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.ColumnSelection;
35 import jalview.datamodel.DBRefEntry;
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.Arrays;
59 import java.util.Collection;
60 import java.util.Collections;
61 import java.util.Hashtable;
62 import java.util.LinkedHashMap;
63 import java.util.List;
65 import java.util.SortedMap;
66 import java.util.TreeMap;
67 import java.util.Vector;
69 import javax.swing.JCheckBoxMenuItem;
70 import javax.swing.JColorChooser;
71 import javax.swing.JMenu;
72 import javax.swing.JMenuItem;
73 import javax.swing.JPopupMenu;
79 * @version $Revision: 1.118 $
81 public class PopupMenu extends JPopupMenu implements ColourChangeListener
83 JMenu groupMenu = new JMenu();
85 JMenuItem groupName = new JMenuItem();
87 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
89 protected JMenuItem modifyPID = new JMenuItem();
91 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
93 protected JMenuItem modifyConservation = new JMenuItem();
97 JMenu sequenceMenu = new JMenu();
99 JMenuItem sequenceName = new JMenuItem();
101 JMenuItem sequenceDetails = new JMenuItem();
103 JMenuItem sequenceSelDetails = new JMenuItem();
105 JMenuItem makeReferenceSeq = new JMenuItem();
107 JMenuItem chooseAnnotations = new JMenuItem();
111 JMenuItem createGroupMenuItem = new JMenuItem();
113 JMenuItem unGroupMenuItem = new JMenuItem();
115 JMenuItem outline = new JMenuItem();
117 JMenu colourMenu = new JMenu();
119 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
121 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
123 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
125 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
127 JMenu editMenu = new JMenu();
129 JMenuItem cut = new JMenuItem();
131 JMenuItem copy = new JMenuItem();
133 JMenuItem upperCase = new JMenuItem();
135 JMenuItem lowerCase = new JMenuItem();
137 JMenuItem toggle = new JMenuItem();
139 JMenu pdbMenu = new JMenu();
141 JMenu outputMenu = new JMenu();
143 JMenu seqShowAnnotationsMenu = new JMenu();
145 JMenu seqHideAnnotationsMenu = new JMenu();
147 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
148 MessageManager.getString("label.add_reference_annotations"));
150 JMenu groupShowAnnotationsMenu = new JMenu();
152 JMenu groupHideAnnotationsMenu = new JMenu();
154 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
155 MessageManager.getString("label.add_reference_annotations"));
157 JMenuItem sequenceFeature = new JMenuItem();
159 JMenuItem textColour = new JMenuItem();
161 JMenu jMenu1 = new JMenu();
163 JMenuItem pdbStructureDialog = new JMenuItem();
165 JMenu rnaStructureMenu = new JMenu();
167 JMenuItem editSequence = new JMenuItem();
169 JMenu groupLinksMenu;
171 JMenuItem hideInsertions = new JMenuItem();
174 * Creates a new PopupMenu object.
181 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
183 this(ap, seq, links, null);
193 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
194 List<String> links, List<String> groupLinks)
196 // /////////////////////////////////////////////////////////
197 // If this is activated from the sequence panel, the user may want to
198 // edit or annotate a particular residue. Therefore display the residue menu
200 // If from the IDPanel, we must display the sequence menu
201 // ////////////////////////////////////////////////////////
205 for (String ff : FileFormats.getInstance().getWritableFormats(true))
207 JMenuItem item = new JMenuItem(ff);
209 item.addActionListener(new ActionListener()
212 public void actionPerformed(ActionEvent e)
214 outputText_actionPerformed(e);
218 outputMenu.add(item);
222 * Build menus for annotation types that may be shown or hidden, and for
223 * 'reference annotations' that may be added to the alignment. First for the
224 * currently selected sequence (if there is one):
226 final List<SequenceI> selectedSequence = (seq == null ? Collections
227 .<SequenceI> emptyList() : Arrays.asList(seq));
228 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
229 seqHideAnnotationsMenu, selectedSequence);
230 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
234 * And repeat for the current selection group (if there is one):
236 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
237 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
239 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
240 groupHideAnnotationsMenu, selectedGroup);
241 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
247 } catch (Exception e)
255 sequenceMenu.setText(sequence.getName());
256 if (seq == ap.av.getAlignment().getSeqrep())
258 makeReferenceSeq.setText(MessageManager
259 .getString("action.unmark_as_reference"));
263 makeReferenceSeq.setText(MessageManager
264 .getString("action.set_as_reference"));
267 if (!ap.av.getAlignment().isNucleotide())
269 remove(rnaStructureMenu);
273 int origCount = rnaStructureMenu.getItemCount();
275 * add menu items to 2D-render any alignment or sequence secondary
276 * structure annotation
278 AlignmentAnnotation[] aas = ap.av.getAlignment()
279 .getAlignmentAnnotation();
282 for (final AlignmentAnnotation aa : aas)
284 if (aa.isValidStruc() && aa.sequenceRef == null)
287 * valid alignment RNA secondary structure annotation
289 menuItem = new JMenuItem();
290 menuItem.setText(MessageManager.formatMessage(
291 "label.2d_rna_structure_line",
292 new Object[] { aa.label }));
293 menuItem.addActionListener(new ActionListener()
296 public void actionPerformed(ActionEvent e)
