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 java.util.Locale;
25 import java.awt.BorderLayout;
26 import java.awt.Color;
27 import java.awt.event.ActionEvent;
28 import java.awt.event.ActionListener;
29 import java.util.ArrayList;
30 import java.util.Arrays;
31 import java.util.BitSet;
32 import java.util.Collection;
33 import java.util.Collections;
34 import java.util.Hashtable;
35 import java.util.LinkedHashMap;
36 import java.util.List;
38 import java.util.Objects;
39 import java.util.SortedMap;
40 import java.util.TreeMap;
41 import java.util.Vector;
43 import javax.swing.ButtonGroup;
44 import javax.swing.JCheckBoxMenuItem;
45 import javax.swing.JInternalFrame;
46 import javax.swing.JLabel;
47 import javax.swing.JMenu;
48 import javax.swing.JMenuItem;
49 import javax.swing.JPanel;
50 import javax.swing.JPopupMenu;
51 import javax.swing.JRadioButtonMenuItem;
52 import javax.swing.JScrollPane;
54 import jalview.analysis.AAFrequency;
55 import jalview.analysis.AlignmentAnnotationUtils;
56 import jalview.analysis.AlignmentUtils;
57 import jalview.analysis.Conservation;
58 import jalview.api.AlignViewportI;
59 import jalview.bin.Console;
60 import jalview.commands.ChangeCaseCommand;
61 import jalview.commands.EditCommand;
62 import jalview.commands.EditCommand.Action;
63 import jalview.datamodel.AlignmentAnnotation;
64 import jalview.datamodel.AlignmentI;
65 import jalview.datamodel.DBRefEntry;
66 import jalview.datamodel.HiddenColumns;
67 import jalview.datamodel.MappedFeatures;
68 import jalview.datamodel.PDBEntry;
69 import jalview.datamodel.SequenceFeature;
70 import jalview.datamodel.SequenceGroup;
71 import jalview.datamodel.SequenceI;
72 import jalview.gui.ColourMenuHelper.ColourChangeListener;
73 import jalview.gui.JalviewColourChooser.ColourChooserListener;
74 import jalview.io.FileFormatI;
75 import jalview.io.FileFormats;
76 import jalview.io.FormatAdapter;
77 import jalview.io.SequenceAnnotationReport;
78 import jalview.schemes.Blosum62ColourScheme;
79 import jalview.schemes.ColourSchemeI;
80 import jalview.schemes.ColourSchemes;
81 import jalview.schemes.PIDColourScheme;
82 import jalview.schemes.ResidueColourScheme;
83 import jalview.util.Comparison;
84 import jalview.util.GroupUrlLink;
85 import jalview.util.GroupUrlLink.UrlStringTooLongException;
86 import jalview.util.MessageManager;
87 import jalview.util.Platform;
88 import jalview.util.StringUtils;
89 import jalview.util.UrlLink;
90 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
93 * The popup menu that is displayed on right-click on a sequence id, or in the
96 public class PopupMenu extends JPopupMenu implements ColourChangeListener
99 * maximum length of feature description to include in popup menu item text
101 private static final int FEATURE_DESC_MAX = 40;
104 * true for ID Panel menu, false for alignment panel menu
106 private final boolean forIdPanel;
108 private final AlignmentPanel ap;
111 * the sequence under the cursor when clicked
112 * (additional sequences may be selected)
114 private final SequenceI sequence;
116 JMenu groupMenu = new JMenu();
118 JMenuItem groupName = new JMenuItem();
120 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
122 protected JMenuItem modifyPID = new JMenuItem();
124 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
126 protected JRadioButtonMenuItem annotationColour;
128 protected JMenuItem modifyConservation = new JMenuItem();
130 JMenu sequenceMenu = new JMenu();
132 JMenuItem makeReferenceSeq = new JMenuItem();
134 JMenuItem createGroupMenuItem = new JMenuItem();
136 JMenuItem unGroupMenuItem = new JMenuItem();
138 JMenu colourMenu = new JMenu();
140 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
142 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
144 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
146 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
148 JMenu editMenu = new JMenu();
150 JMenuItem upperCase = new JMenuItem();
152 JMenuItem lowerCase = new JMenuItem();
154 JMenuItem toggle = new JMenuItem();
156 JMenu outputMenu = new JMenu();
158 JMenu seqShowAnnotationsMenu = new JMenu();
160 JMenu seqHideAnnotationsMenu = new JMenu();
162 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
163 MessageManager.getString("label.add_reference_annotations"));
165 JMenu groupShowAnnotationsMenu = new JMenu();
167 JMenu groupHideAnnotationsMenu = new JMenu();
169 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
170 MessageManager.getString("label.add_reference_annotations"));
172 JMenuItem textColour = new JMenuItem();
174 JMenu editGroupMenu = new JMenu();
176 JMenuItem chooseStructure = new JMenuItem();
178 JMenu rnaStructureMenu = new JMenu();
181 * Constructs a menu with sub-menu items for any hyperlinks for the sequence
182 * and/or features provided. Hyperlinks may include a lookup by sequence id,
183 * or database cross-references, depending on which links are enabled in user
190 protected static JMenu buildLinkMenu(final SequenceI seq,
191 List<SequenceFeature> features)
193 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
195 List<String> nlinks = null;
198 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
199 UrlLink.sort(nlinks);
203 nlinks = new ArrayList<>();
206 if (features != null)
208 for (SequenceFeature sf : features)
210 if (sf.links != null)
212 for (String link : sf.links)
221 * instantiate the hyperlinklink templates from sequence data;
222 * note the order of the templates is preserved in the map
224 Map<String, List<String>> linkset = new LinkedHashMap<>();
225 for (String link : nlinks)
227 UrlLink urlLink = null;
230 urlLink = new UrlLink(link);
231 } catch (Exception foo)
233 Console.error("Exception for URLLink '" + link + "'", foo);
237 if (!urlLink.isValid())
239 Console.error(urlLink.getInvalidMessage());
243 urlLink.createLinksFromSeq(seq, linkset);
247 * construct menu items for the hyperlinks (still preserving
248 * the order of the sorted templates)
250 addUrlLinks(linkMenu, linkset.values());
256 * A helper method that builds menu items from the given links, with action
257 * handlers to open the link URL, and adds them to the linkMenu. Each provided
258 * link should be a list whose second item is the menu text, and whose fourth
259 * item is the URL to open when the menu item is selected.
