.label }));
294 menuItem.addActionListener(new ActionListener()
297 public void actionPerformed(ActionEvent e)
299 new AppVarna(seq, aa, ap);
302 rnaStructureMenu.add(menuItem);
307 if (seq.getAnnotation() != null)
309 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
310 for (final AlignmentAnnotation aa : seqAnns)
312 if (aa.isValidStruc())
315 * valid sequence RNA secondary structure annotation
317 // TODO: make rnastrucF a bit more nice
318 menuItem = new JMenuItem();
319 menuItem.setText(MessageManager.formatMessage(
320 "label.2d_rna_sequence_name",
321 new Object[] { seq.getName() }));
322 menuItem.addActionListener(new ActionListener()
325 public void actionPerformed(ActionEvent e)
327 // TODO: VARNA does'nt print gaps in the sequence
328 new AppVarna(seq, aa, ap);
331 rnaStructureMenu.add(menuItem);
335 if (rnaStructureMenu.getItemCount() == origCount)
337 remove(rnaStructureMenu);
341 menuItem = new JMenuItem(
342 MessageManager.getString("action.hide_sequences"));
343 menuItem.addActionListener(new ActionListener()
346 public void actionPerformed(ActionEvent e)
348 hideSequences(false);
353 if (ap.av.getSelectionGroup() != null
354 && ap.av.getSelectionGroup().getSize() > 1)
356 menuItem = new JMenuItem(MessageManager.formatMessage(
357 "label.represent_group_with",
358 new Object[] { seq.getName() }));
359 menuItem.addActionListener(new ActionListener()
362 public void actionPerformed(ActionEvent e)
367 sequenceMenu.add(menuItem);
370 if (ap.av.hasHiddenRows())
372 final int index = ap.av.getAlignment().findIndex(seq);
374 if (ap.av.adjustForHiddenSeqs(index)
375 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
377 menuItem = new JMenuItem(
378 MessageManager.getString("action.reveal_sequences"));
379 menuItem.addActionListener(new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 ap.av.showSequence(index);
385 if (ap.overviewPanel != null)
387 ap.overviewPanel.updateOverviewImage();
395 // for the case when no sequences are even visible
396 if (ap.av.hasHiddenRows())
399 menuItem = new JMenuItem(
400 MessageManager.getString("action.reveal_all"));
401 menuItem.addActionListener(new ActionListener()
404 public void actionPerformed(ActionEvent e)
406 ap.av.showAllHiddenSeqs();
407 if (ap.overviewPanel != null)
409 ap.overviewPanel.updateOverviewImage();
418 SequenceGroup sg = ap.av.getSelectionGroup();
419 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
420 .getGroups().contains(sg) : false;
422 if (sg != null && sg.getSize() > 0)
424 groupName.setText(MessageManager
425 .getString("label.edit_name_and_description_current_group"));
427 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
429 conservationMenuItem.setEnabled(!sg.isNucleotide());
433 if (sg.cs.conservationApplied())
435 conservationMenuItem.setSelected(true);
437 if (sg.cs.getThreshold() > 0)
439 abovePIDColour.setSelected(true);
442 modifyConservation.setEnabled(conservationMenuItem.isSelected());
443 modifyPID.setEnabled(abovePIDColour.isSelected());
444 displayNonconserved.setSelected(sg.getShowNonconserved());
445 showText.setSelected(sg.getDisplayText());
446 showColourText.setSelected(sg.getColourText());
447 showBoxes.setSelected(sg.getDisplayBoxes());
448 // add any groupURLs to the groupURL submenu and make it visible
449 if (groupLinks != null && groupLinks.size() > 0)
451 buildGroupURLMenu(sg, groupLinks);
453 // Add a 'show all structures' for the current selection
454 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
455 SequenceI sqass = null;
456 for (SequenceI sq : ap.av.getSequenceSelection())
458 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
459 if (pes != null && pes.size() > 0)
461 reppdb.put(pes.get(0).getId(), pes.get(0));
462 for (PDBEntry pe : pes)
464 pdbe.put(pe.getId(), pe);
474 final PDBEntry[] pe = pdbe.values().toArray(
475 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
476 new PDBEntry[reppdb.size()]);
477 final JMenuItem gpdbview, rpdbview;
482 groupMenu.setVisible(false);
483 editMenu.setVisible(false);
488 createGroupMenuItem.setVisible(true);
489 unGroupMenuItem.setVisible(false);
490 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
494 createGroupMenuItem.setVisible(false);
495 unGroupMenuItem.setVisible(true);
496 jMenu1.setText(MessageManager.getString("action.edit_group"));
501 sequenceMenu.setVisible(false);
502 pdbStructureDialog.setVisible(false);
503 rnaStructureMenu.setVisible(false);
506 if (links != null && links.size() > 0)
508 addFeatureLinks(seq, links);
513 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
518 void addFeatureLinks(final SequenceI seq, List<String> links)
520 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
521 Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
523 for (String link : links)
525 UrlLink urlLink = null;
528 urlLink = new UrlLink(link);
529 } catch (Exception foo)
531 Cache.log.error("Exception for URLLink '" + link + "'", foo);
535 if (!urlLink.isValid())
537 Cache.log.error(urlLink.getInvalidMessage());
541 urlLink.createLinksFromSeq(seq, linkset);
544 addshowLinks(linkMenu, linkset.values());
546 // disable link menu if there are no valid entries
547 if (linkMenu.getItemCount() > 0)
549 linkMenu.setEnabled(true);
553 linkMenu.setEnabled(false);
556 if (sequence != null)
558 sequenceMenu.add(linkMenu);
568 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
569 * "All" is added first, followed by a separator. Then add any annotation
570 * types associated with the current selection. Separate menus are built for
571 * the selected sequence group (if any), and the selected sequence.