298 new AppVarna(seq, aa, ap);
301 rnaStructureMenu.add(menuItem);
306 if (seq.getAnnotation() != null)
308 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
309 for (final AlignmentAnnotation aa : seqAnns)
311 if (aa.isValidStruc())
314 * valid sequence RNA secondary structure annotation
316 // TODO: make rnastrucF a bit more nice
317 menuItem = new JMenuItem();
318 menuItem.setText(MessageManager.formatMessage(
319 "label.2d_rna_sequence_name",
320 new Object[] { seq.getName() }));
321 menuItem.addActionListener(new ActionListener()
324 public void actionPerformed(ActionEvent e)
326 // TODO: VARNA does'nt print gaps in the sequence
327 new AppVarna(seq, aa, ap);
330 rnaStructureMenu.add(menuItem);
334 if (rnaStructureMenu.getItemCount() == origCount)
336 remove(rnaStructureMenu);
340 menuItem = new JMenuItem(
341 MessageManager.getString("action.hide_sequences"));
342 menuItem.addActionListener(new ActionListener()
345 public void actionPerformed(ActionEvent e)
347 hideSequences(false);
352 if (ap.av.getSelectionGroup() != null
353 && ap.av.getSelectionGroup().getSize() > 1)
355 menuItem = new JMenuItem(MessageManager.formatMessage(
356 "label.represent_group_with",
357 new Object[] { seq.getName() }));
358 menuItem.addActionListener(new ActionListener()
361 public void actionPerformed(ActionEvent e)
366 sequenceMenu.add(menuItem);
369 if (ap.av.hasHiddenRows())
371 final int index = ap.av.getAlignment().findIndex(seq);
373 if (ap.av.adjustForHiddenSeqs(index)
374 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
376 menuItem = new JMenuItem(
377 MessageManager.getString("action.reveal_sequences"));
378 menuItem.addActionListener(new ActionListener()
381 public void actionPerformed(ActionEvent e)
383 ap.av.showSequence(index);
384 if (ap.overviewPanel != null)
386 ap.overviewPanel.updateOverviewImage();
394 // for the case when no sequences are even visible
395 if (ap.av.hasHiddenRows())
398 menuItem = new JMenuItem(
399 MessageManager.getString("action.reveal_all"));
400 menuItem.addActionListener(new ActionListener()
403 public void actionPerformed(ActionEvent e)
405 ap.av.showAllHiddenSeqs();
406 if (ap.overviewPanel != null)
408 ap.overviewPanel.updateOverviewImage();
417 SequenceGroup sg = ap.av.getSelectionGroup();
418 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
419 .getGroups().contains(sg) : false;
421 if (sg != null && sg.getSize() > 0)
423 groupName.setText(MessageManager
424 .getString("label.edit_name_and_description_current_group"));
426 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
428 conservationMenuItem.setEnabled(!sg.isNucleotide());
432 if (sg.cs.conservationApplied())
434 conservationMenuItem.setSelected(true);
436 if (sg.cs.getThreshold() > 0)
438 abovePIDColour.setSelected(true);
441 modifyConservation.setEnabled(conservationMenuItem.isSelected());
442 modifyPID.setEnabled(abovePIDColour.isSelected());
443 displayNonconserved.setSelected(sg.getShowNonconserved());
444 showText.setSelected(sg.getDisplayText());
445 showColourText.setSelected(sg.getColourText());
446 showBoxes.setSelected(sg.getDisplayBoxes());
447 // add any groupURLs to the groupURL submenu and make it visible
448 if (groupLinks != null && groupLinks.size() > 0)
450 buildGroupURLMenu(sg, groupLinks);
452 // Add a 'show all structures' for the current selection
453 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
454 SequenceI sqass = null;
455 for (SequenceI sq : ap.av.getSequenceSelection())
457 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
458 if (pes != null && pes.size() > 0)
460 reppdb.put(pes.get(0).getId(), pes.get(0));
461 for (PDBEntry pe : pes)
463 pdbe.put(pe.getId(), pe);
473 final PDBEntry[] pe = pdbe.values().toArray(
474 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
475 new PDBEntry[reppdb.size()]);
476 final JMenuItem gpdbview, rpdbview;
481 groupMenu.setVisible(false);
482 editMenu.setVisible(false);
487 createGroupMenuItem.setVisible(true);
488 unGroupMenuItem.setVisible(false);
489 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
493 createGroupMenuItem.setVisible(false);
494 unGroupMenuItem.setVisible(true);
495 jMenu1.setText(MessageManager.getString("action.edit_group"));
500 sequenceMenu.setVisible(false);
501 pdbStructureDialog.setVisible(false);
502 rnaStructureMenu.setVisible(false);
505 if (links != null && links.size() > 0)
507 addFeatureLinks(seq, links);
512 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
517 void addFeatureLinks(final SequenceI seq, List<String> links)
519 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
520 Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
522 for (String link : links)
524 UrlLink urlLink = null;
527 urlLink = new UrlLink(link);
528 } catch (Exception foo)
530 Cache.log.error("Exception for URLLink '" + link + "'", foo);
534 if (!urlLink.isValid())
536 Cache.log.error(urlLink.getInvalidMessage());
540 urlLink.createLinksFromSeq(seq, linkset);
543 addshowLinks(linkMenu, linkset.values());
545 // disable link menu if there are no valid entries
546 if (linkMenu.getItemCount() > 0)
548 linkMenu.setEnabled(true);
552 linkMenu.setEnabled(false);
555 if (sequence != null)
557 sequenceMenu.add(linkMenu);
567 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
568 * "All" is added first, followed by a separator. Then add any annotation
569 * types associated with the current selection. Separate menus are built for
570 * the selected sequence group (if any), and the selected sequence.
