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.gui.JalviewColourChooser.ColourChooserListener;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileFormats;
44 import jalview.io.FormatAdapter;
45 import jalview.io.SequenceAnnotationReport;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.ColourSchemes;
49 import jalview.schemes.PIDColourScheme;
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;
55 import jalview.util.dialogrunner.RunResponse;
57 import java.awt.BorderLayout;
58 import java.awt.Color;
59 import java.awt.event.ActionEvent;
60 import java.awt.event.ActionListener;
61 import java.util.ArrayList;
62 import java.util.Arrays;
63 import java.util.BitSet;
64 import java.util.Collection;
65 import java.util.Collections;
66 import java.util.Hashtable;
67 import java.util.LinkedHashMap;
68 import java.util.List;
70 import java.util.SortedMap;
71 import java.util.TreeMap;
72 import java.util.Vector;
74 import javax.swing.JCheckBoxMenuItem;
75 import javax.swing.JInternalFrame;
76 import javax.swing.JLabel;
77 import javax.swing.JMenu;
78 import javax.swing.JMenuItem;
79 import javax.swing.JPanel;
80 import javax.swing.JPopupMenu;
86 * @version $Revision: 1.118 $
88 public class PopupMenu extends JPopupMenu implements ColourChangeListener
90 JMenu groupMenu = new JMenu();
92 JMenuItem groupName = new JMenuItem();
94 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
96 protected JMenuItem modifyPID = new JMenuItem();
98 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
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 JInternalFrame details;
599 if (/** @j2sNative true || */ false)
601 details = new JInternalFrame();
602 JPanel panel = new JPanel(new BorderLayout());
603 panel.setOpaque(true);
604 panel.setBackground(Color.white);
605 // TODO JAL-3026 set style of table correctly for feature details
606 JLabel reprt = new JLabel(MessageManager.formatMessage("label.html_content",
608 { sf.getDetailsReport()}));
609 reprt.setBackground(Color.WHITE);
610 reprt.setOpaque(true);
611 panel.add(reprt,BorderLayout.CENTER);
612 details.setContentPane(panel);
617 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
618 // it appears Java's CSS does not support border-collaps :-(
619 cap.addStylesheetRule("table { border-collapse: collapse;}");
620 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
621 cap.setText(sf.getDetailsReport());
624 Desktop.addInternalFrame(details,
625 MessageManager.getString("label.feature_details"), 500, 500);
629 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
630 * When seq is not null, these are links for the sequence id, which may be to
631 * external web sites for the sequence accession, and/or links embedded in
632 * non-positional features. When seq is null, only links embedded in the
633 * provided features are added.
638 void addLinks(final SequenceI seq, List<SequenceFeature> features)
640 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
642 List<String> nlinks = null;
645 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
649 nlinks = new ArrayList<>();
652 if (features != null)
654 for (SequenceFeature sf : features)
656 if (sf.links != null)
658 for (String link : sf.links)
666 Map<String, List<String>> linkset = new LinkedHashMap<>();
668 for (String link : nlinks)
670 UrlLink urlLink = null;
673 urlLink = new UrlLink(link);
674 } catch (Exception foo)
676 Cache.log.error("Exception for URLLink '" + link + "'", foo);
680 if (!urlLink.isValid())
682 Cache.log.error(urlLink.getInvalidMessage());
686 urlLink.createLinksFromSeq(seq, linkset);
689 addshowLinks(linkMenu, linkset.values());
691 // only add link menu if it has entries
692 if (linkMenu.getItemCount() > 0)
694 if (sequence != null)
696 sequenceMenu.add(linkMenu);
706 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
707 * "All" is added first, followed by a separator. Then add any annotation
708 * types associated with the current selection. Separate menus are built for
709 * the selected sequence group (if any), and the selected sequence.
711 * Some annotation rows are always rendered together - these can be identified
712 * by a common graphGroup property > -1. Only one of each group will be marked
713 * as visible (to avoid duplication of the display). For such groups we add a
714 * composite type name, e.g.
