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.ColumnSelection;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.FormatAdapter;
42 import jalview.io.SequenceAnnotationReport;
43 import jalview.schemes.AnnotationColourGradient;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.BuriedColourScheme;
46 import jalview.schemes.ClustalxColourScheme;
47 import jalview.schemes.HelixColourScheme;
48 import jalview.schemes.HydrophobicColourScheme;
49 import jalview.schemes.NucleotideColourScheme;
50 import jalview.schemes.PIDColourScheme;
51 import jalview.schemes.PurinePyrimidineColourScheme;
52 import jalview.schemes.StrandColourScheme;
53 import jalview.schemes.TaylorColourScheme;
54 import jalview.schemes.TurnColourScheme;
55 import jalview.schemes.UserColourScheme;
56 import jalview.schemes.ZappoColourScheme;
57 import jalview.util.DBRefUtils;
58 import jalview.util.GroupUrlLink;
59 import jalview.util.GroupUrlLink.UrlStringTooLongException;
60 import jalview.util.MessageManager;
61 import jalview.util.UrlLink;
63 import java.awt.Color;
64 import java.awt.event.ActionEvent;
65 import java.awt.event.ActionListener;
66 import java.util.ArrayList;
67 import java.util.Arrays;
68 import java.util.Collections;
69 import java.util.Hashtable;
70 import java.util.LinkedHashMap;
71 import java.util.List;
73 import java.util.TreeMap;
74 import java.util.Vector;
76 import javax.swing.ButtonGroup;
77 import javax.swing.JCheckBoxMenuItem;
78 import javax.swing.JColorChooser;
79 import javax.swing.JMenu;
80 import javax.swing.JMenuItem;
81 import javax.swing.JOptionPane;
82 import javax.swing.JPopupMenu;
83 import javax.swing.JRadioButtonMenuItem;
89 * @version $Revision: 1.118 $
91 public class PopupMenu extends JPopupMenu
93 JMenu groupMenu = new JMenu();
95 JMenuItem groupName = new JMenuItem();
97 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
113 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
115 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
117 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
119 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
121 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
123 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
125 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
127 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
131 JMenu sequenceMenu = new JMenu();
133 JMenuItem sequenceName = new JMenuItem();
135 JMenuItem sequenceDetails = new JMenuItem();
137 JMenuItem sequenceSelDetails = new JMenuItem();
139 JMenuItem makeReferenceSeq = new JMenuItem();
141 JMenuItem chooseAnnotations = new JMenuItem();
145 JMenuItem createGroupMenuItem = new JMenuItem();
147 JMenuItem unGroupMenuItem = new JMenuItem();
149 JMenuItem outline = new JMenuItem();
151 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
153 JMenu colourMenu = new JMenu();
155 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
157 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
159 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
161 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
163 JMenu editMenu = new JMenu();
165 JMenuItem cut = new JMenuItem();
167 JMenuItem copy = new JMenuItem();
169 JMenuItem upperCase = new JMenuItem();
171 JMenuItem lowerCase = new JMenuItem();
173 JMenuItem toggle = new JMenuItem();
175 JMenu pdbMenu = new JMenu();
177 JMenu outputMenu = new JMenu();
179 JMenu seqShowAnnotationsMenu = new JMenu();
181 JMenu seqHideAnnotationsMenu = new JMenu();
183 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
184 MessageManager.getString("label.add_reference_annotations"));
186 JMenu groupShowAnnotationsMenu = new JMenu();
188 JMenu groupHideAnnotationsMenu = new JMenu();
190 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
191 MessageManager.getString("label.add_reference_annotations"));
193 JMenuItem sequenceFeature = new JMenuItem();
195 JMenuItem textColour = new JMenuItem();
197 JMenu jMenu1 = new JMenu();
199 JMenuItem pdbStructureDialog = new JMenuItem();
201 JMenu rnaStructureMenu = new JMenu();
203 JMenuItem editSequence = new JMenuItem();
205 JMenu groupLinksMenu;
207 JMenuItem hideInsertions = new JMenuItem();
210 * Creates a new PopupMenu object.
