2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.gui.ColourMenuHelper.ColourChangeListener;
41 import jalview.io.FileFormatI;
42 import jalview.io.FileFormats;
43 import jalview.io.FormatAdapter;
44 import jalview.io.SequenceAnnotationReport;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemes;
48 import jalview.schemes.PIDColourScheme;
49 import jalview.util.GroupUrlLink;
50 import jalview.util.GroupUrlLink.UrlStringTooLongException;
51 import jalview.util.MessageManager;
52 import jalview.util.UrlLink;
54 import java.awt.Color;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.util.ArrayList;
58 import java.util.Arrays;
59 import java.util.BitSet;
60 import java.util.Collection;
61 import java.util.Collections;
62 import java.util.Hashtable;
63 import java.util.LinkedHashMap;
64 import java.util.List;
66 import java.util.SortedMap;
67 import java.util.TreeMap;
68 import java.util.Vector;
70 import javax.swing.JCheckBoxMenuItem;
71 import javax.swing.JColorChooser;
72 import javax.swing.JMenu;
73 import javax.swing.JMenuItem;
74 import javax.swing.JPopupMenu;
80 * @version $Revision: 1.118 $
82 public class PopupMenu extends JPopupMenu implements ColourChangeListener
84 JMenu groupMenu = new JMenu();
86 JMenuItem groupName = new JMenuItem();
88 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
90 protected JMenuItem modifyPID = new JMenuItem();
92 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
94 protected JMenuItem modifyConservation = new JMenuItem();
98 JMenu sequenceMenu = new JMenu();
100 JMenuItem sequenceName = new JMenuItem();
102 JMenuItem sequenceDetails = new JMenuItem();
104 JMenuItem sequenceSelDetails = new JMenuItem();
106 JMenuItem makeReferenceSeq = new JMenuItem();
108 JMenuItem chooseAnnotations = new JMenuItem();
112 JMenuItem createGroupMenuItem = new JMenuItem();
114 JMenuItem unGroupMenuItem = new JMenuItem();
116 JMenuItem outline = new JMenuItem();
118 JMenu colourMenu = new JMenu();
120 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
122 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
124 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
126 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
128 JMenu editMenu = new JMenu();
130 JMenuItem cut = new JMenuItem();
132 JMenuItem copy = new JMenuItem();
134 JMenuItem upperCase = new JMenuItem();
136 JMenuItem lowerCase = new JMenuItem();
138 JMenuItem toggle = new JMenuItem();
140 JMenu pdbMenu = new JMenu();
142 JMenu outputMenu = new JMenu();
144 JMenu seqShowAnnotationsMenu = new JMenu();
146 JMenu seqHideAnnotationsMenu = new JMenu();
148 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
149 MessageManager.getString("label.add_reference_annotations"));
151 JMenu groupShowAnnotationsMenu = new JMenu();
153 JMenu groupHideAnnotationsMenu = new JMenu();
155 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
156 MessageManager.getString("label.add_reference_annotations"));
158 JMenuItem sequenceFeature = new JMenuItem();
160 JMenuItem textColour = new JMenuItem();
162 JMenu jMenu1 = new JMenu();
164 JMenuItem pdbStructureDialog = new JMenuItem();
166 JMenu rnaStructureMenu = new JMenu();
168 JMenuItem editSequence = new JMenuItem();
170 JMenu groupLinksMenu;
172 JMenuItem hideInsertions = new JMenuItem();
175 * Creates a new PopupMenu object.
180 * non-positional features (for seq not null), or positional features
181 * at residue (for seq equal to null)
183 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
184 List<SequenceFeature> features)
186 this(ap, seq, features, null);
194 * the sequence under the cursor if in the Id panel, null if in the
197 * non-positional features if in the Id panel, features at the
198 * clicked residue if in the sequence panel
201 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
202 List<SequenceFeature> features, List<String> groupLinks)
204 // /////////////////////////////////////////////////////////
205 // If this is activated from the sequence panel, the user may want to
206 // edit or annotate a particular residue. Therefore display the residue menu
208 // If from the IDPanel, we must display the sequence menu
209 // ////////////////////////////////////////////////////////
210 this.ap = alignPanel;
213 for (String ff : FileFormats.getInstance().getWritableFormats(true))
215 JMenuItem item = new JMenuItem(ff);
217 item.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent e)
222 outputText_actionPerformed(e);
226 outputMenu.add(item);
230 * Build menus for annotation types that may be shown or hidden, and for
231 * 'reference annotations' that may be added to the alignment. First for the
232 * currently selected sequence (if there is one):
234 final List<SequenceI> selectedSequence = (seq == null
235 ? Collections.<SequenceI> emptyList()
236 : Arrays.asList(seq));
237 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
238 seqHideAnnotationsMenu, selectedSequence);
239 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
243 * And repeat for the current selection group (if there is one):
245 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
246 ? Collections.<SequenceI> emptyList()
247 : alignPanel.av.getSelectionGroup().getSequences());
248 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
249 groupHideAnnotationsMenu, selectedGroup);
250 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
256 } catch (Exception e)
264 sequenceMenu.setText(sequence.getName());
265 if (seq == alignPanel.av.getAlignment().getSeqrep())
267 makeReferenceSeq.setText(
