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.gui.JalviewColourChooser.ColourChooserListener;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileFormats;
44 import jalview.io.FormatAdapter;
45 import jalview.io.SequenceAnnotationReport;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.ColourSchemes;
49 import jalview.schemes.FeatureColour;
50 import jalview.schemes.PIDColourScheme;
51 import jalview.util.GroupUrlLink;
52 import jalview.util.GroupUrlLink.UrlStringTooLongException;
53 import jalview.util.MessageManager;
54 import jalview.util.StringUtils;
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.ArrayList;
61 import java.util.Arrays;
62 import java.util.BitSet;
63 import java.util.Collection;
64 import java.util.Collections;
65 import java.util.Hashtable;
66 import java.util.LinkedHashMap;
67 import java.util.List;
69 import java.util.SortedMap;
70 import java.util.TreeMap;
71 import java.util.Vector;
73 import javax.swing.JCheckBoxMenuItem;
74 import javax.swing.JColorChooser;
75 import javax.swing.JDialog;
76 import javax.swing.JMenu;
77 import javax.swing.JMenuItem;
78 import javax.swing.JPopupMenu;
84 * @version $Revision: 1.118 $
86 public class PopupMenu extends JPopupMenu implements ColourChangeListener
88 JMenu groupMenu = new JMenu();
90 JMenuItem groupName = new JMenuItem();
92 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
94 protected JMenuItem modifyPID = new JMenuItem();
96 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
98 protected JMenuItem modifyConservation = new JMenuItem();
102 JMenu sequenceMenu = new JMenu();
104 JMenuItem sequenceName = new JMenuItem();
106 JMenuItem sequenceDetails = new JMenuItem();
108 JMenuItem sequenceSelDetails = new JMenuItem();
110 JMenuItem makeReferenceSeq = new JMenuItem();
112 JMenuItem chooseAnnotations = new JMenuItem();
116 JMenuItem createGroupMenuItem = new JMenuItem();
118 JMenuItem unGroupMenuItem = new JMenuItem();
120 JMenuItem outline = new JMenuItem();
122 JMenu colourMenu = new JMenu();
124 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
126 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
128 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
130 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
132 JMenu editMenu = new JMenu();
134 JMenuItem cut = new JMenuItem();
136 JMenuItem copy = new JMenuItem();
138 JMenuItem upperCase = new JMenuItem();
140 JMenuItem lowerCase = new JMenuItem();
142 JMenuItem toggle = new JMenuItem();
144 JMenu pdbMenu = new JMenu();
146 JMenu outputMenu = new JMenu();
148 JMenu seqShowAnnotationsMenu = new JMenu();
150 JMenu seqHideAnnotationsMenu = new JMenu();
152 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
153 MessageManager.getString("label.add_reference_annotations"));
155 JMenu groupShowAnnotationsMenu = new JMenu();
157 JMenu groupHideAnnotationsMenu = new JMenu();
159 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
160 MessageManager.getString("label.add_reference_annotations"));
162 JMenuItem sequenceFeature = new JMenuItem();
164 JMenuItem textColour = new JMenuItem();
166 JMenu jMenu1 = new JMenu();
168 JMenuItem pdbStructureDialog = new JMenuItem();
170 JMenu rnaStructureMenu = new JMenu();
172 JMenuItem editSequence = new JMenuItem();
174 JMenu groupLinksMenu;
176 JMenuItem hideInsertions = new JMenuItem();
179 * Creates a new PopupMenu object.
184 * non-positional features (for seq not null), or positional features
185 * at residue (for seq equal to null)
187 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
188 List<SequenceFeature> features)
190 this(ap, seq, features, null);
198 * the sequence under the cursor if in the Id panel, null if in the
201 * non-positional features if in the Id panel, features at the
202 * clicked residue if in the sequence panel
205 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
206 List<SequenceFeature> features, List<String> groupLinks)
208 // /////////////////////////////////////////////////////////
209 // If this is activated from the sequence panel, the user may want to
210 // edit or annotate a particular residue. Therefore display the residue menu
212 // If from the IDPanel, we must display the sequence menu
213 // ////////////////////////////////////////////////////////
214 this.ap = alignPanel;
217 for (String ff : FileFormats.getInstance().getWritableFormats(true))
219 JMenuItem item = new JMenuItem(ff);
221 item.addActionListener(new ActionListener()
224 public void actionPerformed(ActionEvent e)
226 outputText_actionPerformed(e);
230 outputMenu.add(item);
234 * Build menus for annotation types that may be shown or hidden, and for
235 * 'reference annotations' that may be added to the alignment. First for the
236 * currently selected sequence (if there is one):
238 final List<SequenceI> selectedSequence = (seq == null
239 ? Collections.<SequenceI> emptyList()
240 : Arrays.asList(seq));
241 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
242 seqHideAnnotationsMenu, selectedSequence);
243 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
247 * And repeat for the current selection group (if there is one):
249 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
250 ? Collections.<SequenceI> emptyList()
251 : alignPanel.av.getSelectionGroup().getSequences());
252 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
253 groupHideAnnotationsMenu, selectedGroup);
254 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
260 } catch (Exception e)
268 sequenceMenu.setText(sequence.getName());
269 if (seq == alignPanel.av.getAlignment().getSeqrep())
271 makeReferenceSeq.setText(
272 MessageManager.getString("action.unmark_as_reference"));
276 makeReferenceSeq.setText(
277 MessageManager.getString("action.set_as_reference"));
280 if (!alignPanel.av.getAlignment().isNucleotide())
282 remove(rnaStructureMenu);
286 int origCount = rnaStructureMenu.getItemCount();
