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();
407 * - in the IdPanel (seq not null) if any sequence is hidden
408 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
410 if (alignPanel.av.hasHiddenRows())
412 boolean addOption = seq != null;
413 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
419 menuItem = new JMenuItem(
420 MessageManager.getString("action.reveal_all"));
421 menuItem.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 alignPanel.av.showAllHiddenSeqs();
427 if (alignPanel.overviewPanel != null)
429 alignPanel.overviewPanel.updateOverviewImage();
437 SequenceGroup sg = alignPanel.av.getSelectionGroup();
438 boolean isDefinedGroup = (sg != null)
439 ? alignPanel.av.getAlignment().getGroups().contains(sg)
442 if (sg != null && sg.getSize() > 0)
444 groupName.setText(MessageManager
445 .getString("label.edit_name_and_description_current_group"));
447 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
449 conservationMenuItem.setEnabled(!sg.isNucleotide());
453 if (sg.cs.conservationApplied())
455 conservationMenuItem.setSelected(true);
457 if (sg.cs.getThreshold() > 0)
459 abovePIDColour.setSelected(true);
462 modifyConservation.setEnabled(conservationMenuItem.isSelected());
463 modifyPID.setEnabled(abovePIDColour.isSelected());
464 displayNonconserved.setSelected(sg.getShowNonconserved());
465 showText.setSelected(sg.getDisplayText());
466 showColourText.setSelected(sg.getColourText());
467 showBoxes.setSelected(sg.getDisplayBoxes());
468 // add any groupURLs to the groupURL submenu and make it visible
469 if (groupLinks != null && groupLinks.size() > 0)
471 buildGroupURLMenu(sg, groupLinks);
473 // Add a 'show all structures' for the current selection
474 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
476 SequenceI sqass = null;
477 for (SequenceI sq : alignPanel.av.getSequenceSelection())
479 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
480 if (pes != null && pes.size() > 0)
482 reppdb.put(pes.get(0).getId(), pes.get(0));
483 for (PDBEntry pe : pes)
485 pdbe.put(pe.getId(), pe);
495 final PDBEntry[] pe = pdbe.values()
496 .toArray(new PDBEntry[pdbe.size()]),
497 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
498 final JMenuItem gpdbview, rpdbview;
503 groupMenu.setVisible(false);
504 editMenu.setVisible(false);
509 createGroupMenuItem.setVisible(true);
510 unGroupMenuItem.setVisible(false);
511 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
515 createGroupMenuItem.setVisible(false);
516 unGroupMenuItem.setVisible(true);
517 jMenu1.setText(MessageManager.getString("action.edit_group"));
522 sequenceMenu.setVisible(false);
523 pdbStructureDialog.setVisible(false);
524 rnaStructureMenu.setVisible(false);
527 addLinks(seq, features);
531 addFeatureDetails(features);
536 * Add a link to show feature details for each sequence feature
540 protected void addFeatureDetails(List<SequenceFeature> features)
542 if (features == null || features.isEmpty())
546 JMenu details = new JMenu(
547 MessageManager.getString("label.feature_details"));
550 for (final SequenceFeature sf : features)
552 int start = sf.getBegin();
553 int end = sf.getEnd();
557 desc = String.format("%s %d", sf.getType(), start);
561 desc = String.format("%s %d-%d", sf.getType(), start, end);
563 String tooltip = desc;
564 String description = sf.getDescription();
565 if (description != null)
567 description = StringUtils.stripHtmlTags(description);
568 if (description.length() > 12)
570 desc = desc + " " + description.substring(0, 12) + "..";
574 desc = desc + " " + description;
576 tooltip = tooltip + " " + description;
578 if (sf.getFeatureGroup() != null)
580 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
582 JMenuItem item = new JMenuItem(desc);
583 item.setToolTipText(tooltip);
584 item.addActionListener(new ActionListener()
587 public void actionPerformed(ActionEvent e)
589 showFeatureDetails(sf);
597 * Opens a panel showing a text report of feature dteails
601 protected void showFeatureDetails(SequenceFeature sf)
603 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
604 // it appears Java's CSS does not support border-collaps :-(
605 cap.addStylesheetRule("table { border-collapse: collapse;}");
606 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
607 cap.setText(sf.getDetailsReport());
609 Desktop.addInternalFrame(cap,
610 MessageManager.getString("label.feature_details"), 500, 500);
614 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
615 * When seq is not null, these are links for the sequence id, which may be to
616 * external web sites for the sequence accession, and/or links embedded in
617 * non-positional features. When seq is null, only links embedded in the
618 * provided features are added.
