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.ResidueCount;
70 import jalview.datamodel.SequenceFeature;
71 import jalview.datamodel.SequenceGroup;
72 import jalview.datamodel.SequenceI;
73 import jalview.gui.ColourMenuHelper.ColourChangeListener;
74 import jalview.gui.JalviewColourChooser.ColourChooserListener;
75 import jalview.io.CountReader;
76 import jalview.io.FileFormatI;
77 import jalview.io.FileFormats;
78 import jalview.io.FormatAdapter;
79 import jalview.io.SequenceAnnotationReport;
80 import jalview.schemes.Blosum62ColourScheme;
81 import jalview.schemes.ColourSchemeI;
82 import jalview.schemes.ColourSchemes;
83 import jalview.schemes.PIDColourScheme;
84 import jalview.schemes.ResidueColourScheme;
85 import jalview.util.Comparison;
86 import jalview.util.GroupUrlLink;
87 import jalview.util.GroupUrlLink.UrlStringTooLongException;
88 import jalview.util.MessageManager;
89 import jalview.util.Platform;
90 import jalview.util.StringUtils;
91 import jalview.util.UrlLink;
92 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
94 import java.io.IOException;
95 import java.net.MalformedURLException;
98 * The popup menu that is displayed on right-click on a sequence id, or in the
101 public class PopupMenu extends JPopupMenu implements ColourChangeListener
104 * maximum length of feature description to include in popup menu item text
106 private static final int FEATURE_DESC_MAX = 40;
109 * true for ID Panel menu, false for alignment panel menu
111 private final boolean forIdPanel;
113 private final AlignmentPanel ap;
116 * the sequence under the cursor when clicked
117 * (additional sequences may be selected)
119 private final SequenceI sequence;
121 JMenu groupMenu = new JMenu();
123 JMenuItem groupName = new JMenuItem();
125 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
127 protected JMenuItem modifyPID = new JMenuItem();
129 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
131 protected JRadioButtonMenuItem annotationColour;
133 protected JMenuItem modifyConservation = new JMenuItem();
135 JMenu sequenceMenu = new JMenu();
137 JMenuItem makeReferenceSeq = new JMenuItem();
139 JMenuItem createGroupMenuItem = new JMenuItem();
141 JMenuItem unGroupMenuItem = new JMenuItem();
143 JMenu colourMenu = new JMenu();
145 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
147 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
149 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
151 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
153 JMenu editMenu = new JMenu();
155 JMenuItem upperCase = new JMenuItem();
157 JMenuItem lowerCase = new JMenuItem();
159 JMenuItem toggle = new JMenuItem();
161 JMenu outputMenu = new JMenu();
163 JMenu seqShowAnnotationsMenu = new JMenu();
165 JMenu seqHideAnnotationsMenu = new JMenu();
167 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
168 MessageManager.getString("label.add_reference_annotations"));
170 JMenu groupShowAnnotationsMenu = new JMenu();
172 JMenu groupHideAnnotationsMenu = new JMenu();
174 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
175 MessageManager.getString("label.add_reference_annotations"));
177 JMenuItem textColour = new JMenuItem();
179 JMenu editGroupMenu = new JMenu();
181 JMenuItem chooseStructure = new JMenuItem();
183 JMenu rnaStructureMenu = new JMenu();
186 * Constructs a menu with sub-menu items for any hyperlinks for the sequence
187 * and/or features provided. Hyperlinks may include a lookup by sequence id,
188 * or database cross-references, depending on which links are enabled in user
195 protected static JMenu buildLinkMenu(final SequenceI seq,
196 List<SequenceFeature> features)
198 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
200 List<String> nlinks = null;
203 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
204 UrlLink.sort(nlinks);
208 nlinks = new ArrayList<>();
211 if (features != null)
213 for (SequenceFeature sf : features)
215 if (sf.links != null)
217 for (String link : sf.links)
226 * instantiate the hyperlinklink templates from sequence data;
227 * note the order of the templates is preserved in the map
229 Map<String, List<String>> linkset = new LinkedHashMap<>();
230 for (String link : nlinks)
232 UrlLink urlLink = null;
235 urlLink = new UrlLink(link);
236 } catch (Exception foo)
238 Cache.log.error("Exception for URLLink '" + link + "'", foo);
242 if (!urlLink.isValid())
244 Cache.log.error(urlLink.getInvalidMessage());
248 urlLink.createLinksFromSeq(seq, linkset);
252 * construct menu items for the hyperlinks (still preserving
253 * the order of the sorted templates)
255 addUrlLinks(linkMenu, linkset.values());
261 * A helper method that builds menu items from the given links, with action
262 * handlers to open the link URL, and adds them to the linkMenu. Each provided
263 * link should be a list whose second item is the menu text, and whose fourth
264 * item is the URL to open when the menu item is selected.
269 static private void addUrlLinks(JMenu linkMenu,
270 Collection<List<String>> linkset)
272 for (List<String> linkstrset : linkset)
274 final String url = linkstrset.get(3);
275 JMenuItem item = new JMenuItem(linkstrset.get(1));
276 item.setToolTipText(MessageManager
277 .formatMessage("label.open_url_param", new Object[]
279 item.addActionListener(new ActionListener()
282 public void actionPerformed(ActionEvent e)
284 new Thread(new Runnable()
299 * Opens the provided url in the default web browser, or shows an error
300 * message if this fails
304 static void showLink(String url)
308 jalview.util.BrowserLauncher.openURL(url);
309 } catch (Exception ex)
311 JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
312 MessageManager.getString("label.web_browser_not_found_unix"),
313 MessageManager.getString("label.web_browser_not_found"),
314 JvOptionPane.WARNING_MESSAGE);
316 ex.printStackTrace();
321 * add a late bound groupURL item to the given linkMenu
325 * - menu label string
326 * @param urlgenerator
327 * GroupURLLink used to generate URL
329 * Object array returned from the makeUrlStubs function.
331 static void addshowLink(JMenu linkMenu, String label,
332 final GroupUrlLink urlgenerator, final Object[] urlstub)
334 JMenuItem item = new JMenuItem(label);
335 item.setToolTipText(MessageManager
336 .formatMessage("label.open_url_seqs_param", new Object[]
337 { urlgenerator.getUrl_prefix(),
338 urlgenerator.getNumberInvolved(urlstub) }));
339 // TODO: put in info about what is being sent.