288 * add menu items to 2D-render any alignment or sequence secondary
289 * structure annotation
291 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
292 .getAlignmentAnnotation();
295 for (final AlignmentAnnotation aa : aas)
297 if (aa.isValidStruc() && aa.sequenceRef == null)
300 * valid alignment RNA secondary structure annotation
302 menuItem = new JMenuItem();
303 menuItem.setText(MessageManager.formatMessage(
304 "label.2d_rna_structure_line", new Object[]
306 menuItem.addActionListener(new ActionListener()
309 public void actionPerformed(ActionEvent e)
311 new AppVarna(seq, aa, alignPanel);
314 rnaStructureMenu.add(menuItem);
319 if (seq.getAnnotation() != null)
321 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
322 for (final AlignmentAnnotation aa : seqAnns)
324 if (aa.isValidStruc())
327 * valid sequence RNA secondary structure annotation
329 // TODO: make rnastrucF a bit more nice
330 menuItem = new JMenuItem();
331 menuItem.setText(MessageManager.formatMessage(
332 "label.2d_rna_sequence_name", new Object[]
334 menuItem.addActionListener(new ActionListener()
337 public void actionPerformed(ActionEvent e)
339 // TODO: VARNA does'nt print gaps in the sequence
340 new AppVarna(seq, aa, alignPanel);
343 rnaStructureMenu.add(menuItem);
347 if (rnaStructureMenu.getItemCount() == origCount)
349 remove(rnaStructureMenu);
353 menuItem = new JMenuItem(
354 MessageManager.getString("action.hide_sequences"));
355 menuItem.addActionListener(new ActionListener()
358 public void actionPerformed(ActionEvent e)
360 hideSequences(false);
365 if (alignPanel.av.getSelectionGroup() != null
366 && alignPanel.av.getSelectionGroup().getSize() > 1)
368 menuItem = new JMenuItem(MessageManager
369 .formatMessage("label.represent_group_with", new Object[]
371 menuItem.addActionListener(new ActionListener()
374 public void actionPerformed(ActionEvent e)
379 sequenceMenu.add(menuItem);
382 if (alignPanel.av.hasHiddenRows())
384 final int index = alignPanel.av.getAlignment().findIndex(seq);
386 if (alignPanel.av.adjustForHiddenSeqs(index)
387 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
389 menuItem = new JMenuItem(
390 MessageManager.getString("action.reveal_sequences"));
391 menuItem.addActionListener(new ActionListener()
394 public void actionPerformed(ActionEvent e)
396 alignPanel.av.showSequence(index);
397 if (alignPanel.overviewPanel != null)
399 alignPanel.overviewPanel.updateOverviewImage();
407 // for the case when no sequences are even visible
408 if (alignPanel.av.hasHiddenRows())
411 menuItem = new JMenuItem(
412 MessageManager.getString("action.reveal_all"));
413 menuItem.addActionListener(new ActionListener()
416 public void actionPerformed(ActionEvent e)
418 alignPanel.av.showAllHiddenSeqs();
419 if (alignPanel.overviewPanel != null)
421 alignPanel.overviewPanel.updateOverviewImage();
430 SequenceGroup sg = alignPanel.av.getSelectionGroup();
431 boolean isDefinedGroup = (sg != null)
432 ? alignPanel.av.getAlignment().getGroups().contains(sg)
435 if (sg != null && sg.getSize() > 0)
437 groupName.setText(MessageManager
438 .getString("label.edit_name_and_description_current_group"));
440 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
442 conservationMenuItem.setEnabled(!sg.isNucleotide());
446 if (sg.cs.conservationApplied())
448 conservationMenuItem.setSelected(true);
450 if (sg.cs.getThreshold() > 0)
452 abovePIDColour.setSelected(true);
455 modifyConservation.setEnabled(conservationMenuItem.isSelected());
456 modifyPID.setEnabled(abovePIDColour.isSelected());
457 displayNonconserved.setSelected(sg.getShowNonconserved());
458 showText.setSelected(sg.getDisplayText());
459 showColourText.setSelected(sg.getColourText());
460 showBoxes.setSelected(sg.getDisplayBoxes());
461 // add any groupURLs to the groupURL submenu and make it visible
462 if (groupLinks != null && groupLinks.size() > 0)
464 buildGroupURLMenu(sg, groupLinks);
466 // Add a 'show all structures' for the current selection
467 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
469 SequenceI sqass = null;
470 for (SequenceI sq : alignPanel.av.getSequenceSelection())
472 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
473 if (pes != null && pes.size() > 0)
475 reppdb.put(pes.get(0).getId(), pes.get(0));
476 for (PDBEntry pe : pes)
478 pdbe.put(pe.getId(), pe);
488 final PDBEntry[] pe = pdbe.values()
489 .toArray(new PDBEntry[pdbe.size()]),
490 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
491 final JMenuItem gpdbview, rpdbview;
496 groupMenu.setVisible(false);
497 editMenu.setVisible(false);
502 createGroupMenuItem.setVisible(true);
503 unGroupMenuItem.setVisible(false);
504 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
508 createGroupMenuItem.setVisible(false);
509 unGroupMenuItem.setVisible(true);
510 jMenu1.setText(MessageManager.getString("action.edit_group"));
515 sequenceMenu.setVisible(false);
516 pdbStructureDialog.setVisible(false);
517 rnaStructureMenu.setVisible(false);
520 addLinks(seq, features);
524 addFeatureDetails(features);
529 * Add a link to show feature details for each sequence feature
533 protected void addFeatureDetails(List<SequenceFeature> features)
535 if (features == null || features.isEmpty())
539 JMenu details = new JMenu(
540 MessageManager.getString("label.feature_details"));
543 for (final SequenceFeature sf : features)
545 int start = sf.getBegin();
546 int end = sf.getEnd();
550 desc = String.format("%s %d", sf.getType(), start);
554 desc = String.format("%s %d-%d", sf.getType(), start, end);
556 String tooltip = desc;
557 String description = sf.getDescription();
558 if (description != null)
560 description = StringUtils.stripHtmlTags(description);
561 if (description.length() > 12)
563 desc = desc + " " + description.substring(0, 12) + "..";
567 desc = desc + " " + description;
569 tooltip = tooltip + " " + description;
