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.FileFormat;
43 import jalview.io.FileFormatI;
44 import jalview.io.FormatAdapter;
45 import jalview.io.SequenceAnnotationReport;
46 import jalview.schemes.AnnotationColourGradient;
47 import jalview.schemes.Blosum62ColourScheme;
48 import jalview.schemes.ColourSchemes;
49 import jalview.schemes.PIDColourScheme;
50 import jalview.schemes.ResidueColourScheme;
51 import jalview.util.GroupUrlLink;
52 import jalview.util.GroupUrlLink.UrlStringTooLongException;
53 import jalview.util.MessageManager;
54 import jalview.util.UrlLink;
56 import java.awt.Color;
57 import java.awt.event.ActionEvent;
58 import java.awt.event.ActionListener;
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 JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
94 JMenu sequenceMenu = new JMenu();
96 JMenuItem sequenceName = new JMenuItem();
98 JMenuItem sequenceDetails = new JMenuItem();
100 JMenuItem sequenceSelDetails = new JMenuItem();
102 JMenuItem makeReferenceSeq = new JMenuItem();
104 JMenuItem chooseAnnotations = new JMenuItem();
108 JMenuItem createGroupMenuItem = new JMenuItem();
110 JMenuItem unGroupMenuItem = new JMenuItem();
112 JMenuItem outline = new JMenuItem();
114 JMenu colourMenu = new JMenu();
116 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
118 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
120 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
122 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
124 JMenu editMenu = new JMenu();
126 JMenuItem cut = new JMenuItem();
128 JMenuItem copy = new JMenuItem();
130 JMenuItem upperCase = new JMenuItem();
132 JMenuItem lowerCase = new JMenuItem();
134 JMenuItem toggle = new JMenuItem();
136 JMenu pdbMenu = new JMenu();
138 JMenu outputMenu = new JMenu();
140 JMenu seqShowAnnotationsMenu = new JMenu();
142 JMenu seqHideAnnotationsMenu = new JMenu();
144 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
145 MessageManager.getString("label.add_reference_annotations"));
147 JMenu groupShowAnnotationsMenu = new JMenu();
149 JMenu groupHideAnnotationsMenu = new JMenu();
151 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
152 MessageManager.getString("label.add_reference_annotations"));
154 JMenuItem sequenceFeature = new JMenuItem();
156 JMenuItem textColour = new JMenuItem();
158 JMenu jMenu1 = new JMenu();
160 JMenuItem pdbStructureDialog = new JMenuItem();
162 JMenu rnaStructureMenu = new JMenu();
164 JMenuItem editSequence = new JMenuItem();
166 JMenu groupLinksMenu;
168 JMenuItem hideInsertions = new JMenuItem();
171 * Creates a new PopupMenu object.
178 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
180 this(ap, seq, links, null);
190 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
191 List<String> links, List<String> groupLinks)
193 // /////////////////////////////////////////////////////////
194 // If this is activated from the sequence panel, the user may want to
195 // edit or annotate a particular residue. Therefore display the residue menu
197 // If from the IDPanel, we must display the sequence menu
198 // ////////////////////////////////////////////////////////
202 for (String ff : FileFormat.getWritableFormats(true))
204 JMenuItem item = new JMenuItem(ff);
206 item.addActionListener(new ActionListener()
209 public void actionPerformed(ActionEvent e)
211 outputText_actionPerformed(e);
215 outputMenu.add(item);
219 * Build menus for annotation types that may be shown or hidden, and for
220 * 'reference annotations' that may be added to the alignment. First for the
221 * currently selected sequence (if there is one):
223 final List<SequenceI> selectedSequence = (seq == null ? Collections
224 .<SequenceI> emptyList() : Arrays.asList(seq));
225 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
226 seqHideAnnotationsMenu, selectedSequence);
227 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
231 * And repeat for the current selection group (if there is one):
233 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
234 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
236 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
237 groupHideAnnotationsMenu, selectedGroup);
238 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
244 } catch (Exception e)
252 sequenceMenu.setText(sequence.getName());
253 if (seq == ap.av.getAlignment().getSeqrep())
255 makeReferenceSeq.setText(MessageManager
256 .getString("action.unmark_as_reference"));
260 makeReferenceSeq.setText(MessageManager
261 .getString("action.set_as_reference"));
264 if (!ap.av.getAlignment().isNucleotide())
266 remove(rnaStructureMenu);
270 int origCount = rnaStructureMenu.getItemCount();
272 * add menu items to 2D-render any alignment or sequence secondary
273 * structure annotation
275 AlignmentAnnotation[] aas = ap.av.getAlignment()
276 .getAlignmentAnnotation();
279 for (final AlignmentAnnotation aa : aas)
281 if (aa.isValidStruc() && aa.sequenceRef == null)
284 * valid alignment RNA secondary structure annotation
286 menuItem = new JMenuItem();
287 menuItem.setText(MessageManager.formatMessage(
288 "label.2d_rna_structure_line",
289 new Object[] { aa.label }));
290 menuItem.addActionListener(new ActionListener()
293 public void actionPerformed(ActionEvent e)
295 new AppVarna(seq, aa, ap);