623 void addLinks(final SequenceI seq, List<SequenceFeature> features)
625 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
627 List<String> nlinks = null;
630 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
634 nlinks = new ArrayList<>();
637 if (features != null)
639 for (SequenceFeature sf : features)
641 if (sf.links != null)
643 for (String link : sf.links)
651 Map<String, List<String>> linkset = new LinkedHashMap<>();
653 for (String link : nlinks)
655 UrlLink urlLink = null;
658 urlLink = new UrlLink(link);
659 } catch (Exception foo)
661 Cache.log.error("Exception for URLLink '" + link + "'", foo);
665 if (!urlLink.isValid())
667 Cache.log.error(urlLink.getInvalidMessage());
671 urlLink.createLinksFromSeq(seq, linkset);
674 addshowLinks(linkMenu, linkset.values());
676 // only add link menu if it has entries
677 if (linkMenu.getItemCount() > 0)
679 if (sequence != null)
681 sequenceMenu.add(linkMenu);
691 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
692 * "All" is added first, followed by a separator. Then add any annotation
693 * types associated with the current selection. Separate menus are built for
694 * the selected sequence group (if any), and the selected sequence.
696 * Some annotation rows are always rendered together - these can be identified
697 * by a common graphGroup property > -1. Only one of each group will be marked
698 * as visible (to avoid duplication of the display). For such groups we add a
699 * composite type name, e.g.
701 * IUPredWS (Long), IUPredWS (Short)
705 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
706 List<SequenceI> forSequences)
708 showMenu.removeAll();
709 hideMenu.removeAll();
711 final List<String> all = Arrays
713 { MessageManager.getString("label.all") });
714 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
716 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
718 showMenu.addSeparator();
719 hideMenu.addSeparator();
721 final AlignmentAnnotation[] annotations = ap.getAlignment()
722 .getAlignmentAnnotation();
725 * Find shown/hidden annotations types, distinguished by source (calcId),
726 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
727 * the insertion order, which is the order of the annotations on the
730 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
731 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
732 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
733 AlignmentAnnotationUtils.asList(annotations), forSequences);
735 for (String calcId : hiddenTypes.keySet())
737 for (List<String> type : hiddenTypes.get(calcId))
739 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
743 // grey out 'show annotations' if none are hidden
744 showMenu.setEnabled(!hiddenTypes.isEmpty());
746 for (String calcId : shownTypes.keySet())
748 for (List<String> type : shownTypes.get(calcId))
750 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
754 // grey out 'hide annotations' if none are shown
755 hideMenu.setEnabled(!shownTypes.isEmpty());
759 * Returns a list of sequences - either the current selection group (if there
760 * is one), else the specified single sequence.
765 protected List<SequenceI> getSequenceScope(SequenceI seq)
767 List<SequenceI> forSequences = null;
768 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
769 if (selectionGroup != null && selectionGroup.getSize() > 0)
771 forSequences = selectionGroup.getSequences();
775 forSequences = seq == null ? Collections.<SequenceI> emptyList()
776 : Arrays.asList(seq);
782 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
785 * @param showOrHideMenu
787 * @param forSequences
788 * the sequences whose annotations may be shown or hidden
793 * if true this is a special label meaning 'All'
794 * @param actionIsShow
795 * if true, the select menu item action is to show the annotation
798 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
799 final List<SequenceI> forSequences, String calcId,
800 final List<String> types, final boolean allTypes,
801 final boolean actionIsShow)
803 String label = types.toString(); // [a, b, c]
804 label = label.substring(1, label.length() - 1); // a, b, c
805 final JMenuItem item = new JMenuItem(label);
806 item.setToolTipText(calcId);
807 item.addActionListener(new ActionListener()
810 public void actionPerformed(ActionEvent e)
812 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
813 types, forSequences, allTypes, actionIsShow);
817 showOrHideMenu.add(item);
820 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
823 // TODO: usability: thread off the generation of group url content so root
825 // sequence only URLs
826 // ID/regex match URLs
827 groupLinksMenu = new JMenu(
828 MessageManager.getString("action.group_link"));
829 // three types of url that might be created.
