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.AnnotationColourGradient;
47 import jalview.schemes.Blosum62ColourScheme;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.schemes.ColourSchemes;
50 import jalview.schemes.PIDColourScheme;
51 import jalview.schemes.ResidueColourScheme;
52 import jalview.util.GroupUrlLink;
53 import jalview.util.GroupUrlLink.UrlStringTooLongException;
54 import jalview.util.MessageManager;
55 import jalview.util.UrlLink;
57 import java.awt.Color;
58 import java.awt.event.ActionEvent;
59 import java.awt.event.ActionListener;
60 import java.util.Arrays;
61 import java.util.Collection;
62 import java.util.Collections;
63 import java.util.Hashtable;
64 import java.util.LinkedHashMap;
65 import java.util.List;
67 import java.util.SortedMap;
68 import java.util.TreeMap;
69 import java.util.Vector;
71 import javax.swing.JCheckBoxMenuItem;
72 import javax.swing.JColorChooser;
73 import javax.swing.JMenu;
74 import javax.swing.JMenuItem;
75 import javax.swing.JPopupMenu;
81 * @version $Revision: 1.118 $
83 public class PopupMenu extends JPopupMenu implements ColourChangeListener
85 JMenu groupMenu = new JMenu();
87 JMenuItem groupName = new JMenuItem();
89 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
91 protected JMenuItem modifyPID = new JMenuItem();
93 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
95 protected JMenuItem modifyConservation = new JMenuItem();
99 JMenu sequenceMenu = new JMenu();
101 JMenuItem sequenceName = new JMenuItem();
103 JMenuItem sequenceDetails = new JMenuItem();
105 JMenuItem sequenceSelDetails = new JMenuItem();
107 JMenuItem makeReferenceSeq = new JMenuItem();
109 JMenuItem chooseAnnotations = new JMenuItem();
113 JMenuItem createGroupMenuItem = new JMenuItem();
115 JMenuItem unGroupMenuItem = new JMenuItem();
117 JMenuItem outline = new JMenuItem();
119 JMenu colourMenu = new JMenu();
121 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
123 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
125 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
127 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
129 JMenu editMenu = new JMenu();
131 JMenuItem cut = new JMenuItem();
133 JMenuItem copy = new JMenuItem();
135 JMenuItem upperCase = new JMenuItem();
137 JMenuItem lowerCase = new JMenuItem();
139 JMenuItem toggle = new JMenuItem();
141 JMenu pdbMenu = new JMenu();
143 JMenu outputMenu = new JMenu();
145 JMenu seqShowAnnotationsMenu = new JMenu();
147 JMenu seqHideAnnotationsMenu = new JMenu();
149 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
150 MessageManager.getString("label.add_reference_annotations"));
152 JMenu groupShowAnnotationsMenu = new JMenu();
154 JMenu groupHideAnnotationsMenu = new JMenu();
156 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
157 MessageManager.getString("label.add_reference_annotations"));
159 JMenuItem sequenceFeature = new JMenuItem();
161 JMenuItem textColour = new JMenuItem();
163 JMenu jMenu1 = new JMenu();
165 JMenuItem pdbStructureDialog = new JMenuItem();
167 JMenu rnaStructureMenu = new JMenu();
169 JMenuItem editSequence = new JMenuItem();
171 JMenu groupLinksMenu;
173 JMenuItem hideInsertions = new JMenuItem();
176 * Creates a new PopupMenu object.
