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.Color;
24 import java.awt.event.ActionEvent;
25 import java.awt.event.ActionListener;
26 import java.util.ArrayList;
27 import java.util.Arrays;
28 import java.util.BitSet;
29 import java.util.Collection;
30 import java.util.Collections;
31 import java.util.Hashtable;
32 import java.util.LinkedHashMap;
33 import java.util.List;
35 import java.util.Objects;
36 import java.util.SortedMap;
37 import java.util.TreeMap;
38 import java.util.Vector;
40 import javax.swing.ButtonGroup;
41 import javax.swing.JCheckBoxMenuItem;
42 import javax.swing.JColorChooser;
43 import javax.swing.JMenu;
44 import javax.swing.JMenuItem;
45 import javax.swing.JPopupMenu;
46 import javax.swing.JRadioButtonMenuItem;
48 import jalview.analysis.AAFrequency;
49 import jalview.analysis.AlignmentAnnotationUtils;
50 import jalview.analysis.AlignmentUtils;
51 import jalview.analysis.Conservation;
52 import jalview.api.AlignViewportI;
53 import jalview.bin.Cache;
54 import jalview.commands.ChangeCaseCommand;
55 import jalview.commands.EditCommand;
56 import jalview.commands.EditCommand.Action;
57 import jalview.datamodel.AlignmentAnnotation;
58 import jalview.datamodel.AlignmentI;
59 import jalview.datamodel.DBRefEntry;
60 import jalview.datamodel.HiddenColumns;
61 import jalview.datamodel.MappedFeatures;
62 import jalview.datamodel.PDBEntry;
63 import jalview.datamodel.SequenceFeature;
64 import jalview.datamodel.SequenceGroup;
65 import jalview.datamodel.SequenceI;
66 import jalview.gui.ColourMenuHelper.ColourChangeListener;
67 import jalview.io.FileFormatI;
68 import jalview.io.FileFormats;
69 import jalview.io.FormatAdapter;
70 import jalview.io.SequenceAnnotationReport;
71 import jalview.schemes.Blosum62ColourScheme;
72 import jalview.schemes.ColourSchemeI;
73 import jalview.schemes.ColourSchemes;
74 import jalview.schemes.PIDColourScheme;
75 import jalview.schemes.ResidueColourScheme;
76 import jalview.util.Comparison;
77 import jalview.util.GroupUrlLink;
78 import jalview.util.GroupUrlLink.UrlStringTooLongException;
79 import jalview.util.MessageManager;
80 import jalview.util.StringUtils;
81 import jalview.util.UrlLink;
82 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
85 * The popup menu that is displayed on right-click on a sequence id, or in the
88 public class PopupMenu extends JPopupMenu implements ColourChangeListener
91 * maximum length of feature description to include in popup menu item text
93 private static final int FEATURE_DESC_MAX = 40;
96 * true for ID Panel menu, false for alignment panel menu
98 private final boolean forIdPanel;
100 private final AlignmentPanel ap;
103 * the sequence under the cursor when clicked
104 * (additional sequences may be selected)
106 private final SequenceI sequence;
108 JMenu groupMenu = new JMenu();
110 JMenuItem groupName = new JMenuItem();
112 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
114 protected JMenuItem modifyPID = new JMenuItem();
116 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
118 protected JRadioButtonMenuItem annotationColour;
120 protected JMenuItem modifyConservation = new JMenuItem();
122 JMenu sequenceMenu = new JMenu();
124 JMenuItem makeReferenceSeq = new JMenuItem();
126 JMenuItem createGroupMenuItem = new JMenuItem();
128 JMenuItem unGroupMenuItem = new JMenuItem();
130 JMenu colourMenu = new JMenu();
132 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
134 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
136 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
138 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
140 JMenu editMenu = new JMenu();
142 JMenuItem upperCase = new JMenuItem();
144 JMenuItem lowerCase = new JMenuItem();
146 JMenuItem toggle = new JMenuItem();
148 JMenu outputMenu = new JMenu();
150 JMenu seqShowAnnotationsMenu = new JMenu();
152 JMenu seqHideAnnotationsMenu = new JMenu();
154 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
155 MessageManager.getString("label.add_reference_annotations"));
157 JMenu groupShowAnnotationsMenu = new JMenu();
159 JMenu groupHideAnnotationsMenu = new JMenu();
161 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
162 MessageManager.getString("label.add_reference_annotations"));
164 JMenuItem textColour = new JMenuItem();
166 JMenu editGroupMenu = new JMenu();
168 JMenuItem chooseStructure = new JMenuItem();
170 JMenu rnaStructureMenu = new JMenu();
173 * Constructs a menu with sub-menu items for any hyperlinks for the sequence
174 * and/or features provided. Hyperlinks may include a lookup by sequence id,
175 * or database cross-references, depending on which links are enabled in user
182 protected static JMenu buildLinkMenu(final SequenceI seq,
183 List<SequenceFeature> features)
185 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
187 List<String> nlinks = null;
190 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
191 UrlLink.sort(nlinks);
195 nlinks = new ArrayList<>();
198 if (features != null)
200 for (SequenceFeature sf : features)
202 if (sf.links != null)
204 for (String link : sf.links)
213 * instantiate the hyperlinklink templates from sequence data;
214 * note the order of the templates is preserved in the map
216 Map<String, List<String>> linkset = new LinkedHashMap<>();
217 for (String link : nlinks)
219 UrlLink urlLink = null;
222 urlLink = new UrlLink(link);
223 } catch (Exception foo)
225 Cache.log.error("Exception for URLLink '" + link + "'", foo);
229 if (!urlLink.isValid())
231 Cache.log.error(urlLink.getInvalidMessage());
235 urlLink.createLinksFromSeq(seq, linkset);
239 * construct menu items for the hyperlinks (still preserving
240 * the order of the sorted templates)
242 addUrlLinks(linkMenu, linkset.values());
248 * A helper method that builds menu items from the given links, with action
249 * handlers to open the link URL, and adds them to the linkMenu. Each provided
250 * link should be a list whose second item is the menu text, and whose fourth
251 * item is the URL to open when the menu item is selected.