572 * Some annotation rows are always rendered together - these can be identified
573 * by a common graphGroup property > -1. Only one of each group will be marked
574 * as visible (to avoid duplication of the display). For such groups we add a
575 * composite type name, e.g.
577 * IUPredWS (Long), IUPredWS (Short)
581 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
582 List<SequenceI> forSequences)
584 showMenu.removeAll();
585 hideMenu.removeAll();
587 final List<String> all = Arrays.asList(new String[] { MessageManager
588 .getString("label.all") });
589 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
590 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
592 showMenu.addSeparator();
593 hideMenu.addSeparator();
595 final AlignmentAnnotation[] annotations = ap.getAlignment()
596 .getAlignmentAnnotation();
599 * Find shown/hidden annotations types, distinguished by source (calcId),
600 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
601 * the insertion order, which is the order of the annotations on the
604 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
605 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
606 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
607 AlignmentAnnotationUtils.asList(annotations), forSequences);
609 for (String calcId : hiddenTypes.keySet())
611 for (List<String> type : hiddenTypes.get(calcId))
613 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
617 // grey out 'show annotations' if none are hidden
618 showMenu.setEnabled(!hiddenTypes.isEmpty());
620 for (String calcId : shownTypes.keySet())
622 for (List<String> type : shownTypes.get(calcId))
624 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
628 // grey out 'hide annotations' if none are shown
629 hideMenu.setEnabled(!shownTypes.isEmpty());
633 * Returns a list of sequences - either the current selection group (if there
634 * is one), else the specified single sequence.
639 protected List<SequenceI> getSequenceScope(SequenceI seq)
641 List<SequenceI> forSequences = null;
642 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
643 if (selectionGroup != null && selectionGroup.getSize() > 0)
645 forSequences = selectionGroup.getSequences();
649 forSequences = seq == null ? Collections.<SequenceI> emptyList()
650 : Arrays.asList(seq);
656 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
659 * @param showOrHideMenu
661 * @param forSequences
662 * the sequences whose annotations may be shown or hidden
667 * if true this is a special label meaning 'All'
668 * @param actionIsShow
669 * if true, the select menu item action is to show the annotation
672 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
673 final List<SequenceI> forSequences, String calcId,
674 final List<String> types, final boolean allTypes,
675 final boolean actionIsShow)
677 String label = types.toString(); // [a, b, c]
678 label = label.substring(1, label.length() - 1); // a, b, c
679 final JMenuItem item = new JMenuItem(label);
680 item.setToolTipText(calcId);
681 item.addActionListener(new ActionListener()
684 public void actionPerformed(ActionEvent e)
686 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
687 types, forSequences, allTypes, actionIsShow);
691 showOrHideMenu.add(item);
694 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
697 // TODO: usability: thread off the generation of group url content so root
699 // sequence only URLs
700 // ID/regex match URLs
701 groupLinksMenu = new JMenu(
702 MessageManager.getString("action.group_link"));
703 // three types of url that might be created.
704 JMenu[] linkMenus = new JMenu[] { null,
705 new JMenu(MessageManager.getString("action.ids")),
706 new JMenu(MessageManager.getString("action.sequences")),
707 new JMenu(MessageManager.getString("action.ids_sequences")) };
709 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
710 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
711 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
712 for (int sq = 0; sq < seqs.length; sq++)
715 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
716 .findPosition(sg.getEndRes());
717 // just collect ids from dataset sequence
718 // TODO: check if IDs collected from selecton group intersects with the
719 // current selection, too
720 SequenceI sqi = seqs[sq];
721 while (sqi.getDatasetSequence() != null)
723 sqi = sqi.getDatasetSequence();
725 DBRefEntry[] dbr = sqi.getDBRefs();
726 if (dbr != null && dbr.length > 0)
728 for (int d = 0; d < dbr.length; d++)
730 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
731 Object[] sarray = commonDbrefs.get(src);
734 sarray = new Object[2];
735 sarray[0] = new int[] { 0 };
736 sarray[1] = new String[seqs.length];
738 commonDbrefs.put(src, sarray);
741 if (((String[]) sarray[1])[sq] == null)
744 || (dbr[d].getMap().locateMappedRange(start, end) != null))
746 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
747 ((int[]) sarray[0])[0]++;
753 // now create group links for all distinct ID/sequence sets.
