2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.gui.ColourMenuHelper.ColourChangeListener;
41 import jalview.io.FileFormatI;
42 import jalview.io.FileFormats;
43 import jalview.io.FormatAdapter;
44 import jalview.io.SequenceAnnotationReport;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemes;
48 import jalview.schemes.PIDColourScheme;
49 import jalview.util.GroupUrlLink;
50 import jalview.util.GroupUrlLink.UrlStringTooLongException;
51 import jalview.util.MessageManager;
52 import jalview.util.UrlLink;
54 import java.awt.Color;
55 import java.awt.event.ActionEvent;
56 import java.awt.event.ActionListener;
57 import java.util.ArrayList;
58 import java.util.Arrays;
59 import java.util.BitSet;
60 import java.util.Collection;
61 import java.util.Collections;
62 import java.util.Hashtable;
63 import java.util.LinkedHashMap;
64 import java.util.List;
66 import java.util.SortedMap;
67 import java.util.TreeMap;
68 import java.util.Vector;
70 import javax.swing.JCheckBoxMenuItem;
71 import javax.swing.JColorChooser;
72 import javax.swing.JMenu;
73 import javax.swing.JMenuItem;
74 import javax.swing.JPopupMenu;
80 * @version $Revision: 1.118 $
82 public class PopupMenu extends JPopupMenu implements ColourChangeListener
84 JMenu groupMenu = new JMenu();
86 JMenuItem groupName = new JMenuItem();
88 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
90 protected JMenuItem modifyPID = new JMenuItem();
92 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
94 protected JMenuItem modifyConservation = new JMenuItem();
98 JMenu sequenceMenu = new JMenu();
100 JMenuItem sequenceName = new JMenuItem();
102 JMenuItem sequenceDetails = new JMenuItem();
104 JMenuItem sequenceSelDetails = new JMenuItem();
106 JMenuItem makeReferenceSeq = new JMenuItem();
108 JMenuItem chooseAnnotations = new JMenuItem();
112 JMenuItem createGroupMenuItem = new JMenuItem();
114 JMenuItem unGroupMenuItem = new JMenuItem();
116 JMenuItem outline = new JMenuItem();
118 JMenu colourMenu = new JMenu();
120 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
122 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
124 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
126 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
128 JMenu editMenu = new JMenu();
130 JMenuItem cut = new JMenuItem();
132 JMenuItem copy = new JMenuItem();
134 JMenuItem upperCase = new JMenuItem();
136 JMenuItem lowerCase = new JMenuItem();
138 JMenuItem toggle = new JMenuItem();
140 JMenu pdbMenu = new JMenu();
142 JMenu outputMenu = new JMenu();
144 JMenu seqShowAnnotationsMenu = new JMenu();
146 JMenu seqHideAnnotationsMenu = new JMenu();
148 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
149 MessageManager.getString("label.add_reference_annotations"));
151 JMenu groupShowAnnotationsMenu = new JMenu();
153 JMenu groupHideAnnotationsMenu = new JMenu();
155 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
156 MessageManager.getString("label.add_reference_annotations"));
158 JMenuItem sequenceFeature = new JMenuItem();
160 JMenuItem textColour = new JMenuItem();
162 JMenu jMenu1 = new JMenu();
164 JMenuItem pdbStructureDialog = new JMenuItem();
166 JMenu rnaStructureMenu = new JMenu();
168 JMenuItem editSequence = new JMenuItem();
170 JMenu groupLinksMenu;
172 JMenuItem hideInsertions = new JMenuItem();
175 * Creates a new PopupMenu object.
180 * non-positional features (for seq not null), or positional features
181 * at residue (for seq equal to null)
183 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
184 List<SequenceFeature> features)
186 this(ap, seq, features, null);
194 * the sequence under the cursor if in the Id panel, null if in the
197 * non-positional features if in the Id panel, features at the
198 * clicked residue if in the sequence panel
201 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
202 List<SequenceFeature> features, List<String> groupLinks)
204 // /////////////////////////////////////////////////////////
205 // If this is activated from the sequence panel, the user may want to
206 // edit or annotate a particular residue. Therefore display the residue menu
208 // If from the IDPanel, we must display the sequence menu
209 // ////////////////////////////////////////////////////////
210 this.ap = alignPanel;
213 for (String ff : FileFormats.getInstance().getWritableFormats(true))
215 JMenuItem item = new JMenuItem(ff);
217 item.addActionListener(new ActionListener()
220 public void actionPerformed(ActionEvent e)
222 outputText_actionPerformed(e);
226 outputMenu.add(item);
230 * Build menus for annotation types that may be shown or hidden, and for
231 * 'reference annotations' that may be added to the alignment. First for the
232 * currently selected sequence (if there is one):
234 final List<SequenceI> selectedSequence = (seq == null
235 ? Collections.<SequenceI> emptyList()
236 : Arrays.asList(seq));
237 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
238 seqHideAnnotationsMenu, selectedSequence);
239 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
243 * And repeat for the current selection group (if there is one):
245 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
246 ? Collections.<SequenceI> emptyList()
247 : alignPanel.av.getSelectionGroup().getSequences());
248 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
249 groupHideAnnotationsMenu, selectedGroup);
250 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
256 } catch (Exception e)
264 sequenceMenu.setText(sequence.getName());
265 if (seq == alignPanel.av.getAlignment().getSeqrep())
267 makeReferenceSeq.setText(
268 MessageManager.getString("action.unmark_as_reference"));
272 makeReferenceSeq.setText(
273 MessageManager.getString("action.set_as_reference"));
276 if (!alignPanel.av.getAlignment().isNucleotide())
278 remove(rnaStructureMenu);
282 int origCount = rnaStructureMenu.getItemCount();
284 * add menu items to 2D-render any alignment or sequence secondary
285 * structure annotation
287 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
288 .getAlignmentAnnotation();
291 for (final AlignmentAnnotation aa : aas)
293 if (aa.isValidStruc() && aa.sequenceRef == null)
296 * valid alignment RNA secondary structure annotation
298 menuItem = new JMenuItem();