830 JMenu[] linkMenus = new JMenu[] { null,
831 new JMenu(MessageManager.getString("action.ids")),
832 new JMenu(MessageManager.getString("action.sequences")),
833 new JMenu(MessageManager.getString("action.ids_sequences")) };
835 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
836 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
837 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
838 for (int sq = 0; sq < seqs.length; sq++)
841 int start = seqs[sq].findPosition(sg.getStartRes()),
842 end = seqs[sq].findPosition(sg.getEndRes());
843 // just collect ids from dataset sequence
844 // TODO: check if IDs collected from selecton group intersects with the
845 // current selection, too
846 SequenceI sqi = seqs[sq];
847 while (sqi.getDatasetSequence() != null)
849 sqi = sqi.getDatasetSequence();
851 DBRefEntry[] dbr = sqi.getDBRefs();
852 if (dbr != null && dbr.length > 0)
854 for (int d = 0; d < dbr.length; d++)
856 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
857 Object[] sarray = commonDbrefs.get(src);
860 sarray = new Object[2];
861 sarray[0] = new int[] { 0 };
862 sarray[1] = new String[seqs.length];
864 commonDbrefs.put(src, sarray);
867 if (((String[]) sarray[1])[sq] == null)
869 if (!dbr[d].hasMap() || (dbr[d].getMap()
870 .locateMappedRange(start, end) != null))
872 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
873 ((int[]) sarray[0])[0]++;
879 // now create group links for all distinct ID/sequence sets.
880 boolean addMenu = false; // indicates if there are any group links to give
882 for (String link : groupLinks)
884 GroupUrlLink urlLink = null;
887 urlLink = new GroupUrlLink(link);
888 } catch (Exception foo)
890 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
894 if (!urlLink.isValid())
896 Cache.log.error(urlLink.getInvalidMessage());
899 final String label = urlLink.getLabel();
900 boolean usingNames = false;
901 // Now see which parts of the group apply for this URL
902 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
903 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
904 String[] seqstr, ids; // input to makeUrl
907 int numinput = ((int[]) idset[0])[0];
908 String[] allids = ((String[]) idset[1]);
909 seqstr = new String[numinput];
910 ids = new String[numinput];
911 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
913 if (allids[sq] != null)
915 ids[idcount] = allids[sq];
916 seqstr[idcount++] = idandseqs[1][sq];
922 // just use the id/seq set
923 seqstr = idandseqs[1];
927 // and try and make the groupURL!
929 Object[] urlset = null;
932 urlset = urlLink.makeUrlStubs(ids, seqstr,
933 "FromJalview" + System.currentTimeMillis(), false);
934 } catch (UrlStringTooLongException e)
939 int type = urlLink.getGroupURLType() & 3;
940 // first two bits ofurlLink type bitfield are sequenceids and sequences
941 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
942 addshowLink(linkMenus[type],
943 label + (((type & 1) == 1)
944 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
952 groupLinksMenu = new JMenu(
953 MessageManager.getString("action.group_link"));
954 for (int m = 0; m < linkMenus.length; m++)
956 if (linkMenus[m] != null
957 && linkMenus[m].getMenuComponentCount() > 0)
959 groupLinksMenu.add(linkMenus[m]);
963 groupMenu.add(groupLinksMenu);
967 private void addshowLinks(JMenu linkMenu,
968 Collection<List<String>> linkset)
970 for (List<String> linkstrset : linkset)
972 // split linkstr into label and url
973 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
978 * add a show URL menu item to the given linkMenu
982 * - menu label string
986 private void addshowLink(JMenu linkMenu, String label, final String url)
988 JMenuItem item = new JMenuItem(label);
989 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
992 item.addActionListener(new ActionListener()
995 public void actionPerformed(ActionEvent e)
997 new Thread(new Runnable()
1014 * add a late bound groupURL item to the given linkMenu
1018 * - menu label string
1019 * @param urlgenerator
1020 * GroupURLLink used to generate URL
1022 * Object array returned from the makeUrlStubs function.
1024 private void addshowLink(JMenu linkMenu, String label,
1025 final GroupUrlLink urlgenerator, final Object[] urlstub)
1027 JMenuItem item = new JMenuItem(label);
1028 item.setToolTipText(MessageManager
1029 .formatMessage("label.open_url_seqs_param", new Object[]
1030 { urlgenerator.getUrl_prefix(),
1031 urlgenerator.getNumberInvolved(urlstub) }));
1032 // TODO: put in info about what is being sent.