256 static private void addUrlLinks(JMenu linkMenu,
257 Collection<List<String>> linkset)
259 for (List<String> linkstrset : linkset)
261 final String url = linkstrset.get(3);
262 JMenuItem item = new JMenuItem(linkstrset.get(1));
263 item.setToolTipText(MessageManager
264 .formatMessage("label.open_url_param", new Object[]
266 item.addActionListener(new ActionListener()
269 public void actionPerformed(ActionEvent e)
271 new Thread(new Runnable()
286 * Opens the provided url in the default web browser, or shows an error
287 * message if this fails
291 static void showLink(String url)
295 jalview.util.BrowserLauncher.openURL(url);
296 } catch (Exception ex)
298 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
299 MessageManager.getString("label.web_browser_not_found_unix"),
300 MessageManager.getString("label.web_browser_not_found"),
301 JvOptionPane.WARNING_MESSAGE);
303 ex.printStackTrace();
308 * add a late bound groupURL item to the given linkMenu
312 * - menu label string
313 * @param urlgenerator
314 * GroupURLLink used to generate URL
316 * Object array returned from the makeUrlStubs function.
318 static void addshowLink(JMenu linkMenu, String label,
319 final GroupUrlLink urlgenerator, final Object[] urlstub)
321 JMenuItem item = new JMenuItem(label);
322 item.setToolTipText(MessageManager
323 .formatMessage("label.open_url_seqs_param", new Object[]
324 { urlgenerator.getUrl_prefix(),
325 urlgenerator.getNumberInvolved(urlstub) }));
326 // TODO: put in info about what is being sent.
327 item.addActionListener(new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 new Thread(new Runnable()
340 showLink(urlgenerator.constructFrom(urlstub));
341 } catch (UrlStringTooLongException e2)
354 * Constructor for a PopupMenu for a click in the alignment panel (on a residue)
357 * the panel in which the mouse is clicked
359 * the sequence under the mouse
360 * @throws NullPointerException
363 public PopupMenu(final AlignmentPanel ap, SequenceI seq, int column)
365 this(false, ap, seq, column, null);
369 * Constructor for a PopupMenu for a click in the sequence id panel
372 * the panel in which the mouse is clicked
374 * the sequence under the mouse click
376 * templates for sequence external links
377 * @throws NullPointerException
380 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
381 List<String> groupLinks)
383 this(true, alignPanel, seq, -1, groupLinks);
387 * Private constructor that constructs a popup menu for either sequence ID
388 * Panel, or alignment context
394 * aligned column position (0...)
397 private PopupMenu(boolean fromIdPanel,
398 final AlignmentPanel alignPanel,
399 final SequenceI seq, final int column, List<String> groupLinks)
401 Objects.requireNonNull(seq);
402 this.forIdPanel = fromIdPanel;
403 this.ap = alignPanel;
406 for (String ff : FileFormats.getInstance().getWritableFormats(true))
408 JMenuItem item = new JMenuItem(ff);
410 item.addActionListener(new ActionListener()
413 public void actionPerformed(ActionEvent e)
415 outputText_actionPerformed(e);
419 outputMenu.add(item);
423 * Build menus for annotation types that may be shown or hidden, and for
424 * 'reference annotations' that may be added to the alignment. First for the
425 * currently selected sequence (if there is one):
427 final List<SequenceI> selectedSequence = (forIdPanel && seq != null
429 : Collections.<SequenceI> emptyList());
430 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
431 seqHideAnnotationsMenu, selectedSequence);
432 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
436 * And repeat for the current selection group (if there is one):
438 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
439 ? Collections.<SequenceI> emptyList()
440 : alignPanel.av.getSelectionGroup().getSequences());
441 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
442 groupHideAnnotationsMenu, selectedGroup);
443 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
449 } catch (Exception e)
457 sequenceMenu.setText(sequence.getName());
458 if (seq == alignPanel.av.getAlignment().getSeqrep())
460 makeReferenceSeq.setText(
461 MessageManager.getString("action.unmark_as_reference"));
465 makeReferenceSeq.setText(
466 MessageManager.getString("action.set_as_reference"));
469 if (!alignPanel.av.getAlignment().isNucleotide())
471 remove(rnaStructureMenu);
475 int origCount = rnaStructureMenu.getItemCount();
477 * add menu items to 2D-render any alignment or sequence secondary
478 * structure annotation
480 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
481 .getAlignmentAnnotation();
484 for (final AlignmentAnnotation aa : aas)
486 if (aa.isValidStruc() && aa.sequenceRef == null)
489 * valid alignment RNA secondary structure annotation
491 menuItem = new JMenuItem();
492 menuItem.setText(MessageManager.formatMessage(
493 "label.2d_rna_structure_line", new Object[]
495 menuItem.addActionListener(new ActionListener()
498 public void actionPerformed(ActionEvent e)
500 new AppVarna(seq, aa, alignPanel);
503 rnaStructureMenu.add(menuItem);
508 if (seq.getAnnotation() != null)
510 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
511 for (final AlignmentAnnotation aa : seqAnns)
513 if (aa.isValidStruc())
516 * valid sequence RNA secondary structure annotation
518 // TODO: make rnastrucF a bit more nice
519 menuItem = new JMenuItem();
520 menuItem.setText(MessageManager.formatMessage(
521 "label.2d_rna_sequence_name", new Object[]
523 menuItem.addActionListener(new ActionListener()
526 public void actionPerformed(ActionEvent e)
528 // TODO: VARNA does'nt print gaps in the sequence
529 new AppVarna(seq, aa, alignPanel);
532 rnaStructureMenu.add(menuItem);
536 if (rnaStructureMenu.getItemCount() == origCount)
538 remove(rnaStructureMenu);
542 menuItem = new JMenuItem(
543 MessageManager.getString("action.hide_sequences"));
544 menuItem.addActionListener(new ActionListener()
547 public void actionPerformed(ActionEvent e)
549 hideSequences(false);
554 if (alignPanel.av.getSelectionGroup() != null
555 && alignPanel.av.getSelectionGroup().getSize() > 1)
557 menuItem = new JMenuItem(MessageManager
558 .formatMessage("label.represent_group_with", new Object[]
560 menuItem.addActionListener(new ActionListener()
563 public void actionPerformed(ActionEvent e)
568 sequenceMenu.add(menuItem);
571 if (alignPanel.av.hasHiddenRows())
573 final int index = alignPanel.av.getAlignment().findIndex(seq);
575 if (alignPanel.av.adjustForHiddenSeqs(index)
576 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
578 menuItem = new JMenuItem(
579 MessageManager.getString("action.reveal_sequences"));
580 menuItem.addActionListener(new ActionListener()
583 public void actionPerformed(ActionEvent e)
585 alignPanel.av.showSequence(index);
586 if (alignPanel.overviewPanel != null)
588 alignPanel.overviewPanel.updateOverviewImage();
599 * - in the IdPanel (seq not null) if any sequence is hidden
600 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
602 if (alignPanel.av.hasHiddenRows())
604 boolean addOption = seq != null;
605 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
611 JMenuItem menuItem = new JMenuItem(
612 MessageManager.getString("action.reveal_all"));