298 rnaStructureMenu.add(menuItem);
303 if (seq.getAnnotation() != null)
305 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
306 for (final AlignmentAnnotation aa : seqAnns)
308 if (aa.isValidStruc())
311 * valid sequence RNA secondary structure annotation
313 // TODO: make rnastrucF a bit more nice
314 menuItem = new JMenuItem();
315 menuItem.setText(MessageManager.formatMessage(
316 "label.2d_rna_sequence_name",
317 new Object[] { seq.getName() }));
318 menuItem.addActionListener(new ActionListener()
321 public void actionPerformed(ActionEvent e)
323 // TODO: VARNA does'nt print gaps in the sequence
324 new AppVarna(seq, aa, ap);
327 rnaStructureMenu.add(menuItem);
331 if (rnaStructureMenu.getItemCount() == origCount)
333 remove(rnaStructureMenu);
337 menuItem = new JMenuItem(
338 MessageManager.getString("action.hide_sequences"));
339 menuItem.addActionListener(new ActionListener()
342 public void actionPerformed(ActionEvent e)
344 hideSequences(false);
349 if (ap.av.getSelectionGroup() != null
350 && ap.av.getSelectionGroup().getSize() > 1)
352 menuItem = new JMenuItem(MessageManager.formatMessage(
353 "label.represent_group_with",
354 new Object[] { seq.getName() }));
355 menuItem.addActionListener(new ActionListener()
358 public void actionPerformed(ActionEvent e)
363 sequenceMenu.add(menuItem);
366 if (ap.av.hasHiddenRows())
368 final int index = ap.av.getAlignment().findIndex(seq);
370 if (ap.av.adjustForHiddenSeqs(index)
371 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
373 menuItem = new JMenuItem(
374 MessageManager.getString("action.reveal_sequences"));
375 menuItem.addActionListener(new ActionListener()
378 public void actionPerformed(ActionEvent e)
380 ap.av.showSequence(index);
381 if (ap.overviewPanel != null)
383 ap.overviewPanel.updateOverviewImage();
391 // for the case when no sequences are even visible
392 if (ap.av.hasHiddenRows())
395 menuItem = new JMenuItem(
396 MessageManager.getString("action.reveal_all"));
397 menuItem.addActionListener(new ActionListener()
400 public void actionPerformed(ActionEvent e)
402 ap.av.showAllHiddenSeqs();
403 if (ap.overviewPanel != null)
405 ap.overviewPanel.updateOverviewImage();
415 SequenceGroup sg = ap.av.getSelectionGroup();
416 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
417 .getGroups().contains(sg) : false;
419 if (sg != null && sg.getSize() > 0)
421 groupName.setText(MessageManager
422 .getString("label.edit_name_and_description_current_group"));
424 ColourMenuHelper.setColourSelected(colourMenu, sg.cs);
428 if (sg.cs.conservationApplied())
430 conservationMenuItem.setSelected(true);
432 if (sg.cs.getThreshold() > 0)
434 abovePIDColour.setSelected(true);
437 displayNonconserved.setSelected(sg.getShowNonconserved());
438 showText.setSelected(sg.getDisplayText());
439 showColourText.setSelected(sg.getColourText());
440 showBoxes.setSelected(sg.getDisplayBoxes());
441 // add any groupURLs to the groupURL submenu and make it visible
442 if (groupLinks != null && groupLinks.size() > 0)
444 buildGroupURLMenu(sg, groupLinks);
446 // Add a 'show all structures' for the current selection
447 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
448 SequenceI sqass = null;
449 for (SequenceI sq : ap.av.getSequenceSelection())
451 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
452 if (pes != null && pes.size() > 0)
454 reppdb.put(pes.get(0).getId(), pes.get(0));
455 for (PDBEntry pe : pes)
457 pdbe.put(pe.getId(), pe);
467 final PDBEntry[] pe = pdbe.values().toArray(
468 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
469 new PDBEntry[reppdb.size()]);
470 final JMenuItem gpdbview, rpdbview;
475 groupMenu.setVisible(false);
476 editMenu.setVisible(false);
481 createGroupMenuItem.setVisible(true);
482 unGroupMenuItem.setVisible(false);
483 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
487 createGroupMenuItem.setVisible(false);
488 unGroupMenuItem.setVisible(true);
489 jMenu1.setText(MessageManager.getString("action.edit_group"));
494 sequenceMenu.setVisible(false);
495 pdbStructureDialog.setVisible(false);
496 rnaStructureMenu.setVisible(false);
499 if (links != null && links.size() > 0)
501 addFeatureLinks(seq, links);
506 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
511 void addFeatureLinks(final SequenceI seq, List<String> links)
513 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
514 Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
516 for (String link : links)
518 UrlLink urlLink = null;
521 urlLink = new UrlLink(link);
522 } catch (Exception foo)
524 Cache.log.error("Exception for URLLink '" + link + "'", foo);
528 if (!urlLink.isValid())
530 Cache.log.error(urlLink.getInvalidMessage());
534 urlLink.createLinksFromSeq(seq, linkset);
537 addshowLinks(linkMenu, linkset.values());
539 // disable link menu if there are no valid entries
540 if (linkMenu.getItemCount() > 0)
542 linkMenu.setEnabled(true);
546 linkMenu.setEnabled(false);
549 if (sequence != null)
551 sequenceMenu.add(linkMenu);
563 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
564 * "All" is added first, followed by a separator. Then add any annotation
565 * types associated with the current selection. Separate menus are built for
566 * the selected sequence group (if any), and the selected sequence.