573 * Some annotation rows are always rendered together - these can be identified
574 * by a common graphGroup property > -1. Only one of each group will be marked
575 * as visible (to avoid duplication of the display). For such groups we add a
576 * composite type name, e.g.
578 * IUPredWS (Long), IUPredWS (Short)
582 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
583 List<SequenceI> forSequences)
585 showMenu.removeAll();
586 hideMenu.removeAll();
588 final List<String> all = Arrays.asList(new String[] { MessageManager
589 .getString("label.all") });
590 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
591 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
593 showMenu.addSeparator();
594 hideMenu.addSeparator();
596 final AlignmentAnnotation[] annotations = ap.getAlignment()
597 .getAlignmentAnnotation();
600 * Find shown/hidden annotations types, distinguished by source (calcId),
601 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
602 * the insertion order, which is the order of the annotations on the
605 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
606 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
607 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
608 AlignmentAnnotationUtils.asList(annotations), forSequences);
610 for (String calcId : hiddenTypes.keySet())
612 for (List<String> type : hiddenTypes.get(calcId))
614 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
618 // grey out 'show annotations' if none are hidden
619 showMenu.setEnabled(!hiddenTypes.isEmpty());
621 for (String calcId : shownTypes.keySet())
623 for (List<String> type : shownTypes.get(calcId))
625 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
629 // grey out 'hide annotations' if none are shown
630 hideMenu.setEnabled(!shownTypes.isEmpty());
634 * Returns a list of sequences - either the current selection group (if there
635 * is one), else the specified single sequence.
640 protected List<SequenceI> getSequenceScope(SequenceI seq)
642 List<SequenceI> forSequences = null;
643 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
644 if (selectionGroup != null && selectionGroup.getSize() > 0)
646 forSequences = selectionGroup.getSequences();
650 forSequences = seq == null ? Collections.<SequenceI> emptyList()
651 : Arrays.asList(seq);
657 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
660 * @param showOrHideMenu
662 * @param forSequences
663 * the sequences whose annotations may be shown or hidden
668 * if true this is a special label meaning 'All'
669 * @param actionIsShow
670 * if true, the select menu item action is to show the annotation
673 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
674 final List<SequenceI> forSequences, String calcId,
675 final List<String> types, final boolean allTypes,
676 final boolean actionIsShow)
678 String label = types.toString(); // [a, b, c]
679 label = label.substring(1, label.length() - 1); // a, b, c
680 final JMenuItem item = new JMenuItem(label);
681 item.setToolTipText(calcId);
682 item.addActionListener(new ActionListener()
685 public void actionPerformed(ActionEvent e)
687 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
688 types, forSequences, allTypes, actionIsShow);
692 showOrHideMenu.add(item);
695 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
698 // TODO: usability: thread off the generation of group url content so root
700 // sequence only URLs
701 // ID/regex match URLs
702 groupLinksMenu = new JMenu(
703 MessageManager.getString("action.group_link"));
704 // three types of url that might be created.