264 static private void addUrlLinks(JMenu linkMenu,
265 Collection<List<String>> linkset)
267 for (List<String> linkstrset : linkset)
269 final String url = linkstrset.get(3);
270 JMenuItem item = new JMenuItem(linkstrset.get(1));
271 item.setToolTipText(MessageManager
272 .formatMessage("label.open_url_param", new Object[]
274 item.addActionListener(new ActionListener()
277 public void actionPerformed(ActionEvent e)
279 new Thread(new Runnable()
294 * Opens the provided url in the default web browser, or shows an error
295 * message if this fails
299 static void showLink(String url)
303 jalview.util.BrowserLauncher.openURL(url);
304 } catch (Exception ex)
306 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
307 MessageManager.getString("label.web_browser_not_found_unix"),
308 MessageManager.getString("label.web_browser_not_found"),
309 JvOptionPane.WARNING_MESSAGE);
311 ex.printStackTrace();
316 * add a late bound groupURL item to the given linkMenu
320 * - menu label string
321 * @param urlgenerator
322 * GroupURLLink used to generate URL
324 * Object array returned from the makeUrlStubs function.
326 static void addshowLink(JMenu linkMenu, String label,
327 final GroupUrlLink urlgenerator, final Object[] urlstub)
329 JMenuItem item = new JMenuItem(label);
330 item.setToolTipText(MessageManager
331 .formatMessage("label.open_url_seqs_param", new Object[]
332 { urlgenerator.getUrl_prefix(),
333 urlgenerator.getNumberInvolved(urlstub) }));
334 // TODO: put in info about what is being sent.
335 item.addActionListener(new ActionListener()
338 public void actionPerformed(ActionEvent e)
340 new Thread(new Runnable()
348 showLink(urlgenerator.constructFrom(urlstub));
349 } catch (UrlStringTooLongException e2)
362 * Constructor for a PopupMenu for a click in the alignment panel (on a
366 * the panel in which the mouse is clicked
368 * the sequence under the mouse
369 * @throws NullPointerException
372 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
374 this(false, ap, seq, column, null);
378 * Constructor for a PopupMenu for a click in the sequence id panel
381 * the panel in which the mouse is clicked
383 * the sequence under the mouse click
385 * templates for sequence external links
386 * @throws NullPointerException
389 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
390 List<String> groupLinks)
392 this(true, alignPanel, seq, -1, groupLinks);
396 * Private constructor that constructs a popup menu for either sequence ID
397 * Panel, or alignment context
403 * aligned column position (0...)
406 private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
407 final SequenceI seq, final int column, List<String> groupLinks)
409 Objects.requireNonNull(seq);
410 this.forIdPanel = fromIdPanel;
411 this.ap = alignPanel;
414 for (String ff : FileFormats.getInstance().getWritableFormats(true))
416 JMenuItem item = new JMenuItem(ff);
418 item.addActionListener(new ActionListener()
421 public void actionPerformed(ActionEvent e)
423 outputText_actionPerformed(e);
427 outputMenu.add(item);
431 * Build menus for annotation types that may be shown or hidden, and for
432 * 'reference annotations' that may be added to the alignment. First for the
433 * currently selected sequence (if there is one):
435 final List<SequenceI> selectedSequence = (forIdPanel && seq != null
437 : Collections.<SequenceI> emptyList());
438 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
439 seqHideAnnotationsMenu, selectedSequence);
440 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
444 * And repeat for the current selection group (if there is one):
446 final List<SequenceI> selectedGroup = (alignPanel.av
447 .getSelectionGroup() == null
448 ? Collections.<SequenceI> emptyList()
449 : alignPanel.av.getSelectionGroup().getSequences());
450 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
451 groupHideAnnotationsMenu, selectedGroup);
452 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
458 } catch (Exception e)
466 sequenceMenu.setText(sequence.getName());
467 if (seq == alignPanel.av.getAlignment().getSeqrep())
469 makeReferenceSeq.setText(
470 MessageManager.getString("action.unmark_as_reference"));
474 makeReferenceSeq.setText(
475 MessageManager.getString("action.set_as_reference"));
478 if (!alignPanel.av.getAlignment().isNucleotide())
480 remove(rnaStructureMenu);
484 int origCount = rnaStructureMenu.getItemCount();
486 * add menu items to 2D-render any alignment or sequence secondary
487 * structure annotation
489 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
490 .getAlignmentAnnotation();
493 for (final AlignmentAnnotation aa : aas)
495 if (aa.isValidStruc() && aa.sequenceRef == null)
498 * valid alignment RNA secondary structure annotation
500 menuItem = new JMenuItem();
501 menuItem.setText(MessageManager.formatMessage(
502 "label.2d_rna_structure_line", new Object[]
504 menuItem.addActionListener(new ActionListener()
507 public void actionPerformed(ActionEvent e)
509 new AppVarna(seq, aa, alignPanel);
512 rnaStructureMenu.add(menuItem);
517 if (seq.getAnnotation() != null)
519 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
520 for (final AlignmentAnnotation aa : seqAnns)
522 if (aa.isValidStruc())
525 * valid sequence RNA secondary structure annotation
527 // TODO: make rnastrucF a bit more nice
528 menuItem = new JMenuItem();
529 menuItem.setText(MessageManager.formatMessage(
530 "label.2d_rna_sequence_name", new Object[]
532 menuItem.addActionListener(new ActionListener()
535 public void actionPerformed(ActionEvent e)
537 // TODO: VARNA does'nt print gaps in the sequence
538 new AppVarna(seq, aa, alignPanel);
541 rnaStructureMenu.add(menuItem);
545 if (rnaStructureMenu.getItemCount() == origCount)
547 remove(rnaStructureMenu);
551 menuItem = new JMenuItem(
552 MessageManager.getString("action.hide_sequences"));
553 menuItem.addActionListener(new ActionListener()
556 public void actionPerformed(ActionEvent e)
558 hideSequences(false);
563 if (alignPanel.av.getSelectionGroup() != null
564 && alignPanel.av.getSelectionGroup().getSize() > 1)
566 menuItem = new JMenuItem(MessageManager
567 .formatMessage("label.represent_group_with", new Object[]
569 menuItem.addActionListener(new ActionListener()
572 public void actionPerformed(ActionEvent e)
577 sequenceMenu.add(menuItem);
580 if (alignPanel.av.hasHiddenRows())
582 final int index = alignPanel.av.getAlignment().findIndex(seq);
584 if (alignPanel.av.adjustForHiddenSeqs(index)
585 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
587 menuItem = new JMenuItem(
588 MessageManager.getString("action.reveal_sequences"));
589 menuItem.addActionListener(new ActionListener()
592 public void actionPerformed(ActionEvent e)
594 alignPanel.av.showSequence(index);
595 if (alignPanel.overviewPanel != null)
597 alignPanel.overviewPanel.updateOverviewImage();
608 * - in the IdPanel (seq not null) if any sequence is hidden
609 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
611 if (alignPanel.av.hasHiddenRows())
613 boolean addOption = seq != null;
614 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
620 JMenuItem menuItem = new JMenuItem(
621 MessageManager.getString("action.reveal_all"));
622 menuItem.addActionListener(new ActionListener()
625 public void actionPerformed(ActionEvent e)
