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.Cache;
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 Cache.log.error("Exception for URLLink '" + link + "'", foo);
237 if (!urlLink.isValid())
239 Cache.log.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 residue)
365 * the panel in which the mouse is clicked
367 * the sequence under the mouse
368 * @throws NullPointerException
371 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
373 this(false, ap, seq, column, null);
377 * Constructor for a PopupMenu for a click in the sequence id panel
380 * the panel in which the mouse is clicked
382 * the sequence under the mouse click
384 * templates for sequence external links
385 * @throws NullPointerException
388 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
389 List<String> groupLinks)
391 this(true, alignPanel, seq, -1, groupLinks);
395 * Private constructor that constructs a popup menu for either sequence ID
396 * Panel, or alignment context
402 * aligned column position (0...)
405 private PopupMenu(boolean fromIdPanel,
406 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.getSelectionGroup() == null
447 ? Collections.<SequenceI> emptyList()
448 : alignPanel.av.getSelectionGroup().getSequences());
449 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
450 groupHideAnnotationsMenu, selectedGroup);
451 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
457 } catch (Exception e)
465 sequenceMenu.setText(sequence.getName());
466 if (seq == alignPanel.av.getAlignment().getSeqrep())
468 makeReferenceSeq.setText(
469 MessageManager.getString("action.unmark_as_reference"));
473 makeReferenceSeq.setText(
474 MessageManager.getString("action.set_as_reference"));
477 if (!alignPanel.av.getAlignment().isNucleotide())
479 remove(rnaStructureMenu);
483 int origCount = rnaStructureMenu.getItemCount();
485 * add menu items to 2D-render any alignment or sequence secondary
486 * structure annotation
488 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
489 .getAlignmentAnnotation();
492 for (final AlignmentAnnotation aa : aas)
494 if (aa.isValidStruc() && aa.sequenceRef == null)
497 * valid alignment RNA secondary structure annotation
499 menuItem = new JMenuItem();
500 menuItem.setText(MessageManager.formatMessage(
501 "label.2d_rna_structure_line", new Object[]
503 menuItem.addActionListener(new ActionListener()
506 public void actionPerformed(ActionEvent e)
508 new AppVarna(seq, aa, alignPanel);
511 rnaStructureMenu.add(menuItem);
516 if (seq.getAnnotation() != null)
518 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
519 for (final AlignmentAnnotation aa : seqAnns)
521 if (aa.isValidStruc())
524 * valid sequence RNA secondary structure annotation
526 // TODO: make rnastrucF a bit more nice
527 menuItem = new JMenuItem();
528 menuItem.setText(MessageManager.formatMessage(
529 "label.2d_rna_sequence_name", new Object[]
531 menuItem.addActionListener(new ActionListener()
534 public void actionPerformed(ActionEvent e)
536 // TODO: VARNA does'nt print gaps in the sequence
537 new AppVarna(seq, aa, alignPanel);
540 rnaStructureMenu.add(menuItem);
544 if (rnaStructureMenu.getItemCount() == origCount)
546 remove(rnaStructureMenu);
550 menuItem = new JMenuItem(
551 MessageManager.getString("action.hide_sequences"));
552 menuItem.addActionListener(new ActionListener()
555 public void actionPerformed(ActionEvent e)
557 hideSequences(false);
562 if (alignPanel.av.getSelectionGroup() != null
563 && alignPanel.av.getSelectionGroup().getSize() > 1)
565 menuItem = new JMenuItem(MessageManager
566 .formatMessage("label.represent_group_with", new Object[]
568 menuItem.addActionListener(new ActionListener()
571 public void actionPerformed(ActionEvent e)
576 sequenceMenu.add(menuItem);
579 if (alignPanel.av.hasHiddenRows())
581 final int index = alignPanel.av.getAlignment().findIndex(seq);
583 if (alignPanel.av.adjustForHiddenSeqs(index)
584 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
586 menuItem = new JMenuItem(
587 MessageManager.getString("action.reveal_sequences"));
588 menuItem.addActionListener(new ActionListener()
591 public void actionPerformed(ActionEvent e)
593 alignPanel.av.showSequence(index);
594 if (alignPanel.overviewPanel != null)
596 alignPanel.overviewPanel.updateOverviewImage();
607 * - in the IdPanel (seq not null) if any sequence is hidden
608 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
610 if (alignPanel.av.hasHiddenRows())
612 boolean addOption = seq != null;
613 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
619 JMenuItem menuItem = new JMenuItem(
620 MessageManager.getString("action.reveal_all"));
621 menuItem.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 alignPanel.av.showAllHiddenSeqs();
627 if (alignPanel.overviewPanel != null)
629 alignPanel.overviewPanel.updateOverviewImage();
