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.awt.BorderLayout;
24 import java.awt.Color;
25 import java.awt.event.ActionEvent;
26 import java.awt.event.ActionListener;
27 import java.util.ArrayList;
28 import java.util.Arrays;
29 import java.util.BitSet;
30 import java.util.Collection;
31 import java.util.Collections;
32 import java.util.Hashtable;
33 import java.util.LinkedHashMap;
34 import java.util.List;
35 import java.util.Locale;
37 import java.util.Objects;
38 import java.util.SortedMap;
39 import java.util.TreeMap;
40 import java.util.Vector;
42 import javax.swing.ButtonGroup;
43 import javax.swing.JCheckBoxMenuItem;
44 import javax.swing.JInternalFrame;
45 import javax.swing.JLabel;
46 import javax.swing.JMenu;
47 import javax.swing.JMenuItem;
48 import javax.swing.JPanel;
49 import javax.swing.JPopupMenu;
50 import javax.swing.JRadioButtonMenuItem;
51 import javax.swing.JScrollPane;
53 import jalview.analysis.AAFrequency;
54 import jalview.analysis.AlignmentAnnotationUtils;
55 import jalview.analysis.AlignmentUtils;
56 import jalview.analysis.Conservation;
57 import jalview.api.AlignCalcWorkerI;
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;
91 import jalview.workers.SecondaryStructureConsensusThread;
94 * The popup menu that is displayed on right-click on a sequence id, or in the
97 public class PopupMenu extends JPopupMenu implements ColourChangeListener
100 * maximum length of feature description to include in popup menu item text
102 private static final int FEATURE_DESC_MAX = 40;
105 * true for ID Panel menu, false for alignment panel menu
107 private final boolean forIdPanel;
109 private final AlignmentPanel ap;
112 * the sequence under the cursor when clicked
113 * (additional sequences may be selected)
115 private final SequenceI sequence;
117 JMenu groupMenu = new JMenu();
119 JMenuItem groupName = new JMenuItem();
121 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
123 protected JMenuItem modifyPID = new JMenuItem();
125 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
127 protected JRadioButtonMenuItem annotationColour;
129 protected JMenuItem modifyConservation = new JMenuItem();
131 JMenu sequenceMenu = new JMenu();
133 JMenuItem makeReferenceSeq = new JMenuItem();
135 JMenuItem createGroupMenuItem = new JMenuItem();
137 JMenuItem unGroupMenuItem = new JMenuItem();
139 JMenu colourMenu = new JMenu();
141 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
143 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
145 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
147 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
149 JMenu editMenu = new JMenu();
151 JMenuItem upperCase = new JMenuItem();
153 JMenuItem lowerCase = new JMenuItem();
155 JMenuItem toggle = new JMenuItem();
157 JMenu outputMenu = new JMenu();
159 JMenu seqShowAnnotationsMenu = new JMenu();
161 JMenu seqHideAnnotationsMenu = new JMenu();
163 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
164 MessageManager.getString("label.add_reference_annotations"));
166 JMenu groupShowAnnotationsMenu = new JMenu();
168 JMenu groupHideAnnotationsMenu = new JMenu();
170 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
171 MessageManager.getString("label.add_reference_annotations"));
173 JMenuItem textColour = new JMenuItem();
175 JMenu editGroupMenu = new JMenu();
177 JMenuItem chooseStructure = new JMenuItem();
179 JMenu rnaStructureMenu = new JMenu();
182 * Constructs a menu with sub-menu items for any hyperlinks for the sequence
183 * and/or features provided. Hyperlinks may include a lookup by sequence id,
184 * or database cross-references, depending on which links are enabled in user
191 protected static JMenu buildLinkMenu(final SequenceI seq,
192 List<SequenceFeature> features)
194 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
196 List<String> nlinks = null;
199 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
200 UrlLink.sort(nlinks);
204 nlinks = new ArrayList<>();
207 if (features != null)
209 for (SequenceFeature sf : features)
211 if (sf.links != null)
213 for (String link : sf.links)
222 * instantiate the hyperlinklink templates from sequence data;
223 * note the order of the templates is preserved in the map
225 Map<String, List<String>> linkset = new LinkedHashMap<>();
226 for (String link : nlinks)
228 UrlLink urlLink = null;
231 urlLink = new UrlLink(link);
232 } catch (Exception foo)
234 Console.error("Exception for URLLink '" + link + "'", foo);
238 if (!urlLink.isValid())
240 Console.error(urlLink.getInvalidMessage());
244 urlLink.createLinksFromSeq(seq, linkset);
248 * construct menu items for the hyperlinks (still preserving
249 * the order of the sorted templates)
251 addUrlLinks(linkMenu, linkset.values());
257 * A helper method that builds menu items from the given links, with action
258 * handlers to open the link URL, and adds them to the linkMenu. Each provided
259 * link should be a list whose second item is the menu text, and whose fourth
260 * item is the URL to open when the menu item is selected.
265 static private void addUrlLinks(JMenu linkMenu,
266 Collection<List<String>> linkset)
268 for (List<String> linkstrset : linkset)
270 final String url = linkstrset.get(3);
271 JMenuItem item = new JMenuItem(linkstrset.get(1));
272 item.setToolTipText(MessageManager
273 .formatMessage("label.open_url_param", new Object[]
275 item.addActionListener(new ActionListener()
278 public void actionPerformed(ActionEvent e)
280 new Thread(new Runnable()
295 * Opens the provided url in the default web browser, or shows an error
296 * message if this fails
300 static void showLink(String url)
304 jalview.util.BrowserLauncher.openURL(url);
305 } catch (Exception ex)
307 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
308 MessageManager.getString("label.web_browser_not_found_unix"),
309 MessageManager.getString("label.web_browser_not_found"),
310 JvOptionPane.WARNING_MESSAGE);
312 ex.printStackTrace();
317 * add a late bound groupURL item to the given linkMenu
321 * - menu label string
322 * @param urlgenerator
323 * GroupURLLink used to generate URL
325 * Object array returned from the makeUrlStubs function.
327 static void addshowLink(JMenu linkMenu, String label,
328 final GroupUrlLink urlgenerator, final Object[] urlstub)
330 JMenuItem item = new JMenuItem(label);
331 item.setToolTipText(MessageManager
332 .formatMessage("label.open_url_seqs_param", new Object[]
333 { urlgenerator.getUrl_prefix(),
334 urlgenerator.getNumberInvolved(urlstub) }));
335 // TODO: put in info about what is being sent.