217 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
219 this(ap, seq, links, null);
229 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
230 List<String> links, List<String> groupLinks)
232 // /////////////////////////////////////////////////////////
233 // If this is activated from the sequence panel, the user may want to
234 // edit or annotate a particular residue. Therefore display the residue menu
236 // If from the IDPanel, we must display the sequence menu
237 // ////////////////////////////////////////////////////////
241 ButtonGroup colours = new ButtonGroup();
242 colours.add(noColourmenuItem);
243 colours.add(clustalColour);
244 colours.add(zappoColour);
245 colours.add(taylorColour);
246 colours.add(hydrophobicityColour);
247 colours.add(helixColour);
248 colours.add(strandColour);
249 colours.add(turnColour);
250 colours.add(buriedColour);
251 colours.add(abovePIDColour);
252 colours.add(userDefinedColour);
253 colours.add(PIDColour);
254 colours.add(BLOSUM62Colour);
255 colours.add(purinePyrimidineColour);
256 colours.add(RNAInteractionColour);
258 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
260 JMenuItem item = new JMenuItem(
261 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
263 item.addActionListener(new java.awt.event.ActionListener()
266 public void actionPerformed(ActionEvent e)
268 outputText_actionPerformed(e);
272 outputMenu.add(item);
276 * Build menus for annotation types that may be shown or hidden, and for
277 * 'reference annotations' that may be added to the alignment. First for the
278 * currently selected sequence (if there is one):
280 final List<SequenceI> selectedSequence = (seq == null ? Collections
281 .<SequenceI> emptyList() : Arrays.asList(seq));
282 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
283 seqHideAnnotationsMenu, selectedSequence);
284 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
288 * And repeat for the current selection group (if there is one):
290 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
291 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
293 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
294 groupHideAnnotationsMenu, selectedGroup);
295 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
301 } catch (Exception e)
309 sequenceMenu.setText(sequence.getName());
310 if (seq == ap.av.getAlignment().getSeqrep())
312 makeReferenceSeq.setText(MessageManager
313 .getString("action.unmark_as_reference"));
317 makeReferenceSeq.setText(MessageManager
318 .getString("action.set_as_reference"));
321 if (!ap.av.getAlignment().isNucleotide())
323 remove(rnaStructureMenu);
327 int origCount = rnaStructureMenu.getItemCount();
329 * add menu items to 2D-render any alignment or sequence secondary
330 * structure annotation
332 AlignmentAnnotation[] aas = ap.av.getAlignment()
333 .getAlignmentAnnotation();
336 for (final AlignmentAnnotation aa : aas)
338 if (aa.isValidStruc() && aa.sequenceRef == null)
341 * valid alignment RNA secondary structure annotation
343 menuItem = new JMenuItem();
344 menuItem.setText(MessageManager.formatMessage(
345 "label.2d_rna_structure_line",
346 new Object[] { aa.label }));
347 menuItem.addActionListener(new java.awt.event.ActionListener()
350 public void actionPerformed(ActionEvent e)
352 new AppVarna(seq, aa, ap);
355 rnaStructureMenu.add(menuItem);
360 if (seq.getAnnotation() != null)
362 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
363 for (final AlignmentAnnotation aa : seqAnns)
365 if (aa.isValidStruc())
368 * valid sequence RNA secondary structure annotation
370 // TODO: make rnastrucF a bit more nice
371 menuItem = new JMenuItem();
372 menuItem.setText(MessageManager.formatMessage(
373 "label.2d_rna_sequence_name",
374 new Object[] { seq.getName() }));
375 menuItem.addActionListener(new java.awt.event.ActionListener()
378 public void actionPerformed(ActionEvent e)
380 // TODO: VARNA does'nt print gaps in the sequence
381 new AppVarna(seq, aa, ap);
384 rnaStructureMenu.add(menuItem);
388 if (rnaStructureMenu.getItemCount() == origCount)
390 remove(rnaStructureMenu);
394 menuItem = new JMenuItem(
395 MessageManager.getString("action.hide_sequences"));
396 menuItem.addActionListener(new java.awt.event.ActionListener()
399 public void actionPerformed(ActionEvent e)
401 hideSequences(false);
406 if (ap.av.getSelectionGroup() != null
407 && ap.av.getSelectionGroup().getSize() > 1)
409 menuItem = new JMenuItem(MessageManager.formatMessage(
410 "label.represent_group_with",
411 new Object[] { seq.getName() }));