568 * Some annotation rows are always rendered together - these can be identified
569 * by a common graphGroup property > -1. Only one of each group will be marked
570 * as visible (to avoid duplication of the display). For such groups we add a
571 * composite type name, e.g.
573 * IUPredWS (Long), IUPredWS (Short)
577 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
578 List<SequenceI> forSequences)
580 showMenu.removeAll();
581 hideMenu.removeAll();
583 final List<String> all = Arrays.asList(new String[] { MessageManager
584 .getString("label.all") });
585 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
586 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
588 showMenu.addSeparator();
589 hideMenu.addSeparator();
591 final AlignmentAnnotation[] annotations = ap.getAlignment()
592 .getAlignmentAnnotation();
595 * Find shown/hidden annotations types, distinguished by source (calcId),
596 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
597 * the insertion order, which is the order of the annotations on the
600 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
601 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
602 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
603 AlignmentAnnotationUtils.asList(annotations), forSequences);
605 for (String calcId : hiddenTypes.keySet())
607 for (List<String> type : hiddenTypes.get(calcId))
609 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
613 // grey out 'show annotations' if none are hidden
614 showMenu.setEnabled(!hiddenTypes.isEmpty());
616 for (String calcId : shownTypes.keySet())
618 for (List<String> type : shownTypes.get(calcId))
620 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
624 // grey out 'hide annotations' if none are shown
625 hideMenu.setEnabled(!shownTypes.isEmpty());
629 * Returns a list of sequences - either the current selection group (if there
630 * is one), else the specified single sequence.
635 protected List<SequenceI> getSequenceScope(SequenceI seq)
637 List<SequenceI> forSequences = null;
638 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
639 if (selectionGroup != null && selectionGroup.getSize() > 0)
641 forSequences = selectionGroup.getSequences();
645 forSequences = seq == null ? Collections.<SequenceI> emptyList()
646 : Arrays.asList(seq);
652 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
655 * @param showOrHideMenu
657 * @param forSequences
658 * the sequences whose annotations may be shown or hidden
663 * if true this is a special label meaning 'All'
664 * @param actionIsShow
665 * if true, the select menu item action is to show the annotation
668 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
669 final List<SequenceI> forSequences, String calcId,
670 final List<String> types, final boolean allTypes,
671 final boolean actionIsShow)
673 String label = types.toString(); // [a, b, c]
674 label = label.substring(1, label.length() - 1); // a, b, c
675 final JMenuItem item = new JMenuItem(label);
676 item.setToolTipText(calcId);
677 item.addActionListener(new ActionListener()
680 public void actionPerformed(ActionEvent e)
682 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
683 types, forSequences, allTypes, actionIsShow);
687 showOrHideMenu.add(item);
690 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
693 // TODO: usability: thread off the generation of group url content so root
695 // sequence only URLs
696 // ID/regex match URLs
697 groupLinksMenu = new JMenu(
698 MessageManager.getString("action.group_link"));
699 // three types of url that might be created.
