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 jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.gui.ColourMenuHelper.ColourChangeListener;
41 import jalview.io.FileFormatI;
42 import jalview.io.FileFormats;
43 import jalview.io.FormatAdapter;
44 import jalview.io.SequenceAnnotationReport;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemes;
48 import jalview.schemes.PIDColourScheme;
49 import jalview.schemes.ResidueColourScheme;
50 import jalview.util.GroupUrlLink;
51 import jalview.util.GroupUrlLink.UrlStringTooLongException;
52 import jalview.util.MessageManager;
53 import jalview.util.StringUtils;
54 import jalview.util.UrlLink;
56 import java.awt.Color;
57 import java.awt.event.ActionEvent;
58 import java.awt.event.ActionListener;
59 import java.util.ArrayList;
60 import java.util.Arrays;
61 import java.util.BitSet;
62 import java.util.Collection;
63 import java.util.Collections;
64 import java.util.Hashtable;
65 import java.util.LinkedHashMap;
66 import java.util.List;
68 import java.util.SortedMap;
69 import java.util.TreeMap;
70 import java.util.Vector;
72 import javax.swing.ButtonGroup;
73 import javax.swing.JCheckBoxMenuItem;
74 import javax.swing.JColorChooser;
75 import javax.swing.JMenu;
76 import javax.swing.JMenuItem;
77 import javax.swing.JPopupMenu;
78 import javax.swing.JRadioButtonMenuItem;
84 * @version $Revision: 1.118 $
86 public class PopupMenu extends JPopupMenu implements ColourChangeListener
88 JMenu groupMenu = new JMenu();
90 JMenuItem groupName = new JMenuItem();
92 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
94 protected JMenuItem modifyPID = new JMenuItem();
96 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
98 protected JRadioButtonMenuItem annotationColour;
100 protected JMenuItem modifyConservation = new JMenuItem();
104 JMenu sequenceMenu = new JMenu();
106 JMenuItem sequenceName = new JMenuItem();
108 JMenuItem sequenceDetails = new JMenuItem();
110 JMenuItem sequenceSelDetails = new JMenuItem();
112 JMenuItem makeReferenceSeq = new JMenuItem();
114 JMenuItem chooseAnnotations = new JMenuItem();
118 JMenuItem createGroupMenuItem = new JMenuItem();
120 JMenuItem unGroupMenuItem = new JMenuItem();
122 JMenuItem outline = new JMenuItem();
124 JMenu colourMenu = new JMenu();
126 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
128 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
130 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
132 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
134 JMenu editMenu = new JMenu();
136 JMenuItem cut = new JMenuItem();
138 JMenuItem copy = new JMenuItem();
140 JMenuItem upperCase = new JMenuItem();
142 JMenuItem lowerCase = new JMenuItem();
144 JMenuItem toggle = new JMenuItem();
146 JMenu pdbMenu = new JMenu();
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 sequenceFeature = new JMenuItem();
166 JMenuItem textColour = new JMenuItem();
168 JMenu jMenu1 = new JMenu();
170 JMenuItem pdbStructureDialog = new JMenuItem();
172 JMenu rnaStructureMenu = new JMenu();
174 JMenuItem editSequence = new JMenuItem();
176 JMenu groupLinksMenu;
178 JMenuItem hideInsertions = new JMenuItem();
181 * Creates a new PopupMenu object.
186 * non-positional features (for seq not null), or positional features
187 * at residue (for seq equal to null)
189 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
190 List<SequenceFeature> features)
192 this(ap, seq, features, null);
200 * the sequence under the cursor if in the Id panel, null if in the
203 * non-positional features if in the Id panel, features at the
204 * clicked residue if in the sequence panel
207 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
208 List<SequenceFeature> features, List<String> groupLinks)
210 // /////////////////////////////////////////////////////////
211 // If this is activated from the sequence panel, the user may want to
212 // edit or annotate a particular residue. Therefore display the residue menu
214 // If from the IDPanel, we must display the sequence menu
215 // ////////////////////////////////////////////////////////
216 this.ap = alignPanel;
219 for (String ff : FileFormats.getInstance().getWritableFormats(true))
221 JMenuItem item = new JMenuItem(ff);
223 item.addActionListener(new ActionListener()
226 public void actionPerformed(ActionEvent e)
228 outputText_actionPerformed(e);
232 outputMenu.add(item);
236 * Build menus for annotation types that may be shown or hidden, and for
237 * 'reference annotations' that may be added to the alignment. First for the
238 * currently selected sequence (if there is one):
240 final List<SequenceI> selectedSequence = (seq == null
241 ? Collections.<SequenceI> emptyList()
242 : Arrays.asList(seq));
243 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
244 seqHideAnnotationsMenu, selectedSequence);
245 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
249 * And repeat for the current selection group (if there is one):
251 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
252 ? Collections.<SequenceI> emptyList()
253 : alignPanel.av.getSelectionGroup().getSequences());
254 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
255 groupHideAnnotationsMenu, selectedGroup);
256 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
262 } catch (Exception e)
270 sequenceMenu.setText(sequence.getName());
271 if (seq == alignPanel.av.getAlignment().getSeqrep())
273 makeReferenceSeq.setText(
274 MessageManager.getString("action.unmark_as_reference"));
278 makeReferenceSeq.setText(
279 MessageManager.getString("action.set_as_reference"));
282 if (!alignPanel.av.getAlignment().isNucleotide())
284 remove(rnaStructureMenu);
288 int origCount = rnaStructureMenu.getItemCount();
290 * add menu items to 2D-render any alignment or sequence secondary
291 * structure annotation
293 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
294 .getAlignmentAnnotation();
297 for (final AlignmentAnnotation aa : aas)
299 if (aa.isValidStruc() && aa.sequenceRef == null)
302 * valid alignment RNA secondary structure annotation
304 menuItem = new JMenuItem();
305 menuItem.setText(MessageManager.formatMessage(
306 "label.2d_rna_structure_line", new Object[]
308 menuItem.addActionListener(new ActionListener()
311 public void actionPerformed(ActionEvent e)
313 new AppVarna(seq, aa, alignPanel);