716 * IUPredWS (Long), IUPredWS (Short)
720 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
721 List<SequenceI> forSequences)
723 showMenu.removeAll();
724 hideMenu.removeAll();
726 final List<String> all = Arrays
728 { MessageManager.getString("label.all") });
729 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
731 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
733 showMenu.addSeparator();
734 hideMenu.addSeparator();
736 final AlignmentAnnotation[] annotations = ap.getAlignment()
737 .getAlignmentAnnotation();
740 * Find shown/hidden annotations types, distinguished by source (calcId),
741 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
742 * the insertion order, which is the order of the annotations on the
745 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
746 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
747 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
748 AlignmentAnnotationUtils.asList(annotations), forSequences);
750 for (String calcId : hiddenTypes.keySet())
752 for (List<String> type : hiddenTypes.get(calcId))
754 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
758 // grey out 'show annotations' if none are hidden
759 showMenu.setEnabled(!hiddenTypes.isEmpty());
761 for (String calcId : shownTypes.keySet())
763 for (List<String> type : shownTypes.get(calcId))
765 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
769 // grey out 'hide annotations' if none are shown
770 hideMenu.setEnabled(!shownTypes.isEmpty());
774 * Returns a list of sequences - either the current selection group (if there
775 * is one), else the specified single sequence.
780 protected List<SequenceI> getSequenceScope(SequenceI seq)
782 List<SequenceI> forSequences = null;
783 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
784 if (selectionGroup != null && selectionGroup.getSize() > 0)
786 forSequences = selectionGroup.getSequences();
790 forSequences = seq == null ? Collections.<SequenceI> emptyList()
791 : Arrays.asList(seq);
797 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
800 * @param showOrHideMenu
802 * @param forSequences
803 * the sequences whose annotations may be shown or hidden
808 * if true this is a special label meaning 'All'
809 * @param actionIsShow
810 * if true, the select menu item action is to show the annotation
813 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
814 final List<SequenceI> forSequences, String calcId,
815 final List<String> types, final boolean allTypes,
816 final boolean actionIsShow)
818 String label = types.toString(); // [a, b, c]
819 label = label.substring(1, label.length() - 1); // a, b, c
820 final JMenuItem item = new JMenuItem(label);
821 item.setToolTipText(calcId);
822 item.addActionListener(new ActionListener()
825 public void actionPerformed(ActionEvent e)
827 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
828 types, forSequences, allTypes, actionIsShow);
832 showOrHideMenu.add(item);
835 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
838 // TODO: usability: thread off the generation of group url content so root
840 // sequence only URLs
841 // ID/regex match URLs
842 groupLinksMenu = new JMenu(
843 MessageManager.getString("action.group_link"));
844 // three types of url that might be created.
845 JMenu[] linkMenus = new JMenu[] { null,
846 new JMenu(MessageManager.getString("action.ids")),
847 new JMenu(MessageManager.getString("action.sequences")),
848 new JMenu(MessageManager.getString("action.ids_sequences")) };
850 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
851 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
852 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
853 for (int sq = 0; sq < seqs.length; sq++)
856 int start = seqs[sq].findPosition(sg.getStartRes()),
857 end = seqs[sq].findPosition(sg.getEndRes());
858 // just collect ids from dataset sequence
859 // TODO: check if IDs collected from selecton group intersects with the
860 // current selection, too
861 SequenceI sqi = seqs[sq];
862 while (sqi.getDatasetSequence() != null)
864 sqi = sqi.getDatasetSequence();
866 DBRefEntry[] dbr = sqi.getDBRefs();
867 if (dbr != null && dbr.length > 0)
869 for (int d = 0; d < dbr.length; d++)
871 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
872 Object[] sarray = commonDbrefs.get(src);
875 sarray = new Object[2];
876 sarray[0] = new int[] { 0 };
877 sarray[1] = new String[seqs.length];
879 commonDbrefs.put(src, sarray);
882 if (((String[]) sarray[1])[sq] == null)
884 if (!dbr[d].hasMap() || (dbr[d].getMap()
885 .locateMappedRange(start, end) != null))
887 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
888 ((int[]) sarray[0])[0]++;
894 // now create group links for all distinct ID/sequence sets.
895 boolean addMenu = false; // indicates if there are any group links to give
897 for (String link : groupLinks)
899 GroupUrlLink urlLink = null;
902 urlLink = new GroupUrlLink(link);
903 } catch (Exception foo)
905 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
909 if (!urlLink.isValid())
911 Cache.log.error(urlLink.getInvalidMessage());
914 final String label = urlLink.getLabel();
915 boolean usingNames = false;
916 // Now see which parts of the group apply for this URL
917 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
918 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
919 String[] seqstr, ids; // input to makeUrl
922 int numinput = ((int[]) idset[0])[0];
923 String[] allids = ((String[]) idset[1]);
924 seqstr = new String[numinput];
925 ids = new String[numinput];
926 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
928 if (allids[sq] != null)
930 ids[idcount] = allids[sq];
931 seqstr[idcount++] = idandseqs[1][sq];
937 // just use the id/seq set
938 seqstr = idandseqs[1];
942 // and try and make the groupURL!