268 MessageManager.getString("action.unmark_as_reference"));
272 makeReferenceSeq.setText(
273 MessageManager.getString("action.set_as_reference"));
276 if (!alignPanel.av.getAlignment().isNucleotide())
278 remove(rnaStructureMenu);
282 int origCount = rnaStructureMenu.getItemCount();
284 * add menu items to 2D-render any alignment or sequence secondary
285 * structure annotation
287 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
288 .getAlignmentAnnotation();
291 for (final AlignmentAnnotation aa : aas)
293 if (aa.isValidStruc() && aa.sequenceRef == null)
296 * valid alignment RNA secondary structure annotation
298 menuItem = new JMenuItem();
299 menuItem.setText(MessageManager.formatMessage(
300 "label.2d_rna_structure_line", new Object[]
302 menuItem.addActionListener(new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 new AppVarna(seq, aa, alignPanel);
310 rnaStructureMenu.add(menuItem);
315 if (seq.getAnnotation() != null)
317 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
318 for (final AlignmentAnnotation aa : seqAnns)
320 if (aa.isValidStruc())
323 * valid sequence RNA secondary structure annotation
325 // TODO: make rnastrucF a bit more nice
326 menuItem = new JMenuItem();
327 menuItem.setText(MessageManager.formatMessage(
328 "label.2d_rna_sequence_name", new Object[]
330 menuItem.addActionListener(new ActionListener()
333 public void actionPerformed(ActionEvent e)
335 // TODO: VARNA does'nt print gaps in the sequence
336 new AppVarna(seq, aa, alignPanel);
339 rnaStructureMenu.add(menuItem);
343 if (rnaStructureMenu.getItemCount() == origCount)
345 remove(rnaStructureMenu);
349 menuItem = new JMenuItem(
350 MessageManager.getString("action.hide_sequences"));
351 menuItem.addActionListener(new ActionListener()
354 public void actionPerformed(ActionEvent e)
356 hideSequences(false);
361 if (alignPanel.av.getSelectionGroup() != null
362 && alignPanel.av.getSelectionGroup().getSize() > 1)
364 menuItem = new JMenuItem(MessageManager
365 .formatMessage("label.represent_group_with", new Object[]
367 menuItem.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
375 sequenceMenu.add(menuItem);
378 if (alignPanel.av.hasHiddenRows())
380 final int index = alignPanel.av.getAlignment().findIndex(seq);
382 if (alignPanel.av.adjustForHiddenSeqs(index)
383 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
385 menuItem = new JMenuItem(
386 MessageManager.getString("action.reveal_sequences"));
387 menuItem.addActionListener(new ActionListener()
390 public void actionPerformed(ActionEvent e)
392 alignPanel.av.showSequence(index);
393 if (alignPanel.overviewPanel != null)
395 alignPanel.overviewPanel.updateOverviewImage();
403 // for the case when no sequences are even visible
404 if (alignPanel.av.hasHiddenRows())
407 menuItem = new JMenuItem(
408 MessageManager.getString("action.reveal_all"));
409 menuItem.addActionListener(new ActionListener()
412 public void actionPerformed(ActionEvent e)
414 alignPanel.av.showAllHiddenSeqs();
415 if (alignPanel.overviewPanel != null)
417 alignPanel.overviewPanel.updateOverviewImage();
426 SequenceGroup sg = alignPanel.av.getSelectionGroup();
427 boolean isDefinedGroup = (sg != null)
428 ? alignPanel.av.getAlignment().getGroups().contains(sg)
431 if (sg != null && sg.getSize() > 0)
433 groupName.setText(MessageManager
434 .getString("label.edit_name_and_description_current_group"));
436 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
438 conservationMenuItem.setEnabled(!sg.isNucleotide());
442 if (sg.cs.conservationApplied())
444 conservationMenuItem.setSelected(true);
446 if (sg.cs.getThreshold() > 0)
448 abovePIDColour.setSelected(true);
451 modifyConservation.setEnabled(conservationMenuItem.isSelected());
452 modifyPID.setEnabled(abovePIDColour.isSelected());
453 displayNonconserved.setSelected(sg.getShowNonconserved());
454 showText.setSelected(sg.getDisplayText());
455 showColourText.setSelected(sg.getColourText());
456 showBoxes.setSelected(sg.getDisplayBoxes());
457 // add any groupURLs to the groupURL submenu and make it visible
458 if (groupLinks != null && groupLinks.size() > 0)
460 buildGroupURLMenu(sg, groupLinks);
462 // Add a 'show all structures' for the current selection
463 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
465 SequenceI sqass = null;
466 for (SequenceI sq : alignPanel.av.getSequenceSelection())
468 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
469 if (pes != null && pes.size() > 0)
471 reppdb.put(pes.get(0).getId(), pes.get(0));
472 for (PDBEntry pe : pes)
474 pdbe.put(pe.getId(), pe);
484 final PDBEntry[] pe = pdbe.values()
485 .toArray(new PDBEntry[pdbe.size()]),
486 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
487 final JMenuItem gpdbview, rpdbview;
492 groupMenu.setVisible(false);
493 editMenu.setVisible(false);
498 createGroupMenuItem.setVisible(true);
499 unGroupMenuItem.setVisible(false);
500 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
504 createGroupMenuItem.setVisible(false);
505 unGroupMenuItem.setVisible(true);
506 jMenu1.setText(MessageManager.getString("action.edit_group"));
511 sequenceMenu.setVisible(false);
512 pdbStructureDialog.setVisible(false);
513 rnaStructureMenu.setVisible(false);
516 addLinks(seq, features);
520 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
521 * When seq is not null, these are links for the sequence id, which may be to
522 * external web sites for the sequence accession, and/or links embedded in
523 * non-positional features. When seq is null, only links embedded in the
524 * provided features are added.