613 menuItem.addActionListener(new ActionListener()
616 public void actionPerformed(ActionEvent e)
618 alignPanel.av.showAllHiddenSeqs();
619 if (alignPanel.overviewPanel != null)
621 alignPanel.overviewPanel.updateOverviewImage();
629 SequenceGroup sg = alignPanel.av.getSelectionGroup();
630 boolean isDefinedGroup = (sg != null)
631 ? alignPanel.av.getAlignment().getGroups().contains(sg)
634 if (sg != null && sg.getSize() > 0)
636 groupName.setText(MessageManager
637 .getString("label.edit_name_and_description_current_group"));
639 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
641 conservationMenuItem.setEnabled(!sg.isNucleotide());
645 if (sg.cs.conservationApplied())
647 conservationMenuItem.setSelected(true);
649 if (sg.cs.getThreshold() > 0)
651 abovePIDColour.setSelected(true);
654 modifyConservation.setEnabled(conservationMenuItem.isSelected());
655 modifyPID.setEnabled(abovePIDColour.isSelected());
656 displayNonconserved.setSelected(sg.getShowNonconserved());
657 showText.setSelected(sg.getDisplayText());
658 showColourText.setSelected(sg.getColourText());
659 showBoxes.setSelected(sg.getDisplayBoxes());
660 // add any groupURLs to the groupURL submenu and make it visible
661 if (groupLinks != null && groupLinks.size() > 0)
663 buildGroupURLMenu(sg, groupLinks);
665 // Add a 'show all structures' for the current selection
666 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
668 SequenceI sqass = null;
669 for (SequenceI sq : alignPanel.av.getSequenceSelection())
671 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
672 if (pes != null && pes.size() > 0)
674 reppdb.put(pes.get(0).getId(), pes.get(0));
675 for (PDBEntry pe : pes)
677 pdbe.put(pe.getId(), pe);
687 final PDBEntry[] pe = pdbe.values()
688 .toArray(new PDBEntry[pdbe.size()]),
689 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
690 final JMenuItem gpdbview, rpdbview;
695 groupMenu.setVisible(false);
696 editMenu.setVisible(false);
701 createGroupMenuItem.setVisible(true);
702 unGroupMenuItem.setVisible(false);
703 editGroupMenu.setText(MessageManager.getString("action.edit_new_group"));
707 createGroupMenuItem.setVisible(false);
708 unGroupMenuItem.setVisible(true);
709 editGroupMenu.setText(MessageManager.getString("action.edit_group"));
714 sequenceMenu.setVisible(false);
715 chooseStructure.setVisible(false);
716 rnaStructureMenu.setVisible(false);
719 addLinksAndFeatures(seq, column);
725 * <li>configured sequence database links (ID panel popup menu)</li>
726 * <li>non-positional feature links (ID panel popup menu)</li>
727 * <li>positional feature links (alignment panel popup menu)</li>
728 * <li>feature details links (alignment panel popup menu)</li>
730 * If this panel is also showed complementary (CDS/protein) features, then links
731 * to their feature details are also added.
736 void addLinksAndFeatures(final SequenceI seq, final int column)
738 List<SequenceFeature> features = null;
741 features = sequence.getFeatures().getNonPositionalFeatures();
745 features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
749 addLinks(seq, features);
753 addFeatureDetails(features, seq, column);
758 * Add a menu item to show feature details for each sequence feature. Any
759 * linked 'virtual' features (CDS/protein) are also optionally found and
766 protected void addFeatureDetails(List<SequenceFeature> features,
767 final SequenceI seq, final int column)
770 * add features in CDS/protein complement at the corresponding
771 * position if configured to do so
773 MappedFeatures mf = null;
774 if (ap.av.isShowComplementFeatures())
776 if (!Comparison.isGap(sequence.getCharAt(column)))
778 AlignViewportI complement = ap.getAlignViewport()
779 .getCodingComplement();
780 AlignFrame af = Desktop.getAlignFrameFor(complement);
781 FeatureRendererModel fr2 = af.getFeatureRenderer();
782 int seqPos = sequence.findPosition(column);
783 mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
787 if (features.isEmpty() && mf == null)
790 * no features to show at this position
795 JMenu details = new JMenu(
796 MessageManager.getString("label.feature_details"));
799 String name = seq.getName();
800 for (final SequenceFeature sf : features)
802 addFeatureDetailsMenuItem(details, name, sf, null);
807 for (final SequenceFeature sf : mf.features)
809 addFeatureDetailsMenuItem(details, name, sf, mf);
815 * A helper method to add one menu item whose action is to show details for
816 * one feature. The menu text includes feature description, but this may be
824 void addFeatureDetailsMenuItem(JMenu details, final String seqName,
825 final SequenceFeature sf, MappedFeatures mf)
827 int start = sf.getBegin();
828 int end = sf.getEnd();
832 * show local rather than linked feature coordinates
834 int[] beginRange = mf.getMappedPositions(start, start);
835 int[] endRange = mf.getMappedPositions(end, end);
836 if (beginRange == null || endRange == null)
838 // e.g. variant extending to stop codon so not mappable
841 start = beginRange[0];
842 end = endRange[endRange.length - 1];
843 int[] localRange = mf.getMappedPositions(start, end);
844 if (localRange == null)
848 start = localRange[0];
849 end = localRange[localRange.length - 1];
851 StringBuilder desc = new StringBuilder();
852 desc.append(sf.getType()).append(" ").append(String.valueOf(start));
855 desc.append(sf.isContactFeature() ? ":" : "-");
856 desc.append(String.valueOf(end));
858 String description = sf.getDescription();
859 if (description != null)
862 description = StringUtils.stripHtmlTags(description);
865 * truncate overlong descriptions unless they contain an href
866 * (as truncation could leave corrupted html)
868 boolean hasLink = description.indexOf("a href") > -1;
869 if (description.length() > FEATURE_DESC_MAX && !hasLink)
871 description = description.substring(0, FEATURE_DESC_MAX) + "...";
873 desc.append(description);
875 String featureGroup = sf.getFeatureGroup();
876 if (featureGroup != null)
878 desc.append(" (").append(featureGroup).append(")");
880 String htmlText = JvSwingUtils.wrapTooltip(true, desc.toString());
881 JMenuItem item = new JMenuItem(htmlText);
882 item.addActionListener(new ActionListener()
885 public void actionPerformed(ActionEvent e)
887 showFeatureDetails(sf, seqName, mf);
894 * Opens a panel showing a text report of feature details
900 protected void showFeatureDetails(SequenceFeature sf, String seqName,
903 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
904 // it appears Java's CSS does not support border-collapse :-(
905 cap.addStylesheetRule("table { border-collapse: collapse;}");
906 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
907 cap.setText(sf.getDetailsReport(seqName, mf));
909 Desktop.addInternalFrame(cap,
910 MessageManager.getString("label.feature_details"), 500, 500);
914 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
915 * When seq is not null, these are links for the sequence id, which may be to
916 * external web sites for the sequence accession, and/or links embedded in
917 * non-positional features. When seq is null, only links embedded in the
918 * provided features are added. If no links are found, the menu is not added.