637 SequenceGroup sg = alignPanel.av.getSelectionGroup();
638 boolean isDefinedGroup = (sg != null)
639 ? alignPanel.av.getAlignment().getGroups().contains(sg)
642 if (sg != null && sg.getSize() > 0)
644 groupName.setText(MessageManager
645 .getString("label.edit_name_and_description_current_group"));
647 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
649 conservationMenuItem.setEnabled(!sg.isNucleotide());
653 if (sg.cs.conservationApplied())
655 conservationMenuItem.setSelected(true);
657 if (sg.cs.getThreshold() > 0)
659 abovePIDColour.setSelected(true);
662 modifyConservation.setEnabled(conservationMenuItem.isSelected());
663 modifyPID.setEnabled(abovePIDColour.isSelected());
664 displayNonconserved.setSelected(sg.getShowNonconserved());
665 showText.setSelected(sg.getDisplayText());
666 showColourText.setSelected(sg.getColourText());
667 showBoxes.setSelected(sg.getDisplayBoxes());
668 // add any groupURLs to the groupURL submenu and make it visible
669 if (groupLinks != null && groupLinks.size() > 0)
671 buildGroupURLMenu(sg, groupLinks);
673 // Add a 'show all structures' for the current selection
674 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
676 SequenceI sqass = null;
677 for (SequenceI sq : alignPanel.av.getSequenceSelection())
679 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
680 if (pes != null && pes.size() > 0)
682 reppdb.put(pes.get(0).getId(), pes.get(0));
683 for (PDBEntry pe : pes)
685 pdbe.put(pe.getId(), pe);
695 final PDBEntry[] pe = pdbe.values()
696 .toArray(new PDBEntry[pdbe.size()]),
697 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
698 final JMenuItem gpdbview, rpdbview;
703 groupMenu.setVisible(false);
704 editMenu.setVisible(false);
709 createGroupMenuItem.setVisible(true);
710 unGroupMenuItem.setVisible(false);
711 editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
715 createGroupMenuItem.setVisible(false);
716 unGroupMenuItem.setVisible(true);
717 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
722 sequenceMenu.setVisible(false);
723 chooseStructure.setVisible(false);
724 rnaStructureMenu.setVisible(false);
727 addLinksAndFeatures(seq, column);
733 * <li>configured sequence database links (ID panel popup menu)</li>
734 * <li>non-positional feature links (ID panel popup menu)</li>
735 * <li>positional feature links (alignment panel popup menu)</li>
736 * <li>feature details links (alignment panel popup menu)</li>
738 * If this panel is also showed complementary (CDS/protein) features, then links
739 * to their feature details are also added.
744 void addLinksAndFeatures(final SequenceI seq, final int column)
746 List<SequenceFeature> features = null;
749 features = sequence.getFeatures().getNonPositionalFeatures();
753 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
757 addLinks(seq, features);
761 addFeatureDetails(features, seq, column);
766 * Add a menu item to show feature details for each sequence feature. Any
767 * linked 'virtual' features (CDS/protein) are also optionally found and
774 protected void addFeatureDetails(List<SequenceFeature> features,
775 final SequenceI seq, final int column)
778 * add features in CDS/protein complement at the corresponding
779 * position if configured to do so
781 MappedFeatures mf = null;
782 if (ap.av.isShowComplementFeatures())
784 if (!Comparison.isGap(sequence.getCharAt(column)))
786 AlignViewportI complement = ap.getAlignViewport()
787 .getCodingComplement();
788 AlignFrame af = Desktop.getAlignFrameFor(complement);
789 FeatureRendererModel fr2 = af.getFeatureRenderer();
790 int seqPos = sequence.findPosition(column);
791 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
795 if (features.isEmpty() && mf == null)
798 * no features to show at this position
803 JMenu details = new JMenu(
804 MessageManager.getString("label.feature_details"));
807 String name = seq.getName();
808 for (final SequenceFeature sf : features)
810 addFeatureDetailsMenuItem(details, name, sf, null);
815 for (final SequenceFeature sf : mf.features)
817 addFeatureDetailsMenuItem(details, name, sf, mf);
823 * A helper method to add one menu item whose action is to show details for
824 * one feature. The menu text includes feature description, but this may be
832 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
833 final SequenceFeature sf, MappedFeatures mf)
835 int start = sf.getBegin();
836 int end = sf.getEnd();
840 * show local rather than linked feature coordinates
842 int[] beginRange = mf.getMappedPositions(start, start);
843 int[] endRange = mf.getMappedPositions(end, end);
844 if (beginRange == null || endRange == null)
846 // e.g. variant extending to stop codon so not mappable
849 start = beginRange[0];
850 end = endRange[endRange.length - 1];
852 StringBuilder desc = new StringBuilder();
853 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