571 if (sf.getFeatureGroup() != null)
573 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
575 JMenuItem item = new JMenuItem(desc);
576 item.setToolTipText(tooltip);
577 item.addActionListener(new ActionListener()
580 public void actionPerformed(ActionEvent e)
582 showFeatureDetails(sf);
590 * Opens a panel showing a text report of feature dteails
594 protected void showFeatureDetails(SequenceFeature sf)
596 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
597 // it appears Java's CSS does not support border-collaps :-(
598 cap.addStylesheetRule("table { border-collapse: collapse;}");
599 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
600 cap.setText(sf.getDetailsReport());
602 Desktop.addInternalFrame(cap,
603 MessageManager.getString("label.feature_details"), 500, 500);
607 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
608 * When seq is not null, these are links for the sequence id, which may be to
609 * external web sites for the sequence accession, and/or links embedded in
610 * non-positional features. When seq is null, only links embedded in the
611 * provided features are added.
616 void addLinks(final SequenceI seq, List<SequenceFeature> features)
618 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
620 List<String> nlinks = null;
623 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
627 nlinks = new ArrayList<>();
630 if (features != null)
632 for (SequenceFeature sf : features)
634 if (sf.links != null)
636 for (String link : sf.links)
644 Map<String, List<String>> linkset = new LinkedHashMap<>();
646 for (String link : nlinks)
648 UrlLink urlLink = null;
651 urlLink = new UrlLink(link);
652 } catch (Exception foo)
654 Cache.log.error("Exception for URLLink '" + link + "'", foo);
658 if (!urlLink.isValid())
660 Cache.log.error(urlLink.getInvalidMessage());
664 urlLink.createLinksFromSeq(seq, linkset);
667 addshowLinks(linkMenu, linkset.values());
669 // only add link menu if it has entries
670 if (linkMenu.getItemCount() > 0)
672 if (sequence != null)
674 sequenceMenu.add(linkMenu);
684 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
685 * "All" is added first, followed by a separator. Then add any annotation
686 * types associated with the current selection. Separate menus are built for
687 * the selected sequence group (if any), and the selected sequence.
689 * Some annotation rows are always rendered together - these can be identified
690 * by a common graphGroup property > -1. Only one of each group will be marked
691 * as visible (to avoid duplication of the display). For such groups we add a
692 * composite type name, e.g.
694 * IUPredWS (Long), IUPredWS (Short)
698 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
699 List<SequenceI> forSequences)
701 showMenu.removeAll();
702 hideMenu.removeAll();
704 final List<String> all = Arrays
706 { MessageManager.getString("label.all") });
707 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
709 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
711 showMenu.addSeparator();
712 hideMenu.addSeparator();
714 final AlignmentAnnotation[] annotations = ap.getAlignment()
715 .getAlignmentAnnotation();
718 * Find shown/hidden annotations types, distinguished by source (calcId),
719 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
720 * the insertion order, which is the order of the annotations on the
723 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
724 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
725 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
726 AlignmentAnnotationUtils.asList(annotations), forSequences);
728 for (String calcId : hiddenTypes.keySet())
730 for (List<String> type : hiddenTypes.get(calcId))
732 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
736 // grey out 'show annotations' if none are hidden
737 showMenu.setEnabled(!hiddenTypes.isEmpty());
739 for (String calcId : shownTypes.keySet())
741 for (List<String> type : shownTypes.get(calcId))
743 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
747 // grey out 'hide annotations' if none are shown
748 hideMenu.setEnabled(!shownTypes.isEmpty());
752 * Returns a list of sequences - either the current selection group (if there
753 * is one), else the specified single sequence.
758 protected List<SequenceI> getSequenceScope(SequenceI seq)
760 List<SequenceI> forSequences = null;
761 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
762 if (selectionGroup != null && selectionGroup.getSize() > 0)
764 forSequences = selectionGroup.getSequences();
768 forSequences = seq == null ? Collections.<SequenceI> emptyList()
769 : Arrays.asList(seq);
775 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
778 * @param showOrHideMenu
780 * @param forSequences
781 * the sequences whose annotations may be shown or hidden
786 * if true this is a special label meaning 'All'
787 * @param actionIsShow
788 * if true, the select menu item action is to show the annotation
791 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
792 final List<SequenceI> forSequences, String calcId,
793 final List<String> types, final boolean allTypes,
794 final boolean actionIsShow)
796 String label = types.toString(); // [a, b, c]
797 label = label.substring(1, label.length() - 1); // a, b, c
798 final JMenuItem item = new JMenuItem(label);
799 item.setToolTipText(calcId);
800 item.addActionListener(new ActionListener()
803 public void actionPerformed(ActionEvent e)
805 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
806 types, forSequences, allTypes, actionIsShow);
810 showOrHideMenu.add(item);
813 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
816 // TODO: usability: thread off the generation of group url content so root
818 // sequence only URLs
819 // ID/regex match URLs
820 groupLinksMenu = new JMenu(
821 MessageManager.getString("action.group_link"));
822 // three types of url that might be created.
