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.StringUtils;
53 import jalview.util.UrlLink;
55 import java.awt.Color;
56 import java.awt.event.ActionEvent;
57 import java.awt.event.ActionListener;
58 import java.util.ArrayList;
59 import java.util.Arrays;
60 import java.util.BitSet;
61 import java.util.Collection;
62 import java.util.Collections;
63 import java.util.Hashtable;
64 import java.util.LinkedHashMap;
65 import java.util.List;
67 import java.util.SortedMap;
68 import java.util.TreeMap;
69 import java.util.Vector;
71 import javax.swing.JCheckBoxMenuItem;
72 import javax.swing.JColorChooser;
73 import javax.swing.JMenu;
74 import javax.swing.JMenuItem;
75 import javax.swing.JPopupMenu;
81 * @version $Revision: 1.118 $
83 public class PopupMenu extends JPopupMenu implements ColourChangeListener
85 JMenu groupMenu = new JMenu();
87 JMenuItem groupName = new JMenuItem();
89 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
91 protected JMenuItem modifyPID = new JMenuItem();
93 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
95 protected JMenuItem modifyConservation = new JMenuItem();
99 JMenu sequenceMenu = new JMenu();
101 JMenuItem sequenceName = new JMenuItem();
103 JMenuItem sequenceDetails = new JMenuItem();
105 JMenuItem sequenceSelDetails = new JMenuItem();
107 JMenuItem makeReferenceSeq = new JMenuItem();
109 JMenuItem chooseAnnotations = new JMenuItem();
113 JMenuItem createGroupMenuItem = new JMenuItem();
115 JMenuItem unGroupMenuItem = new JMenuItem();
117 JMenuItem outline = new JMenuItem();
119 JMenu colourMenu = new JMenu();
121 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
123 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
125 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
127 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
129 JMenu editMenu = new JMenu();
131 JMenuItem cut = new JMenuItem();
133 JMenuItem copy = new JMenuItem();
135 JMenuItem upperCase = new JMenuItem();
137 JMenuItem lowerCase = new JMenuItem();
139 JMenuItem toggle = new JMenuItem();
141 JMenu pdbMenu = new JMenu();
143 JMenu outputMenu = new JMenu();
145 JMenu seqShowAnnotationsMenu = new JMenu();
147 JMenu seqHideAnnotationsMenu = new JMenu();
149 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
150 MessageManager.getString("label.add_reference_annotations"));
152 JMenu groupShowAnnotationsMenu = new JMenu();
154 JMenu groupHideAnnotationsMenu = new JMenu();
156 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
157 MessageManager.getString("label.add_reference_annotations"));
159 JMenuItem sequenceFeature = new JMenuItem();
161 JMenuItem textColour = new JMenuItem();
163 JMenu jMenu1 = new JMenu();
165 JMenuItem pdbStructureDialog = new JMenuItem();
167 JMenu rnaStructureMenu = new JMenu();
169 JMenuItem editSequence = new JMenuItem();
171 JMenu groupLinksMenu;
173 JMenuItem hideInsertions = new JMenuItem();
176 * Creates a new PopupMenu object.
181 * non-positional features (for seq not null), or positional features
182 * at residue (for seq equal to null)
184 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
185 List<SequenceFeature> features)
187 this(ap, seq, features, null);
195 * the sequence under the cursor if in the Id panel, null if in the
198 * non-positional features if in the Id panel, features at the
199 * clicked residue if in the sequence panel
202 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
203 List<SequenceFeature> features, List<String> groupLinks)
205 // /////////////////////////////////////////////////////////
206 // If this is activated from the sequence panel, the user may want to
207 // edit or annotate a particular residue. Therefore display the residue menu
209 // If from the IDPanel, we must display the sequence menu
210 // ////////////////////////////////////////////////////////
211 this.ap = alignPanel;
214 for (String ff : FileFormats.getInstance().getWritableFormats(true))
216 JMenuItem item = new JMenuItem(ff);
218 item.addActionListener(new ActionListener()
221 public void actionPerformed(ActionEvent e)
223 outputText_actionPerformed(e);
227 outputMenu.add(item);
231 * Build menus for annotation types that may be shown or hidden, and for
232 * 'reference annotations' that may be added to the alignment. First for the
233 * currently selected sequence (if there is one):
235 final List<SequenceI> selectedSequence = (seq == null
236 ? Collections.<SequenceI> emptyList()
237 : Arrays.asList(seq));
238 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
239 seqHideAnnotationsMenu, selectedSequence);
240 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
244 * And repeat for the current selection group (if there is one):
246 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
247 ? Collections.<SequenceI> emptyList()
248 : alignPanel.av.getSelectionGroup().getSequences());
249 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
250 groupHideAnnotationsMenu, selectedGroup);
251 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
257 } catch (Exception e)
265 sequenceMenu.setText(sequence.getName());
266 if (seq == alignPanel.av.getAlignment().getSeqrep())
268 makeReferenceSeq.setText(
269 MessageManager.getString("action.unmark_as_reference"));
273 makeReferenceSeq.setText(
274 MessageManager.getString("action.set_as_reference"));
277 if (!alignPanel.av.getAlignment().isNucleotide())
279 remove(rnaStructureMenu);
283 int origCount = rnaStructureMenu.getItemCount();
285 * add menu items to 2D-render any alignment or sequence secondary
286 * structure annotation
288 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
289 .getAlignmentAnnotation();
292 for (final AlignmentAnnotation aa : aas)
294 if (aa.isValidStruc() && aa.sequenceRef == null)
297 * valid alignment RNA secondary structure annotation
299 menuItem = new JMenuItem();
300 menuItem.setText(MessageManager.formatMessage(
301 "label.2d_rna_structure_line", new Object[]
303 menuItem.addActionListener(new ActionListener()
306 public void actionPerformed(ActionEvent e)
308 new AppVarna(seq, aa, alignPanel);
311 rnaStructureMenu.add(menuItem);
316 if (seq.getAnnotation() != null)
318 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