856 desc.append(sf.isContactFeature() ? ":" : "-");
857 desc.append(String.valueOf(end));
859 String description = sf.getDescription();
860 if (description != null)
863 description = StringUtils.stripHtmlTags(description);
866 * truncate overlong descriptions unless they contain an href
867 * (as truncation could leave corrupted html)
869 boolean hasLink = description.indexOf("a href") > -1;
870 if (description.length() > FEATURE_DESC_MAX && !hasLink)
872 description = description.substring(0, FEATURE_DESC_MAX) + "...";
874 desc.append(description);
876 String featureGroup = sf.getFeatureGroup();
877 if (featureGroup != null)
879 desc.append(" (").append(featureGroup).append(")");
881 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
882 JMenuItem item = new JMenuItem(htmlText);
883 item.addActionListener(new ActionListener()
886 public void actionPerformed(ActionEvent e)
888 showFeatureDetails(sf, seqName, mf);
895 * Opens a panel showing a text report of feature details
901 protected void showFeatureDetails(SequenceFeature sf, String seqName,
904 JInternalFrame details;
907 details = new JInternalFrame();
908 JPanel panel = new JPanel(new BorderLayout());
909 panel.setOpaque(true);
910 panel.setBackground(Color.white);
911 // TODO JAL-3026 set style of table correctly for feature details
912 JLabel reprt = new JLabel(MessageManager
913 .formatMessage("label.html_content", new Object[]
914 { sf.getDetailsReport(seqName, mf) }));
915 reprt.setBackground(Color.WHITE);
916 reprt.setOpaque(true);
917 panel.add(reprt, BorderLayout.CENTER);
918 details.setContentPane(panel);
928 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
929 // it appears Java's CSS does not support border-collapse :-(
930 cap.addStylesheetRule("table { border-collapse: collapse;}");
931 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
932 cap.setText(sf.getDetailsReport(seqName, mf));
935 Desktop.addInternalFrame(details,
936 MessageManager.getString("label.feature_details"), 500, 500);
940 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
941 * When seq is not null, these are links for the sequence id, which may be to
942 * external web sites for the sequence accession, and/or links embedded in
943 * non-positional features. When seq is null, only links embedded in the
944 * provided features are added. If no links are found, the menu is not added.
949 void addLinks(final SequenceI seq, List<SequenceFeature> features)
951 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
953 // only add link menu if it has entries
954 if (linkMenu.getItemCount() > 0)
958 sequenceMenu.add(linkMenu);
968 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
969 * "All" is added first, followed by a separator. Then add any annotation
970 * types associated with the current selection. Separate menus are built for
971 * the selected sequence group (if any), and the selected sequence.
973 * Some annotation rows are always rendered together - these can be identified
974 * by a common graphGroup property > -1. Only one of each group will be marked
975 * as visible (to avoid duplication of the display). For such groups we add a
976 * composite type name, e.g.
978 * IUPredWS (Long), IUPredWS (Short)
982 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
983 List<SequenceI> forSequences)
985 showMenu.removeAll();
986 hideMenu.removeAll();
988 final List<String> all = Arrays
990 { MessageManager.getString("label.all") });
991 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
993 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
995 showMenu.addSeparator();
996 hideMenu.addSeparator();
998 final AlignmentAnnotation[] annotations = ap.getAlignment()
999 .getAlignmentAnnotation();
1002 * Find shown/hidden annotations types, distinguished by source (calcId),
1003 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1004 * the insertion order, which is the order of the annotations on the
1007 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
1008 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
1009 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1010 AlignmentAnnotationUtils.asList(annotations), forSequences);
1012 for (String calcId : hiddenTypes.keySet())
1014 for (List<String> type : hiddenTypes.get(calcId))
1016 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1020 // grey out 'show annotations' if none are hidden
1021 showMenu.setEnabled(!hiddenTypes.isEmpty());
1023 for (String calcId : shownTypes.keySet())
1025 for (List<String> type : shownTypes.get(calcId))
1027 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1031 // grey out 'hide annotations' if none are shown
1032 hideMenu.setEnabled(!shownTypes.isEmpty());
1036 * Returns a list of sequences - either the current selection group (if there
1037 * is one), else the specified single sequence.