627 alignPanel.av.showAllHiddenSeqs();
628 if (alignPanel.overviewPanel != null)
630 alignPanel.overviewPanel.updateOverviewImage();
638 SequenceGroup sg = alignPanel.av.getSelectionGroup();
639 boolean isDefinedGroup = (sg != null)
640 ? alignPanel.av.getAlignment().getGroups().contains(sg)
643 if (sg != null && sg.getSize() > 0)
645 groupName.setText(MessageManager
646 .getString("label.edit_name_and_description_current_group"));
648 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
650 conservationMenuItem.setEnabled(!sg.isNucleotide());
654 if (sg.cs.conservationApplied())
656 conservationMenuItem.setSelected(true);
658 if (sg.cs.getThreshold() > 0)
660 abovePIDColour.setSelected(true);
663 modifyConservation.setEnabled(conservationMenuItem.isSelected());
664 modifyPID.setEnabled(abovePIDColour.isSelected());
665 displayNonconserved.setSelected(sg.getShowNonconserved());
666 showText.setSelected(sg.getDisplayText());
667 showColourText.setSelected(sg.getColourText());
668 showBoxes.setSelected(sg.getDisplayBoxes());
669 // add any groupURLs to the groupURL submenu and make it visible
670 if (groupLinks != null && groupLinks.size() > 0)
672 buildGroupURLMenu(sg, groupLinks);
674 // Add a 'show all structures' for the current selection
675 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
676 reppdb = new Hashtable<>();
678 SequenceI sqass = null;
679 for (SequenceI sq : alignPanel.av.getSequenceSelection())
681 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
682 if (pes != null && pes.size() > 0)
684 reppdb.put(pes.get(0).getId(), pes.get(0));
685 for (PDBEntry pe : pes)
687 pdbe.put(pe.getId(), pe);
697 final PDBEntry[] pe = pdbe.values()
698 .toArray(new PDBEntry[pdbe.size()]),
699 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
700 final JMenuItem gpdbview, rpdbview;
705 groupMenu.setVisible(false);
706 editMenu.setVisible(false);
711 createGroupMenuItem.setVisible(true);
712 unGroupMenuItem.setVisible(false);
714 .setText(MessageManager.getString("action.edit_new_group"));
718 createGroupMenuItem.setVisible(false);
719 unGroupMenuItem.setVisible(true);
720 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
725 sequenceMenu.setVisible(false);
726 chooseStructure.setVisible(false);
727 rnaStructureMenu.setVisible(false);
730 addLinksAndFeatures(seq, column);
736 * <li>configured sequence database links (ID panel popup menu)</li>
737 * <li>non-positional feature links (ID panel popup menu)</li>
738 * <li>positional feature links (alignment panel popup menu)</li>
739 * <li>feature details links (alignment panel popup menu)</li>
741 * If this panel is also showed complementary (CDS/protein) features, then
742 * links to their feature details are also added.
747 void addLinksAndFeatures(final SequenceI seq, final int column)
749 List<SequenceFeature> features = null;
752 features = sequence.getFeatures().getNonPositionalFeatures();
756 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
760 addLinks(seq, features);
764 addFeatureDetails(features, seq, column);
769 * Add a menu item to show feature details for each sequence feature. Any
770 * linked 'virtual' features (CDS/protein) are also optionally found and
777 protected void addFeatureDetails(List<SequenceFeature> features,
778 final SequenceI seq, final int column)
781 * add features in CDS/protein complement at the corresponding
782 * position if configured to do so
784 MappedFeatures mf = null;
785 if (ap.av.isShowComplementFeatures())
787 if (!Comparison.isGap(sequence.getCharAt(column)))
789 AlignViewportI complement = ap.getAlignViewport()
790 .getCodingComplement();
791 AlignFrame af = Desktop.getAlignFrameFor(complement);
792 FeatureRendererModel fr2 = af.getFeatureRenderer();
793 int seqPos = sequence.findPosition(column);
794 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
798 if (features.isEmpty() && mf == null)
801 * no features to show at this position
806 JMenu details = new JMenu(
807 MessageManager.getString("label.feature_details"));
810 String name = seq.getName();
811 for (final SequenceFeature sf : features)
813 addFeatureDetailsMenuItem(details, name, sf, null);
818 for (final SequenceFeature sf : mf.features)
820 addFeatureDetailsMenuItem(details, name, sf, mf);
826 * A helper method to add one menu item whose action is to show details for
827 * one feature. The menu text includes feature description, but this may be
835 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
836 final SequenceFeature sf, MappedFeatures mf)
838 int start = sf.getBegin();
839 int end = sf.getEnd();
843 * show local rather than linked feature coordinates
845 int[] localRange = mf.getMappedPositions(start, end);
846 if (localRange == null)
848 // e.g. variant extending to stop codon so not mappable
851 start = localRange[0];
852 end = localRange[localRange.length - 1];
854 StringBuilder desc = new StringBuilder();
855 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
858 desc.append(sf.isContactFeature() ? ":" : "-");
859 desc.append(String.valueOf(end));
861 String description = sf.getDescription();
862 if (description != null)
865 description = StringUtils.stripHtmlTags(description);
868 * truncate overlong descriptions unless they contain an href
869 * (as truncation could leave corrupted html)
871 boolean hasLink = description.indexOf("a href") > -1;
872 if (description.length() > FEATURE_DESC_MAX && !hasLink)
874 description = description.substring(0, FEATURE_DESC_MAX) + "...";
876 desc.append(description);
878 String featureGroup = sf.getFeatureGroup();
879 if (featureGroup != null)
881 desc.append(" (").append(featureGroup).append(")");
883 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
884 JMenuItem item = new JMenuItem(htmlText);
885 item.addActionListener(new ActionListener()
888 public void actionPerformed(ActionEvent e)
890 showFeatureDetails(sf, seqName, mf);
897 * Opens a panel showing a text report of feature details
903 protected void showFeatureDetails(SequenceFeature sf, String seqName,
906 JInternalFrame details;
909 details = new JInternalFrame();
910 JPanel panel = new JPanel(new BorderLayout());
911 panel.setOpaque(true);
912 panel.setBackground(Color.white);
913 // TODO JAL-3026 set style of table correctly for feature details
914 JLabel reprt = new JLabel(MessageManager
915 .formatMessage("label.html_content", new Object[]
916 { sf.getDetailsReport(seqName, mf) }));
917 reprt.setBackground(Color.WHITE);
918 reprt.setOpaque(true);
919 panel.add(reprt, BorderLayout.CENTER);
920 details.setContentPane(panel);
930 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
931 // it appears Java's CSS does not support border-collapse :-(
932 cap.addStylesheetRule("table { border-collapse: collapse;}");
933 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
934 cap.setText(sf.getDetailsReport(seqName, mf));
937 Desktop.addInternalFrame(details,
938 MessageManager.getString("label.feature_details"), 500, 500);
942 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
943 * When seq is not null, these are links for the sequence id, which may be to
944 * external web sites for the sequence accession, and/or links embedded in
945 * non-positional features. When seq is null, only links embedded in the
946 * provided features are added. If no links are found, the menu is not added.