944 Object[] urlset = null;
947 urlset = urlLink.makeUrlStubs(ids, seqstr,
948 "FromJalview" + System.currentTimeMillis(), false);
949 } catch (UrlStringTooLongException e)
954 int type = urlLink.getGroupURLType() & 3;
955 // first two bits ofurlLink type bitfield are sequenceids and sequences
956 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
957 addshowLink(linkMenus[type],
958 label + (((type & 1) == 1)
959 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
967 groupLinksMenu = new JMenu(
968 MessageManager.getString("action.group_link"));
969 for (int m = 0; m < linkMenus.length; m++)
971 if (linkMenus[m] != null
972 && linkMenus[m].getMenuComponentCount() > 0)
974 groupLinksMenu.add(linkMenus[m]);
978 groupMenu.add(groupLinksMenu);
982 private void addshowLinks(JMenu linkMenu,
983 Collection<List<String>> linkset)
985 for (List<String> linkstrset : linkset)
987 // split linkstr into label and url
988 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
993 * add a show URL menu item to the given linkMenu
997 * - menu label string
1001 private void addshowLink(JMenu linkMenu, String label, final String url)
1003 JMenuItem item = new JMenuItem(label);
1004 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
1007 item.addActionListener(new ActionListener()
1010 public void actionPerformed(ActionEvent e)
1012 new Thread(new Runnable()
1029 * add a late bound groupURL item to the given linkMenu
1033 * - menu label string
1034 * @param urlgenerator
1035 * GroupURLLink used to generate URL
1037 * Object array returned from the makeUrlStubs function.
1039 private void addshowLink(JMenu linkMenu, String label,
1040 final GroupUrlLink urlgenerator, final Object[] urlstub)
1042 JMenuItem item = new JMenuItem(label);
1043 item.setToolTipText(MessageManager
1044 .formatMessage("label.open_url_seqs_param", new Object[]
1045 { urlgenerator.getUrl_prefix(),
1046 urlgenerator.getNumberInvolved(urlstub) }));
1047 // TODO: put in info about what is being sent.
1048 item.addActionListener(new ActionListener()
1051 public void actionPerformed(ActionEvent e)
1053 new Thread(new Runnable()
1061 showLink(urlgenerator.constructFrom(urlstub));
1062 } catch (UrlStringTooLongException e2)
1080 private void jbInit() throws Exception
1082 groupMenu.setText(MessageManager.getString("label.selection"));
1083 groupName.setText(MessageManager.getString("label.name"));
1084 groupName.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 groupName_actionPerformed();
1092 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1093 sequenceName.setText(
1094 MessageManager.getString("label.edit_name_description"));
1095 sequenceName.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 sequenceName_actionPerformed();
1104 .setText(MessageManager.getString("action.choose_annotations"));
1105 chooseAnnotations.addActionListener(new ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 chooseAnnotations_actionPerformed(e);
1114 .setText(MessageManager.getString("label.sequence_details"));
1115 sequenceDetails.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 sequenceDetails_actionPerformed();
1124 .setText(MessageManager.getString("label.sequence_details"));
1125 sequenceSelDetails.addActionListener(new ActionListener()
1128 public void actionPerformed(ActionEvent e)
1130 sequenceSelectionDetails_actionPerformed();
1135 .setText(MessageManager.getString("action.remove_group"));
1136 unGroupMenuItem.addActionListener(new ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 unGroupMenuItem_actionPerformed();
1145 .setText(MessageManager.getString("action.create_group"));
1146 createGroupMenuItem.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent e)
1151 createGroupMenuItem_actionPerformed();
1155 outline.setText(MessageManager.getString("action.border_colour"));
1156 outline.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 outline_actionPerformed();
1164 showBoxes.setText(MessageManager.getString("action.boxes"));
1165 showBoxes.setState(true);