823 JMenu[] linkMenus = new JMenu[] { null,
824 new JMenu(MessageManager.getString("action.ids")),
825 new JMenu(MessageManager.getString("action.sequences")),
826 new JMenu(MessageManager.getString("action.ids_sequences")) };
828 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
829 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
830 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
831 for (int sq = 0; sq < seqs.length; sq++)
834 int start = seqs[sq].findPosition(sg.getStartRes()),
835 end = seqs[sq].findPosition(sg.getEndRes());
836 // just collect ids from dataset sequence
837 // TODO: check if IDs collected from selecton group intersects with the
838 // current selection, too
839 SequenceI sqi = seqs[sq];
840 while (sqi.getDatasetSequence() != null)
842 sqi = sqi.getDatasetSequence();
844 DBRefEntry[] dbr = sqi.getDBRefs();
845 if (dbr != null && dbr.length > 0)
847 for (int d = 0; d < dbr.length; d++)
849 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
850 Object[] sarray = commonDbrefs.get(src);
853 sarray = new Object[2];
854 sarray[0] = new int[] { 0 };
855 sarray[1] = new String[seqs.length];
857 commonDbrefs.put(src, sarray);
860 if (((String[]) sarray[1])[sq] == null)
862 if (!dbr[d].hasMap() || (dbr[d].getMap()
863 .locateMappedRange(start, end) != null))
865 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
866 ((int[]) sarray[0])[0]++;
872 // now create group links for all distinct ID/sequence sets.
873 boolean addMenu = false; // indicates if there are any group links to give
875 for (String link : groupLinks)
877 GroupUrlLink urlLink = null;
880 urlLink = new GroupUrlLink(link);
881 } catch (Exception foo)
883 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
887 if (!urlLink.isValid())
889 Cache.log.error(urlLink.getInvalidMessage());
892 final String label = urlLink.getLabel();
893 boolean usingNames = false;
894 // Now see which parts of the group apply for this URL
895 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
896 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
897 String[] seqstr, ids; // input to makeUrl
900 int numinput = ((int[]) idset[0])[0];
901 String[] allids = ((String[]) idset[1]);
902 seqstr = new String[numinput];
903 ids = new String[numinput];
904 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
906 if (allids[sq] != null)
908 ids[idcount] = allids[sq];
909 seqstr[idcount++] = idandseqs[1][sq];
915 // just use the id/seq set
916 seqstr = idandseqs[1];
920 // and try and make the groupURL!
922 Object[] urlset = null;
925 urlset = urlLink.makeUrlStubs(ids, seqstr,
926 "FromJalview" + System.currentTimeMillis(), false);
927 } catch (UrlStringTooLongException e)
932 int type = urlLink.getGroupURLType() & 3;
933 // first two bits ofurlLink type bitfield are sequenceids and sequences
934 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
935 addshowLink(linkMenus[type],
936 label + (((type & 1) == 1)
937 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
945 groupLinksMenu = new JMenu(
946 MessageManager.getString("action.group_link"));
947 for (int m = 0; m < linkMenus.length; m++)
949 if (linkMenus[m] != null
950 && linkMenus[m].getMenuComponentCount() > 0)
952 groupLinksMenu.add(linkMenus[m]);
956 groupMenu.add(groupLinksMenu);
960 private void addshowLinks(JMenu linkMenu,
961 Collection<List<String>> linkset)
963 for (List<String> linkstrset : linkset)
965 // split linkstr into label and url
966 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
971 * add a show URL menu item to the given linkMenu
975 * - menu label string
979 private void addshowLink(JMenu linkMenu, String label, final String url)
981 JMenuItem item = new JMenuItem(label);
982 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
985 item.addActionListener(new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 new Thread(new Runnable()
1007 * add a late bound groupURL item to the given linkMenu
1011 * - menu label string
1012 * @param urlgenerator
1013 * GroupURLLink used to generate URL
1015 * Object array returned from the makeUrlStubs function.
1017 private void addshowLink(JMenu linkMenu, String label,
1018 final GroupUrlLink urlgenerator, final Object[] urlstub)
1020 JMenuItem item = new JMenuItem(label);
1021 item.setToolTipText(MessageManager
1022 .formatMessage("label.open_url_seqs_param", new Object[]
1023 { urlgenerator.getUrl_prefix(),
1024 urlgenerator.getNumberInvolved(urlstub) }));
1025 // TODO: put in info about what is being sent.