316 rnaStructureMenu.add(menuItem);
321 if (seq.getAnnotation() != null)
323 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
324 for (final AlignmentAnnotation aa : seqAnns)
326 if (aa.isValidStruc())
329 * valid sequence RNA secondary structure annotation
331 // TODO: make rnastrucF a bit more nice
332 menuItem = new JMenuItem();
333 menuItem.setText(MessageManager.formatMessage(
334 "label.2d_rna_sequence_name", new Object[]
336 menuItem.addActionListener(new ActionListener()
339 public void actionPerformed(ActionEvent e)
341 // TODO: VARNA does'nt print gaps in the sequence
342 new AppVarna(seq, aa, alignPanel);
345 rnaStructureMenu.add(menuItem);
349 if (rnaStructureMenu.getItemCount() == origCount)
351 remove(rnaStructureMenu);
355 menuItem = new JMenuItem(
356 MessageManager.getString("action.hide_sequences"));
357 menuItem.addActionListener(new ActionListener()
360 public void actionPerformed(ActionEvent e)
362 hideSequences(false);
367 if (alignPanel.av.getSelectionGroup() != null
368 && alignPanel.av.getSelectionGroup().getSize() > 1)
370 menuItem = new JMenuItem(MessageManager
371 .formatMessage("label.represent_group_with", new Object[]
373 menuItem.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent e)
381 sequenceMenu.add(menuItem);
384 if (alignPanel.av.hasHiddenRows())
386 final int index = alignPanel.av.getAlignment().findIndex(seq);
388 if (alignPanel.av.adjustForHiddenSeqs(index)
389 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
391 menuItem = new JMenuItem(
392 MessageManager.getString("action.reveal_sequences"));
393 menuItem.addActionListener(new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 alignPanel.av.showSequence(index);
399 if (alignPanel.overviewPanel != null)
401 alignPanel.overviewPanel.updateOverviewImage();
409 // for the case when no sequences are even visible
410 if (alignPanel.av.hasHiddenRows())
413 menuItem = new JMenuItem(
414 MessageManager.getString("action.reveal_all"));
415 menuItem.addActionListener(new ActionListener()
418 public void actionPerformed(ActionEvent e)
420 alignPanel.av.showAllHiddenSeqs();
421 if (alignPanel.overviewPanel != null)
423 alignPanel.overviewPanel.updateOverviewImage();
432 SequenceGroup sg = alignPanel.av.getSelectionGroup();
433 boolean isDefinedGroup = (sg != null)
434 ? alignPanel.av.getAlignment().getGroups().contains(sg)
437 if (sg != null && sg.getSize() > 0)
439 groupName.setText(MessageManager
440 .getString("label.edit_name_and_description_current_group"));
442 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
444 conservationMenuItem.setEnabled(!sg.isNucleotide());
448 if (sg.cs.conservationApplied())
450 conservationMenuItem.setSelected(true);
452 if (sg.cs.getThreshold() > 0)
454 abovePIDColour.setSelected(true);
457 modifyConservation.setEnabled(conservationMenuItem.isSelected());
458 modifyPID.setEnabled(abovePIDColour.isSelected());
459 displayNonconserved.setSelected(sg.getShowNonconserved());
460 showText.setSelected(sg.getDisplayText());
461 showColourText.setSelected(sg.getColourText());
462 showBoxes.setSelected(sg.getDisplayBoxes());
463 // add any groupURLs to the groupURL submenu and make it visible
464 if (groupLinks != null && groupLinks.size() > 0)
466 buildGroupURLMenu(sg, groupLinks);
468 // Add a 'show all structures' for the current selection
469 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
471 SequenceI sqass = null;
472 for (SequenceI sq : alignPanel.av.getSequenceSelection())
474 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
475 if (pes != null && pes.size() > 0)
477 reppdb.put(pes.get(0).getId(), pes.get(0));
478 for (PDBEntry pe : pes)
480 pdbe.put(pe.getId(), pe);
490 final PDBEntry[] pe = pdbe.values()
491 .toArray(new PDBEntry[pdbe.size()]),
492 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
493 final JMenuItem gpdbview, rpdbview;
498 groupMenu.setVisible(false);
499 editMenu.setVisible(false);
504 createGroupMenuItem.setVisible(true);
505 unGroupMenuItem.setVisible(false);
506 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
510 createGroupMenuItem.setVisible(false);
511 unGroupMenuItem.setVisible(true);
512 jMenu1.setText(MessageManager.getString("action.edit_group"));
517 sequenceMenu.setVisible(false);
518 pdbStructureDialog.setVisible(false);
519 rnaStructureMenu.setVisible(false);
522 addLinks(seq, features);
526 addFeatureDetails(features);
531 * Add a link to show feature details for each sequence feature
535 protected void addFeatureDetails(List<SequenceFeature> features)
537 if (features == null || features.isEmpty())
541 JMenu details = new JMenu(
542 MessageManager.getString("label.feature_details"));
545 for (final SequenceFeature sf : features)
547 int start = sf.getBegin();
548 int end = sf.getEnd();
552 desc = String.format("%s %d", sf.getType(), start);
556 desc = String.format("%s %d-%d", sf.getType(), start, end);
558 String tooltip = desc;
559 String description = sf.getDescription();
560 if (description != null)
562 description = StringUtils.stripHtmlTags(description);
563 if (description.length() > 12)
565 desc = desc + " " + description.substring(0, 12) + "..";
569 desc = desc + " " + description;
571 tooltip = tooltip + " " + description;
573 if (sf.getFeatureGroup() != null)
575 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
577 JMenuItem item = new JMenuItem(desc);
578 item.setToolTipText(tooltip);
579 item.addActionListener(new ActionListener()
582 public void actionPerformed(ActionEvent e)
584 showFeatureDetails(sf);
592 * Opens a panel showing a text report of feature dteails
596 protected void showFeatureDetails(SequenceFeature sf)
598 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
599 // it appears Java's CSS does not support border-collaps :-(
600 cap.addStylesheetRule("table { border-collapse: collapse;}");
601 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
602 cap.setText(sf.getDetailsReport());
604 Desktop.addInternalFrame(cap,
605 MessageManager.getString("label.feature_details"), 500, 500);
609 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
610 * When seq is not null, these are links for the sequence id, which may be to
611 * external web sites for the sequence accession, and/or links embedded in
612 * non-positional features. When seq is null, only links embedded in the
613 * provided features are added.