340 item.addActionListener(new ActionListener()
343 public void actionPerformed(ActionEvent e)
345 new Thread(new Runnable()
353 showLink(urlgenerator.constructFrom(urlstub));
354 } catch (UrlStringTooLongException e2)
367 * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
370 * the panel in which the mouse is clicked
372 * the sequence under the mouse
373 * @throws NullPointerException
376 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
378 this(false, ap, seq, column, null);
382 * Constructor for a PopupMenu for a click in the sequence id panel
385 * the panel in which the mouse is clicked
387 * the sequence under the mouse click
389 * templates for sequence external links
390 * @throws NullPointerException
393 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
394 List<String> groupLinks)
396 this(true, alignPanel, seq, -1, groupLinks);
400 * Private constructor that constructs a popup menu for either sequence ID
401 * Panel, or alignment context
407 * aligned column position (0...)
410 private PopupMenu(boolean fromIdPanel,
411 final AlignmentPanel alignPanel,
412 final SequenceI seq, final int column, List<String> groupLinks)
414 Objects.requireNonNull(seq);
415 this.forIdPanel = fromIdPanel;
416 this.ap = alignPanel;
419 for (String ff : FileFormats.getInstance().getWritableFormats(true))
421 JMenuItem item = new JMenuItem(ff);
423 item.addActionListener(new ActionListener()
426 public void actionPerformed(ActionEvent e)
428 outputText_actionPerformed(e);
432 outputMenu.add(item);
436 * Build menus for annotation types that may be shown or hidden, and for
437 * 'reference annotations' that may be added to the alignment. First for the
438 * currently selected sequence (if there is one):
440 final List<SequenceI> selectedSequence = (forIdPanel && seq != null
442 : Collections.<SequenceI> emptyList());
443 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
444 seqHideAnnotationsMenu, selectedSequence);
445 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
449 * And repeat for the current selection group (if there is one):
451 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
452 ? Collections.<SequenceI> emptyList()
453 : alignPanel.av.getSelectionGroup().getSequences());
454 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
455 groupHideAnnotationsMenu, selectedGroup);
456 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
462 } catch (Exception e)
470 sequenceMenu.setText(sequence.getName());
471 if (seq == alignPanel.av.getAlignment().getSeqrep())
473 makeReferenceSeq.setText(
474 MessageManager.getString("action.unmark_as_reference"));
478 makeReferenceSeq.setText(
479 MessageManager.getString("action.set_as_reference"));
482 if (!alignPanel.av.getAlignment().isNucleotide())
484 remove(rnaStructureMenu);
488 int origCount = rnaStructureMenu.getItemCount();
490 * add menu items to 2D-render any alignment or sequence secondary
491 * structure annotation
493 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
494 .getAlignmentAnnotation();
497 for (final AlignmentAnnotation aa : aas)
499 if (aa.isValidStruc() && aa.sequenceRef == null)
502 * valid alignment RNA secondary structure annotation
504 menuItem = new JMenuItem();
505 menuItem.setText(MessageManager.formatMessage(
506 "label.2d_rna_structure_line", new Object[]
508 menuItem.addActionListener(new ActionListener()
511 public void actionPerformed(ActionEvent e)
513 new AppVarna(seq, aa, alignPanel);
516 rnaStructureMenu.add(menuItem);
521 if (seq.getAnnotation() != null)
523 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
524 for (final AlignmentAnnotation aa : seqAnns)
526 if (aa.isValidStruc())
529 * valid sequence RNA secondary structure annotation
531 // TODO: make rnastrucF a bit more nice
532 menuItem = new JMenuItem();
533 menuItem.setText(MessageManager.formatMessage(
534 "label.2d_rna_sequence_name", new Object[]
536 menuItem.addActionListener(new ActionListener()
539 public void actionPerformed(ActionEvent e)
541 // TODO: VARNA does'nt print gaps in the sequence
542 new AppVarna(seq, aa, alignPanel);
545 rnaStructureMenu.add(menuItem);
549 if (rnaStructureMenu.getItemCount() == origCount)
551 remove(rnaStructureMenu);
555 if (seq.hasHMMProfile())
557 menuItem = new JMenuItem(MessageManager
558 .getString("action.add_background_frequencies"));
559 menuItem.addActionListener(new ActionListener()
562 public void actionPerformed(ActionEvent e)
566 ResidueCount counts = CountReader.getBackgroundFrequencies(ap,
570 seq.getHMM().setBackgroundFrequencies(counts);
571 ap.alignFrame.buildColourMenu();
573 } catch (MalformedURLException e1)
575 e1.printStackTrace();
576 } catch (IOException e1)
578 e1.printStackTrace();
585 menuItem = new JMenuItem(
586 MessageManager.getString("action.hide_sequences"));
587 menuItem.addActionListener(new ActionListener()
590 public void actionPerformed(ActionEvent e)
592 hideSequences(false);
597 if (alignPanel.av.getSelectionGroup() != null
598 && alignPanel.av.getSelectionGroup().getSize() > 1)
600 menuItem = new JMenuItem(MessageManager
601 .formatMessage("label.represent_group_with", new Object[]
603 menuItem.addActionListener(new ActionListener()
606 public void actionPerformed(ActionEvent e)
611 sequenceMenu.add(menuItem);
614 if (alignPanel.av.hasHiddenRows())
616 final int index = alignPanel.av.getAlignment().findIndex(seq);
618 if (alignPanel.av.adjustForHiddenSeqs(index)
619 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
621 menuItem = new JMenuItem(
622 MessageManager.getString("action.reveal_sequences"));
623 menuItem.addActionListener(new ActionListener()
626 public void actionPerformed(ActionEvent e)
628 alignPanel.av.showSequence(index);
629 if (alignPanel.overviewPanel != null)
631 alignPanel.overviewPanel.updateOverviewImage();
642 * - in the IdPanel (seq not null) if any sequence is hidden
643 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
645 if (alignPanel.av.hasHiddenRows())
647 boolean addOption = seq != null;
648 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
654 JMenuItem menuItem = new JMenuItem(
655 MessageManager.getString("action.reveal_all"));
656 menuItem.addActionListener(new ActionListener()
659 public void actionPerformed(ActionEvent e)
661 alignPanel.av.showAllHiddenSeqs();
662 if (alignPanel.overviewPanel != null)
664 alignPanel.overviewPanel.updateOverviewImage();
672 SequenceGroup sg = alignPanel.av.getSelectionGroup();
673 boolean isDefinedGroup = (sg != null)
674 ? alignPanel.av.getAlignment().getGroups().contains(sg)
677 if (sg != null && sg.getSize() > 0)
679 groupName.setText(MessageManager
680 .getString("label.edit_name_and_description_current_group"));
682 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
684 conservationMenuItem.setEnabled(!sg.isNucleotide());