299 menuItem.setText(MessageManager.formatMessage(
300 "label.2d_rna_structure_line", new Object[]
302 menuItem.addActionListener(new ActionListener()
305 public void actionPerformed(ActionEvent e)
307 new AppVarna(seq, aa, alignPanel);
310 rnaStructureMenu.add(menuItem);
315 if (seq.getAnnotation() != null)
317 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
318 for (final AlignmentAnnotation aa : seqAnns)
320 if (aa.isValidStruc())
323 * valid sequence RNA secondary structure annotation
325 // TODO: make rnastrucF a bit more nice
326 menuItem = new JMenuItem();
327 menuItem.setText(MessageManager.formatMessage(
328 "label.2d_rna_sequence_name", new Object[]
330 menuItem.addActionListener(new ActionListener()
333 public void actionPerformed(ActionEvent e)
335 // TODO: VARNA does'nt print gaps in the sequence
336 new AppVarna(seq, aa, alignPanel);
339 rnaStructureMenu.add(menuItem);
343 if (rnaStructureMenu.getItemCount() == origCount)
345 remove(rnaStructureMenu);
349 menuItem = new JMenuItem(
350 MessageManager.getString("action.hide_sequences"));
351 menuItem.addActionListener(new ActionListener()
354 public void actionPerformed(ActionEvent e)
356 hideSequences(false);
361 if (alignPanel.av.getSelectionGroup() != null
362 && alignPanel.av.getSelectionGroup().getSize() > 1)
364 menuItem = new JMenuItem(MessageManager
365 .formatMessage("label.represent_group_with", new Object[]
367 menuItem.addActionListener(new ActionListener()
370 public void actionPerformed(ActionEvent e)
375 sequenceMenu.add(menuItem);
378 if (alignPanel.av.hasHiddenRows())
380 final int index = alignPanel.av.getAlignment().findIndex(seq);
382 if (alignPanel.av.adjustForHiddenSeqs(index)
383 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
385 menuItem = new JMenuItem(
386 MessageManager.getString("action.reveal_sequences"));
387 menuItem.addActionListener(new ActionListener()
390 public void actionPerformed(ActionEvent e)
392 alignPanel.av.showSequence(index);
393 if (alignPanel.overviewPanel != null)
395 alignPanel.overviewPanel.updateOverviewImage();
403 // for the case when no sequences are even visible
404 if (alignPanel.av.hasHiddenRows())
407 menuItem = new JMenuItem(
408 MessageManager.getString("action.reveal_all"));
409 menuItem.addActionListener(new ActionListener()
412 public void actionPerformed(ActionEvent e)
414 alignPanel.av.showAllHiddenSeqs();
415 if (alignPanel.overviewPanel != null)
417 alignPanel.overviewPanel.updateOverviewImage();
426 SequenceGroup sg = alignPanel.av.getSelectionGroup();
427 boolean isDefinedGroup = (sg != null)
428 ? alignPanel.av.getAlignment().getGroups().contains(sg)
431 if (sg != null && sg.getSize() > 0)
433 groupName.setText(MessageManager
434 .getString("label.edit_name_and_description_current_group"));
436 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
438 conservationMenuItem.setEnabled(!sg.isNucleotide());
442 if (sg.cs.conservationApplied())
444 conservationMenuItem.setSelected(true);
446 if (sg.cs.getThreshold() > 0)
448 abovePIDColour.setSelected(true);
451 modifyConservation.setEnabled(conservationMenuItem.isSelected());
452 modifyPID.setEnabled(abovePIDColour.isSelected());
453 displayNonconserved.setSelected(sg.getShowNonconserved());
454 showText.setSelected(sg.getDisplayText());
455 showColourText.setSelected(sg.getColourText());
456 showBoxes.setSelected(sg.getDisplayBoxes());
457 // add any groupURLs to the groupURL submenu and make it visible
458 if (groupLinks != null && groupLinks.size() > 0)
460 buildGroupURLMenu(sg, groupLinks);
462 // Add a 'show all structures' for the current selection
463 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
465 SequenceI sqass = null;
466 for (SequenceI sq : alignPanel.av.getSequenceSelection())
468 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
469 if (pes != null && pes.size() > 0)
471 reppdb.put(pes.get(0).getId(), pes.get(0));
472 for (PDBEntry pe : pes)
474 pdbe.put(pe.getId(), pe);
484 final PDBEntry[] pe = pdbe.values()
485 .toArray(new PDBEntry[pdbe.size()]),
486 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
487 final JMenuItem gpdbview, rpdbview;
492 groupMenu.setVisible(false);
493 editMenu.setVisible(false);
498 createGroupMenuItem.setVisible(true);
499 unGroupMenuItem.setVisible(false);
500 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
504 createGroupMenuItem.setVisible(false);
505 unGroupMenuItem.setVisible(true);
506 jMenu1.setText(MessageManager.getString("action.edit_group"));
511 sequenceMenu.setVisible(false);
512 pdbStructureDialog.setVisible(false);
513 rnaStructureMenu.setVisible(false);
516 addLinks(seq, features);
520 addFeatureDetails(features);
525 * Add a link to show feature details for each sequence feature
529 protected void addFeatureDetails(List<SequenceFeature> features)
531 if (features == null || features.isEmpty())
535 JMenu details = new JMenu(
536 MessageManager.getString("label.feature_details"));
539 for (final SequenceFeature sf : features)
541 int start = sf.getBegin();
542 int end = sf.getEnd();
546 desc = String.format("%s %d", sf.getType(), start);
550 desc = String.format("%s %d-%d", sf.getType(), start, end);
552 String description = sf.getDescription();
553 if (description != null)
555 if (description.length() <= 6)
557 desc = desc + " " + description;
561 desc = desc + " " + description.substring(0, 6) + "..";
564 if (sf.getFeatureGroup() != null)
566 desc = desc + " (" + sf.getFeatureGroup() + ")";
568 JMenuItem item = new JMenuItem(desc);
569 item.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
574 showFeatureDetails(sf);
582 * Opens a panel showing a text report of feature dteails
586 protected void showFeatureDetails(SequenceFeature sf)
588 CutAndPasteTransfer cap = new CutAndPasteTransfer();
589 cap.setText(sf.getDetailsReport());
590 Desktop.addInternalFrame(cap,
591 MessageManager.getString("label.feature_details"), 500, 500);
595 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
596 * When seq is not null, these are links for the sequence id, which may be to
597 * external web sites for the sequence accession, and/or links embedded in
598 * non-positional features. When seq is null, only links embedded in the
599 * provided features are added.