1042 protected List<SequenceI> getSequenceScope(SequenceI seq)
1044 List<SequenceI> forSequences = null;
1045 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1046 if (selectionGroup != null && selectionGroup.getSize() > 0)
1048 forSequences = selectionGroup.getSequences();
1052 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1053 : Arrays.asList(seq);
1055 return forSequences;
1059 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1062 * @param showOrHideMenu
1063 * the menu to add to
1064 * @param forSequences
1065 * the sequences whose annotations may be shown or hidden
1070 * if true this is a special label meaning 'All'
1071 * @param actionIsShow
1072 * if true, the select menu item action is to show the annotation
1075 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1076 final List<SequenceI> forSequences, String calcId,
1077 final List<String> types, final boolean allTypes,
1078 final boolean actionIsShow)
1080 String label = types.toString(); // [a, b, c]
1081 label = label.substring(1, label.length() - 1); // a, b, c
1082 final JMenuItem item = new JMenuItem(label);
1083 item.setToolTipText(calcId);
1084 item.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1090 types, forSequences, allTypes, actionIsShow);
1094 showOrHideMenu.add(item);
1097 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1100 // TODO: usability: thread off the generation of group url content so root
1101 // menu appears asap
1102 // sequence only URLs
1103 // ID/regex match URLs
1104 JMenu groupLinksMenu = new JMenu(
1105 MessageManager.getString("action.group_link"));
1106 // three types of url that might be created.
1107 JMenu[] linkMenus = new JMenu[] { null,
1108 new JMenu(MessageManager.getString("action.ids")),
1109 new JMenu(MessageManager.getString("action.sequences")),
1110 new JMenu(MessageManager.getString("action.ids_sequences")) };
1112 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1113 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1114 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1115 for (int sq = 0; sq < seqs.length; sq++)
1118 int start = seqs[sq].findPosition(sg.getStartRes()),
1119 end = seqs[sq].findPosition(sg.getEndRes());
1120 // just collect ids from dataset sequence
1121 // TODO: check if IDs collected from selecton group intersects with the
1122 // current selection, too
1123 SequenceI sqi = seqs[sq];
1124 while (sqi.getDatasetSequence() != null)
1126 sqi = sqi.getDatasetSequence();
1128 List<DBRefEntry> dbr = sqi.getDBRefs();
1130 if (dbr != null && (nd = dbr.size()) > 0)
1132 for (int d = 0; d < nd; d++)
1134 DBRefEntry e = dbr.get(d);
1135 String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
1136 Object[] sarray = commonDbrefs.get(src);
1139 sarray = new Object[2];
1140 sarray[0] = new int[] { 0 };
1141 sarray[1] = new String[seqs.length];
1143 commonDbrefs.put(src, sarray);
1146 if (((String[]) sarray[1])[sq] == null)
1148 if (!e.hasMap() || (e.getMap()
1149 .locateMappedRange(start, end) != null))
1151 ((String[]) sarray[1])[sq] = e.getAccessionId();
1152 ((int[]) sarray[0])[0]++;
1158 // now create group links for all distinct ID/sequence sets.
1159 boolean addMenu = false; // indicates if there are any group links to give
1161 for (String link : groupLinks)
1163 GroupUrlLink urlLink = null;
1166 urlLink = new GroupUrlLink(link);
1167 } catch (Exception foo)
1169 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
1172 if (!urlLink.isValid())
1174 Cache.log.error(urlLink.getInvalidMessage());
1177 final String label = urlLink.getLabel();
1178 boolean usingNames = false;
1179 // Now see which parts of the group apply for this URL
1180 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1181 Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
1182 String[] seqstr, ids; // input to makeUrl
1185 int numinput = ((int[]) idset[0])[0];
1186 String[] allids = ((String[]) idset[1]);
1187 seqstr = new String[numinput];
1188 ids = new String[numinput];
1189 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1191 if (allids[sq] != null)
1193 ids[idcount] = allids[sq];
1194 seqstr[idcount++] = idandseqs[1][sq];
1200 // just use the id/seq set
1201 seqstr = idandseqs[1];
1205 // and try and make the groupURL!