1033 item.addActionListener(new ActionListener()
1036 public void actionPerformed(ActionEvent e)
1038 new Thread(new Runnable()
1046 showLink(urlgenerator.constructFrom(urlstub));
1047 } catch (UrlStringTooLongException e2)
1065 private void jbInit() throws Exception
1067 groupMenu.setText(MessageManager.getString("label.selection"));
1068 groupName.setText(MessageManager.getString("label.name"));
1069 groupName.addActionListener(new ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 groupName_actionPerformed();
1077 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1078 sequenceName.setText(
1079 MessageManager.getString("label.edit_name_description"));
1080 sequenceName.addActionListener(new ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 sequenceName_actionPerformed();
1089 .setText(MessageManager.getString("action.choose_annotations"));
1090 chooseAnnotations.addActionListener(new ActionListener()
1093 public void actionPerformed(ActionEvent e)
1095 chooseAnnotations_actionPerformed(e);
1099 .setText(MessageManager.getString("label.sequence_details"));
1100 sequenceDetails.addActionListener(new ActionListener()
1103 public void actionPerformed(ActionEvent e)
1105 sequenceDetails_actionPerformed();
1109 .setText(MessageManager.getString("label.sequence_details"));
1110 sequenceSelDetails.addActionListener(new ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 sequenceSelectionDetails_actionPerformed();
1120 .setText(MessageManager.getString("action.remove_group"));
1121 unGroupMenuItem.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 unGroupMenuItem_actionPerformed();
1130 .setText(MessageManager.getString("action.create_group"));
1131 createGroupMenuItem.addActionListener(new ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 createGroupMenuItem_actionPerformed();
1140 outline.setText(MessageManager.getString("action.border_colour"));
1141 outline.addActionListener(new ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 outline_actionPerformed();
1149 showBoxes.setText(MessageManager.getString("action.boxes"));
1150 showBoxes.setState(true);
1151 showBoxes.addActionListener(new ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 showBoxes_actionPerformed();
1159 showText.setText(MessageManager.getString("action.text"));
1160 showText.setState(true);
1161 showText.addActionListener(new ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 showText_actionPerformed();
1169 showColourText.setText(MessageManager.getString("label.colour_text"));
1170 showColourText.addActionListener(new ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 showColourText_actionPerformed();
1179 .setText(MessageManager.getString("label.show_non_conserved"));
1180 displayNonconserved.setState(true);
1181 displayNonconserved.addActionListener(new ActionListener()
1184 public void actionPerformed(ActionEvent e)
1186 showNonconserved_actionPerformed();
1189 editMenu.setText(MessageManager.getString("action.edit"));
1190 cut.setText(MessageManager.getString("action.cut"));
1191 cut.addActionListener(new ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 cut_actionPerformed();
1199 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1200 upperCase.addActionListener(new ActionListener()
1203 public void actionPerformed(ActionEvent e)
1208 copy.setText(MessageManager.getString("action.copy"));
1209 copy.addActionListener(new ActionListener()
1212 public void actionPerformed(ActionEvent e)
1214 copy_actionPerformed();
1217 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1218 lowerCase.addActionListener(new ActionListener()
1221 public void actionPerformed(ActionEvent e)
1226 toggle.setText(MessageManager.getString("label.toggle_case"));
1227 toggle.addActionListener(new ActionListener()
1230 public void actionPerformed(ActionEvent e)
1236 MessageManager.getString("label.out_to_textbox") + "...");
1237 seqShowAnnotationsMenu
1238 .setText(MessageManager.getString("label.show_annotations"));
1239 seqHideAnnotationsMenu
1240 .setText(MessageManager.getString("label.hide_annotations"));
1241 groupShowAnnotationsMenu
1242 .setText(MessageManager.getString("label.show_annotations"));
1243 groupHideAnnotationsMenu
1244 .setText(MessageManager.getString("label.hide_annotations"));
1245 sequenceFeature.setText(
1246 MessageManager.getString("label.create_sequence_feature"));
1247 sequenceFeature.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1252 sequenceFeature_actionPerformed();
1255 jMenu1.setText(MessageManager.getString("label.group"));
1256 pdbStructureDialog.setText(
1257 MessageManager.getString("label.show_pdbstruct_dialog"));
1258 pdbStructureDialog.addActionListener(new ActionListener()
1261 public void actionPerformed(ActionEvent actionEvent)
1263 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1264 if (ap.av.getSelectionGroup() != null)
1266 selectedSeqs = ap.av.getSequenceSelection();
1268 new StructureChooser(selectedSeqs, sequence, ap);
1273 .setText(MessageManager.getString("label.view_rna_structure"));
1275 // colStructureMenu.setText("Colour By Structure");
1276 editSequence.setText(
1277 MessageManager.getString("label.edit_sequence") + "...");
1278 editSequence.addActionListener(new ActionListener()
1281 public void actionPerformed(ActionEvent actionEvent)
1283 editSequence_actionPerformed(actionEvent);
1286 makeReferenceSeq.setText(
1287 MessageManager.getString("label.mark_as_representative"));
1288 makeReferenceSeq.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent actionEvent)
1294 makeReferenceSeq_actionPerformed(actionEvent);
1299 .setText(MessageManager.getString("label.hide_insertions"));
1300 hideInsertions.addActionListener(new ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 hideInsertions_actionPerformed(e);
1310 groupMenu.add(sequenceSelDetails);
1313 add(rnaStructureMenu);
1314 add(pdbStructureDialog);
1315 if (sequence != null)
1317 add(hideInsertions);
1319 // annotations configuration panel suppressed for now
1320 // groupMenu.add(chooseAnnotations);
1323 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1324 * (if a selection group is in force).