604 void addLinks(final SequenceI seq, List<SequenceFeature> features)
606 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
608 List<String> nlinks = null;
611 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
615 nlinks = new ArrayList<>();
618 if (features != null)
620 for (SequenceFeature sf : features)
622 if (sf.links != null)
624 for (String link : sf.links)
632 Map<String, List<String>> linkset = new LinkedHashMap<>();
634 for (String link : nlinks)
636 UrlLink urlLink = null;
639 urlLink = new UrlLink(link);
640 } catch (Exception foo)
642 Cache.log.error("Exception for URLLink '" + link + "'", foo);
646 if (!urlLink.isValid())
648 Cache.log.error(urlLink.getInvalidMessage());
652 urlLink.createLinksFromSeq(seq, linkset);
655 addshowLinks(linkMenu, linkset.values());
657 // only add link menu if it has entries
658 if (linkMenu.getItemCount() > 0)
660 if (sequence != null)
662 sequenceMenu.add(linkMenu);
672 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
673 * "All" is added first, followed by a separator. Then add any annotation
674 * types associated with the current selection. Separate menus are built for
675 * the selected sequence group (if any), and the selected sequence.
677 * Some annotation rows are always rendered together - these can be identified
678 * by a common graphGroup property > -1. Only one of each group will be marked
679 * as visible (to avoid duplication of the display). For such groups we add a
680 * composite type name, e.g.
682 * IUPredWS (Long), IUPredWS (Short)
686 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
687 List<SequenceI> forSequences)
689 showMenu.removeAll();
690 hideMenu.removeAll();
692 final List<String> all = Arrays
694 { MessageManager.getString("label.all") });
695 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
697 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
699 showMenu.addSeparator();
700 hideMenu.addSeparator();
702 final AlignmentAnnotation[] annotations = ap.getAlignment()
703 .getAlignmentAnnotation();
706 * Find shown/hidden annotations types, distinguished by source (calcId),
707 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
708 * the insertion order, which is the order of the annotations on the
711 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
712 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
713 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
714 AlignmentAnnotationUtils.asList(annotations), forSequences);
716 for (String calcId : hiddenTypes.keySet())
718 for (List<String> type : hiddenTypes.get(calcId))
720 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
724 // grey out 'show annotations' if none are hidden
725 showMenu.setEnabled(!hiddenTypes.isEmpty());
727 for (String calcId : shownTypes.keySet())
729 for (List<String> type : shownTypes.get(calcId))
731 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
735 // grey out 'hide annotations' if none are shown
736 hideMenu.setEnabled(!shownTypes.isEmpty());
740 * Returns a list of sequences - either the current selection group (if there
741 * is one), else the specified single sequence.
746 protected List<SequenceI> getSequenceScope(SequenceI seq)
748 List<SequenceI> forSequences = null;
749 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
750 if (selectionGroup != null && selectionGroup.getSize() > 0)
752 forSequences = selectionGroup.getSequences();
756 forSequences = seq == null ? Collections.<SequenceI> emptyList()
757 : Arrays.asList(seq);
763 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
766 * @param showOrHideMenu
768 * @param forSequences
769 * the sequences whose annotations may be shown or hidden
774 * if true this is a special label meaning 'All'
775 * @param actionIsShow
776 * if true, the select menu item action is to show the annotation
779 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
780 final List<SequenceI> forSequences, String calcId,
781 final List<String> types, final boolean allTypes,
782 final boolean actionIsShow)
784 String label = types.toString(); // [a, b, c]
785 label = label.substring(1, label.length() - 1); // a, b, c
786 final JMenuItem item = new JMenuItem(label);
787 item.setToolTipText(calcId);
788 item.addActionListener(new ActionListener()
791 public void actionPerformed(ActionEvent e)
793 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
794 types, forSequences, allTypes, actionIsShow);
798 showOrHideMenu.add(item);
801 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
804 // TODO: usability: thread off the generation of group url content so root
806 // sequence only URLs
807 // ID/regex match URLs
808 groupLinksMenu = new JMenu(
809 MessageManager.getString("action.group_link"));
810 // three types of url that might be created.