412 menuItem.addActionListener(new java.awt.event.ActionListener()
415 public void actionPerformed(ActionEvent e)
420 sequenceMenu.add(menuItem);
423 if (ap.av.hasHiddenRows())
425 final int index = ap.av.getAlignment().findIndex(seq);
427 if (ap.av.adjustForHiddenSeqs(index)
428 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
430 menuItem = new JMenuItem(
431 MessageManager.getString("action.reveal_sequences"));
432 menuItem.addActionListener(new ActionListener()
435 public void actionPerformed(ActionEvent e)
437 ap.av.showSequence(index);
438 if (ap.overviewPanel != null)
440 ap.overviewPanel.updateOverviewImage();
448 // for the case when no sequences are even visible
449 if (ap.av.hasHiddenRows())
452 menuItem = new JMenuItem(
453 MessageManager.getString("action.reveal_all"));
454 menuItem.addActionListener(new ActionListener()
457 public void actionPerformed(ActionEvent e)
459 ap.av.showAllHiddenSeqs();
460 if (ap.overviewPanel != null)
462 ap.overviewPanel.updateOverviewImage();
472 SequenceGroup sg = ap.av.getSelectionGroup();
473 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
474 .getGroups().contains(sg) : false;
476 if (sg != null && sg.getSize() > 0)
478 groupName.setText(MessageManager
479 .getString("label.edit_name_and_description_current_group"));
481 if (sg.cs instanceof ZappoColourScheme)
483 zappoColour.setSelected(true);
485 else if (sg.cs instanceof TaylorColourScheme)
487 taylorColour.setSelected(true);
489 else if (sg.cs instanceof PIDColourScheme)
491 PIDColour.setSelected(true);
493 else if (sg.cs instanceof Blosum62ColourScheme)
495 BLOSUM62Colour.setSelected(true);
497 else if (sg.cs instanceof UserColourScheme)
499 userDefinedColour.setSelected(true);
501 else if (sg.cs instanceof HydrophobicColourScheme)
503 hydrophobicityColour.setSelected(true);
505 else if (sg.cs instanceof HelixColourScheme)
507 helixColour.setSelected(true);
509 else if (sg.cs instanceof StrandColourScheme)
511 strandColour.setSelected(true);
513 else if (sg.cs instanceof TurnColourScheme)
515 turnColour.setSelected(true);
517 else if (sg.cs instanceof BuriedColourScheme)
519 buriedColour.setSelected(true);
521 else if (sg.cs instanceof ClustalxColourScheme)
523 clustalColour.setSelected(true);
525 else if (sg.cs instanceof PurinePyrimidineColourScheme)
527 purinePyrimidineColour.setSelected(true);
531 * else if (sg.cs instanceof CovariationColourScheme) {
532 * covariationColour.setSelected(true); }
536 noColourmenuItem.setSelected(true);
539 if (sg.cs != null && sg.cs.conservationApplied())
541 conservationMenuItem.setSelected(true);
543 displayNonconserved.setSelected(sg.getShowNonconserved());
544 showText.setSelected(sg.getDisplayText());
545 showColourText.setSelected(sg.getColourText());
546 showBoxes.setSelected(sg.getDisplayBoxes());
547 // add any groupURLs to the groupURL submenu and make it visible
548 if (groupLinks != null && groupLinks.size() > 0)
550 buildGroupURLMenu(sg, groupLinks);
552 // Add a 'show all structures' for the current selection
553 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
554 SequenceI sqass = null;
555 for (SequenceI sq : ap.av.getSequenceSelection())
557 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
558 if (pes != null && pes.size() > 0)
560 reppdb.put(pes.get(0).getId(), pes.get(0));
561 for (PDBEntry pe : pes)
563 pdbe.put(pe.getId(), pe);
573 final PDBEntry[] pe = pdbe.values().toArray(
574 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
575 new PDBEntry[reppdb.size()]);
576 final JMenuItem gpdbview, rpdbview;
581 groupMenu.setVisible(false);
582 editMenu.setVisible(false);
587 createGroupMenuItem.setVisible(true);
588 unGroupMenuItem.setVisible(false);
589 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
593 createGroupMenuItem.setVisible(false);
594 unGroupMenuItem.setVisible(true);
595 jMenu1.setText(MessageManager.getString("action.edit_group"));
600 sequenceMenu.setVisible(false);
601 pdbStructureDialog.setVisible(false);
602 rnaStructureMenu.setVisible(false);
605 if (links != null && links.size() > 0)
607 addFeatureLinks(seq, links);
612 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
617 void addFeatureLinks(final SequenceI seq, List<String> links)
619 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
620 List<String> linkset = new ArrayList<String>();
621 for (String link : links)
623 UrlLink urlLink = null;
626 urlLink = new UrlLink(link);
627 } catch (Exception foo)
629 Cache.log.error("Exception for URLLink '" + link + "'", foo);