319 for (final AlignmentAnnotation aa : seqAnns)
321 if (aa.isValidStruc())
324 * valid sequence RNA secondary structure annotation
326 // TODO: make rnastrucF a bit more nice
327 menuItem = new JMenuItem();
328 menuItem.setText(MessageManager.formatMessage(
329 "label.2d_rna_sequence_name", new Object[]
331 menuItem.addActionListener(new ActionListener()
334 public void actionPerformed(ActionEvent e)
336 // TODO: VARNA does'nt print gaps in the sequence
337 new AppVarna(seq, aa, alignPanel);
340 rnaStructureMenu.add(menuItem);
344 if (rnaStructureMenu.getItemCount() == origCount)
346 remove(rnaStructureMenu);
350 menuItem = new JMenuItem(
351 MessageManager.getString("action.hide_sequences"));
352 menuItem.addActionListener(new ActionListener()
355 public void actionPerformed(ActionEvent e)
357 hideSequences(false);
362 if (alignPanel.av.getSelectionGroup() != null
363 && alignPanel.av.getSelectionGroup().getSize() > 1)
365 menuItem = new JMenuItem(MessageManager
366 .formatMessage("label.represent_group_with", new Object[]
368 menuItem.addActionListener(new ActionListener()
371 public void actionPerformed(ActionEvent e)
376 sequenceMenu.add(menuItem);
379 if (alignPanel.av.hasHiddenRows())
381 final int index = alignPanel.av.getAlignment().findIndex(seq);
383 if (alignPanel.av.adjustForHiddenSeqs(index)
384 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
386 menuItem = new JMenuItem(
387 MessageManager.getString("action.reveal_sequences"));
388 menuItem.addActionListener(new ActionListener()
391 public void actionPerformed(ActionEvent e)
393 alignPanel.av.showSequence(index);
394 if (alignPanel.overviewPanel != null)
396 alignPanel.overviewPanel.updateOverviewImage();
404 // for the case when no sequences are even visible
405 if (alignPanel.av.hasHiddenRows())
408 menuItem = new JMenuItem(
409 MessageManager.getString("action.reveal_all"));
410 menuItem.addActionListener(new ActionListener()
413 public void actionPerformed(ActionEvent e)
415 alignPanel.av.showAllHiddenSeqs();
416 if (alignPanel.overviewPanel != null)
418 alignPanel.overviewPanel.updateOverviewImage();
427 SequenceGroup sg = alignPanel.av.getSelectionGroup();
428 boolean isDefinedGroup = (sg != null)
429 ? alignPanel.av.getAlignment().getGroups().contains(sg)
432 if (sg != null && sg.getSize() > 0)
434 groupName.setText(MessageManager
435 .getString("label.edit_name_and_description_current_group"));
437 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
439 conservationMenuItem.setEnabled(!sg.isNucleotide());
443 if (sg.cs.conservationApplied())
445 conservationMenuItem.setSelected(true);
447 if (sg.cs.getThreshold() > 0)
449 abovePIDColour.setSelected(true);
452 modifyConservation.setEnabled(conservationMenuItem.isSelected());
453 modifyPID.setEnabled(abovePIDColour.isSelected());
454 displayNonconserved.setSelected(sg.getShowNonconserved());
455 showText.setSelected(sg.getDisplayText());
456 showColourText.setSelected(sg.getColourText());
457 showBoxes.setSelected(sg.getDisplayBoxes());
458 // add any groupURLs to the groupURL submenu and make it visible
459 if (groupLinks != null && groupLinks.size() > 0)
461 buildGroupURLMenu(sg, groupLinks);
463 // Add a 'show all structures' for the current selection
464 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
466 SequenceI sqass = null;
467 for (SequenceI sq : alignPanel.av.getSequenceSelection())
469 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
470 if (pes != null && pes.size() > 0)
472 reppdb.put(pes.get(0).getId(), pes.get(0));
473 for (PDBEntry pe : pes)
475 pdbe.put(pe.getId(), pe);
485 final PDBEntry[] pe = pdbe.values()
486 .toArray(new PDBEntry[pdbe.size()]),
487 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
488 final JMenuItem gpdbview, rpdbview;
493 groupMenu.setVisible(false);
494 editMenu.setVisible(false);
499 createGroupMenuItem.setVisible(true);
500 unGroupMenuItem.setVisible(false);
501 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
505 createGroupMenuItem.setVisible(false);
506 unGroupMenuItem.setVisible(true);
507 jMenu1.setText(MessageManager.getString("action.edit_group"));
512 sequenceMenu.setVisible(false);
513 pdbStructureDialog.setVisible(false);
514 rnaStructureMenu.setVisible(false);
517 addLinks(seq, features);
521 addFeatureDetails(features);
526 * Add a link to show feature details for each sequence feature
530 protected void addFeatureDetails(List<SequenceFeature> features)
532 if (features == null || features.isEmpty())
536 JMenu details = new JMenu(
537 MessageManager.getString("label.feature_details"));
540 for (final SequenceFeature sf : features)
542 int start = sf.getBegin();
543 int end = sf.getEnd();
547 desc = String.format("%s %d", sf.getType(), start);
551 desc = String.format("%s %d-%d", sf.getType(), start, end);
553 String description = sf.getDescription();
554 if (description != null)
556 description = StringUtils.stripHtmlTags(description);
557 if (description.length() <= 6)
559 desc = desc + " " + description;
563 desc = desc + " " + description.substring(0, 6) + "..";
566 if (sf.getFeatureGroup() != null)
568 desc = desc + " (" + sf.getFeatureGroup() + ")";
570 JMenuItem item = new JMenuItem(desc);
571 item.addActionListener(new ActionListener()
574 public void actionPerformed(ActionEvent e)
576 showFeatureDetails(sf);
584 * Opens a panel showing a text report of feature dteails
588 protected void showFeatureDetails(SequenceFeature sf)
590 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
591 // it appears Java's CSS does not support border-collaps :-(
592 cap.addStylesheetRule("table { border-collapse: collapse;}");
593 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
594 cap.setText(sf.getDetailsReport());
596 Desktop.addInternalFrame(cap,
597 MessageManager.getString("label.feature_details"), 500, 500);
601 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
602 * When seq is not null, these are links for the sequence id, which may be to
603 * external web sites for the sequence accession, and/or links embedded in
604 * non-positional features. When seq is null, only links embedded in the
605 * provided features are added.