811 JMenu[] linkMenus = new JMenu[] { null,
812 new JMenu(MessageManager.getString("action.ids")),
813 new JMenu(MessageManager.getString("action.sequences")),
814 new JMenu(MessageManager.getString("action.ids_sequences")) };
816 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
817 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
818 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
819 for (int sq = 0; sq < seqs.length; sq++)
822 int start = seqs[sq].findPosition(sg.getStartRes()),
823 end = seqs[sq].findPosition(sg.getEndRes());
824 // just collect ids from dataset sequence
825 // TODO: check if IDs collected from selecton group intersects with the
826 // current selection, too
827 SequenceI sqi = seqs[sq];
828 while (sqi.getDatasetSequence() != null)
830 sqi = sqi.getDatasetSequence();
832 DBRefEntry[] dbr = sqi.getDBRefs();
833 if (dbr != null && dbr.length > 0)
835 for (int d = 0; d < dbr.length; d++)
837 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
838 Object[] sarray = commonDbrefs.get(src);
841 sarray = new Object[2];
842 sarray[0] = new int[] { 0 };
843 sarray[1] = new String[seqs.length];
845 commonDbrefs.put(src, sarray);
848 if (((String[]) sarray[1])[sq] == null)
850 if (!dbr[d].hasMap() || (dbr[d].getMap()
851 .locateMappedRange(start, end) != null))
853 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
854 ((int[]) sarray[0])[0]++;
860 // now create group links for all distinct ID/sequence sets.
861 boolean addMenu = false; // indicates if there are any group links to give
863 for (String link : groupLinks)
865 GroupUrlLink urlLink = null;
868 urlLink = new GroupUrlLink(link);
869 } catch (Exception foo)
871 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
875 if (!urlLink.isValid())
877 Cache.log.error(urlLink.getInvalidMessage());
880 final String label = urlLink.getLabel();
881 boolean usingNames = false;
882 // Now see which parts of the group apply for this URL
883 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
884 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
885 String[] seqstr, ids; // input to makeUrl
888 int numinput = ((int[]) idset[0])[0];
889 String[] allids = ((String[]) idset[1]);
890 seqstr = new String[numinput];
891 ids = new String[numinput];
892 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
894 if (allids[sq] != null)
896 ids[idcount] = allids[sq];
897 seqstr[idcount++] = idandseqs[1][sq];
903 // just use the id/seq set
904 seqstr = idandseqs[1];
908 // and try and make the groupURL!
910 Object[] urlset = null;
913 urlset = urlLink.makeUrlStubs(ids, seqstr,
914 "FromJalview" + System.currentTimeMillis(), false);
915 } catch (UrlStringTooLongException e)
920 int type = urlLink.getGroupURLType() & 3;
921 // first two bits ofurlLink type bitfield are sequenceids and sequences
922 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
923 addshowLink(linkMenus[type],
924 label + (((type & 1) == 1)
925 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
933 groupLinksMenu = new JMenu(
934 MessageManager.getString("action.group_link"));
935 for (int m = 0; m < linkMenus.length; m++)
937 if (linkMenus[m] != null
938 && linkMenus[m].getMenuComponentCount() > 0)
940 groupLinksMenu.add(linkMenus[m]);
944 groupMenu.add(groupLinksMenu);
948 private void addshowLinks(JMenu linkMenu,
949 Collection<List<String>> linkset)
951 for (List<String> linkstrset : linkset)
953 // split linkstr into label and url
954 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
959 * add a show URL menu item to the given linkMenu
963 * - menu label string
967 private void addshowLink(JMenu linkMenu, String label, final String url)
969 JMenuItem item = new JMenuItem(label);
970 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
973 item.addActionListener(new ActionListener()
976 public void actionPerformed(ActionEvent e)
978 new Thread(new Runnable()
995 * add a late bound groupURL item to the given linkMenu
999 * - menu label string
1000 * @param urlgenerator
1001 * GroupURLLink used to generate URL
1003 * Object array returned from the makeUrlStubs function.
1005 private void addshowLink(JMenu linkMenu, String label,
1006 final GroupUrlLink urlgenerator, final Object[] urlstub)
1008 JMenuItem item = new JMenuItem(label);
1009 item.setToolTipText(MessageManager
1010 .formatMessage("label.open_url_seqs_param", new Object[]
1011 { urlgenerator.getUrl_prefix(),
1012 urlgenerator.getNumberInvolved(urlstub) }));
1013 // TODO: put in info about what is being sent.