336 item.addActionListener(new ActionListener()
339 public void actionPerformed(ActionEvent e)
341 new Thread(new Runnable()
349 showLink(urlgenerator.constructFrom(urlstub));
350 } catch (UrlStringTooLongException e2)
363 * Constructor for a PopupMenu for a click in the alignment panel (on a
367 * the panel in which the mouse is clicked
369 * the sequence under the mouse
370 * @throws NullPointerException
373 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
375 this(false, ap, seq, column, null);
379 * Constructor for a PopupMenu for a click in the sequence id panel
382 * the panel in which the mouse is clicked
384 * the sequence under the mouse click
386 * templates for sequence external links
387 * @throws NullPointerException
390 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
391 List<String> groupLinks)
393 this(true, alignPanel, seq, -1, groupLinks);
397 * Private constructor that constructs a popup menu for either sequence ID
398 * Panel, or alignment context
404 * aligned column position (0...)
407 private PopupMenu(boolean fromIdPanel, final AlignmentPanel alignPanel,
408 final SequenceI seq, final int column, List<String> groupLinks)
410 Objects.requireNonNull(seq);
411 this.forIdPanel = fromIdPanel;
412 this.ap = alignPanel;
415 for (String ff : FileFormats.getInstance().getWritableFormats(true))
417 JMenuItem item = new JMenuItem(ff);
419 item.addActionListener(new ActionListener()
422 public void actionPerformed(ActionEvent e)
424 outputText_actionPerformed(e);
428 outputMenu.add(item);
432 * Build menus for annotation types that may be shown or hidden, and for
433 * 'reference annotations' that may be added to the alignment. First for the
434 * currently selected sequence (if there is one):
436 final List<SequenceI> selectedSequence = (forIdPanel && seq != null
438 : Collections.<SequenceI> emptyList());
439 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
440 seqHideAnnotationsMenu, selectedSequence);
441 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
445 * And repeat for the current selection group (if there is one):
447 final List<SequenceI> selectedGroup = (alignPanel.av
448 .getSelectionGroup() == null
449 ? Collections.<SequenceI> emptyList()
450 : alignPanel.av.getSelectionGroup().getSequences());
451 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
452 groupHideAnnotationsMenu, selectedGroup);
453 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
459 } catch (Exception e)
467 sequenceMenu.setText(sequence.getName());
468 if (seq == alignPanel.av.getAlignment().getSeqrep())
470 makeReferenceSeq.setText(
471 MessageManager.getString("action.unmark_as_reference"));
475 makeReferenceSeq.setText(
476 MessageManager.getString("action.set_as_reference"));
479 if (!alignPanel.av.getAlignment().isNucleotide())
481 remove(rnaStructureMenu);
485 int origCount = rnaStructureMenu.getItemCount();
487 * add menu items to 2D-render any alignment or sequence secondary
488 * structure annotation
490 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
491 .getAlignmentAnnotation();
494 for (final AlignmentAnnotation aa : aas)
496 if (aa.isValidStruc() && aa.sequenceRef == null)
499 * valid alignment RNA secondary structure annotation
501 menuItem = new JMenuItem();
502 menuItem.setText(MessageManager.formatMessage(
503 "label.2d_rna_structure_line", new Object[]
505 menuItem.addActionListener(new ActionListener()
508 public void actionPerformed(ActionEvent e)
510 new AppVarna(seq, aa, alignPanel);
513 rnaStructureMenu.add(menuItem);
518 if (seq.getAnnotation() != null)
520 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
521 for (final AlignmentAnnotation aa : seqAnns)
523 if (aa.isValidStruc())
526 * valid sequence RNA secondary structure annotation
528 // TODO: make rnastrucF a bit more nice
529 menuItem = new JMenuItem();
530 menuItem.setText(MessageManager.formatMessage(
531 "label.2d_rna_sequence_name", new Object[]
533 menuItem.addActionListener(new ActionListener()
536 public void actionPerformed(ActionEvent e)
538 // TODO: VARNA does'nt print gaps in the sequence
539 new AppVarna(seq, aa, alignPanel);
542 rnaStructureMenu.add(menuItem);
546 if (rnaStructureMenu.getItemCount() == origCount)
548 remove(rnaStructureMenu);
552 menuItem = new JMenuItem(
553 MessageManager.getString("action.hide_sequences"));
554 menuItem.addActionListener(new ActionListener()
557 public void actionPerformed(ActionEvent e)
559 hideSequences(false);
564 if (alignPanel.av.getSelectionGroup() != null
565 && alignPanel.av.getSelectionGroup().getSize() > 1)
567 menuItem = new JMenuItem(MessageManager
568 .formatMessage("label.represent_group_with", new Object[]
570 menuItem.addActionListener(new ActionListener()
573 public void actionPerformed(ActionEvent e)
578 sequenceMenu.add(menuItem);
581 if (alignPanel.av.hasHiddenRows())
583 final int index = alignPanel.av.getAlignment().findIndex(seq);
585 if (alignPanel.av.adjustForHiddenSeqs(index)
586 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
588 menuItem = new JMenuItem(
589 MessageManager.getString("action.reveal_sequences"));
590 menuItem.addActionListener(new ActionListener()
593 public void actionPerformed(ActionEvent e)
595 alignPanel.av.showSequence(index);
596 if (alignPanel.overviewPanel != null)
598 alignPanel.overviewPanel.updateOverviewImage();
609 * - in the IdPanel (seq not null) if any sequence is hidden
610 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
612 if (alignPanel.av.hasHiddenRows())
614 boolean addOption = seq != null;
615 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
621 JMenuItem menuItem = new JMenuItem(
622 MessageManager.getString("action.reveal_all"));
623 menuItem.addActionListener(new ActionListener()
626 public void actionPerformed(ActionEvent e)
628 alignPanel.av.showAllHiddenSeqs();
629 if (alignPanel.overviewPanel != null)
631 alignPanel.overviewPanel.updateOverviewImage();
639 SequenceGroup sg = alignPanel.av.getSelectionGroup();
640 boolean isDefinedGroup = (sg != null)
641 ? alignPanel.av.getAlignment().getGroups().contains(sg)
644 if (sg != null && sg.getSize() > 0)
646 groupName.setText(MessageManager
647 .getString("label.edit_name_and_description_current_group"));
649 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
651 conservationMenuItem.setEnabled(!sg.isNucleotide());
655 if (sg.cs.conservationApplied())
657 conservationMenuItem.setSelected(true);
659 if (sg.cs.getThreshold() > 0)
661 abovePIDColour.setSelected(true);
664 modifyConservation.setEnabled(conservationMenuItem.isSelected());