923 void addLinks(final SequenceI seq, List<SequenceFeature> features)
925 JMenu linkMenu = buildLinkMenu(forIdPanel ? seq : null, features);
927 // only add link menu if it has entries
928 if (linkMenu.getItemCount() > 0)
932 sequenceMenu.add(linkMenu);
942 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
943 * "All" is added first, followed by a separator. Then add any annotation
944 * types associated with the current selection. Separate menus are built for
945 * the selected sequence group (if any), and the selected sequence.
947 * Some annotation rows are always rendered together - these can be identified
948 * by a common graphGroup property > -1. Only one of each group will be marked
949 * as visible (to avoid duplication of the display). For such groups we add a
950 * composite type name, e.g.
952 * IUPredWS (Long), IUPredWS (Short)
956 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
957 List<SequenceI> forSequences)
959 showMenu.removeAll();
960 hideMenu.removeAll();
962 final List<String> all = Arrays
964 { MessageManager.getString("label.all") });
965 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
967 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
969 showMenu.addSeparator();
970 hideMenu.addSeparator();
972 final AlignmentAnnotation[] annotations = ap.getAlignment()
973 .getAlignmentAnnotation();
976 * Find shown/hidden annotations types, distinguished by source (calcId),
977 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
978 * the insertion order, which is the order of the annotations on the
981 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
982 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
983 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
984 AlignmentAnnotationUtils.asList(annotations), forSequences);
986 for (String calcId : hiddenTypes.keySet())
988 for (List<String> type : hiddenTypes.get(calcId))
990 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
994 // grey out 'show annotations' if none are hidden
995 showMenu.setEnabled(!hiddenTypes.isEmpty());
997 for (String calcId : shownTypes.keySet())
999 for (List<String> type : shownTypes.get(calcId))
1001 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
1005 // grey out 'hide annotations' if none are shown
1006 hideMenu.setEnabled(!shownTypes.isEmpty());
1010 * Returns a list of sequences - either the current selection group (if there
1011 * is one), else the specified single sequence.
1016 protected List<SequenceI> getSequenceScope(SequenceI seq)
1018 List<SequenceI> forSequences = null;
1019 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
1020 if (selectionGroup != null && selectionGroup.getSize() > 0)
1022 forSequences = selectionGroup.getSequences();
1026 forSequences = seq == null ? Collections.<SequenceI> emptyList()
1027 : Arrays.asList(seq);
1029 return forSequences;
1033 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
1036 * @param showOrHideMenu
1037 * the menu to add to
1038 * @param forSequences
1039 * the sequences whose annotations may be shown or hidden
1044 * if true this is a special label meaning 'All'
1045 * @param actionIsShow
1046 * if true, the select menu item action is to show the annotation
1049 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
1050 final List<SequenceI> forSequences, String calcId,
1051 final List<String> types, final boolean allTypes,
1052 final boolean actionIsShow)
1054 String label = types.toString(); // [a, b, c]
1055 label = label.substring(1, label.length() - 1); // a, b, c
1056 final JMenuItem item = new JMenuItem(label);
1057 item.setToolTipText(calcId);
1058 item.addActionListener(new ActionListener()
1061 public void actionPerformed(ActionEvent e)
1063 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
1064 types, forSequences, allTypes, actionIsShow);
1068 showOrHideMenu.add(item);
1071 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
1074 // TODO: usability: thread off the generation of group url content so root
1075 // menu appears asap
1076 // sequence only URLs
1077 // ID/regex match URLs
1078 JMenu groupLinksMenu = new JMenu(
1079 MessageManager.getString("action.group_link"));
1080 // three types of url that might be created.
1081 JMenu[] linkMenus = new JMenu[] { null,
1082 new JMenu(MessageManager.getString("action.ids")),
1083 new JMenu(MessageManager.getString("action.sequences")),
1084 new JMenu(MessageManager.getString("action.ids_sequences")) };
1086 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
1087 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
1088 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
1089 for (int sq = 0; sq < seqs.length; sq++)
1092 int start = seqs[sq].findPosition(sg.getStartRes()),
1093 end = seqs[sq].findPosition(sg.getEndRes());
1094 // just collect ids from dataset sequence
1095 // TODO: check if IDs collected from selecton group intersects with the
1096 // current selection, too
1097 SequenceI sqi = seqs[sq];
1098 while (sqi.getDatasetSequence() != null)
1100 sqi = sqi.getDatasetSequence();
1102 DBRefEntry[] dbr = sqi.getDBRefs();
1103 if (dbr != null && dbr.length > 0)
1105 for (int d = 0; d < dbr.length; d++)
1107 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
1108 Object[] sarray = commonDbrefs.get(src);
1111 sarray = new Object[2];
1112 sarray[0] = new int[] { 0 };
1113 sarray[1] = new String[seqs.length];
1115 commonDbrefs.put(src, sarray);
1118 if (((String[]) sarray[1])[sq] == null)
1120 if (!dbr[d].hasMap() || (dbr[d].getMap()
1121 .locateMappedRange(start, end) != null))
1123 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
1124 ((int[]) sarray[0])[0]++;
1130 // now create group links for all distinct ID/sequence sets.