610 void addLinks(final SequenceI seq, List<SequenceFeature> features)
612 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
614 List<String> nlinks = null;
617 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
621 nlinks = new ArrayList<>();
624 if (features != null)
626 for (SequenceFeature sf : features)
628 if (sf.links != null)
630 for (String link : sf.links)
638 Map<String, List<String>> linkset = new LinkedHashMap<>();
640 for (String link : nlinks)
642 UrlLink urlLink = null;
645 urlLink = new UrlLink(link);
646 } catch (Exception foo)
648 Cache.log.error("Exception for URLLink '" + link + "'", foo);
652 if (!urlLink.isValid())
654 Cache.log.error(urlLink.getInvalidMessage());
658 urlLink.createLinksFromSeq(seq, linkset);
661 addshowLinks(linkMenu, linkset.values());
663 // only add link menu if it has entries
664 if (linkMenu.getItemCount() > 0)
666 if (sequence != null)
668 sequenceMenu.add(linkMenu);
678 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
679 * "All" is added first, followed by a separator. Then add any annotation
680 * types associated with the current selection. Separate menus are built for
681 * the selected sequence group (if any), and the selected sequence.
683 * Some annotation rows are always rendered together - these can be identified
684 * by a common graphGroup property > -1. Only one of each group will be marked
685 * as visible (to avoid duplication of the display). For such groups we add a
686 * composite type name, e.g.
688 * IUPredWS (Long), IUPredWS (Short)
692 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
693 List<SequenceI> forSequences)
695 showMenu.removeAll();
696 hideMenu.removeAll();
698 final List<String> all = Arrays
700 { MessageManager.getString("label.all") });
701 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
703 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
705 showMenu.addSeparator();
706 hideMenu.addSeparator();
708 final AlignmentAnnotation[] annotations = ap.getAlignment()
709 .getAlignmentAnnotation();
712 * Find shown/hidden annotations types, distinguished by source (calcId),
713 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
714 * the insertion order, which is the order of the annotations on the
717 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
718 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
719 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
720 AlignmentAnnotationUtils.asList(annotations), forSequences);
722 for (String calcId : hiddenTypes.keySet())
724 for (List<String> type : hiddenTypes.get(calcId))
726 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
730 // grey out 'show annotations' if none are hidden
731 showMenu.setEnabled(!hiddenTypes.isEmpty());
733 for (String calcId : shownTypes.keySet())
735 for (List<String> type : shownTypes.get(calcId))
737 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
741 // grey out 'hide annotations' if none are shown
742 hideMenu.setEnabled(!shownTypes.isEmpty());
746 * Returns a list of sequences - either the current selection group (if there
747 * is one), else the specified single sequence.
752 protected List<SequenceI> getSequenceScope(SequenceI seq)
754 List<SequenceI> forSequences = null;
755 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
756 if (selectionGroup != null && selectionGroup.getSize() > 0)
758 forSequences = selectionGroup.getSequences();
762 forSequences = seq == null ? Collections.<SequenceI> emptyList()
763 : Arrays.asList(seq);
769 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
772 * @param showOrHideMenu
774 * @param forSequences
775 * the sequences whose annotations may be shown or hidden
780 * if true this is a special label meaning 'All'
781 * @param actionIsShow
782 * if true, the select menu item action is to show the annotation
785 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
786 final List<SequenceI> forSequences, String calcId,
787 final List<String> types, final boolean allTypes,
788 final boolean actionIsShow)
790 String label = types.toString(); // [a, b, c]
791 label = label.substring(1, label.length() - 1); // a, b, c
792 final JMenuItem item = new JMenuItem(label);
793 item.setToolTipText(calcId);
794 item.addActionListener(new ActionListener()
797 public void actionPerformed(ActionEvent e)
799 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
800 types, forSequences, allTypes, actionIsShow);
804 showOrHideMenu.add(item);
807 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
810 // TODO: usability: thread off the generation of group url content so root
812 // sequence only URLs
813 // ID/regex match URLs
814 groupLinksMenu = new JMenu(
815 MessageManager.getString("action.group_link"));
816 // three types of url that might be created.