618 void addLinks(final SequenceI seq, List<SequenceFeature> features)
620 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
622 List<String> nlinks = null;
625 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
629 nlinks = new ArrayList<>();
632 if (features != null)
634 for (SequenceFeature sf : features)
636 if (sf.links != null)
638 for (String link : sf.links)
646 Map<String, List<String>> linkset = new LinkedHashMap<>();
648 for (String link : nlinks)
650 UrlLink urlLink = null;
653 urlLink = new UrlLink(link);
654 } catch (Exception foo)
656 Cache.log.error("Exception for URLLink '" + link + "'", foo);
660 if (!urlLink.isValid())
662 Cache.log.error(urlLink.getInvalidMessage());
666 urlLink.createLinksFromSeq(seq, linkset);
669 addshowLinks(linkMenu, linkset.values());
671 // only add link menu if it has entries
672 if (linkMenu.getItemCount() > 0)
674 if (sequence != null)
676 sequenceMenu.add(linkMenu);
686 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
687 * "All" is added first, followed by a separator. Then add any annotation
688 * types associated with the current selection. Separate menus are built for
689 * the selected sequence group (if any), and the selected sequence.
691 * Some annotation rows are always rendered together - these can be identified
692 * by a common graphGroup property > -1. Only one of each group will be marked
693 * as visible (to avoid duplication of the display). For such groups we add a
694 * composite type name, e.g.
696 * IUPredWS (Long), IUPredWS (Short)
700 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
701 List<SequenceI> forSequences)
703 showMenu.removeAll();
704 hideMenu.removeAll();
706 final List<String> all = Arrays
708 { MessageManager.getString("label.all") });
709 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
711 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
713 showMenu.addSeparator();
714 hideMenu.addSeparator();
716 final AlignmentAnnotation[] annotations = ap.getAlignment()
717 .getAlignmentAnnotation();
720 * Find shown/hidden annotations types, distinguished by source (calcId),
721 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
722 * the insertion order, which is the order of the annotations on the
725 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
726 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
727 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
728 AlignmentAnnotationUtils.asList(annotations), forSequences);
730 for (String calcId : hiddenTypes.keySet())
732 for (List<String> type : hiddenTypes.get(calcId))
734 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
738 // grey out 'show annotations' if none are hidden
739 showMenu.setEnabled(!hiddenTypes.isEmpty());
741 for (String calcId : shownTypes.keySet())
743 for (List<String> type : shownTypes.get(calcId))
745 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
749 // grey out 'hide annotations' if none are shown
750 hideMenu.setEnabled(!shownTypes.isEmpty());
754 * Returns a list of sequences - either the current selection group (if there
755 * is one), else the specified single sequence.
760 protected List<SequenceI> getSequenceScope(SequenceI seq)
762 List<SequenceI> forSequences = null;
763 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
764 if (selectionGroup != null && selectionGroup.getSize() > 0)
766 forSequences = selectionGroup.getSequences();
770 forSequences = seq == null ? Collections.<SequenceI> emptyList()
771 : Arrays.asList(seq);
777 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
780 * @param showOrHideMenu
782 * @param forSequences
783 * the sequences whose annotations may be shown or hidden
788 * if true this is a special label meaning 'All'
789 * @param actionIsShow
790 * if true, the select menu item action is to show the annotation
793 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
794 final List<SequenceI> forSequences, String calcId,
795 final List<String> types, final boolean allTypes,
796 final boolean actionIsShow)
798 String label = types.toString(); // [a, b, c]
799 label = label.substring(1, label.length() - 1); // a, b, c
800 final JMenuItem item = new JMenuItem(label);
801 item.setToolTipText(calcId);
802 item.addActionListener(new ActionListener()
805 public void actionPerformed(ActionEvent e)
807 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
808 types, forSequences, allTypes, actionIsShow);
812 showOrHideMenu.add(item);
815 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
818 // TODO: usability: thread off the generation of group url content so root
820 // sequence only URLs
821 // ID/regex match URLs
822 groupLinksMenu = new JMenu(
823 MessageManager.getString("action.group_link"));
824 // three types of url that might be created.