1131 boolean addMenu = false; // indicates if there are any group links to give
1133 for (String link : groupLinks)
1135 GroupUrlLink urlLink = null;
1138 urlLink = new GroupUrlLink(link);
1139 } catch (Exception foo)
1141 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
1145 if (!urlLink.isValid())
1147 Cache.log.error(urlLink.getInvalidMessage());
1150 final String label = urlLink.getLabel();
1151 boolean usingNames = false;
1152 // Now see which parts of the group apply for this URL
1153 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
1154 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
1155 String[] seqstr, ids; // input to makeUrl
1158 int numinput = ((int[]) idset[0])[0];
1159 String[] allids = ((String[]) idset[1]);
1160 seqstr = new String[numinput];
1161 ids = new String[numinput];
1162 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
1164 if (allids[sq] != null)
1166 ids[idcount] = allids[sq];
1167 seqstr[idcount++] = idandseqs[1][sq];
1173 // just use the id/seq set
1174 seqstr = idandseqs[1];
1178 // and try and make the groupURL!
1180 Object[] urlset = null;
1183 urlset = urlLink.makeUrlStubs(ids, seqstr,
1184 "FromJalview" + System.currentTimeMillis(), false);
1185 } catch (UrlStringTooLongException e)
1190 int type = urlLink.getGroupURLType() & 3;
1191 // first two bits ofurlLink type bitfield are sequenceids and sequences
1192 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1193 addshowLink(linkMenus[type],
1194 label + (((type & 1) == 1)
1195 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
1203 groupLinksMenu = new JMenu(
1204 MessageManager.getString("action.group_link"));
1205 for (int m = 0; m < linkMenus.length; m++)
1207 if (linkMenus[m] != null
1208 && linkMenus[m].getMenuComponentCount() > 0)
1210 groupLinksMenu.add(linkMenus[m]);
1214 groupMenu.add(groupLinksMenu);
1224 private void jbInit() throws Exception
1226 groupMenu.setText(MessageManager.getString("label.selection"));
1227 groupName.setText(MessageManager.getString("label.name"));
1228 groupName.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 groupName_actionPerformed();
1236 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1238 JMenuItem sequenceName = new JMenuItem(
1239 MessageManager.getString("label.edit_name_description"));
1240 sequenceName.addActionListener(new ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 sequenceName_actionPerformed();
1248 JMenuItem chooseAnnotations = new JMenuItem(
1249 MessageManager.getString("action.choose_annotations"));
1250 chooseAnnotations.addActionListener(new ActionListener()
1253 public void actionPerformed(ActionEvent e)
1255 chooseAnnotations_actionPerformed(e);
1258 JMenuItem sequenceDetails = new JMenuItem(
1259 MessageManager.getString("label.sequence_details"));
1260 sequenceDetails.addActionListener(new ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 createSequenceDetailsReport(new SequenceI[] { sequence });
1268 JMenuItem sequenceSelDetails = new JMenuItem(
1269 MessageManager.getString("label.sequence_details"));
1270 sequenceSelDetails.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1275 createSequenceDetailsReport(ap.av.getSequenceSelection());
1280 .setText(MessageManager.getString("action.remove_group"));
1281 unGroupMenuItem.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1286 unGroupMenuItem_actionPerformed();
1290 .setText(MessageManager.getString("action.create_group"));
1291 createGroupMenuItem.addActionListener(new ActionListener()
1294 public void actionPerformed(ActionEvent e)
1296 createGroupMenuItem_actionPerformed();
1300 JMenuItem outline = new JMenuItem(
1301 MessageManager.getString("action.border_colour"));
1302 outline.addActionListener(new ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 outline_actionPerformed();
1310 showBoxes.setText(MessageManager.getString("action.boxes"));
1311 showBoxes.setState(true);
1312 showBoxes.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent e)
1317 showBoxes_actionPerformed();
1320 showText.setText(MessageManager.getString("action.text"));
1321 showText.setState(true);
1322 showText.addActionListener(new ActionListener()
1325 public void actionPerformed(ActionEvent e)
1327 showText_actionPerformed();
1330 showColourText.setText(MessageManager.getString("label.colour_text"));
1331 showColourText.addActionListener(new ActionListener()
1334 public void actionPerformed(ActionEvent e)
1336 showColourText_actionPerformed();
1340 .setText(MessageManager.getString("label.show_non_conserved"));
1341 displayNonconserved.setState(true);
1342 displayNonconserved.addActionListener(new ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 showNonconserved_actionPerformed();
1350 editMenu.setText(MessageManager.getString("action.edit"));
1351 JMenuItem cut = new JMenuItem(MessageManager.getString("action.cut"));
1352 cut.addActionListener(new ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 cut_actionPerformed();
1360 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1361 upperCase.addActionListener(new ActionListener()
1364 public void actionPerformed(ActionEvent e)
1369 JMenuItem copy = new JMenuItem(MessageManager.getString("action.copy"));
1370 copy.addActionListener(new ActionListener()
1373 public void actionPerformed(ActionEvent e)
1375 copy_actionPerformed();
1378 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1379 lowerCase.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent e)
1387 toggle.setText(MessageManager.getString("label.toggle_case"));
1388 toggle.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1397 MessageManager.getString("label.out_to_textbox") + "...");
1398 seqShowAnnotationsMenu
1399 .setText(MessageManager.getString("label.show_annotations"));
1400 seqHideAnnotationsMenu
1401 .setText(MessageManager.getString("label.hide_annotations"));
1402 groupShowAnnotationsMenu
1403 .setText(MessageManager.getString("label.show_annotations"));
1404 groupHideAnnotationsMenu
1405 .setText(MessageManager.getString("label.hide_annotations"));
1406 JMenuItem sequenceFeature = new JMenuItem(