529 void addLinks(final SequenceI seq, List<SequenceFeature> features)
531 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
533 List<String> nlinks = null;
536 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
540 nlinks = new ArrayList<>();
543 if (features != null)
545 for (SequenceFeature sf : features)
547 if (sf.links != null)
549 for (String link : sf.links)
557 Map<String, List<String>> linkset = new LinkedHashMap<>();
559 for (String link : nlinks)
561 UrlLink urlLink = null;
564 urlLink = new UrlLink(link);
565 } catch (Exception foo)
567 Cache.log.error("Exception for URLLink '" + link + "'", foo);
571 if (!urlLink.isValid())
573 Cache.log.error(urlLink.getInvalidMessage());
577 urlLink.createLinksFromSeq(seq, linkset);
580 addshowLinks(linkMenu, linkset.values());
582 // only add link menu if it has entries
583 if (linkMenu.getItemCount() > 0)
585 if (sequence != null)
587 sequenceMenu.add(linkMenu);
597 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
598 * "All" is added first, followed by a separator. Then add any annotation
599 * types associated with the current selection. Separate menus are built for
600 * the selected sequence group (if any), and the selected sequence.
602 * Some annotation rows are always rendered together - these can be identified
603 * by a common graphGroup property > -1. Only one of each group will be marked
604 * as visible (to avoid duplication of the display). For such groups we add a
605 * composite type name, e.g.
607 * IUPredWS (Long), IUPredWS (Short)
611 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
612 List<SequenceI> forSequences)
614 showMenu.removeAll();
615 hideMenu.removeAll();
617 final List<String> all = Arrays
619 { MessageManager.getString("label.all") });
620 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
622 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
624 showMenu.addSeparator();
625 hideMenu.addSeparator();
627 final AlignmentAnnotation[] annotations = ap.getAlignment()
628 .getAlignmentAnnotation();
631 * Find shown/hidden annotations types, distinguished by source (calcId),
632 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
633 * the insertion order, which is the order of the annotations on the
636 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
637 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
638 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
639 AlignmentAnnotationUtils.asList(annotations), forSequences);
641 for (String calcId : hiddenTypes.keySet())
643 for (List<String> type : hiddenTypes.get(calcId))
645 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
649 // grey out 'show annotations' if none are hidden
650 showMenu.setEnabled(!hiddenTypes.isEmpty());
652 for (String calcId : shownTypes.keySet())
654 for (List<String> type : shownTypes.get(calcId))
656 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
660 // grey out 'hide annotations' if none are shown
661 hideMenu.setEnabled(!shownTypes.isEmpty());
665 * Returns a list of sequences - either the current selection group (if there
666 * is one), else the specified single sequence.
671 protected List<SequenceI> getSequenceScope(SequenceI seq)
673 List<SequenceI> forSequences = null;
674 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
675 if (selectionGroup != null && selectionGroup.getSize() > 0)
677 forSequences = selectionGroup.getSequences();
681 forSequences = seq == null ? Collections.<SequenceI> emptyList()
682 : Arrays.asList(seq);
688 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
691 * @param showOrHideMenu
693 * @param forSequences
694 * the sequences whose annotations may be shown or hidden
699 * if true this is a special label meaning 'All'
700 * @param actionIsShow
701 * if true, the select menu item action is to show the annotation
704 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
705 final List<SequenceI> forSequences, String calcId,
706 final List<String> types, final boolean allTypes,
707 final boolean actionIsShow)
709 String label = types.toString(); // [a, b, c]
710 label = label.substring(1, label.length() - 1); // a, b, c
711 final JMenuItem item = new JMenuItem(label);
712 item.setToolTipText(calcId);
713 item.addActionListener(new ActionListener()
716 public void actionPerformed(ActionEvent e)
718 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
719 types, forSequences, allTypes, actionIsShow);
723 showOrHideMenu.add(item);
726 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
729 // TODO: usability: thread off the generation of group url content so root
731 // sequence only URLs
732 // ID/regex match URLs
733 groupLinksMenu = new JMenu(
734 MessageManager.getString("action.group_link"));
735 // three types of url that might be created.
736 JMenu[] linkMenus = new JMenu[] { null,
737 new JMenu(MessageManager.getString("action.ids")),
738 new JMenu(MessageManager.getString("action.sequences")),
739 new JMenu(MessageManager.getString("action.ids_sequences")) };
741 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
742 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
743 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
744 for (int sq = 0; sq < seqs.length; sq++)
747 int start = seqs[sq].findPosition(sg.getStartRes()),
748 end = seqs[sq].findPosition(sg.getEndRes());
749 // just collect ids from dataset sequence
750 // TODO: check if IDs collected from selecton group intersects with the
751 // current selection, too
752 SequenceI sqi = seqs[sq];
753 while (sqi.getDatasetSequence() != null)
755 sqi = sqi.getDatasetSequence();
757 DBRefEntry[] dbr = sqi.getDBRefs();
758 if (dbr != null && dbr.length > 0)
760 for (int d = 0; d < dbr.length; d++)
762 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
763 Object[] sarray = commonDbrefs.get(src);
766 sarray = new Object[2];
767 sarray[0] = new int[] { 0 };
768 sarray[1] = new String[seqs.length];
770 commonDbrefs.put(src, sarray);
773 if (((String[]) sarray[1])[sq] == null)
775 if (!dbr[d].hasMap() || (dbr[d].getMap()
776 .locateMappedRange(start, end) != null))
778 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
779 ((int[]) sarray[0])[0]++;
785 // now create group links for all distinct ID/sequence sets.
