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;
36 import java.util.Objects;
37 import java.util.SortedMap;
38 import java.util.TreeMap;
39 import java.util.Vector;
41 import javax.swing.ButtonGroup;
42 import javax.swing.JCheckBoxMenuItem;
43 import javax.swing.JInternalFrame;
44 import javax.swing.JLabel;
45 import javax.swing.JMenu;
46 import javax.swing.JMenuItem;
47 import javax.swing.JPanel;
48 import javax.swing.JPopupMenu;
49 import javax.swing.JRadioButtonMenuItem;
50 import javax.swing.JScrollPane;
52 import jalview.analysis.AAFrequency;
53 import jalview.analysis.AlignmentAnnotationUtils;
54 import jalview.analysis.AlignmentUtils;
55 import jalview.analysis.Conservation;
56 import jalview.api.AlignViewportI;
57 import jalview.bin.Cache;
58 import jalview.commands.ChangeCaseCommand;
59 import jalview.commands.EditCommand;
60 import jalview.commands.EditCommand.Action;
61 import jalview.datamodel.AlignmentAnnotation;
62 import jalview.datamodel.AlignmentI;
63 import jalview.datamodel.DBRefEntry;
64 import jalview.datamodel.HiddenColumns;
65 import jalview.datamodel.MappedFeatures;
66 import jalview.datamodel.PDBEntry;
67 import jalview.datamodel.ResidueCount;
68 import jalview.datamodel.SequenceFeature;
69 import jalview.datamodel.SequenceGroup;
70 import jalview.datamodel.SequenceI;
71 import jalview.gui.ColourMenuHelper.ColourChangeListener;
72 import jalview.gui.JalviewColourChooser.ColourChooserListener;
73 import jalview.io.CountReader;
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;
92 import java.io.IOException;
93 import java.net.MalformedURLException;
96 * The popup menu that is displayed on right-click on a sequence id, or in the
99 public class PopupMenu extends JPopupMenu implements ColourChangeListener
102 * maximum length of feature description to include in popup menu item text
104 private static final int FEATURE_DESC_MAX = 40;
107 * true for ID Panel menu, false for alignment panel menu
109 private final boolean forIdPanel;
111 private final AlignmentPanel ap;
114 * the sequence under the cursor when clicked
115 * (additional sequences may be selected)
117 private final SequenceI sequence;
119 JMenu groupMenu = new JMenu();
121 JMenuItem groupName = new JMenuItem();
123 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
125 protected JMenuItem modifyPID = new JMenuItem();
127 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
129 protected JRadioButtonMenuItem annotationColour;
131 protected JMenuItem modifyConservation = new JMenuItem();
133 JMenu sequenceMenu = new JMenu();
135 JMenuItem makeReferenceSeq = new JMenuItem();
137 JMenuItem createGroupMenuItem = new JMenuItem();
139 JMenuItem unGroupMenuItem = new JMenuItem();
141 JMenu colourMenu = new JMenu();
143 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
145 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
147 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
149 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
151 JMenu editMenu = new JMenu();
153 JMenuItem upperCase = new JMenuItem();
155 JMenuItem lowerCase = new JMenuItem();
157 JMenuItem toggle = new JMenuItem();
159 JMenu outputMenu = new JMenu();
161 JMenu seqShowAnnotationsMenu = new JMenu();
163 JMenu seqHideAnnotationsMenu = new JMenu();
165 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
166 MessageManager.getString("label.add_reference_annotations"));
168 JMenu groupShowAnnotationsMenu = new JMenu();
170 JMenu groupHideAnnotationsMenu = new JMenu();
172 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
173 MessageManager.getString("label.add_reference_annotations"));
175 JMenuItem textColour = new JMenuItem();
177 JMenu editGroupMenu = new JMenu();
179 JMenuItem chooseStructure = new JMenuItem();
181 JMenu rnaStructureMenu = new JMenu();
184 * Constructs a menu with sub-menu items for any hyperlinks for the sequence
185 * and/or features provided. Hyperlinks may include a lookup by sequence id,
186 * or database cross-references, depending on which links are enabled in user
193 protected static JMenu buildLinkMenu(final SequenceI seq,
194 List<SequenceFeature> features)
196 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
198 List<String> nlinks = null;
201 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
202 UrlLink.sort(nlinks);
206 nlinks = new ArrayList<>();
209 if (features != null)
211 for (SequenceFeature sf : features)
213 if (sf.links != null)
215 for (String link : sf.links)
224 * instantiate the hyperlinklink templates from sequence data;
225 * note the order of the templates is preserved in the map
227 Map<String, List<String>> linkset = new LinkedHashMap<>();
228 for (String link : nlinks)
230 UrlLink urlLink = null;
233 urlLink = new UrlLink(link);
234 } catch (Exception foo)
236 Cache.log.error("Exception for URLLink '" + link + "'", foo);
240 if (!urlLink.isValid())
242 Cache.log.error(urlLink.getInvalidMessage());
246 urlLink.createLinksFromSeq(seq, linkset);
250 * construct menu items for the hyperlinks (still preserving
251 * the order of the sorted templates)
253 addUrlLinks(linkMenu, linkset.values());
259 * A helper method that builds menu items from the given links, with action
260 * handlers to open the link URL, and adds them to the linkMenu. Each provided
261 * link should be a list whose second item is the menu text, and whose fourth
262 * item is the URL to open when the menu item is selected.