665 modifyPID.setEnabled(abovePIDColour.isSelected());
666 displayNonconserved.setSelected(sg.getShowNonconserved());
667 showText.setSelected(sg.getDisplayText());
668 showColourText.setSelected(sg.getColourText());
669 showBoxes.setSelected(sg.getDisplayBoxes());
670 // add any groupURLs to the groupURL submenu and make it visible
671 if (groupLinks != null && groupLinks.size() > 0)
673 buildGroupURLMenu(sg, groupLinks);
675 // Add a 'show all structures' for the current selection
676 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(),
677 reppdb = new Hashtable<>();
679 SequenceI sqass = null;
680 for (SequenceI sq : alignPanel.av.getSequenceSelection())
682 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
683 if (pes != null && pes.size() > 0)
685 reppdb.put(pes.get(0).getId(), pes.get(0));
686 for (PDBEntry pe : pes)
688 pdbe.put(pe.getId(), pe);
698 final PDBEntry[] pe = pdbe.values()
699 .toArray(new PDBEntry[pdbe.size()]),
700 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
701 final JMenuItem gpdbview, rpdbview;
706 groupMenu.setVisible(false);
707 editMenu.setVisible(false);
712 createGroupMenuItem.setVisible(true);
713 unGroupMenuItem.setVisible(false);
715 .setText(MessageManager.getString("action.edit_new_group"));
719 createGroupMenuItem.setVisible(false);
720 unGroupMenuItem.setVisible(true);
721 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
726 sequenceMenu.setVisible(false);
727 chooseStructure.setVisible(false);
728 rnaStructureMenu.setVisible(false);
731 addLinksAndFeatures(seq, column);
737 * <li>configured sequence database links (ID panel popup menu)</li>
738 * <li>non-positional feature links (ID panel popup menu)</li>
739 * <li>positional feature links (alignment panel popup menu)</li>
740 * <li>feature details links (alignment panel popup menu)</li>
742 * If this panel is also showed complementary (CDS/protein) features, then
743 * links to their feature details are also added.
748 void addLinksAndFeatures(final SequenceI seq, final int column)
750 List<SequenceFeature> features = null;
753 features = sequence.getFeatures().getNonPositionalFeatures();
757 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
761 addLinks(seq, features);
765 addFeatureDetails(features, seq, column);
770 * Add a menu item to show feature details for each sequence feature. Any
771 * linked 'virtual' features (CDS/protein) are also optionally found and
778 protected void addFeatureDetails(List<SequenceFeature> features,
779 final SequenceI seq, final int column)
782 * add features in CDS/protein complement at the corresponding
783 * position if configured to do so
785 MappedFeatures mf = null;
786 if (ap.av.isShowComplementFeatures())
788 if (!Comparison.isGap(sequence.getCharAt(column)))
790 AlignViewportI complement = ap.getAlignViewport()
791 .getCodingComplement();
792 AlignFrame af = Desktop.getAlignFrameFor(complement);
793 FeatureRendererModel fr2 = af.getFeatureRenderer();
794 int seqPos = sequence.findPosition(column);
795 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
799 if (features.isEmpty() && mf == null)
802 * no features to show at this position
807 JMenu details = new JMenu(
808 MessageManager.getString("label.feature_details"));
811 String name = seq.getName();
812 for (final SequenceFeature sf : features)
814 addFeatureDetailsMenuItem(details, name, sf, null);
819 for (final SequenceFeature sf : mf.features)
821 addFeatureDetailsMenuItem(details, name, sf, mf);
827 * A helper method to add one menu item whose action is to show details for
828 * one feature. The menu text includes feature description, but this may be
836 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
837 final SequenceFeature sf, MappedFeatures mf)
839 int start = sf.getBegin();
840 int end = sf.getEnd();
844 * show local rather than linked feature coordinates
846 int[] localRange = mf.getMappedPositions(start, end);
847 if (localRange == null)
849 // e.g. variant extending to stop codon so not mappable
852 start = localRange[0];
853 end = localRange[localRange.length - 1];
855 StringBuilder desc = new StringBuilder();
856 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
859 desc.append(sf.isContactFeature() ? ":" : "-");
860 desc.append(String.valueOf(end));
862 String description = sf.getDescription();
863 if (description != null)
866 description = StringUtils.stripHtmlTags(description);
869 * truncate overlong descriptions unless they contain an href
870 * (as truncation could leave corrupted html)
872 boolean hasLink = description.indexOf("a href") > -1;
873 if (description.length() > FEATURE_DESC_MAX && !hasLink)
875 description = description.substring(0, FEATURE_DESC_MAX) + "...";
877 desc.append(description);
879 String featureGroup = sf.getFeatureGroup();
880 if (featureGroup != null)
882 desc.append(" (").append(featureGroup).append(")");
884 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
885 JMenuItem item = new JMenuItem(htmlText);
886 item.addActionListener(new ActionListener()
889 public void actionPerformed(ActionEvent e)
891 showFeatureDetails(sf, seqName, mf);
898 * Opens a panel showing a text report of feature details
904 protected void showFeatureDetails(SequenceFeature sf, String seqName,
907 JInternalFrame details;
910 details = new JInternalFrame();
911 details.setFrameIcon(null);
912 JPanel panel = new JPanel(new BorderLayout());
913 panel.setOpaque(true);
914 panel.setBackground(Color.white);
915 // TODO JAL-3026 set style of table correctly for feature details
916 JLabel reprt = new JLabel(MessageManager
917 .formatMessage("label.html_content", new Object[]
918 { sf.getDetailsReport(seqName, mf) }));
919 reprt.setBackground(Color.WHITE);
920 reprt.setOpaque(true);
921 panel.add(reprt, BorderLayout.CENTER);
922 details.setContentPane(panel);
932 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
933 // it appears Java's CSS does not support border-collapse :-(
934 cap.addStylesheetRule("table { border-collapse: collapse;}");
935 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
936 cap.setText(sf.getDetailsReport(seqName, mf));
939 Desktop.addInternalFrame(details,
940 MessageManager.getString("label.feature_details"), 500, 500);
944 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
945 * When seq is not null, these are links for the sequence id, which may be to
946 * external web sites for the sequence accession, and/or links embedded in
947 * non-positional features. When seq is null, only links embedded in the
948 * provided features are added. If no links are found, the menu is not added.