825 JMenu[] linkMenus = new JMenu[] { null,
826 new JMenu(MessageManager.getString("action.ids")),
827 new JMenu(MessageManager.getString("action.sequences")),
828 new JMenu(MessageManager.getString("action.ids_sequences")) };
830 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
831 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
832 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
833 for (int sq = 0; sq < seqs.length; sq++)
836 int start = seqs[sq].findPosition(sg.getStartRes()),
837 end = seqs[sq].findPosition(sg.getEndRes());
838 // just collect ids from dataset sequence
839 // TODO: check if IDs collected from selecton group intersects with the
840 // current selection, too
841 SequenceI sqi = seqs[sq];
842 while (sqi.getDatasetSequence() != null)
844 sqi = sqi.getDatasetSequence();
846 DBRefEntry[] dbr = sqi.getDBRefs();
847 if (dbr != null && dbr.length > 0)
849 for (int d = 0; d < dbr.length; d++)
851 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
852 Object[] sarray = commonDbrefs.get(src);
855 sarray = new Object[2];
856 sarray[0] = new int[] { 0 };
857 sarray[1] = new String[seqs.length];
859 commonDbrefs.put(src, sarray);
862 if (((String[]) sarray[1])[sq] == null)
864 if (!dbr[d].hasMap() || (dbr[d].getMap()
865 .locateMappedRange(start, end) != null))
867 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
868 ((int[]) sarray[0])[0]++;
874 // now create group links for all distinct ID/sequence sets.
875 boolean addMenu = false; // indicates if there are any group links to give
877 for (String link : groupLinks)
879 GroupUrlLink urlLink = null;
882 urlLink = new GroupUrlLink(link);
883 } catch (Exception foo)
885 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
889 if (!urlLink.isValid())
891 Cache.log.error(urlLink.getInvalidMessage());
894 final String label = urlLink.getLabel();
895 boolean usingNames = false;
896 // Now see which parts of the group apply for this URL
897 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
898 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
899 String[] seqstr, ids; // input to makeUrl
902 int numinput = ((int[]) idset[0])[0];
903 String[] allids = ((String[]) idset[1]);
904 seqstr = new String[numinput];
905 ids = new String[numinput];
906 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
908 if (allids[sq] != null)
910 ids[idcount] = allids[sq];
911 seqstr[idcount++] = idandseqs[1][sq];
917 // just use the id/seq set
918 seqstr = idandseqs[1];
922 // and try and make the groupURL!
924 Object[] urlset = null;
927 urlset = urlLink.makeUrlStubs(ids, seqstr,
928 "FromJalview" + System.currentTimeMillis(), false);
929 } catch (UrlStringTooLongException e)
934 int type = urlLink.getGroupURLType() & 3;
935 // first two bits ofurlLink type bitfield are sequenceids and sequences
936 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
937 addshowLink(linkMenus[type],
938 label + (((type & 1) == 1)
939 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
947 groupLinksMenu = new JMenu(
948 MessageManager.getString("action.group_link"));
949 for (int m = 0; m < linkMenus.length; m++)
951 if (linkMenus[m] != null
952 && linkMenus[m].getMenuComponentCount() > 0)
954 groupLinksMenu.add(linkMenus[m]);
958 groupMenu.add(groupLinksMenu);
962 private void addshowLinks(JMenu linkMenu,
963 Collection<List<String>> linkset)
965 for (List<String> linkstrset : linkset)
967 // split linkstr into label and url
968 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
973 * add a show URL menu item to the given linkMenu
977 * - menu label string
981 private void addshowLink(JMenu linkMenu, String label, final String url)
983 JMenuItem item = new JMenuItem(label);
984 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
987 item.addActionListener(new ActionListener()
990 public void actionPerformed(ActionEvent e)
992 new Thread(new Runnable()
1009 * add a late bound groupURL item to the given linkMenu
1013 * - menu label string
1014 * @param urlgenerator
1015 * GroupURLLink used to generate URL
1017 * Object array returned from the makeUrlStubs function.
1019 private void addshowLink(JMenu linkMenu, String label,
1020 final GroupUrlLink urlgenerator, final Object[] urlstub)
1022 JMenuItem item = new JMenuItem(label);
1023 item.setToolTipText(MessageManager
1024 .formatMessage("label.open_url_seqs_param", new Object[]
1025 { urlgenerator.getUrl_prefix(),
1026 urlgenerator.getNumberInvolved(urlstub) }));
1027 // TODO: put in info about what is being sent.