1026 item.addActionListener(new ActionListener()
1029 public void actionPerformed(ActionEvent e)
1031 new Thread(new Runnable()
1039 showLink(urlgenerator.constructFrom(urlstub));
1040 } catch (UrlStringTooLongException e2)
1058 private void jbInit() throws Exception
1060 groupMenu.setText(MessageManager.getString("label.selection"));
1061 groupName.setText(MessageManager.getString("label.name"));
1062 groupName.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 groupName_actionPerformed();
1070 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1071 sequenceName.setText(
1072 MessageManager.getString("label.edit_name_description"));
1073 sequenceName.addActionListener(new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 sequenceName_actionPerformed();
1082 .setText(MessageManager.getString("action.choose_annotations"));
1083 chooseAnnotations.addActionListener(new ActionListener()
1086 public void actionPerformed(ActionEvent e)
1088 chooseAnnotations_actionPerformed(e);
1092 .setText(MessageManager.getString("label.sequence_details"));
1093 sequenceDetails.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent e)
1098 sequenceDetails_actionPerformed();
1102 .setText(MessageManager.getString("label.sequence_details"));
1103 sequenceSelDetails.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 sequenceSelectionDetails_actionPerformed();
1113 .setText(MessageManager.getString("action.remove_group"));
1114 unGroupMenuItem.addActionListener(new ActionListener()
1117 public void actionPerformed(ActionEvent e)
1119 unGroupMenuItem_actionPerformed();
1123 .setText(MessageManager.getString("action.create_group"));
1124 createGroupMenuItem.addActionListener(new ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 createGroupMenuItem_actionPerformed();
1133 outline.setText(MessageManager.getString("action.border_colour"));
1134 outline.addActionListener(new ActionListener()
1137 public void actionPerformed(ActionEvent e)
1139 outline_actionPerformed();
1142 showBoxes.setText(MessageManager.getString("action.boxes"));
1143 showBoxes.setState(true);
1144 showBoxes.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 showBoxes_actionPerformed();
1152 showText.setText(MessageManager.getString("action.text"));
1153 showText.setState(true);
1154 showText.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 showText_actionPerformed();
1162 showColourText.setText(MessageManager.getString("label.colour_text"));
1163 showColourText.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 showColourText_actionPerformed();
1172 .setText(MessageManager.getString("label.show_non_conserved"));
1173 displayNonconserved.setState(true);
1174 displayNonconserved.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 showNonconserved_actionPerformed();
1182 editMenu.setText(MessageManager.getString("action.edit"));
1183 cut.setText(MessageManager.getString("action.cut"));
1184 cut.addActionListener(new ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 cut_actionPerformed();
1192 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1193 upperCase.addActionListener(new ActionListener()
1196 public void actionPerformed(ActionEvent e)
1201 copy.setText(MessageManager.getString("action.copy"));
1202 copy.addActionListener(new ActionListener()
1205 public void actionPerformed(ActionEvent e)
1207 copy_actionPerformed();
1210 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1211 lowerCase.addActionListener(new ActionListener()
1214 public void actionPerformed(ActionEvent e)
1219 toggle.setText(MessageManager.getString("label.toggle_case"));
1220 toggle.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent e)
1229 MessageManager.getString("label.out_to_textbox") + "...");
1230 seqShowAnnotationsMenu
1231 .setText(MessageManager.getString("label.show_annotations"));
1232 seqHideAnnotationsMenu
1233 .setText(MessageManager.getString("label.hide_annotations"));
1234 groupShowAnnotationsMenu
1235 .setText(MessageManager.getString("label.show_annotations"));
1236 groupHideAnnotationsMenu
1237 .setText(MessageManager.getString("label.hide_annotations"));
1238 sequenceFeature.setText(
1239 MessageManager.getString("label.create_sequence_feature"));
1240 sequenceFeature.addActionListener(new ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 sequenceFeature_actionPerformed();
1248 jMenu1.setText(MessageManager.getString("label.group"));
1249 pdbStructureDialog.setText(
1250 MessageManager.getString("label.show_pdbstruct_dialog"));
1251 pdbStructureDialog.addActionListener(new ActionListener()
1254 public void actionPerformed(ActionEvent actionEvent)
1256 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1257 if (ap.av.getSelectionGroup() != null)
1259 selectedSeqs = ap.av.getSequenceSelection();
1261 new StructureChooser(selectedSeqs, sequence, ap);
1266 .setText(MessageManager.getString("label.view_rna_structure"));
1268 // colStructureMenu.setText("Colour By Structure");
1269 editSequence.setText(
1270 MessageManager.getString("label.edit_sequence") + "...");
1271 editSequence.addActionListener(new ActionListener()
1274 public void actionPerformed(ActionEvent actionEvent)
1276 editSequence_actionPerformed(actionEvent);
1279 makeReferenceSeq.setText(
1280 MessageManager.getString("label.mark_as_representative"));
1281 makeReferenceSeq.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent actionEvent)
1287 makeReferenceSeq_actionPerformed(actionEvent);
1292 .setText(MessageManager.getString("label.hide_insertions"));
1293 hideInsertions.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 hideInsertions_actionPerformed(e);
1303 groupMenu.add(sequenceSelDetails);
1306 add(rnaStructureMenu);
1307 add(pdbStructureDialog);
1308 if (sequence != null)
1310 add(hideInsertions);
1312 // annotations configuration panel suppressed for now
1313 // groupMenu.add(chooseAnnotations);
1316 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1317 * (if a selection group is in force).