688 if (sg.cs.conservationApplied())
690 conservationMenuItem.setSelected(true);
692 if (sg.cs.getThreshold() > 0)
694 abovePIDColour.setSelected(true);
697 modifyConservation.setEnabled(conservationMenuItem.isSelected());
698 modifyPID.setEnabled(abovePIDColour.isSelected());
699 displayNonconserved.setSelected(sg.getShowNonconserved());
700 showText.setSelected(sg.getDisplayText());
701 showColourText.setSelected(sg.getColourText());
702 showBoxes.setSelected(sg.getDisplayBoxes());
703 // add any groupURLs to the groupURL submenu and make it visible
704 if (groupLinks != null && groupLinks.size() > 0)
706 buildGroupURLMenu(sg, groupLinks);
708 // Add a 'show all structures' for the current selection
709 Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
710 Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
712 SequenceI sqass = null;
713 for (SequenceI sq : alignPanel.av.getSequenceSelection())
715 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
716 if (pes != null && pes.size() > 0)
718 reppdb.put(pes.get(0).getId(), pes.get(0));
719 for (PDBEntry pe : pes)
721 pdbe.put(pe.getId(), pe);
731 final PDBEntry[] pe = pdbe.values()
732 .toArray(new PDBEntry[pdbe.size()]),
733 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
734 final JMenuItem gpdbview, rpdbview;
739 groupMenu.setVisible(false);
740 editMenu.setVisible(false);
745 createGroupMenuItem.setVisible(true);
746 unGroupMenuItem.setVisible(false);
747 editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
751 createGroupMenuItem.setVisible(false);
752 unGroupMenuItem.setVisible(true);
753 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
758 sequenceMenu.setVisible(false);
759 chooseStructure.setVisible(false);
760 rnaStructureMenu.setVisible(false);
763 addLinksAndFeatures(seq, column);
769 * <li>configured sequence database links (ID panel popup menu)</li>
770 * <li>non-positional feature links (ID panel popup menu)</li>
771 * <li>positional feature links (alignment panel popup menu)</li>
772 * <li>feature details links (alignment panel popup menu)</li>
774 * If this panel is also showed complementary (CDS/protein) features, then links
775 * to their feature details are also added.
780 void addLinksAndFeatures(final SequenceI seq, final int column)
782 List<SequenceFeature> features = null;
785 features = sequence.getFeatures().getNonPositionalFeatures();
789 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
793 addLinks(seq, features);
797 addFeatureDetails(features, seq, column);
802 * Add a menu item to show feature details for each sequence feature. Any
803 * linked 'virtual' features (CDS/protein) are also optionally found and
810 protected void addFeatureDetails(List<SequenceFeature> features,
811 final SequenceI seq, final int column)
814 * add features in CDS/protein complement at the corresponding
815 * position if configured to do so
817 MappedFeatures mf = null;
818 if (ap.av.isShowComplementFeatures())
820 if (!Comparison.isGap(sequence.getCharAt(column)))
822 AlignViewportI complement = ap.getAlignViewport()
823 .getCodingComplement();
824 AlignFrame af = Desktop.getAlignFrameFor(complement);
825 FeatureRendererModel fr2 = af.getFeatureRenderer();
826 int seqPos = sequence.findPosition(column);
827 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
831 if (features.isEmpty() && mf == null)
834 * no features to show at this position
839 JMenu details = new JMenu(
840 MessageManager.getString("label.feature_details"));
843 String name = seq.getName();
844 for (final SequenceFeature sf : features)
846 addFeatureDetailsMenuItem(details, name, sf, null);
851 for (final SequenceFeature sf : mf.features)
853 addFeatureDetailsMenuItem(details, name, sf, mf);
859 * A helper method to add one menu item whose action is to show details for
860 * one feature. The menu text includes feature description, but this may be
868 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
869 final SequenceFeature sf, MappedFeatures mf)
871 int start = sf.getBegin();
872 int end = sf.getEnd();
876 * show local rather than linked feature coordinates
878 int[] beginRange = mf.getMappedPositions(start, start);
879 start = beginRange[0];
880 int[] endRange = mf.getMappedPositions(end, end);
881 end = endRange[endRange.length - 1];
883 StringBuilder desc = new StringBuilder();
884 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
887 desc.append(sf.isContactFeature() ? ":" : "-");
888 desc.append(String.valueOf(end));
890 String description = sf.getDescription();
891 if (description != null)
894 description = StringUtils.stripHtmlTags(description);
897 * truncate overlong descriptions unless they contain an href
898 * (as truncation could leave corrupted html)
900 boolean hasLink = description.indexOf("a href") > -1;
901 if (description.length() > FEATURE_DESC_MAX && !hasLink)
903 description = description.substring(0, FEATURE_DESC_MAX) + "...";
905 desc.append(description);
907 String featureGroup = sf.getFeatureGroup();
908 if (featureGroup != null)
910 desc.append(" (").append(featureGroup).append(")");
912 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
913 JMenuItem item = new JMenuItem(htmlText);
914 item.addActionListener(new ActionListener()
917 public void actionPerformed(ActionEvent e)
919 showFeatureDetails(sf, seqName, mf);
926 * Opens a panel showing a text report of feature details
932 protected void showFeatureDetails(SequenceFeature sf, String seqName,
935 JInternalFrame details;
938 details = new JInternalFrame();
939 JPanel panel = new JPanel(new BorderLayout());
940 panel.setOpaque(true);
941 panel.setBackground(Color.white);
942 // TODO JAL-3026 set style of table correctly for feature details
943 JLabel reprt = new JLabel(MessageManager
944 .formatMessage("label.html_content", new Object[]
945 { sf.getDetailsReport(seqName, mf) }));
946 reprt.setBackground(Color.WHITE);
947 reprt.setOpaque(true);
948 panel.add(reprt, BorderLayout.CENTER);
949 details.setContentPane(panel);
959 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
960 // it appears Java's CSS does not support border-collapse :-(
961 cap.addStylesheetRule("table { border-collapse: collapse;}");
962 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
963 cap.setText(sf.getDetailsReport(seqName, mf));
966 Desktop.addInternalFrame(details,
967 MessageManager.getString("label.feature_details"), 500, 500);
971 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
972 * When seq is not null, these are links for the sequence id, which may be to
973 * external web sites for the sequence accession, and/or links embedded in
974 * non-positional features. When seq is null, only links embedded in the
975 * provided features are added. If no links are found, the menu is not added.