1028 item.addActionListener(new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 new Thread(new Runnable()
1041 showLink(urlgenerator.constructFrom(urlstub));
1042 } catch (UrlStringTooLongException e2)
1060 private void jbInit() throws Exception
1062 groupMenu.setText(MessageManager.getString("label.selection"));
1063 groupName.setText(MessageManager.getString("label.name"));
1064 groupName.addActionListener(new ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 groupName_actionPerformed();
1072 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1073 sequenceName.setText(
1074 MessageManager.getString("label.edit_name_description"));
1075 sequenceName.addActionListener(new ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 sequenceName_actionPerformed();
1084 .setText(MessageManager.getString("action.choose_annotations"));
1085 chooseAnnotations.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 chooseAnnotations_actionPerformed(e);
1094 .setText(MessageManager.getString("label.sequence_details"));
1095 sequenceDetails.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 sequenceDetails_actionPerformed();
1104 .setText(MessageManager.getString("label.sequence_details"));
1105 sequenceSelDetails.addActionListener(new ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 sequenceSelectionDetails_actionPerformed();
1115 .setText(MessageManager.getString("action.remove_group"));
1116 unGroupMenuItem.addActionListener(new ActionListener()
1119 public void actionPerformed(ActionEvent e)
1121 unGroupMenuItem_actionPerformed();
1125 .setText(MessageManager.getString("action.create_group"));
1126 createGroupMenuItem.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1131 createGroupMenuItem_actionPerformed();
1135 outline.setText(MessageManager.getString("action.border_colour"));
1136 outline.addActionListener(new ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 outline_actionPerformed();
1144 showBoxes.setText(MessageManager.getString("action.boxes"));
1145 showBoxes.setState(true);
1146 showBoxes.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent e)
1151 showBoxes_actionPerformed();
1154 showText.setText(MessageManager.getString("action.text"));
1155 showText.setState(true);
1156 showText.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 showText_actionPerformed();
1164 showColourText.setText(MessageManager.getString("label.colour_text"));
1165 showColourText.addActionListener(new ActionListener()
1168 public void actionPerformed(ActionEvent e)
1170 showColourText_actionPerformed();
1174 .setText(MessageManager.getString("label.show_non_conserved"));
1175 displayNonconserved.setState(true);
1176 displayNonconserved.addActionListener(new ActionListener()
1179 public void actionPerformed(ActionEvent e)
1181 showNonconserved_actionPerformed();
1184 editMenu.setText(MessageManager.getString("action.edit"));
1185 cut.setText(MessageManager.getString("action.cut"));
1186 cut.addActionListener(new ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 cut_actionPerformed();
1194 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1195 upperCase.addActionListener(new ActionListener()
1198 public void actionPerformed(ActionEvent e)
1203 copy.setText(MessageManager.getString("action.copy"));
1204 copy.addActionListener(new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 copy_actionPerformed();
1212 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1213 lowerCase.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1221 toggle.setText(MessageManager.getString("label.toggle_case"));
1222 toggle.addActionListener(new ActionListener()
1225 public void actionPerformed(ActionEvent e)
1231 MessageManager.getString("label.out_to_textbox") + "...");
1232 seqShowAnnotationsMenu
1233 .setText(MessageManager.getString("label.show_annotations"));
1234 seqHideAnnotationsMenu
1235 .setText(MessageManager.getString("label.hide_annotations"));
1236 groupShowAnnotationsMenu
1237 .setText(MessageManager.getString("label.show_annotations"));
1238 groupHideAnnotationsMenu
1239 .setText(MessageManager.getString("label.hide_annotations"));
1240 sequenceFeature.setText(
1241 MessageManager.getString("label.create_sequence_feature"));
1242 sequenceFeature.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1247 sequenceFeature_actionPerformed();
1250 jMenu1.setText(MessageManager.getString("label.group"));
1251 pdbStructureDialog.setText(
1252 MessageManager.getString("label.show_pdbstruct_dialog"));
1253 pdbStructureDialog.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent actionEvent)
1258 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1259 if (ap.av.getSelectionGroup() != null)
1261 selectedSeqs = ap.av.getSequenceSelection();
1263 new StructureChooser(selectedSeqs, sequence, ap);
1268 .setText(MessageManager.getString("label.view_rna_structure"));
1270 // colStructureMenu.setText("Colour By Structure");
1271 editSequence.setText(
1272 MessageManager.getString("label.edit_sequence") + "...");
1273 editSequence.addActionListener(new ActionListener()
1276 public void actionPerformed(ActionEvent actionEvent)
1278 editSequence_actionPerformed(actionEvent);
1281 makeReferenceSeq.setText(
1282 MessageManager.getString("label.mark_as_representative"));
1283 makeReferenceSeq.addActionListener(new ActionListener()
1287 public void actionPerformed(ActionEvent actionEvent)
1289 makeReferenceSeq_actionPerformed(actionEvent);
1294 .setText(MessageManager.getString("label.hide_insertions"));
1295 hideInsertions.addActionListener(new ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 hideInsertions_actionPerformed(e);
1305 groupMenu.add(sequenceSelDetails);
1308 add(rnaStructureMenu);
1309 add(pdbStructureDialog);
1310 if (sequence != null)
1312 add(hideInsertions);
1314 // annotations configuration panel suppressed for now
1315 // groupMenu.add(chooseAnnotations);
1318 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1319 * (if a selection group is in force).