705 JMenu[] linkMenus = new JMenu[] { null,
706 new JMenu(MessageManager.getString("action.ids")),
707 new JMenu(MessageManager.getString("action.sequences")),
708 new JMenu(MessageManager.getString("action.ids_sequences")) };
710 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
711 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
712 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
713 for (int sq = 0; sq < seqs.length; sq++)
716 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
717 .findPosition(sg.getEndRes());
718 // just collect ids from dataset sequence
719 // TODO: check if IDs collected from selecton group intersects with the
720 // current selection, too
721 SequenceI sqi = seqs[sq];
722 while (sqi.getDatasetSequence() != null)
724 sqi = sqi.getDatasetSequence();
726 DBRefEntry[] dbr = sqi.getDBRefs();
727 if (dbr != null && dbr.length > 0)
729 for (int d = 0; d < dbr.length; d++)
731 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
732 Object[] sarray = commonDbrefs.get(src);
735 sarray = new Object[2];
736 sarray[0] = new int[] { 0 };
737 sarray[1] = new String[seqs.length];
739 commonDbrefs.put(src, sarray);
742 if (((String[]) sarray[1])[sq] == null)
745 || (dbr[d].getMap().locateMappedRange(start, end) != null))
747 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
748 ((int[]) sarray[0])[0]++;
754 // now create group links for all distinct ID/sequence sets.
755 boolean addMenu = false; // indicates if there are any group links to give
757 for (String link : groupLinks)
759 GroupUrlLink urlLink = null;
762 urlLink = new GroupUrlLink(link);
763 } catch (Exception foo)
765 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
769 if (!urlLink.isValid())
771 Cache.log.error(urlLink.getInvalidMessage());
774 final String label = urlLink.getLabel();
775 boolean usingNames = false;
776 // Now see which parts of the group apply for this URL
777 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
778 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
779 String[] seqstr, ids; // input to makeUrl
782 int numinput = ((int[]) idset[0])[0];
783 String[] allids = ((String[]) idset[1]);
784 seqstr = new String[numinput];
785 ids = new String[numinput];
786 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
788 if (allids[sq] != null)
790 ids[idcount] = allids[sq];
791 seqstr[idcount++] = idandseqs[1][sq];
797 // just use the id/seq set
798 seqstr = idandseqs[1];
802 // and try and make the groupURL!
804 Object[] urlset = null;
807 urlset = urlLink.makeUrlStubs(ids, seqstr,
808 "FromJalview" + System.currentTimeMillis(), false);
809 } catch (UrlStringTooLongException e)
814 int type = urlLink.getGroupURLType() & 3;
815 // first two bits ofurlLink type bitfield are sequenceids and sequences
816 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
817 addshowLink(linkMenus[type], label
818 + (((type & 1) == 1) ? ("("
819 + (usingNames ? "Names" : ltarget) + ")") : ""),
826 groupLinksMenu = new JMenu(
827 MessageManager.getString("action.group_link"));
828 for (int m = 0; m < linkMenus.length; m++)
830 if (linkMenus[m] != null
831 && linkMenus[m].getMenuComponentCount() > 0)
833 groupLinksMenu.add(linkMenus[m]);
837 groupMenu.add(groupLinksMenu);
841 private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
843 for (List<String> linkstrset : linkset)
845 // split linkstr into label and url
846 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
851 * add a show URL menu item to the given linkMenu
855 * - menu label string
859 private void addshowLink(JMenu linkMenu, String label, final String url)
861 JMenuItem item = new JMenuItem(label);
862 item.setToolTipText(MessageManager.formatMessage(
863 "label.open_url_param", new Object[] { url }));
864 item.addActionListener(new ActionListener()
867 public void actionPerformed(ActionEvent e)
869 new Thread(new Runnable()
886 * add a late bound groupURL item to the given linkMenu
890 * - menu label string
891 * @param urlgenerator
892 * GroupURLLink used to generate URL
894 * Object array returned from the makeUrlStubs function.
896 private void addshowLink(JMenu linkMenu, String label,
897 final GroupUrlLink urlgenerator, final Object[] urlstub)
899 JMenuItem item = new JMenuItem(label);
900 item.setToolTipText(MessageManager.formatMessage(
901 "label.open_url_seqs_param",
902 new Object[] { urlgenerator.getUrl_prefix(),
903 urlgenerator.getNumberInvolved(urlstub) }));
904 // TODO: put in info about what is being sent.