1166 showBoxes.addActionListener(new ActionListener()
1169 public void actionPerformed(ActionEvent e)
1171 showBoxes_actionPerformed();
1174 showText.setText(MessageManager.getString("action.text"));
1175 showText.setState(true);
1176 showText.addActionListener(new ActionListener()
1179 public void actionPerformed(ActionEvent e)
1181 showText_actionPerformed();
1184 showColourText.setText(MessageManager.getString("label.colour_text"));
1185 showColourText.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 showColourText_actionPerformed();
1194 .setText(MessageManager.getString("label.show_non_conserved"));
1195 displayNonconserved.setState(true);
1196 displayNonconserved.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 showNonconserved_actionPerformed();
1204 editMenu.setText(MessageManager.getString("action.edit"));
1205 cut.setText(MessageManager.getString("action.cut"));
1206 cut.addActionListener(new ActionListener()
1209 public void actionPerformed(ActionEvent e)
1211 cut_actionPerformed();
1214 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1215 upperCase.addActionListener(new ActionListener()
1218 public void actionPerformed(ActionEvent e)
1223 copy.setText(MessageManager.getString("action.copy"));
1224 copy.addActionListener(new ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 copy_actionPerformed();
1232 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1233 lowerCase.addActionListener(new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1241 toggle.setText(MessageManager.getString("label.toggle_case"));
1242 toggle.addActionListener(new ActionListener()
1245 public void actionPerformed(ActionEvent e)
1251 MessageManager.getString("label.out_to_textbox") + "...");
1252 seqShowAnnotationsMenu
1253 .setText(MessageManager.getString("label.show_annotations"));
1254 seqHideAnnotationsMenu
1255 .setText(MessageManager.getString("label.hide_annotations"));
1256 groupShowAnnotationsMenu
1257 .setText(MessageManager.getString("label.show_annotations"));
1258 groupHideAnnotationsMenu
1259 .setText(MessageManager.getString("label.hide_annotations"));
1260 sequenceFeature.setText(
1261 MessageManager.getString("label.create_sequence_feature"));
1262 sequenceFeature.addActionListener(new ActionListener()
1265 public void actionPerformed(ActionEvent e)
1267 sequenceFeature_actionPerformed();
1270 jMenu1.setText(MessageManager.getString("label.group"));
1271 pdbStructureDialog.setText(
1272 MessageManager.getString("label.show_pdbstruct_dialog"));
1273 pdbStructureDialog.addActionListener(new ActionListener()
1276 public void actionPerformed(ActionEvent actionEvent)
1278 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1279 if (ap.av.getSelectionGroup() != null)
1281 selectedSeqs = ap.av.getSequenceSelection();
1283 new StructureChooser(selectedSeqs, sequence, ap);
1288 .setText(MessageManager.getString("label.view_rna_structure"));
1290 // colStructureMenu.setText("Colour By Structure");
1291 editSequence.setText(
1292 MessageManager.getString("label.edit_sequence") + "...");
1293 editSequence.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent actionEvent)
1298 editSequence_actionPerformed();
1301 makeReferenceSeq.setText(
1302 MessageManager.getString("label.mark_as_representative"));
1303 makeReferenceSeq.addActionListener(new ActionListener()
1307 public void actionPerformed(ActionEvent actionEvent)
1309 makeReferenceSeq_actionPerformed(actionEvent);
1314 .setText(MessageManager.getString("label.hide_insertions"));
1315 hideInsertions.addActionListener(new ActionListener()
1319 public void actionPerformed(ActionEvent e)
1321 hideInsertions_actionPerformed(e);
1325 groupMenu.add(sequenceSelDetails);
1328 add(rnaStructureMenu);
1329 add(pdbStructureDialog);
1330 if (sequence != null)
1332 add(hideInsertions);
1334 // annotations configuration panel suppressed for now
1335 // groupMenu.add(chooseAnnotations);
1338 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1339 * (if a selection group is in force).