267 static private void addUrlLinks(JMenu linkMenu,
268 Collection<List<String>> linkset)
270 for (List<String> linkstrset : linkset)
272 final String url = linkstrset.get(3);
273 JMenuItem item = new JMenuItem(linkstrset.get(1));
274 item.setToolTipText(MessageManager
275 .formatMessage("label.open_url_param", new Object[]
277 item.addActionListener(new ActionListener()
280 public void actionPerformed(ActionEvent e)
282 new Thread(new Runnable()
297 * Opens the provided url in the default web browser, or shows an error
298 * message if this fails
302 static void showLink(String url)
306 jalview.util.BrowserLauncher.openURL(url);
307 } catch (Exception ex)
309 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
310 MessageManager.getString("label.web_browser_not_found_unix"),
311 MessageManager.getString("label.web_browser_not_found"),
312 JvOptionPane.WARNING_MESSAGE);
314 ex.printStackTrace();
319 * add a late bound groupURL item to the given linkMenu
323 * - menu label string
324 * @param urlgenerator
325 * GroupURLLink used to generate URL
327 * Object array returned from the makeUrlStubs function.
329 static void addshowLink(JMenu linkMenu, String label,
330 final GroupUrlLink urlgenerator, final Object[] urlstub)
332 JMenuItem item = new JMenuItem(label);
333 item.setToolTipText(MessageManager
334 .formatMessage("label.open_url_seqs_param", new Object[]
335 { urlgenerator.getUrl_prefix(),
336 urlgenerator.getNumberInvolved(urlstub) }));
337 // TODO: put in info about what is being sent.
338 item.addActionListener(new ActionListener()
341 public void actionPerformed(ActionEvent e)
343 new Thread(new Runnable()
351 showLink(urlgenerator.constructFrom(urlstub));
352 } catch (UrlStringTooLongException e2)
365 * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
368 * the panel in which the mouse is clicked
370 * the sequence under the mouse
371 * @throws NullPointerException
374 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
376 this(false, ap, seq, column, null);
380 * Constructor for a PopupMenu for a click in the sequence id panel
383 * the panel in which the mouse is clicked
385 * the sequence under the mouse click
387 * templates for sequence external links
388 * @throws NullPointerException
391 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
392 List<String> groupLinks)
394 this(true, alignPanel, seq, -1, groupLinks);
398 * Private constructor that constructs a popup menu for either sequence ID
399 * Panel, or alignment context
405 * aligned column position (0...)
408 private PopupMenu(boolean fromIdPanel,
409 final AlignmentPanel alignPanel,
410 final SequenceI seq, final int column, List<String> groupLinks)
412 Objects.requireNonNull(seq);
413 this.forIdPanel = fromIdPanel;
414 this.ap = alignPanel;
417 for (String ff : FileFormats.getInstance().getWritableFormats(true))
419 JMenuItem item = new JMenuItem(ff);
421 item.addActionListener(new ActionListener()
424 public void actionPerformed(ActionEvent e)
426 outputText_actionPerformed(e);
430 outputMenu.add(item);
434 * Build menus for annotation types that may be shown or hidden, and for
435 * 'reference annotations' that may be added to the alignment. First for the
436 * currently selected sequence (if there is one):
438 final List<SequenceI> selectedSequence = (forIdPanel && seq != null
440 : Collections.<SequenceI> emptyList());
441 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
442 seqHideAnnotationsMenu, selectedSequence);
443 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
447 * And repeat for the current selection group (if there is one):
449 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
450 ? Collections.<SequenceI> emptyList()
451 : alignPanel.av.getSelectionGroup().getSequences());
452 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
453 groupHideAnnotationsMenu, selectedGroup);
454 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
460 } catch (Exception e)
468 sequenceMenu.setText(sequence.getName());
469 if (seq == alignPanel.av.getAlignment().getSeqrep())
471 makeReferenceSeq.setText(
472 MessageManager.getString("action.unmark_as_reference"));
476 makeReferenceSeq.setText(
477 MessageManager.getString("action.set_as_reference"));
480 if (!alignPanel.av.getAlignment().isNucleotide())
482 remove(rnaStructureMenu);
486 int origCount = rnaStructureMenu.getItemCount();
488 * add menu items to 2D-render any alignment or sequence secondary
489 * structure annotation
491 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
492 .getAlignmentAnnotation();
495 for (final AlignmentAnnotation aa : aas)
497 if (aa.isValidStruc() && aa.sequenceRef == null)
500 * valid alignment RNA secondary structure annotation
502 menuItem = new JMenuItem();
503 menuItem.setText(MessageManager.formatMessage(
504 "label.2d_rna_structure_line", new Object[]
506 menuItem.addActionListener(new ActionListener()
509 public void actionPerformed(ActionEvent e)
511 new AppVarna(seq, aa, alignPanel);
514 rnaStructureMenu.add(menuItem);
519 if (seq.getAnnotation() != null)
521 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
522 for (final AlignmentAnnotation aa : seqAnns)
524 if (aa.isValidStruc())
527 * valid sequence RNA secondary structure annotation