905 item.addActionListener(new ActionListener()
908 public void actionPerformed(ActionEvent e)
910 new Thread(new Runnable()
918 showLink(urlgenerator.constructFrom(urlstub));
919 } catch (UrlStringTooLongException e2)
937 private void jbInit() throws Exception
939 groupMenu.setText(MessageManager.getString("label.selection"));
940 groupName.setText(MessageManager.getString("label.name"));
941 groupName.addActionListener(new ActionListener()
944 public void actionPerformed(ActionEvent e)
946 groupName_actionPerformed();
949 sequenceMenu.setText(MessageManager.getString("label.sequence"));
950 sequenceName.setText(MessageManager
951 .getString("label.edit_name_description"));
952 sequenceName.addActionListener(new ActionListener()
955 public void actionPerformed(ActionEvent e)
957 sequenceName_actionPerformed();
960 chooseAnnotations.setText(MessageManager
961 .getString("action.choose_annotations"));
962 chooseAnnotations.addActionListener(new ActionListener()
965 public void actionPerformed(ActionEvent e)
967 chooseAnnotations_actionPerformed(e);
970 sequenceDetails.setText(MessageManager
971 .getString("label.sequence_details"));
972 sequenceDetails.addActionListener(new ActionListener()
975 public void actionPerformed(ActionEvent e)
977 sequenceDetails_actionPerformed();
980 sequenceSelDetails.setText(MessageManager
981 .getString("label.sequence_details"));
982 sequenceSelDetails.addActionListener(new ActionListener()
985 public void actionPerformed(ActionEvent e)
987 sequenceSelectionDetails_actionPerformed();
992 .setText(MessageManager.getString("action.remove_group"));
993 unGroupMenuItem.addActionListener(new ActionListener()
996 public void actionPerformed(ActionEvent e)
998 unGroupMenuItem_actionPerformed();
1001 createGroupMenuItem.setText(MessageManager
1002 .getString("action.create_group"));
1003 createGroupMenuItem.addActionListener(new ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 createGroupMenuItem_actionPerformed();
1012 outline.setText(MessageManager.getString("action.border_colour"));
1013 outline.addActionListener(new ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 outline_actionPerformed();
1021 showBoxes.setText(MessageManager.getString("action.boxes"));
1022 showBoxes.setState(true);
1023 showBoxes.addActionListener(new ActionListener()
1026 public void actionPerformed(ActionEvent e)
1028 showBoxes_actionPerformed();
1031 showText.setText(MessageManager.getString("action.text"));
1032 showText.setState(true);
1033 showText.addActionListener(new ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 showText_actionPerformed();
1041 showColourText.setText(MessageManager.getString("label.colour_text"));
1042 showColourText.addActionListener(new ActionListener()
1045 public void actionPerformed(ActionEvent e)
1047 showColourText_actionPerformed();
1050 displayNonconserved.setText(MessageManager
1051 .getString("label.show_non_conserved"));
1052 displayNonconserved.setState(true);
1053 displayNonconserved.addActionListener(new ActionListener()
1056 public void actionPerformed(ActionEvent e)
1058 showNonconserved_actionPerformed();
1061 editMenu.setText(MessageManager.getString("action.edit"));
1062 cut.setText(MessageManager.getString("action.cut"));
1063 cut.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 cut_actionPerformed();
1071 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1072 upperCase.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1080 copy.setText(MessageManager.getString("action.copy"));
1081 copy.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 copy_actionPerformed();
1089 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1090 lowerCase.addActionListener(new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1098 toggle.setText(MessageManager.getString("label.toggle_case"));
1099 toggle.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent e)
1107 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1109 seqShowAnnotationsMenu.setText(MessageManager
1110 .getString("label.show_annotations"));
1111 seqHideAnnotationsMenu.setText(MessageManager
1112 .getString("label.hide_annotations"));
1113 groupShowAnnotationsMenu.setText(MessageManager
1114 .getString("label.show_annotations"));
1115 groupHideAnnotationsMenu.setText(MessageManager
1116 .getString("label.hide_annotations"));
1117 sequenceFeature.setText(MessageManager
1118 .getString("label.create_sequence_feature"));
1119 sequenceFeature.addActionListener(new ActionListener()
1122 public void actionPerformed(ActionEvent e)
1124 sequenceFeature_actionPerformed();
1127 jMenu1.setText(MessageManager.getString("label.group"));
1128 pdbStructureDialog.setText(MessageManager
1129 .getString("label.show_pdbstruct_dialog"));
1130 pdbStructureDialog.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent actionEvent)
1135 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1136 if (ap.av.getSelectionGroup() != null)
1138 selectedSeqs = ap.av.getSequenceSelection();
1140 new StructureChooser(selectedSeqs, sequence, ap);
1144 rnaStructureMenu.setText(MessageManager
1145 .getString("label.view_rna_structure"));
1147 // colStructureMenu.setText("Colour By Structure");
1148 editSequence.setText(MessageManager.getString("label.edit_sequence")
1150 editSequence.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent actionEvent)
1155 editSequence_actionPerformed(actionEvent);
1158 makeReferenceSeq.setText(MessageManager
1159 .getString("label.mark_as_representative"));
1160 makeReferenceSeq.addActionListener(new ActionListener()
1164 public void actionPerformed(ActionEvent actionEvent)
1166 makeReferenceSeq_actionPerformed(actionEvent);
1170 hideInsertions.setText(MessageManager
1171 .getString("label.hide_insertions"));
1172 hideInsertions.addActionListener(new ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 hideInsertions_actionPerformed(e);
1182 groupMenu.add(sequenceSelDetails);
1185 add(rnaStructureMenu);
1186 add(pdbStructureDialog);
1187 if (sequence != null)
1189 add(hideInsertions);
1191 // annotations configuration panel suppressed for now
1192 // groupMenu.add(chooseAnnotations);
1195 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1196 * (if a selection group is in force).