700 JMenu[] linkMenus = new JMenu[] { null,
701 new JMenu(MessageManager.getString("action.ids")),
702 new JMenu(MessageManager.getString("action.sequences")),
703 new JMenu(MessageManager.getString("action.ids_sequences")) };
705 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
706 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
707 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
708 for (int sq = 0; sq < seqs.length; sq++)
711 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
712 .findPosition(sg.getEndRes());
713 // just collect ids from dataset sequence
714 // TODO: check if IDs collected from selecton group intersects with the
715 // current selection, too
716 SequenceI sqi = seqs[sq];
717 while (sqi.getDatasetSequence() != null)
719 sqi = sqi.getDatasetSequence();
721 DBRefEntry[] dbr = sqi.getDBRefs();
722 if (dbr != null && dbr.length > 0)
724 for (int d = 0; d < dbr.length; d++)
726 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
727 Object[] sarray = commonDbrefs.get(src);
730 sarray = new Object[2];
731 sarray[0] = new int[] { 0 };
732 sarray[1] = new String[seqs.length];
734 commonDbrefs.put(src, sarray);
737 if (((String[]) sarray[1])[sq] == null)
740 || (dbr[d].getMap().locateMappedRange(start, end) != null))
742 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
743 ((int[]) sarray[0])[0]++;
749 // now create group links for all distinct ID/sequence sets.
750 boolean addMenu = false; // indicates if there are any group links to give
752 for (String link : groupLinks)
754 GroupUrlLink urlLink = null;
757 urlLink = new GroupUrlLink(link);
758 } catch (Exception foo)
760 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
764 if (!urlLink.isValid())
766 Cache.log.error(urlLink.getInvalidMessage());
769 final String label = urlLink.getLabel();
770 boolean usingNames = false;
771 // Now see which parts of the group apply for this URL
772 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
773 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
774 String[] seqstr, ids; // input to makeUrl
777 int numinput = ((int[]) idset[0])[0];
778 String[] allids = ((String[]) idset[1]);
779 seqstr = new String[numinput];
780 ids = new String[numinput];
781 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
783 if (allids[sq] != null)
785 ids[idcount] = allids[sq];
786 seqstr[idcount++] = idandseqs[1][sq];
792 // just use the id/seq set
793 seqstr = idandseqs[1];
797 // and try and make the groupURL!
799 Object[] urlset = null;
802 urlset = urlLink.makeUrlStubs(ids, seqstr,
803 "FromJalview" + System.currentTimeMillis(), false);
804 } catch (UrlStringTooLongException e)
809 int type = urlLink.getGroupURLType() & 3;
810 // first two bits ofurlLink type bitfield are sequenceids and sequences
811 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
812 addshowLink(linkMenus[type], label
813 + (((type & 1) == 1) ? ("("
814 + (usingNames ? "Names" : ltarget) + ")") : ""),
821 groupLinksMenu = new JMenu(
822 MessageManager.getString("action.group_link"));
823 for (int m = 0; m < linkMenus.length; m++)
825 if (linkMenus[m] != null
826 && linkMenus[m].getMenuComponentCount() > 0)
828 groupLinksMenu.add(linkMenus[m]);
832 groupMenu.add(groupLinksMenu);
836 private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
838 for (List<String> linkstrset : linkset)
840 // split linkstr into label and url
841 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
846 * add a show URL menu item to the given linkMenu
850 * - menu label string
854 private void addshowLink(JMenu linkMenu, String label, final String url)
856 JMenuItem item = new JMenuItem(label);
857 item.setToolTipText(MessageManager.formatMessage(
858 "label.open_url_param", new Object[] { url }));
859 item.addActionListener(new ActionListener()
862 public void actionPerformed(ActionEvent e)
864 new Thread(new Runnable()
881 * add a late bound groupURL item to the given linkMenu
885 * - menu label string
886 * @param urlgenerator
887 * GroupURLLink used to generate URL
889 * Object array returned from the makeUrlStubs function.
891 private void addshowLink(JMenu linkMenu, String label,
892 final GroupUrlLink urlgenerator, final Object[] urlstub)
894 JMenuItem item = new JMenuItem(label);
895 item.setToolTipText(MessageManager.formatMessage(
896 "label.open_url_seqs_param",
897 new Object[] { urlgenerator.getUrl_prefix(),
898 urlgenerator.getNumberInvolved(urlstub) }));
899 // TODO: put in info about what is being sent.