633 if (!urlLink.isValid())
635 Cache.log.error(urlLink.getInvalidMessage());
638 final String label = urlLink.getLabel();
640 // collect id string too
641 String id = seq.getName();
642 String descr = seq.getDescription();
643 if (descr != null && descr.length() < 1)
648 if (seq != null && urlLink.usesSeqId()) // link is ID
650 // collect matching db-refs
651 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
652 new String[] { urlLink.getTarget() });
654 // if there are any dbrefs which match up with the link
657 for (int r = 0; r < dbr.length; r++)
659 if (id != null && dbr[r].getAccessionId().equals(id))
661 // suppress duplicate link creation for the bare sequence ID
662 // string with this link
665 // create Bare ID link for this URL
666 createBareURLLink(urlLink, dbr[r].getAccessionId(), linkset,
667 linkMenu, label, true);
671 // Create urls from description but only for URL links which are regex
673 if (descr != null && urlLink.getRegexReplace() != null)
675 // create link for this URL from description where regex matches
676 createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
680 else if (seq != null && !urlLink.usesSeqId()) // link is name
684 // create Bare ID link for this URL
685 createBareURLLink(urlLink, id, linkset, linkMenu, label, false);
687 // Create urls from description but only for URL links which are regex
689 if (descr != null && urlLink.getRegexReplace() != null)
691 // create link for this URL from description where regex matches
692 createBareURLLink(urlLink, descr, linkset, linkMenu, label, false);
697 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
699 linkset.add(label + "|" + urlLink.getUrl_prefix());
700 // Add a non-dynamic link
701 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
706 if (sequence != null)
708 sequenceMenu.add(linkMenu);
717 * Create a bare URL Link
719 private void createBareURLLink(UrlLink urlLink, String id,
720 List<String> linkset, JMenu linkMenu, String label,
721 Boolean addSepToLabel)
723 String[] urls = urlLink.makeUrls(id, true);
726 for (int u = 0; u < urls.length; u += 2)
728 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
730 linkset.add(urls[u] + "|" + urls[u + 1]);
733 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
737 addshowLink(linkMenu, label, urls[u + 1]);
745 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
746 * "All" is added first, followed by a separator. Then add any annotation
747 * types associated with the current selection. Separate menus are built for
748 * the selected sequence group (if any), and the selected sequence.
750 * Some annotation rows are always rendered together - these can be identified
751 * by a common graphGroup property > -1. Only one of each group will be marked
752 * as visible (to avoid duplication of the display). For such groups we add a
753 * composite type name, e.g.
755 * IUPredWS (Long), IUPredWS (Short)
759 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
760 List<SequenceI> forSequences)
762 showMenu.removeAll();
763 hideMenu.removeAll();
765 final List<String> all = Arrays.asList(new String[] { MessageManager
766 .getString("label.all") });
767 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
768 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
770 showMenu.addSeparator();
771 hideMenu.addSeparator();
773 final AlignmentAnnotation[] annotations = ap.getAlignment()
774 .getAlignmentAnnotation();
777 * Find shown/hidden annotations types, distinguished by source (calcId),
778 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
779 * the insertion order, which is the order of the annotations on the
782 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
783 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
784 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
785 AlignmentAnnotationUtils.asList(annotations), forSequences);
787 for (String calcId : hiddenTypes.keySet())
789 for (List<String> type : hiddenTypes.get(calcId))
791 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
795 // grey out 'show annotations' if none are hidden
796 showMenu.setEnabled(!hiddenTypes.isEmpty());
798 for (String calcId : shownTypes.keySet())
800 for (List<String> type : shownTypes.get(calcId))
802 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
806 // grey out 'hide annotations' if none are shown
807 hideMenu.setEnabled(!shownTypes.isEmpty());
811 * Returns a list of sequences - either the current selection group (if there
812 * is one), else the specified single sequence.