1321 sequenceMenu.add(seqShowAnnotationsMenu);
1322 sequenceMenu.add(seqHideAnnotationsMenu);
1323 sequenceMenu.add(seqAddReferenceAnnotations);
1324 groupMenu.add(groupShowAnnotationsMenu);
1325 groupMenu.add(groupHideAnnotationsMenu);
1326 groupMenu.add(groupAddReferenceAnnotations);
1327 groupMenu.add(editMenu);
1328 groupMenu.add(outputMenu);
1329 groupMenu.add(sequenceFeature);
1330 groupMenu.add(createGroupMenuItem);
1331 groupMenu.add(unGroupMenuItem);
1332 groupMenu.add(jMenu1);
1333 sequenceMenu.add(sequenceName);
1334 sequenceMenu.add(sequenceDetails);
1335 sequenceMenu.add(makeReferenceSeq);
1342 editMenu.add(editSequence);
1343 editMenu.add(upperCase);
1344 editMenu.add(lowerCase);
1345 editMenu.add(toggle);
1346 // JBPNote: These shouldn't be added here - should appear in a generic
1347 // 'apply web service to this sequence menu'
1348 // pdbMenu.add(RNAFold);
1349 // pdbMenu.add(ContraFold);
1350 jMenu1.add(groupName);
1351 jMenu1.add(colourMenu);
1352 jMenu1.add(showBoxes);
1353 jMenu1.add(showText);
1354 jMenu1.add(showColourText);
1355 jMenu1.add(outline);
1356 jMenu1.add(displayNonconserved);
1360 * Constructs the entries for the colour menu
1362 protected void initColourMenu()
1364 colourMenu.setText(MessageManager.getString("label.group_colour"));
1365 textColour.setText(MessageManager.getString("label.text_colour"));
1366 textColour.addActionListener(new ActionListener()
1369 public void actionPerformed(ActionEvent e)
1371 textColour_actionPerformed();
1375 abovePIDColour.setText(
1376 MessageManager.getString("label.above_identity_threshold"));
1377 abovePIDColour.addActionListener(new ActionListener()
1380 public void actionPerformed(ActionEvent e)
1382 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1387 MessageManager.getString("label.modify_identity_threshold"));
1388 modifyPID.addActionListener(new ActionListener()
1391 public void actionPerformed(ActionEvent e)
1393 modifyPID_actionPerformed();
1397 conservationMenuItem
1398 .setText(MessageManager.getString("action.by_conservation"));
1399 conservationMenuItem.addActionListener(new ActionListener()
1402 public void actionPerformed(ActionEvent e)
1404 conservationMenuItem_actionPerformed(
1405 conservationMenuItem.isSelected());
1409 annotationColour = new JRadioButtonMenuItem(
1410 MessageManager.getString("action.by_annotation"));
1411 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1412 annotationColour.setEnabled(false);
1413 annotationColour.setToolTipText(
1414 MessageManager.getString("label.by_annotation_tooltip"));
1416 modifyConservation.setText(MessageManager
1417 .getString("label.modify_conservation_threshold"));
1418 modifyConservation.addActionListener(new ActionListener()
1421 public void actionPerformed(ActionEvent e)
1423 modifyConservation_actionPerformed();
1429 * Builds the group colour sub-menu, including any user-defined colours which
1430 * were loaded at startup or during the Jalview session
1432 protected void buildColourMenu()
1434 SequenceGroup sg = ap.av.getSelectionGroup();
1438 * popup menu with no sequence group scope
1442 colourMenu.removeAll();
1443 colourMenu.add(textColour);
1444 colourMenu.addSeparator();
1446 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1448 bg.add(annotationColour);
1449 colourMenu.add(annotationColour);
1451 colourMenu.addSeparator();
1452 colourMenu.add(conservationMenuItem);
1453 colourMenu.add(modifyConservation);
1454 colourMenu.add(abovePIDColour);
1455 colourMenu.add(modifyPID);
1458 protected void modifyConservation_actionPerformed()
1460 SequenceGroup sg = getGroup();
1463 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1464 SliderPanel.showConservationSlider();
1468 protected void modifyPID_actionPerformed()
1470 SequenceGroup sg = getGroup();
1473 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1475 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1476 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1477 SliderPanel.showPIDSlider();
1482 * Check for any annotations on the underlying dataset sequences (for the
1483 * current selection group) which are not 'on the alignment'.If any are found,
1484 * enable the option to add them to the alignment. The criteria for 'on the
1485 * alignment' is finding an alignment annotation on the alignment, matched on
1486 * calcId, label and sequenceRef.
1488 * A tooltip is also constructed that displays the source (calcId) and type
1489 * (label) of the annotations that can be added.
1492 * @param forSequences
1494 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1495 List<SequenceI> forSequences)
1497 menuItem.setEnabled(false);
1500 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1501 * Using TreeMap means calcIds are shown in alphabetical order.
1503 SortedMap<String, String> tipEntries = new TreeMap<>();
1504 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1505 AlignmentI al = this.ap.av.getAlignment();
1506 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1508 if (!candidates.isEmpty())
1510 StringBuilder tooltip = new StringBuilder(64);
1511 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1514 * Found annotations that could be added. Enable the menu item, and
1515 * configure its tooltip and action.
1517 menuItem.setEnabled(true);
1518 for (String calcId : tipEntries.keySet())
1520 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1522 String tooltipText = JvSwingUtils.wrapTooltip(true,
1523 tooltip.toString());
1524 menuItem.setToolTipText(tooltipText);
1526 menuItem.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 addReferenceAnnotations_actionPerformed(candidates);
1538 * Add annotations to the sequences and to the alignment.