529 // TODO: make rnastrucF a bit more nice
530 menuItem = new JMenuItem();
531 menuItem.setText(MessageManager.formatMessage(
532 "label.2d_rna_sequence_name", new Object[]
534 menuItem.addActionListener(new ActionListener()
537 public void actionPerformed(ActionEvent e)
539 // TODO: VARNA does'nt print gaps in the sequence
540 new AppVarna(seq, aa, alignPanel);
543 rnaStructureMenu.add(menuItem);
547 if (rnaStructureMenu.getItemCount() == origCount)
549 remove(rnaStructureMenu);
553 if (seq.hasHMMProfile())
555 menuItem = new JMenuItem(MessageManager
556 .getString("action.add_background_frequencies"));
557 menuItem.addActionListener(new ActionListener()
560 public void actionPerformed(ActionEvent e)
564 ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
568 seq.getHMM().setBackgroundFrequencies(counts);
569 ap.alignFrame.buildColourMenu();
571 } catch (MalformedURLException e1)
573 e1.printStackTrace();
574 } catch (IOException e1)
576 e1.printStackTrace();
583 menuItem = new JMenuItem(
584 MessageManager.getString("action.hide_sequences"));
585 menuItem.addActionListener(new ActionListener()
588 public void actionPerformed(ActionEvent e)
590 hideSequences(false);
595 if (alignPanel.av.getSelectionGroup() != null
596 && alignPanel.av.getSelectionGroup().getSize() > 1)
598 menuItem = new JMenuItem(MessageManager
599 .formatMessage("label.represent_group_with", new Object[]
601 menuItem.addActionListener(new ActionListener()
604 public void actionPerformed(ActionEvent e)
609 sequenceMenu.add(menuItem);
612 if (alignPanel.av.hasHiddenRows())
614 final int index = alignPanel.av.getAlignment().findIndex(seq);
616 if (alignPanel.av.adjustForHiddenSeqs(index)
617 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
619 menuItem = new JMenuItem(
620 MessageManager.getString("action.reveal_sequences"));
621 menuItem.addActionListener(new ActionListener()
624 public void actionPerformed(ActionEvent e)
626 alignPanel.av.showSequence(index);
627 if (alignPanel.overviewPanel != null)
629 alignPanel.overviewPanel.updateOverviewImage();
640 * - in the IdPanel (seq not null) if any sequence is hidden
641 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
643 if (alignPanel.av.hasHiddenRows())
645 boolean addOption = seq != null;
646 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
652 JMenuItem menuItem = new JMenuItem(
653 MessageManager.getString("action.reveal_all"));
654 menuItem.addActionListener(new ActionListener()
657 public void actionPerformed(ActionEvent e)
659 alignPanel.av.showAllHiddenSeqs();
660 if (alignPanel.overviewPanel != null)
662 alignPanel.overviewPanel.updateOverviewImage();
670 SequenceGroup sg = alignPanel.av.getSelectionGroup();
671 boolean isDefinedGroup = (sg != null)
672 ? alignPanel.av.getAlignment().getGroups().contains(sg)
675 if (sg != null && sg.getSize() > 0)
677 groupName.setText(MessageManager
678 .getString("label.edit_name_and_description_current_group"));
680 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
682 conservationMenuItem.setEnabled(!sg.isNucleotide());
686 if (sg.cs.conservationApplied())
688 conservationMenuItem.setSelected(true);
690 if (sg.cs.getThreshold() > 0)
692 abovePIDColour.setSelected(true);
695 modifyConservation.setEnabled(conservationMenuItem.isSelected());
696 modifyPID.setEnabled(abovePIDColour.isSelected());
697 displayNonconserved.setSelected(sg.getShowNonconserved());
698 showText.setSelected(sg.getDisplayText());
699 showColourText.setSelected(sg.getColourText());
700 showBoxes.setSelected(sg.getDisplayBoxes());
701 // add any groupURLs to the groupURL submenu and make it visible
702 if (groupLinks != null && groupLinks.size() > 0)
704 buildGroupURLMenu(sg, groupLinks);
706 // Add a 'show all structures' for the current selection
707 Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
708 Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
710 SequenceI sqass = null;
711 for (SequenceI sq : alignPanel.av.getSequenceSelection())
713 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
714 if (pes != null && pes.size() > 0)
716 reppdb.put(pes.get(0).getId(), pes.get(0));
717 for (PDBEntry pe : pes)
719 pdbe.put(pe.getId(), pe);
729 final PDBEntry[] pe = pdbe.values()
730 .toArray(new PDBEntry[pdbe.size()]),
731 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
732 final JMenuItem gpdbview, rpdbview;
737 groupMenu.setVisible(false);
738 editMenu.setVisible(false);
743 createGroupMenuItem.setVisible(true);
744 unGroupMenuItem.setVisible(false);
745 editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
749 createGroupMenuItem.setVisible(false);
750 unGroupMenuItem.setVisible(true);
751 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
756 sequenceMenu.setVisible(false);
757 chooseStructure.setVisible(false);
758 rnaStructureMenu.setVisible(false);
761 addLinksAndFeatures(seq, column);
767 * <li>configured sequence database links (ID panel popup menu)</li>
768 * <li>non-positional feature links (ID panel popup menu)</li>
769 * <li>positional feature links (alignment panel popup menu)</li>
770 * <li>feature details links (alignment panel popup menu)</li>
772 * If this panel is also showed complementary (CDS/protein) features, then links
773 * to their feature details are also added.