900 item.addActionListener(new ActionListener()
903 public void actionPerformed(ActionEvent e)
905 new Thread(new Runnable()
913 showLink(urlgenerator.constructFrom(urlstub));
914 } catch (UrlStringTooLongException e2)
932 private void jbInit() throws Exception
934 groupMenu.setText(MessageManager.getString("label.selection"));
935 groupName.setText(MessageManager.getString("label.name"));
936 groupName.addActionListener(new ActionListener()
939 public void actionPerformed(ActionEvent e)
941 groupName_actionPerformed();
944 sequenceMenu.setText(MessageManager.getString("label.sequence"));
945 sequenceName.setText(MessageManager
946 .getString("label.edit_name_description"));
947 sequenceName.addActionListener(new ActionListener()
950 public void actionPerformed(ActionEvent e)
952 sequenceName_actionPerformed();
955 chooseAnnotations.setText(MessageManager
956 .getString("action.choose_annotations"));
957 chooseAnnotations.addActionListener(new ActionListener()
960 public void actionPerformed(ActionEvent e)
962 chooseAnnotations_actionPerformed(e);
965 sequenceDetails.setText(MessageManager
966 .getString("label.sequence_details"));
967 sequenceDetails.addActionListener(new ActionListener()
970 public void actionPerformed(ActionEvent e)
972 sequenceDetails_actionPerformed();
975 sequenceSelDetails.setText(MessageManager
976 .getString("label.sequence_details"));
977 sequenceSelDetails.addActionListener(new ActionListener()
980 public void actionPerformed(ActionEvent e)
982 sequenceSelectionDetails_actionPerformed();
986 .setText(MessageManager.getString("action.remove_group"));
987 unGroupMenuItem.addActionListener(new ActionListener()
990 public void actionPerformed(ActionEvent e)
992 unGroupMenuItem_actionPerformed();
995 createGroupMenuItem.setText(MessageManager
996 .getString("action.create_group"));
997 createGroupMenuItem.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 createGroupMenuItem_actionPerformed();
1006 outline.setText(MessageManager.getString("action.border_colour"));
1007 outline.addActionListener(new ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 outline_actionPerformed();
1015 showBoxes.setText(MessageManager.getString("action.boxes"));
1016 showBoxes.setState(true);
1017 showBoxes.addActionListener(new ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 showBoxes_actionPerformed();
1025 showText.setText(MessageManager.getString("action.text"));
1026 showText.setState(true);
1027 showText.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 showText_actionPerformed();
1035 showColourText.setText(MessageManager.getString("label.colour_text"));
1036 showColourText.addActionListener(new ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 showColourText_actionPerformed();
1044 displayNonconserved.setText(MessageManager
1045 .getString("label.show_non_conserved"));
1046 displayNonconserved.setState(true);
1047 displayNonconserved.addActionListener(new ActionListener()
1050 public void actionPerformed(ActionEvent e)
1052 showNonconserved_actionPerformed();
1055 editMenu.setText(MessageManager.getString("action.edit"));
1056 cut.setText(MessageManager.getString("action.cut"));
1057 cut.addActionListener(new ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 cut_actionPerformed();
1065 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1066 upperCase.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1074 copy.setText(MessageManager.getString("action.copy"));
1075 copy.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 copy_actionPerformed();
1083 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1084 lowerCase.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1092 toggle.setText(MessageManager.getString("label.toggle_case"));
1093 toggle.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1101 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1103 seqShowAnnotationsMenu.setText(MessageManager
1104 .getString("label.show_annotations"));
1105 seqHideAnnotationsMenu.setText(MessageManager
1106 .getString("label.hide_annotations"));
1107 groupShowAnnotationsMenu.setText(MessageManager
1108 .getString("label.show_annotations"));
1109 groupHideAnnotationsMenu.setText(MessageManager
1110 .getString("label.hide_annotations"));
1111 sequenceFeature.setText(MessageManager
1112 .getString("label.create_sequence_feature"));
1113 sequenceFeature.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 sequenceFeature_actionPerformed();
1121 jMenu1.setText(MessageManager.getString("label.group"));
1122 pdbStructureDialog.setText(MessageManager
1123 .getString("label.show_pdbstruct_dialog"));
1124 pdbStructureDialog.addActionListener(new ActionListener()
1127 public void actionPerformed(ActionEvent actionEvent)
1129 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1130 if (ap.av.getSelectionGroup() != null)
1132 selectedSeqs = ap.av.getSequenceSelection();
1134 new StructureChooser(selectedSeqs, sequence, ap);
1138 rnaStructureMenu.setText(MessageManager
1139 .getString("label.view_rna_structure"));
1141 // colStructureMenu.setText("Colour By Structure");
1142 editSequence.setText(MessageManager.getString("label.edit_sequence")
1144 editSequence.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent actionEvent)
1149 editSequence_actionPerformed(actionEvent);
1152 makeReferenceSeq.setText(MessageManager
1153 .getString("label.mark_as_representative"));
1154 makeReferenceSeq.addActionListener(new ActionListener()
1158 public void actionPerformed(ActionEvent actionEvent)
1160 makeReferenceSeq_actionPerformed(actionEvent);
1164 hideInsertions.setText(MessageManager
1165 .getString("label.hide_insertions"));
1166 hideInsertions.addActionListener(new ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 hideInsertions_actionPerformed(e);
1176 * annotationMenuItem.setText("By Annotation");
1177 * annotationMenuItem.addActionListener(new ActionListener() { public void
1178 * actionPerformed(ActionEvent actionEvent) {
1179 * annotationMenuItem_actionPerformed(actionEvent); } });
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();