1319 sequenceMenu.add(seqShowAnnotationsMenu);
1320 sequenceMenu.add(seqHideAnnotationsMenu);
1321 sequenceMenu.add(seqAddReferenceAnnotations);
1322 groupMenu.add(groupShowAnnotationsMenu);
1323 groupMenu.add(groupHideAnnotationsMenu);
1324 groupMenu.add(groupAddReferenceAnnotations);
1325 groupMenu.add(editMenu);
1326 groupMenu.add(outputMenu);
1327 groupMenu.add(sequenceFeature);
1328 groupMenu.add(createGroupMenuItem);
1329 groupMenu.add(unGroupMenuItem);
1330 groupMenu.add(jMenu1);
1331 sequenceMenu.add(sequenceName);
1332 sequenceMenu.add(sequenceDetails);
1333 sequenceMenu.add(makeReferenceSeq);
1340 editMenu.add(editSequence);
1341 editMenu.add(upperCase);
1342 editMenu.add(lowerCase);
1343 editMenu.add(toggle);
1344 // JBPNote: These shouldn't be added here - should appear in a generic
1345 // 'apply web service to this sequence menu'
1346 // pdbMenu.add(RNAFold);
1347 // pdbMenu.add(ContraFold);
1348 jMenu1.add(groupName);
1349 jMenu1.add(colourMenu);
1350 jMenu1.add(showBoxes);
1351 jMenu1.add(showText);
1352 jMenu1.add(showColourText);
1353 jMenu1.add(outline);
1354 jMenu1.add(displayNonconserved);
1358 * Constructs the entries for the colour menu
1360 protected void initColourMenu()
1362 colourMenu.setText(MessageManager.getString("label.group_colour"));
1363 textColour.setText(MessageManager.getString("label.text_colour"));
1364 textColour.addActionListener(new ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 textColour_actionPerformed();
1373 abovePIDColour.setText(
1374 MessageManager.getString("label.above_identity_threshold"));
1375 abovePIDColour.addActionListener(new ActionListener()
1378 public void actionPerformed(ActionEvent e)
1380 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1385 MessageManager.getString("label.modify_identity_threshold"));
1386 modifyPID.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 modifyPID_actionPerformed();
1395 conservationMenuItem
1396 .setText(MessageManager.getString("action.by_conservation"));
1397 conservationMenuItem.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 conservationMenuItem_actionPerformed(
1403 conservationMenuItem.isSelected());
1407 modifyConservation.setText(MessageManager
1408 .getString("label.modify_conservation_threshold"));
1409 modifyConservation.addActionListener(new ActionListener()
1412 public void actionPerformed(ActionEvent e)
1414 modifyConservation_actionPerformed();
1420 * Builds the group colour sub-menu, including any user-defined colours which
1421 * were loaded at startup or during the Jalview session
1423 protected void buildColourMenu()
1425 SequenceGroup sg = ap.av.getSelectionGroup();
1429 * popup menu with no sequence group scope
1433 colourMenu.removeAll();
1434 colourMenu.add(textColour);
1435 colourMenu.addSeparator();
1437 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1439 colourMenu.addSeparator();
1440 colourMenu.add(conservationMenuItem);
1441 colourMenu.add(modifyConservation);
1442 colourMenu.add(abovePIDColour);
1443 colourMenu.add(modifyPID);
1446 protected void modifyConservation_actionPerformed()
1448 SequenceGroup sg = getGroup();
1451 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1452 SliderPanel.showConservationSlider();
1456 protected void modifyPID_actionPerformed()
1458 SequenceGroup sg = getGroup();
1461 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1463 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1464 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1465 SliderPanel.showPIDSlider();
1470 * Check for any annotations on the underlying dataset sequences (for the
1471 * current selection group) which are not 'on the alignment'.If any are found,
1472 * enable the option to add them to the alignment. The criteria for 'on the
1473 * alignment' is finding an alignment annotation on the alignment, matched on
1474 * calcId, label and sequenceRef.
1476 * A tooltip is also constructed that displays the source (calcId) and type
1477 * (label) of the annotations that can be added.
1480 * @param forSequences
1482 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1483 List<SequenceI> forSequences)
1485 menuItem.setEnabled(false);
1488 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1489 * Using TreeMap means calcIds are shown in alphabetical order.
1491 SortedMap<String, String> tipEntries = new TreeMap<>();
1492 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1493 AlignmentI al = this.ap.av.getAlignment();
1494 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1496 if (!candidates.isEmpty())
1498 StringBuilder tooltip = new StringBuilder(64);
1499 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1502 * Found annotations that could be added. Enable the menu item, and
1503 * configure its tooltip and action.
1505 menuItem.setEnabled(true);
1506 for (String calcId : tipEntries.keySet())
1508 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1510 String tooltipText = JvSwingUtils.wrapTooltip(true,
1511 tooltip.toString());
1512 menuItem.setToolTipText(tooltipText);
1514 menuItem.addActionListener(new ActionListener()
1517 public void actionPerformed(ActionEvent e)
1519 addReferenceAnnotations_actionPerformed(candidates);
1526 * Add annotations to the sequences and to the alignment.