951 void addLinks(final SequenceI seq, List<SequenceFeature> features)
953 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
955 // only add link menu if it has entries
956 if (linkMenu.getItemCount() > 0)
960 sequenceMenu.add(linkMenu);
970 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
971 * "All" is added first, followed by a separator. Then add any annotation
972 * types associated with the current selection. Separate menus are built for
973 * the selected sequence group (if any), and the selected sequence.
975 * Some annotation rows are always rendered together - these can be identified
976 * by a common graphGroup property > -1. Only one of each group will be marked
977 * as visible (to avoid duplication of the display). For such groups we add a
978 * composite type name, e.g.
980 * IUPredWS (Long), IUPredWS (Short)
984 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
985 List<SequenceI> forSequences)
987 showMenu.removeAll();
988 hideMenu.removeAll();
990 final List<String> all = Arrays
992 { MessageManager.getString("label.all") });
993 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
995 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
997 showMenu.addSeparator();
998 hideMenu.addSeparator();
1000 final AlignmentAnnotation[] annotations = ap.getAlignment()
1001 .getAlignmentAnnotation();
1004 * Find shown/hidden annotations types, distinguished by source (calcId),
1005 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1006 * the insertion order, which is the order of the annotations on the
1009 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
1010 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
1011 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1012 AlignmentAnnotationUtils.asList(annotations), forSequences);
1014 for (String calcId : hiddenTypes.keySet())
1016 for (List<String> type : hiddenTypes.get(calcId))
1018 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1022 // grey out 'show annotations' if none are hidden
1023 showMenu.setEnabled(!hiddenTypes.isEmpty());
1025 for (String calcId : shownTypes.keySet())
1027 for (List<String> type : shownTypes.get(calcId))
1029 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1033 // grey out 'hide annotations' if none are shown
1034 hideMenu.setEnabled(!shownTypes.isEmpty());
1038 * Returns a list of sequences - either the current selection group (if there
1039 * is one), else the specified single sequence.
1044 protected List<SequenceI> getSequenceScope(SequenceI seq)
1046 List<SequenceI> forSequences = null;
1047 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1048 if (selectionGroup != null && selectionGroup.getSize() > 0)
1050 forSequences = selectionGroup.getSequences();
1054 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1055 : Arrays.asList(seq);
1057 return forSequences;
1061 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1064 * @param showOrHideMenu
1065 * the menu to add to
1066 * @param forSequences
1067 * the sequences whose annotations may be shown or hidden
1072 * if true this is a special label meaning 'All'
1073 * @param actionIsShow
1074 * if true, the select menu item action is to show the annotation
1077 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1078 final List<SequenceI> forSequences, String calcId,
1079 final List<String> types, final boolean allTypes,
1080 final boolean actionIsShow)
1082 String label = types.toString(); // [a, b, c]
1083 label = label.substring(1, label.length() - 1); // a, b, c
1084 final JMenuItem item = new JMenuItem(label);
1085 item.setToolTipText(calcId);
1086 item.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1092 types, forSequences, allTypes, actionIsShow);
1096 showOrHideMenu.add(item);
1099 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1102 // TODO: usability: thread off the generation of group url content so root
1103 // menu appears asap
1104 // sequence only URLs
1105 // ID/regex match URLs
1106 JMenu groupLinksMenu = new JMenu(
1107 MessageManager.getString("action.group_link"));
1108 // three types of url that might be created.
1109 JMenu[] linkMenus = new JMenu[] { null,
1110 new JMenu(MessageManager.getString("action.ids")),
1111 new JMenu(MessageManager.getString("action.sequences")),
1112 new JMenu(MessageManager.getString("action.ids_sequences")) };
1114 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1115 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1116 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1117 for (int sq = 0; sq < seqs.length; sq++)
1120 int start = seqs[sq].findPosition(sg.getStartRes()),
1121 end = seqs[sq].findPosition(sg.getEndRes());
1122 // just collect ids from dataset sequence
1123 // TODO: check if IDs collected from selecton group intersects with the
1124 // current selection, too
1125 SequenceI sqi = seqs[sq];
1126 while (sqi.getDatasetSequence() != null)
1128 sqi = sqi.getDatasetSequence();
1130 List<DBRefEntry> dbr = sqi.getDBRefs();
1132 if (dbr != null && (nd = dbr.size()) > 0)
1134 for (int d = 0; d < nd; d++)
1136 DBRefEntry e = dbr.get(d);
1137 String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
1138 Object[] sarray = commonDbrefs.get(src);
1141 sarray = new Object[2];
1142 sarray[0] = new int[] { 0 };
1143 sarray[1] = new String[seqs.length];
1145 commonDbrefs.put(src, sarray);
1148 if (((String[]) sarray[1])[sq] == null)
1151 || (e.getMap().locateMappedRange(start, end) != null))
1153 ((String[]) sarray[1])[sq] = e.getAccessionId();
1154 ((int[]) sarray[0])[0]++;
1160 // now create group links for all distinct ID/sequence sets.