1207 Object[] urlset = null;
1210 urlset = urlLink.makeUrlStubs(ids, seqstr,
1211 "FromJalview" + System.currentTimeMillis(), false);
1212 } catch (UrlStringTooLongException e)
1217 int type = urlLink.getGroupURLType() & 3;
1218 // first two bits ofurlLink type bitfield are sequenceids and sequences
1219 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1220 addshowLink(linkMenus[type],
1221 label + (((type & 1) == 1)
1222 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1230 groupLinksMenu = new JMenu(
1231 MessageManager.getString("action.group_link"));
1232 for (int m = 0; m < linkMenus.length; m++)
1234 if (linkMenus[m] != null
1235 && linkMenus[m].getMenuComponentCount() > 0)
1237 groupLinksMenu.add(linkMenus[m]);
1241 groupMenu.add(groupLinksMenu);
1251 private void jbInit() throws Exception
1253 groupMenu.setText(MessageManager.getString("label.selection"));
1254 groupName.setText(MessageManager.getString("label.name"));
1255 groupName.addActionListener(new ActionListener()
1258 public void actionPerformed(ActionEvent e)
1260 groupName_actionPerformed();
1263 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1265 JMenuItem sequenceName = new JMenuItem(
1266 MessageManager.getString("label.edit_name_description"));
1267 sequenceName.addActionListener(new ActionListener()
1270 public void actionPerformed(ActionEvent e)
1272 sequenceName_actionPerformed();
1275 JMenuItem chooseAnnotations = new JMenuItem(
1276 MessageManager.getString("action.choose_annotations"));
1277 chooseAnnotations.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 chooseAnnotations_actionPerformed(e);
1285 JMenuItem sequenceDetails = new JMenuItem(
1286 MessageManager.getString("label.sequence_details"));
1287 sequenceDetails.addActionListener(new ActionListener()
1290 public void actionPerformed(ActionEvent e)
1292 createSequenceDetailsReport(new SequenceI[] { sequence });
1295 JMenuItem sequenceSelDetails = new JMenuItem(
1296 MessageManager.getString("label.sequence_details"));
1297 sequenceSelDetails.addActionListener(new ActionListener()
1300 public void actionPerformed(ActionEvent e)
1302 createSequenceDetailsReport(ap.av.getSequenceSelection());
1307 .setText(MessageManager.getString("action.remove_group"));
1308 unGroupMenuItem.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 unGroupMenuItem_actionPerformed();
1317 .setText(MessageManager.getString("action.create_group"));
1318 createGroupMenuItem.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 createGroupMenuItem_actionPerformed();
1327 JMenuItem outline = new JMenuItem(
1328 MessageManager.getString("action.border_colour"));
1329 outline.addActionListener(new ActionListener()
1332 public void actionPerformed(ActionEvent e)
1334 outline_actionPerformed();
1337 showBoxes.setText(MessageManager.getString("action.boxes"));
1338 showBoxes.setState(true);
1339 showBoxes.addActionListener(new ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 showBoxes_actionPerformed();
1347 showText.setText(MessageManager.getString("action.text"));
1348 showText.setState(true);
1349 showText.addActionListener(new ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 showText_actionPerformed();
1357 showColourText.setText(MessageManager.getString("label.colour_text"));
1358 showColourText.addActionListener(new ActionListener()
1361 public void actionPerformed(ActionEvent e)
1363 showColourText_actionPerformed();
1367 .setText(MessageManager.getString("label.show_non_conserved"));
1368 displayNonconserved.setState(true);
1369 displayNonconserved.addActionListener(new ActionListener()
1372 public void actionPerformed(ActionEvent e)
1374 showNonconserved_actionPerformed();
1377 editMenu.setText(MessageManager.getString("action.edit"));
1378 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1379 cut.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1384 cut_actionPerformed();
1387 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1388 upperCase.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1396 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1397 copy.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 copy_actionPerformed();
1405 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1406 lowerCase.addActionListener(new ActionListener()
1409 public void actionPerformed(ActionEvent e)
1414 toggle.setText(MessageManager.getString("label.toggle_case"));
1415 toggle.addActionListener(new ActionListener()
1418 public void actionPerformed(ActionEvent e)
1424 MessageManager.getString("label.out_to_textbox") + "...");
1425 seqShowAnnotationsMenu
1426 .setText(MessageManager.getString("label.show_annotations"));
1427 seqHideAnnotationsMenu
1428 .setText(MessageManager.getString("label.hide_annotations"));
1429 groupShowAnnotationsMenu
1430 .setText(MessageManager.getString("label.show_annotations"));
1431 groupHideAnnotationsMenu
1432 .setText(MessageManager.getString("label.hide_annotations"));
1433 JMenuItem sequenceFeature = new JMenuItem(
1434 MessageManager.getString("label.create_sequence_feature"));
1435 sequenceFeature.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1440 sequenceFeature_actionPerformed();
1443 editGroupMenu.setText(MessageManager.getString("label.group"));
1444 chooseStructure.setText(
1445 MessageManager.getString("label.show_pdbstruct_dialog"));
1446 chooseStructure.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent actionEvent)
1451 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1452 if (ap.av.getSelectionGroup() != null)
1454 selectedSeqs = ap.av.getSequenceSelection();
1456 new StructureChooser(selectedSeqs, sequence, ap);
1461 .setText(MessageManager.getString("label.view_rna_structure"));
1463 // colStructureMenu.setText("Colour By Structure");
1464 JMenuItem editSequence = new JMenuItem(
1465 MessageManager.getString("label.edit_sequence") + "...");
1466 editSequence.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent actionEvent)
1471 editSequence_actionPerformed();
1474 makeReferenceSeq.setText(
1475 MessageManager.getString("label.mark_as_representative"));
1476 makeReferenceSeq.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent actionEvent)
1482 makeReferenceSeq_actionPerformed(actionEvent);
1487 groupMenu.add(sequenceSelDetails);
1490 add(rnaStructureMenu);
1491 add(chooseStructure);
1494 JMenuItem hideInsertions = new JMenuItem(
1495 MessageManager.getString("label.hide_insertions"));
1496 hideInsertions.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 hideInsertions_actionPerformed(e);
1505 add(hideInsertions);
1507 // annotations configuration panel suppressed for now
1508 // groupMenu.add(chooseAnnotations);
1511 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1512 * (if a selection group is in force).