817 protected List<SequenceI> getSequenceScope(SequenceI seq)
819 List<SequenceI> forSequences = null;
820 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
821 if (selectionGroup != null && selectionGroup.getSize() > 0)
823 forSequences = selectionGroup.getSequences();
827 forSequences = seq == null ? Collections.<SequenceI> emptyList()
828 : Arrays.asList(seq);
834 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
837 * @param showOrHideMenu
839 * @param forSequences
840 * the sequences whose annotations may be shown or hidden
845 * if true this is a special label meaning 'All'
846 * @param actionIsShow
847 * if true, the select menu item action is to show the annotation
850 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
851 final List<SequenceI> forSequences, String calcId,
852 final List<String> types, final boolean allTypes,
853 final boolean actionIsShow)
855 String label = types.toString(); // [a, b, c]
856 label = label.substring(1, label.length() - 1); // a, b, c
857 final JMenuItem item = new JMenuItem(label);
858 item.setToolTipText(calcId);
859 item.addActionListener(new java.awt.event.ActionListener()
862 public void actionPerformed(ActionEvent e)
864 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
865 types, forSequences, allTypes, actionIsShow);
869 showOrHideMenu.add(item);
872 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
875 // TODO: usability: thread off the generation of group url content so root
877 // sequence only URLs
878 // ID/regex match URLs
879 groupLinksMenu = new JMenu(
880 MessageManager.getString("action.group_link"));
881 // three types of url that might be created.
882 JMenu[] linkMenus = new JMenu[] { null,
883 new JMenu(MessageManager.getString("action.ids")),
884 new JMenu(MessageManager.getString("action.sequences")),
885 new JMenu(MessageManager.getString("action.ids_sequences")) };
887 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
888 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
889 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
890 for (int sq = 0; sq < seqs.length; sq++)
893 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
894 .findPosition(sg.getEndRes());
895 // just collect ids from dataset sequence
896 // TODO: check if IDs collected from selecton group intersects with the
897 // current selection, too
898 SequenceI sqi = seqs[sq];
899 while (sqi.getDatasetSequence() != null)
901 sqi = sqi.getDatasetSequence();
903 DBRefEntry[] dbr = sqi.getDBRefs();
904 if (dbr != null && dbr.length > 0)
906 for (int d = 0; d < dbr.length; d++)
908 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
909 Object[] sarray = commonDbrefs.get(src);
912 sarray = new Object[2];
913 sarray[0] = new int[] { 0 };
914 sarray[1] = new String[seqs.length];
916 commonDbrefs.put(src, sarray);
919 if (((String[]) sarray[1])[sq] == null)
922 || (dbr[d].getMap().locateMappedRange(start, end) != null))
924 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
925 ((int[]) sarray[0])[0]++;
931 // now create group links for all distinct ID/sequence sets.
932 boolean addMenu = false; // indicates if there are any group links to give
934 for (String link : groupLinks)
936 GroupUrlLink urlLink = null;
939 urlLink = new GroupUrlLink(link);
940 } catch (Exception foo)
942 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
946 if (!urlLink.isValid())
948 Cache.log.error(urlLink.getInvalidMessage());
951 final String label = urlLink.getLabel();
952 boolean usingNames = false;
953 // Now see which parts of the group apply for this URL
954 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
955 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
956 String[] seqstr, ids; // input to makeUrl
959 int numinput = ((int[]) idset[0])[0];
960 String[] allids = ((String[]) idset[1]);
961 seqstr = new String[numinput];
962 ids = new String[numinput];
963 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
965 if (allids[sq] != null)
967 ids[idcount] = allids[sq];
968 seqstr[idcount++] = idandseqs[1][sq];
974 // just use the id/seq set
975 seqstr = idandseqs[1];
979 // and try and make the groupURL!