1161 boolean addMenu = false; // indicates if there are any group links to give
1163 for (String link : groupLinks)
1165 GroupUrlLink urlLink = null;
1168 urlLink = new GroupUrlLink(link);
1169 } catch (Exception foo)
1171 Console.error("Exception for GroupURLLink '" + link + "'", foo);
1174 if (!urlLink.isValid())
1176 Console.error(urlLink.getInvalidMessage());
1179 final String label = urlLink.getLabel();
1180 boolean usingNames = false;
1181 // Now see which parts of the group apply for this URL
1182 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1183 Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
1184 String[] seqstr, ids; // input to makeUrl
1187 int numinput = ((int[]) idset[0])[0];
1188 String[] allids = ((String[]) idset[1]);
1189 seqstr = new String[numinput];
1190 ids = new String[numinput];
1191 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1193 if (allids[sq] != null)
1195 ids[idcount] = allids[sq];
1196 seqstr[idcount++] = idandseqs[1][sq];
1202 // just use the id/seq set
1203 seqstr = idandseqs[1];
1207 // and try and make the groupURL!
1209 Object[] urlset = null;
1212 urlset = urlLink.makeUrlStubs(ids, seqstr,
1213 "FromJalview" + System.currentTimeMillis(), false);
1214 } catch (UrlStringTooLongException e)
1219 int type = urlLink.getGroupURLType() & 3;
1220 // first two bits ofurlLink type bitfield are sequenceids and sequences
1221 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1222 addshowLink(linkMenus[type],
1223 label + (((type & 1) == 1)
1224 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1232 groupLinksMenu = new JMenu(
1233 MessageManager.getString("action.group_link"));
1234 for (int m = 0; m < linkMenus.length; m++)
1236 if (linkMenus[m] != null
1237 && linkMenus[m].getMenuComponentCount() > 0)
1239 groupLinksMenu.add(linkMenus[m]);
1243 groupMenu.add(groupLinksMenu);
1253 private void jbInit() throws Exception
1255 groupMenu.setText(MessageManager.getString("label.selection"));
1256 groupName.setText(MessageManager.getString("label.name"));
1257 groupName.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 groupName_actionPerformed();
1265 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1267 JMenuItem sequenceName = new JMenuItem(
1268 MessageManager.getString("label.edit_name_description"));
1269 sequenceName.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 sequenceName_actionPerformed();
1277 JMenuItem chooseAnnotations = new JMenuItem(
1278 MessageManager.getString("action.choose_annotations"));
1279 chooseAnnotations.addActionListener(new ActionListener()
1282 public void actionPerformed(ActionEvent e)
1284 chooseAnnotations_actionPerformed(e);
1287 JMenuItem sequenceDetails = new JMenuItem(
1288 MessageManager.getString("label.sequence_details"));
1289 sequenceDetails.addActionListener(new ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 createSequenceDetailsReport(new SequenceI[] { sequence });
1297 JMenuItem sequenceSelDetails = new JMenuItem(
1298 MessageManager.getString("label.sequence_details"));
1299 sequenceSelDetails.addActionListener(new ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 createSequenceDetailsReport(ap.av.getSequenceSelection());
1309 .setText(MessageManager.getString("action.remove_group"));
1310 unGroupMenuItem.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent e)
1315 unGroupMenuItem_actionPerformed();
1319 .setText(MessageManager.getString("action.create_group"));
1320 createGroupMenuItem.addActionListener(new ActionListener()
1323 public void actionPerformed(ActionEvent e)
1325 createGroupMenuItem_actionPerformed();
1329 JMenuItem outline = new JMenuItem(
1330 MessageManager.getString("action.border_colour"));
1331 outline.addActionListener(new ActionListener()
1334 public void actionPerformed(ActionEvent e)
1336 outline_actionPerformed();
1339 showBoxes.setText(MessageManager.getString("action.boxes"));
1340 showBoxes.setState(true);
1341 showBoxes.addActionListener(new ActionListener()
1344 public void actionPerformed(ActionEvent e)
1346 showBoxes_actionPerformed();
1349 showText.setText(MessageManager.getString("action.text"));
1350 showText.setState(true);
1351 showText.addActionListener(new ActionListener()
1354 public void actionPerformed(ActionEvent e)
1356 showText_actionPerformed();
1359 showColourText.setText(MessageManager.getString("label.colour_text"));
1360 showColourText.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 showColourText_actionPerformed();
1369 .setText(MessageManager.getString("label.show_non_conserved"));
1370 displayNonconserved.setState(true);
1371 displayNonconserved.addActionListener(new ActionListener()
1374 public void actionPerformed(ActionEvent e)
1376 showNonconserved_actionPerformed();
1379 editMenu.setText(MessageManager.getString("action.edit"));
1380 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1381 cut.addActionListener(new ActionListener()
1384 public void actionPerformed(ActionEvent e)
1386 cut_actionPerformed();
1389 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1390 upperCase.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1398 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1399 copy.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 copy_actionPerformed();
1407 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1408 lowerCase.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1416 toggle.setText(MessageManager.getString("label.toggle_case"));
1417 toggle.addActionListener(new ActionListener()
1420 public void actionPerformed(ActionEvent e)
1426 MessageManager.getString("label.out_to_textbox") + "...");
1427 seqShowAnnotationsMenu
1428 .setText(MessageManager.getString("label.show_annotations"));
1429 seqHideAnnotationsMenu
1430 .setText(MessageManager.getString("label.hide_annotations"));
1431 groupShowAnnotationsMenu
1432 .setText(MessageManager.getString("label.show_annotations"));
1433 groupHideAnnotationsMenu
1434 .setText(MessageManager.getString("label.hide_annotations"));
1435 JMenuItem sequenceFeature = new JMenuItem(
1436 MessageManager.getString("label.create_sequence_feature"));
1437 sequenceFeature.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1442 sequenceFeature_actionPerformed();
1445 editGroupMenu.setText(MessageManager.getString("label.group"));
1446 chooseStructure.setText(
1447 MessageManager.getString("label.show_pdbstruct_dialog"));
1448 chooseStructure.addActionListener(new ActionListener()
1451 public void actionPerformed(ActionEvent actionEvent)
1453 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1454 if (ap.av.getSelectionGroup() != null)
1456 selectedSeqs = ap.av.getSequenceSelection();
1458 new StructureChooser(selectedSeqs, sequence, ap);
1463 .setText(MessageManager.getString("label.view_rna_structure"));
1465 // colStructureMenu.setText("Colour By Structure");
1466 JMenuItem editSequence = new JMenuItem(
1467 MessageManager.getString("label.edit_sequence") + "...");
1468 editSequence.addActionListener(new ActionListener()
1471 public void actionPerformed(ActionEvent actionEvent)
1473 editSequence_actionPerformed();
1476 makeReferenceSeq.setText(
1477 MessageManager.getString("label.mark_as_representative"));
1478 makeReferenceSeq.addActionListener(new ActionListener()
1482 public void actionPerformed(ActionEvent actionEvent)
1484 makeReferenceSeq_actionPerformed(actionEvent);
1489 groupMenu.add(sequenceSelDetails);
1492 add(rnaStructureMenu);
1493 add(chooseStructure);
1496 JMenuItem hideInsertions = new JMenuItem(
1497 MessageManager.getString("label.hide_insertions"));
1498 hideInsertions.addActionListener(new ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 hideInsertions_actionPerformed(e);
1507 add(hideInsertions);
1509 // annotations configuration panel suppressed for now
1510 // groupMenu.add(chooseAnnotations);
1513 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1514 * (if a selection group is in force).