1341 sequenceMenu.add(seqShowAnnotationsMenu);
1342 sequenceMenu.add(seqHideAnnotationsMenu);
1343 sequenceMenu.add(seqAddReferenceAnnotations);
1344 groupMenu.add(groupShowAnnotationsMenu);
1345 groupMenu.add(groupHideAnnotationsMenu);
1346 groupMenu.add(groupAddReferenceAnnotations);
1347 groupMenu.add(editMenu);
1348 groupMenu.add(outputMenu);
1349 groupMenu.add(sequenceFeature);
1350 groupMenu.add(createGroupMenuItem);
1351 groupMenu.add(unGroupMenuItem);
1352 groupMenu.add(jMenu1);
1353 sequenceMenu.add(sequenceName);
1354 sequenceMenu.add(sequenceDetails);
1355 sequenceMenu.add(makeReferenceSeq);
1362 editMenu.add(editSequence);
1363 editMenu.add(upperCase);
1364 editMenu.add(lowerCase);
1365 editMenu.add(toggle);
1366 // JBPNote: These shouldn't be added here - should appear in a generic
1367 // 'apply web service to this sequence menu'
1368 // pdbMenu.add(RNAFold);
1369 // pdbMenu.add(ContraFold);
1370 jMenu1.add(groupName);
1371 jMenu1.add(colourMenu);
1372 jMenu1.add(showBoxes);
1373 jMenu1.add(showText);
1374 jMenu1.add(showColourText);
1375 jMenu1.add(outline);
1376 jMenu1.add(displayNonconserved);
1380 * Constructs the entries for the colour menu
1382 protected void initColourMenu()
1384 colourMenu.setText(MessageManager.getString("label.group_colour"));
1385 textColour.setText(MessageManager.getString("label.text_colour"));
1386 textColour.addActionListener(new ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 textColour_actionPerformed();
1395 abovePIDColour.setText(
1396 MessageManager.getString("label.above_identity_threshold"));
1397 abovePIDColour.addActionListener(new ActionListener()
1400 public void actionPerformed(ActionEvent e)
1402 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1407 MessageManager.getString("label.modify_identity_threshold"));
1408 modifyPID.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 modifyPID_actionPerformed();
1417 conservationMenuItem
1418 .setText(MessageManager.getString("action.by_conservation"));
1419 conservationMenuItem.addActionListener(new ActionListener()
1422 public void actionPerformed(ActionEvent e)
1424 conservationMenuItem_actionPerformed(
1425 conservationMenuItem.isSelected());
1429 modifyConservation.setText(MessageManager
1430 .getString("label.modify_conservation_threshold"));
1431 modifyConservation.addActionListener(new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 modifyConservation_actionPerformed();
1442 * Builds the group colour sub-menu, including any user-defined colours which
1443 * were loaded at startup or during the Jalview session
1445 protected void buildColourMenu()
1447 SequenceGroup sg = ap.av.getSelectionGroup();
1451 * popup menu with no sequence group scope
1455 colourMenu.removeAll();
1456 colourMenu.add(textColour);
1457 colourMenu.addSeparator();
1459 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1461 colourMenu.addSeparator();
1462 colourMenu.add(conservationMenuItem);
1463 colourMenu.add(modifyConservation);
1464 colourMenu.add(abovePIDColour);
1465 colourMenu.add(modifyPID);
1468 protected void modifyConservation_actionPerformed()
1470 SequenceGroup sg = getGroup();
1473 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1474 SliderPanel.showConservationSlider();
1478 protected void modifyPID_actionPerformed()
1480 SequenceGroup sg = getGroup();
1483 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1485 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1486 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1487 SliderPanel.showPIDSlider();
1492 * Check for any annotations on the underlying dataset sequences (for the
1493 * current selection group) which are not 'on the alignment'.If any are found,
1494 * enable the option to add them to the alignment. The criteria for 'on the
1495 * alignment' is finding an alignment annotation on the alignment, matched on
1496 * calcId, label and sequenceRef.
1498 * A tooltip is also constructed that displays the source (calcId) and type
1499 * (label) of the annotations that can be added.
1502 * @param forSequences
1504 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1505 List<SequenceI> forSequences)
1507 menuItem.setEnabled(false);
1510 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1511 * Using TreeMap means calcIds are shown in alphabetical order.
1513 SortedMap<String, String> tipEntries = new TreeMap<>();
1514 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1515 AlignmentI al = this.ap.av.getAlignment();
1516 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1518 if (!candidates.isEmpty())
1520 StringBuilder tooltip = new StringBuilder(64);
1521 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1524 * Found annotations that could be added. Enable the menu item, and
1525 * configure its tooltip and action.