817 JMenu[] linkMenus = new JMenu[] { null,
818 new JMenu(MessageManager.getString("action.ids")),
819 new JMenu(MessageManager.getString("action.sequences")),
820 new JMenu(MessageManager.getString("action.ids_sequences")) };
822 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
823 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
824 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
825 for (int sq = 0; sq < seqs.length; sq++)
828 int start = seqs[sq].findPosition(sg.getStartRes()),
829 end = seqs[sq].findPosition(sg.getEndRes());
830 // just collect ids from dataset sequence
831 // TODO: check if IDs collected from selecton group intersects with the
832 // current selection, too
833 SequenceI sqi = seqs[sq];
834 while (sqi.getDatasetSequence() != null)
836 sqi = sqi.getDatasetSequence();
838 DBRefEntry[] dbr = sqi.getDBRefs();
839 if (dbr != null && dbr.length > 0)
841 for (int d = 0; d < dbr.length; d++)
843 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
844 Object[] sarray = commonDbrefs.get(src);
847 sarray = new Object[2];
848 sarray[0] = new int[] { 0 };
849 sarray[1] = new String[seqs.length];
851 commonDbrefs.put(src, sarray);
854 if (((String[]) sarray[1])[sq] == null)
856 if (!dbr[d].hasMap() || (dbr[d].getMap()
857 .locateMappedRange(start, end) != null))
859 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
860 ((int[]) sarray[0])[0]++;
866 // now create group links for all distinct ID/sequence sets.
867 boolean addMenu = false; // indicates if there are any group links to give
869 for (String link : groupLinks)
871 GroupUrlLink urlLink = null;
874 urlLink = new GroupUrlLink(link);
875 } catch (Exception foo)
877 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
881 if (!urlLink.isValid())
883 Cache.log.error(urlLink.getInvalidMessage());
886 final String label = urlLink.getLabel();
887 boolean usingNames = false;
888 // Now see which parts of the group apply for this URL
889 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
890 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
891 String[] seqstr, ids; // input to makeUrl
894 int numinput = ((int[]) idset[0])[0];
895 String[] allids = ((String[]) idset[1]);
896 seqstr = new String[numinput];
897 ids = new String[numinput];
898 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
900 if (allids[sq] != null)
902 ids[idcount] = allids[sq];
903 seqstr[idcount++] = idandseqs[1][sq];
909 // just use the id/seq set
910 seqstr = idandseqs[1];
914 // and try and make the groupURL!
916 Object[] urlset = null;
919 urlset = urlLink.makeUrlStubs(ids, seqstr,
920 "FromJalview" + System.currentTimeMillis(), false);
921 } catch (UrlStringTooLongException e)
926 int type = urlLink.getGroupURLType() & 3;
927 // first two bits ofurlLink type bitfield are sequenceids and sequences
928 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
929 addshowLink(linkMenus[type],
930 label + (((type & 1) == 1)
931 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
939 groupLinksMenu = new JMenu(
940 MessageManager.getString("action.group_link"));
941 for (int m = 0; m < linkMenus.length; m++)
943 if (linkMenus[m] != null
944 && linkMenus[m].getMenuComponentCount() > 0)
946 groupLinksMenu.add(linkMenus[m]);
950 groupMenu.add(groupLinksMenu);
954 private void addshowLinks(JMenu linkMenu,
955 Collection<List<String>> linkset)
957 for (List<String> linkstrset : linkset)
959 // split linkstr into label and url
960 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
965 * add a show URL menu item to the given linkMenu
969 * - menu label string
973 private void addshowLink(JMenu linkMenu, String label, final String url)
975 JMenuItem item = new JMenuItem(label);
976 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
979 item.addActionListener(new ActionListener()
982 public void actionPerformed(ActionEvent e)
984 new Thread(new Runnable()
1001 * add a late bound groupURL item to the given linkMenu
1005 * - menu label string
1006 * @param urlgenerator
1007 * GroupURLLink used to generate URL
1009 * Object array returned from the makeUrlStubs function.
1011 private void addshowLink(JMenu linkMenu, String label,
1012 final GroupUrlLink urlgenerator, final Object[] urlstub)
1014 JMenuItem item = new JMenuItem(label);
1015 item.setToolTipText(MessageManager
1016 .formatMessage("label.open_url_seqs_param", new Object[]
1017 { urlgenerator.getUrl_prefix(),
1018 urlgenerator.getNumberInvolved(urlstub) }));
1019 // TODO: put in info about what is being sent.