1516 sequenceMenu.add(seqShowAnnotationsMenu);
1517 sequenceMenu.add(seqHideAnnotationsMenu);
1518 sequenceMenu.add(seqAddReferenceAnnotations);
1519 groupMenu.add(groupShowAnnotationsMenu);
1520 groupMenu.add(groupHideAnnotationsMenu);
1521 groupMenu.add(groupAddReferenceAnnotations);
1522 groupMenu.add(editMenu);
1523 groupMenu.add(outputMenu);
1524 groupMenu.add(sequenceFeature);
1525 groupMenu.add(createGroupMenuItem);
1526 groupMenu.add(unGroupMenuItem);
1527 groupMenu.add(editGroupMenu);
1528 sequenceMenu.add(sequenceName);
1529 sequenceMenu.add(sequenceDetails);
1530 sequenceMenu.add(makeReferenceSeq);
1537 editMenu.add(editSequence);
1538 editMenu.add(upperCase);
1539 editMenu.add(lowerCase);
1540 editMenu.add(toggle);
1541 editGroupMenu.add(groupName);
1542 editGroupMenu.add(colourMenu);
1543 editGroupMenu.add(showBoxes);
1544 editGroupMenu.add(showText);
1545 editGroupMenu.add(showColourText);
1546 editGroupMenu.add(outline);
1547 editGroupMenu.add(displayNonconserved);
1551 * Constructs the entries for the colour menu
1553 protected void initColourMenu()
1555 colourMenu.setText(MessageManager.getString("label.group_colour"));
1556 textColour.setText(MessageManager.getString("label.text_colour"));
1557 textColour.addActionListener(new ActionListener()
1560 public void actionPerformed(ActionEvent e)
1562 textColour_actionPerformed();
1566 abovePIDColour.setText(
1567 MessageManager.getString("label.above_identity_threshold"));
1568 abovePIDColour.addActionListener(new ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1578 MessageManager.getString("label.modify_identity_threshold"));
1579 modifyPID.addActionListener(new ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 modifyPID_actionPerformed();
1588 conservationMenuItem
1589 .setText(MessageManager.getString("action.by_conservation"));
1590 conservationMenuItem.addActionListener(new ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 conservationMenuItem_actionPerformed(
1596 conservationMenuItem.isSelected());
1600 annotationColour = new JRadioButtonMenuItem(
1601 MessageManager.getString("action.by_annotation"));
1602 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1603 annotationColour.setEnabled(false);
1604 annotationColour.setToolTipText(
1605 MessageManager.getString("label.by_annotation_tooltip"));
1607 modifyConservation.setText(MessageManager
1608 .getString("label.modify_conservation_threshold"));
1609 modifyConservation.addActionListener(new ActionListener()
1612 public void actionPerformed(ActionEvent e)
1614 modifyConservation_actionPerformed();
1620 * Builds the group colour sub-menu, including any user-defined colours which
1621 * were loaded at startup or during the Jalview session
1623 protected void buildColourMenu()
1625 SequenceGroup sg = ap.av.getSelectionGroup();
1629 * popup menu with no sequence group scope
1633 colourMenu.removeAll();
1634 colourMenu.add(textColour);
1635 colourMenu.addSeparator();
1637 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1639 bg.add(annotationColour);
1640 colourMenu.add(annotationColour);
1642 colourMenu.addSeparator();
1643 colourMenu.add(conservationMenuItem);
1644 colourMenu.add(modifyConservation);
1645 colourMenu.add(abovePIDColour);
1646 colourMenu.add(modifyPID);
1649 protected void modifyConservation_actionPerformed()
1651 SequenceGroup sg = getGroup();
1654 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1655 SliderPanel.showConservationSlider();
1659 protected void modifyPID_actionPerformed()
1661 SequenceGroup sg = getGroup();
1664 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1666 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1667 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1668 SliderPanel.showPIDSlider();
1673 * Check for any annotations on the underlying dataset sequences (for the
1674 * current selection group) which are not 'on the alignment'.If any are found,
1675 * enable the option to add them to the alignment. The criteria for 'on the
1676 * alignment' is finding an alignment annotation on the alignment, matched on
1677 * calcId, label and sequenceRef.
1679 * A tooltip is also constructed that displays the source (calcId) and type
1680 * (label) of the annotations that can be added.
1683 * @param forSequences
1685 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1686 List<SequenceI> forSequences)
1688 menuItem.setEnabled(false);
1691 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1692 * Using TreeMap means calcIds are shown in alphabetical order.
1694 SortedMap<String, String> tipEntries = new TreeMap<>();
1695 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1696 AlignmentI al = this.ap.av.getAlignment();
1697 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1699 if (!candidates.isEmpty())
1701 StringBuilder tooltip = new StringBuilder(64);
1702 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1705 * Found annotations that could be added. Enable the menu item, and
1706 * configure its tooltip and action.