1198 sequenceMenu.add(seqShowAnnotationsMenu);
1199 sequenceMenu.add(seqHideAnnotationsMenu);
1200 sequenceMenu.add(seqAddReferenceAnnotations);
1201 groupMenu.add(groupShowAnnotationsMenu);
1202 groupMenu.add(groupHideAnnotationsMenu);
1203 groupMenu.add(groupAddReferenceAnnotations);
1204 groupMenu.add(editMenu);
1205 groupMenu.add(outputMenu);
1206 groupMenu.add(sequenceFeature);
1207 groupMenu.add(createGroupMenuItem);
1208 groupMenu.add(unGroupMenuItem);
1209 groupMenu.add(jMenu1);
1210 sequenceMenu.add(sequenceName);
1211 sequenceMenu.add(sequenceDetails);
1212 sequenceMenu.add(makeReferenceSeq);
1219 editMenu.add(editSequence);
1220 editMenu.add(upperCase);
1221 editMenu.add(lowerCase);
1222 editMenu.add(toggle);
1223 // JBPNote: These shouldn't be added here - should appear in a generic
1224 // 'apply web service to this sequence menu'
1225 // pdbMenu.add(RNAFold);
1226 // pdbMenu.add(ContraFold);
1227 jMenu1.add(groupName);
1228 jMenu1.add(colourMenu);
1229 jMenu1.add(showBoxes);
1230 jMenu1.add(showText);
1231 jMenu1.add(showColourText);
1232 jMenu1.add(outline);
1233 jMenu1.add(displayNonconserved);
1237 * Constructs the entries for the colour menu
1239 protected void initColourMenu()
1241 colourMenu.setText(MessageManager.getString("label.group_colour"));
1242 textColour.setText(MessageManager.getString("label.text_colour"));
1243 textColour.addActionListener(new ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 textColour_actionPerformed();
1252 abovePIDColour.setText(MessageManager
1253 .getString("label.above_identity_threshold"));
1254 abovePIDColour.addActionListener(new ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1263 modifyPID.setText(MessageManager
1264 .getString("label.modify_identity_threshold"));
1265 modifyPID.addActionListener(new ActionListener()
1268 public void actionPerformed(ActionEvent e)
1270 modifyPID_actionPerformed();
1274 conservationMenuItem.setText(MessageManager
1275 .getString("action.by_conservation"));
1276 conservationMenuItem.addActionListener(new ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 conservationMenuItem_actionPerformed(conservationMenuItem
1286 modifyConservation.setText(MessageManager
1287 .getString("label.modify_conservation_threshold"));
1288 modifyConservation.addActionListener(new ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 modifyConservation_actionPerformed();
1299 * Builds the group colour sub-menu, including any user-defined colours which
1300 * were loaded at startup or during the Jalview session
1302 protected void buildColourMenu()
1304 SequenceGroup sg = ap.av.getSelectionGroup();
1308 * popup menu with no sequence group scope
1312 colourMenu.removeAll();
1313 colourMenu.add(textColour);
1314 colourMenu.addSeparator();
1316 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1318 colourMenu.addSeparator();
1319 colourMenu.add(conservationMenuItem);
1320 colourMenu.add(modifyConservation);
1321 colourMenu.add(abovePIDColour);
1322 colourMenu.add(modifyPID);
1325 protected void modifyConservation_actionPerformed()
1327 SequenceGroup sg = getGroup();
1330 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1331 SliderPanel.showConservationSlider();
1335 protected void modifyPID_actionPerformed()
1337 SequenceGroup sg = getGroup();
1340 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1342 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1343 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1345 SliderPanel.showPIDSlider();
1350 * Check for any annotations on the underlying dataset sequences (for the
1351 * current selection group) which are not 'on the alignment'.If any are found,
1352 * enable the option to add them to the alignment. The criteria for 'on the
1353 * alignment' is finding an alignment annotation on the alignment, matched on
1354 * calcId, label and sequenceRef.