1529 * a map whose keys are sequences on the alignment, and values a list
1530 * of annotations to add to each sequence
1532 protected void addReferenceAnnotations_actionPerformed(
1533 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1535 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1536 final AlignmentI alignment = this.ap.getAlignment();
1537 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1542 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1544 if (!ap.av.getAlignment().hasSeqrep())
1546 // initialise the display flags so the user sees something happen
1547 ap.av.setDisplayReferenceSeq(true);
1548 ap.av.setColourByReferenceSeq(true);
1549 ap.av.getAlignment().setSeqrep(sequence);
1553 if (ap.av.getAlignment().getSeqrep() == sequence)
1555 ap.av.getAlignment().setSeqrep(null);
1559 ap.av.getAlignment().setSeqrep(sequence);
1565 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1567 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1568 BitSet inserts = new BitSet();
1570 boolean markedPopup = false;
1571 // mark inserts in current selection
1572 if (ap.av.getSelectionGroup() != null)
1574 // mark just the columns in the selection group to be hidden
1575 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1576 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1578 // now clear columns without gaps
1579 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1585 inserts.and(sq.getInsertionsAsBits());
1587 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1588 ap.av.getSelectionGroup().getEndRes());
1591 // now mark for sequence under popup if we haven't already done it
1592 else if (!markedPopup && sequence != null)
1594 inserts.or(sequence.getInsertionsAsBits());
1596 // and set hidden columns accordingly
1597 hidden.hideColumns(inserts);
1602 protected void sequenceSelectionDetails_actionPerformed()
1604 createSequenceDetailsReport(ap.av.getSequenceSelection());
1607 protected void sequenceDetails_actionPerformed()
1609 createSequenceDetailsReport(new SequenceI[] { sequence });
1612 public void createSequenceDetailsReport(SequenceI[] sequences)
1614 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1615 StringBuilder contents = new StringBuilder(128);
1616 for (SequenceI seq : sequences)
1618 contents.append("<p><h2>" + MessageManager.formatMessage(
1619 "label.create_sequence_details_report_annotation_for",
1621 { seq.getDisplayId(true) }) + "</h2></p><p>");
1622 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1623 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1624 contents.append("</p>");
1626 cap.setText("<html>" + contents.toString() + "</html>");
1628 Desktop.addInternalFrame(cap,
1629 MessageManager.formatMessage("label.sequence_details_for",
1630 (sequences.length == 1 ? new Object[]
1631 { sequences[0].getDisplayId(true) }
1634 .getString("label.selection") })),
1639 protected void showNonconserved_actionPerformed()
1641 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1646 * call to refresh view after settings change
1650 ap.updateAnnotation();
1651 // removed paintAlignment(true) here:
1652 // updateAnnotation calls paintAlignment already, so don't need to call
1655 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1659 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1660 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1670 public void abovePIDColour_actionPerformed(boolean selected)
1672 SequenceGroup sg = getGroup();
1680 sg.cs.setConsensus(AAFrequency.calculate(
1681 sg.getSequences(ap.av.getHiddenRepSequences()),
1682 sg.getStartRes(), sg.getEndRes() + 1));
1684 int threshold = SliderPanel.setPIDSliderSource(ap,
1685 sg.getGroupColourScheme(), getGroup().getName());
1687 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1689 SliderPanel.showPIDSlider();
1692 // remove PIDColouring
1694 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1695 SliderPanel.hidePIDSlider();
1697 modifyPID.setEnabled(selected);
1703 * Open a panel where the user can choose which types of sequence annotation
1708 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1710 // todo correct way to guard against opening a duplicate panel?
1711 new AnnotationChooser(ap);
1720 public void conservationMenuItem_actionPerformed(boolean selected)
1722 SequenceGroup sg = getGroup();
1730 // JBPNote: Conservation name shouldn't be i18n translated
1731 Conservation c = new Conservation("Group",
1732 sg.getSequences(ap.av.getHiddenRepSequences()),
1733 sg.getStartRes(), sg.getEndRes() + 1);
1736 c.verdict(false, ap.av.getConsPercGaps());
1737 sg.cs.setConservation(c);
1739 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1741 SliderPanel.showConservationSlider();
1744 // remove ConservationColouring
1746 sg.cs.setConservation(null);
1747 SliderPanel.hideConservationSlider();
1749 modifyConservation.setEnabled(selected);
1760 protected void groupName_actionPerformed()
1763 SequenceGroup sg = getGroup();
1764 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1765 sg.getDescription(),
1766 " " + MessageManager.getString("label.group_name") + " ",
1767 MessageManager.getString("label.group_description") + " ",
1768 MessageManager.getString("label.edit_group_name_description"),
1776 sg.setName(dialog.getName());
1777 sg.setDescription(dialog.getDescription());
1782 * Get selection group - adding it to the alignment if necessary.
1784 * @return sequence group to operate on
1786 SequenceGroup getGroup()
1788 SequenceGroup sg = ap.av.getSelectionGroup();
1789 // this method won't add a new group if it already exists
1792 ap.av.getAlignment().addGroup(sg);
1804 void sequenceName_actionPerformed()
1806 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1807 sequence.getDescription(),
1808 " " + MessageManager.getString("label.sequence_name")
1810 MessageManager.getString("label.sequence_description") + " ",
1811 MessageManager.getString(
1812 "label.edit_sequence_name_description"),
1820 if (dialog.getName() != null)
1822 if (dialog.getName().indexOf(" ") > -1)
1824 JvOptionPane.showMessageDialog(ap,
1826 .getString("label.spaces_converted_to_backslashes"),
1828 .getString("label.no_spaces_allowed_sequence_name"),
1829 JvOptionPane.WARNING_MESSAGE);
1832 sequence.setName(dialog.getName().replace(' ', '_'));
1833 ap.paintAlignment(false, false);
1836 sequence.setDescription(dialog.getDescription());
1838 ap.av.firePropertyChange("alignment", null,
1839 ap.av.getAlignment().getSequences());