1514 sequenceMenu.add(seqShowAnnotationsMenu);
1515 sequenceMenu.add(seqHideAnnotationsMenu);
1516 sequenceMenu.add(seqAddReferenceAnnotations);
1517 groupMenu.add(groupShowAnnotationsMenu);
1518 groupMenu.add(groupHideAnnotationsMenu);
1519 groupMenu.add(groupAddReferenceAnnotations);
1520 groupMenu.add(editMenu);
1521 groupMenu.add(outputMenu);
1522 groupMenu.add(sequenceFeature);
1523 groupMenu.add(createGroupMenuItem);
1524 groupMenu.add(unGroupMenuItem);
1525 groupMenu.add(editGroupMenu);
1526 sequenceMenu.add(sequenceName);
1527 sequenceMenu.add(sequenceDetails);
1528 sequenceMenu.add(makeReferenceSeq);
1535 editMenu.add(editSequence);
1536 editMenu.add(upperCase);
1537 editMenu.add(lowerCase);
1538 editMenu.add(toggle);
1539 editGroupMenu.add(groupName);
1540 editGroupMenu.add(colourMenu);
1541 editGroupMenu.add(showBoxes);
1542 editGroupMenu.add(showText);
1543 editGroupMenu.add(showColourText);
1544 editGroupMenu.add(outline);
1545 editGroupMenu.add(displayNonconserved);
1549 * Constructs the entries for the colour menu
1551 protected void initColourMenu()
1553 colourMenu.setText(MessageManager.getString("label.group_colour"));
1554 textColour.setText(MessageManager.getString("label.text_colour"));
1555 textColour.addActionListener(new ActionListener()
1558 public void actionPerformed(ActionEvent e)
1560 textColour_actionPerformed();
1564 abovePIDColour.setText(
1565 MessageManager.getString("label.above_identity_threshold"));
1566 abovePIDColour.addActionListener(new ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1576 MessageManager.getString("label.modify_identity_threshold"));
1577 modifyPID.addActionListener(new ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 modifyPID_actionPerformed();
1586 conservationMenuItem
1587 .setText(MessageManager.getString("action.by_conservation"));
1588 conservationMenuItem.addActionListener(new ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 conservationMenuItem_actionPerformed(
1594 conservationMenuItem.isSelected());
1598 annotationColour = new JRadioButtonMenuItem(
1599 MessageManager.getString("action.by_annotation"));
1600 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1601 annotationColour.setEnabled(false);
1602 annotationColour.setToolTipText(
1603 MessageManager.getString("label.by_annotation_tooltip"));
1605 modifyConservation.setText(MessageManager
1606 .getString("label.modify_conservation_threshold"));
1607 modifyConservation.addActionListener(new ActionListener()
1610 public void actionPerformed(ActionEvent e)
1612 modifyConservation_actionPerformed();
1618 * Builds the group colour sub-menu, including any user-defined colours which
1619 * were loaded at startup or during the Jalview session
1621 protected void buildColourMenu()
1623 SequenceGroup sg = ap.av.getSelectionGroup();
1627 * popup menu with no sequence group scope
1631 colourMenu.removeAll();
1632 colourMenu.add(textColour);
1633 colourMenu.addSeparator();
1635 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1637 bg.add(annotationColour);
1638 colourMenu.add(annotationColour);
1640 colourMenu.addSeparator();
1641 colourMenu.add(conservationMenuItem);
1642 colourMenu.add(modifyConservation);
1643 colourMenu.add(abovePIDColour);
1644 colourMenu.add(modifyPID);
1647 protected void modifyConservation_actionPerformed()
1649 SequenceGroup sg = getGroup();
1652 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1653 SliderPanel.showConservationSlider();
1657 protected void modifyPID_actionPerformed()
1659 SequenceGroup sg = getGroup();
1662 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1664 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1665 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1666 SliderPanel.showPIDSlider();
1671 * Check for any annotations on the underlying dataset sequences (for the
1672 * current selection group) which are not 'on the alignment'.If any are found,
1673 * enable the option to add them to the alignment. The criteria for 'on the
1674 * alignment' is finding an alignment annotation on the alignment, matched on
1675 * calcId, label and sequenceRef.