1020 item.addActionListener(new ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 new Thread(new Runnable()
1033 showLink(urlgenerator.constructFrom(urlstub));
1034 } catch (UrlStringTooLongException e2)
1052 private void jbInit() throws Exception
1054 groupMenu.setText(MessageManager.getString("label.selection"));
1055 groupName.setText(MessageManager.getString("label.name"));
1056 groupName.addActionListener(new ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 groupName_actionPerformed();
1064 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1065 sequenceName.setText(
1066 MessageManager.getString("label.edit_name_description"));
1067 sequenceName.addActionListener(new ActionListener()
1070 public void actionPerformed(ActionEvent e)
1072 sequenceName_actionPerformed();
1076 .setText(MessageManager.getString("action.choose_annotations"));
1077 chooseAnnotations.addActionListener(new ActionListener()
1080 public void actionPerformed(ActionEvent e)
1082 chooseAnnotations_actionPerformed(e);
1086 .setText(MessageManager.getString("label.sequence_details"));
1087 sequenceDetails.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 sequenceDetails_actionPerformed();
1096 .setText(MessageManager.getString("label.sequence_details"));
1097 sequenceSelDetails.addActionListener(new ActionListener()
1100 public void actionPerformed(ActionEvent e)
1102 sequenceSelectionDetails_actionPerformed();
1107 .setText(MessageManager.getString("action.remove_group"));
1108 unGroupMenuItem.addActionListener(new ActionListener()
1111 public void actionPerformed(ActionEvent e)
1113 unGroupMenuItem_actionPerformed();
1117 .setText(MessageManager.getString("action.create_group"));
1118 createGroupMenuItem.addActionListener(new ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 createGroupMenuItem_actionPerformed();
1127 outline.setText(MessageManager.getString("action.border_colour"));
1128 outline.addActionListener(new ActionListener()
1131 public void actionPerformed(ActionEvent e)
1133 outline_actionPerformed();
1136 showBoxes.setText(MessageManager.getString("action.boxes"));
1137 showBoxes.setState(true);
1138 showBoxes.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 showBoxes_actionPerformed();
1146 showText.setText(MessageManager.getString("action.text"));
1147 showText.setState(true);
1148 showText.addActionListener(new ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 showText_actionPerformed();
1156 showColourText.setText(MessageManager.getString("label.colour_text"));
1157 showColourText.addActionListener(new ActionListener()
1160 public void actionPerformed(ActionEvent e)
1162 showColourText_actionPerformed();
1166 .setText(MessageManager.getString("label.show_non_conserved"));
1167 displayNonconserved.setState(true);
1168 displayNonconserved.addActionListener(new ActionListener()
1171 public void actionPerformed(ActionEvent e)
1173 showNonconserved_actionPerformed();
1176 editMenu.setText(MessageManager.getString("action.edit"));
1177 cut.setText(MessageManager.getString("action.cut"));
1178 cut.addActionListener(new ActionListener()
1181 public void actionPerformed(ActionEvent e)
1183 cut_actionPerformed();
1186 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1187 upperCase.addActionListener(new ActionListener()
1190 public void actionPerformed(ActionEvent e)
1195 copy.setText(MessageManager.getString("action.copy"));
1196 copy.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 copy_actionPerformed();
1204 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1205 lowerCase.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent e)
1213 toggle.setText(MessageManager.getString("label.toggle_case"));
1214 toggle.addActionListener(new ActionListener()
1217 public void actionPerformed(ActionEvent e)
1223 MessageManager.getString("label.out_to_textbox") + "...");
1224 seqShowAnnotationsMenu
1225 .setText(MessageManager.getString("label.show_annotations"));
1226 seqHideAnnotationsMenu
1227 .setText(MessageManager.getString("label.hide_annotations"));
1228 groupShowAnnotationsMenu
1229 .setText(MessageManager.getString("label.show_annotations"));
1230 groupHideAnnotationsMenu
1231 .setText(MessageManager.getString("label.hide_annotations"));
1232 sequenceFeature.setText(
1233 MessageManager.getString("label.create_sequence_feature"));
1234 sequenceFeature.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 sequenceFeature_actionPerformed();
1242 jMenu1.setText(MessageManager.getString("label.group"));
1243 pdbStructureDialog.setText(
1244 MessageManager.getString("label.show_pdbstruct_dialog"));
1245 pdbStructureDialog.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent actionEvent)
1250 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1251 if (ap.av.getSelectionGroup() != null)
1253 selectedSeqs = ap.av.getSequenceSelection();
1255 new StructureChooser(selectedSeqs, sequence, ap);
1260 .setText(MessageManager.getString("label.view_rna_structure"));
1262 // colStructureMenu.setText("Colour By Structure");
1263 editSequence.setText(
1264 MessageManager.getString("label.edit_sequence") + "...");
1265 editSequence.addActionListener(new ActionListener()
1268 public void actionPerformed(ActionEvent actionEvent)
1270 editSequence_actionPerformed(actionEvent);
1273 makeReferenceSeq.setText(
1274 MessageManager.getString("label.mark_as_representative"));
1275 makeReferenceSeq.addActionListener(new ActionListener()
1279 public void actionPerformed(ActionEvent actionEvent)
1281 makeReferenceSeq_actionPerformed(actionEvent);
1286 .setText(MessageManager.getString("label.hide_insertions"));
1287 hideInsertions.addActionListener(new ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 hideInsertions_actionPerformed(e);
1297 groupMenu.add(sequenceSelDetails);
1300 add(rnaStructureMenu);
1301 add(pdbStructureDialog);
1302 if (sequence != null)
1304 add(hideInsertions);
1306 // annotations configuration panel suppressed for now
1307 // groupMenu.add(chooseAnnotations);
1310 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1311 * (if a selection group is in force).