980 void addLinks(final SequenceI seq, List<SequenceFeature> features)
982 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
984 // only add link menu if it has entries
985 if (linkMenu.getItemCount() > 0)
989 sequenceMenu.add(linkMenu);
999 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
1000 * "All" is added first, followed by a separator. Then add any annotation
1001 * types associated with the current selection. Separate menus are built for
1002 * the selected sequence group (if any), and the selected sequence.
1004 * Some annotation rows are always rendered together - these can be identified
1005 * by a common graphGroup property > -1. Only one of each group will be marked
1006 * as visible (to avoid duplication of the display). For such groups we add a
1007 * composite type name, e.g.
1009 * IUPredWS (Long), IUPredWS (Short)
1013 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
1014 List<SequenceI> forSequences)
1016 showMenu.removeAll();
1017 hideMenu.removeAll();
1019 final List<String> all = Arrays
1020 .asList(new String[]
1021 { MessageManager.getString("label.all") });
1022 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
1024 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
1026 showMenu.addSeparator();
1027 hideMenu.addSeparator();
1029 final AlignmentAnnotation[] annotations = ap.getAlignment()
1030 .getAlignmentAnnotation();
1033 * Find shown/hidden annotations types, distinguished by source (calcId),
1034 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
1035 * the insertion order, which is the order of the annotations on the
1038 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
1039 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
1040 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
1041 AlignmentAnnotationUtils.asList(annotations), forSequences);
1043 for (String calcId : hiddenTypes.keySet())
1045 for (List<String> type : hiddenTypes.get(calcId))
1047 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
1051 // grey out 'show annotations' if none are hidden
1052 showMenu.setEnabled(!hiddenTypes.isEmpty());
1054 for (String calcId : shownTypes.keySet())
1056 for (List<String> type : shownTypes.get(calcId))
1058 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1062 // grey out 'hide annotations' if none are shown
1063 hideMenu.setEnabled(!shownTypes.isEmpty());
1067 * Returns a list of sequences - either the current selection group (if there
1068 * is one), else the specified single sequence.
1073 protected List<SequenceI> getSequenceScope(SequenceI seq)
1075 List<SequenceI> forSequences = null;
1076 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1077 if (selectionGroup != null && selectionGroup.getSize() > 0)
1079 forSequences = selectionGroup.getSequences();
1083 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1084 : Arrays.asList(seq);
1086 return forSequences;
1090 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1093 * @param showOrHideMenu
1094 * the menu to add to
1095 * @param forSequences
1096 * the sequences whose annotations may be shown or hidden
1101 * if true this is a special label meaning 'All'
1102 * @param actionIsShow
1103 * if true, the select menu item action is to show the annotation
1106 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1107 final List<SequenceI> forSequences, String calcId,
1108 final List<String> types, final boolean allTypes,
1109 final boolean actionIsShow)
1111 String label = types.toString(); // [a, b, c]
1112 label = label.substring(1, label.length() - 1); // a, b, c
1113 final JMenuItem item = new JMenuItem(label);
1114 item.setToolTipText(calcId);
1115 item.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1121 types, forSequences, allTypes, actionIsShow);
1125 showOrHideMenu.add(item);
1128 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1131 // TODO: usability: thread off the generation of group url content so root
1132 // menu appears asap
1133 // sequence only URLs
1134 // ID/regex match URLs
1135 JMenu groupLinksMenu = new JMenu(
1136 MessageManager.getString("action.group_link"));
1137 // three types of url that might be created.
1138 JMenu[] linkMenus = new JMenu[] { null,
1139 new JMenu(MessageManager.getString("action.ids")),
1140 new JMenu(MessageManager.getString("action.sequences")),
1141 new JMenu(MessageManager.getString("action.ids_sequences")) };
1143 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1144 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1145 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1146 for (int sq = 0; sq < seqs.length; sq++)
1149 int start = seqs[sq].findPosition(sg.getStartRes()),
1150 end = seqs[sq].findPosition(sg.getEndRes());
1151 // just collect ids from dataset sequence
1152 // TODO: check if IDs collected from selecton group intersects with the
1153 // current selection, too
1154 SequenceI sqi = seqs[sq];
1155 while (sqi.getDatasetSequence() != null)
1157 sqi = sqi.getDatasetSequence();
1159 List<DBRefEntry> dbr = sqi.getDBRefs();
1161 if (dbr != null && (nd = dbr.size()) > 0)
1163 for (int d = 0; d < nd; d++)
1165 DBRefEntry e = dbr.get(d);
1166 String src = e.getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase(Locale.ROOT);
1167 Object[] sarray = commonDbrefs.get(src);
1170 sarray = new Object[2];
1171 sarray[0] = new int[] { 0 };
1172 sarray[1] = new String[seqs.length];
1174 commonDbrefs.put(src, sarray);
1177 if (((String[]) sarray[1])[sq] == null)
1179 if (!e.hasMap() || (e.getMap()
1180 .locateMappedRange(start, end) != null))
1182 ((String[]) sarray[1])[sq] = e.getAccessionId();
1183 ((int[]) sarray[0])[0]++;
1189 // now create group links for all distinct ID/sequence sets.