1677 * A tooltip is also constructed that displays the source (calcId) and type
1678 * (label) of the annotations that can be added.
1681 * @param forSequences
1683 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1684 List<SequenceI> forSequences)
1686 menuItem.setEnabled(false);
1689 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1690 * Using TreeMap means calcIds are shown in alphabetical order.
1692 SortedMap<String, String> tipEntries = new TreeMap<>();
1693 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1694 AlignmentI al = this.ap.av.getAlignment();
1695 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1697 if (!candidates.isEmpty())
1699 StringBuilder tooltip = new StringBuilder(64);
1700 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1703 * Found annotations that could be added. Enable the menu item, and
1704 * configure its tooltip and action.
1706 menuItem.setEnabled(true);
1707 for (String calcId : tipEntries.keySet())
1709 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1711 String tooltipText = JvSwingUtils.wrapTooltip(true,
1712 tooltip.toString());
1713 menuItem.setToolTipText(tooltipText);
1715 menuItem.addActionListener(new ActionListener()
1718 public void actionPerformed(ActionEvent e)
1720 addReferenceAnnotations_actionPerformed(candidates);
1727 * Add annotations to the sequences and to the alignment.
1730 * a map whose keys are sequences on the alignment, and values a list
1731 * of annotations to add to each sequence
1733 protected void addReferenceAnnotations_actionPerformed(
1734 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1736 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1737 final AlignmentI alignment = this.ap.getAlignment();
1738 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1743 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1745 if (!ap.av.getAlignment().hasSeqrep())
1747 // initialise the display flags so the user sees something happen
1748 ap.av.setDisplayReferenceSeq(true);
1749 ap.av.setColourByReferenceSeq(true);
1750 ap.av.getAlignment().setSeqrep(sequence);
1754 if (ap.av.getAlignment().getSeqrep() == sequence)
1756 ap.av.getAlignment().setSeqrep(null);
1760 ap.av.getAlignment().setSeqrep(sequence);
1766 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1768 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1769 BitSet inserts = new BitSet();
1771 boolean markedPopup = false;
1772 // mark inserts in current selection
1773 if (ap.av.getSelectionGroup() != null)
1775 // mark just the columns in the selection group to be hidden
1776 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1777 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1779 // now clear columns without gaps
1780 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1786 inserts.and(sq.getInsertionsAsBits());
1788 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1789 ap.av.getSelectionGroup().getEndRes());
1792 // now mark for sequence under popup if we haven't already done it
1793 else if (!markedPopup && sequence != null)
1795 inserts.or(sequence.getInsertionsAsBits());
1797 // and set hidden columns accordingly
1798 hidden.hideColumns(inserts);
1803 protected void sequenceSelectionDetails_actionPerformed()
1805 createSequenceDetailsReport(ap.av.getSequenceSelection());
1808 public void createSequenceDetailsReport(SequenceI[] sequences)
1810 StringBuilder contents = new StringBuilder(128);
1811 contents.append("<html><body>");
1812 for (SequenceI seq : sequences)
1814 contents.append("<p><h2>" + MessageManager.formatMessage(
1815 "label.create_sequence_details_report_annotation_for",
1817 { seq.getDisplayId(true) }) + "</h2></p><p>");
1818 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1819 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1820 contents.append("</p>");
1822 contents.append("</body></html>");
1823 String report = contents.toString();
1825 JInternalFrame frame;
1826 if (Platform.isJS())
1828 JLabel textLabel = new JLabel();
1829 textLabel.setText(report);
1830 textLabel.setBackground(Color.WHITE);
1831 JPanel pane = new JPanel(new BorderLayout());
1832 pane.setOpaque(true);
1833 pane.setBackground(Color.WHITE);
1834 pane.add(textLabel, BorderLayout.NORTH);
1835 frame = new JInternalFrame();
1836 frame.getContentPane().add(new JScrollPane(pane));
1845 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1846 cap.setText(report);
1850 Desktop.addInternalFrame(frame,
1851 MessageManager.formatMessage("label.sequence_details_for",
1852 (sequences.length == 1 ? new Object[]
1853 { sequences[0].getDisplayId(true) }
1856 .getString("label.selection") })),
1860 protected void showNonconserved_actionPerformed()
1862 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1867 * call to refresh view after settings change
1871 ap.updateAnnotation();
1872 // removed paintAlignment(true) here:
1873 // updateAnnotation calls paintAlignment already, so don't need to call
1876 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1880 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1881 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1891 public void abovePIDColour_actionPerformed(boolean selected)
1893 SequenceGroup sg = getGroup();
1901 sg.cs.setConsensus(AAFrequency.calculate(
1902 sg.getSequences(ap.av.getHiddenRepSequences()),
1903 sg.getStartRes(), sg.getEndRes() + 1));
1905 int threshold = SliderPanel.setPIDSliderSource(ap,
1906 sg.getGroupColourScheme(), getGroup().getName());
1908 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1910 SliderPanel.showPIDSlider();
1913 // remove PIDColouring
1915 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1916 SliderPanel.hidePIDSlider();
1918 modifyPID.setEnabled(selected);
1924 * Open a panel where the user can choose which types of sequence annotation
1929 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1931 // todo correct way to guard against opening a duplicate panel?