1313 sequenceMenu.add(seqShowAnnotationsMenu);
1314 sequenceMenu.add(seqHideAnnotationsMenu);
1315 sequenceMenu.add(seqAddReferenceAnnotations);
1316 groupMenu.add(groupShowAnnotationsMenu);
1317 groupMenu.add(groupHideAnnotationsMenu);
1318 groupMenu.add(groupAddReferenceAnnotations);
1319 groupMenu.add(editMenu);
1320 groupMenu.add(outputMenu);
1321 groupMenu.add(sequenceFeature);
1322 groupMenu.add(createGroupMenuItem);
1323 groupMenu.add(unGroupMenuItem);
1324 groupMenu.add(jMenu1);
1325 sequenceMenu.add(sequenceName);
1326 sequenceMenu.add(sequenceDetails);
1327 sequenceMenu.add(makeReferenceSeq);
1334 editMenu.add(editSequence);
1335 editMenu.add(upperCase);
1336 editMenu.add(lowerCase);
1337 editMenu.add(toggle);
1338 // JBPNote: These shouldn't be added here - should appear in a generic
1339 // 'apply web service to this sequence menu'
1340 // pdbMenu.add(RNAFold);
1341 // pdbMenu.add(ContraFold);
1342 jMenu1.add(groupName);
1343 jMenu1.add(colourMenu);
1344 jMenu1.add(showBoxes);
1345 jMenu1.add(showText);
1346 jMenu1.add(showColourText);
1347 jMenu1.add(outline);
1348 jMenu1.add(displayNonconserved);
1352 * Constructs the entries for the colour menu
1354 protected void initColourMenu()
1356 colourMenu.setText(MessageManager.getString("label.group_colour"));
1357 textColour.setText(MessageManager.getString("label.text_colour"));
1358 textColour.addActionListener(new ActionListener()
1361 public void actionPerformed(ActionEvent e)
1363 textColour_actionPerformed();
1367 abovePIDColour.setText(
1368 MessageManager.getString("label.above_identity_threshold"));
1369 abovePIDColour.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1379 MessageManager.getString("label.modify_identity_threshold"));
1380 modifyPID.addActionListener(new ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 modifyPID_actionPerformed();
1389 conservationMenuItem
1390 .setText(MessageManager.getString("action.by_conservation"));
1391 conservationMenuItem.addActionListener(new ActionListener()
1394 public void actionPerformed(ActionEvent e)
1396 conservationMenuItem_actionPerformed(
1397 conservationMenuItem.isSelected());
1401 modifyConservation.setText(MessageManager
1402 .getString("label.modify_conservation_threshold"));
1403 modifyConservation.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 modifyConservation_actionPerformed();
1414 * Builds the group colour sub-menu, including any user-defined colours which
1415 * were loaded at startup or during the Jalview session
1417 protected void buildColourMenu()
1419 SequenceGroup sg = ap.av.getSelectionGroup();
1423 * popup menu with no sequence group scope
1427 colourMenu.removeAll();
1428 colourMenu.add(textColour);
1429 colourMenu.addSeparator();
1431 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1433 colourMenu.addSeparator();
1434 colourMenu.add(conservationMenuItem);
1435 colourMenu.add(modifyConservation);
1436 colourMenu.add(abovePIDColour);
1437 colourMenu.add(modifyPID);
1440 protected void modifyConservation_actionPerformed()
1442 SequenceGroup sg = getGroup();
1445 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1446 SliderPanel.showConservationSlider();
1450 protected void modifyPID_actionPerformed()
1452 SequenceGroup sg = getGroup();
1455 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1457 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1458 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1459 SliderPanel.showPIDSlider();
1464 * Check for any annotations on the underlying dataset sequences (for the
1465 * current selection group) which are not 'on the alignment'.If any are found,
1466 * enable the option to add them to the alignment. The criteria for 'on the
1467 * alignment' is finding an alignment annotation on the alignment, matched on
1468 * calcId, label and sequenceRef.
1470 * A tooltip is also constructed that displays the source (calcId) and type
1471 * (label) of the annotations that can be added.
1474 * @param forSequences
1476 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1477 List<SequenceI> forSequences)
1479 menuItem.setEnabled(false);
1482 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1483 * Using TreeMap means calcIds are shown in alphabetical order.
1485 SortedMap<String, String> tipEntries = new TreeMap<>();
1486 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1487 AlignmentI al = this.ap.av.getAlignment();
1488 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1490 if (!candidates.isEmpty())
1492 StringBuilder tooltip = new StringBuilder(64);
1493 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1496 * Found annotations that could be added. Enable the menu item, and
1497 * configure its tooltip and action.
1499 menuItem.setEnabled(true);
1500 for (String calcId : tipEntries.keySet())
1502 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1504 String tooltipText = JvSwingUtils.wrapTooltip(true,
1505 tooltip.toString());
1506 menuItem.setToolTipText(tooltipText);
1508 menuItem.addActionListener(new ActionListener()
1511 public void actionPerformed(ActionEvent e)
1513 addReferenceAnnotations_actionPerformed(candidates);
1520 * Add annotations to the sequences and to the alignment.