183 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
185 this(ap, seq, links, null);
195 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
196 List<String> links, List<String> groupLinks)
198 // /////////////////////////////////////////////////////////
199 // If this is activated from the sequence panel, the user may want to
200 // edit or annotate a particular residue. Therefore display the residue menu
202 // If from the IDPanel, we must display the sequence menu
203 // ////////////////////////////////////////////////////////
207 for (String ff : FileFormats.getInstance().getWritableFormats(true))
209 JMenuItem item = new JMenuItem(ff);
211 item.addActionListener(new ActionListener()
214 public void actionPerformed(ActionEvent e)
216 outputText_actionPerformed(e);
220 outputMenu.add(item);
224 * Build menus for annotation types that may be shown or hidden, and for
225 * 'reference annotations' that may be added to the alignment. First for the
226 * currently selected sequence (if there is one):
228 final List<SequenceI> selectedSequence = (seq == null ? Collections
229 .<SequenceI> emptyList() : Arrays.asList(seq));
230 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
231 seqHideAnnotationsMenu, selectedSequence);
232 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
236 * And repeat for the current selection group (if there is one):
238 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
239 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
241 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
242 groupHideAnnotationsMenu, selectedGroup);
243 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
249 } catch (Exception e)
257 sequenceMenu.setText(sequence.getName());
258 if (seq == ap.av.getAlignment().getSeqrep())
260 makeReferenceSeq.setText(MessageManager
261 .getString("action.unmark_as_reference"));
265 makeReferenceSeq.setText(MessageManager
266 .getString("action.set_as_reference"));
269 if (!ap.av.getAlignment().isNucleotide())
271 remove(rnaStructureMenu);
275 int origCount = rnaStructureMenu.getItemCount();
277 * add menu items to 2D-render any alignment or sequence secondary
278 * structure annotation
280 AlignmentAnnotation[] aas = ap.av.getAlignment()
281 .getAlignmentAnnotation();
284 for (final AlignmentAnnotation aa : aas)
286 if (aa.isValidStruc() && aa.sequenceRef == null)
289 * valid alignment RNA secondary structure annotation
291 menuItem = new JMenuItem();
292 menuItem.setText(MessageManager.formatMessage(
293 "label.2d_rna_structure_line",
294 new Object[] { aa.label }));
295 menuItem.addActionListener(new ActionListener()
298 public void actionPerformed(ActionEvent e)
300 new AppVarna(seq, aa, ap);
303 rnaStructureMenu.add(menuItem);
308 if (seq.getAnnotation() != null)
310 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
311 for (final AlignmentAnnotation aa : seqAnns)
313 if (aa.isValidStruc())
316 * valid sequence RNA secondary structure annotation
318 // TODO: make rnastrucF a bit more nice
319 menuItem = new JMenuItem();
320 menuItem.setText(MessageManager.formatMessage(
321 "label.2d_rna_sequence_name",
322 new Object[] { seq.getName() }));
323 menuItem.addActionListener(new ActionListener()
326 public void actionPerformed(ActionEvent e)
328 // TODO: VARNA does'nt print gaps in the sequence
329 new AppVarna(seq, aa, ap);
332 rnaStructureMenu.add(menuItem);
336 if (rnaStructureMenu.getItemCount() == origCount)
338 remove(rnaStructureMenu);
342 menuItem = new JMenuItem(
343 MessageManager.getString("action.hide_sequences"));
344 menuItem.addActionListener(new ActionListener()
347 public void actionPerformed(ActionEvent e)
349 hideSequences(false);
354 if (ap.av.getSelectionGroup() != null
355 && ap.av.getSelectionGroup().getSize() > 1)
357 menuItem = new JMenuItem(MessageManager.formatMessage(
358 "label.represent_group_with",
359 new Object[] { seq.getName() }));
360 menuItem.addActionListener(new ActionListener()
363 public void actionPerformed(ActionEvent e)
368 sequenceMenu.add(menuItem);
371 if (ap.av.hasHiddenRows())
373 final int index = ap.av.getAlignment().findIndex(seq);
375 if (ap.av.adjustForHiddenSeqs(index)
376 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
378 menuItem = new JMenuItem(
379 MessageManager.getString("action.reveal_sequences"));
380 menuItem.addActionListener(new ActionListener()
383 public void actionPerformed(ActionEvent e)
385 ap.av.showSequence(index);
386 if (ap.overviewPanel != null)
388 ap.overviewPanel.updateOverviewImage();
396 // for the case when no sequences are even visible
397 if (ap.av.hasHiddenRows())
400 menuItem = new JMenuItem(
401 MessageManager.getString("action.reveal_all"));
402 menuItem.addActionListener(new ActionListener()
405 public void actionPerformed(ActionEvent e)
407 ap.av.showAllHiddenSeqs();
408 if (ap.overviewPanel != null)
410 ap.overviewPanel.updateOverviewImage();
420 SequenceGroup sg = ap.av.getSelectionGroup();
421 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
422 .getGroups().contains(sg) : false;
424 if (sg != null && sg.getSize() > 0)
426 groupName.setText(MessageManager
427 .getString("label.edit_name_and_description_current_group"));
429 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
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 * annotationMenuItem.setText("By Annotation");
1183 * annotationMenuItem.addActionListener(new ActionListener() { public void
1184 * actionPerformed(ActionEvent actionEvent) {
1185 * annotationMenuItem_actionPerformed(actionEvent); } });
1187 groupMenu.add(sequenceSelDetails);
1190 add(rnaStructureMenu);
1191 add(pdbStructureDialog);
1192 if (sequence != null)
1194 add(hideInsertions);
1196 // annotations configuration panel suppressed for now
1197 // groupMenu.add(chooseAnnotations);
1200 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1201 * (if a selection group is in force).