1541 * a map whose keys are sequences on the alignment, and values a list
1542 * of annotations to add to each sequence
1544 protected void addReferenceAnnotations_actionPerformed(
1545 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1547 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1548 final AlignmentI alignment = this.ap.getAlignment();
1549 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1554 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1556 if (!ap.av.getAlignment().hasSeqrep())
1558 // initialise the display flags so the user sees something happen
1559 ap.av.setDisplayReferenceSeq(true);
1560 ap.av.setColourByReferenceSeq(true);
1561 ap.av.getAlignment().setSeqrep(sequence);
1565 if (ap.av.getAlignment().getSeqrep() == sequence)
1567 ap.av.getAlignment().setSeqrep(null);
1571 ap.av.getAlignment().setSeqrep(sequence);
1577 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1579 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1580 BitSet inserts = new BitSet();
1582 boolean markedPopup = false;
1583 // mark inserts in current selection
1584 if (ap.av.getSelectionGroup() != null)
1586 // mark just the columns in the selection group to be hidden
1587 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1588 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1590 // now clear columns without gaps
1591 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1597 inserts.and(sq.getInsertionsAsBits());
1599 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1600 ap.av.getSelectionGroup().getEndRes());
1603 // now mark for sequence under popup if we haven't already done it
1604 else if (!markedPopup && sequence != null)
1606 inserts.or(sequence.getInsertionsAsBits());
1608 // and set hidden columns accordingly
1609 hidden.hideColumns(inserts);
1614 protected void sequenceSelectionDetails_actionPerformed()
1616 createSequenceDetailsReport(ap.av.getSequenceSelection());
1619 protected void sequenceDetails_actionPerformed()
1621 createSequenceDetailsReport(new SequenceI[] { sequence });
1624 public void createSequenceDetailsReport(SequenceI[] sequences)
1626 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1627 StringBuilder contents = new StringBuilder(128);
1628 for (SequenceI seq : sequences)
1630 contents.append("<p><h2>" + MessageManager.formatMessage(
1631 "label.create_sequence_details_report_annotation_for",
1633 { seq.getDisplayId(true) }) + "</h2></p><p>");
1634 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1635 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1636 contents.append("</p>");
1638 cap.setText("<html>" + contents.toString() + "</html>");
1640 Desktop.addInternalFrame(cap,
1641 MessageManager.formatMessage("label.sequence_details_for",
1642 (sequences.length == 1 ? new Object[]
1643 { sequences[0].getDisplayId(true) }
1646 .getString("label.selection") })),
1651 protected void showNonconserved_actionPerformed()
1653 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1658 * call to refresh view after settings change
1662 ap.updateAnnotation();
1663 // removed paintAlignment(true) here:
1664 // updateAnnotation calls paintAlignment already, so don't need to call
1667 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1671 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1672 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1682 public void abovePIDColour_actionPerformed(boolean selected)
1684 SequenceGroup sg = getGroup();
1692 sg.cs.setConsensus(AAFrequency.calculate(
1693 sg.getSequences(ap.av.getHiddenRepSequences()),
1694 sg.getStartRes(), sg.getEndRes() + 1));
1696 int threshold = SliderPanel.setPIDSliderSource(ap,
1697 sg.getGroupColourScheme(), getGroup().getName());
1699 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1701 SliderPanel.showPIDSlider();
1704 // remove PIDColouring
1706 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1707 SliderPanel.hidePIDSlider();
1709 modifyPID.setEnabled(selected);
1715 * Open a panel where the user can choose which types of sequence annotation
1720 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1722 // todo correct way to guard against opening a duplicate panel?
1723 new AnnotationChooser(ap);
1732 public void conservationMenuItem_actionPerformed(boolean selected)
1734 SequenceGroup sg = getGroup();
1742 // JBPNote: Conservation name shouldn't be i18n translated
1743 Conservation c = new Conservation("Group",
1744 sg.getSequences(ap.av.getHiddenRepSequences()),
1745 sg.getStartRes(), sg.getEndRes() + 1);
1748 c.verdict(false, ap.av.getConsPercGaps());
1749 sg.cs.setConservation(c);
1751 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1753 SliderPanel.showConservationSlider();
1756 // remove ConservationColouring
1758 sg.cs.setConservation(null);
1759 SliderPanel.hideConservationSlider();
1761 modifyConservation.setEnabled(selected);
1772 protected void groupName_actionPerformed()
1775 SequenceGroup sg = getGroup();
1776 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1777 sg.getDescription(),
1778 " " + MessageManager.getString("label.group_name") + " ",
1779 MessageManager.getString("label.group_description") + " ",
1780 MessageManager.getString("label.edit_group_name_description"),
1788 sg.setName(dialog.getName());
1789 sg.setDescription(dialog.getDescription());
1794 * Get selection group - adding it to the alignment if necessary.
1796 * @return sequence group to operate on
1798 SequenceGroup getGroup()
1800 SequenceGroup sg = ap.av.getSelectionGroup();
1801 // this method won't add a new group if it already exists
1804 ap.av.getAlignment().addGroup(sg);
1816 void sequenceName_actionPerformed()
1818 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1819 sequence.getDescription(),
1820 " " + MessageManager.getString("label.sequence_name")
1822 MessageManager.getString("label.sequence_description") + " ",
1823 MessageManager.getString(
1824 "label.edit_sequence_name_description"),
1832 if (dialog.getName() != null)
1834 if (dialog.getName().indexOf(" ") > -1)
1836 JvOptionPane.showMessageDialog(ap,
1838 .getString("label.spaces_converted_to_backslashes"),
1840 .getString("label.no_spaces_allowed_sequence_name"),
1841 JvOptionPane.WARNING_MESSAGE);
1844 sequence.setName(dialog.getName().replace(' ', '_'));
1845 ap.paintAlignment(false, false);
1848 sequence.setDescription(dialog.getDescription());