754 boolean addMenu = false; // indicates if there are any group links to give
756 for (String link : groupLinks)
758 GroupUrlLink urlLink = null;
761 urlLink = new GroupUrlLink(link);
762 } catch (Exception foo)
764 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
768 if (!urlLink.isValid())
770 Cache.log.error(urlLink.getInvalidMessage());
773 final String label = urlLink.getLabel();
774 boolean usingNames = false;
775 // Now see which parts of the group apply for this URL
776 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
777 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
778 String[] seqstr, ids; // input to makeUrl
781 int numinput = ((int[]) idset[0])[0];
782 String[] allids = ((String[]) idset[1]);
783 seqstr = new String[numinput];
784 ids = new String[numinput];
785 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
787 if (allids[sq] != null)
789 ids[idcount] = allids[sq];
790 seqstr[idcount++] = idandseqs[1][sq];
796 // just use the id/seq set
797 seqstr = idandseqs[1];
801 // and try and make the groupURL!
803 Object[] urlset = null;
806 urlset = urlLink.makeUrlStubs(ids, seqstr,
807 "FromJalview" + System.currentTimeMillis(), false);
808 } catch (UrlStringTooLongException e)
813 int type = urlLink.getGroupURLType() & 3;
814 // first two bits ofurlLink type bitfield are sequenceids and sequences
815 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
816 addshowLink(linkMenus[type], label
817 + (((type & 1) == 1) ? ("("
818 + (usingNames ? "Names" : ltarget) + ")") : ""),
825 groupLinksMenu = new JMenu(
826 MessageManager.getString("action.group_link"));
827 for (int m = 0; m < linkMenus.length; m++)
829 if (linkMenus[m] != null
830 && linkMenus[m].getMenuComponentCount() > 0)
832 groupLinksMenu.add(linkMenus[m]);
836 groupMenu.add(groupLinksMenu);
840 private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
842 for (List<String> linkstrset : linkset)
844 // split linkstr into label and url
845 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
850 * add a show URL menu item to the given linkMenu
854 * - menu label string
858 private void addshowLink(JMenu linkMenu, String label, final String url)
860 JMenuItem item = new JMenuItem(label);
861 item.setToolTipText(MessageManager.formatMessage(
862 "label.open_url_param", new Object[] { url }));
863 item.addActionListener(new ActionListener()
866 public void actionPerformed(ActionEvent e)
868 new Thread(new Runnable()
885 * add a late bound groupURL item to the given linkMenu
889 * - menu label string
890 * @param urlgenerator
891 * GroupURLLink used to generate URL
893 * Object array returned from the makeUrlStubs function.
895 private void addshowLink(JMenu linkMenu, String label,
896 final GroupUrlLink urlgenerator, final Object[] urlstub)
898 JMenuItem item = new JMenuItem(label);
899 item.setToolTipText(MessageManager.formatMessage(
900 "label.open_url_seqs_param",
901 new Object[] { urlgenerator.getUrl_prefix(),
902 urlgenerator.getNumberInvolved(urlstub) }));
903 // TODO: put in info about what is being sent.
904 item.addActionListener(new ActionListener()
907 public void actionPerformed(ActionEvent e)
909 new Thread(new Runnable()
917 showLink(urlgenerator.constructFrom(urlstub));
918 } catch (UrlStringTooLongException e2)
936 private void jbInit() throws Exception
938 groupMenu.setText(MessageManager.getString("label.selection"));
939 groupName.setText(MessageManager.getString("label.name"));
940 groupName.addActionListener(new ActionListener()
943 public void actionPerformed(ActionEvent e)
945 groupName_actionPerformed();
948 sequenceMenu.setText(MessageManager.getString("label.sequence"));
949 sequenceName.setText(MessageManager
950 .getString("label.edit_name_description"));
951 sequenceName.addActionListener(new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 sequenceName_actionPerformed();
959 chooseAnnotations.setText(MessageManager
960 .getString("action.choose_annotations"));
961 chooseAnnotations.addActionListener(new ActionListener()
964 public void actionPerformed(ActionEvent e)
966 chooseAnnotations_actionPerformed(e);
969 sequenceDetails.setText(MessageManager
970 .getString("label.sequence_details"));
971 sequenceDetails.addActionListener(new ActionListener()
974 public void actionPerformed(ActionEvent e)
976 sequenceDetails_actionPerformed();
979 sequenceSelDetails.setText(MessageManager
980 .getString("label.sequence_details"));
981 sequenceSelDetails.addActionListener(new ActionListener()
984 public void actionPerformed(ActionEvent e)
986 sequenceSelectionDetails_actionPerformed();
991 .setText(MessageManager.getString("action.remove_group"));