1203 sequenceMenu.add(seqShowAnnotationsMenu);
1204 sequenceMenu.add(seqHideAnnotationsMenu);
1205 sequenceMenu.add(seqAddReferenceAnnotations);
1206 groupMenu.add(groupShowAnnotationsMenu);
1207 groupMenu.add(groupHideAnnotationsMenu);
1208 groupMenu.add(groupAddReferenceAnnotations);
1209 groupMenu.add(editMenu);
1210 groupMenu.add(outputMenu);
1211 groupMenu.add(sequenceFeature);
1212 groupMenu.add(createGroupMenuItem);
1213 groupMenu.add(unGroupMenuItem);
1214 groupMenu.add(jMenu1);
1215 sequenceMenu.add(sequenceName);
1216 sequenceMenu.add(sequenceDetails);
1217 sequenceMenu.add(makeReferenceSeq);
1224 editMenu.add(editSequence);
1225 editMenu.add(upperCase);
1226 editMenu.add(lowerCase);
1227 editMenu.add(toggle);
1228 // JBPNote: These shouldn't be added here - should appear in a generic
1229 // 'apply web service to this sequence menu'
1230 // pdbMenu.add(RNAFold);
1231 // pdbMenu.add(ContraFold);
1232 jMenu1.add(groupName);
1233 jMenu1.add(colourMenu);
1234 jMenu1.add(showBoxes);
1235 jMenu1.add(showText);
1236 jMenu1.add(showColourText);
1237 jMenu1.add(outline);
1238 jMenu1.add(displayNonconserved);
1242 * Constructs the entries for the colour menu
1244 protected void initColourMenu()
1246 colourMenu.setText(MessageManager.getString("label.group_colour"));
1247 textColour.setText(MessageManager.getString("label.text_colour"));
1248 textColour.addActionListener(new ActionListener()
1251 public void actionPerformed(ActionEvent e)
1253 textColour_actionPerformed();
1257 abovePIDColour.setText(MessageManager
1258 .getString("label.above_identity_threshold"));
1259 abovePIDColour.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1268 modifyPID.setText(MessageManager
1269 .getString("label.modify_identity_threshold"));
1270 modifyPID.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 modifyPID_actionPerformed();
1279 conservationMenuItem.setText(MessageManager
1280 .getString("action.by_conservation"));
1281 conservationMenuItem.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 conservationMenuItem_actionPerformed(conservationMenuItem
1291 modifyConservation.setText(MessageManager
1292 .getString("label.modify_conservation_threshold"));
1293 modifyConservation.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 modifyConservation_actionPerformed();
1304 * Builds the group colour sub-menu, including any user-defined colours which
1305 * were loaded at startup or during the Jalview session
1307 protected void buildColourMenu()
1309 SequenceGroup sg = ap.av.getSelectionGroup();
1313 * popup menu with no sequence group scope
1317 colourMenu.removeAll();
1318 colourMenu.add(textColour);
1319 colourMenu.addSeparator();
1321 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1323 colourMenu.addSeparator();
1324 colourMenu.add(conservationMenuItem);
1325 colourMenu.add(modifyConservation);
1326 colourMenu.add(abovePIDColour);
1327 colourMenu.add(modifyPID);
1330 protected void modifyConservation_actionPerformed()
1332 SequenceGroup sg = getGroup();
1335 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1336 SliderPanel.showConservationSlider();
1340 protected void modifyPID_actionPerformed()
1342 SequenceGroup sg = getGroup();
1345 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1347 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1348 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1350 SliderPanel.showPIDSlider();
1355 * Check for any annotations on the underlying dataset sequences (for the
1356 * current selection group) which are not 'on the alignment'.If any are found,
1357 * enable the option to add them to the alignment. The criteria for 'on the
1358 * alignment' is finding an alignment annotation on the alignment, matched on
1359 * calcId, label and sequenceRef.