1407 MessageManager.getString("label.create_sequence_feature"));
1408 sequenceFeature.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 sequenceFeature_actionPerformed();
1416 editGroupMenu.setText(MessageManager.getString("label.group"));
1417 chooseStructure.setText(
1418 MessageManager.getString("label.show_pdbstruct_dialog"));
1419 chooseStructure.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent actionEvent)
1424 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1425 if (ap.av.getSelectionGroup() != null)
1427 selectedSeqs = ap.av.getSequenceSelection();
1429 new StructureChooser(selectedSeqs, sequence, ap);
1434 .setText(MessageManager.getString("label.view_rna_structure"));
1436 // colStructureMenu.setText("Colour By Structure");
1437 JMenuItem editSequence = new JMenuItem(
1438 MessageManager.getString("label.edit_sequence") + "...");
1439 editSequence.addActionListener(new ActionListener()
1442 public void actionPerformed(ActionEvent actionEvent)
1444 editSequence_actionPerformed(actionEvent);
1447 makeReferenceSeq.setText(
1448 MessageManager.getString("label.mark_as_representative"));
1449 makeReferenceSeq.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent actionEvent)
1455 makeReferenceSeq_actionPerformed(actionEvent);
1460 groupMenu.add(sequenceSelDetails);
1463 add(rnaStructureMenu);
1464 add(chooseStructure);
1467 JMenuItem hideInsertions = new JMenuItem(
1468 MessageManager.getString("label.hide_insertions"));
1469 hideInsertions.addActionListener(new ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 hideInsertions_actionPerformed(e);
1478 add(hideInsertions);
1480 // annotations configuration panel suppressed for now
1481 // groupMenu.add(chooseAnnotations);
1484 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1485 * (if a selection group is in force).
1487 sequenceMenu.add(seqShowAnnotationsMenu);
1488 sequenceMenu.add(seqHideAnnotationsMenu);
1489 sequenceMenu.add(seqAddReferenceAnnotations);
1490 groupMenu.add(groupShowAnnotationsMenu);
1491 groupMenu.add(groupHideAnnotationsMenu);
1492 groupMenu.add(groupAddReferenceAnnotations);
1493 groupMenu.add(editMenu);
1494 groupMenu.add(outputMenu);
1495 groupMenu.add(sequenceFeature);
1496 groupMenu.add(createGroupMenuItem);
1497 groupMenu.add(unGroupMenuItem);
1498 groupMenu.add(editGroupMenu);
1499 sequenceMenu.add(sequenceName);
1500 sequenceMenu.add(sequenceDetails);
1501 sequenceMenu.add(makeReferenceSeq);
1508 editMenu.add(editSequence);
1509 editMenu.add(upperCase);
1510 editMenu.add(lowerCase);
1511 editMenu.add(toggle);
1512 editGroupMenu.add(groupName);
1513 editGroupMenu.add(colourMenu);
1514 editGroupMenu.add(showBoxes);
1515 editGroupMenu.add(showText);
1516 editGroupMenu.add(showColourText);
1517 editGroupMenu.add(outline);
1518 editGroupMenu.add(displayNonconserved);
1522 * Constructs the entries for the colour menu
1524 protected void initColourMenu()
1526 colourMenu.setText(MessageManager.getString("label.group_colour"));
1527 textColour.setText(MessageManager.getString("label.text_colour"));
1528 textColour.addActionListener(new ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 textColour_actionPerformed();
1537 abovePIDColour.setText(
1538 MessageManager.getString("label.above_identity_threshold"));
1539 abovePIDColour.addActionListener(new ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1549 MessageManager.getString("label.modify_identity_threshold"));
1550 modifyPID.addActionListener(new ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 modifyPID_actionPerformed();
1559 conservationMenuItem
1560 .setText(MessageManager.getString("action.by_conservation"));
1561 conservationMenuItem.addActionListener(new ActionListener()
1564 public void actionPerformed(ActionEvent e)
1566 conservationMenuItem_actionPerformed(
1567 conservationMenuItem.isSelected());
1571 annotationColour = new JRadioButtonMenuItem(
1572 MessageManager.getString("action.by_annotation"));
1573 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1574 annotationColour.setEnabled(false);
1575 annotationColour.setToolTipText(
1576 MessageManager.getString("label.by_annotation_tooltip"));
1578 modifyConservation.setText(MessageManager
1579 .getString("label.modify_conservation_threshold"));
1580 modifyConservation.addActionListener(new ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 modifyConservation_actionPerformed();
1591 * Builds the group colour sub-menu, including any user-defined colours which
1592 * were loaded at startup or during the Jalview session
1594 protected void buildColourMenu()
1596 SequenceGroup sg = ap.av.getSelectionGroup();
1600 * popup menu with no sequence group scope
1604 colourMenu.removeAll();
1605 colourMenu.add(textColour);
1606 colourMenu.addSeparator();
1608 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1610 bg.add(annotationColour);
1611 colourMenu.add(annotationColour);
1613 colourMenu.addSeparator();
1614 colourMenu.add(conservationMenuItem);
1615 colourMenu.add(modifyConservation);
1616 colourMenu.add(abovePIDColour);
1617 colourMenu.add(modifyPID);
1620 protected void modifyConservation_actionPerformed()
1622 SequenceGroup sg = getGroup();
1625 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1626 SliderPanel.showConservationSlider();
1630 protected void modifyPID_actionPerformed()
1632 SequenceGroup sg = getGroup();
1635 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1637 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1638 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1639 SliderPanel.showPIDSlider();
1644 * Check for any annotations on the underlying dataset sequences (for the
1645 * current selection group) which are not 'on the alignment'.If any are found,
1646 * enable the option to add them to the alignment. The criteria for 'on the
1647 * alignment' is finding an alignment annotation on the alignment, matched on
1648 * calcId, label and sequenceRef.
1650 * A tooltip is also constructed that displays the source (calcId) and type
1651 * (label) of the annotations that can be added.