1850 ap.av.firePropertyChange("alignment", null,
1851 ap.av.getAlignment().getSequences());
1861 void unGroupMenuItem_actionPerformed()
1863 SequenceGroup sg = ap.av.getSelectionGroup();
1864 ap.av.getAlignment().deleteGroup(sg);
1865 ap.av.setSelectionGroup(null);
1869 void createGroupMenuItem_actionPerformed()
1871 getGroup(); // implicitly creates group - note - should apply defaults / use
1872 // standard alignment window logic for this
1882 protected void outline_actionPerformed()
1884 SequenceGroup sg = getGroup();
1885 Color col = JColorChooser.showDialog(this,
1886 MessageManager.getString("label.select_outline_colour"),
1891 sg.setOutlineColour(col);
1903 public void showBoxes_actionPerformed()
1905 getGroup().setDisplayBoxes(showBoxes.isSelected());
1915 public void showText_actionPerformed()
1917 getGroup().setDisplayText(showText.isSelected());
1927 public void showColourText_actionPerformed()
1929 getGroup().setColourText(showColourText.isSelected());
1933 public void showLink(String url)
1937 jalview.util.BrowserLauncher.openURL(url);
1938 } catch (Exception ex)
1940 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1941 MessageManager.getString("label.web_browser_not_found_unix"),
1942 MessageManager.getString("label.web_browser_not_found"),
1943 JvOptionPane.WARNING_MESSAGE);
1945 ex.printStackTrace();
1949 void hideSequences(boolean representGroup)
1951 ap.av.hideSequences(sequence, representGroup);
1954 public void copy_actionPerformed()
1956 ap.alignFrame.copy_actionPerformed(null);
1959 public void cut_actionPerformed()
1961 ap.alignFrame.cut_actionPerformed(null);
1964 void changeCase(ActionEvent e)
1966 Object source = e.getSource();
1967 SequenceGroup sg = ap.av.getSelectionGroup();
1971 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1972 sg.getStartRes(), sg.getEndRes() + 1);
1977 if (source == toggle)
1979 description = MessageManager.getString("label.toggle_case");
1980 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1982 else if (source == upperCase)
1984 description = MessageManager.getString("label.to_upper_case");
1985 caseChange = ChangeCaseCommand.TO_UPPER;
1989 description = MessageManager.getString("label.to_lower_case");
1990 caseChange = ChangeCaseCommand.TO_LOWER;
1993 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1994 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1995 startEnd, caseChange);
1997 ap.alignFrame.addHistoryItem(caseCommand);
1999 ap.av.firePropertyChange("alignment", null,
2000 ap.av.getAlignment().getSequences());
2005 public void outputText_actionPerformed(ActionEvent e)
2007 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2008 cap.setForInput(null);
2009 Desktop.addInternalFrame(cap, MessageManager
2010 .formatMessage("label.alignment_output_command", new Object[]
2011 { e.getActionCommand() }), 600, 500);
2013 String[] omitHidden = null;
2015 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2016 // or we simply trust the user wants
2017 // wysiwig behaviour
2019 FileFormatI fileFormat = FileFormats.getInstance()
2020 .forName(e.getActionCommand());
2022 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2025 public void sequenceFeature_actionPerformed()
2027 SequenceGroup sg = ap.av.getSelectionGroup();
2033 List<SequenceI> seqs = new ArrayList<>();
2034 List<SequenceFeature> features = new ArrayList<>();
2037 * assemble dataset sequences, and template new sequence features,
2038 * for the amend features dialog
2040 int gSize = sg.getSize();
2041 for (int i = 0; i < gSize; i++)
2043 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2044 int end = sg.findEndRes(sg.getSequenceAt(i));
2047 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2048 features.add(new SequenceFeature(null, null, start, end, null));
2053 * an entirely gapped region will generate empty lists of sequence / features
2055 if (!seqs.isEmpty())
2057 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2058 .amendFeatures(seqs, features, true, ap))
2060 ap.alignFrame.setShowSeqFeatures(true);
2061 ap.av.setSearchResults(null); // clear highlighting
2062 ap.repaint(); // draw new/amended features
2067 public void textColour_actionPerformed()
2069 SequenceGroup sg = getGroup();
2072 new TextColourChooser().chooseColour(ap, sg);
2076 public void colourByStructure(String pdbid)
2078 Annotation[] anots = ap.av.getStructureSelectionManager()
2079 .colourSequenceFromStructure(sequence, pdbid);
2081 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2082 "Coloured by " + pdbid, anots);
2084 ap.av.getAlignment().addAnnotation(an);
2085 an.createSequenceMapping(sequence, 0, true);
2086 // an.adjustForAlignment();
2087 ap.av.getAlignment().setAnnotationIndex(an, 0);
2089 ap.adjustAnnotationHeight();
2091 sequence.addAlignmentAnnotation(an);
2095 public void editSequence_actionPerformed(ActionEvent actionEvent)
2097 SequenceGroup sg = ap.av.getSelectionGroup();
2101 if (sequence == null)
2103 sequence = sg.getSequenceAt(0);
2106 EditNameDialog dialog = new EditNameDialog(
2107 sequence.getSequenceAsString(sg.getStartRes(),
2108 sg.getEndRes() + 1),
2109 null, MessageManager.getString("label.edit_sequence"), null,
2110 MessageManager.getString("label.edit_sequence"),
2115 EditCommand editCommand = new EditCommand(
2116 MessageManager.getString("label.edit_sequences"),
2118 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2119 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2120 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2122 ap.alignFrame.addHistoryItem(editCommand);
2124 ap.av.firePropertyChange("alignment", null,
2125 ap.av.getAlignment().getSequences());
2131 * Action on user selecting an item from the colour menu (that does not have
2132 * its bespoke action handler)
2137 public void changeColour_actionPerformed(String colourSchemeName)
2139 SequenceGroup sg = getGroup();
2141 * switch to the chosen colour scheme (or null for None)
2143 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2144 .getColourScheme(colourSchemeName, sg,
2145 ap.av.getHiddenRepSequences());
2146 sg.setColourScheme(colourScheme);
2147 if (colourScheme instanceof Blosum62ColourScheme
2148 || colourScheme instanceof PIDColourScheme)
2150 sg.cs.setConsensus(AAFrequency.calculate(
2151 sg.getSequences(ap.av.getHiddenRepSequences()),
2152 sg.getStartRes(), sg.getEndRes() + 1));