953 void addLinks(final SequenceI seq, List<SequenceFeature> features)
955 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
957 // only add link menu if it has entries
958 if (linkMenu.getItemCount() > 0)
962 sequenceMenu.add(linkMenu);
972 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
973 * "All" is added first, followed by a separator. Then add any annotation
974 * types associated with the current selection. Separate menus are built for
975 * the selected sequence group (if any), and the selected sequence.
977 * Some annotation rows are always rendered together - these can be identified
978 * by a common graphGroup property > -1. Only one of each group will be marked
979 * as visible (to avoid duplication of the display). For such groups we add a
980 * composite type name, e.g.
982 * IUPredWS (Long), IUPredWS (Short)
986 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
987 List<SequenceI> forSequences)
989 showMenu.removeAll();
990 hideMenu.removeAll();
992 final List<String> all = Arrays
994 { MessageManager.getString("label.all") });
995 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
997 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
999 showMenu.addSeparator();
1000 hideMenu.addSeparator();
1002 final AlignmentAnnotation[] annotations = ap.getAlignment()
1003 .getAlignmentAnnotation();
1006 * Find shown/hidden annotations types, distinguished by source (calcId),
1007 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1008 * the insertion order, which is the order of the annotations on the
1011 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
1012 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
1013 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1014 AlignmentAnnotationUtils.asList(annotations), forSequences);
1016 for (String calcId : hiddenTypes.keySet())
1018 for (List<String> type : hiddenTypes.get(calcId))
1020 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1024 // grey out 'show annotations' if none are hidden
1025 showMenu.setEnabled(!hiddenTypes.isEmpty());
1027 for (String calcId : shownTypes.keySet())
1029 for (List<String> type : shownTypes.get(calcId))
1031 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1035 // grey out 'hide annotations' if none are shown
1036 hideMenu.setEnabled(!shownTypes.isEmpty());
1040 * Returns a list of sequences - either the current selection group (if there
1041 * is one), else the specified single sequence.
1046 protected List<SequenceI> getSequenceScope(SequenceI seq)
1048 List<SequenceI> forSequences = null;
1049 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1050 if (selectionGroup != null && selectionGroup.getSize() > 0)
1052 forSequences = selectionGroup.getSequences();
1056 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1057 : Arrays.asList(seq);
1059 return forSequences;
1063 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1066 * @param showOrHideMenu
1067 * the menu to add to
1068 * @param forSequences
1069 * the sequences whose annotations may be shown or hidden
1074 * if true this is a special label meaning 'All'
1075 * @param actionIsShow
1076 * if true, the select menu item action is to show the annotation
1079 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1080 final List<SequenceI> forSequences, String calcId,
1081 final List<String> types, final boolean allTypes,
1082 final boolean actionIsShow)
1084 String label = types.toString(); // [a, b, c]
1085 label = label.substring(1, label.length() - 1); // a, b, c
1086 final JMenuItem item = new JMenuItem(label);
1087 item.setToolTipText(calcId);
1088 item.addActionListener(new ActionListener()
1091 public void actionPerformed(ActionEvent e)
1093 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1094 types, forSequences, allTypes, actionIsShow);
1098 showOrHideMenu.add(item);
1101 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1104 // TODO: usability: thread off the generation of group url content so root
1105 // menu appears asap
1106 // sequence only URLs
1107 // ID/regex match URLs
1108 JMenu groupLinksMenu = new JMenu(
1109 MessageManager.getString("action.group_link"));
1110 // three types of url that might be created.
1111 JMenu[] linkMenus = new JMenu[] { null,
1112 new JMenu(MessageManager.getString("action.ids")),
1113 new JMenu(MessageManager.getString("action.sequences")),
1114 new JMenu(MessageManager.getString("action.ids_sequences")) };
1116 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1117 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1118 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1119 for (int sq = 0; sq < seqs.length; sq++)
1122 int start = seqs[sq].findPosition(sg.getStartRes()),
1123 end = seqs[sq].findPosition(sg.getEndRes());
1124 // just collect ids from dataset sequence
1125 // TODO: check if IDs collected from selecton group intersects with the
1126 // current selection, too
1127 SequenceI sqi = seqs[sq];
1128 while (sqi.getDatasetSequence() != null)
1130 sqi = sqi.getDatasetSequence();
1132 List<DBRefEntry> dbr = sqi.getDBRefs();
1134 if (dbr != null && (nd = dbr.size()) > 0)
1136 for (int d = 0; d < nd; d++)
1138 DBRefEntry e = dbr.get(d);
1139 String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
1140 Object[] sarray = commonDbrefs.get(src);
1143 sarray = new Object[2];
1144 sarray[0] = new int[] { 0 };
1145 sarray[1] = new String[seqs.length];
1147 commonDbrefs.put(src, sarray);
1150 if (((String[]) sarray[1])[sq] == null)
1153 || (e.getMap().locateMappedRange(start, end) != null))
1155 ((String[]) sarray[1])[sq] = e.getAccessionId();
1156 ((int[]) sarray[0])[0]++;
1162 // now create group links for all distinct ID/sequence sets.
1163 boolean addMenu = false; // indicates if there are any group links to give
1165 for (String link : groupLinks)
1167 GroupUrlLink urlLink = null;
1170 urlLink = new GroupUrlLink(link);
1171 } catch (Exception foo)
1173 Console.error("Exception for GroupURLLink '" + link + "'", foo);
1176 if (!urlLink.isValid())
1178 Console.error(urlLink.getInvalidMessage());
1181 final String label = urlLink.getLabel();
1182 boolean usingNames = false;
1183 // Now see which parts of the group apply for this URL
1184 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1185 Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
1186 String[] seqstr, ids; // input to makeUrl
1189 int numinput = ((int[]) idset[0])[0];
1190 String[] allids = ((String[]) idset[1]);
1191 seqstr = new String[numinput];
1192 ids = new String[numinput];
1193 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1195 if (allids[sq] != null)
1197 ids[idcount] = allids[sq];
1198 seqstr[idcount++] = idandseqs[1][sq];
1204 // just use the id/seq set
1205 seqstr = idandseqs[1];
1209 // and try and make the groupURL!