1250 abovePIDColour.setText(MessageManager
1251 .getString("label.above_identity_threshold"));
1252 abovePIDColour.addActionListener(new ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 abovePIDColour_actionPerformed();
1261 conservationMenuItem.setText(MessageManager
1262 .getString("action.by_conservation"));
1263 conservationMenuItem.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 conservationMenuItem_actionPerformed();
1274 * Builds the group colour sub-menu, including any user-defined colours which
1275 * were loaded at startup or during the Jalview session
1277 protected void buildColourMenu()
1279 SequenceGroup sg = ap.av.getSelectionGroup();
1283 * popup menu with no sequence group scope
1287 colourMenu.removeAll();
1288 colourMenu.add(textColour);
1289 colourMenu.addSeparator();
1291 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1293 colourMenu.addSeparator();
1294 colourMenu.add(conservationMenuItem);
1295 colourMenu.add(abovePIDColour);
1299 * Check for any annotations on the underlying dataset sequences (for the
1300 * current selection group) which are not 'on the alignment'.If any are found,
1301 * enable the option to add them to the alignment. The criteria for 'on the
1302 * alignment' is finding an alignment annotation on the alignment, matched on
1303 * calcId, label and sequenceRef.
1305 * A tooltip is also constructed that displays the source (calcId) and type
1306 * (label) of the annotations that can be added.
1309 * @param forSequences
1311 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1312 List<SequenceI> forSequences)
1314 menuItem.setEnabled(false);
1317 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1318 * Using TreeMap means calcIds are shown in alphabetical order.
1320 SortedMap<String, String> tipEntries = new TreeMap<String, String>();
1321 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1322 AlignmentI al = this.ap.av.getAlignment();
1323 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1324 tipEntries, candidates, al);
1325 if (!candidates.isEmpty())
1327 StringBuilder tooltip = new StringBuilder(64);
1328 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1331 * Found annotations that could be added. Enable the menu item, and
1332 * configure its tooltip and action.
1334 menuItem.setEnabled(true);
1335 for (String calcId : tipEntries.keySet())
1337 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1339 String tooltipText = JvSwingUtils.wrapTooltip(true,
1340 tooltip.toString());
1341 menuItem.setToolTipText(tooltipText);
1343 menuItem.addActionListener(new ActionListener()
1346 public void actionPerformed(ActionEvent e)
1348 addReferenceAnnotations_actionPerformed(candidates);
1355 * Add annotations to the sequences and to the alignment.
1358 * a map whose keys are sequences on the alignment, and values a list
1359 * of annotations to add to each sequence
1361 protected void addReferenceAnnotations_actionPerformed(
1362 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1364 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1365 final AlignmentI alignment = this.ap.getAlignment();
1366 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1371 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1373 if (!ap.av.getAlignment().hasSeqrep())
1375 // initialise the display flags so the user sees something happen
1376 ap.av.setDisplayReferenceSeq(true);
1377 ap.av.setColourByReferenceSeq(true);
1378 ap.av.getAlignment().setSeqrep(sequence);
1382 if (ap.av.getAlignment().getSeqrep() == sequence)
1384 ap.av.getAlignment().setSeqrep(null);
1388 ap.av.getAlignment().setSeqrep(sequence);
1394 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1396 if (sequence != null)
1398 ColumnSelection cs = ap.av.getColumnSelection();
1401 cs = new ColumnSelection();
1403 cs.hideInsertionsFor(sequence);
1404 ap.av.setColumnSelection(cs);
1409 protected void sequenceSelectionDetails_actionPerformed()
1411 createSequenceDetailsReport(ap.av.getSequenceSelection());
1414 protected void sequenceDetails_actionPerformed()
1416 createSequenceDetailsReport(new SequenceI[] { sequence });
1419 public void createSequenceDetailsReport(SequenceI[] sequences)
1421 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1422 StringBuilder contents = new StringBuilder(128);
1423 for (SequenceI seq : sequences)
1425 contents.append("<p><h2>"
1428 "label.create_sequence_details_report_annotation_for",
1429 new Object[] { seq.getDisplayId(true) })
1431 new SequenceAnnotationReport(null)
1432 .createSequenceAnnotationReport(
1437 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1438 .getSeqPanel().seqCanvas.fr.getMinMax()
1440 contents.append("</p>");
1442 cap.setText("<html>" + contents.toString() + "</html>");
1444 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1445 "label.sequence_details_for",
1446 (sequences.length == 1 ? new Object[] { sequences[0]
1447 .getDisplayId(true) } : new Object[] { MessageManager
1448 .getString("label.selection") })), 500, 400);
1452 protected void showNonconserved_actionPerformed()
1454 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1459 * call to refresh view after settings change
1463 ap.updateAnnotation();
1464 ap.paintAlignment(true);
1466 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1470 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1471 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1479 protected void abovePIDColour_actionPerformed()
1481 SequenceGroup sg = getGroup();
1487 if (abovePIDColour.isSelected())
1489 sg.cs.setConsensus(AAFrequency.calculate(
1490 sg.getSequences(ap.av.getHiddenRepSequences()),
1491 sg.getStartRes(), sg.getEndRes() + 1));
1493 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1496 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1498 SliderPanel.showPIDSlider();
1501 // remove PIDColouring
1503 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1510 * Open a panel where the user can choose which types of sequence annotation
1515 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1517 // todo correct way to guard against opening a duplicate panel?