778 void addLinksAndFeatures(final SequenceI seq, final int column)
780 List<SequenceFeature> features = null;
783 features = sequence.getFeatures().getNonPositionalFeatures();
787 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
791 addLinks(seq, features);
795 addFeatureDetails(features, seq, column);
800 * Add a menu item to show feature details for each sequence feature. Any
801 * linked 'virtual' features (CDS/protein) are also optionally found and
808 protected void addFeatureDetails(List<SequenceFeature> features,
809 final SequenceI seq, final int column)
812 * add features in CDS/protein complement at the corresponding
813 * position if configured to do so
815 MappedFeatures mf = null;
816 if (ap.av.isShowComplementFeatures())
818 if (!Comparison.isGap(sequence.getCharAt(column)))
820 AlignViewportI complement = ap.getAlignViewport()
821 .getCodingComplement();
822 AlignFrame af = Desktop.getAlignFrameFor(complement);
823 FeatureRendererModel fr2 = af.getFeatureRenderer();
824 int seqPos = sequence.findPosition(column);
825 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
829 if (features.isEmpty() && mf == null)
832 * no features to show at this position
837 JMenu details = new JMenu(
838 MessageManager.getString("label.feature_details"));
841 String name = seq.getName();
842 for (final SequenceFeature sf : features)
844 addFeatureDetailsMenuItem(details, name, sf, null);
849 for (final SequenceFeature sf : mf.features)
851 addFeatureDetailsMenuItem(details, name, sf, mf);
857 * A helper method to add one menu item whose action is to show details for
858 * one feature. The menu text includes feature description, but this may be
866 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
867 final SequenceFeature sf, MappedFeatures mf)
869 int start = sf.getBegin();
870 int end = sf.getEnd();
874 * show local rather than linked feature coordinates
876 int[] beginRange = mf.getMappedPositions(start, start);
877 start = beginRange[0];
878 int[] endRange = mf.getMappedPositions(end, end);
879 end = endRange[endRange.length - 1];
881 StringBuilder desc = new StringBuilder();
882 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
885 desc.append(sf.isContactFeature() ? ":" : "-");
886 desc.append(String.valueOf(end));
888 String description = sf.getDescription();
889 if (description != null)
892 description = StringUtils.stripHtmlTags(description);
895 * truncate overlong descriptions unless they contain an href
896 * (as truncation could leave corrupted html)
898 boolean hasLink = description.indexOf("a href") > -1;
899 if (description.length() > FEATURE_DESC_MAX && !hasLink)
901 description = description.substring(0, FEATURE_DESC_MAX) + "...";
903 desc.append(description);
905 String featureGroup = sf.getFeatureGroup();
906 if (featureGroup != null)
908 desc.append(" (").append(featureGroup).append(")");
910 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
911 JMenuItem item = new JMenuItem(htmlText);
912 item.addActionListener(new ActionListener()
915 public void actionPerformed(ActionEvent e)
917 showFeatureDetails(sf, seqName, mf);
924 * Opens a panel showing a text report of feature details
930 protected void showFeatureDetails(SequenceFeature sf, String seqName,
933 JInternalFrame details;
936 details = new JInternalFrame();
937 JPanel panel = new JPanel(new BorderLayout());
938 panel.setOpaque(true);
939 panel.setBackground(Color.white);
940 // TODO JAL-3026 set style of table correctly for feature details
941 JLabel reprt = new JLabel(MessageManager
942 .formatMessage("label.html_content", new Object[]
943 { sf.getDetailsReport(seqName, mf) }));
944 reprt.setBackground(Color.WHITE);
945 reprt.setOpaque(true);
946 panel.add(reprt, BorderLayout.CENTER);
947 details.setContentPane(panel);
957 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
958 // it appears Java's CSS does not support border-collapse :-(
959 cap.addStylesheetRule("table { border-collapse: collapse;}");
960 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
961 cap.setText(sf.getDetailsReport(seqName, mf));
964 Desktop.addInternalFrame(details,
965 MessageManager.getString("label.feature_details"), 500, 500);
969 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
970 * When seq is not null, these are links for the sequence id, which may be to
971 * external web sites for the sequence accession, and/or links embedded in
972 * non-positional features. When seq is null, only links embedded in the
973 * provided features are added. If no links are found, the menu is not added.
978 void addLinks(final SequenceI seq, List<SequenceFeature> features)
980 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
982 // only add link menu if it has entries
983 if (linkMenu.getItemCount() > 0)
987 sequenceMenu.add(linkMenu);
997 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
998 * "All" is added first, followed by a separator. Then add any annotation
999 * types associated with the current selection. Separate menus are built for
1000 * the selected sequence group (if any), and the selected sequence.
1002 * Some annotation rows are always rendered together - these can be identified
1003 * by a common graphGroup property > -1. Only one of each group will be marked
1004 * as visible (to avoid duplication of the display). For such groups we add a
1005 * composite type name, e.g.
1007 * IUPredWS (Long), IUPredWS (Short)
1011 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
1012 List<SequenceI> forSequences)
1014 showMenu.removeAll();
1015 hideMenu.removeAll();
1017 final List<String> all = Arrays
1018 .asList(new String[]
1019 { MessageManager.getString("label.all") });
1020 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
1022 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
1024 showMenu.addSeparator();
1025 hideMenu.addSeparator();
1027 final AlignmentAnnotation[] annotations = ap.getAlignment()
1028 .getAlignmentAnnotation();
1031 * Find shown/hidden annotations types, distinguished by source (calcId),
1032 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1033 * the insertion order, which is the order of the annotations on the
1036 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
1037 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
1038 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1039 AlignmentAnnotationUtils.asList(annotations), forSequences);
1041 for (String calcId : hiddenTypes.keySet())
1043 for (List<String> type : hiddenTypes.get(calcId))
1045 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1049 // grey out 'show annotations' if none are hidden
1050 showMenu.setEnabled(!hiddenTypes.isEmpty());
1052 for (String calcId : shownTypes.keySet())
1054 for (List<String> type : shownTypes.get(calcId))
1056 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1060 // grey out 'hide annotations' if none are shown
1061 hideMenu.setEnabled(!shownTypes.isEmpty());
1065 * Returns a list of sequences - either the current selection group (if there
1066 * is one), else the specified single sequence.