1654 * @param forSequences
1656 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1657 List<SequenceI> forSequences)
1659 menuItem.setEnabled(false);
1662 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1663 * Using TreeMap means calcIds are shown in alphabetical order.
1665 SortedMap<String, String> tipEntries = new TreeMap<>();
1666 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1667 AlignmentI al = this.ap.av.getAlignment();
1668 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1670 if (!candidates.isEmpty())
1672 StringBuilder tooltip = new StringBuilder(64);
1673 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1676 * Found annotations that could be added. Enable the menu item, and
1677 * configure its tooltip and action.
1679 menuItem.setEnabled(true);
1680 for (String calcId : tipEntries.keySet())
1682 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1684 String tooltipText = JvSwingUtils.wrapTooltip(true,
1685 tooltip.toString());
1686 menuItem.setToolTipText(tooltipText);
1688 menuItem.addActionListener(new ActionListener()
1691 public void actionPerformed(ActionEvent e)
1693 addReferenceAnnotations_actionPerformed(candidates);
1700 * Add annotations to the sequences and to the alignment.
1703 * a map whose keys are sequences on the alignment, and values a list
1704 * of annotations to add to each sequence
1706 protected void addReferenceAnnotations_actionPerformed(
1707 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1709 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1710 final AlignmentI alignment = this.ap.getAlignment();
1711 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1716 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1718 if (!ap.av.getAlignment().hasSeqrep())
1720 // initialise the display flags so the user sees something happen
1721 ap.av.setDisplayReferenceSeq(true);
1722 ap.av.setColourByReferenceSeq(true);
1723 ap.av.getAlignment().setSeqrep(sequence);
1727 if (ap.av.getAlignment().getSeqrep() == sequence)
1729 ap.av.getAlignment().setSeqrep(null);
1733 ap.av.getAlignment().setSeqrep(sequence);
1739 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1741 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1742 BitSet inserts = new BitSet();
1744 boolean markedPopup = false;
1745 // mark inserts in current selection
1746 if (ap.av.getSelectionGroup() != null)
1748 // mark just the columns in the selection group to be hidden
1749 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1750 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1752 // now clear columns without gaps
1753 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1759 inserts.and(sq.getInsertionsAsBits());
1761 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1762 ap.av.getSelectionGroup().getEndRes());
1765 // now mark for sequence under popup if we haven't already done it
1766 else if (!markedPopup && sequence != null)
1768 inserts.or(sequence.getInsertionsAsBits());
1770 // and set hidden columns accordingly
1771 hidden.hideColumns(inserts);
1776 protected void sequenceSelectionDetails_actionPerformed()
1778 createSequenceDetailsReport(ap.av.getSequenceSelection());
1781 public void createSequenceDetailsReport(SequenceI[] sequences)
1783 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1784 StringBuilder contents = new StringBuilder(128);
1785 for (SequenceI seq : sequences)
1787 contents.append("<p><h2>" + MessageManager.formatMessage(
1788 "label.create_sequence_details_report_annotation_for",
1790 { seq.getDisplayId(true) }) + "</h2></p><p>");
1791 new SequenceAnnotationReport(false).createSequenceAnnotationReport(
1792 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1793 contents.append("</p>");
1795 cap.setText("<html>" + contents.toString() + "</html>");
1797 Desktop.addInternalFrame(cap,
1798 MessageManager.formatMessage("label.sequence_details_for",
1799 (sequences.length == 1 ? new Object[]
1800 { sequences[0].getDisplayId(true) }
1803 .getString("label.selection") })),
1808 protected void showNonconserved_actionPerformed()
1810 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1815 * call to refresh view after settings change
1819 ap.updateAnnotation();
1820 // removed paintAlignment(true) here:
1821 // updateAnnotation calls paintAlignment already, so don't need to call
1824 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1828 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1829 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1839 public void abovePIDColour_actionPerformed(boolean selected)
1841 SequenceGroup sg = getGroup();
1849 sg.cs.setConsensus(AAFrequency.calculate(
1850 sg.getSequences(ap.av.getHiddenRepSequences()),
1851 sg.getStartRes(), sg.getEndRes() + 1));
1853 int threshold = SliderPanel.setPIDSliderSource(ap,
1854 sg.getGroupColourScheme(), getGroup().getName());
1856 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1858 SliderPanel.showPIDSlider();
1861 // remove PIDColouring
1863 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1864 SliderPanel.hidePIDSlider();
1866 modifyPID.setEnabled(selected);
1872 * Open a panel where the user can choose which types of sequence annotation
1877 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1879 // todo correct way to guard against opening a duplicate panel?
1880 new AnnotationChooser(ap);
1889 public void conservationMenuItem_actionPerformed(boolean selected)
1891 SequenceGroup sg = getGroup();
1899 // JBPNote: Conservation name shouldn't be i18n translated
1900 Conservation c = new Conservation("Group",
1901 sg.getSequences(ap.av.getHiddenRepSequences()),
1902 sg.getStartRes(), sg.getEndRes() + 1);
1905 c.verdict(false, ap.av.getConsPercGaps());
1906 sg.cs.setConservation(c);
1908 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1910 SliderPanel.showConservationSlider();
1913 // remove ConservationColouring
1915 sg.cs.setConservation(null);
1916 SliderPanel.hideConservationSlider();
1918 modifyConservation.setEnabled(selected);
1929 protected void groupName_actionPerformed()
1932 SequenceGroup sg = getGroup();
1933 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1934 sg.getDescription(),
1935 " " + MessageManager.getString("label.group_name") + " ",
1936 MessageManager.getString("label.group_description") + " ",
1937 MessageManager.getString("label.edit_group_name_description"),
1945 sg.setName(dialog.getName());
1946 sg.setDescription(dialog.getDescription());
1951 * Get selection group - adding it to the alignment if necessary.