786 boolean addMenu = false; // indicates if there are any group links to give
788 for (String link : groupLinks)
790 GroupUrlLink urlLink = null;
793 urlLink = new GroupUrlLink(link);
794 } catch (Exception foo)
796 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
800 if (!urlLink.isValid())
802 Cache.log.error(urlLink.getInvalidMessage());
805 final String label = urlLink.getLabel();
806 boolean usingNames = false;
807 // Now see which parts of the group apply for this URL
808 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
809 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
810 String[] seqstr, ids; // input to makeUrl
813 int numinput = ((int[]) idset[0])[0];
814 String[] allids = ((String[]) idset[1]);
815 seqstr = new String[numinput];
816 ids = new String[numinput];
817 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
819 if (allids[sq] != null)
821 ids[idcount] = allids[sq];
822 seqstr[idcount++] = idandseqs[1][sq];
828 // just use the id/seq set
829 seqstr = idandseqs[1];
833 // and try and make the groupURL!
835 Object[] urlset = null;
838 urlset = urlLink.makeUrlStubs(ids, seqstr,
839 "FromJalview" + System.currentTimeMillis(), false);
840 } catch (UrlStringTooLongException e)
845 int type = urlLink.getGroupURLType() & 3;
846 // first two bits ofurlLink type bitfield are sequenceids and sequences
847 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
848 addshowLink(linkMenus[type],
849 label + (((type & 1) == 1)
850 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
858 groupLinksMenu = new JMenu(
859 MessageManager.getString("action.group_link"));
860 for (int m = 0; m < linkMenus.length; m++)
862 if (linkMenus[m] != null
863 && linkMenus[m].getMenuComponentCount() > 0)
865 groupLinksMenu.add(linkMenus[m]);
869 groupMenu.add(groupLinksMenu);
873 private void addshowLinks(JMenu linkMenu,
874 Collection<List<String>> linkset)
876 for (List<String> linkstrset : linkset)
878 // split linkstr into label and url
879 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
884 * add a show URL menu item to the given linkMenu
888 * - menu label string
892 private void addshowLink(JMenu linkMenu, String label, final String url)
894 JMenuItem item = new JMenuItem(label);
895 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
898 item.addActionListener(new ActionListener()
901 public void actionPerformed(ActionEvent e)
903 new Thread(new Runnable()
920 * add a late bound groupURL item to the given linkMenu
924 * - menu label string
925 * @param urlgenerator
926 * GroupURLLink used to generate URL
928 * Object array returned from the makeUrlStubs function.
930 private void addshowLink(JMenu linkMenu, String label,
931 final GroupUrlLink urlgenerator, final Object[] urlstub)
933 JMenuItem item = new JMenuItem(label);
934 item.setToolTipText(MessageManager
935 .formatMessage("label.open_url_seqs_param", new Object[]
936 { urlgenerator.getUrl_prefix(),
937 urlgenerator.getNumberInvolved(urlstub) }));
938 // TODO: put in info about what is being sent.
939 item.addActionListener(new ActionListener()
942 public void actionPerformed(ActionEvent e)
944 new Thread(new Runnable()
952 showLink(urlgenerator.constructFrom(urlstub));
953 } catch (UrlStringTooLongException e2)
971 private void jbInit() throws Exception
973 groupMenu.setText(MessageManager.getString("label.selection"));
974 groupName.setText(MessageManager.getString("label.name"));
975 groupName.addActionListener(new ActionListener()
978 public void actionPerformed(ActionEvent e)
980 groupName_actionPerformed();
983 sequenceMenu.setText(MessageManager.getString("label.sequence"));
984 sequenceName.setText(
985 MessageManager.getString("label.edit_name_description"));
986 sequenceName.addActionListener(new ActionListener()
989 public void actionPerformed(ActionEvent e)
991 sequenceName_actionPerformed();
995 .setText(MessageManager.getString("action.choose_annotations"));
996 chooseAnnotations.addActionListener(new ActionListener()
999 public void actionPerformed(ActionEvent e)
1001 chooseAnnotations_actionPerformed(e);
1005 .setText(MessageManager.getString("label.sequence_details"));
1006 sequenceDetails.addActionListener(new ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 sequenceDetails_actionPerformed();
1015 .setText(MessageManager.getString("label.sequence_details"));
1016 sequenceSelDetails.addActionListener(new ActionListener()
1019 public void actionPerformed(ActionEvent e)
1021 sequenceSelectionDetails_actionPerformed();
1026 .setText(MessageManager.getString("action.remove_group"));
1027 unGroupMenuItem.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 unGroupMenuItem_actionPerformed();
1036 .setText(MessageManager.getString("action.create_group"));
1037 createGroupMenuItem.addActionListener(new ActionListener()
1040 public void actionPerformed(ActionEvent e)
1042 createGroupMenuItem_actionPerformed();
1046 outline.setText(MessageManager.getString("action.border_colour"));
1047 outline.addActionListener(new ActionListener()
1050 public void actionPerformed(ActionEvent e)
1052 outline_actionPerformed();
1055 showBoxes.setText(MessageManager.getString("action.boxes"));
1056 showBoxes.setState(true);
1057 showBoxes.addActionListener(new ActionListener()
1060 public void actionPerformed(ActionEvent e)
1062 showBoxes_actionPerformed();
1065 showText.setText(MessageManager.getString("action.text"));
1066 showText.setState(true);
1067 showText.addActionListener(new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 showText_actionPerformed();