1211 Object[] urlset = null;
1214 urlset = urlLink.makeUrlStubs(ids, seqstr,
1215 "FromJalview" + System.currentTimeMillis(), false);
1216 } catch (UrlStringTooLongException e)
1221 int type = urlLink.getGroupURLType() & 3;
1222 // first two bits ofurlLink type bitfield are sequenceids and sequences
1223 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1224 addshowLink(linkMenus[type],
1225 label + (((type & 1) == 1)
1226 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1234 groupLinksMenu = new JMenu(
1235 MessageManager.getString("action.group_link"));
1236 for (int m = 0; m < linkMenus.length; m++)
1238 if (linkMenus[m] != null
1239 && linkMenus[m].getMenuComponentCount() > 0)
1241 groupLinksMenu.add(linkMenus[m]);
1245 groupMenu.add(groupLinksMenu);
1255 private void jbInit() throws Exception
1257 groupMenu.setText(MessageManager.getString("label.selection"));
1258 groupName.setText(MessageManager.getString("label.name"));
1259 groupName.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 groupName_actionPerformed();
1267 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1269 JMenuItem sequenceName = new JMenuItem(
1270 MessageManager.getString("label.edit_name_description"));
1271 sequenceName.addActionListener(new ActionListener()
1274 public void actionPerformed(ActionEvent e)
1276 sequenceName_actionPerformed();
1279 JMenuItem chooseAnnotations = new JMenuItem(
1280 MessageManager.getString("action.choose_annotations"));
1281 chooseAnnotations.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 chooseAnnotations_actionPerformed(e);
1289 JMenuItem sequenceDetails = new JMenuItem(
1290 MessageManager.getString("label.sequence_details"));
1291 sequenceDetails.addActionListener(new ActionListener()
1294 public void actionPerformed(ActionEvent e)
1296 createSequenceDetailsReport(new SequenceI[] { sequence });
1299 JMenuItem sequenceSelDetails = new JMenuItem(
1300 MessageManager.getString("label.sequence_details"));
1301 sequenceSelDetails.addActionListener(new ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 createSequenceDetailsReport(ap.av.getSequenceSelection());
1311 .setText(MessageManager.getString("action.remove_group"));
1312 unGroupMenuItem.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 unGroupMenuItem_actionPerformed();
1321 .setText(MessageManager.getString("action.create_group"));
1322 createGroupMenuItem.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 createGroupMenuItem_actionPerformed();
1331 JMenuItem outline = new JMenuItem(
1332 MessageManager.getString("action.border_colour"));
1333 outline.addActionListener(new ActionListener()
1336 public void actionPerformed(ActionEvent e)
1338 outline_actionPerformed();
1341 showBoxes.setText(MessageManager.getString("action.boxes"));
1342 showBoxes.setState(true);
1343 showBoxes.addActionListener(new ActionListener()
1346 public void actionPerformed(ActionEvent e)
1348 showBoxes_actionPerformed();
1351 showText.setText(MessageManager.getString("action.text"));
1352 showText.setState(true);
1353 showText.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 showText_actionPerformed();
1361 showColourText.setText(MessageManager.getString("label.colour_text"));
1362 showColourText.addActionListener(new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 showColourText_actionPerformed();
1371 .setText(MessageManager.getString("label.show_non_conserved"));
1372 displayNonconserved.setState(true);
1373 displayNonconserved.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 showNonconserved_actionPerformed();
1381 editMenu.setText(MessageManager.getString("action.edit"));
1382 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1383 cut.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent e)
1388 cut_actionPerformed();
1391 JMenuItem justifyLeftMenuItem = new JMenuItem(
1392 MessageManager.getString("action.left_justify"));
1393 justifyLeftMenuItem.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 ap.alignFrame.avc.justify_Region(true);
1402 JMenuItem justifyRightMenuItem = new JMenuItem(
1403 MessageManager.getString("action.right_justify"));
1404 justifyRightMenuItem.addActionListener(new ActionListener()
1408 public void actionPerformed(ActionEvent e)
1410 ap.alignFrame.avc.justify_Region(false);
1414 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1415 upperCase.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1423 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1424 copy.addActionListener(new ActionListener()
1427 public void actionPerformed(ActionEvent e)
1429 copy_actionPerformed();
1432 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1433 lowerCase.addActionListener(new ActionListener()
1436 public void actionPerformed(ActionEvent e)
1441 toggle.setText(MessageManager.getString("label.toggle_case"));
1442 toggle.addActionListener(new ActionListener()
1445 public void actionPerformed(ActionEvent e)
1451 MessageManager.getString("label.out_to_textbox") + "...");
1452 seqShowAnnotationsMenu
1453 .setText(MessageManager.getString("label.show_annotations"));
1454 seqHideAnnotationsMenu
1455 .setText(MessageManager.getString("label.hide_annotations"));
1456 groupShowAnnotationsMenu
1457 .setText(MessageManager.getString("label.show_annotations"));
1458 groupHideAnnotationsMenu
1459 .setText(MessageManager.getString("label.hide_annotations"));
1460 JMenuItem sequenceFeature = new JMenuItem(
1461 MessageManager.getString("label.create_sequence_feature"));
1462 sequenceFeature.addActionListener(new ActionListener()
1465 public void actionPerformed(ActionEvent e)
1467 sequenceFeature_actionPerformed();
1470 editGroupMenu.setText(MessageManager.getString("label.group"));
1471 chooseStructure.setText(
1472 MessageManager.getString("label.show_pdbstruct_dialog"));
1473 chooseStructure.addActionListener(new ActionListener()
1476 public void actionPerformed(ActionEvent actionEvent)
1478 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1479 if (ap.av.getSelectionGroup() != null)
1481 selectedSeqs = ap.av.getSequenceSelection();
1483 new StructureChooser(selectedSeqs, sequence, ap);
1488 .setText(MessageManager.getString("label.view_rna_structure"));
1490 // colStructureMenu.setText("Colour By Structure");
1491 JMenuItem editSequence = new JMenuItem(
1492 MessageManager.getString("label.edit_sequence") + "...");
1493 editSequence.addActionListener(new ActionListener()
1496 public void actionPerformed(ActionEvent actionEvent)
1498 editSequence_actionPerformed();
1501 makeReferenceSeq.setText(
1502 MessageManager.getString("label.mark_as_representative"));
1503 makeReferenceSeq.addActionListener(new ActionListener()
1507 public void actionPerformed(ActionEvent actionEvent)
1509 makeReferenceSeq_actionPerformed(actionEvent);
1514 groupMenu.add(sequenceSelDetails);
1517 add(rnaStructureMenu);
1518 add(chooseStructure);
1521 JMenuItem hideInsertions = new JMenuItem(
1522 MessageManager.getString("label.hide_insertions"));
1523 hideInsertions.addActionListener(new ActionListener()
1527 public void actionPerformed(ActionEvent e)
1529 hideInsertions_actionPerformed(e);
1532 add(hideInsertions);
1534 // annotations configuration panel suppressed for now
1535 // groupMenu.add(chooseAnnotations);
1538 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1539 * (if a selection group is in force).