1356 * A tooltip is also constructed that displays the source (calcId) and type
1357 * (label) of the annotations that can be added.
1360 * @param forSequences
1362 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1363 List<SequenceI> forSequences)
1365 menuItem.setEnabled(false);
1368 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1369 * Using TreeMap means calcIds are shown in alphabetical order.
1371 SortedMap<String, String> tipEntries = new TreeMap<String, String>();
1372 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1373 AlignmentI al = this.ap.av.getAlignment();
1374 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1375 tipEntries, candidates, al);
1376 if (!candidates.isEmpty())
1378 StringBuilder tooltip = new StringBuilder(64);
1379 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1382 * Found annotations that could be added. Enable the menu item, and
1383 * configure its tooltip and action.
1385 menuItem.setEnabled(true);
1386 for (String calcId : tipEntries.keySet())
1388 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1390 String tooltipText = JvSwingUtils.wrapTooltip(true,
1391 tooltip.toString());
1392 menuItem.setToolTipText(tooltipText);
1394 menuItem.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 addReferenceAnnotations_actionPerformed(candidates);
1406 * Add annotations to the sequences and to the alignment.
1409 * a map whose keys are sequences on the alignment, and values a list
1410 * of annotations to add to each sequence
1412 protected void addReferenceAnnotations_actionPerformed(
1413 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1415 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1416 final AlignmentI alignment = this.ap.getAlignment();
1417 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1422 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1424 if (!ap.av.getAlignment().hasSeqrep())
1426 // initialise the display flags so the user sees something happen
1427 ap.av.setDisplayReferenceSeq(true);
1428 ap.av.setColourByReferenceSeq(true);
1429 ap.av.getAlignment().setSeqrep(sequence);
1433 if (ap.av.getAlignment().getSeqrep() == sequence)
1435 ap.av.getAlignment().setSeqrep(null);
1439 ap.av.getAlignment().setSeqrep(sequence);
1445 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1447 if (sequence != null)
1449 /* ColumnSelection cs = ap.av.getColumnSelection();
1452 cs = new ColumnSelection();
1454 cs.hideInsertionsFor(sequence);
1455 ap.av.setColumnSelection(cs);*/
1457 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1460 hidden = new HiddenColumns();
1462 hidden.hideInsertionsFor(sequence);
1463 ap.av.getAlignment().setHiddenColumns(hidden);
1468 protected void sequenceSelectionDetails_actionPerformed()
1470 createSequenceDetailsReport(ap.av.getSequenceSelection());
1473 protected void sequenceDetails_actionPerformed()
1475 createSequenceDetailsReport(new SequenceI[] { sequence });
1478 public void createSequenceDetailsReport(SequenceI[] sequences)
1480 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1481 StringBuilder contents = new StringBuilder(128);
1482 for (SequenceI seq : sequences)
1484 contents.append("<p><h2>"
1487 "label.create_sequence_details_report_annotation_for",
1488 new Object[] { seq.getDisplayId(true) })
1490 new SequenceAnnotationReport(null)
1491 .createSequenceAnnotationReport(
1496 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1497 .getSeqPanel().seqCanvas.fr.getMinMax()
1499 contents.append("</p>");
1501 cap.setText("<html>" + contents.toString() + "</html>");
1503 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1504 "label.sequence_details_for",
1505 (sequences.length == 1 ? new Object[] { sequences[0]
1506 .getDisplayId(true) } : new Object[] { MessageManager
1507 .getString("label.selection") })), 500, 400);
1511 protected void showNonconserved_actionPerformed()
1513 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1518 * call to refresh view after settings change
1522 ap.updateAnnotation();
1523 ap.paintAlignment(true);
1525 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1529 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1530 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1540 public void abovePIDColour_actionPerformed(boolean selected)
1542 SequenceGroup sg = getGroup();
1550 sg.cs.setConsensus(AAFrequency.calculate(
1551 sg.getSequences(ap.av.getHiddenRepSequences()),
1552 sg.getStartRes(), sg.getEndRes() + 1));
1554 int threshold = SliderPanel.setPIDSliderSource(ap,
1555 sg.getGroupColourScheme(), getGroup()
1558 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1560 SliderPanel.showPIDSlider();
1563 // remove PIDColouring
1565 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1566 SliderPanel.hidePIDSlider();
1568 modifyPID.setEnabled(selected);
1574 * Open a panel where the user can choose which types of sequence annotation
1579 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1581 // todo correct way to guard against opening a duplicate panel?