1075 showColourText.setText(MessageManager.getString("label.colour_text"));
1076 showColourText.addActionListener(new ActionListener()
1079 public void actionPerformed(ActionEvent e)
1081 showColourText_actionPerformed();
1085 .setText(MessageManager.getString("label.show_non_conserved"));
1086 displayNonconserved.setState(true);
1087 displayNonconserved.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 showNonconserved_actionPerformed();
1095 editMenu.setText(MessageManager.getString("action.edit"));
1096 cut.setText(MessageManager.getString("action.cut"));
1097 cut.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 cut_actionPerformed();
1105 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1106 upperCase.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent e)
1114 copy.setText(MessageManager.getString("action.copy"));
1115 copy.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 copy_actionPerformed();
1123 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1124 lowerCase.addActionListener(new ActionListener()
1127 public void actionPerformed(ActionEvent e)
1132 toggle.setText(MessageManager.getString("label.toggle_case"));
1133 toggle.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1142 MessageManager.getString("label.out_to_textbox") + "...");
1143 seqShowAnnotationsMenu
1144 .setText(MessageManager.getString("label.show_annotations"));
1145 seqHideAnnotationsMenu
1146 .setText(MessageManager.getString("label.hide_annotations"));
1147 groupShowAnnotationsMenu
1148 .setText(MessageManager.getString("label.show_annotations"));
1149 groupHideAnnotationsMenu
1150 .setText(MessageManager.getString("label.hide_annotations"));
1151 sequenceFeature.setText(
1152 MessageManager.getString("label.create_sequence_feature"));
1153 sequenceFeature.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 sequenceFeature_actionPerformed();
1161 jMenu1.setText(MessageManager.getString("label.group"));
1162 pdbStructureDialog.setText(
1163 MessageManager.getString("label.show_pdbstruct_dialog"));
1164 pdbStructureDialog.addActionListener(new ActionListener()
1167 public void actionPerformed(ActionEvent actionEvent)
1169 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1170 if (ap.av.getSelectionGroup() != null)
1172 selectedSeqs = ap.av.getSequenceSelection();
1174 new StructureChooser(selectedSeqs, sequence, ap);
1179 .setText(MessageManager.getString("label.view_rna_structure"));
1181 // colStructureMenu.setText("Colour By Structure");
1182 editSequence.setText(
1183 MessageManager.getString("label.edit_sequence") + "...");
1184 editSequence.addActionListener(new ActionListener()
1187 public void actionPerformed(ActionEvent actionEvent)
1189 editSequence_actionPerformed(actionEvent);
1192 makeReferenceSeq.setText(
1193 MessageManager.getString("label.mark_as_representative"));
1194 makeReferenceSeq.addActionListener(new ActionListener()
1198 public void actionPerformed(ActionEvent actionEvent)
1200 makeReferenceSeq_actionPerformed(actionEvent);
1205 .setText(MessageManager.getString("label.hide_insertions"));
1206 hideInsertions.addActionListener(new ActionListener()
1210 public void actionPerformed(ActionEvent e)
1212 hideInsertions_actionPerformed(e);
1216 groupMenu.add(sequenceSelDetails);
1219 add(rnaStructureMenu);
1220 add(pdbStructureDialog);
1221 if (sequence != null)
1223 add(hideInsertions);
1225 // annotations configuration panel suppressed for now
1226 // groupMenu.add(chooseAnnotations);
1229 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1230 * (if a selection group is in force).
1232 sequenceMenu.add(seqShowAnnotationsMenu);
1233 sequenceMenu.add(seqHideAnnotationsMenu);
1234 sequenceMenu.add(seqAddReferenceAnnotations);
1235 groupMenu.add(groupShowAnnotationsMenu);
1236 groupMenu.add(groupHideAnnotationsMenu);
1237 groupMenu.add(groupAddReferenceAnnotations);
1238 groupMenu.add(editMenu);
1239 groupMenu.add(outputMenu);
1240 groupMenu.add(sequenceFeature);
1241 groupMenu.add(createGroupMenuItem);
1242 groupMenu.add(unGroupMenuItem);
1243 groupMenu.add(jMenu1);
1244 sequenceMenu.add(sequenceName);
1245 sequenceMenu.add(sequenceDetails);
1246 sequenceMenu.add(makeReferenceSeq);
1253 editMenu.add(editSequence);
1254 editMenu.add(upperCase);
1255 editMenu.add(lowerCase);
1256 editMenu.add(toggle);
1257 // JBPNote: These shouldn't be added here - should appear in a generic
1258 // 'apply web service to this sequence menu'
1259 // pdbMenu.add(RNAFold);
1260 // pdbMenu.add(ContraFold);
1261 jMenu1.add(groupName);
1262 jMenu1.add(colourMenu);
1263 jMenu1.add(showBoxes);
1264 jMenu1.add(showText);
1265 jMenu1.add(showColourText);
1266 jMenu1.add(outline);
1267 jMenu1.add(displayNonconserved);
1271 * Constructs the entries for the colour menu
1273 protected void initColourMenu()
1275 colourMenu.setText(MessageManager.getString("label.group_colour"));
1276 textColour.setText(MessageManager.getString("label.text_colour"));
1277 textColour.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 textColour_actionPerformed();
1286 abovePIDColour.setText(
1287 MessageManager.getString("label.above_identity_threshold"));
1288 abovePIDColour.addActionListener(new ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1298 MessageManager.getString("label.modify_identity_threshold"));
1299 modifyPID.addActionListener(new ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 modifyPID_actionPerformed();
1308 conservationMenuItem