992 unGroupMenuItem.addActionListener(new ActionListener()
995 public void actionPerformed(ActionEvent e)
997 unGroupMenuItem_actionPerformed();
1000 createGroupMenuItem.setText(MessageManager
1001 .getString("action.create_group"));
1002 createGroupMenuItem.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 createGroupMenuItem_actionPerformed();
1011 outline.setText(MessageManager.getString("action.border_colour"));
1012 outline.addActionListener(new ActionListener()
1015 public void actionPerformed(ActionEvent e)
1017 outline_actionPerformed();
1020 showBoxes.setText(MessageManager.getString("action.boxes"));
1021 showBoxes.setState(true);
1022 showBoxes.addActionListener(new ActionListener()
1025 public void actionPerformed(ActionEvent e)
1027 showBoxes_actionPerformed();
1030 showText.setText(MessageManager.getString("action.text"));
1031 showText.setState(true);
1032 showText.addActionListener(new ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 showText_actionPerformed();
1040 showColourText.setText(MessageManager.getString("label.colour_text"));
1041 showColourText.addActionListener(new ActionListener()
1044 public void actionPerformed(ActionEvent e)
1046 showColourText_actionPerformed();
1049 displayNonconserved.setText(MessageManager
1050 .getString("label.show_non_conserved"));
1051 displayNonconserved.setState(true);
1052 displayNonconserved.addActionListener(new ActionListener()
1055 public void actionPerformed(ActionEvent e)
1057 showNonconserved_actionPerformed();
1060 editMenu.setText(MessageManager.getString("action.edit"));
1061 cut.setText(MessageManager.getString("action.cut"));
1062 cut.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 cut_actionPerformed();
1070 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1071 upperCase.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1079 copy.setText(MessageManager.getString("action.copy"));
1080 copy.addActionListener(new ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 copy_actionPerformed();
1088 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1089 lowerCase.addActionListener(new ActionListener()
1092 public void actionPerformed(ActionEvent e)
1097 toggle.setText(MessageManager.getString("label.toggle_case"));
1098 toggle.addActionListener(new ActionListener()
1101 public void actionPerformed(ActionEvent e)
1106 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1108 seqShowAnnotationsMenu.setText(MessageManager
1109 .getString("label.show_annotations"));
1110 seqHideAnnotationsMenu.setText(MessageManager
1111 .getString("label.hide_annotations"));
1112 groupShowAnnotationsMenu.setText(MessageManager
1113 .getString("label.show_annotations"));
1114 groupHideAnnotationsMenu.setText(MessageManager
1115 .getString("label.hide_annotations"));
1116 sequenceFeature.setText(MessageManager
1117 .getString("label.create_sequence_feature"));
1118 sequenceFeature.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 sequenceFeature_actionPerformed();
1126 jMenu1.setText(MessageManager.getString("label.group"));
1127 pdbStructureDialog.setText(MessageManager
1128 .getString("label.show_pdbstruct_dialog"));
1129 pdbStructureDialog.addActionListener(new ActionListener()
1132 public void actionPerformed(ActionEvent actionEvent)
1134 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1135 if (ap.av.getSelectionGroup() != null)
1137 selectedSeqs = ap.av.getSequenceSelection();
1139 new StructureChooser(selectedSeqs, sequence, ap);
1143 rnaStructureMenu.setText(MessageManager
1144 .getString("label.view_rna_structure"));
1146 // colStructureMenu.setText("Colour By Structure");
1147 editSequence.setText(MessageManager.getString("label.edit_sequence")
1149 editSequence.addActionListener(new ActionListener()
1152 public void actionPerformed(ActionEvent actionEvent)
1154 editSequence_actionPerformed(actionEvent);
1157 makeReferenceSeq.setText(MessageManager
1158 .getString("label.mark_as_representative"));
1159 makeReferenceSeq.addActionListener(new ActionListener()
1163 public void actionPerformed(ActionEvent actionEvent)
1165 makeReferenceSeq_actionPerformed(actionEvent);
1169 hideInsertions.setText(MessageManager
1170 .getString("label.hide_insertions"));
1171 hideInsertions.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 hideInsertions_actionPerformed(e);
1181 groupMenu.add(sequenceSelDetails);
1184 add(rnaStructureMenu);
1185 add(pdbStructureDialog);
1186 if (sequence != null)
1188 add(hideInsertions);
1190 // annotations configuration panel suppressed for now
1191 // groupMenu.add(chooseAnnotations);
1194 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1195 * (if a selection group is in force).