1361 * A tooltip is also constructed that displays the source (calcId) and type
1362 * (label) of the annotations that can be added.
1365 * @param forSequences
1367 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1368 List<SequenceI> forSequences)
1370 menuItem.setEnabled(false);
1373 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1374 * Using TreeMap means calcIds are shown in alphabetical order.
1376 SortedMap<String, String> tipEntries = new TreeMap<String, String>();
1377 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1378 AlignmentI al = this.ap.av.getAlignment();
1379 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1380 tipEntries, candidates, al);
1381 if (!candidates.isEmpty())
1383 StringBuilder tooltip = new StringBuilder(64);
1384 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1387 * Found annotations that could be added. Enable the menu item, and
1388 * configure its tooltip and action.
1390 menuItem.setEnabled(true);
1391 for (String calcId : tipEntries.keySet())
1393 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1395 String tooltipText = JvSwingUtils.wrapTooltip(true,
1396 tooltip.toString());
1397 menuItem.setToolTipText(tooltipText);
1399 menuItem.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 addReferenceAnnotations_actionPerformed(candidates);
1411 * Add annotations to the sequences and to the alignment.
1414 * a map whose keys are sequences on the alignment, and values a list
1415 * of annotations to add to each sequence
1417 protected void addReferenceAnnotations_actionPerformed(
1418 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1420 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1421 final AlignmentI alignment = this.ap.getAlignment();
1422 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1427 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1429 if (!ap.av.getAlignment().hasSeqrep())
1431 // initialise the display flags so the user sees something happen
1432 ap.av.setDisplayReferenceSeq(true);
1433 ap.av.setColourByReferenceSeq(true);
1434 ap.av.getAlignment().setSeqrep(sequence);
1438 if (ap.av.getAlignment().getSeqrep() == sequence)
1440 ap.av.getAlignment().setSeqrep(null);
1444 ap.av.getAlignment().setSeqrep(sequence);
1450 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1452 if (sequence != null)
1454 ColumnSelection cs = ap.av.getColumnSelection();
1457 cs = new ColumnSelection();
1459 cs.hideInsertionsFor(sequence);
1460 ap.av.setColumnSelection(cs);
1465 protected void sequenceSelectionDetails_actionPerformed()
1467 createSequenceDetailsReport(ap.av.getSequenceSelection());
1470 protected void sequenceDetails_actionPerformed()
1472 createSequenceDetailsReport(new SequenceI[] { sequence });
1475 public void createSequenceDetailsReport(SequenceI[] sequences)
1477 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1478 StringBuilder contents = new StringBuilder(128);
1479 for (SequenceI seq : sequences)
1481 contents.append("<p><h2>"
1484 "label.create_sequence_details_report_annotation_for",
1485 new Object[] { seq.getDisplayId(true) })
1487 new SequenceAnnotationReport(null)
1488 .createSequenceAnnotationReport(
1493 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1494 .getSeqPanel().seqCanvas.fr.getMinMax()
1496 contents.append("</p>");
1498 cap.setText("<html>" + contents.toString() + "</html>");
1500 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1501 "label.sequence_details_for",
1502 (sequences.length == 1 ? new Object[] { sequences[0]
1503 .getDisplayId(true) } : new Object[] { MessageManager
1504 .getString("label.selection") })), 500, 400);
1508 protected void showNonconserved_actionPerformed()
1510 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1515 * call to refresh view after settings change
1519 ap.updateAnnotation();
1520 ap.paintAlignment(true);
1522 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1526 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1527 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1537 public void abovePIDColour_actionPerformed(boolean selected)
1539 SequenceGroup sg = getGroup();
1547 sg.cs.setConsensus(AAFrequency.calculate(
1548 sg.getSequences(ap.av.getHiddenRepSequences()),
1549 sg.getStartRes(), sg.getEndRes() + 1));
1551 int threshold = SliderPanel.setPIDSliderSource(ap,
1552 sg.getGroupColourScheme(), getGroup()
1555 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1557 SliderPanel.showPIDSlider();
1560 // remove PIDColouring
1562 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1563 SliderPanel.hidePIDSlider();
1565 modifyPID.setEnabled(selected);
1571 * Open a panel where the user can choose which types of sequence annotation
1576 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1578 // todo correct way to guard against opening a duplicate panel?