1527 menuItem.setEnabled(true);
1528 for (String calcId : tipEntries.keySet())
1530 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1532 String tooltipText = JvSwingUtils.wrapTooltip(true,
1533 tooltip.toString());
1534 menuItem.setToolTipText(tooltipText);
1536 menuItem.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 addReferenceAnnotations_actionPerformed(candidates);
1548 * Add annotations to the sequences and to the alignment.
1551 * a map whose keys are sequences on the alignment, and values a list
1552 * of annotations to add to each sequence
1554 protected void addReferenceAnnotations_actionPerformed(
1555 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1557 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1558 final AlignmentI alignment = this.ap.getAlignment();
1559 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1564 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1566 if (!ap.av.getAlignment().hasSeqrep())
1568 // initialise the display flags so the user sees something happen
1569 ap.av.setDisplayReferenceSeq(true);
1570 ap.av.setColourByReferenceSeq(true);
1571 ap.av.getAlignment().setSeqrep(sequence);
1575 if (ap.av.getAlignment().getSeqrep() == sequence)
1577 ap.av.getAlignment().setSeqrep(null);
1581 ap.av.getAlignment().setSeqrep(sequence);
1587 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1589 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1590 BitSet inserts = new BitSet();
1592 boolean markedPopup = false;
1593 // mark inserts in current selection
1594 if (ap.av.getSelectionGroup() != null)
1596 // mark just the columns in the selection group to be hidden
1597 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1598 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1600 // now clear columns without gaps
1601 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1607 inserts.and(sq.getInsertionsAsBits());
1609 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1610 ap.av.getSelectionGroup().getEndRes());
1613 // now mark for sequence under popup if we haven't already done it
1614 else if (!markedPopup && sequence != null)
1616 inserts.or(sequence.getInsertionsAsBits());
1618 // and set hidden columns accordingly
1619 hidden.hideColumns(inserts);
1624 protected void sequenceSelectionDetails_actionPerformed()
1626 createSequenceDetailsReport(ap.av.getSequenceSelection());
1629 protected void sequenceDetails_actionPerformed()
1631 createSequenceDetailsReport(new SequenceI[] { sequence });
1634 public void createSequenceDetailsReport(SequenceI[] sequences)
1636 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1637 StringBuilder contents = new StringBuilder(128);
1638 for (SequenceI seq : sequences)
1640 contents.append("<p><h2>" + MessageManager.formatMessage(
1641 "label.create_sequence_details_report_annotation_for",
1643 { seq.getDisplayId(true) }) + "</h2></p><p>");
1644 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1645 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1646 contents.append("</p>");
1648 cap.setText("<html>" + contents.toString() + "</html>");
1650 Desktop.addInternalFrame(cap,
1651 MessageManager.formatMessage("label.sequence_details_for",
1652 (sequences.length == 1 ? new Object[]
1653 { sequences[0].getDisplayId(true) }
1656 .getString("label.selection") })),
1661 protected void showNonconserved_actionPerformed()
1663 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1668 * call to refresh view after settings change
1672 ap.updateAnnotation();
1673 // removed paintAlignment(true) here:
1674 // updateAnnotation calls paintAlignment already, so don't need to call
1677 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1681 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1682 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1692 public void abovePIDColour_actionPerformed(boolean selected)
1694 SequenceGroup sg = getGroup();
1702 sg.cs.setConsensus(AAFrequency.calculate(
1703 sg.getSequences(ap.av.getHiddenRepSequences()),
1704 sg.getStartRes(), sg.getEndRes() + 1));
1706 int threshold = SliderPanel.setPIDSliderSource(ap,
1707 sg.getGroupColourScheme(), getGroup().getName());
1709 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1711 SliderPanel.showPIDSlider();
1714 // remove PIDColouring
1716 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1717 SliderPanel.hidePIDSlider();
1719 modifyPID.setEnabled(selected);
1725 * Open a panel where the user can choose which types of sequence annotation
1730 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1732 // todo correct way to guard against opening a duplicate panel?