1014 item.addActionListener(new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1019 new Thread(new Runnable()
1027 showLink(urlgenerator.constructFrom(urlstub));
1028 } catch (UrlStringTooLongException e2)
1046 private void jbInit() throws Exception
1048 groupMenu.setText(MessageManager.getString("label.selection"));
1049 groupName.setText(MessageManager.getString("label.name"));
1050 groupName.addActionListener(new ActionListener()
1053 public void actionPerformed(ActionEvent e)
1055 groupName_actionPerformed();
1058 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1059 sequenceName.setText(
1060 MessageManager.getString("label.edit_name_description"));
1061 sequenceName.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 sequenceName_actionPerformed();
1070 .setText(MessageManager.getString("action.choose_annotations"));
1071 chooseAnnotations.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 chooseAnnotations_actionPerformed(e);
1080 .setText(MessageManager.getString("label.sequence_details"));
1081 sequenceDetails.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 sequenceDetails_actionPerformed();
1090 .setText(MessageManager.getString("label.sequence_details"));
1091 sequenceSelDetails.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 sequenceSelectionDetails_actionPerformed();
1101 .setText(MessageManager.getString("action.remove_group"));
1102 unGroupMenuItem.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 unGroupMenuItem_actionPerformed();
1111 .setText(MessageManager.getString("action.create_group"));
1112 createGroupMenuItem.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 createGroupMenuItem_actionPerformed();
1121 outline.setText(MessageManager.getString("action.border_colour"));
1122 outline.addActionListener(new ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 outline_actionPerformed();
1130 showBoxes.setText(MessageManager.getString("action.boxes"));
1131 showBoxes.setState(true);
1132 showBoxes.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 showBoxes_actionPerformed();
1140 showText.setText(MessageManager.getString("action.text"));
1141 showText.setState(true);
1142 showText.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 showText_actionPerformed();
1150 showColourText.setText(MessageManager.getString("label.colour_text"));
1151 showColourText.addActionListener(new ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 showColourText_actionPerformed();
1160 .setText(MessageManager.getString("label.show_non_conserved"));
1161 displayNonconserved.setState(true);
1162 displayNonconserved.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 showNonconserved_actionPerformed();
1170 editMenu.setText(MessageManager.getString("action.edit"));
1171 cut.setText(MessageManager.getString("action.cut"));
1172 cut.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 cut_actionPerformed();
1180 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1181 upperCase.addActionListener(new ActionListener()
1184 public void actionPerformed(ActionEvent e)
1189 copy.setText(MessageManager.getString("action.copy"));
1190 copy.addActionListener(new ActionListener()
1193 public void actionPerformed(ActionEvent e)
1195 copy_actionPerformed();
1198 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1199 lowerCase.addActionListener(new ActionListener()
1202 public void actionPerformed(ActionEvent e)
1207 toggle.setText(MessageManager.getString("label.toggle_case"));
1208 toggle.addActionListener(new ActionListener()
1211 public void actionPerformed(ActionEvent e)
1217 MessageManager.getString("label.out_to_textbox") + "...");
1218 seqShowAnnotationsMenu
1219 .setText(MessageManager.getString("label.show_annotations"));
1220 seqHideAnnotationsMenu
1221 .setText(MessageManager.getString("label.hide_annotations"));
1222 groupShowAnnotationsMenu
1223 .setText(MessageManager.getString("label.show_annotations"));
1224 groupHideAnnotationsMenu
1225 .setText(MessageManager.getString("label.hide_annotations"));
1226 sequenceFeature.setText(
1227 MessageManager.getString("label.create_sequence_feature"));
1228 sequenceFeature.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 sequenceFeature_actionPerformed();
1236 jMenu1.setText(MessageManager.getString("label.group"));
1237 pdbStructureDialog.setText(
1238 MessageManager.getString("label.show_pdbstruct_dialog"));
1239 pdbStructureDialog.addActionListener(new ActionListener()
1242 public void actionPerformed(ActionEvent actionEvent)
1244 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1245 if (ap.av.getSelectionGroup() != null)
1247 selectedSeqs = ap.av.getSequenceSelection();
1249 new StructureChooser(selectedSeqs, sequence, ap);
1254 .setText(MessageManager.getString("label.view_rna_structure"));
1256 // colStructureMenu.setText("Colour By Structure");
1257 editSequence.setText(
1258 MessageManager.getString("label.edit_sequence") + "...");
1259 editSequence.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent actionEvent)
1264 editSequence_actionPerformed(actionEvent);
1267 makeReferenceSeq.setText(
1268 MessageManager.getString("label.mark_as_representative"));
1269 makeReferenceSeq.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent actionEvent)
1275 makeReferenceSeq_actionPerformed(actionEvent);
1280 .setText(MessageManager.getString("label.hide_insertions"));
1281 hideInsertions.addActionListener(new ActionListener()
1285 public void actionPerformed(ActionEvent e)
1287 hideInsertions_actionPerformed(e);
1291 groupMenu.add(sequenceSelDetails);
1294 add(rnaStructureMenu);
1295 add(pdbStructureDialog);
1296 if (sequence != null)
1298 add(hideInsertions);
1300 // annotations configuration panel suppressed for now
1301 // groupMenu.add(chooseAnnotations);
1304 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1305 * (if a selection group is in force).