1326 sequenceMenu.add(seqShowAnnotationsMenu);
1327 sequenceMenu.add(seqHideAnnotationsMenu);
1328 sequenceMenu.add(seqAddReferenceAnnotations);
1329 groupMenu.add(groupShowAnnotationsMenu);
1330 groupMenu.add(groupHideAnnotationsMenu);
1331 groupMenu.add(groupAddReferenceAnnotations);
1332 groupMenu.add(editMenu);
1333 groupMenu.add(outputMenu);
1334 groupMenu.add(sequenceFeature);
1335 groupMenu.add(createGroupMenuItem);
1336 groupMenu.add(unGroupMenuItem);
1337 groupMenu.add(jMenu1);
1338 sequenceMenu.add(sequenceName);
1339 sequenceMenu.add(sequenceDetails);
1340 sequenceMenu.add(makeReferenceSeq);
1347 editMenu.add(editSequence);
1348 editMenu.add(upperCase);
1349 editMenu.add(lowerCase);
1350 editMenu.add(toggle);
1351 // JBPNote: These shouldn't be added here - should appear in a generic
1352 // 'apply web service to this sequence menu'
1353 // pdbMenu.add(RNAFold);
1354 // pdbMenu.add(ContraFold);
1355 jMenu1.add(groupName);
1356 jMenu1.add(colourMenu);
1357 jMenu1.add(showBoxes);
1358 jMenu1.add(showText);
1359 jMenu1.add(showColourText);
1360 jMenu1.add(outline);
1361 jMenu1.add(displayNonconserved);
1365 * Constructs the entries for the colour menu
1367 protected void initColourMenu()
1369 colourMenu.setText(MessageManager.getString("label.group_colour"));
1370 textColour.setText(MessageManager.getString("label.text_colour"));
1371 textColour.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 textColour_actionPerformed();
1380 abovePIDColour.setText(
1381 MessageManager.getString("label.above_identity_threshold"));
1382 abovePIDColour.addActionListener(new ActionListener()
1385 public void actionPerformed(ActionEvent e)
1387 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1392 MessageManager.getString("label.modify_identity_threshold"));
1393 modifyPID.addActionListener(new ActionListener()
1396 public void actionPerformed(ActionEvent e)
1398 modifyPID_actionPerformed();
1402 conservationMenuItem
1403 .setText(MessageManager.getString("action.by_conservation"));
1404 conservationMenuItem.addActionListener(new ActionListener()
1407 public void actionPerformed(ActionEvent e)
1409 conservationMenuItem_actionPerformed(
1410 conservationMenuItem.isSelected());
1414 modifyConservation.setText(MessageManager
1415 .getString("label.modify_conservation_threshold"));
1416 modifyConservation.addActionListener(new ActionListener()
1419 public void actionPerformed(ActionEvent e)
1421 modifyConservation_actionPerformed();
1427 * Builds the group colour sub-menu, including any user-defined colours which
1428 * were loaded at startup or during the Jalview session
1430 protected void buildColourMenu()
1432 SequenceGroup sg = ap.av.getSelectionGroup();
1436 * popup menu with no sequence group scope
1440 colourMenu.removeAll();
1441 colourMenu.add(textColour);
1442 colourMenu.addSeparator();
1444 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1446 colourMenu.addSeparator();
1447 colourMenu.add(conservationMenuItem);
1448 colourMenu.add(modifyConservation);
1449 colourMenu.add(abovePIDColour);
1450 colourMenu.add(modifyPID);
1453 protected void modifyConservation_actionPerformed()
1455 SequenceGroup sg = getGroup();
1458 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1459 SliderPanel.showConservationSlider();
1463 protected void modifyPID_actionPerformed()
1465 SequenceGroup sg = getGroup();
1468 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1470 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1471 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1472 SliderPanel.showPIDSlider();
1477 * Check for any annotations on the underlying dataset sequences (for the
1478 * current selection group) which are not 'on the alignment'.If any are found,
1479 * enable the option to add them to the alignment. The criteria for 'on the
1480 * alignment' is finding an alignment annotation on the alignment, matched on
1481 * calcId, label and sequenceRef.