981 Object[] urlset = null;
984 urlset = urlLink.makeUrlStubs(ids, seqstr,
985 "FromJalview" + System.currentTimeMillis(), false);
986 } catch (UrlStringTooLongException e)
991 int type = urlLink.getGroupURLType() & 3;
992 // first two bits ofurlLink type bitfield are sequenceids and sequences
993 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
994 addshowLink(linkMenus[type], label
995 + (((type & 1) == 1) ? ("("
996 + (usingNames ? "Names" : ltarget) + ")") : ""),
1003 groupLinksMenu = new JMenu(
1004 MessageManager.getString("action.group_link"));
1005 for (int m = 0; m < linkMenus.length; m++)
1007 if (linkMenus[m] != null
1008 && linkMenus[m].getMenuComponentCount() > 0)
1010 groupLinksMenu.add(linkMenus[m]);
1014 groupMenu.add(groupLinksMenu);
1019 * add a show URL menu item to the given linkMenu
1023 * - menu label string
1027 private void addshowLink(JMenu linkMenu, String label, final String url)
1029 JMenuItem item = new JMenuItem(label);
1030 item.setToolTipText(MessageManager.formatMessage(
1031 "label.open_url_param", new Object[] { url }));
1032 item.addActionListener(new java.awt.event.ActionListener()
1035 public void actionPerformed(ActionEvent e)
1037 new Thread(new Runnable()
1054 * add a late bound groupURL item to the given linkMenu
1058 * - menu label string
1059 * @param urlgenerator
1060 * GroupURLLink used to generate URL
1062 * Object array returned from the makeUrlStubs function.
1064 private void addshowLink(JMenu linkMenu, String label,
1065 final GroupUrlLink urlgenerator, final Object[] urlstub)
1067 JMenuItem item = new JMenuItem(label);
1068 item.setToolTipText(MessageManager.formatMessage(
1069 "label.open_url_seqs_param",
1070 new Object[] { urlgenerator.getUrl_prefix(),
1071 urlgenerator.getNumberInvolved(urlstub) }));
1072 // TODO: put in info about what is being sent.
1073 item.addActionListener(new ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 new Thread(new Runnable()
1086 showLink(urlgenerator.constructFrom(urlstub));
1087 } catch (UrlStringTooLongException e2)
1105 private void jbInit() throws Exception
1107 groupMenu.setText(MessageManager.getString("label.selection"));
1108 groupName.setText(MessageManager.getString("label.name"));
1109 groupName.addActionListener(new java.awt.event.ActionListener()
1112 public void actionPerformed(ActionEvent e)
1114 groupName_actionPerformed();
1117 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1118 sequenceName.setText(MessageManager
1119 .getString("label.edit_name_description"));
1120 sequenceName.addActionListener(new java.awt.event.ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 sequenceName_actionPerformed();
1128 chooseAnnotations.setText(MessageManager
1129 .getString("action.choose_annotations"));
1130 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 chooseAnnotations_actionPerformed(e);
1138 sequenceDetails.setText(MessageManager
1139 .getString("label.sequence_details"));
1140 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1143 public void actionPerformed(ActionEvent e)
1145 sequenceDetails_actionPerformed();
1148 sequenceSelDetails.setText(MessageManager
1149 .getString("label.sequence_details"));
1151 .addActionListener(new java.awt.event.ActionListener()
1154 public void actionPerformed(ActionEvent e)
1156 sequenceSelectionDetails_actionPerformed();
1159 PIDColour.setFocusPainted(false);
1161 .setText(MessageManager.getString("action.remove_group"));
1162 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 unGroupMenuItem_actionPerformed();
1170 createGroupMenuItem.setText(MessageManager
1171 .getString("action.create_group"));
1173 .addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 createGroupMenuItem_actionPerformed();
1182 outline.setText(MessageManager.getString("action.border_colour"));
1183 outline.addActionListener(new java.awt.event.ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 outline_actionPerformed();
1192 .setText(MessageManager.getString("label.nucleotide"));
1193 nucleotideMenuItem.addActionListener(new ActionListener()
1196 public void actionPerformed(ActionEvent e)
1198 nucleotideMenuItem_actionPerformed();
1201 colourMenu.setText(MessageManager.getString("label.group_colour"));
1202 showBoxes.setText(MessageManager.getString("action.boxes"));
1203 showBoxes.setState(true);
1204 showBoxes.addActionListener(new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 showBoxes_actionPerformed();
1212 showText.setText(MessageManager.getString("action.text"));
1213 showText.setState(true);
1214 showText.addActionListener(new ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 showText_actionPerformed();
1222 showColourText.setText(MessageManager.getString("label.colour_text"));