1733 new AnnotationChooser(ap);
1742 public void conservationMenuItem_actionPerformed(boolean selected)
1744 SequenceGroup sg = getGroup();
1752 // JBPNote: Conservation name shouldn't be i18n translated
1753 Conservation c = new Conservation("Group",
1754 sg.getSequences(ap.av.getHiddenRepSequences()),
1755 sg.getStartRes(), sg.getEndRes() + 1);
1758 c.verdict(false, ap.av.getConsPercGaps());
1759 sg.cs.setConservation(c);
1761 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1763 SliderPanel.showConservationSlider();
1766 // remove ConservationColouring
1768 sg.cs.setConservation(null);
1769 SliderPanel.hideConservationSlider();
1771 modifyConservation.setEnabled(selected);
1777 * Shows a dialog where group name and description may be edited
1779 protected void groupName_actionPerformed()
1781 SequenceGroup sg = getGroup();
1782 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1783 sg.getDescription(),
1784 MessageManager.getString("label.group_name"),
1785 MessageManager.getString("label.group_description"));
1786 dialog.showDialog(ap.alignFrame,
1787 MessageManager.getString("label.edit_group_name_description"),
1788 new RunResponse(JvOptionPane.OK_OPTION)
1793 sg.setName(dialog.getName());
1794 sg.setDescription(dialog.getDescription());
1801 * Get selection group - adding it to the alignment if necessary.
1803 * @return sequence group to operate on
1805 SequenceGroup getGroup()
1807 SequenceGroup sg = ap.av.getSelectionGroup();
1808 // this method won't add a new group if it already exists
1811 ap.av.getAlignment().addGroup(sg);
1818 * Shows a dialog where sequence name and description may be edited
1820 void sequenceName_actionPerformed()
1822 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1823 sequence.getDescription(),
1824 MessageManager.getString("label.sequence_name"),
1825 MessageManager.getString("label.sequence_description"));
1826 dialog.showDialog(ap.alignFrame,
1827 MessageManager.getString(
1828 "label.edit_sequence_name_description"),
1829 new RunResponse(JvOptionPane.OK_OPTION)
1834 if (dialog.getName() != null)
1836 if (dialog.getName().indexOf(" ") > -1)
1838 JvOptionPane.showMessageDialog(ap,
1839 MessageManager.getString(
1840 "label.spaces_converted_to_underscores"),
1841 MessageManager.getString(
1842 "label.no_spaces_allowed_sequence_name"),
1843 JvOptionPane.WARNING_MESSAGE);
1845 sequence.setName(dialog.getName().replace(' ', '_'));
1846 ap.paintAlignment(false, false);
1848 sequence.setDescription(dialog.getDescription());
1849 ap.av.firePropertyChange("alignment", null,
1850 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
1877 * Offers a colour chooser and sets the selected colour as the group outline
1879 protected void outline_actionPerformed()
1881 String title = MessageManager
1882 .getString("label.select_outline_colour");
1883 ColourChooserListener listener = new ColourChooserListener()
1886 public void colourSelected(Color c)
1888 getGroup().setOutlineColour(c);
1892 JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
1893 title, Color.BLUE, listener);
1902 public void showBoxes_actionPerformed()
1904 getGroup().setDisplayBoxes(showBoxes.isSelected());
1914 public void showText_actionPerformed()
1916 getGroup().setDisplayText(showText.isSelected());
1926 public void showColourText_actionPerformed()
1928 getGroup().setColourText(showColourText.isSelected());
1932 public void showLink(String url)
1936 jalview.util.BrowserLauncher.openURL(url);
1937 } catch (Exception ex)
1939 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1940 MessageManager.getString("label.web_browser_not_found_unix"),
1941 MessageManager.getString("label.web_browser_not_found"),
1942 JvOptionPane.WARNING_MESSAGE);
1944 ex.printStackTrace();
1948 void hideSequences(boolean representGroup)
1950 ap.av.hideSequences(sequence, representGroup);
1953 public void copy_actionPerformed()
1955 ap.alignFrame.copy_actionPerformed(null);
1958 public void cut_actionPerformed()
1960 ap.alignFrame.cut_actionPerformed(null);
1963 void changeCase(ActionEvent e)
1965 Object source = e.getSource();
1966 SequenceGroup sg = ap.av.getSelectionGroup();
1970 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1971 sg.getStartRes(), sg.getEndRes() + 1);
1976 if (source == toggle)
1978 description = MessageManager.getString("label.toggle_case");
1979 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1981 else if (source == upperCase)