1309 .setText(MessageManager.getString("action.by_conservation"));
1310 conservationMenuItem.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 conservationMenuItem_actionPerformed(
1316 conservationMenuItem.isSelected());
1320 modifyConservation.setText(MessageManager
1321 .getString("label.modify_conservation_threshold"));
1322 modifyConservation.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 modifyConservation_actionPerformed();
1333 * Builds the group colour sub-menu, including any user-defined colours which
1334 * were loaded at startup or during the Jalview session
1336 protected void buildColourMenu()
1338 SequenceGroup sg = ap.av.getSelectionGroup();
1342 * popup menu with no sequence group scope
1346 colourMenu.removeAll();
1347 colourMenu.add(textColour);
1348 colourMenu.addSeparator();
1350 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1352 colourMenu.addSeparator();
1353 colourMenu.add(conservationMenuItem);
1354 colourMenu.add(modifyConservation);
1355 colourMenu.add(abovePIDColour);
1356 colourMenu.add(modifyPID);
1359 protected void modifyConservation_actionPerformed()
1361 SequenceGroup sg = getGroup();
1364 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1365 SliderPanel.showConservationSlider();
1369 protected void modifyPID_actionPerformed()
1371 SequenceGroup sg = getGroup();
1374 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1376 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1377 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1378 SliderPanel.showPIDSlider();
1383 * Check for any annotations on the underlying dataset sequences (for the
1384 * current selection group) which are not 'on the alignment'.If any are found,
1385 * enable the option to add them to the alignment. The criteria for 'on the
1386 * alignment' is finding an alignment annotation on the alignment, matched on
1387 * calcId, label and sequenceRef.
1389 * A tooltip is also constructed that displays the source (calcId) and type
1390 * (label) of the annotations that can be added.
1393 * @param forSequences
1395 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1396 List<SequenceI> forSequences)
1398 menuItem.setEnabled(false);
1401 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1402 * Using TreeMap means calcIds are shown in alphabetical order.
1404 SortedMap<String, String> tipEntries = new TreeMap<>();
1405 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1406 AlignmentI al = this.ap.av.getAlignment();
1407 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1409 if (!candidates.isEmpty())
1411 StringBuilder tooltip = new StringBuilder(64);
1412 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1415 * Found annotations that could be added. Enable the menu item, and
1416 * configure its tooltip and action.
1418 menuItem.setEnabled(true);
1419 for (String calcId : tipEntries.keySet())
1421 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1423 String tooltipText = JvSwingUtils.wrapTooltip(true,
1424 tooltip.toString());
1425 menuItem.setToolTipText(tooltipText);
1427 menuItem.addActionListener(new ActionListener()
1430 public void actionPerformed(ActionEvent e)
1432 addReferenceAnnotations_actionPerformed(candidates);
1439 * Add annotations to the sequences and to the alignment.
1442 * a map whose keys are sequences on the alignment, and values a list
1443 * of annotations to add to each sequence
1445 protected void addReferenceAnnotations_actionPerformed(
1446 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1448 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1449 final AlignmentI alignment = this.ap.getAlignment();
1450 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1455 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1457 if (!ap.av.getAlignment().hasSeqrep())
1459 // initialise the display flags so the user sees something happen
1460 ap.av.setDisplayReferenceSeq(true);
1461 ap.av.setColourByReferenceSeq(true);
1462 ap.av.getAlignment().setSeqrep(sequence);
1466 if (ap.av.getAlignment().getSeqrep() == sequence)
1468 ap.av.getAlignment().setSeqrep(null);
1472 ap.av.getAlignment().setSeqrep(sequence);
1478 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1481 HiddenColumns hidden = new HiddenColumns();
1482 BitSet inserts = new BitSet(), mask = new BitSet();
1484 // set mask to preserve existing hidden columns outside selected group
1485 if (ap.av.hasHiddenColumns())
1487 ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
1490 boolean markedPopup = false;
1491 // mark inserts in current selection
1492 if (ap.av.getSelectionGroup() != null)
1494 // mark just the columns in the selection group to be hidden
1495 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1496 ap.av.getSelectionGroup().getEndRes() + 1);
1498 // and clear that part of the mask
1499 mask.andNot(inserts);
1501 // now clear columns without gaps
1502 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1508 inserts.and(sq.getInsertionsAsBits());
1513 // initially, mark all columns to be hidden
1514 inserts.set(0, ap.av.getAlignment().getWidth());
1516 // and clear out old hidden regions completely
1520 // now mark for sequence under popup if we haven't already done it
1521 if (!markedPopup && sequence != null)
1523 inserts.and(sequence.getInsertionsAsBits());
1526 // finally, preserve hidden regions outside selection
1529 // and set hidden columns accordingly
1530 hidden.hideMarkedBits(inserts);
1532 ap.av.getAlignment().setHiddenColumns(hidden);