1197 sequenceMenu.add(seqShowAnnotationsMenu);
1198 sequenceMenu.add(seqHideAnnotationsMenu);
1199 sequenceMenu.add(seqAddReferenceAnnotations);
1200 groupMenu.add(groupShowAnnotationsMenu);
1201 groupMenu.add(groupHideAnnotationsMenu);
1202 groupMenu.add(groupAddReferenceAnnotations);
1203 groupMenu.add(editMenu);
1204 groupMenu.add(outputMenu);
1205 groupMenu.add(sequenceFeature);
1206 groupMenu.add(createGroupMenuItem);
1207 groupMenu.add(unGroupMenuItem);
1208 groupMenu.add(jMenu1);
1209 sequenceMenu.add(sequenceName);
1210 sequenceMenu.add(sequenceDetails);
1211 sequenceMenu.add(makeReferenceSeq);
1218 editMenu.add(editSequence);
1219 editMenu.add(upperCase);
1220 editMenu.add(lowerCase);
1221 editMenu.add(toggle);
1222 // JBPNote: These shouldn't be added here - should appear in a generic
1223 // 'apply web service to this sequence menu'
1224 // pdbMenu.add(RNAFold);
1225 // pdbMenu.add(ContraFold);
1226 jMenu1.add(groupName);
1227 jMenu1.add(colourMenu);
1228 jMenu1.add(showBoxes);
1229 jMenu1.add(showText);
1230 jMenu1.add(showColourText);
1231 jMenu1.add(outline);
1232 jMenu1.add(displayNonconserved);
1236 * Constructs the entries for the colour menu
1238 protected void initColourMenu()
1240 colourMenu.setText(MessageManager.getString("label.group_colour"));
1241 textColour.setText(MessageManager.getString("label.text_colour"));
1242 textColour.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 textColour_actionPerformed();
1251 abovePIDColour.setText(MessageManager
1252 .getString("label.above_identity_threshold"));
1253 abovePIDColour.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1262 modifyPID.setText(MessageManager
1263 .getString("label.modify_identity_threshold"));
1264 modifyPID.addActionListener(new ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 modifyPID_actionPerformed();
1273 conservationMenuItem.setText(MessageManager
1274 .getString("action.by_conservation"));
1275 conservationMenuItem.addActionListener(new ActionListener()
1278 public void actionPerformed(ActionEvent e)
1280 conservationMenuItem_actionPerformed(conservationMenuItem
1285 modifyConservation.setText(MessageManager
1286 .getString("label.modify_conservation_threshold"));
1287 modifyConservation.addActionListener(new ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 modifyConservation_actionPerformed();
1298 * Builds the group colour sub-menu, including any user-defined colours which
1299 * were loaded at startup or during the Jalview session
1301 protected void buildColourMenu()
1303 SequenceGroup sg = ap.av.getSelectionGroup();
1307 * popup menu with no sequence group scope
1311 colourMenu.removeAll();
1312 colourMenu.add(textColour);
1313 colourMenu.addSeparator();
1315 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1317 colourMenu.addSeparator();
1318 colourMenu.add(conservationMenuItem);
1319 colourMenu.add(modifyConservation);
1320 colourMenu.add(abovePIDColour);
1321 colourMenu.add(modifyPID);
1324 protected void modifyConservation_actionPerformed()
1326 SequenceGroup sg = getGroup();
1329 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1330 SliderPanel.showConservationSlider();
1334 protected void modifyPID_actionPerformed()
1336 SequenceGroup sg = getGroup();
1339 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1341 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1342 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1344 SliderPanel.showPIDSlider();
1349 * Check for any annotations on the underlying dataset sequences (for the
1350 * current selection group) which are not 'on the alignment'.If any are found,
1351 * enable the option to add them to the alignment. The criteria for 'on the
1352 * alignment' is finding an alignment annotation on the alignment, matched on
1353 * calcId, label and sequenceRef.
1355 * A tooltip is also constructed that displays the source (calcId) and type
1356 * (label) of the annotations that can be added.
1359 * @param forSequences
1361 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1362 List<SequenceI> forSequences)
1364 menuItem.setEnabled(false);
1367 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1368 * Using TreeMap means calcIds are shown in alphabetical order.
1370 SortedMap<String, String> tipEntries = new TreeMap<String, String>();
1371 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1372 AlignmentI al = this.ap.av.getAlignment();
1373 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1374 tipEntries, candidates, al);
1375 if (!candidates.isEmpty())
1377 StringBuilder tooltip = new StringBuilder(64);
1378 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1381 * Found annotations that could be added. Enable the menu item, and
1382 * configure its tooltip and action.
1384 menuItem.setEnabled(true);
1385 for (String calcId : tipEntries.keySet())
1387 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1389 String tooltipText = JvSwingUtils.wrapTooltip(true,
1390 tooltip.toString());
1391 menuItem.setToolTipText(tooltipText);
1393 menuItem.addActionListener(new ActionListener()
1396 public void actionPerformed(ActionEvent e)
1398 addReferenceAnnotations_actionPerformed(candidates);
1405 * Add annotations to the sequences and to the alignment.