1953 * @return sequence group to operate on
1955 SequenceGroup getGroup()
1957 SequenceGroup sg = ap.av.getSelectionGroup();
1958 // this method won't add a new group if it already exists
1961 ap.av.getAlignment().addGroup(sg);
1968 * Shows a dialog where the sequence name and description may be edited. If a
1969 * name containing spaces is entered, these are converted to underscores, with a
1972 void sequenceName_actionPerformed()
1974 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1975 sequence.getDescription(),
1976 " " + MessageManager.getString("label.sequence_name")
1978 MessageManager.getString("label.sequence_description") + " ",
1979 MessageManager.getString(
1980 "label.edit_sequence_name_description"),
1988 String name = dialog.getName();
1991 if (name.indexOf(" ") > -1)
1993 JvOptionPane.showMessageDialog(ap,
1995 .getString("label.spaces_converted_to_backslashes"),
1997 .getString("label.no_spaces_allowed_sequence_name"),
1998 JvOptionPane.WARNING_MESSAGE);
1999 name = name.replace(' ', '_');
2002 sequence.setName(name);
2003 ap.paintAlignment(false, false);
2006 sequence.setDescription(dialog.getDescription());
2008 ap.av.firePropertyChange("alignment", null,
2009 ap.av.getAlignment().getSequences());
2019 void unGroupMenuItem_actionPerformed()
2021 SequenceGroup sg = ap.av.getSelectionGroup();
2022 ap.av.getAlignment().deleteGroup(sg);
2023 ap.av.setSelectionGroup(null);
2027 void createGroupMenuItem_actionPerformed()
2029 getGroup(); // implicitly creates group - note - should apply defaults / use
2030 // standard alignment window logic for this
2040 protected void outline_actionPerformed()
2042 SequenceGroup sg = getGroup();
2043 Color col = JColorChooser.showDialog(this,
2044 MessageManager.getString("label.select_outline_colour"),
2049 sg.setOutlineColour(col);
2061 public void showBoxes_actionPerformed()
2063 getGroup().setDisplayBoxes(showBoxes.isSelected());
2073 public void showText_actionPerformed()
2075 getGroup().setDisplayText(showText.isSelected());
2085 public void showColourText_actionPerformed()
2087 getGroup().setColourText(showColourText.isSelected());
2091 void hideSequences(boolean representGroup)
2093 ap.av.hideSequences(sequence, representGroup);
2096 public void copy_actionPerformed()
2098 ap.alignFrame.copy_actionPerformed(null);
2101 public void cut_actionPerformed()
2103 ap.alignFrame.cut_actionPerformed(null);
2106 void changeCase(ActionEvent e)
2108 Object source = e.getSource();
2109 SequenceGroup sg = ap.av.getSelectionGroup();
2113 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2114 sg.getStartRes(), sg.getEndRes() + 1);
2119 if (source == toggle)
2121 description = MessageManager.getString("label.toggle_case");
2122 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2124 else if (source == upperCase)
2126 description = MessageManager.getString("label.to_upper_case");
2127 caseChange = ChangeCaseCommand.TO_UPPER;
2131 description = MessageManager.getString("label.to_lower_case");
2132 caseChange = ChangeCaseCommand.TO_LOWER;
2135 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2136 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2137 startEnd, caseChange);
2139 ap.alignFrame.addHistoryItem(caseCommand);
2141 ap.av.firePropertyChange("alignment", null,
2142 ap.av.getAlignment().getSequences());
2147 public void outputText_actionPerformed(ActionEvent e)
2149 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2150 cap.setForInput(null);
2151 Desktop.addInternalFrame(cap, MessageManager
2152 .formatMessage("label.alignment_output_command", new Object[]
2153 { e.getActionCommand() }), 600, 500);
2155 String[] omitHidden = null;
2157 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2158 // or we simply trust the user wants
2159 // wysiwig behaviour
2161 FileFormatI fileFormat = FileFormats.getInstance()
2162 .forName(e.getActionCommand());
2164 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2167 public void sequenceFeature_actionPerformed()
2169 SequenceGroup sg = ap.av.getSelectionGroup();
2175 List<SequenceI> seqs = new ArrayList<>();
2176 List<SequenceFeature> features = new ArrayList<>();
2179 * assemble dataset sequences, and template new sequence features,
2180 * for the amend features dialog
2182 int gSize = sg.getSize();
2183 for (int i = 0; i < gSize; i++)
2185 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2186 int end = sg.findEndRes(sg.getSequenceAt(i));
2189 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2190 features.add(new SequenceFeature(null, null, start, end, null));
2195 * an entirely gapped region will generate empty lists of sequence / features
2197 if (!seqs.isEmpty())
2199 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2200 .amendFeatures(seqs, features, true, ap))
2202 ap.alignFrame.setShowSeqFeatures(true);
2203 ap.av.setSearchResults(null); // clear highlighting
2204 ap.repaint(); // draw new/amended features
2209 public void textColour_actionPerformed()
2211 SequenceGroup sg = getGroup();
2214 new TextColourChooser().chooseColour(ap, sg);
2218 public void editSequence_actionPerformed(ActionEvent actionEvent)
2220 SequenceGroup sg = ap.av.getSelectionGroup();
2222 SequenceI seq = sequence;
2227 seq = sg.getSequenceAt(0);
2230 EditNameDialog dialog = new EditNameDialog(
2231 seq.getSequenceAsString(sg.getStartRes(),
2232 sg.getEndRes() + 1),
2233 null, MessageManager.getString("label.edit_sequence"), null,
2234 MessageManager.getString("label.edit_sequence"),
2239 EditCommand editCommand = new EditCommand(
2240 MessageManager.getString("label.edit_sequences"),
2242 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2243 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2244 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2246 ap.alignFrame.addHistoryItem(editCommand);
2248 ap.av.firePropertyChange("alignment", null,
2249 ap.av.getAlignment().getSequences());
2255 * Action on user selecting an item from the colour menu (that does not have
2256 * its bespoke action handler)
2261 public void changeColour_actionPerformed(String colourSchemeName)
2263 SequenceGroup sg = getGroup();
2265 * switch to the chosen colour scheme (or null for None)
2267 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2268 .getColourScheme(colourSchemeName, ap.av, sg,
2269 ap.av.getHiddenRepSequences());
2270 sg.setColourScheme(colourScheme);
2271 if (colourScheme instanceof Blosum62ColourScheme
2272 || colourScheme instanceof PIDColourScheme)
2274 sg.cs.setConsensus(AAFrequency.calculate(
2275 sg.getSequences(ap.av.getHiddenRepSequences()),
2276 sg.getStartRes(), sg.getEndRes() + 1));