1518 new AnnotationChooser(ap);
1527 protected void conservationMenuItem_actionPerformed()
1529 SequenceGroup sg = getGroup();
1535 if (conservationMenuItem.isSelected())
1537 // JBPNote: Conservation name shouldn't be i18n translated
1538 Conservation c = new Conservation("Group", sg.getSequences(ap.av
1539 .getHiddenRepSequences()), sg.getStartRes(),
1540 sg.getEndRes() + 1);
1543 c.verdict(false, ap.av.getConsPercGaps());
1545 sg.cs.setConservation(c);
1547 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1548 SliderPanel.showConservationSlider();
1551 // remove ConservationColouring
1553 sg.cs.setConservation(null);
1559 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1561 SequenceGroup sg = getGroup();
1567 AnnotationColourGradient acg = new AnnotationColourGradient(
1568 sequence.getAnnotation()[0], null,
1569 AnnotationColourGradient.NO_THRESHOLD);
1571 acg.setPredefinedColours(true);
1583 protected void groupName_actionPerformed()
1586 SequenceGroup sg = getGroup();
1587 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1588 sg.getDescription(), " "
1589 + MessageManager.getString("label.group_name") + " ",
1590 MessageManager.getString("label.group_description") + " ",
1591 MessageManager.getString("label.edit_group_name_description"),
1599 sg.setName(dialog.getName());
1600 sg.setDescription(dialog.getDescription());
1605 * Get selection group - adding it to the alignment if necessary.
1607 * @return sequence group to operate on
1609 SequenceGroup getGroup()
1611 SequenceGroup sg = ap.av.getSelectionGroup();
1612 // this method won't add a new group if it already exists
1615 ap.av.getAlignment().addGroup(sg);
1627 void sequenceName_actionPerformed()
1629 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1630 sequence.getDescription(),
1631 " " + MessageManager.getString("label.sequence_name")
1633 MessageManager.getString("label.sequence_description") + " ",
1635 .getString("label.edit_sequence_name_description"),
1643 if (dialog.getName() != null)
1645 if (dialog.getName().indexOf(" ") > -1)
1651 .getString("label.spaces_converted_to_backslashes"),
1653 .getString("label.no_spaces_allowed_sequence_name"),
1654 JvOptionPane.WARNING_MESSAGE);
1657 sequence.setName(dialog.getName().replace(' ', '_'));
1658 ap.paintAlignment(false);
1661 sequence.setDescription(dialog.getDescription());
1663 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1674 void unGroupMenuItem_actionPerformed()
1676 SequenceGroup sg = ap.av.getSelectionGroup();
1677 ap.av.getAlignment().deleteGroup(sg);
1678 ap.av.setSelectionGroup(null);
1682 void createGroupMenuItem_actionPerformed()
1684 getGroup(); // implicitly creates group - note - should apply defaults / use
1685 // standard alignment window logic for this
1695 protected void outline_actionPerformed()
1697 SequenceGroup sg = getGroup();
1698 Color col = JColorChooser.showDialog(this,
1699 MessageManager.getString("label.select_outline_colour"),
1704 sg.setOutlineColour(col);
1716 public void showBoxes_actionPerformed()
1718 getGroup().setDisplayBoxes(showBoxes.isSelected());
1728 public void showText_actionPerformed()
1730 getGroup().setDisplayText(showText.isSelected());
1740 public void showColourText_actionPerformed()
1742 getGroup().setColourText(showColourText.isSelected());
1746 public void showLink(String url)
1750 jalview.util.BrowserLauncher.openURL(url);
1751 } catch (Exception ex)
1753 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1754 MessageManager.getString("label.web_browser_not_found_unix"),
1755 MessageManager.getString("label.web_browser_not_found"),
1756 JvOptionPane.WARNING_MESSAGE);
1758 ex.printStackTrace();
1762 void hideSequences(boolean representGroup)
1764 ap.av.hideSequences(sequence, representGroup);
1767 public void copy_actionPerformed()
1769 ap.alignFrame.copy_actionPerformed(null);
1772 public void cut_actionPerformed()
1774 ap.alignFrame.cut_actionPerformed(null);
1777 void changeCase(ActionEvent e)
1779 Object source = e.getSource();
1780 SequenceGroup sg = ap.av.getSelectionGroup();
1784 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1785 sg.getStartRes(), sg.getEndRes() + 1);
1790 if (source == toggle)
1792 description = MessageManager.getString("label.toggle_case");
1793 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1795 else if (source == upperCase)