1190 boolean addMenu = false; // indicates if there are any group links to give
1192 for (String link : groupLinks)
1194 GroupUrlLink urlLink = null;
1197 urlLink = new GroupUrlLink(link);
1198 } catch (Exception foo)
1200 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
1203 if (!urlLink.isValid())
1205 Cache.log.error(urlLink.getInvalidMessage());
1208 final String label = urlLink.getLabel();
1209 boolean usingNames = false;
1210 // Now see which parts of the group apply for this URL
1211 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1212 Object[] idset = commonDbrefs.get(ltarget.toUpperCase(Locale.ROOT));
1213 String[] seqstr, ids; // input to makeUrl
1216 int numinput = ((int[]) idset[0])[0];
1217 String[] allids = ((String[]) idset[1]);
1218 seqstr = new String[numinput];
1219 ids = new String[numinput];
1220 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1222 if (allids[sq] != null)
1224 ids[idcount] = allids[sq];
1225 seqstr[idcount++] = idandseqs[1][sq];
1231 // just use the id/seq set
1232 seqstr = idandseqs[1];
1236 // and try and make the groupURL!
1238 Object[] urlset = null;
1241 urlset = urlLink.makeUrlStubs(ids, seqstr,
1242 "FromJalview" + System.currentTimeMillis(), false);
1243 } catch (UrlStringTooLongException e)
1248 int type = urlLink.getGroupURLType() & 3;
1249 // first two bits ofurlLink type bitfield are sequenceids and sequences
1250 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1251 addshowLink(linkMenus[type],
1252 label + (((type & 1) == 1)
1253 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1261 groupLinksMenu = new JMenu(
1262 MessageManager.getString("action.group_link"));
1263 for (int m = 0; m < linkMenus.length; m++)
1265 if (linkMenus[m] != null
1266 && linkMenus[m].getMenuComponentCount() > 0)
1268 groupLinksMenu.add(linkMenus[m]);
1272 groupMenu.add(groupLinksMenu);
1282 private void jbInit() throws Exception
1284 groupMenu.setText(MessageManager.getString("label.selection"));
1285 groupName.setText(MessageManager.getString("label.name"));
1286 groupName.addActionListener(new ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 groupName_actionPerformed();
1294 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1296 JMenuItem sequenceName = new JMenuItem(
1297 MessageManager.getString("label.edit_name_description"));
1298 sequenceName.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 sequenceName_actionPerformed();
1306 JMenuItem chooseAnnotations = new JMenuItem(
1307 MessageManager.getString("action.choose_annotations"));
1308 chooseAnnotations.addActionListener(new ActionListener()
1311 public void actionPerformed(ActionEvent e)
1313 chooseAnnotations_actionPerformed(e);
1316 JMenuItem sequenceDetails = new JMenuItem(
1317 MessageManager.getString("label.sequence_details"));
1318 sequenceDetails.addActionListener(new ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 createSequenceDetailsReport(new SequenceI[] { sequence });
1326 JMenuItem sequenceSelDetails = new JMenuItem(
1327 MessageManager.getString("label.sequence_details"));
1328 sequenceSelDetails.addActionListener(new ActionListener()
1331 public void actionPerformed(ActionEvent e)
1333 createSequenceDetailsReport(ap.av.getSequenceSelection());
1338 .setText(MessageManager.getString("action.remove_group"));
1339 unGroupMenuItem.addActionListener(new ActionListener()
1342 public void actionPerformed(ActionEvent e)
1344 unGroupMenuItem_actionPerformed();
1348 .setText(MessageManager.getString("action.create_group"));
1349 createGroupMenuItem.addActionListener(new ActionListener()
1352 public void actionPerformed(ActionEvent e)
1354 createGroupMenuItem_actionPerformed();
1358 JMenuItem outline = new JMenuItem(
1359 MessageManager.getString("action.border_colour"));
1360 outline.addActionListener(new ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 outline_actionPerformed();
1368 showBoxes.setText(MessageManager.getString("action.boxes"));
1369 showBoxes.setState(true);
1370 showBoxes.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 showBoxes_actionPerformed();
1378 showText.setText(MessageManager.getString("action.text"));
1379 showText.setState(true);
1380 showText.addActionListener(new ActionListener()
1383 public void actionPerformed(ActionEvent e)
1385 showText_actionPerformed();
1388 showColourText.setText(MessageManager.getString("label.colour_text"));
1389 showColourText.addActionListener(new ActionListener()
1392 public void actionPerformed(ActionEvent e)
1394 showColourText_actionPerformed();
1398 .setText(MessageManager.getString("label.show_non_conserved"));
1399 displayNonconserved.setState(true);
1400 displayNonconserved.addActionListener(new ActionListener()
1403 public void actionPerformed(ActionEvent e)
1405 showNonconserved_actionPerformed();
1408 editMenu.setText(MessageManager.getString("action.edit"));
1409 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1410 cut.addActionListener(new ActionListener()
1413 public void actionPerformed(ActionEvent e)
1415 cut_actionPerformed();
1418 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1419 upperCase.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1427 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1428 copy.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 copy_actionPerformed();
1436 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1437 lowerCase.addActionListener(new ActionListener()
1440 public void actionPerformed(ActionEvent e)
1445 toggle.setText(MessageManager.getString("label.toggle_case"));
1446 toggle.addActionListener(new ActionListener()
1449 public void actionPerformed(ActionEvent e)
1455 MessageManager.getString("label.out_to_textbox") + "...");
1456 seqShowAnnotationsMenu
1457 .setText(MessageManager.getString("label.show_annotations"));
1458 seqHideAnnotationsMenu
1459 .setText(MessageManager.getString("label.hide_annotations"));
1460 groupShowAnnotationsMenu
1461 .setText(MessageManager.getString("label.show_annotations"));
1462 groupHideAnnotationsMenu
1463 .setText(MessageManager.getString("label.hide_annotations"));
1464 JMenuItem sequenceFeature = new JMenuItem(
1465 MessageManager.getString("label.create_sequence_feature"));
1466 sequenceFeature.addActionListener(new ActionListener()
1469 public void actionPerformed(ActionEvent e)
1471 sequenceFeature_actionPerformed();
1474 editGroupMenu.setText(MessageManager.getString("label.group"));
1475 chooseStructure.setText(
1476 MessageManager.getString("label.show_pdbstruct_dialog"));
1477 chooseStructure.addActionListener(new ActionListener()
1480 public void actionPerformed(ActionEvent actionEvent)
1482 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1483 if (ap.av.getSelectionGroup() != null)
1485 selectedSeqs = ap.av.getSequenceSelection();
1487 new StructureChooser(selectedSeqs, sequence, ap);
1492 .setText(MessageManager.getString("label.view_rna_structure"));
1494 // colStructureMenu.setText("Colour By Structure");
1495 JMenuItem editSequence = new JMenuItem(
1496 MessageManager.getString("label.edit_sequence") + "...");
1497 editSequence.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent actionEvent)
1502 editSequence_actionPerformed();
1505 makeReferenceSeq.setText(
1506 MessageManager.getString("label.mark_as_representative"));
1507 makeReferenceSeq.addActionListener(new ActionListener()
1511 public void actionPerformed(ActionEvent actionEvent)
1513 makeReferenceSeq_actionPerformed(actionEvent);
1518 groupMenu.add(sequenceSelDetails);
1521 add(rnaStructureMenu);
1522 add(chooseStructure);
1525 JMenuItem hideInsertions = new JMenuItem(
1526 MessageManager.getString("label.hide_insertions"));
1527 hideInsertions.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 hideInsertions_actionPerformed(e);
1536 add(hideInsertions);
1538 // annotations configuration panel suppressed for now
1539 // groupMenu.add(chooseAnnotations);
1542 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1543 * (if a selection group is in force).