1708 menuItem.setEnabled(true);
1709 for (String calcId : tipEntries.keySet())
1711 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1713 String tooltipText = JvSwingUtils.wrapTooltip(true,
1714 tooltip.toString());
1715 menuItem.setToolTipText(tooltipText);
1717 menuItem.addActionListener(new ActionListener()
1720 public void actionPerformed(ActionEvent e)
1722 addReferenceAnnotations_actionPerformed(candidates);
1729 * Add annotations to the sequences and to the alignment.
1732 * a map whose keys are sequences on the alignment, and values a list
1733 * of annotations to add to each sequence
1735 protected void addReferenceAnnotations_actionPerformed(
1736 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1738 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1739 final AlignmentI alignment = this.ap.getAlignment();
1740 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1745 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1747 if (!ap.av.getAlignment().hasSeqrep())
1749 // initialise the display flags so the user sees something happen
1750 ap.av.setDisplayReferenceSeq(true);
1751 ap.av.setColourByReferenceSeq(true);
1752 ap.av.getAlignment().setSeqrep(sequence);
1756 if (ap.av.getAlignment().getSeqrep() == sequence)
1758 ap.av.getAlignment().setSeqrep(null);
1762 ap.av.getAlignment().setSeqrep(sequence);
1768 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1770 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1771 BitSet inserts = new BitSet();
1773 boolean markedPopup = false;
1774 // mark inserts in current selection
1775 if (ap.av.getSelectionGroup() != null)
1777 // mark just the columns in the selection group to be hidden
1778 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1779 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1781 // now clear columns without gaps
1782 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1788 inserts.and(sq.getInsertionsAsBits());
1790 hidden.clearAndHideColumns(inserts,
1791 ap.av.getSelectionGroup().getStartRes(),
1792 ap.av.getSelectionGroup().getEndRes());
1795 // now mark for sequence under popup if we haven't already done it
1796 else if (!markedPopup && sequence != null)
1798 inserts.or(sequence.getInsertionsAsBits());
1800 // and set hidden columns accordingly
1801 hidden.hideColumns(inserts);
1806 protected void sequenceSelectionDetails_actionPerformed()
1808 createSequenceDetailsReport(ap.av.getSequenceSelection());
1811 public void createSequenceDetailsReport(SequenceI[] sequences)
1813 StringBuilder contents = new StringBuilder(128);
1814 contents.append("<html><body>");
1815 for (SequenceI seq : sequences)
1817 contents.append("<p><h2>" + MessageManager.formatMessage(
1818 "label.create_sequence_details_report_annotation_for",
1820 { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
1821 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1822 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1823 contents.append("</p>");
1825 contents.append("</body></html>");
1826 String report = contents.toString();
1828 JInternalFrame frame;
1829 if (Platform.isJS())
1831 JLabel textLabel = new JLabel();
1832 textLabel.setText(report);
1833 textLabel.setBackground(Color.WHITE);
1834 JPanel pane = new JPanel(new BorderLayout());
1835 pane.setOpaque(true);
1836 pane.setBackground(Color.WHITE);
1837 pane.add(textLabel, BorderLayout.NORTH);
1838 frame = new JInternalFrame();
1839 frame.getContentPane().add(new JScrollPane(pane));
1848 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1849 cap.setText(report);
1853 Desktop.addInternalFrame(frame,
1854 MessageManager.formatMessage("label.sequence_details_for",
1855 (sequences.length == 1 ? new Object[]
1856 { sequences[0].getDisplayId(true) }
1859 .getString("label.selection") })),
1863 protected void showNonconserved_actionPerformed()
1865 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1870 * call to refresh view after settings change
1874 ap.updateAnnotation();
1875 // removed paintAlignment(true) here:
1876 // updateAnnotation calls paintAlignment already, so don't need to call
1879 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1883 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1884 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1894 public void abovePIDColour_actionPerformed(boolean selected)
1896 SequenceGroup sg = getGroup();
1904 sg.cs.setConsensus(AAFrequency.calculate(
1905 sg.getSequences(ap.av.getHiddenRepSequences()),
1906 sg.getStartRes(), sg.getEndRes() + 1));
1908 int threshold = SliderPanel.setPIDSliderSource(ap,
1909 sg.getGroupColourScheme(), getGroup().getName());
1911 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1913 SliderPanel.showPIDSlider();
1916 // remove PIDColouring
1918 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1919 SliderPanel.hidePIDSlider();
1921 modifyPID.setEnabled(selected);
1927 * Open a panel where the user can choose which types of sequence annotation
1932 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1934 // todo correct way to guard against opening a duplicate panel?
1935 new AnnotationChooser(ap);
1944 public void conservationMenuItem_actionPerformed(boolean selected)
1946 SequenceGroup sg = getGroup();
1954 // JBPNote: Conservation name shouldn't be i18n translated
1955 Conservation c = new Conservation("Group",
1956 sg.getSequences(ap.av.getHiddenRepSequences()),
1957 sg.getStartRes(), sg.getEndRes() + 1);
1960 c.verdict(false, ap.av.getConsPercGaps());
1961 sg.cs.setConservation(c);
1963 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1965 SliderPanel.showConservationSlider();
1968 // remove ConservationColouring
1970 sg.cs.setConservation(null);
1971 SliderPanel.hideConservationSlider();
1973 modifyConservation.setEnabled(selected);
1979 * Shows a dialog where group name and description may be edited
1981 protected void groupName_actionPerformed()
1983 SequenceGroup sg = getGroup();
1984 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1985 sg.getDescription(),
1986 MessageManager.getString("label.group_name"),
1987 MessageManager.getString("label.group_description"));
1988 dialog.showDialog(ap.alignFrame,
1989 MessageManager.getString("label.edit_group_name_description"),
1995 sg.setName(dialog.getName());
1996 sg.setDescription(dialog.getDescription());
2003 * Get selection group - adding it to the alignment if necessary.
2005 * @return sequence group to operate on
2007 SequenceGroup getGroup()
2009 SequenceGroup sg = ap.av.getSelectionGroup();
2010 // this method won't add a new group if it already exists
2013 ap.av.getAlignment().addGroup(sg);
2020 * Shows a dialog where the sequence name and description may be edited. If a
2021 * name containing spaces is entered, these are converted to underscores, with
2022 * a warning message.