1541 sequenceMenu.add(seqShowAnnotationsMenu);
1542 sequenceMenu.add(seqHideAnnotationsMenu);
1543 sequenceMenu.add(seqAddReferenceAnnotations);
1544 groupMenu.add(groupShowAnnotationsMenu);
1545 groupMenu.add(groupHideAnnotationsMenu);
1546 groupMenu.add(groupAddReferenceAnnotations);
1547 groupMenu.add(editMenu);
1548 groupMenu.add(outputMenu);
1549 groupMenu.add(sequenceFeature);
1550 groupMenu.add(createGroupMenuItem);
1551 groupMenu.add(unGroupMenuItem);
1552 groupMenu.add(editGroupMenu);
1553 sequenceMenu.add(sequenceName);
1554 sequenceMenu.add(sequenceDetails);
1555 sequenceMenu.add(makeReferenceSeq);
1562 editMenu.add(justifyLeftMenuItem);
1563 editMenu.add(justifyRightMenuItem);
1564 editMenu.add(editSequence);
1565 editMenu.add(upperCase);
1566 editMenu.add(lowerCase);
1567 editMenu.add(toggle);
1568 editGroupMenu.add(groupName);
1569 editGroupMenu.add(colourMenu);
1570 editGroupMenu.add(showBoxes);
1571 editGroupMenu.add(showText);
1572 editGroupMenu.add(showColourText);
1573 editGroupMenu.add(outline);
1574 editGroupMenu.add(displayNonconserved);
1578 * Constructs the entries for the colour menu
1580 protected void initColourMenu()
1582 colourMenu.setText(MessageManager.getString("label.group_colour"));
1583 textColour.setText(MessageManager.getString("label.text_colour"));
1584 textColour.addActionListener(new ActionListener()
1587 public void actionPerformed(ActionEvent e)
1589 textColour_actionPerformed();
1593 abovePIDColour.setText(
1594 MessageManager.getString("label.above_identity_threshold"));
1595 abovePIDColour.addActionListener(new ActionListener()
1598 public void actionPerformed(ActionEvent e)
1600 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1605 MessageManager.getString("label.modify_identity_threshold"));
1606 modifyPID.addActionListener(new ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 modifyPID_actionPerformed();
1615 conservationMenuItem
1616 .setText(MessageManager.getString("action.by_conservation"));
1617 conservationMenuItem.addActionListener(new ActionListener()
1620 public void actionPerformed(ActionEvent e)
1622 conservationMenuItem_actionPerformed(
1623 conservationMenuItem.isSelected());
1627 annotationColour = new JRadioButtonMenuItem(
1628 MessageManager.getString("action.by_annotation"));
1629 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1630 annotationColour.setEnabled(false);
1631 annotationColour.setToolTipText(
1632 MessageManager.getString("label.by_annotation_tooltip"));
1634 modifyConservation.setText(MessageManager
1635 .getString("label.modify_conservation_threshold"));
1636 modifyConservation.addActionListener(new ActionListener()
1639 public void actionPerformed(ActionEvent e)
1641 modifyConservation_actionPerformed();
1647 * Builds the group colour sub-menu, including any user-defined colours which
1648 * were loaded at startup or during the Jalview session
1650 protected void buildColourMenu()
1652 SequenceGroup sg = ap.av.getSelectionGroup();
1656 * popup menu with no sequence group scope
1660 colourMenu.removeAll();
1661 colourMenu.add(textColour);
1662 colourMenu.addSeparator();
1664 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1666 bg.add(annotationColour);
1667 colourMenu.add(annotationColour);
1669 colourMenu.addSeparator();
1670 colourMenu.add(conservationMenuItem);
1671 colourMenu.add(modifyConservation);
1672 colourMenu.add(abovePIDColour);
1673 colourMenu.add(modifyPID);
1676 protected void modifyConservation_actionPerformed()
1678 SequenceGroup sg = getGroup();
1681 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1682 SliderPanel.showConservationSlider();
1686 protected void modifyPID_actionPerformed()
1688 SequenceGroup sg = getGroup();
1691 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1693 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1694 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1695 SliderPanel.showPIDSlider();
1700 * Check for any annotations on the underlying dataset sequences (for the
1701 * current selection group) which are not 'on the alignment'.If any are found,
1702 * enable the option to add them to the alignment. The criteria for 'on the
1703 * alignment' is finding an alignment annotation on the alignment, matched on
1704 * calcId, label and sequenceRef.
1706 * A tooltip is also constructed that displays the source (calcId) and type
1707 * (label) of the annotations that can be added.
1710 * @param forSequences
1712 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1713 List<SequenceI> forSequences)
1715 menuItem.setEnabled(false);
1718 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1719 * Using TreeMap means calcIds are shown in alphabetical order.
1721 SortedMap<String, String> tipEntries = new TreeMap<>();
1722 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1723 AlignmentI al = this.ap.av.getAlignment();
1724 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1726 if (!candidates.isEmpty())
1728 StringBuilder tooltip = new StringBuilder(64);
1729 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1732 * Found annotations that could be added. Enable the menu item, and
1733 * configure its tooltip and action.
1735 menuItem.setEnabled(true);
1736 for (String calcId : tipEntries.keySet())
1738 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1740 String tooltipText = JvSwingUtils.wrapTooltip(true,
1741 tooltip.toString());
1742 menuItem.setToolTipText(tooltipText);
1744 menuItem.addActionListener(new ActionListener()
1747 public void actionPerformed(ActionEvent e)
1749 addReferenceAnnotations_actionPerformed(candidates);
1756 * Add annotations to the sequences and to the alignment.