1483 * A tooltip is also constructed that displays the source (calcId) and type
1484 * (label) of the annotations that can be added.
1487 * @param forSequences
1489 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1490 List<SequenceI> forSequences)
1492 menuItem.setEnabled(false);
1495 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1496 * Using TreeMap means calcIds are shown in alphabetical order.
1498 SortedMap<String, String> tipEntries = new TreeMap<>();
1499 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1500 AlignmentI al = this.ap.av.getAlignment();
1501 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1503 if (!candidates.isEmpty())
1505 StringBuilder tooltip = new StringBuilder(64);
1506 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1509 * Found annotations that could be added. Enable the menu item, and
1510 * configure its tooltip and action.
1512 menuItem.setEnabled(true);
1513 for (String calcId : tipEntries.keySet())
1515 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1517 String tooltipText = JvSwingUtils.wrapTooltip(true,
1518 tooltip.toString());
1519 menuItem.setToolTipText(tooltipText);
1521 menuItem.addActionListener(new ActionListener()
1524 public void actionPerformed(ActionEvent e)
1526 addReferenceAnnotations_actionPerformed(candidates);
1533 * Add annotations to the sequences and to the alignment.
1536 * a map whose keys are sequences on the alignment, and values a list
1537 * of annotations to add to each sequence
1539 protected void addReferenceAnnotations_actionPerformed(
1540 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1542 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1543 final AlignmentI alignment = this.ap.getAlignment();
1544 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1549 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1551 if (!ap.av.getAlignment().hasSeqrep())
1553 // initialise the display flags so the user sees something happen
1554 ap.av.setDisplayReferenceSeq(true);
1555 ap.av.setColourByReferenceSeq(true);
1556 ap.av.getAlignment().setSeqrep(sequence);
1560 if (ap.av.getAlignment().getSeqrep() == sequence)
1562 ap.av.getAlignment().setSeqrep(null);
1566 ap.av.getAlignment().setSeqrep(sequence);
1572 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1574 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1575 BitSet inserts = new BitSet();
1577 boolean markedPopup = false;
1578 // mark inserts in current selection
1579 if (ap.av.getSelectionGroup() != null)
1581 // mark just the columns in the selection group to be hidden
1582 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1583 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1585 // now clear columns without gaps
1586 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1592 inserts.and(sq.getInsertionsAsBits());
1594 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1595 ap.av.getSelectionGroup().getEndRes());
1598 // now mark for sequence under popup if we haven't already done it
1599 else if (!markedPopup && sequence != null)
1601 inserts.or(sequence.getInsertionsAsBits());
1603 // and set hidden columns accordingly
1604 hidden.hideColumns(inserts);
1609 protected void sequenceSelectionDetails_actionPerformed()
1611 createSequenceDetailsReport(ap.av.getSequenceSelection());
1614 protected void sequenceDetails_actionPerformed()
1616 createSequenceDetailsReport(new SequenceI[] { sequence });
1619 public void createSequenceDetailsReport(SequenceI[] sequences)
1621 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1622 StringBuilder contents = new StringBuilder(128);
1623 for (SequenceI seq : sequences)
1625 contents.append("<p><h2>" + MessageManager.formatMessage(
1626 "label.create_sequence_details_report_annotation_for",
1628 { seq.getDisplayId(true) }) + "</h2></p><p>");
1629 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1630 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1631 contents.append("</p>");
1633 cap.setText("<html>" + contents.toString() + "</html>");
1635 Desktop.addInternalFrame(cap,
1636 MessageManager.formatMessage("label.sequence_details_for",
1637 (sequences.length == 1 ? new Object[]
1638 { sequences[0].getDisplayId(true) }
1641 .getString("label.selection") })),
1646 protected void showNonconserved_actionPerformed()
1648 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1653 * call to refresh view after settings change
1657 ap.updateAnnotation();
1658 // removed paintAlignment(true) here:
1659 // updateAnnotation calls paintAlignment already, so don't need to call
1662 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1666 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1667 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1677 public void abovePIDColour_actionPerformed(boolean selected)
1679 SequenceGroup sg = getGroup();
1687 sg.cs.setConsensus(AAFrequency.calculate(
1688 sg.getSequences(ap.av.getHiddenRepSequences()),
1689 sg.getStartRes(), sg.getEndRes() + 1));
1691 int threshold = SliderPanel.setPIDSliderSource(ap,
1692 sg.getGroupColourScheme(), getGroup().getName());
1694 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1696 SliderPanel.showPIDSlider();
1699 // remove PIDColouring
1701 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1702 SliderPanel.hidePIDSlider();
1704 modifyPID.setEnabled(selected);
1710 * Open a panel where the user can choose which types of sequence annotation
1715 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1717 // todo correct way to guard against opening a duplicate panel?