2024 void sequenceName_actionPerformed()
2026 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2027 sequence.getDescription(),
2028 MessageManager.getString("label.sequence_name"),
2029 MessageManager.getString("label.sequence_description"));
2030 dialog.showDialog(ap.alignFrame, MessageManager.getString(
2031 "label.edit_sequence_name_description"), new Runnable()
2036 if (dialog.getName() != null)
2038 if (dialog.getName().indexOf(" ") > -1)
2040 JvOptionPane.showMessageDialog(ap,
2041 MessageManager.getString(
2042 "label.spaces_converted_to_underscores"),
2043 MessageManager.getString(
2044 "label.no_spaces_allowed_sequence_name"),
2045 JvOptionPane.WARNING_MESSAGE);
2047 sequence.setName(dialog.getName().replace(' ', '_'));
2048 ap.paintAlignment(false, false);
2050 sequence.setDescription(dialog.getDescription());
2051 ap.av.firePropertyChange("alignment", null,
2052 ap.av.getAlignment().getSequences());
2063 void unGroupMenuItem_actionPerformed()
2065 SequenceGroup sg = ap.av.getSelectionGroup();
2066 ap.av.getAlignment().deleteGroup(sg);
2067 ap.av.setSelectionGroup(null);
2071 void createGroupMenuItem_actionPerformed()
2073 getGroup(); // implicitly creates group - note - should apply defaults / use
2074 // standard alignment window logic for this
2079 * Offers a colour chooser and sets the selected colour as the group outline
2081 protected void outline_actionPerformed()
2083 String title = MessageManager.getString("label.select_outline_colour");
2084 ColourChooserListener listener = new ColourChooserListener()
2087 public void colourSelected(Color c)
2089 getGroup().setOutlineColour(c);
2093 JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
2094 Color.BLUE, listener);
2103 public void showBoxes_actionPerformed()
2105 getGroup().setDisplayBoxes(showBoxes.isSelected());
2115 public void showText_actionPerformed()
2117 getGroup().setDisplayText(showText.isSelected());
2127 public void showColourText_actionPerformed()
2129 getGroup().setColourText(showColourText.isSelected());
2133 void hideSequences(boolean representGroup)
2135 ap.av.hideSequences(sequence, representGroup);
2138 public void copy_actionPerformed()
2140 ap.alignFrame.copy_actionPerformed();
2143 public void cut_actionPerformed()
2145 ap.alignFrame.cut_actionPerformed();
2148 void changeCase(ActionEvent e)
2150 Object source = e.getSource();
2151 SequenceGroup sg = ap.av.getSelectionGroup();
2155 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2156 sg.getStartRes(), sg.getEndRes() + 1);
2161 if (source == toggle)
2163 description = MessageManager.getString("label.toggle_case");
2164 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2166 else if (source == upperCase)
2168 description = MessageManager.getString("label.to_upper_case");
2169 caseChange = ChangeCaseCommand.TO_UPPER;
2173 description = MessageManager.getString("label.to_lower_case");
2174 caseChange = ChangeCaseCommand.TO_LOWER;
2177 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2178 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2179 startEnd, caseChange);
2181 ap.alignFrame.addHistoryItem(caseCommand);
2183 ap.av.firePropertyChange("alignment", null,
2184 ap.av.getAlignment().getSequences());
2189 public void outputText_actionPerformed(ActionEvent e)
2191 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2192 cap.setForInput(null);
2193 Desktop.addInternalFrame(cap, MessageManager
2194 .formatMessage("label.alignment_output_command", new Object[]
2195 { e.getActionCommand() }), 600, 500);
2197 String[] omitHidden = null;
2199 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2200 // or we simply trust the user wants
2201 // wysiwig behaviour
2203 FileFormatI fileFormat = FileFormats.getInstance()
2204 .forName(e.getActionCommand());
2206 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2209 public void sequenceFeature_actionPerformed()
2211 SequenceGroup sg = ap.av.getSelectionGroup();
2217 List<SequenceI> seqs = new ArrayList<>();
2218 List<SequenceFeature> features = new ArrayList<>();
2221 * assemble dataset sequences, and template new sequence features,
2222 * for the amend features dialog
2224 int gSize = sg.getSize();
2225 for (int i = 0; i < gSize; i++)
2227 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2228 int end = sg.findEndRes(sg.getSequenceAt(i));
2231 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2232 features.add(new SequenceFeature(null, null, start, end, null));
2237 * an entirely gapped region will generate empty lists of sequence / features
2239 if (!seqs.isEmpty())
2241 new FeatureEditor(ap, seqs, features, true).showDialog();
2245 public void textColour_actionPerformed()
2247 SequenceGroup sg = getGroup();
2250 new TextColourChooser().chooseColour(ap, sg);
2255 * Shows a dialog where sequence characters may be edited. Any changes are
2256 * applied, and added as an available 'Undo' item in the edit commands
2259 public void editSequence_actionPerformed()
2261 SequenceGroup sg = ap.av.getSelectionGroup();
2263 SequenceI seq = sequence;
2268 seq = sg.getSequenceAt(0);
2271 EditNameDialog dialog = new EditNameDialog(
2272 seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
2273 null, MessageManager.getString("label.edit_sequence"), null);
2274 dialog.showDialog(ap.alignFrame,
2275 MessageManager.getString("label.edit_sequence"),
2281 EditCommand editCommand = new EditCommand(
2282 MessageManager.getString("label.edit_sequences"),
2284 dialog.getName().replace(' ',
2285 ap.av.getGapCharacter()),
2286 sg.getSequencesAsArray(
2287 ap.av.getHiddenRepSequences()),
2288 sg.getStartRes(), sg.getEndRes() + 1,
2289 ap.av.getAlignment());
2290 ap.alignFrame.addHistoryItem(editCommand);
2291 ap.av.firePropertyChange("alignment", null,
2292 ap.av.getAlignment().getSequences());
2299 * Action on user selecting an item from the colour menu (that does not have
2300 * its bespoke action handler)
2305 public void changeColour_actionPerformed(String colourSchemeName)
2307 SequenceGroup sg = getGroup();
2309 * switch to the chosen colour scheme (or null for None)
2311 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2312 .getColourScheme(colourSchemeName, ap.av, sg,
2313 ap.av.getHiddenRepSequences());
2314 sg.setColourScheme(colourScheme);
2315 if (colourScheme instanceof Blosum62ColourScheme
2316 || colourScheme instanceof PIDColourScheme)
2318 sg.cs.setConsensus(AAFrequency.calculate(
2319 sg.getSequences(ap.av.getHiddenRepSequences()),
2320 sg.getStartRes(), sg.getEndRes() + 1));