1307 sequenceMenu.add(seqShowAnnotationsMenu);
1308 sequenceMenu.add(seqHideAnnotationsMenu);
1309 sequenceMenu.add(seqAddReferenceAnnotations);
1310 groupMenu.add(groupShowAnnotationsMenu);
1311 groupMenu.add(groupHideAnnotationsMenu);
1312 groupMenu.add(groupAddReferenceAnnotations);
1313 groupMenu.add(editMenu);
1314 groupMenu.add(outputMenu);
1315 groupMenu.add(sequenceFeature);
1316 groupMenu.add(createGroupMenuItem);
1317 groupMenu.add(unGroupMenuItem);
1318 groupMenu.add(jMenu1);
1319 sequenceMenu.add(sequenceName);
1320 sequenceMenu.add(sequenceDetails);
1321 sequenceMenu.add(makeReferenceSeq);
1328 editMenu.add(editSequence);
1329 editMenu.add(upperCase);
1330 editMenu.add(lowerCase);
1331 editMenu.add(toggle);
1332 // JBPNote: These shouldn't be added here - should appear in a generic
1333 // 'apply web service to this sequence menu'
1334 // pdbMenu.add(RNAFold);
1335 // pdbMenu.add(ContraFold);
1336 jMenu1.add(groupName);
1337 jMenu1.add(colourMenu);
1338 jMenu1.add(showBoxes);
1339 jMenu1.add(showText);
1340 jMenu1.add(showColourText);
1341 jMenu1.add(outline);
1342 jMenu1.add(displayNonconserved);
1346 * Constructs the entries for the colour menu
1348 protected void initColourMenu()
1350 colourMenu.setText(MessageManager.getString("label.group_colour"));
1351 textColour.setText(MessageManager.getString("label.text_colour"));
1352 textColour.addActionListener(new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 textColour_actionPerformed();
1361 abovePIDColour.setText(
1362 MessageManager.getString("label.above_identity_threshold"));
1363 abovePIDColour.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1373 MessageManager.getString("label.modify_identity_threshold"));
1374 modifyPID.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 modifyPID_actionPerformed();
1383 conservationMenuItem
1384 .setText(MessageManager.getString("action.by_conservation"));
1385 conservationMenuItem.addActionListener(new ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 conservationMenuItem_actionPerformed(
1391 conservationMenuItem.isSelected());
1395 modifyConservation.setText(MessageManager
1396 .getString("label.modify_conservation_threshold"));
1397 modifyConservation.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 modifyConservation_actionPerformed();
1408 * Builds the group colour sub-menu, including any user-defined colours which
1409 * were loaded at startup or during the Jalview session
1411 protected void buildColourMenu()
1413 SequenceGroup sg = ap.av.getSelectionGroup();
1417 * popup menu with no sequence group scope
1421 colourMenu.removeAll();
1422 colourMenu.add(textColour);
1423 colourMenu.addSeparator();
1425 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1427 colourMenu.addSeparator();
1428 colourMenu.add(conservationMenuItem);
1429 colourMenu.add(modifyConservation);
1430 colourMenu.add(abovePIDColour);
1431 colourMenu.add(modifyPID);
1434 protected void modifyConservation_actionPerformed()
1436 SequenceGroup sg = getGroup();
1439 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1440 SliderPanel.showConservationSlider();
1444 protected void modifyPID_actionPerformed()
1446 SequenceGroup sg = getGroup();
1449 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1451 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1452 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1453 SliderPanel.showPIDSlider();
1458 * Check for any annotations on the underlying dataset sequences (for the
1459 * current selection group) which are not 'on the alignment'.If any are found,
1460 * enable the option to add them to the alignment. The criteria for 'on the
1461 * alignment' is finding an alignment annotation on the alignment, matched on
1462 * calcId, label and sequenceRef.
1464 * A tooltip is also constructed that displays the source (calcId) and type
1465 * (label) of the annotations that can be added.
1468 * @param forSequences
1470 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1471 List<SequenceI> forSequences)
1473 menuItem.setEnabled(false);
1476 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1477 * Using TreeMap means calcIds are shown in alphabetical order.
1479 SortedMap<String, String> tipEntries = new TreeMap<>();
1480 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1481 AlignmentI al = this.ap.av.getAlignment();
1482 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1484 if (!candidates.isEmpty())
1486 StringBuilder tooltip = new StringBuilder(64);
1487 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1490 * Found annotations that could be added. Enable the menu item, and
1491 * configure its tooltip and action.
1493 menuItem.setEnabled(true);
1494 for (String calcId : tipEntries.keySet())
1496 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1498 String tooltipText = JvSwingUtils.wrapTooltip(true,
1499 tooltip.toString());
1500 menuItem.setToolTipText(tooltipText);
1502 menuItem.addActionListener(new ActionListener()
1505 public void actionPerformed(ActionEvent e)
1507 addReferenceAnnotations_actionPerformed(candidates);
1514 * Add annotations to the sequences and to the alignment.
1517 * a map whose keys are sequences on the alignment, and values a list
1518 * of annotations to add to each sequence
1520 protected void addReferenceAnnotations_actionPerformed(
1521 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1523 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1524 final AlignmentI alignment = this.ap.getAlignment();
1525 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1530 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1532 if (!ap.av.getAlignment().hasSeqrep())
1534 // initialise the display flags so the user sees something happen
1535 ap.av.setDisplayReferenceSeq(true);
1536 ap.av.setColourByReferenceSeq(true);
1537 ap.av.getAlignment().setSeqrep(sequence);
1541 if (ap.av.getAlignment().getSeqrep() == sequence)
1543 ap.av.getAlignment().setSeqrep(null);
1547 ap.av.getAlignment().setSeqrep(sequence);
1553 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1556 HiddenColumns hidden = new HiddenColumns();