1759 * a map whose keys are sequences on the alignment, and values a list
1760 * of annotations to add to each sequence
1762 protected void addReferenceAnnotations_actionPerformed(
1763 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1765 final AlignmentI alignment = this.ap.getAlignment();
1766 AlignmentUtils.addReferenceAnnotations(candidates, alignment, null);
1768 if(AlignmentUtils.isSSAnnotationPresent(candidates)) {
1769 restartSSConsensusWorker();
1776 private void restartSSConsensusWorker() {
1778 List<AlignCalcWorkerI> workers = ap.alignFrame.getViewport().getCalcManager()
1779 .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class);
1780 if (!workers.isEmpty()) {
1782 ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0));
1790 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1792 if (!ap.av.getAlignment().hasSeqrep())
1794 // initialise the display flags so the user sees something happen
1795 ap.av.setDisplayReferenceSeq(true);
1796 ap.av.setColourByReferenceSeq(true);
1797 ap.av.getAlignment().setSeqrep(sequence);
1801 if (ap.av.getAlignment().getSeqrep() == sequence)
1803 ap.av.getAlignment().setSeqrep(null);
1807 ap.av.getAlignment().setSeqrep(sequence);
1813 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1815 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1816 BitSet inserts = new BitSet();
1818 boolean markedPopup = false;
1819 // mark inserts in current selection
1820 if (ap.av.getSelectionGroup() != null)
1822 // mark just the columns in the selection group to be hidden
1823 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1824 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1826 // now clear columns without gaps
1827 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1833 inserts.and(sq.getInsertionsAsBits());
1835 hidden.clearAndHideColumns(inserts,
1836 ap.av.getSelectionGroup().getStartRes(),
1837 ap.av.getSelectionGroup().getEndRes());
1840 // now mark for sequence under popup if we haven't already done it
1841 else if (!markedPopup && sequence != null)
1843 inserts.or(sequence.getInsertionsAsBits());
1845 // and set hidden columns accordingly
1846 hidden.hideColumns(inserts);
1851 protected void sequenceSelectionDetails_actionPerformed()
1853 createSequenceDetailsReport(ap.av.getSequenceSelection());
1856 public void createSequenceDetailsReport(SequenceI[] sequences)
1858 StringBuilder contents = new StringBuilder(128);
1859 contents.append("<html><body>");
1860 for (SequenceI seq : sequences)
1862 contents.append("<p><h2>" + MessageManager.formatMessage(
1863 "label.create_sequence_details_report_annotation_for",
1865 { seq.getDisplayId(true) }) + "</h2></p>\n<p>");
1866 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1867 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1868 contents.append("</p>");
1870 contents.append("</body></html>");
1871 String report = contents.toString();
1873 JInternalFrame frame;
1874 if (Platform.isJS())
1876 JLabel textLabel = new JLabel();
1877 textLabel.setText(report);
1878 textLabel.setBackground(Color.WHITE);
1879 JPanel pane = new JPanel(new BorderLayout());
1880 pane.setOpaque(true);
1881 pane.setBackground(Color.WHITE);
1882 pane.add(textLabel, BorderLayout.NORTH);
1883 frame = new JInternalFrame();
1884 frame.setFrameIcon(null);
1885 frame.getContentPane().add(new JScrollPane(pane));
1894 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1895 cap.setText(report);
1899 Desktop.addInternalFrame(frame,
1900 MessageManager.formatMessage("label.sequence_details_for",
1901 (sequences.length == 1 ? new Object[]
1902 { sequences[0].getDisplayId(true) }
1905 .getString("label.selection") })),
1909 protected void showNonconserved_actionPerformed()
1911 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1916 * call to refresh view after settings change
1920 ap.updateAnnotation();
1921 // removed paintAlignment(true) here:
1922 // updateAnnotation calls paintAlignment already, so don't need to call
1925 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1929 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1930 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1940 public void abovePIDColour_actionPerformed(boolean selected)
1942 SequenceGroup sg = getGroup();
1950 sg.cs.setConsensus(AAFrequency.calculate(
1951 sg.getSequences(ap.av.getHiddenRepSequences()),
1952 sg.getStartRes(), sg.getEndRes() + 1));
1954 int threshold = SliderPanel.setPIDSliderSource(ap,
1955 sg.getGroupColourScheme(), getGroup().getName());
1957 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1959 SliderPanel.showPIDSlider();
1962 // remove PIDColouring
1964 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1965 SliderPanel.hidePIDSlider();
1967 modifyPID.setEnabled(selected);
1973 * Open a panel where the user can choose which types of sequence annotation
1978 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1980 // todo correct way to guard against opening a duplicate panel?
1981 new AnnotationChooser(ap);
1990 public void conservationMenuItem_actionPerformed(boolean selected)
1992 SequenceGroup sg = getGroup();
2000 // JBPNote: Conservation name shouldn't be i18n translated
2001 Conservation c = new Conservation("Group",
2002 sg.getSequences(ap.av.getHiddenRepSequences()),
2003 sg.getStartRes(), sg.getEndRes() + 1);
2006 c.verdict(false, ap.av.getConsPercGaps());
2007 sg.cs.setConservation(c);
2009 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
2011 SliderPanel.showConservationSlider();
2014 // remove ConservationColouring
2016 sg.cs.setConservation(null);
2017 SliderPanel.hideConservationSlider();
2019 modifyConservation.setEnabled(selected);
2025 * Shows a dialog where group name and description may be edited
2027 protected void groupName_actionPerformed()
2029 SequenceGroup sg = getGroup();
2030 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2031 sg.getDescription(),
2032 MessageManager.getString("label.group_name"),
2033 MessageManager.getString("label.group_description"));
2034 dialog.showDialog(ap.alignFrame,
2035 MessageManager.getString("label.edit_group_name_description"),
2037 sg.setName(dialog.getName());
2038 sg.setDescription(dialog.getDescription());
2044 * Get selection group - adding it to the alignment if necessary.
2046 * @return sequence group to operate on
2048 SequenceGroup getGroup()
2050 SequenceGroup sg = ap.av.getSelectionGroup();
2051 // this method won't add a new group if it already exists
2054 ap.av.getAlignment().addGroup(sg);
2061 * Shows a dialog where the sequence name and description may be edited. If a
2062 * name containing spaces is entered, these are converted to underscores, with
2063 * a warning message.