1545 sequenceMenu.add(seqShowAnnotationsMenu);
1546 sequenceMenu.add(seqHideAnnotationsMenu);
1547 sequenceMenu.add(seqAddReferenceAnnotations);
1548 groupMenu.add(groupShowAnnotationsMenu);
1549 groupMenu.add(groupHideAnnotationsMenu);
1550 groupMenu.add(groupAddReferenceAnnotations);
1551 groupMenu.add(editMenu);
1552 groupMenu.add(outputMenu);
1553 groupMenu.add(sequenceFeature);
1554 groupMenu.add(createGroupMenuItem);
1555 groupMenu.add(unGroupMenuItem);
1556 groupMenu.add(editGroupMenu);
1557 sequenceMenu.add(sequenceName);
1558 sequenceMenu.add(sequenceDetails);
1559 sequenceMenu.add(makeReferenceSeq);
1566 editMenu.add(editSequence);
1567 editMenu.add(upperCase);
1568 editMenu.add(lowerCase);
1569 editMenu.add(toggle);
1570 editGroupMenu.add(groupName);
1571 editGroupMenu.add(colourMenu);
1572 editGroupMenu.add(showBoxes);
1573 editGroupMenu.add(showText);
1574 editGroupMenu.add(showColourText);
1575 editGroupMenu.add(outline);
1576 editGroupMenu.add(displayNonconserved);
1580 * Constructs the entries for the colour menu
1582 protected void initColourMenu()
1584 colourMenu.setText(MessageManager.getString("label.group_colour"));
1585 textColour.setText(MessageManager.getString("label.text_colour"));
1586 textColour.addActionListener(new ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 textColour_actionPerformed();
1595 abovePIDColour.setText(
1596 MessageManager.getString("label.above_identity_threshold"));
1597 abovePIDColour.addActionListener(new ActionListener()
1600 public void actionPerformed(ActionEvent e)
1602 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1607 MessageManager.getString("label.modify_identity_threshold"));
1608 modifyPID.addActionListener(new ActionListener()
1611 public void actionPerformed(ActionEvent e)
1613 modifyPID_actionPerformed();
1617 conservationMenuItem
1618 .setText(MessageManager.getString("action.by_conservation"));
1619 conservationMenuItem.addActionListener(new ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 conservationMenuItem_actionPerformed(
1625 conservationMenuItem.isSelected());
1629 annotationColour = new JRadioButtonMenuItem(
1630 MessageManager.getString("action.by_annotation"));
1631 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1632 annotationColour.setEnabled(false);
1633 annotationColour.setToolTipText(
1634 MessageManager.getString("label.by_annotation_tooltip"));
1636 modifyConservation.setText(MessageManager
1637 .getString("label.modify_conservation_threshold"));
1638 modifyConservation.addActionListener(new ActionListener()
1641 public void actionPerformed(ActionEvent e)
1643 modifyConservation_actionPerformed();
1649 * Builds the group colour sub-menu, including any user-defined colours which
1650 * were loaded at startup or during the Jalview session
1652 protected void buildColourMenu()
1654 SequenceGroup sg = ap.av.getSelectionGroup();
1658 * popup menu with no sequence group scope
1662 colourMenu.removeAll();
1663 colourMenu.add(textColour);
1664 colourMenu.addSeparator();
1666 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1668 bg.add(annotationColour);
1669 colourMenu.add(annotationColour);
1671 colourMenu.addSeparator();
1672 colourMenu.add(conservationMenuItem);
1673 colourMenu.add(modifyConservation);
1674 colourMenu.add(abovePIDColour);
1675 colourMenu.add(modifyPID);
1678 protected void modifyConservation_actionPerformed()
1680 SequenceGroup sg = getGroup();
1683 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1684 SliderPanel.showConservationSlider();
1688 protected void modifyPID_actionPerformed()
1690 SequenceGroup sg = getGroup();
1693 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1695 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1696 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1697 SliderPanel.showPIDSlider();
1702 * Check for any annotations on the underlying dataset sequences (for the
1703 * current selection group) which are not 'on the alignment'.If any are found,
1704 * enable the option to add them to the alignment. The criteria for 'on the
1705 * alignment' is finding an alignment annotation on the alignment, matched on
1706 * calcId, label and sequenceRef.
1708 * A tooltip is also constructed that displays the source (calcId) and type
1709 * (label) of the annotations that can be added.
1712 * @param forSequences
1714 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1715 List<SequenceI> forSequences)
1717 menuItem.setEnabled(false);
1720 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1721 * Using TreeMap means calcIds are shown in alphabetical order.
1723 SortedMap<String, String> tipEntries = new TreeMap<>();
1724 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1725 AlignmentI al = this.ap.av.getAlignment();
1726 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1728 if (!candidates.isEmpty())
1730 StringBuilder tooltip = new StringBuilder(64);
1731 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1734 * Found annotations that could be added. Enable the menu item, and
1735 * configure its tooltip and action.