1797 description = MessageManager.getString("label.to_upper_case");
1798 caseChange = ChangeCaseCommand.TO_UPPER;
1802 description = MessageManager.getString("label.to_lower_case");
1803 caseChange = ChangeCaseCommand.TO_LOWER;
1806 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1807 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1808 startEnd, caseChange);
1810 ap.alignFrame.addHistoryItem(caseCommand);
1812 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1818 public void outputText_actionPerformed(ActionEvent e)
1820 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1821 cap.setForInput(null);
1822 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1823 "label.alignment_output_command",
1824 new Object[] { e.getActionCommand() }), 600, 500);
1826 String[] omitHidden = null;
1828 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1829 // or we simply trust the user wants
1830 // wysiwig behaviour
1832 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
1833 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
1836 public void sequenceFeature_actionPerformed()
1838 SequenceGroup sg = ap.av.getSelectionGroup();
1844 int rsize = 0, gSize = sg.getSize();
1845 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1846 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1848 for (int i = 0; i < gSize; i++)
1850 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1851 int end = sg.findEndRes(sg.getSequenceAt(i));
1854 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1855 features[rsize] = new SequenceFeature(null, null, null, start, end,
1860 rseqs = new SequenceI[rsize];
1861 tfeatures = new SequenceFeature[rsize];
1862 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1863 System.arraycopy(features, 0, tfeatures, 0, rsize);
1864 features = tfeatures;
1866 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1867 features, true, ap))
1869 ap.alignFrame.setShowSeqFeatures(true);
1870 ap.highlightSearchResults(null);
1874 public void textColour_actionPerformed()
1876 SequenceGroup sg = getGroup();
1879 new TextColourChooser().chooseColour(ap, sg);
1883 public void colourByStructure(String pdbid)
1885 Annotation[] anots = ap.av.getStructureSelectionManager()
1886 .colourSequenceFromStructure(sequence, pdbid);
1888 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1889 "Coloured by " + pdbid, anots);
1891 ap.av.getAlignment().addAnnotation(an);
1892 an.createSequenceMapping(sequence, 0, true);
1893 // an.adjustForAlignment();
1894 ap.av.getAlignment().setAnnotationIndex(an, 0);
1896 ap.adjustAnnotationHeight();
1898 sequence.addAlignmentAnnotation(an);
1902 public void editSequence_actionPerformed(ActionEvent actionEvent)
1904 SequenceGroup sg = ap.av.getSelectionGroup();
1908 if (sequence == null)
1910 sequence = sg.getSequenceAt(0);
1913 EditNameDialog dialog = new EditNameDialog(
1914 sequence.getSequenceAsString(sg.getStartRes(),
1915 sg.getEndRes() + 1), null,
1916 MessageManager.getString("label.edit_sequence"), null,
1917 MessageManager.getString("label.edit_sequence"),
1922 EditCommand editCommand = new EditCommand(
1923 MessageManager.getString("label.edit_sequences"),
1924 Action.REPLACE, dialog.getName().replace(' ',
1925 ap.av.getGapCharacter()),
1926 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1927 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
1929 ap.alignFrame.addHistoryItem(editCommand);
1931 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1938 * Action on user selecting an item from the colour menu (that does not have
1939 * its bespoke action handler)
1942 public void changeColour_actionPerformed(String colourSchemeName)
1944 SequenceGroup sg = getGroup();
1945 if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
1948 * open a panel to load or configure a user-defined colour scheme
1950 new UserDefinedColours(ap, sg);
1955 * switch to the chosen colour scheme (or null for None)
1957 sg.cs = ColourSchemes.getInstance().getColourScheme(colourSchemeName,
1958 sg, ap.av.getHiddenRepSequences());
1959 if (sg.cs instanceof Blosum62ColourScheme
1960 || sg.cs instanceof PIDColourScheme)
1962 sg.cs.setConsensus(AAFrequency.calculate(
1963 sg.getSequences(ap.av.getHiddenRepSequences()),
1964 sg.getStartRes(), sg.getEndRes() + 1));