1408 * a map whose keys are sequences on the alignment, and values a list
1409 * of annotations to add to each sequence
1411 protected void addReferenceAnnotations_actionPerformed(
1412 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1414 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1415 final AlignmentI alignment = this.ap.getAlignment();
1416 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1421 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1423 if (!ap.av.getAlignment().hasSeqrep())
1425 // initialise the display flags so the user sees something happen
1426 ap.av.setDisplayReferenceSeq(true);
1427 ap.av.setColourByReferenceSeq(true);
1428 ap.av.getAlignment().setSeqrep(sequence);
1432 if (ap.av.getAlignment().getSeqrep() == sequence)
1434 ap.av.getAlignment().setSeqrep(null);
1438 ap.av.getAlignment().setSeqrep(sequence);
1444 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1446 if (sequence != null)
1448 ColumnSelection cs = ap.av.getColumnSelection();
1451 cs = new ColumnSelection();
1453 cs.hideInsertionsFor(sequence);
1454 ap.av.setColumnSelection(cs);
1459 protected void sequenceSelectionDetails_actionPerformed()
1461 createSequenceDetailsReport(ap.av.getSequenceSelection());
1464 protected void sequenceDetails_actionPerformed()
1466 createSequenceDetailsReport(new SequenceI[] { sequence });
1469 public void createSequenceDetailsReport(SequenceI[] sequences)
1471 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1472 StringBuilder contents = new StringBuilder(128);
1473 for (SequenceI seq : sequences)
1475 contents.append("<p><h2>"
1478 "label.create_sequence_details_report_annotation_for",
1479 new Object[] { seq.getDisplayId(true) })
1481 new SequenceAnnotationReport(null)
1482 .createSequenceAnnotationReport(
1487 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1488 .getSeqPanel().seqCanvas.fr.getMinMax()
1490 contents.append("</p>");
1492 cap.setText("<html>" + contents.toString() + "</html>");
1494 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1495 "label.sequence_details_for",
1496 (sequences.length == 1 ? new Object[] { sequences[0]
1497 .getDisplayId(true) } : new Object[] { MessageManager
1498 .getString("label.selection") })), 500, 400);
1502 protected void showNonconserved_actionPerformed()
1504 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1509 * call to refresh view after settings change
1513 ap.updateAnnotation();
1514 ap.paintAlignment(true);
1516 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1520 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1521 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1531 public void abovePIDColour_actionPerformed(boolean selected)
1533 SequenceGroup sg = getGroup();
1541 sg.cs.setConsensus(AAFrequency.calculate(
1542 sg.getSequences(ap.av.getHiddenRepSequences()),
1543 sg.getStartRes(), sg.getEndRes() + 1));
1545 int threshold = SliderPanel.setPIDSliderSource(ap,
1546 sg.getGroupColourScheme(), getGroup()
1549 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1551 SliderPanel.showPIDSlider();
1554 // remove PIDColouring
1556 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1557 SliderPanel.hidePIDSlider();
1559 modifyPID.setEnabled(selected);
1565 * Open a panel where the user can choose which types of sequence annotation
1570 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1572 // todo correct way to guard against opening a duplicate panel?
1573 new AnnotationChooser(ap);
1582 public void conservationMenuItem_actionPerformed(boolean selected)
1584 SequenceGroup sg = getGroup();
1592 // JBPNote: Conservation name shouldn't be i18n translated
1593 Conservation c = new Conservation("Group", sg.getSequences(ap.av
1594 .getHiddenRepSequences()), sg.getStartRes(),
1595 sg.getEndRes() + 1);
1598 c.verdict(false, ap.av.getConsPercGaps());
1599 sg.cs.setConservation(c);
1601 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1603 SliderPanel.showConservationSlider();
1606 // remove ConservationColouring
1608 sg.cs.setConservation(null);
1609 SliderPanel.hideConservationSlider();
1611 modifyConservation.setEnabled(selected);
1622 protected void groupName_actionPerformed()
1625 SequenceGroup sg = getGroup();
1626 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1627 sg.getDescription(), " "
1628 + MessageManager.getString("label.group_name") + " ",
1629 MessageManager.getString("label.group_description") + " ",
1630 MessageManager.getString("label.edit_group_name_description"),
1638 sg.setName(dialog.getName());
1639 sg.setDescription(dialog.getDescription());
1644 * Get selection group - adding it to the alignment if necessary.
1646 * @return sequence group to operate on
1648 SequenceGroup getGroup()
1650 SequenceGroup sg = ap.av.getSelectionGroup();
1651 // this method won't add a new group if it already exists
1654 ap.av.getAlignment().addGroup(sg);
1666 void sequenceName_actionPerformed()
1668 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1669 sequence.getDescription(),
1670 " " + MessageManager.getString("label.sequence_name")
1672 MessageManager.getString("label.sequence_description") + " ",
1674 .getString("label.edit_sequence_name_description"),
1682 if (dialog.getName() != null)
1684 if (dialog.getName().indexOf(" ") > -1)
1690 .getString("label.spaces_converted_to_backslashes"),
1692 .getString("label.no_spaces_allowed_sequence_name"),
1693 JvOptionPane.WARNING_MESSAGE);
1696 sequence.setName(dialog.getName().replace(' ', '_'));
1697 ap.paintAlignment(false);
1700 sequence.setDescription(dialog.getDescription());
1702 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1713 void unGroupMenuItem_actionPerformed()
1715 SequenceGroup sg = ap.av.getSelectionGroup();
1716 ap.av.getAlignment().deleteGroup(sg);
1717 ap.av.setSelectionGroup(null);
1721 void createGroupMenuItem_actionPerformed()