1582 new AnnotationChooser(ap);
1591 public void conservationMenuItem_actionPerformed(boolean selected)
1593 SequenceGroup sg = getGroup();
1601 // JBPNote: Conservation name shouldn't be i18n translated
1602 Conservation c = new Conservation("Group", sg.getSequences(ap.av
1603 .getHiddenRepSequences()), sg.getStartRes(),
1604 sg.getEndRes() + 1);
1607 c.verdict(false, ap.av.getConsPercGaps());
1608 sg.cs.setConservation(c);
1610 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1612 SliderPanel.showConservationSlider();
1615 // remove ConservationColouring
1617 sg.cs.setConservation(null);
1618 SliderPanel.hideConservationSlider();
1620 modifyConservation.setEnabled(selected);
1631 protected void groupName_actionPerformed()
1634 SequenceGroup sg = getGroup();
1635 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1636 sg.getDescription(), " "
1637 + MessageManager.getString("label.group_name") + " ",
1638 MessageManager.getString("label.group_description") + " ",
1639 MessageManager.getString("label.edit_group_name_description"),
1647 sg.setName(dialog.getName());
1648 sg.setDescription(dialog.getDescription());
1653 * Get selection group - adding it to the alignment if necessary.
1655 * @return sequence group to operate on
1657 SequenceGroup getGroup()
1659 SequenceGroup sg = ap.av.getSelectionGroup();
1660 // this method won't add a new group if it already exists
1663 ap.av.getAlignment().addGroup(sg);
1675 void sequenceName_actionPerformed()
1677 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1678 sequence.getDescription(),
1679 " " + MessageManager.getString("label.sequence_name")
1681 MessageManager.getString("label.sequence_description") + " ",
1683 .getString("label.edit_sequence_name_description"),
1691 if (dialog.getName() != null)
1693 if (dialog.getName().indexOf(" ") > -1)
1699 .getString("label.spaces_converted_to_backslashes"),
1701 .getString("label.no_spaces_allowed_sequence_name"),
1702 JvOptionPane.WARNING_MESSAGE);
1705 sequence.setName(dialog.getName().replace(' ', '_'));
1706 ap.paintAlignment(false);
1709 sequence.setDescription(dialog.getDescription());
1711 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1722 void unGroupMenuItem_actionPerformed()
1724 SequenceGroup sg = ap.av.getSelectionGroup();
1725 ap.av.getAlignment().deleteGroup(sg);
1726 ap.av.setSelectionGroup(null);
1730 void createGroupMenuItem_actionPerformed()
1732 getGroup(); // implicitly creates group - note - should apply defaults / use
1733 // standard alignment window logic for this
1743 protected void outline_actionPerformed()
1745 SequenceGroup sg = getGroup();
1746 Color col = JColorChooser.showDialog(this,
1747 MessageManager.getString("label.select_outline_colour"),
1752 sg.setOutlineColour(col);
1764 public void showBoxes_actionPerformed()
1766 getGroup().setDisplayBoxes(showBoxes.isSelected());
1776 public void showText_actionPerformed()
1778 getGroup().setDisplayText(showText.isSelected());
1788 public void showColourText_actionPerformed()
1790 getGroup().setColourText(showColourText.isSelected());
1794 public void showLink(String url)
1798 jalview.util.BrowserLauncher.openURL(url);
1799 } catch (Exception ex)
1801 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1802 MessageManager.getString("label.web_browser_not_found_unix"),
1803 MessageManager.getString("label.web_browser_not_found"),
1804 JvOptionPane.WARNING_MESSAGE);
1806 ex.printStackTrace();
1810 void hideSequences(boolean representGroup)
1812 ap.av.hideSequences(sequence, representGroup);
1815 public void copy_actionPerformed()
1817 ap.alignFrame.copy_actionPerformed(null);
1820 public void cut_actionPerformed()
1822 ap.alignFrame.cut_actionPerformed(null);
1825 void changeCase(ActionEvent e)
1827 Object source = e.getSource();
1828 SequenceGroup sg = ap.av.getSelectionGroup();
1832 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1833 sg.getStartRes(), sg.getEndRes() + 1);
1838 if (source == toggle)
1840 description = MessageManager.getString("label.toggle_case");
1841 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1843 else if (source == upperCase)