1849 void unGroupMenuItem_actionPerformed()
1851 SequenceGroup sg = ap.av.getSelectionGroup();
1852 ap.av.getAlignment().deleteGroup(sg);
1853 ap.av.setSelectionGroup(null);
1857 void createGroupMenuItem_actionPerformed()
1859 getGroup(); // implicitly creates group - note - should apply defaults / use
1860 // standard alignment window logic for this
1865 * Offers a colour chooser and sets the selected colour as the group outline
1867 protected void outline_actionPerformed()
1869 String title = MessageManager
1870 .getString("label.select_outline_colour");
1871 ColourChooserListener listener = new ColourChooserListener()
1874 public void colourSelected(Color c)
1876 getGroup().setOutlineColour(c);
1880 JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
1881 title, Color.BLUE, listener);
1890 public void showBoxes_actionPerformed()
1892 getGroup().setDisplayBoxes(showBoxes.isSelected());
1902 public void showText_actionPerformed()
1904 getGroup().setDisplayText(showText.isSelected());
1914 public void showColourText_actionPerformed()
1916 getGroup().setColourText(showColourText.isSelected());
1920 public void showLink(String url)
1924 jalview.util.BrowserLauncher.openURL(url);
1925 } catch (Exception ex)
1927 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1928 MessageManager.getString("label.web_browser_not_found_unix"),
1929 MessageManager.getString("label.web_browser_not_found"),
1930 JvOptionPane.WARNING_MESSAGE);
1932 ex.printStackTrace();
1936 void hideSequences(boolean representGroup)
1938 ap.av.hideSequences(sequence, representGroup);
1941 public void copy_actionPerformed()
1943 ap.alignFrame.copy_actionPerformed(null);
1946 public void cut_actionPerformed()
1948 ap.alignFrame.cut_actionPerformed(null);
1951 void changeCase(ActionEvent e)
1953 Object source = e.getSource();
1954 SequenceGroup sg = ap.av.getSelectionGroup();
1958 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1959 sg.getStartRes(), sg.getEndRes() + 1);
1964 if (source == toggle)
1966 description = MessageManager.getString("label.toggle_case");
1967 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1969 else if (source == upperCase)
1971 description = MessageManager.getString("label.to_upper_case");
1972 caseChange = ChangeCaseCommand.TO_UPPER;
1976 description = MessageManager.getString("label.to_lower_case");
1977 caseChange = ChangeCaseCommand.TO_LOWER;
1980 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1981 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1982 startEnd, caseChange);
1984 ap.alignFrame.addHistoryItem(caseCommand);
1986 ap.av.firePropertyChange("alignment", null,
1987 ap.av.getAlignment().getSequences());
1992 public void outputText_actionPerformed(ActionEvent e)
1994 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1995 cap.setForInput(null);
1996 Desktop.addInternalFrame(cap, MessageManager
1997 .formatMessage("label.alignment_output_command", new Object[]
1998 { e.getActionCommand() }), 600, 500);
2000 String[] omitHidden = null;
2002 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2003 // or we simply trust the user wants
2004 // wysiwig behaviour
2006 FileFormatI fileFormat = FileFormats.getInstance()
2007 .forName(e.getActionCommand());
2009 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2012 public void sequenceFeature_actionPerformed()
2014 SequenceGroup sg = ap.av.getSelectionGroup();
2020 List<SequenceI> seqs = new ArrayList<>();
2021 List<SequenceFeature> features = new ArrayList<>();
2024 * assemble dataset sequences, and template new sequence features,
2025 * for the amend features dialog
2027 int gSize = sg.getSize();
2028 for (int i = 0; i < gSize; i++)
2030 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2031 int end = sg.findEndRes(sg.getSequenceAt(i));
2034 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2035 features.add(new SequenceFeature(null, null, start, end, null));
2040 * an entirely gapped region will generate empty lists of sequence / features
2042 if (!seqs.isEmpty())
2044 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2045 .amendFeatures(seqs, features, true, ap))
2047 ap.alignFrame.setShowSeqFeatures(true);
2048 ap.av.setSearchResults(null); // clear highlighting
2049 ap.repaint(); // draw new/amended features
2054 public void textColour_actionPerformed()
2056 SequenceGroup sg = getGroup();
2059 new TextColourChooser().chooseColour(ap, sg);
2063 public void colourByStructure(String pdbid)
2065 Annotation[] anots = ap.av.getStructureSelectionManager()
2066 .colourSequenceFromStructure(sequence, pdbid);
2068 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2069 "Coloured by " + pdbid, anots);
2071 ap.av.getAlignment().addAnnotation(an);
2072 an.createSequenceMapping(sequence, 0, true);
2073 // an.adjustForAlignment();
2074 ap.av.getAlignment().setAnnotationIndex(an, 0);
2076 ap.adjustAnnotationHeight();
2078 sequence.addAlignmentAnnotation(an);
2082 public void editSequence_actionPerformed(ActionEvent actionEvent)
2084 SequenceGroup sg = ap.av.getSelectionGroup();
2088 if (sequence == null)
2090 sequence = sg.getSequenceAt(0);
2093 EditNameDialog dialog = new EditNameDialog(
2094 sequence.getSequenceAsString(sg.getStartRes(),
2095 sg.getEndRes() + 1),
2096 null, MessageManager.getString("label.edit_sequence"), null,
2097 MessageManager.getString("label.edit_sequence"),
2102 EditCommand editCommand = new EditCommand(
2103 MessageManager.getString("label.edit_sequences"),
2105 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2106 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2107 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2109 ap.alignFrame.addHistoryItem(editCommand);
2111 ap.av.firePropertyChange("alignment", null,
2112 ap.av.getAlignment().getSequences());
2118 * Action on user selecting an item from the colour menu (that does not have
2119 * its bespoke action handler)
2124 public void changeColour_actionPerformed(String colourSchemeName)
2126 SequenceGroup sg = getGroup();
2128 * switch to the chosen colour scheme (or null for None)
2130 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2131 .getColourScheme(colourSchemeName, sg,
2132 ap.av.getHiddenRepSequences());
2133 sg.setColourScheme(colourScheme);
2134 if (colourScheme instanceof Blosum62ColourScheme
2135 || colourScheme instanceof PIDColourScheme)
2137 sg.cs.setConsensus(AAFrequency.calculate(
2138 sg.getSequences(ap.av.getHiddenRepSequences()),
2139 sg.getStartRes(), sg.getEndRes() + 1));