1523 * a map whose keys are sequences on the alignment, and values a list
1524 * of annotations to add to each sequence
1526 protected void addReferenceAnnotations_actionPerformed(
1527 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1529 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1530 final AlignmentI alignment = this.ap.getAlignment();
1531 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1536 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1538 if (!ap.av.getAlignment().hasSeqrep())
1540 // initialise the display flags so the user sees something happen
1541 ap.av.setDisplayReferenceSeq(true);
1542 ap.av.setColourByReferenceSeq(true);
1543 ap.av.getAlignment().setSeqrep(sequence);
1547 if (ap.av.getAlignment().getSeqrep() == sequence)
1549 ap.av.getAlignment().setSeqrep(null);
1553 ap.av.getAlignment().setSeqrep(sequence);
1559 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1562 HiddenColumns hidden = new HiddenColumns();
1563 BitSet inserts = new BitSet(), mask = new BitSet();
1565 // set mask to preserve existing hidden columns outside selected group
1566 if (ap.av.hasHiddenColumns())
1568 ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
1571 boolean markedPopup = false;
1572 // mark inserts in current selection
1573 if (ap.av.getSelectionGroup() != null)
1575 // mark just the columns in the selection group to be hidden
1576 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1577 ap.av.getSelectionGroup().getEndRes() + 1);
1579 // and clear that part of the mask
1580 mask.andNot(inserts);
1582 // now clear columns without gaps
1583 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1589 inserts.and(sq.getInsertionsAsBits());
1594 // initially, mark all columns to be hidden
1595 inserts.set(0, ap.av.getAlignment().getWidth());
1597 // and clear out old hidden regions completely
1601 // now mark for sequence under popup if we haven't already done it
1602 if (!markedPopup && sequence != null)
1604 inserts.and(sequence.getInsertionsAsBits());
1607 // finally, preserve hidden regions outside selection
1610 // and set hidden columns accordingly
1611 hidden.hideMarkedBits(inserts);
1613 ap.av.getAlignment().setHiddenColumns(hidden);
1617 protected void sequenceSelectionDetails_actionPerformed()
1619 createSequenceDetailsReport(ap.av.getSequenceSelection());
1622 protected void sequenceDetails_actionPerformed()
1624 createSequenceDetailsReport(new SequenceI[] { sequence });
1627 public void createSequenceDetailsReport(SequenceI[] sequences)
1629 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1630 StringBuilder contents = new StringBuilder(128);
1631 for (SequenceI seq : sequences)
1633 contents.append("<p><h2>" + MessageManager.formatMessage(
1634 "label.create_sequence_details_report_annotation_for",
1636 { seq.getDisplayId(true) }) + "</h2></p><p>");
1637 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1638 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1639 contents.append("</p>");
1641 cap.setText("<html>" + contents.toString() + "</html>");
1643 Desktop.addInternalFrame(cap,
1644 MessageManager.formatMessage("label.sequence_details_for",
1645 (sequences.length == 1 ? new Object[]
1646 { sequences[0].getDisplayId(true) }
1649 .getString("label.selection") })),
1654 protected void showNonconserved_actionPerformed()
1656 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1661 * call to refresh view after settings change
1665 ap.updateAnnotation();
1666 // removed paintAlignment(true) here:
1667 // updateAnnotation calls paintAlignment already, so don't need to call
1670 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1674 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1675 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1685 public void abovePIDColour_actionPerformed(boolean selected)
1687 SequenceGroup sg = getGroup();
1695 sg.cs.setConsensus(AAFrequency.calculate(
1696 sg.getSequences(ap.av.getHiddenRepSequences()),
1697 sg.getStartRes(), sg.getEndRes() + 1));
1699 int threshold = SliderPanel.setPIDSliderSource(ap,
1700 sg.getGroupColourScheme(), getGroup().getName());
1702 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1704 SliderPanel.showPIDSlider();
1707 // remove PIDColouring
1709 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1710 SliderPanel.hidePIDSlider();
1712 modifyPID.setEnabled(selected);
1718 * Open a panel where the user can choose which types of sequence annotation
1723 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1725 // todo correct way to guard against opening a duplicate panel?
1726 new AnnotationChooser(ap);
1735 public void conservationMenuItem_actionPerformed(boolean selected)
1737 SequenceGroup sg = getGroup();
1745 // JBPNote: Conservation name shouldn't be i18n translated
1746 Conservation c = new Conservation("Group",
1747 sg.getSequences(ap.av.getHiddenRepSequences()),
1748 sg.getStartRes(), sg.getEndRes() + 1);
1751 c.verdict(false, ap.av.getConsPercGaps());
1752 sg.cs.setConservation(c);
1754 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1756 SliderPanel.showConservationSlider();
1759 // remove ConservationColouring
1761 sg.cs.setConservation(null);
1762 SliderPanel.hideConservationSlider();
1764 modifyConservation.setEnabled(selected);
1775 protected void groupName_actionPerformed()
1778 SequenceGroup sg = getGroup();
1779 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1780 sg.getDescription(),
1781 " " + MessageManager.getString("label.group_name") + " ",
1782 MessageManager.getString("label.group_description") + " ",
1783 MessageManager.getString("label.edit_group_name_description"),
1791 sg.setName(dialog.getName());
1792 sg.setDescription(dialog.getDescription());
1797 * Get selection group - adding it to the alignment if necessary.
1799 * @return sequence group to operate on
1801 SequenceGroup getGroup()
1803 SequenceGroup sg = ap.av.getSelectionGroup();
1804 // this method won't add a new group if it already exists
1807 ap.av.getAlignment().addGroup(sg);
1819 void sequenceName_actionPerformed()
1821 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1822 sequence.getDescription(),
1823 " " + MessageManager.getString("label.sequence_name")
1825 MessageManager.getString("label.sequence_description") + " ",
1826 MessageManager.getString(
1827 "label.edit_sequence_name_description"),
1835 if (dialog.getName() != null)
1837 if (dialog.getName().indexOf(" ") > -1)
1839 JvOptionPane.showMessageDialog(ap,
1841 .getString("label.spaces_converted_to_backslashes"),
1843 .getString("label.no_spaces_allowed_sequence_name"),