1845 description = MessageManager.getString("label.to_upper_case");
1846 caseChange = ChangeCaseCommand.TO_UPPER;
1850 description = MessageManager.getString("label.to_lower_case");
1851 caseChange = ChangeCaseCommand.TO_LOWER;
1854 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1855 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1856 startEnd, caseChange);
1858 ap.alignFrame.addHistoryItem(caseCommand);
1860 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1866 public void outputText_actionPerformed(ActionEvent e)
1868 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1869 cap.setForInput(null);
1870 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1871 "label.alignment_output_command",
1872 new Object[] { e.getActionCommand() }), 600, 500);
1874 String[] omitHidden = null;
1876 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1877 // or we simply trust the user wants
1878 // wysiwig behaviour
1880 FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
1881 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
1884 public void sequenceFeature_actionPerformed()
1886 SequenceGroup sg = ap.av.getSelectionGroup();
1892 List<SequenceI> seqs = new ArrayList<SequenceI>();
1893 List<SequenceFeature> features = new ArrayList<SequenceFeature>();
1896 * assemble dataset sequences, and template new sequence features,
1897 * for the amend features dialog
1899 int gSize = sg.getSize();
1900 for (int i = 0; i < gSize; i++)
1902 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1903 int end = sg.findEndRes(sg.getSequenceAt(i));
1906 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
1907 features.add(new SequenceFeature(null, null, null, start, end,
1912 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1913 features, true, ap, null))
1915 ap.alignFrame.setShowSeqFeatures(true);
1916 ap.highlightSearchResults(null);
1920 public void textColour_actionPerformed()
1922 SequenceGroup sg = getGroup();
1925 new TextColourChooser().chooseColour(ap, sg);
1929 public void colourByStructure(String pdbid)
1931 Annotation[] anots = ap.av.getStructureSelectionManager()
1932 .colourSequenceFromStructure(sequence, pdbid);
1934 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1935 "Coloured by " + pdbid, anots);
1937 ap.av.getAlignment().addAnnotation(an);
1938 an.createSequenceMapping(sequence, 0, true);
1939 // an.adjustForAlignment();
1940 ap.av.getAlignment().setAnnotationIndex(an, 0);
1942 ap.adjustAnnotationHeight();
1944 sequence.addAlignmentAnnotation(an);
1948 public void editSequence_actionPerformed(ActionEvent actionEvent)
1950 SequenceGroup sg = ap.av.getSelectionGroup();
1954 if (sequence == null)
1956 sequence = sg.getSequenceAt(0);
1959 EditNameDialog dialog = new EditNameDialog(
1960 sequence.getSequenceAsString(sg.getStartRes(),
1961 sg.getEndRes() + 1), null,
1962 MessageManager.getString("label.edit_sequence"), null,
1963 MessageManager.getString("label.edit_sequence"),
1968 EditCommand editCommand = new EditCommand(
1969 MessageManager.getString("label.edit_sequences"),
1970 Action.REPLACE, dialog.getName().replace(' ',
1971 ap.av.getGapCharacter()),
1972 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1973 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
1975 ap.alignFrame.addHistoryItem(editCommand);
1977 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1984 * Action on user selecting an item from the colour menu (that does not have
1985 * its bespoke action handler)
1990 public void changeColour_actionPerformed(String colourSchemeName)
1992 SequenceGroup sg = getGroup();
1994 * switch to the chosen colour scheme (or null for None)
1996 ColourSchemeI colourScheme = ColourSchemes.getInstance()
1997 .getColourScheme(colourSchemeName, sg,
1998 ap.av.getHiddenRepSequences());
1999 sg.setColourScheme(colourScheme);
2000 if (colourScheme instanceof Blosum62ColourScheme
2001 || colourScheme instanceof PIDColourScheme)
2003 sg.cs.setConsensus(AAFrequency.calculate(
2004 sg.getSequences(ap.av.getHiddenRepSequences()),
2005 sg.getStartRes(), sg.getEndRes() + 1));