1579 new AnnotationChooser(ap);
1588 public void conservationMenuItem_actionPerformed(boolean selected)
1590 SequenceGroup sg = getGroup();
1598 // JBPNote: Conservation name shouldn't be i18n translated
1599 Conservation c = new Conservation("Group", sg.getSequences(ap.av
1600 .getHiddenRepSequences()), sg.getStartRes(),
1601 sg.getEndRes() + 1);
1604 c.verdict(false, ap.av.getConsPercGaps());
1605 sg.cs.setConservation(c);
1607 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1609 SliderPanel.showConservationSlider();
1612 // remove ConservationColouring
1614 sg.cs.setConservation(null);
1615 SliderPanel.hideConservationSlider();
1617 modifyConservation.setEnabled(selected);
1622 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1624 SequenceGroup sg = getGroup();
1630 AnnotationColourGradient acg = new AnnotationColourGradient(
1631 sequence.getAnnotation()[0], null,
1632 AnnotationColourGradient.NO_THRESHOLD);
1634 acg.setPredefinedColours(true);
1635 sg.setColourScheme(acg);
1646 protected void groupName_actionPerformed()
1649 SequenceGroup sg = getGroup();
1650 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1651 sg.getDescription(), " "
1652 + MessageManager.getString("label.group_name") + " ",
1653 MessageManager.getString("label.group_description") + " ",
1654 MessageManager.getString("label.edit_group_name_description"),
1662 sg.setName(dialog.getName());
1663 sg.setDescription(dialog.getDescription());
1668 * Get selection group - adding it to the alignment if necessary.
1670 * @return sequence group to operate on
1672 SequenceGroup getGroup()
1674 SequenceGroup sg = ap.av.getSelectionGroup();
1675 // this method won't add a new group if it already exists
1678 ap.av.getAlignment().addGroup(sg);
1690 void sequenceName_actionPerformed()
1692 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1693 sequence.getDescription(),
1694 " " + MessageManager.getString("label.sequence_name")
1696 MessageManager.getString("label.sequence_description") + " ",
1698 .getString("label.edit_sequence_name_description"),
1706 if (dialog.getName() != null)
1708 if (dialog.getName().indexOf(" ") > -1)
1714 .getString("label.spaces_converted_to_backslashes"),
1716 .getString("label.no_spaces_allowed_sequence_name"),
1717 JvOptionPane.WARNING_MESSAGE);
1720 sequence.setName(dialog.getName().replace(' ', '_'));
1721 ap.paintAlignment(false);
1724 sequence.setDescription(dialog.getDescription());
1726 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1737 void unGroupMenuItem_actionPerformed()
1739 SequenceGroup sg = ap.av.getSelectionGroup();
1740 ap.av.getAlignment().deleteGroup(sg);
1741 ap.av.setSelectionGroup(null);
1745 void createGroupMenuItem_actionPerformed()
1747 getGroup(); // implicitly creates group - note - should apply defaults / use
1748 // standard alignment window logic for this
1758 protected void outline_actionPerformed()
1760 SequenceGroup sg = getGroup();
1761 Color col = JColorChooser.showDialog(this,
1762 MessageManager.getString("label.select_outline_colour"),
1767 sg.setOutlineColour(col);
1779 public void showBoxes_actionPerformed()
1781 getGroup().setDisplayBoxes(showBoxes.isSelected());
1791 public void showText_actionPerformed()
1793 getGroup().setDisplayText(showText.isSelected());
1803 public void showColourText_actionPerformed()
1805 getGroup().setColourText(showColourText.isSelected());
1809 public void showLink(String url)
1813 jalview.util.BrowserLauncher.openURL(url);
1814 } catch (Exception ex)
1816 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1817 MessageManager.getString("label.web_browser_not_found_unix"),
1818 MessageManager.getString("label.web_browser_not_found"),
1819 JvOptionPane.WARNING_MESSAGE);
1821 ex.printStackTrace();
1825 void hideSequences(boolean representGroup)
1827 ap.av.hideSequences(sequence, representGroup);
1830 public void copy_actionPerformed()
1832 ap.alignFrame.copy_actionPerformed(null);
1835 public void cut_actionPerformed()
1837 ap.alignFrame.cut_actionPerformed(null);
1840 void changeCase(ActionEvent e)
1842 Object source = e.getSource();
1843 SequenceGroup sg = ap.av.getSelectionGroup();
1847 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1848 sg.getStartRes(), sg.getEndRes() + 1);
1853 if (source == toggle)
1855 description = MessageManager.getString("label.toggle_case");
1856 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1858 else if (source == upperCase)