1737 menuItem.setEnabled(true);
1738 for (String calcId : tipEntries.keySet())
1740 tooltip.append("<br>" + calcId + "/" + tipEntries.get(calcId));
1742 String tooltipText = JvSwingUtils.wrapTooltip(true,
1743 tooltip.toString());
1744 menuItem.setToolTipText(tooltipText);
1746 menuItem.addActionListener(new ActionListener()
1749 public void actionPerformed(ActionEvent e)
1751 addReferenceAnnotations_actionPerformed(candidates);
1758 * Add annotations to the sequences and to the alignment.
1761 * a map whose keys are sequences on the alignment, and values a list
1762 * of annotations to add to each sequence
1764 protected void addReferenceAnnotations_actionPerformed(
1765 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1767 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1768 final AlignmentI alignment = this.ap.getAlignment();
1769 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1774 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1776 if (!ap.av.getAlignment().hasSeqrep())
1778 // initialise the display flags so the user sees something happen
1779 ap.av.setDisplayReferenceSeq(true);
1780 ap.av.setColourByReferenceSeq(true);
1781 ap.av.getAlignment().setSeqrep(sequence);
1785 if (ap.av.getAlignment().getSeqrep() == sequence)
1787 ap.av.getAlignment().setSeqrep(null);
1791 ap.av.getAlignment().setSeqrep(sequence);
1797 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1799 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1800 BitSet inserts = new BitSet();
1802 boolean markedPopup = false;
1803 // mark inserts in current selection
1804 if (ap.av.getSelectionGroup() != null)
1806 // mark just the columns in the selection group to be hidden
1807 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1808 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1810 // now clear columns without gaps
1811 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1817 inserts.and(sq.getInsertionsAsBits());
1819 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1820 ap.av.getSelectionGroup().getEndRes());
1823 // now mark for sequence under popup if we haven't already done it
1824 else if (!markedPopup && sequence != null)
1826 inserts.or(sequence.getInsertionsAsBits());
1828 // and set hidden columns accordingly
1829 hidden.hideColumns(inserts);
1834 protected void sequenceSelectionDetails_actionPerformed()
1836 createSequenceDetailsReport(ap.av.getSequenceSelection());
1839 public void createSequenceDetailsReport(SequenceI[] sequences)
1841 StringBuilder contents = new StringBuilder(128);
1842 contents.append("<html><body>");
1843 for (SequenceI seq : sequences)
1845 contents.append("<p><h2>" + MessageManager.formatMessage(
1846 "label.create_sequence_details_report_annotation_for",
1848 { seq.getDisplayId(true) }) + "</h2></p><p>");
1849 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1850 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1851 contents.append("</p>");
1853 contents.append("</body></html>");
1854 String report = contents.toString();
1856 JInternalFrame frame;
1857 if (Platform.isJS())
1859 JLabel textLabel = new JLabel();
1860 textLabel.setText(report);
1861 textLabel.setBackground(Color.WHITE);
1862 JPanel pane = new JPanel(new BorderLayout());
1863 pane.setOpaque(true);
1864 pane.setBackground(Color.WHITE);
1865 pane.add(textLabel, BorderLayout.NORTH);
1866 frame = new JInternalFrame();
1867 frame.getContentPane().add(new JScrollPane(pane));
1876 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1877 cap.setText(report);
1881 Desktop.addInternalFrame(frame,
1882 MessageManager.formatMessage("label.sequence_details_for",
1883 (sequences.length == 1 ? new Object[]
1884 { sequences[0].getDisplayId(true) }
1887 .getString("label.selection") })),
1891 protected void showNonconserved_actionPerformed()
1893 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1898 * call to refresh view after settings change
1902 ap.updateAnnotation();
1903 // removed paintAlignment(true) here:
1904 // updateAnnotation calls paintAlignment already, so don't need to call
1907 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1911 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1912 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1922 public void abovePIDColour_actionPerformed(boolean selected)
1924 SequenceGroup sg = getGroup();
1932 sg.cs.setConsensus(AAFrequency.calculate(
1933 sg.getSequences(ap.av.getHiddenRepSequences()),
1934 sg.getStartRes(), sg.getEndRes() + 1));
1936 int threshold = SliderPanel.setPIDSliderSource(ap,
1937 sg.getGroupColourScheme(), getGroup().getName());
1939 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1941 SliderPanel.showPIDSlider();
1944 // remove PIDColouring
1946 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1947 SliderPanel.hidePIDSlider();
1949 modifyPID.setEnabled(selected);
1955 * Open a panel where the user can choose which types of sequence annotation
1960 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1962 // todo correct way to guard against opening a duplicate panel?
1963 new AnnotationChooser(ap);
1972 public void conservationMenuItem_actionPerformed(boolean selected)
1974 SequenceGroup sg = getGroup();
1982 // JBPNote: Conservation name shouldn't be i18n translated
1983 Conservation c = new Conservation("Group",
1984 sg.getSequences(ap.av.getHiddenRepSequences()),
1985 sg.getStartRes(), sg.getEndRes() + 1);
1988 c.verdict(false, ap.av.getConsPercGaps());
1989 sg.cs.setConservation(c);
1991 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1993 SliderPanel.showConservationSlider();
1996 // remove ConservationColouring
1998 sg.cs.setConservation(null);
1999 SliderPanel.hideConservationSlider();
2001 modifyConservation.setEnabled(selected);
2007 * Shows a dialog where group name and description may be edited
2009 protected void groupName_actionPerformed()
2011 SequenceGroup sg = getGroup();
2012 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2013 sg.getDescription(),
2014 MessageManager.getString("label.group_name"),
2015 MessageManager.getString("label.group_description"));
2016 dialog.showDialog(ap.alignFrame,
2017 MessageManager.getString("label.edit_group_name_description"),
2023 sg.setName(dialog.getName());
2024 sg.setDescription(dialog.getDescription());
2031 * Get selection group - adding it to the alignment if necessary.