2065 void sequenceName_actionPerformed()
2067 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2068 sequence.getDescription(),
2069 MessageManager.getString("label.sequence_name"),
2070 MessageManager.getString("label.sequence_description"));
2071 dialog.showDialog(ap.alignFrame, MessageManager
2072 .getString("label.edit_sequence_name_description"), () -> {
2073 if (dialog.getName() != null)
2075 if (dialog.getName().indexOf(" ") > -1)
2077 String ok = MessageManager.getString("action.ok");
2078 String cancel = MessageManager.getString("action.cancel");
2079 String message = MessageManager.getString(
2080 "label.spaces_converted_to_underscores");
2081 String title = MessageManager.getString(
2082 "label.no_spaces_allowed_sequence_name");
2083 Object[] options = new Object[] { ok, cancel };
2085 JvOptionPane.frameDialog(message, title,
2086 JvOptionPane.WARNING_MESSAGE, null, null, null,
2089 sequence.setName(dialog.getName().replace(' ', '_'));
2090 ap.paintAlignment(false, false);
2092 sequence.setDescription(dialog.getDescription());
2093 ap.av.firePropertyChange("alignment", null,
2094 ap.av.getAlignment().getSequences());
2104 void unGroupMenuItem_actionPerformed()
2106 SequenceGroup sg = ap.av.getSelectionGroup();
2107 ap.av.getAlignment().deleteGroup(sg);
2108 ap.av.setSelectionGroup(null);
2112 void createGroupMenuItem_actionPerformed()
2114 getGroup(); // implicitly creates group - note - should apply defaults / use
2115 // standard alignment window logic for this
2120 * Offers a colour chooser and sets the selected colour as the group outline
2122 protected void outline_actionPerformed()
2124 String title = MessageManager.getString("label.select_outline_colour");
2125 ColourChooserListener listener = new ColourChooserListener()
2128 public void colourSelected(Color c)
2130 getGroup().setOutlineColour(c);
2134 JalviewColourChooser.showColourChooser(Desktop.getDesktop(), title,
2135 Color.BLUE, listener);
2144 public void showBoxes_actionPerformed()
2146 getGroup().setDisplayBoxes(showBoxes.isSelected());
2156 public void showText_actionPerformed()
2158 getGroup().setDisplayText(showText.isSelected());
2168 public void showColourText_actionPerformed()
2170 getGroup().setColourText(showColourText.isSelected());
2174 void hideSequences(boolean representGroup)
2176 ap.av.hideSequences(sequence, representGroup);
2179 public void copy_actionPerformed()
2181 ap.alignFrame.copy_actionPerformed();
2184 public void cut_actionPerformed()
2186 ap.alignFrame.cut_actionPerformed();
2189 void changeCase(ActionEvent e)
2191 Object source = e.getSource();
2192 SequenceGroup sg = ap.av.getSelectionGroup();
2196 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2197 sg.getStartRes(), sg.getEndRes() + 1);
2202 if (source == toggle)
2204 description = MessageManager.getString("label.toggle_case");
2205 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2207 else if (source == upperCase)
2209 description = MessageManager.getString("label.to_upper_case");
2210 caseChange = ChangeCaseCommand.TO_UPPER;
2214 description = MessageManager.getString("label.to_lower_case");
2215 caseChange = ChangeCaseCommand.TO_LOWER;
2218 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2219 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2220 startEnd, caseChange);
2222 ap.alignFrame.addHistoryItem(caseCommand);
2224 ap.av.firePropertyChange("alignment", null,
2225 ap.av.getAlignment().getSequences());
2230 public void outputText_actionPerformed(ActionEvent e)
2232 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2233 cap.setForInput(null);
2234 Desktop.addInternalFrame(cap, MessageManager
2235 .formatMessage("label.alignment_output_command", new Object[]
2236 { e.getActionCommand() }), 600, 500);
2238 String[] omitHidden = null;
2240 jalview.bin.Console.outPrintln("PROMPT USER HERE"); // TODO: decide if a
2242 // or we simply trust the user wants
2243 // wysiwig behaviour
2245 FileFormatI fileFormat = FileFormats.getInstance()
2246 .forName(e.getActionCommand());
2248 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2251 public void sequenceFeature_actionPerformed()
2253 SequenceGroup sg = ap.av.getSelectionGroup();
2259 List<SequenceI> seqs = new ArrayList<>();
2260 List<SequenceFeature> features = new ArrayList<>();
2263 * assemble dataset sequences, and template new sequence features,
2264 * for the amend features dialog
2266 int gSize = sg.getSize();
2267 for (int i = 0; i < gSize; i++)
2269 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2270 int end = sg.findEndRes(sg.getSequenceAt(i));
2273 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2274 features.add(new SequenceFeature(null, null, start, end, null));
2279 * an entirely gapped region will generate empty lists of sequence / features
2281 if (!seqs.isEmpty())
2283 new FeatureEditor(ap, seqs, features, true).showDialog();
2287 public void textColour_actionPerformed()
2289 SequenceGroup sg = getGroup();
2292 new TextColourChooser().chooseColour(ap, sg);
2297 * Shows a dialog where sequence characters may be edited. Any changes are
2298 * applied, and added as an available 'Undo' item in the edit commands
2301 public void editSequence_actionPerformed()
2303 SequenceGroup sg = ap.av.getSelectionGroup();
2305 SequenceI seq = sequence;
2310 seq = sg.getSequenceAt(0);
2313 EditNameDialog dialog = new EditNameDialog(
2314 seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
2315 null, MessageManager.getString("label.edit_sequence"), null);
2316 dialog.showDialog(ap.alignFrame,
2317 MessageManager.getString("label.edit_sequence"), () -> {
2318 EditCommand editCommand = new EditCommand(
2319 MessageManager.getString("label.edit_sequences"),
2321 dialog.getName().replace(' ',
2322 ap.av.getGapCharacter()),
2323 sg.getSequencesAsArray(
2324 ap.av.getHiddenRepSequences()),
2325 sg.getStartRes(), sg.getEndRes() + 1,
2326 ap.av.getAlignment());
2327 ap.alignFrame.addHistoryItem(editCommand);
2328 ap.av.firePropertyChange("alignment", null,
2329 ap.av.getAlignment().getSequences());
2335 * Action on user selecting an item from the colour menu (that does not have
2336 * its bespoke action handler)
2341 public void changeColour_actionPerformed(String colourSchemeName)
2343 SequenceGroup sg = getGroup();
2345 * switch to the chosen colour scheme (or null for None)
2347 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2348 .getColourScheme(colourSchemeName, ap.av, sg,
2349 ap.av.getHiddenRepSequences());
2350 sg.setColourScheme(colourScheme);
2351 if (colourScheme instanceof Blosum62ColourScheme
2352 || colourScheme instanceof PIDColourScheme)
2354 sg.cs.setConsensus(AAFrequency.calculate(
2355 sg.getSequences(ap.av.getHiddenRepSequences()),
2356 sg.getStartRes(), sg.getEndRes() + 1));