1723 getGroup(); // implicitly creates group - note - should apply defaults / use
1724 // standard alignment window logic for this
1734 protected void outline_actionPerformed()
1736 SequenceGroup sg = getGroup();
1737 Color col = JColorChooser.showDialog(this,
1738 MessageManager.getString("label.select_outline_colour"),
1743 sg.setOutlineColour(col);
1755 public void showBoxes_actionPerformed()
1757 getGroup().setDisplayBoxes(showBoxes.isSelected());
1767 public void showText_actionPerformed()
1769 getGroup().setDisplayText(showText.isSelected());
1779 public void showColourText_actionPerformed()
1781 getGroup().setColourText(showColourText.isSelected());
1785 public void showLink(String url)
1789 jalview.util.BrowserLauncher.openURL(url);
1790 } catch (Exception ex)
1792 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1793 MessageManager.getString("label.web_browser_not_found_unix"),
1794 MessageManager.getString("label.web_browser_not_found"),
1795 JvOptionPane.WARNING_MESSAGE);
1797 ex.printStackTrace();
1801 void hideSequences(boolean representGroup)
1803 ap.av.hideSequences(sequence, representGroup);
1806 public void copy_actionPerformed()
1808 ap.alignFrame.copy_actionPerformed(null);
1811 public void cut_actionPerformed()
1813 ap.alignFrame.cut_actionPerformed(null);
1816 void changeCase(ActionEvent e)
1818 Object source = e.getSource();
1819 SequenceGroup sg = ap.av.getSelectionGroup();
1823 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1824 sg.getStartRes(), sg.getEndRes() + 1);
1829 if (source == toggle)
1831 description = MessageManager.getString("label.toggle_case");
1832 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1834 else if (source == upperCase)
1836 description = MessageManager.getString("label.to_upper_case");
1837 caseChange = ChangeCaseCommand.TO_UPPER;
1841 description = MessageManager.getString("label.to_lower_case");
1842 caseChange = ChangeCaseCommand.TO_LOWER;
1845 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1846 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1847 startEnd, caseChange);
1849 ap.alignFrame.addHistoryItem(caseCommand);
1851 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1857 public void outputText_actionPerformed(ActionEvent e)
1859 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1860 cap.setForInput(null);
1861 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1862 "label.alignment_output_command",
1863 new Object[] { e.getActionCommand() }), 600, 500);
1865 String[] omitHidden = null;
1867 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1868 // or we simply trust the user wants
1869 // wysiwig behaviour
1871 FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
1872 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
1875 public void sequenceFeature_actionPerformed()
1877 SequenceGroup sg = ap.av.getSelectionGroup();
1883 int rsize = 0, gSize = sg.getSize();
1884 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1885 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1887 for (int i = 0; i < gSize; i++)
1889 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1890 int end = sg.findEndRes(sg.getSequenceAt(i));
1893 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1894 features[rsize] = new SequenceFeature(null, null, null, start, end,
1899 rseqs = new SequenceI[rsize];
1900 tfeatures = new SequenceFeature[rsize];
1901 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1902 System.arraycopy(features, 0, tfeatures, 0, rsize);
1903 features = tfeatures;
1905 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1906 features, true, ap))
1908 ap.alignFrame.setShowSeqFeatures(true);
1909 ap.highlightSearchResults(null);
1913 public void textColour_actionPerformed()
1915 SequenceGroup sg = getGroup();
1918 new TextColourChooser().chooseColour(ap, sg);
1922 public void colourByStructure(String pdbid)
1924 Annotation[] anots = ap.av.getStructureSelectionManager()
1925 .colourSequenceFromStructure(sequence, pdbid);
1927 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1928 "Coloured by " + pdbid, anots);
1930 ap.av.getAlignment().addAnnotation(an);
1931 an.createSequenceMapping(sequence, 0, true);
1932 // an.adjustForAlignment();
1933 ap.av.getAlignment().setAnnotationIndex(an, 0);
1935 ap.adjustAnnotationHeight();
1937 sequence.addAlignmentAnnotation(an);
1941 public void editSequence_actionPerformed(ActionEvent actionEvent)
1943 SequenceGroup sg = ap.av.getSelectionGroup();
1947 if (sequence == null)
1949 sequence = sg.getSequenceAt(0);
1952 EditNameDialog dialog = new EditNameDialog(
1953 sequence.getSequenceAsString(sg.getStartRes(),
1954 sg.getEndRes() + 1), null,
1955 MessageManager.getString("label.edit_sequence"), null,
1956 MessageManager.getString("label.edit_sequence"),
1961 EditCommand editCommand = new EditCommand(
1962 MessageManager.getString("label.edit_sequences"),
1963 Action.REPLACE, dialog.getName().replace(' ',
1964 ap.av.getGapCharacter()),
1965 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1966 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
1968 ap.alignFrame.addHistoryItem(editCommand);
1970 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1977 * Action on user selecting an item from the colour menu (that does not have
1978 * its bespoke action handler)
1983 public void changeColour_actionPerformed(String colourSchemeName)
1985 SequenceGroup sg = getGroup();
1987 * switch to the chosen colour scheme (or null for None)
1989 ColourSchemeI colourScheme = ColourSchemes.getInstance()
1990 .getColourScheme(colourSchemeName, sg,
1991 ap.av.getHiddenRepSequences());
1992 sg.setColourScheme(colourScheme);
1993 if (colourScheme instanceof Blosum62ColourScheme
1994 || colourScheme instanceof PIDColourScheme)
1996 sg.cs.setConsensus(AAFrequency.calculate(
1997 sg.getSequences(ap.av.getHiddenRepSequences()),
1998 sg.getStartRes(), sg.getEndRes() + 1));