1718 new AnnotationChooser(ap);
1727 public void conservationMenuItem_actionPerformed(boolean selected)
1729 SequenceGroup sg = getGroup();
1737 // JBPNote: Conservation name shouldn't be i18n translated
1738 Conservation c = new Conservation("Group",
1739 sg.getSequences(ap.av.getHiddenRepSequences()),
1740 sg.getStartRes(), sg.getEndRes() + 1);
1743 c.verdict(false, ap.av.getConsPercGaps());
1744 sg.cs.setConservation(c);
1746 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1748 SliderPanel.showConservationSlider();
1751 // remove ConservationColouring
1753 sg.cs.setConservation(null);
1754 SliderPanel.hideConservationSlider();
1756 modifyConservation.setEnabled(selected);
1767 protected void groupName_actionPerformed()
1770 SequenceGroup sg = getGroup();
1771 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1772 sg.getDescription(),
1773 " " + MessageManager.getString("label.group_name") + " ",
1774 MessageManager.getString("label.group_description") + " ",
1775 MessageManager.getString("label.edit_group_name_description"),
1783 sg.setName(dialog.getName());
1784 sg.setDescription(dialog.getDescription());
1789 * Get selection group - adding it to the alignment if necessary.
1791 * @return sequence group to operate on
1793 SequenceGroup getGroup()
1795 SequenceGroup sg = ap.av.getSelectionGroup();
1796 // this method won't add a new group if it already exists
1799 ap.av.getAlignment().addGroup(sg);
1811 void sequenceName_actionPerformed()
1813 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1814 sequence.getDescription(),
1815 " " + MessageManager.getString("label.sequence_name")
1817 MessageManager.getString("label.sequence_description") + " ",
1818 MessageManager.getString(
1819 "label.edit_sequence_name_description"),
1827 if (dialog.getName() != null)
1829 if (dialog.getName().indexOf(" ") > -1)
1831 JvOptionPane.showMessageDialog(ap,
1833 .getString("label.spaces_converted_to_backslashes"),
1835 .getString("label.no_spaces_allowed_sequence_name"),
1836 JvOptionPane.WARNING_MESSAGE);
1839 sequence.setName(dialog.getName().replace(' ', '_'));
1840 ap.paintAlignment(false, false);
1843 sequence.setDescription(dialog.getDescription());
1845 ap.av.firePropertyChange("alignment", null,
1846 ap.av.getAlignment().getSequences());
1856 void unGroupMenuItem_actionPerformed()
1858 SequenceGroup sg = ap.av.getSelectionGroup();
1859 ap.av.getAlignment().deleteGroup(sg);
1860 ap.av.setSelectionGroup(null);
1864 void createGroupMenuItem_actionPerformed()
1866 getGroup(); // implicitly creates group - note - should apply defaults / use
1867 // standard alignment window logic for this
1877 protected void outline_actionPerformed()
1879 SequenceGroup sg = getGroup();
1880 Color col = JColorChooser.showDialog(this,
1881 MessageManager.getString("label.select_outline_colour"),
1886 sg.setOutlineColour(col);
1898 public void showBoxes_actionPerformed()
1900 getGroup().setDisplayBoxes(showBoxes.isSelected());
1910 public void showText_actionPerformed()
1912 getGroup().setDisplayText(showText.isSelected());
1922 public void showColourText_actionPerformed()
1924 getGroup().setColourText(showColourText.isSelected());
1928 public void showLink(String url)
1932 jalview.util.BrowserLauncher.openURL(url);
1933 } catch (Exception ex)
1935 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1936 MessageManager.getString("label.web_browser_not_found_unix"),
1937 MessageManager.getString("label.web_browser_not_found"),
1938 JvOptionPane.WARNING_MESSAGE);
1940 ex.printStackTrace();
1944 void hideSequences(boolean representGroup)
1946 ap.av.hideSequences(sequence, representGroup);
1949 public void copy_actionPerformed()
1951 ap.alignFrame.copy_actionPerformed(null);
1954 public void cut_actionPerformed()
1956 ap.alignFrame.cut_actionPerformed(null);
1959 void changeCase(ActionEvent e)
1961 Object source = e.getSource();
1962 SequenceGroup sg = ap.av.getSelectionGroup();
1966 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1967 sg.getStartRes(), sg.getEndRes() + 1);
1972 if (source == toggle)
1974 description = MessageManager.getString("label.toggle_case");
1975 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1977 else if (source == upperCase)
1979 description = MessageManager.getString("label.to_upper_case");