1071 protected List<SequenceI> getSequenceScope(SequenceI seq)
1073 List<SequenceI> forSequences = null;
1074 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1075 if (selectionGroup != null && selectionGroup.getSize() > 0)
1077 forSequences = selectionGroup.getSequences();
1081 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1082 : Arrays.asList(seq);
1084 return forSequences;
1088 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1091 * @param showOrHideMenu
1092 * the menu to add to
1093 * @param forSequences
1094 * the sequences whose annotations may be shown or hidden
1099 * if true this is a special label meaning 'All'
1100 * @param actionIsShow
1101 * if true, the select menu item action is to show the annotation
1104 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1105 final List<SequenceI> forSequences, String calcId,
1106 final List<String> types, final boolean allTypes,
1107 final boolean actionIsShow)
1109 String label = types.toString(); // [a, b, c]
1110 label = label.substring(1, label.length() - 1); // a, b, c
1111 final JMenuItem item = new JMenuItem(label);
1112 item.setToolTipText(calcId);
1113 item.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1119 types, forSequences, allTypes, actionIsShow);
1123 showOrHideMenu.add(item);
1126 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1129 // TODO: usability: thread off the generation of group url content so root
1130 // menu appears asap
1131 // sequence only URLs
1132 // ID/regex match URLs
1133 JMenu groupLinksMenu = new JMenu(
1134 MessageManager.getString("action.group_link"));
1135 // three types of url that might be created.
1136 JMenu[] linkMenus = new JMenu[] { null,
1137 new JMenu(MessageManager.getString("action.ids")),
1138 new JMenu(MessageManager.getString("action.sequences")),
1139 new JMenu(MessageManager.getString("action.ids_sequences")) };
1141 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1142 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1143 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1144 for (int sq = 0; sq < seqs.length; sq++)
1147 int start = seqs[sq].findPosition(sg.getStartRes()),
1148 end = seqs[sq].findPosition(sg.getEndRes());
1149 // just collect ids from dataset sequence
1150 // TODO: check if IDs collected from selecton group intersects with the
1151 // current selection, too
1152 SequenceI sqi = seqs[sq];
1153 while (sqi.getDatasetSequence() != null)
1155 sqi = sqi.getDatasetSequence();
1157 List<DBRefEntry> dbr = sqi.getDBRefs();
1159 if (dbr != null && (nd = dbr.size()) > 0)
1161 for (int d = 0; d < nd; d++)
1163 DBRefEntry e = dbr.get(d);
1164 String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
1165 Object[] sarray = commonDbrefs.get(src);
1168 sarray = new Object[2];
1169 sarray[0] = new int[] { 0 };
1170 sarray[1] = new String[seqs.length];
1172 commonDbrefs.put(src, sarray);
1175 if (((String[]) sarray[1])[sq] == null)
1177 if (!e.hasMap() || (e.getMap()
1178 .locateMappedRange(start, end) != null))
1180 ((String[]) sarray[1])[sq] = e.getAccessionId();
1181 ((int[]) sarray[0])[0]++;
1187 // now create group links for all distinct ID/sequence sets.
1188 boolean addMenu = false; // indicates if there are any group links to give
1190 for (String link : groupLinks)
1192 GroupUrlLink urlLink = null;
1195 urlLink = new GroupUrlLink(link);
1196 } catch (Exception foo)
1198 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
1201 if (!urlLink.isValid())
1203 Cache.log.error(urlLink.getInvalidMessage());
1206 final String label = urlLink.getLabel();
1207 boolean usingNames = false;
1208 // Now see which parts of the group apply for this URL
1209 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1210 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
1211 String[] seqstr, ids; // input to makeUrl
1214 int numinput = ((int[]) idset[0])[0];
1215 String[] allids = ((String[]) idset[1]);
1216 seqstr = new String[numinput];
1217 ids = new String[numinput];
1218 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1220 if (allids[sq] != null)
1222 ids[idcount] = allids[sq];
1223 seqstr[idcount++] = idandseqs[1][sq];
1229 // just use the id/seq set
1230 seqstr = idandseqs[1];
1234 // and try and make the groupURL!
1236 Object[] urlset = null;
1239 urlset = urlLink.makeUrlStubs(ids, seqstr,
1240 "FromJalview" + System.currentTimeMillis(), false);
1241 } catch (UrlStringTooLongException e)
1246 int type = urlLink.getGroupURLType() & 3;
1247 // first two bits ofurlLink type bitfield are sequenceids and sequences
1248 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1249 addshowLink(linkMenus[type],
1250 label + (((type & 1) == 1)
1251 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1259 groupLinksMenu = new JMenu(
1260 MessageManager.getString("action.group_link"));
1261 for (int m = 0; m < linkMenus.length; m++)
1263 if (linkMenus[m] != null
1264 && linkMenus[m].getMenuComponentCount() > 0)
1266 groupLinksMenu.add(linkMenus[m]);
1270 groupMenu.add(groupLinksMenu);
1280 private void jbInit() throws Exception
1282 groupMenu.setText(MessageManager.getString("label.selection"));
1283 groupName.setText(MessageManager.getString("label.name"));
1284 groupName.addActionListener(new ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 groupName_actionPerformed();
1292 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1294 JMenuItem sequenceName = new JMenuItem(
1295 MessageManager.getString("label.edit_name_description"));
1296 sequenceName.addActionListener(new ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 sequenceName_actionPerformed();