1557 BitSet inserts = new BitSet(), mask = new BitSet();
1559 // set mask to preserve existing hidden columns outside selected group
1560 if (ap.av.hasHiddenColumns())
1562 ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask);
1565 boolean markedPopup = false;
1566 // mark inserts in current selection
1567 if (ap.av.getSelectionGroup() != null)
1569 // mark just the columns in the selection group to be hidden
1570 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1571 ap.av.getSelectionGroup().getEndRes() + 1);
1573 // and clear that part of the mask
1574 mask.andNot(inserts);
1576 // now clear columns without gaps
1577 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1583 inserts.and(sq.getInsertionsAsBits());
1588 // initially, mark all columns to be hidden
1589 inserts.set(0, ap.av.getAlignment().getWidth());
1591 // and clear out old hidden regions completely
1595 // now mark for sequence under popup if we haven't already done it
1596 if (!markedPopup && sequence != null)
1598 inserts.and(sequence.getInsertionsAsBits());
1601 // finally, preserve hidden regions outside selection
1604 // and set hidden columns accordingly
1605 hidden.hideMarkedBits(inserts);
1607 ap.av.getAlignment().setHiddenColumns(hidden);
1611 protected void sequenceSelectionDetails_actionPerformed()
1613 createSequenceDetailsReport(ap.av.getSequenceSelection());
1616 protected void sequenceDetails_actionPerformed()
1618 createSequenceDetailsReport(new SequenceI[] { sequence });
1621 public void createSequenceDetailsReport(SequenceI[] sequences)
1623 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1624 StringBuilder contents = new StringBuilder(128);
1625 for (SequenceI seq : sequences)
1627 contents.append("<p><h2>" + MessageManager.formatMessage(
1628 "label.create_sequence_details_report_annotation_for",
1630 { seq.getDisplayId(true) }) + "</h2></p><p>");
1631 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1632 contents, seq, true, true,
1633 (ap.getSeqPanel().seqCanvas.fr != null)
1634 ? ap.getSeqPanel().seqCanvas.fr.getMinMax()
1636 contents.append("</p>");
1638 cap.setText("<html>" + contents.toString() + "</html>");
1640 Desktop.addInternalFrame(cap,
1641 MessageManager.formatMessage("label.sequence_details_for",
1642 (sequences.length == 1 ? new Object[]
1643 { sequences[0].getDisplayId(true) }
1646 .getString("label.selection") })),
1651 protected void showNonconserved_actionPerformed()
1653 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1658 * call to refresh view after settings change
1662 ap.updateAnnotation();
1663 // removed paintAlignment(true) here:
1664 // updateAnnotation calls paintAlignment already, so don't need to call
1667 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1671 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1672 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1682 public void abovePIDColour_actionPerformed(boolean selected)
1684 SequenceGroup sg = getGroup();
1692 sg.cs.setConsensus(AAFrequency.calculate(
1693 sg.getSequences(ap.av.getHiddenRepSequences()),
1694 sg.getStartRes(), sg.getEndRes() + 1));
1696 int threshold = SliderPanel.setPIDSliderSource(ap,
1697 sg.getGroupColourScheme(), getGroup().getName());
1699 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1701 SliderPanel.showPIDSlider();
1704 // remove PIDColouring
1706 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1707 SliderPanel.hidePIDSlider();
1709 modifyPID.setEnabled(selected);
1715 * Open a panel where the user can choose which types of sequence annotation
1720 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1722 // todo correct way to guard against opening a duplicate panel?
1723 new AnnotationChooser(ap);
1732 public void conservationMenuItem_actionPerformed(boolean selected)
1734 SequenceGroup sg = getGroup();
1742 // JBPNote: Conservation name shouldn't be i18n translated
1743 Conservation c = new Conservation("Group",
1744 sg.getSequences(ap.av.getHiddenRepSequences()),
1745 sg.getStartRes(), sg.getEndRes() + 1);
1748 c.verdict(false, ap.av.getConsPercGaps());
1749 sg.cs.setConservation(c);
1751 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1753 SliderPanel.showConservationSlider();
1756 // remove ConservationColouring
1758 sg.cs.setConservation(null);
1759 SliderPanel.hideConservationSlider();
1761 modifyConservation.setEnabled(selected);
1772 protected void groupName_actionPerformed()
1775 SequenceGroup sg = getGroup();
1776 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1777 sg.getDescription(),
1778 " " + MessageManager.getString("label.group_name") + " ",
1779 MessageManager.getString("label.group_description") + " ",
1780 MessageManager.getString("label.edit_group_name_description"),
1788 sg.setName(dialog.getName());
1789 sg.setDescription(dialog.getDescription());
1794 * Get selection group - adding it to the alignment if necessary.
1796 * @return sequence group to operate on
1798 SequenceGroup getGroup()
1800 SequenceGroup sg = ap.av.getSelectionGroup();
1801 // this method won't add a new group if it already exists
1804 ap.av.getAlignment().addGroup(sg);
1816 void sequenceName_actionPerformed()
1818 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1819 sequence.getDescription(),
1820 " " + MessageManager.getString("label.sequence_name")
1822 MessageManager.getString("label.sequence_description") + " ",
1823 MessageManager.getString(
1824 "label.edit_sequence_name_description"),
1832 if (dialog.getName() != null)
1834 if (dialog.getName().indexOf(" ") > -1)
1836 JvOptionPane.showMessageDialog(ap,
1838 .getString("label.spaces_converted_to_backslashes"),
1840 .getString("label.no_spaces_allowed_sequence_name"),
1841 JvOptionPane.WARNING_MESSAGE);
1844 sequence.setName(dialog.getName().replace(' ', '_'));
1845 ap.paintAlignment(false);
1848 sequence.setDescription(dialog.getDescription());
1850 ap.av.firePropertyChange("alignment", null,
1851 ap.av.getAlignment().getSequences());
1861 void unGroupMenuItem_actionPerformed()
1863 SequenceGroup sg = ap.av.getSelectionGroup();
1864 ap.av.getAlignment().deleteGroup(sg);