1932 new AnnotationChooser(ap);
1941 public void conservationMenuItem_actionPerformed(boolean selected)
1943 SequenceGroup sg = getGroup();
1951 // JBPNote: Conservation name shouldn't be i18n translated
1952 Conservation c = new Conservation("Group",
1953 sg.getSequences(ap.av.getHiddenRepSequences()),
1954 sg.getStartRes(), sg.getEndRes() + 1);
1957 c.verdict(false, ap.av.getConsPercGaps());
1958 sg.cs.setConservation(c);
1960 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1962 SliderPanel.showConservationSlider();
1965 // remove ConservationColouring
1967 sg.cs.setConservation(null);
1968 SliderPanel.hideConservationSlider();
1970 modifyConservation.setEnabled(selected);
1976 * Shows a dialog where group name and description may be edited
1978 protected void groupName_actionPerformed()
1980 SequenceGroup sg = getGroup();
1981 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1982 sg.getDescription(),
1983 MessageManager.getString("label.group_name"),
1984 MessageManager.getString("label.group_description"));
1985 dialog.showDialog(ap.alignFrame,
1986 MessageManager.getString("label.edit_group_name_description"),
1992 sg.setName(dialog.getName());
1993 sg.setDescription(dialog.getDescription());
2000 * Get selection group - adding it to the alignment if necessary.
2002 * @return sequence group to operate on
2004 SequenceGroup getGroup()
2006 SequenceGroup sg = ap.av.getSelectionGroup();
2007 // this method won't add a new group if it already exists
2010 ap.av.getAlignment().addGroup(sg);
2017 * Shows a dialog where the sequence name and description may be edited. If a
2018 * name containing spaces is entered, these are converted to underscores, with a
2021 void sequenceName_actionPerformed()
2023 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2024 sequence.getDescription(),
2025 MessageManager.getString("label.sequence_name"),
2026 MessageManager.getString("label.sequence_description"));
2027 dialog.showDialog(ap.alignFrame,
2028 MessageManager.getString(
2029 "label.edit_sequence_name_description"),
2035 if (dialog.getName() != null)
2037 if (dialog.getName().indexOf(" ") > -1)
2039 JvOptionPane.showMessageDialog(ap,
2040 MessageManager.getString(
2041 "label.spaces_converted_to_underscores"),
2042 MessageManager.getString(
2043 "label.no_spaces_allowed_sequence_name"),
2044 JvOptionPane.WARNING_MESSAGE);
2046 sequence.setName(dialog.getName().replace(' ', '_'));
2047 ap.paintAlignment(false, false);
2049 sequence.setDescription(dialog.getDescription());
2050 ap.av.firePropertyChange("alignment", null,
2051 ap.av.getAlignment().getSequences());
2062 void unGroupMenuItem_actionPerformed()
2064 SequenceGroup sg = ap.av.getSelectionGroup();
2065 ap.av.getAlignment().deleteGroup(sg);
2066 ap.av.setSelectionGroup(null);
2070 void createGroupMenuItem_actionPerformed()
2072 getGroup(); // implicitly creates group - note - should apply defaults / use
2073 // standard alignment window logic for this
2078 * Offers a colour chooser and sets the selected colour as the group outline
2080 protected void outline_actionPerformed()
2082 String title = MessageManager
2083 .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(),
2094 title, 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));