1983 description = MessageManager.getString("label.to_upper_case");
1984 caseChange = ChangeCaseCommand.TO_UPPER;
1988 description = MessageManager.getString("label.to_lower_case");
1989 caseChange = ChangeCaseCommand.TO_LOWER;
1992 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1993 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1994 startEnd, caseChange);
1996 ap.alignFrame.addHistoryItem(caseCommand);
1998 ap.av.firePropertyChange("alignment", null,
1999 ap.av.getAlignment().getSequences());
2004 public void outputText_actionPerformed(ActionEvent e)
2006 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2007 cap.setForInput(null);
2008 Desktop.addInternalFrame(cap, MessageManager
2009 .formatMessage("label.alignment_output_command", new Object[]
2010 { e.getActionCommand() }), 600, 500);
2012 String[] omitHidden = null;
2014 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2015 // or we simply trust the user wants
2016 // wysiwig behaviour
2018 FileFormatI fileFormat = FileFormats.getInstance()
2019 .forName(e.getActionCommand());
2021 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2024 public void sequenceFeature_actionPerformed()
2026 SequenceGroup sg = ap.av.getSelectionGroup();
2032 List<SequenceI> seqs = new ArrayList<>();
2033 List<SequenceFeature> features = new ArrayList<>();
2036 * assemble dataset sequences, and template new sequence features,
2037 * for the amend features dialog
2039 int gSize = sg.getSize();
2040 for (int i = 0; i < gSize; i++)
2042 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2043 int end = sg.findEndRes(sg.getSequenceAt(i));
2046 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2047 features.add(new SequenceFeature(null, null, start, end, null));
2052 * an entirely gapped region will generate empty lists of sequence / features
2054 if (!seqs.isEmpty())
2056 new FeatureEditor(ap, seqs, features, true).showDialog();
2060 public void textColour_actionPerformed()
2062 SequenceGroup sg = getGroup();
2065 new TextColourChooser().chooseColour(ap, sg);
2069 public void colourByStructure(String pdbid)
2071 Annotation[] anots = ap.av.getStructureSelectionManager()
2072 .colourSequenceFromStructure(sequence, pdbid);
2074 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2075 "Coloured by " + pdbid, anots);
2077 ap.av.getAlignment().addAnnotation(an);
2078 an.createSequenceMapping(sequence, 0, true);
2079 // an.adjustForAlignment();
2080 ap.av.getAlignment().setAnnotationIndex(an, 0);
2082 ap.adjustAnnotationHeight();
2084 sequence.addAlignmentAnnotation(an);
2089 * Shows a dialog where sequence characters may be edited. Any changes are
2090 * applied, and added as an available 'Undo' item in the edit commands
2093 public void editSequence_actionPerformed()
2095 SequenceGroup sg = ap.av.getSelectionGroup();
2099 if (sequence == null)
2101 sequence = sg.getSequenceAt(0);
2104 EditNameDialog dialog = new EditNameDialog(
2105 sequence.getSequenceAsString(sg.getStartRes(),
2106 sg.getEndRes() + 1),
2107 null, MessageManager.getString("label.edit_sequence"), null);
2108 dialog.showDialog(ap.alignFrame,
2109 MessageManager.getString("label.edit_sequence"),
2110 new RunResponse(JvOptionPane.OK_OPTION)
2115 EditCommand editCommand = new EditCommand(
2116 MessageManager.getString("label.edit_sequences"),
2118 dialog.getName().replace(' ',
2119 ap.av.getGapCharacter()),
2120 sg.getSequencesAsArray(
2121 ap.av.getHiddenRepSequences()),
2122 sg.getStartRes(), sg.getEndRes() + 1,
2123 ap.av.getAlignment());
2124 ap.alignFrame.addHistoryItem(editCommand);
2125 ap.av.firePropertyChange("alignment", null,
2126 ap.av.getAlignment().getSequences());
2133 * Action on user selecting an item from the colour menu (that does not have
2134 * its bespoke action handler)
2139 public void changeColour_actionPerformed(String colourSchemeName)
2141 SequenceGroup sg = getGroup();
2143 * switch to the chosen colour scheme (or null for None)
2145 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2146 .getColourScheme(colourSchemeName, sg,
2147 ap.av.getHiddenRepSequences());
2148 sg.setColourScheme(colourScheme);
2149 if (colourScheme instanceof Blosum62ColourScheme
2150 || colourScheme instanceof PIDColourScheme)
2152 sg.cs.setConsensus(AAFrequency.calculate(
2153 sg.getSequences(ap.av.getHiddenRepSequences()),
2154 sg.getStartRes(), sg.getEndRes() + 1));