1304 JMenuItem chooseAnnotations = new JMenuItem(
1305 MessageManager.getString("action.choose_annotations"));
1306 chooseAnnotations.addActionListener(new ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 chooseAnnotations_actionPerformed(e);
1314 JMenuItem sequenceDetails = new JMenuItem(
1315 MessageManager.getString("label.sequence_details"));
1316 sequenceDetails.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 createSequenceDetailsReport(new SequenceI[] { sequence });
1324 JMenuItem sequenceSelDetails = new JMenuItem(
1325 MessageManager.getString("label.sequence_details"));
1326 sequenceSelDetails.addActionListener(new ActionListener()
1329 public void actionPerformed(ActionEvent e)
1331 createSequenceDetailsReport(ap.av.getSequenceSelection());
1336 .setText(MessageManager.getString("action.remove_group"));
1337 unGroupMenuItem.addActionListener(new ActionListener()
1340 public void actionPerformed(ActionEvent e)
1342 unGroupMenuItem_actionPerformed();
1346 .setText(MessageManager.getString("action.create_group"));
1347 createGroupMenuItem.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent e)
1352 createGroupMenuItem_actionPerformed();
1356 JMenuItem outline = new JMenuItem(
1357 MessageManager.getString("action.border_colour"));
1358 outline.addActionListener(new ActionListener()
1361 public void actionPerformed(ActionEvent e)
1363 outline_actionPerformed();
1366 showBoxes.setText(MessageManager.getString("action.boxes"));
1367 showBoxes.setState(true);
1368 showBoxes.addActionListener(new ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 showBoxes_actionPerformed();
1376 showText.setText(MessageManager.getString("action.text"));
1377 showText.setState(true);
1378 showText.addActionListener(new ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 showText_actionPerformed();
1386 showColourText.setText(MessageManager.getString("label.colour_text"));
1387 showColourText.addActionListener(new ActionListener()
1390 public void actionPerformed(ActionEvent e)
1392 showColourText_actionPerformed();
1396 .setText(MessageManager.getString("label.show_non_conserved"));
1397 displayNonconserved.setState(true);
1398 displayNonconserved.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 showNonconserved_actionPerformed();
1406 editMenu.setText(MessageManager.getString("action.edit"));
1407 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1408 cut.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 cut_actionPerformed();
1416 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1417 upperCase.addActionListener(new ActionListener()
1420 public void actionPerformed(ActionEvent e)
1425 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1426 copy.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent e)
1431 copy_actionPerformed();
1434 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1435 lowerCase.addActionListener(new ActionListener()
1438 public void actionPerformed(ActionEvent e)
1443 toggle.setText(MessageManager.getString("label.toggle_case"));
1444 toggle.addActionListener(new ActionListener()
1447 public void actionPerformed(ActionEvent e)
1453 MessageManager.getString("label.out_to_textbox") + "...");
1454 seqShowAnnotationsMenu
1455 .setText(MessageManager.getString("label.show_annotations"));
1456 seqHideAnnotationsMenu
1457 .setText(MessageManager.getString("label.hide_annotations"));
1458 groupShowAnnotationsMenu
1459 .setText(MessageManager.getString("label.show_annotations"));
1460 groupHideAnnotationsMenu
1461 .setText(MessageManager.getString("label.hide_annotations"));
1462 JMenuItem sequenceFeature = new JMenuItem(
1463 MessageManager.getString("label.create_sequence_feature"));
1464 sequenceFeature.addActionListener(new ActionListener()
1467 public void actionPerformed(ActionEvent e)
1469 sequenceFeature_actionPerformed();
1472 editGroupMenu.setText(MessageManager.getString("label.group"));
1473 chooseStructure.setText(
1474 MessageManager.getString("label.show_pdbstruct_dialog"));
1475 chooseStructure.addActionListener(new ActionListener()
1478 public void actionPerformed(ActionEvent actionEvent)
1480 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1481 if (ap.av.getSelectionGroup() != null)
1483 selectedSeqs = ap.av.getSequenceSelection();
1485 new StructureChooser(selectedSeqs, sequence, ap);
1490 .setText(MessageManager.getString("label.view_rna_structure"));
1492 // colStructureMenu.setText("Colour By Structure");
1493 JMenuItem editSequence = new JMenuItem(
1494 MessageManager.getString("label.edit_sequence") + "...");
1495 editSequence.addActionListener(new ActionListener()
1498 public void actionPerformed(ActionEvent actionEvent)
1500 editSequence_actionPerformed();
1503 makeReferenceSeq.setText(
1504 MessageManager.getString("label.mark_as_representative"));
1505 makeReferenceSeq.addActionListener(new ActionListener()
1509 public void actionPerformed(ActionEvent actionEvent)
1511 makeReferenceSeq_actionPerformed(actionEvent);
1516 groupMenu.add(sequenceSelDetails);
1519 add(rnaStructureMenu);
1520 add(chooseStructure);
1523 JMenuItem hideInsertions = new JMenuItem(
1524 MessageManager.getString("label.hide_insertions"));
1525 hideInsertions.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 hideInsertions_actionPerformed(e);
1534 add(hideInsertions);
1536 // annotations configuration panel suppressed for now
1537 // groupMenu.add(chooseAnnotations);
1540 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1541 * (if a selection group is in force).