1980 caseChange = ChangeCaseCommand.TO_UPPER;
1984 description = MessageManager.getString("label.to_lower_case");
1985 caseChange = ChangeCaseCommand.TO_LOWER;
1988 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1989 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1990 startEnd, caseChange);
1992 ap.alignFrame.addHistoryItem(caseCommand);
1994 ap.av.firePropertyChange("alignment", null,
1995 ap.av.getAlignment().getSequences());
2000 public void outputText_actionPerformed(ActionEvent e)
2002 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2003 cap.setForInput(null);
2004 Desktop.addInternalFrame(cap, MessageManager
2005 .formatMessage("label.alignment_output_command", new Object[]
2006 { e.getActionCommand() }), 600, 500);
2008 String[] omitHidden = null;
2010 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2011 // or we simply trust the user wants
2012 // wysiwig behaviour
2014 FileFormatI fileFormat = FileFormats.getInstance()
2015 .forName(e.getActionCommand());
2017 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2020 public void sequenceFeature_actionPerformed()
2022 SequenceGroup sg = ap.av.getSelectionGroup();
2028 List<SequenceI> seqs = new ArrayList<>();
2029 List<SequenceFeature> features = new ArrayList<>();
2032 * assemble dataset sequences, and template new sequence features,
2033 * for the amend features dialog
2035 int gSize = sg.getSize();
2036 for (int i = 0; i < gSize; i++)
2038 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2039 int end = sg.findEndRes(sg.getSequenceAt(i));
2042 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2043 features.add(new SequenceFeature(null, null, start, end, null));
2048 * an entirely gapped region will generate empty lists of sequence / features
2050 if (!seqs.isEmpty())
2052 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2053 .amendFeatures(seqs, features, true, ap))
2055 ap.alignFrame.setShowSeqFeatures(true);
2056 ap.av.setSearchResults(null); // clear highlighting
2057 ap.repaint(); // draw new/amended features
2062 public void textColour_actionPerformed()
2064 SequenceGroup sg = getGroup();
2067 new TextColourChooser().chooseColour(ap, sg);
2071 public void colourByStructure(String pdbid)
2073 Annotation[] anots = ap.av.getStructureSelectionManager()
2074 .colourSequenceFromStructure(sequence, pdbid);
2076 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2077 "Coloured by " + pdbid, anots);
2079 ap.av.getAlignment().addAnnotation(an);
2080 an.createSequenceMapping(sequence, 0, true);
2081 // an.adjustForAlignment();
2082 ap.av.getAlignment().setAnnotationIndex(an, 0);
2084 ap.adjustAnnotationHeight();
2086 sequence.addAlignmentAnnotation(an);
2090 public void editSequence_actionPerformed(ActionEvent actionEvent)
2092 SequenceGroup sg = ap.av.getSelectionGroup();
2096 if (sequence == null)
2098 sequence = sg.getSequenceAt(0);
2101 EditNameDialog dialog = new EditNameDialog(
2102 sequence.getSequenceAsString(sg.getStartRes(),
2103 sg.getEndRes() + 1),
2104 null, MessageManager.getString("label.edit_sequence"), null,
2105 MessageManager.getString("label.edit_sequence"),
2110 EditCommand editCommand = new EditCommand(
2111 MessageManager.getString("label.edit_sequences"),
2113 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2114 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2115 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2117 ap.alignFrame.addHistoryItem(editCommand);
2119 ap.av.firePropertyChange("alignment", null,
2120 ap.av.getAlignment().getSequences());
2126 * Action on user selecting an item from the colour menu (that does not have
2127 * its bespoke action handler)
2132 public void changeColour_actionPerformed(String colourSchemeName)
2134 SequenceGroup sg = getGroup();
2136 * switch to the chosen colour scheme (or null for None)
2138 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2139 .getColourScheme(colourSchemeName, sg,
2140 ap.av.getHiddenRepSequences());
2141 sg.setColourScheme(colourScheme);
2142 if (colourScheme instanceof Blosum62ColourScheme
2143 || colourScheme instanceof PIDColourScheme)
2145 sg.cs.setConsensus(AAFrequency.calculate(
2146 sg.getSequences(ap.av.getHiddenRepSequences()),
2147 sg.getStartRes(), sg.getEndRes() + 1));