1860 description = MessageManager.getString("label.to_upper_case");
1861 caseChange = ChangeCaseCommand.TO_UPPER;
1865 description = MessageManager.getString("label.to_lower_case");
1866 caseChange = ChangeCaseCommand.TO_LOWER;
1869 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1870 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1871 startEnd, caseChange);
1873 ap.alignFrame.addHistoryItem(caseCommand);
1875 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1881 public void outputText_actionPerformed(ActionEvent e)
1883 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1884 cap.setForInput(null);
1885 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1886 "label.alignment_output_command",
1887 new Object[] { e.getActionCommand() }), 600, 500);
1889 String[] omitHidden = null;
1891 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1892 // or we simply trust the user wants
1893 // wysiwig behaviour
1895 FileFormatI fileFormat = FileFormats.getInstance().forName(e.getActionCommand());
1896 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
1899 public void sequenceFeature_actionPerformed()
1901 SequenceGroup sg = ap.av.getSelectionGroup();
1907 int rsize = 0, gSize = sg.getSize();
1908 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1909 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1911 for (int i = 0; i < gSize; i++)
1913 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1914 int end = sg.findEndRes(sg.getSequenceAt(i));
1917 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1918 features[rsize] = new SequenceFeature(null, null, null, start, end,
1923 rseqs = new SequenceI[rsize];
1924 tfeatures = new SequenceFeature[rsize];
1925 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1926 System.arraycopy(features, 0, tfeatures, 0, rsize);
1927 features = tfeatures;
1929 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1930 features, true, ap))
1932 ap.alignFrame.setShowSeqFeatures(true);
1933 ap.highlightSearchResults(null);
1937 public void textColour_actionPerformed()
1939 SequenceGroup sg = getGroup();
1942 new TextColourChooser().chooseColour(ap, sg);
1946 public void colourByStructure(String pdbid)
1948 Annotation[] anots = ap.av.getStructureSelectionManager()
1949 .colourSequenceFromStructure(sequence, pdbid);
1951 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1952 "Coloured by " + pdbid, anots);
1954 ap.av.getAlignment().addAnnotation(an);
1955 an.createSequenceMapping(sequence, 0, true);
1956 // an.adjustForAlignment();
1957 ap.av.getAlignment().setAnnotationIndex(an, 0);
1959 ap.adjustAnnotationHeight();
1961 sequence.addAlignmentAnnotation(an);
1965 public void editSequence_actionPerformed(ActionEvent actionEvent)
1967 SequenceGroup sg = ap.av.getSelectionGroup();
1971 if (sequence == null)
1973 sequence = sg.getSequenceAt(0);
1976 EditNameDialog dialog = new EditNameDialog(
1977 sequence.getSequenceAsString(sg.getStartRes(),
1978 sg.getEndRes() + 1), null,
1979 MessageManager.getString("label.edit_sequence"), null,
1980 MessageManager.getString("label.edit_sequence"),
1985 EditCommand editCommand = new EditCommand(
1986 MessageManager.getString("label.edit_sequences"),
1987 Action.REPLACE, dialog.getName().replace(' ',
1988 ap.av.getGapCharacter()),
1989 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1990 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
1992 ap.alignFrame.addHistoryItem(editCommand);
1994 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2001 * Action on user selecting an item from the colour menu (that does not have
2002 * its bespoke action handler)
2007 public void changeColour_actionPerformed(String colourSchemeName)
2009 SequenceGroup sg = getGroup();
2010 if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName))
2013 * open a panel to load or configure a user-defined colour scheme
2015 new UserDefinedColours(ap, sg);
2020 * switch to the chosen colour scheme (or null for None)
2022 ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme(
2023 colourSchemeName, sg, ap.av.getHiddenRepSequences());
2024 sg.setColourScheme(colourScheme);
2025 if (colourScheme instanceof Blosum62ColourScheme
2026 || colourScheme instanceof PIDColourScheme)
2028 sg.cs.setConsensus(AAFrequency.calculate(
2029 sg.getSequences(ap.av.getHiddenRepSequences()),
2030 sg.getStartRes(), sg.getEndRes() + 1));