1543 sequenceMenu.add(seqShowAnnotationsMenu);
1544 sequenceMenu.add(seqHideAnnotationsMenu);
1545 sequenceMenu.add(seqAddReferenceAnnotations);
1546 groupMenu.add(groupShowAnnotationsMenu);
1547 groupMenu.add(groupHideAnnotationsMenu);
1548 groupMenu.add(groupAddReferenceAnnotations);
1549 groupMenu.add(editMenu);
1550 groupMenu.add(outputMenu);
1551 groupMenu.add(sequenceFeature);
1552 groupMenu.add(createGroupMenuItem);
1553 groupMenu.add(unGroupMenuItem);
1554 groupMenu.add(editGroupMenu);
1555 sequenceMenu.add(sequenceName);
1556 sequenceMenu.add(sequenceDetails);
1557 sequenceMenu.add(makeReferenceSeq);
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 SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1766 final AlignmentI alignment = this.ap.getAlignment();
1767 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1772 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1774 if (!ap.av.getAlignment().hasSeqrep())
1776 // initialise the display flags so the user sees something happen
1777 ap.av.setDisplayReferenceSeq(true);
1778 ap.av.setColourByReferenceSeq(true);
1779 ap.av.getAlignment().setSeqrep(sequence);
1783 if (ap.av.getAlignment().getSeqrep() == sequence)
1785 ap.av.getAlignment().setSeqrep(null);
1789 ap.av.getAlignment().setSeqrep(sequence);
1795 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1797 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1798 BitSet inserts = new BitSet();
1800 boolean markedPopup = false;
1801 // mark inserts in current selection
1802 if (ap.av.getSelectionGroup() != null)
1804 // mark just the columns in the selection group to be hidden
1805 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1806 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1808 // now clear columns without gaps
1809 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1815 inserts.and(sq.getInsertionsAsBits());
1817 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1818 ap.av.getSelectionGroup().getEndRes());
1821 // now mark for sequence under popup if we haven't already done it
1822 else if (!markedPopup && sequence != null)
1824 inserts.or(sequence.getInsertionsAsBits());
1826 // and set hidden columns accordingly
1827 hidden.hideColumns(inserts);
1832 protected void sequenceSelectionDetails_actionPerformed()
1834 createSequenceDetailsReport(ap.av.getSequenceSelection());
1837 public void createSequenceDetailsReport(SequenceI[] sequences)
1839 StringBuilder contents = new StringBuilder(128);
1840 contents.append("<html><body>");
1841 for (SequenceI seq : sequences)
1843 contents.append("<p><h2>" + MessageManager.formatMessage(
1844 "label.create_sequence_details_report_annotation_for",
1846 { seq.getDisplayId(true) }) + "</h2></p><p>");
1847 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1848 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1849 contents.append("</p>");
1851 contents.append("</body></html>");
1852 String report = contents.toString();
1854 JInternalFrame frame;
1855 if (Platform.isJS())
1857 JLabel textLabel = new JLabel();
1858 textLabel.setText(report);
1859 textLabel.setBackground(Color.WHITE);
1860 JPanel pane = new JPanel(new BorderLayout());
1861 pane.setOpaque(true);
1862 pane.setBackground(Color.WHITE);
1863 pane.add(textLabel, BorderLayout.NORTH);
1864 frame = new JInternalFrame();
1865 frame.getContentPane().add(new JScrollPane(pane));
1874 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1875 cap.setText(report);
1879 Desktop.addInternalFrame(frame,
1880 MessageManager.formatMessage("label.sequence_details_for",
1881 (sequences.length == 1 ? new Object[]
1882 { sequences[0].getDisplayId(true) }
1885 .getString("label.selection") })),
1889 protected void showNonconserved_actionPerformed()
1891 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1896 * call to refresh view after settings change
1900 ap.updateAnnotation();
1901 // removed paintAlignment(true) here:
1902 // updateAnnotation calls paintAlignment already, so don't need to call
1905 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1909 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1910 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1920 public void abovePIDColour_actionPerformed(boolean selected)
1922 SequenceGroup sg = getGroup();
1930 sg.cs.setConsensus(AAFrequency.calculate(
1931 sg.getSequences(ap.av.getHiddenRepSequences()),
1932 sg.getStartRes(), sg.getEndRes() + 1));
1934 int threshold = SliderPanel.setPIDSliderSource(ap,
1935 sg.getGroupColourScheme(), getGroup().getName());
1937 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1939 SliderPanel.showPIDSlider();
1942 // remove PIDColouring
1944 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1945 SliderPanel.hidePIDSlider();
1947 modifyPID.setEnabled(selected);
1953 * Open a panel where the user can choose which types of sequence annotation
1958 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1960 // todo correct way to guard against opening a duplicate panel?
1961 new AnnotationChooser(ap);
1970 public void conservationMenuItem_actionPerformed(boolean selected)
1972 SequenceGroup sg = getGroup();
1980 // JBPNote: Conservation name shouldn't be i18n translated
1981 Conservation c = new Conservation("Group",
1982 sg.getSequences(ap.av.getHiddenRepSequences()),
1983 sg.getStartRes(), sg.getEndRes() + 1);
1986 c.verdict(false, ap.av.getConsPercGaps());
1987 sg.cs.setConservation(c);
1989 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1991 SliderPanel.showConservationSlider();
1994 // remove ConservationColouring
1996 sg.cs.setConservation(null);
1997 SliderPanel.hideConservationSlider();
1999 modifyConservation.setEnabled(selected);
2005 * Shows a dialog where group name and description may be edited
2007 protected void groupName_actionPerformed()
2009 SequenceGroup sg = getGroup();
2010 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2011 sg.getDescription(),
2012 MessageManager.getString("label.group_name"),
2013 MessageManager.getString("label.group_description"));
2014 dialog.showDialog(ap.alignFrame,
2015 MessageManager.getString("label.edit_group_name_description"),
2021 sg.setName(dialog.getName());
2022 sg.setDescription(dialog.getDescription());
2029 * Get selection group - adding it to the alignment if necessary.