2033 * @return sequence group to operate on
2035 SequenceGroup getGroup()
2037 SequenceGroup sg = ap.av.getSelectionGroup();
2038 // this method won't add a new group if it already exists
2041 ap.av.getAlignment().addGroup(sg);
2048 * Shows a dialog where the sequence name and description may be edited. If a
2049 * name containing spaces is entered, these are converted to underscores, with a
2052 void sequenceName_actionPerformed()
2054 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2055 sequence.getDescription(),
2056 MessageManager.getString("label.sequence_name"),
2057 MessageManager.getString("label.sequence_description"));
2058 dialog.showDialog(ap.alignFrame,
2059 MessageManager.getString(
2060 "label.edit_sequence_name_description"),
2066 if (dialog.getName() != null)
2068 if (dialog.getName().indexOf(" ") > -1)
2070 JvOptionPane.showMessageDialog(ap,
2071 MessageManager.getString(
2072 "label.spaces_converted_to_underscores"),
2073 MessageManager.getString(
2074 "label.no_spaces_allowed_sequence_name"),
2075 JvOptionPane.WARNING_MESSAGE);
2077 sequence.setName(dialog.getName().replace(' ', '_'));
2078 ap.paintAlignment(false, false);
2080 sequence.setDescription(dialog.getDescription());
2081 ap.av.notifyAlignment();
2092 void unGroupMenuItem_actionPerformed()
2094 SequenceGroup sg = ap.av.getSelectionGroup();
2095 ap.av.getAlignment().deleteGroup(sg);
2096 ap.av.setSelectionGroup(null);
2100 void createGroupMenuItem_actionPerformed()
2102 getGroup(); // implicitly creates group - note - should apply defaults / use
2103 // standard alignment window logic for this
2108 * Offers a colour chooser and sets the selected colour as the group outline
2110 protected void outline_actionPerformed()
2112 String title = MessageManager
2113 .getString("label.select_outline_colour");
2114 ColourChooserListener listener = new ColourChooserListener()
2117 public void colourSelected(Color c)
2119 getGroup().setOutlineColour(c);
2123 JalviewColourChooser.showColourChooser(Desktop.getDesktopPane(),
2124 title, Color.BLUE, listener);
2133 public void showBoxes_actionPerformed()
2135 getGroup().setDisplayBoxes(showBoxes.isSelected());
2145 public void showText_actionPerformed()
2147 getGroup().setDisplayText(showText.isSelected());
2157 public void showColourText_actionPerformed()
2159 getGroup().setColourText(showColourText.isSelected());
2163 void hideSequences(boolean representGroup)
2165 ap.av.hideSequences(sequence, representGroup);
2168 public void copy_actionPerformed()
2170 ap.alignFrame.copy_actionPerformed();
2173 public void cut_actionPerformed()
2175 ap.alignFrame.cut_actionPerformed();
2178 void changeCase(ActionEvent e)
2180 Object source = e.getSource();
2181 SequenceGroup sg = ap.av.getSelectionGroup();
2185 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2186 sg.getStartRes(), sg.getEndRes() + 1);
2191 if (source == toggle)
2193 description = MessageManager.getString("label.toggle_case");
2194 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2196 else if (source == upperCase)
2198 description = MessageManager.getString("label.to_upper_case");
2199 caseChange = ChangeCaseCommand.TO_UPPER;
2203 description = MessageManager.getString("label.to_lower_case");
2204 caseChange = ChangeCaseCommand.TO_LOWER;
2207 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2208 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2209 startEnd, caseChange);
2211 ap.alignFrame.addHistoryItem(caseCommand);
2212 ap.av.notifyAlignment();
2218 public void outputText_actionPerformed(ActionEvent e)
2220 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2221 cap.setForInput(null);
2222 Desktop.addInternalFrame(cap, MessageManager
2223 .formatMessage("label.alignment_output_command", new Object[]
2224 { e.getActionCommand() }), 600, 500);
2226 String[] omitHidden = null;
2228 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2229 // or we simply trust the user wants
2230 // wysiwig behaviour
2232 FileFormatI fileFormat = FileFormats.getInstance()
2233 .forName(e.getActionCommand());
2235 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2238 public void sequenceFeature_actionPerformed()
2240 SequenceGroup sg = ap.av.getSelectionGroup();
2246 List<SequenceI> seqs = new ArrayList<>();
2247 List<SequenceFeature> features = new ArrayList<>();
2250 * assemble dataset sequences, and template new sequence features,
2251 * for the amend features dialog
2253 int gSize = sg.getSize();
2254 for (int i = 0; i < gSize; i++)
2256 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2257 int end = sg.findEndRes(sg.getSequenceAt(i));
2260 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2261 features.add(new SequenceFeature(null, null, start, end, null));
2266 * an entirely gapped region will generate empty lists of sequence / features
2268 if (!seqs.isEmpty())
2270 new FeatureEditor(ap, seqs, features, true).showDialog();
2274 public void textColour_actionPerformed()
2276 SequenceGroup sg = getGroup();
2279 new TextColourChooser().chooseColour(ap, sg);
2284 * Shows a dialog where sequence characters may be edited. Any changes are
2285 * applied, and added as an available 'Undo' item in the edit commands
2288 public void editSequence_actionPerformed()
2290 SequenceGroup sg = ap.av.getSelectionGroup();
2292 SequenceI seq = sequence;
2297 seq = sg.getSequenceAt(0);
2300 EditNameDialog dialog = new EditNameDialog(
2301 seq.getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
2302 null, MessageManager.getString("label.edit_sequence"), null);
2303 dialog.showDialog(ap.alignFrame,
2304 MessageManager.getString("label.edit_sequence"),
2310 EditCommand editCommand = new EditCommand(
2311 MessageManager.getString("label.edit_sequences"),
2313 dialog.getName().replace(' ',
2314 ap.av.getGapCharacter()),
2315 sg.getSequencesAsArray(
2316 ap.av.getHiddenRepSequences()),
2317 sg.getStartRes(), sg.getEndRes() + 1,
2318 ap.av.getAlignment());
2319 ap.alignFrame.addHistoryItem(editCommand);
2320 ap.av.notifyAlignment();
2327 * Action on user selecting an item from the colour menu (that does not have
2328 * its bespoke action handler)
2333 public void changeColour_actionPerformed(String colourSchemeName)
2335 SequenceGroup sg = getGroup();
2337 * switch to the chosen colour scheme (or null for None)
2339 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2340 .getColourScheme(colourSchemeName, ap.av, sg,
2341 ap.av.getHiddenRepSequences());
2342 sg.setColourScheme(colourScheme);
2343 if (colourScheme instanceof Blosum62ColourScheme
2344 || colourScheme instanceof PIDColourScheme)
2346 sg.cs.setConsensus(AAFrequency.calculate(
2347 sg.getSequences(ap.av.getHiddenRepSequences()),
2348 sg.getStartRes(), sg.getEndRes() + 1));