1865 ap.av.setSelectionGroup(null);
1869 void createGroupMenuItem_actionPerformed()
1871 getGroup(); // implicitly creates group - note - should apply defaults / use
1872 // standard alignment window logic for this
1882 protected void outline_actionPerformed()
1884 SequenceGroup sg = getGroup();
1885 Color col = JColorChooser.showDialog(this,
1886 MessageManager.getString("label.select_outline_colour"),
1891 sg.setOutlineColour(col);
1903 public void showBoxes_actionPerformed()
1905 getGroup().setDisplayBoxes(showBoxes.isSelected());
1915 public void showText_actionPerformed()
1917 getGroup().setDisplayText(showText.isSelected());
1927 public void showColourText_actionPerformed()
1929 getGroup().setColourText(showColourText.isSelected());
1933 public void showLink(String url)
1937 jalview.util.BrowserLauncher.openURL(url);
1938 } catch (Exception ex)
1940 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1941 MessageManager.getString("label.web_browser_not_found_unix"),
1942 MessageManager.getString("label.web_browser_not_found"),
1943 JvOptionPane.WARNING_MESSAGE);
1945 ex.printStackTrace();
1949 void hideSequences(boolean representGroup)
1951 ap.av.hideSequences(sequence, representGroup);
1954 public void copy_actionPerformed()
1956 ap.alignFrame.copy_actionPerformed(null);
1959 public void cut_actionPerformed()
1961 ap.alignFrame.cut_actionPerformed(null);
1964 void changeCase(ActionEvent e)
1966 Object source = e.getSource();
1967 SequenceGroup sg = ap.av.getSelectionGroup();
1971 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1972 sg.getStartRes(), sg.getEndRes() + 1);
1977 if (source == toggle)
1979 description = MessageManager.getString("label.toggle_case");
1980 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1982 else if (source == upperCase)
1984 description = MessageManager.getString("label.to_upper_case");
1985 caseChange = ChangeCaseCommand.TO_UPPER;
1989 description = MessageManager.getString("label.to_lower_case");
1990 caseChange = ChangeCaseCommand.TO_LOWER;
1993 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1994 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1995 startEnd, caseChange);
1997 ap.alignFrame.addHistoryItem(caseCommand);
1999 ap.av.firePropertyChange("alignment", null,
2000 ap.av.getAlignment().getSequences());
2005 public void outputText_actionPerformed(ActionEvent e)
2007 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2008 cap.setForInput(null);
2009 Desktop.addInternalFrame(cap, MessageManager
2010 .formatMessage("label.alignment_output_command", new Object[]
2011 { e.getActionCommand() }), 600, 500);
2013 String[] omitHidden = null;
2015 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2016 // or we simply trust the user wants
2017 // wysiwig behaviour
2019 FileFormatI fileFormat = FileFormats.getInstance()
2020 .forName(e.getActionCommand());
2022 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2025 public void sequenceFeature_actionPerformed()
2027 SequenceGroup sg = ap.av.getSelectionGroup();
2033 List<SequenceI> seqs = new ArrayList<>();
2034 List<SequenceFeature> features = new ArrayList<>();
2037 * assemble dataset sequences, and template new sequence features,
2038 * for the amend features dialog
2040 int gSize = sg.getSize();
2041 for (int i = 0; i < gSize; i++)
2043 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2044 int end = sg.findEndRes(sg.getSequenceAt(i));
2047 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2048 features.add(new SequenceFeature(null, null, start, end, null));
2053 * an entirely gapped region will generate empty lists of sequence / features
2055 if (!seqs.isEmpty())
2057 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2058 .amendFeatures(seqs, features, true, ap))
2060 ap.alignFrame.setShowSeqFeatures(true);
2061 ap.av.setSearchResults(null); // clear highlighting
2062 ap.repaint(); // draw new/amended features
2067 public void textColour_actionPerformed()
2069 SequenceGroup sg = getGroup();
2072 new TextColourChooser().chooseColour(ap, sg);
2076 public void colourByStructure(String pdbid)
2078 Annotation[] anots = ap.av.getStructureSelectionManager()
2079 .colourSequenceFromStructure(sequence, pdbid);
2081 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2082 "Coloured by " + pdbid, anots);
2084 ap.av.getAlignment().addAnnotation(an);
2085 an.createSequenceMapping(sequence, 0, true);
2086 // an.adjustForAlignment();
2087 ap.av.getAlignment().setAnnotationIndex(an, 0);
2089 ap.adjustAnnotationHeight();
2091 sequence.addAlignmentAnnotation(an);
2095 public void editSequence_actionPerformed(ActionEvent actionEvent)
2097 SequenceGroup sg = ap.av.getSelectionGroup();
2101 if (sequence == null)
2103 sequence = sg.getSequenceAt(0);
2106 EditNameDialog dialog = new EditNameDialog(
2107 sequence.getSequenceAsString(sg.getStartRes(),
2108 sg.getEndRes() + 1),
2109 null, MessageManager.getString("label.edit_sequence"), null,
2110 MessageManager.getString("label.edit_sequence"),
2115 EditCommand editCommand = new EditCommand(
2116 MessageManager.getString("label.edit_sequences"),
2118 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2119 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2120 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2122 ap.alignFrame.addHistoryItem(editCommand);
2124 ap.av.firePropertyChange("alignment", null,
2125 ap.av.getAlignment().getSequences());
2131 * Action on user selecting an item from the colour menu (that does not have
2132 * its bespoke action handler)
2137 public void changeColour_actionPerformed(String colourSchemeName)
2139 SequenceGroup sg = getGroup();
2141 * switch to the chosen colour scheme (or null for None)
2143 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2144 .getColourScheme(colourSchemeName, sg,
2145 ap.av.getHiddenRepSequences());
2146 sg.setColourScheme(colourScheme);
2147 if (colourScheme instanceof Blosum62ColourScheme
2148 || colourScheme instanceof PIDColourScheme)
2150 sg.cs.setConsensus(AAFrequency.calculate(
2151 sg.getSequences(ap.av.getHiddenRepSequences()),
2152 sg.getStartRes(), sg.getEndRes() + 1));