2031 * @return sequence group to operate on
2033 SequenceGroup getGroup()
2035 SequenceGroup sg = ap.av.getSelectionGroup();
2036 // this method won't add a new group if it already exists
2039 ap.av.getAlignment().addGroup(sg);
2046 * Shows a dialog where the sequence name and description may be edited. If a
2047 * name containing spaces is entered, these are converted to underscores, with a
2050 void sequenceName_actionPerformed()
2052 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2053 sequence.getDescription(),
2054 MessageManager.getString("label.sequence_name"),
2055 MessageManager.getString("label.sequence_description"));
2056 dialog.showDialog(ap.alignFrame,
2057 MessageManager.getString(
2058 "label.edit_sequence_name_description"),
2064 if (dialog.getName() != null)
2066 if (dialog.getName().indexOf(" ") > -1)
2068 JvOptionPane.showMessageDialog(ap,
2069 MessageManager.getString(
2070 "label.spaces_converted_to_underscores"),
2071 MessageManager.getString(
2072 "label.no_spaces_allowed_sequence_name"),
2073 JvOptionPane.WARNING_MESSAGE);
2075 sequence.setName(dialog.getName().replace(' ', '_'));
2076 ap.paintAlignment(false, false);
2078 sequence.setDescription(dialog.getDescription());
2079 ap.av.notifyAlignment();
2090 void unGroupMenuItem_actionPerformed()
2092 SequenceGroup sg = ap.av.getSelectionGroup();
2093 ap.av.getAlignment().deleteGroup(sg);
2094 ap.av.setSelectionGroup(null);
2098 void createGroupMenuItem_actionPerformed()
2100 getGroup(); // implicitly creates group - note - should apply defaults / use
2101 // standard alignment window logic for this
2106 * Offers a colour chooser and sets the selected colour as the group outline
2108 protected void outline_actionPerformed()
2110 String title = MessageManager
2111 .getString("label.select_outline_colour");
2112 ColourChooserListener listener = new ColourChooserListener()
2115 public void colourSelected(Color c)
2117 getGroup().setOutlineColour(c);
2121 JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
2122 title, Color.BLUE, listener);
2131 public void showBoxes_actionPerformed()
2133 getGroup().setDisplayBoxes(showBoxes.isSelected());
2143 public void showText_actionPerformed()
2145 getGroup().setDisplayText(showText.isSelected());
2155 public void showColourText_actionPerformed()
2157 getGroup().setColourText(showColourText.isSelected());
2161 void hideSequences(boolean representGroup)
2163 ap.av.hideSequences(sequence, representGroup);
2166 public void copy_actionPerformed()
2168 ap.alignFrame.copy_actionPerformed();
2171 public void cut_actionPerformed()
2173 ap.alignFrame.cut_actionPerformed();
2176 void changeCase(ActionEvent e)
2178 Object source = e.getSource();
2179 SequenceGroup sg = ap.av.getSelectionGroup();
2183 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2184 sg.getStartRes(), sg.getEndRes() + 1);
2189 if (source == toggle)
2191 description = MessageManager.getString("label.toggle_case");
2192 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2194 else if (source == upperCase)
2196 description = MessageManager.getString("label.to_upper_case");
2197 caseChange = ChangeCaseCommand.TO_UPPER;
2201 description = MessageManager.getString("label.to_lower_case");
2202 caseChange = ChangeCaseCommand.TO_LOWER;
2205 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2206 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2207 startEnd, caseChange);
2209 ap.alignFrame.addHistoryItem(caseCommand);
2210 ap.av.notifyAlignment();
2216 public void outputText_actionPerformed(ActionEvent e)
2218 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2219 cap.setForInput(null);
2220 Desktop.addInternalFrame(cap, MessageManager
2221 .formatMessage("label.alignment_output_command", new Object[]
2222 { e.getActionCommand() }), 600, 500);
2224 String[] omitHidden = null;
2226 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2227 // or we simply trust the user wants
2228 // wysiwig behaviour
2230 FileFormatI fileFormat = FileFormats.getInstance()
2231 .forName(e.getActionCommand());
2233 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2236 public void sequenceFeature_actionPerformed()
2238 SequenceGroup sg = ap.av.getSelectionGroup();
2244 List<SequenceI> seqs = new ArrayList<>();
2245 List<SequenceFeature> features = new ArrayList<>();
2248 * assemble dataset sequences, and template new sequence features,
2249 * for the amend features dialog
2251 int gSize = sg.getSize();
2252 for (int i = 0; i < gSize; i++)
2254 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2255 int end = sg.findEndRes(sg.getSequenceAt(i));
2258 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2259 features.add(new SequenceFeature(null, null, start, end, null));
2264 * an entirely gapped region will generate empty lists of sequence / features
2266 if (!seqs.isEmpty())
2268 new FeatureEditor(ap, seqs, features, true).showDialog();
2272 public void textColour_actionPerformed()
2274 SequenceGroup sg = getGroup();
2277 new TextColourChooser().chooseColour(ap, sg);
2282 * Shows a dialog where sequence characters may be edited. Any changes are
2283 * applied, and added as an available 'Undo' item in the edit commands
2286 public void editSequence_actionPerformed()
2288 SequenceGroup sg = ap.av.getSelectionGroup();
2290 SequenceI seq = sequence;
2295 seq = sg.getSequenceAt(0);
2298 EditNameDialog dialog = new EditNameDialog(
2299 seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
2300 null, MessageManager.getString("label.edit_sequence"), null);
2301 dialog.showDialog(ap.alignFrame,
2302 MessageManager.getString("label.edit_sequence"),
2308 EditCommand editCommand = new EditCommand(
2309 MessageManager.getString("label.edit_sequences"),
2311 dialog.getName().replace(' ',
2312 ap.av.getGapCharacter()),
2313 sg.getSequencesAsArray(
2314 ap.av.getHiddenRepSequences()),
2315 sg.getStartRes(), sg.getEndRes() + 1,
2316 ap.av.getAlignment());
2317 ap.alignFrame.addHistoryItem(editCommand);
2318 ap.av.notifyAlignment();
2325 * Action on user selecting an item from the colour menu (that does not have
2326 * its bespoke action handler)
2331 public void changeColour_actionPerformed(String colourSchemeName)
2333 SequenceGroup sg = getGroup();
2335 * switch to the chosen colour scheme (or null for None)
2337 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2338 .getColourScheme(colourSchemeName, ap.av, sg,
2339 ap.av.getHiddenRepSequences());
2340 sg.setColourScheme(colourScheme);
2341 if (colourScheme instanceof Blosum62ColourScheme
2342 || colourScheme instanceof PIDColourScheme)
2344 sg.cs.setConsensus(AAFrequency.calculate(
2345 sg.getSequences(ap.av.getHiddenRepSequences()),
2346 sg.getStartRes(), sg.getEndRes() + 1));