1536 protected void sequenceSelectionDetails_actionPerformed()
1538 createSequenceDetailsReport(ap.av.getSequenceSelection());
1541 protected void sequenceDetails_actionPerformed()
1543 createSequenceDetailsReport(new SequenceI[] { sequence });
1546 public void createSequenceDetailsReport(SequenceI[] sequences)
1548 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1549 StringBuilder contents = new StringBuilder(128);
1550 for (SequenceI seq : sequences)
1552 contents.append("<p><h2>" + MessageManager.formatMessage(
1553 "label.create_sequence_details_report_annotation_for",
1555 { seq.getDisplayId(true) }) + "</h2></p><p>");
1556 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1557 contents, seq, true, true,
1558 (ap.getSeqPanel().seqCanvas.fr != null)
1559 ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
1561 contents.append("</p>");
1563 cap.setText("<html>" + contents.toString() + "</html>");
1565 Desktop.addInternalFrame(cap,
1566 MessageManager.formatMessage("label.sequence_details_for",
1567 (sequences.length == 1 ? new Object[]
1568 { sequences[0].getDisplayId(true) }
1571 .getString("label.selection") })),
1576 protected void showNonconserved_actionPerformed()
1578 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1583 * call to refresh view after settings change
1587 ap.updateAnnotation();
1588 // removed paintAlignment(true) here:
1589 // updateAnnotation calls paintAlignment already, so don't need to call
1592 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1596 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1597 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1607 public void abovePIDColour_actionPerformed(boolean selected)
1609 SequenceGroup sg = getGroup();
1617 sg.cs.setConsensus(AAFrequency.calculate(
1618 sg.getSequences(ap.av.getHiddenRepSequences()),
1619 sg.getStartRes(), sg.getEndRes() + 1));
1621 int threshold = SliderPanel.setPIDSliderSource(ap,
1622 sg.getGroupColourScheme(), getGroup().getName());
1624 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1626 SliderPanel.showPIDSlider();
1629 // remove PIDColouring
1631 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1632 SliderPanel.hidePIDSlider();
1634 modifyPID.setEnabled(selected);
1640 * Open a panel where the user can choose which types of sequence annotation
1645 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1647 // todo correct way to guard against opening a duplicate panel?
1648 new AnnotationChooser(ap);
1657 public void conservationMenuItem_actionPerformed(boolean selected)
1659 SequenceGroup sg = getGroup();
1667 // JBPNote: Conservation name shouldn't be i18n translated
1668 Conservation c = new Conservation("Group",
1669 sg.getSequences(ap.av.getHiddenRepSequences()),
1670 sg.getStartRes(), sg.getEndRes() + 1);
1673 c.verdict(false, ap.av.getConsPercGaps());
1674 sg.cs.setConservation(c);
1676 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1678 SliderPanel.showConservationSlider();
1681 // remove ConservationColouring
1683 sg.cs.setConservation(null);
1684 SliderPanel.hideConservationSlider();
1686 modifyConservation.setEnabled(selected);
1697 protected void groupName_actionPerformed()
1700 SequenceGroup sg = getGroup();
1701 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1702 sg.getDescription(),
1703 " " + MessageManager.getString("label.group_name") + " ",
1704 MessageManager.getString("label.group_description") + " ",
1705 MessageManager.getString("label.edit_group_name_description"),
1713 sg.setName(dialog.getName());
1714 sg.setDescription(dialog.getDescription());
1719 * Get selection group - adding it to the alignment if necessary.
1721 * @return sequence group to operate on
1723 SequenceGroup getGroup()
1725 SequenceGroup sg = ap.av.getSelectionGroup();
1726 // this method won't add a new group if it already exists
1729 ap.av.getAlignment().addGroup(sg);
1741 void sequenceName_actionPerformed()
1743 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1744 sequence.getDescription(),
1745 " " + MessageManager.getString("label.sequence_name")
1747 MessageManager.getString("label.sequence_description") + " ",
1748 MessageManager.getString(
1749 "label.edit_sequence_name_description"),
1757 if (dialog.getName() != null)
1759 if (dialog.getName().indexOf(" ") > -1)
1761 JvOptionPane.showMessageDialog(ap,
1763 .getString("label.spaces_converted_to_backslashes"),
1765 .getString("label.no_spaces_allowed_sequence_name"),
1766 JvOptionPane.WARNING_MESSAGE);
1769 sequence.setName(dialog.getName().replace(' ', '_'));
1770 ap.paintAlignment(false);
1773 sequence.setDescription(dialog.getDescription());
1775 ap.av.firePropertyChange("alignment", null,
1776 ap.av.getAlignment().getSequences());
1786 void unGroupMenuItem_actionPerformed()
1788 SequenceGroup sg = ap.av.getSelectionGroup();
1789 ap.av.getAlignment().deleteGroup(sg);
1790 ap.av.setSelectionGroup(null);
1794 void createGroupMenuItem_actionPerformed()
1796 getGroup(); // implicitly creates group - note - should apply defaults / use
1797 // standard alignment window logic for this
1807 protected void outline_actionPerformed()
1809 SequenceGroup sg = getGroup();
1810 Color col = JColorChooser.showDialog(this,
1811 MessageManager.getString("label.select_outline_colour"),
1816 sg.setOutlineColour(col);
1828 public void showBoxes_actionPerformed()
1830 getGroup().setDisplayBoxes(showBoxes.isSelected());
1840 public void showText_actionPerformed()
1842 getGroup().setDisplayText(showText.isSelected());