1844 JvOptionPane.WARNING_MESSAGE);
1847 sequence.setName(dialog.getName().replace(' ', '_'));
1848 ap.paintAlignment(false, false);
1851 sequence.setDescription(dialog.getDescription());
1853 ap.av.firePropertyChange("alignment", null,
1854 ap.av.getAlignment().getSequences());
1864 void unGroupMenuItem_actionPerformed()
1866 SequenceGroup sg = ap.av.getSelectionGroup();
1867 ap.av.getAlignment().deleteGroup(sg);
1868 ap.av.setSelectionGroup(null);
1872 void createGroupMenuItem_actionPerformed()
1874 getGroup(); // implicitly creates group - note - should apply defaults / use
1875 // standard alignment window logic for this
1885 protected void outline_actionPerformed()
1887 SequenceGroup sg = getGroup();
1888 Color col = JColorChooser.showDialog(this,
1889 MessageManager.getString("label.select_outline_colour"),
1894 sg.setOutlineColour(col);
1906 public void showBoxes_actionPerformed()
1908 getGroup().setDisplayBoxes(showBoxes.isSelected());
1918 public void showText_actionPerformed()
1920 getGroup().setDisplayText(showText.isSelected());
1930 public void showColourText_actionPerformed()
1932 getGroup().setColourText(showColourText.isSelected());
1936 public void showLink(String url)
1940 jalview.util.BrowserLauncher.openURL(url);
1941 } catch (Exception ex)
1943 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1944 MessageManager.getString("label.web_browser_not_found_unix"),
1945 MessageManager.getString("label.web_browser_not_found"),
1946 JvOptionPane.WARNING_MESSAGE);
1948 ex.printStackTrace();
1952 void hideSequences(boolean representGroup)
1954 ap.av.hideSequences(sequence, representGroup);
1957 public void copy_actionPerformed()
1959 ap.alignFrame.copy_actionPerformed(null);
1962 public void cut_actionPerformed()
1964 ap.alignFrame.cut_actionPerformed(null);
1967 void changeCase(ActionEvent e)
1969 Object source = e.getSource();
1970 SequenceGroup sg = ap.av.getSelectionGroup();
1974 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1975 sg.getStartRes(), sg.getEndRes() + 1);
1980 if (source == toggle)
1982 description = MessageManager.getString("label.toggle_case");
1983 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1985 else if (source == upperCase)
1987 description = MessageManager.getString("label.to_upper_case");
1988 caseChange = ChangeCaseCommand.TO_UPPER;
1992 description = MessageManager.getString("label.to_lower_case");
1993 caseChange = ChangeCaseCommand.TO_LOWER;
1996 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1997 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1998 startEnd, caseChange);
2000 ap.alignFrame.addHistoryItem(caseCommand);
2002 ap.av.firePropertyChange("alignment", null,
2003 ap.av.getAlignment().getSequences());
2008 public void outputText_actionPerformed(ActionEvent e)
2010 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2011 cap.setForInput(null);
2012 Desktop.addInternalFrame(cap, MessageManager
2013 .formatMessage("label.alignment_output_command", new Object[]
2014 { e.getActionCommand() }), 600, 500);
2016 String[] omitHidden = null;
2018 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2019 // or we simply trust the user wants
2020 // wysiwig behaviour
2022 FileFormatI fileFormat = FileFormats.getInstance()
2023 .forName(e.getActionCommand());
2025 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2028 public void sequenceFeature_actionPerformed()
2030 SequenceGroup sg = ap.av.getSelectionGroup();
2036 List<SequenceI> seqs = new ArrayList<>();
2037 List<SequenceFeature> features = new ArrayList<>();
2040 * assemble dataset sequences, and template new sequence features,
2041 * for the amend features dialog
2043 int gSize = sg.getSize();
2044 for (int i = 0; i < gSize; i++)
2046 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2047 int end = sg.findEndRes(sg.getSequenceAt(i));
2050 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2051 features.add(new SequenceFeature(null, null, start, end, null));
2056 * an entirely gapped region will generate empty lists of sequence / features
2058 if (!seqs.isEmpty())
2060 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2061 .amendFeatures(seqs, features, true, ap))
2063 ap.alignFrame.setShowSeqFeatures(true);
2064 ap.av.setSearchResults(null); // clear highlighting
2065 ap.repaint(); // draw new/amended features
2070 public void textColour_actionPerformed()
2072 SequenceGroup sg = getGroup();
2075 new TextColourChooser().chooseColour(ap, sg);
2079 public void colourByStructure(String pdbid)
2081 Annotation[] anots = ap.av.getStructureSelectionManager()
2082 .colourSequenceFromStructure(sequence, pdbid);
2084 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2085 "Coloured by " + pdbid, anots);
2087 ap.av.getAlignment().addAnnotation(an);
2088 an.createSequenceMapping(sequence, 0, true);
2089 // an.adjustForAlignment();
2090 ap.av.getAlignment().setAnnotationIndex(an, 0);
2092 ap.adjustAnnotationHeight();
2094 sequence.addAlignmentAnnotation(an);
2098 public void editSequence_actionPerformed(ActionEvent actionEvent)
2100 SequenceGroup sg = ap.av.getSelectionGroup();
2104 if (sequence == null)
2106 sequence = sg.getSequenceAt(0);
2109 EditNameDialog dialog = new EditNameDialog(
2110 sequence.getSequenceAsString(sg.getStartRes(),
2111 sg.getEndRes() + 1),
2112 null, MessageManager.getString("label.edit_sequence"), null,
2113 MessageManager.getString("label.edit_sequence"),
2118 EditCommand editCommand = new EditCommand(
2119 MessageManager.getString("label.edit_sequences"),
2121 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2122 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2123 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2125 ap.alignFrame.addHistoryItem(editCommand);
2127 ap.av.firePropertyChange("alignment", null,
2128 ap.av.getAlignment().getSequences());
2134 * Action on user selecting an item from the colour menu (that does not have
2135 * its bespoke action handler)
2140 public void changeColour_actionPerformed(String colourSchemeName)
2142 SequenceGroup sg = getGroup();
2144 * switch to the chosen colour scheme (or null for None)
2146 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2147 .getColourScheme(colourSchemeName, sg,
2148 ap.av.getHiddenRepSequences());
2149 sg.setColourScheme(colourScheme);
2150 if (colourScheme instanceof Blosum62ColourScheme
2151 || colourScheme instanceof PIDColourScheme)
2153 sg.cs.setConsensus(AAFrequency.calculate(
2154 sg.getSequences(ap.av.getHiddenRepSequences()),
2155 sg.getStartRes(), sg.getEndRes() + 1));