1852 public void showColourText_actionPerformed()
1854 getGroup().setColourText(showColourText.isSelected());
1858 public void showLink(String url)
1862 jalview.util.BrowserLauncher.openURL(url);
1863 } catch (Exception ex)
1865 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1866 MessageManager.getString("label.web_browser_not_found_unix"),
1867 MessageManager.getString("label.web_browser_not_found"),
1868 JvOptionPane.WARNING_MESSAGE);
1870 ex.printStackTrace();
1874 void hideSequences(boolean representGroup)
1876 ap.av.hideSequences(sequence, representGroup);
1879 public void copy_actionPerformed()
1881 ap.alignFrame.copy_actionPerformed(null);
1884 public void cut_actionPerformed()
1886 ap.alignFrame.cut_actionPerformed(null);
1889 void changeCase(ActionEvent e)
1891 Object source = e.getSource();
1892 SequenceGroup sg = ap.av.getSelectionGroup();
1896 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1897 sg.getStartRes(), sg.getEndRes() + 1);
1902 if (source == toggle)
1904 description = MessageManager.getString("label.toggle_case");
1905 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1907 else if (source == upperCase)
1909 description = MessageManager.getString("label.to_upper_case");
1910 caseChange = ChangeCaseCommand.TO_UPPER;
1914 description = MessageManager.getString("label.to_lower_case");
1915 caseChange = ChangeCaseCommand.TO_LOWER;
1918 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1919 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1920 startEnd, caseChange);
1922 ap.alignFrame.addHistoryItem(caseCommand);
1924 ap.av.firePropertyChange("alignment", null,
1925 ap.av.getAlignment().getSequences());
1930 public void outputText_actionPerformed(ActionEvent e)
1932 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1933 cap.setForInput(null);
1934 Desktop.addInternalFrame(cap, MessageManager
1935 .formatMessage("label.alignment_output_command", new Object[]
1936 { e.getActionCommand() }), 600, 500);
1938 String[] omitHidden = null;
1940 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1941 // or we simply trust the user wants
1942 // wysiwig behaviour
1944 FileFormatI fileFormat = FileFormats.getInstance()
1945 .forName(e.getActionCommand());
1947 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
1950 public void sequenceFeature_actionPerformed()
1952 SequenceGroup sg = ap.av.getSelectionGroup();
1958 List<SequenceI> seqs = new ArrayList<>();
1959 List<SequenceFeature> features = new ArrayList<>();
1962 * assemble dataset sequences, and template new sequence features,
1963 * for the amend features dialog
1965 int gSize = sg.getSize();
1966 for (int i = 0; i < gSize; i++)
1968 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1969 int end = sg.findEndRes(sg.getSequenceAt(i));
1972 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
1973 features.add(new SequenceFeature(null, null, start, end, null));
1978 * an entirely gapped region will generate empty lists of sequence / features
1980 if (!seqs.isEmpty())
1982 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
1983 .amendFeatures(seqs, features, true, ap))
1985 ap.alignFrame.setShowSeqFeatures(true);
1986 ap.av.setSearchResults(null); // clear highlighting
1987 ap.repaint(); // draw new/amended features
1992 public void textColour_actionPerformed()
1994 SequenceGroup sg = getGroup();
1997 new TextColourChooser().chooseColour(ap, sg);
2001 public void colourByStructure(String pdbid)
2003 Annotation[] anots = ap.av.getStructureSelectionManager()
2004 .colourSequenceFromStructure(sequence, pdbid);
2006 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2007 "Coloured by " + pdbid, anots);
2009 ap.av.getAlignment().addAnnotation(an);
2010 an.createSequenceMapping(sequence, 0, true);
2011 // an.adjustForAlignment();
2012 ap.av.getAlignment().setAnnotationIndex(an, 0);
2014 ap.adjustAnnotationHeight();
2016 sequence.addAlignmentAnnotation(an);
2020 public void editSequence_actionPerformed(ActionEvent actionEvent)
2022 SequenceGroup sg = ap.av.getSelectionGroup();
2026 if (sequence == null)
2028 sequence = sg.getSequenceAt(0);
2031 EditNameDialog dialog = new EditNameDialog(
2032 sequence.getSequenceAsString(sg.getStartRes(),
2033 sg.getEndRes() + 1),
2034 null, MessageManager.getString("label.edit_sequence"), null,
2035 MessageManager.getString("label.edit_sequence"),
2040 EditCommand editCommand = new EditCommand(
2041 MessageManager.getString("label.edit_sequences"),
2043 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2044 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2045 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2047 ap.alignFrame.addHistoryItem(editCommand);
2049 ap.av.firePropertyChange("alignment", null,
2050 ap.av.getAlignment().getSequences());
2056 * Action on user selecting an item from the colour menu (that does not have
2057 * its bespoke action handler)
2062 public void changeColour_actionPerformed(String colourSchemeName)
2064 SequenceGroup sg = getGroup();
2066 * switch to the chosen colour scheme (or null for None)
2068 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2069 .getColourScheme(colourSchemeName, sg,
2070 ap.av.getHiddenRepSequences());
2071 sg.setColourScheme(colourScheme);
2072 if (colourScheme instanceof Blosum62ColourScheme
2073 || colourScheme instanceof PIDColourScheme)
2075 sg.cs.setConsensus(AAFrequency.calculate(
2076 sg.getSequences(ap.av.getHiddenRepSequences()),
2077 sg.getStartRes(), sg.getEndRes() + 1));