1223 showColourText.addActionListener(new ActionListener()
1226 public void actionPerformed(ActionEvent e)
1228 showColourText_actionPerformed();
1231 displayNonconserved.setText(MessageManager
1232 .getString("label.show_non_conversed"));
1233 displayNonconserved.setState(true);
1234 displayNonconserved.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 showNonconserved_actionPerformed();
1242 editMenu.setText(MessageManager.getString("action.edit"));
1243 cut.setText(MessageManager.getString("action.cut"));
1244 cut.addActionListener(new ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 cut_actionPerformed();
1252 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1253 upperCase.addActionListener(new ActionListener()
1256 public void actionPerformed(ActionEvent e)
1261 copy.setText(MessageManager.getString("action.copy"));
1262 copy.addActionListener(new ActionListener()
1265 public void actionPerformed(ActionEvent e)
1267 copy_actionPerformed();
1270 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1271 lowerCase.addActionListener(new ActionListener()
1274 public void actionPerformed(ActionEvent e)
1279 toggle.setText(MessageManager.getString("label.toggle_case"));
1280 toggle.addActionListener(new ActionListener()
1283 public void actionPerformed(ActionEvent e)
1288 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1290 seqShowAnnotationsMenu.setText(MessageManager
1291 .getString("label.show_annotations"));
1292 seqHideAnnotationsMenu.setText(MessageManager
1293 .getString("label.hide_annotations"));
1294 groupShowAnnotationsMenu.setText(MessageManager
1295 .getString("label.show_annotations"));
1296 groupHideAnnotationsMenu.setText(MessageManager
1297 .getString("label.hide_annotations"));
1298 sequenceFeature.setText(MessageManager
1299 .getString("label.create_sequence_feature"));
1300 sequenceFeature.addActionListener(new ActionListener()
1303 public void actionPerformed(ActionEvent e)
1305 sequenceFeature_actionPerformed();
1308 textColour.setText(MessageManager.getString("label.text_colour"));
1309 textColour.addActionListener(new ActionListener()
1312 public void actionPerformed(ActionEvent e)
1314 textColour_actionPerformed();
1317 jMenu1.setText(MessageManager.getString("label.group"));
1318 pdbStructureDialog.setText(MessageManager
1319 .getString("label.show_pdbstruct_dialog"));
1320 pdbStructureDialog.addActionListener(new ActionListener()
1323 public void actionPerformed(ActionEvent actionEvent)
1325 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1326 if (ap.av.getSelectionGroup() != null)
1328 selectedSeqs = ap.av.getSequenceSelection();
1330 new StructureChooser(selectedSeqs, sequence, ap);
1334 rnaStructureMenu.setText(MessageManager
1335 .getString("label.view_rna_structure"));
1337 // colStructureMenu.setText("Colour By Structure");
1338 editSequence.setText(MessageManager.getString("label.edit_sequence")
1340 editSequence.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent actionEvent)
1345 editSequence_actionPerformed(actionEvent);
1348 makeReferenceSeq.setText(MessageManager
1349 .getString("label.mark_as_representative"));
1350 makeReferenceSeq.addActionListener(new ActionListener()
1354 public void actionPerformed(ActionEvent actionEvent)
1356 makeReferenceSeq_actionPerformed(actionEvent);
1360 hideInsertions.setText(MessageManager
1361 .getString("label.hide_insertions"));
1362 hideInsertions.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 hideInsertions_actionPerformed(e);
1372 * annotationMenuItem.setText("By Annotation");
1373 * annotationMenuItem.addActionListener(new ActionListener() { public void
1374 * actionPerformed(ActionEvent actionEvent) {
1375 * annotationMenuItem_actionPerformed(actionEvent); } });
1377 groupMenu.add(sequenceSelDetails);
1380 add(rnaStructureMenu);
1381 add(pdbStructureDialog);
1382 if (sequence != null)
1384 add(hideInsertions);
1386 // annotations configuration panel suppressed for now
1387 // groupMenu.add(chooseAnnotations);
1390 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1391 * (if a selection group is in force).
1393 sequenceMenu.add(seqShowAnnotationsMenu);
1394 sequenceMenu.add(seqHideAnnotationsMenu);
1395 sequenceMenu.add(seqAddReferenceAnnotations);
1396 groupMenu.add(groupShowAnnotationsMenu);
1397 groupMenu.add(groupHideAnnotationsMenu);
1398 groupMenu.add(groupAddReferenceAnnotations);
1399 groupMenu.add(editMenu);
1400 groupMenu.add(outputMenu);
1401 groupMenu.add(sequenceFeature);
1402 groupMenu.add(createGroupMenuItem);
1403 groupMenu.add(unGroupMenuItem);
1404 groupMenu.add(jMenu1);
1405 sequenceMenu.add(sequenceName);
1406 sequenceMenu.add(sequenceDetails);
1407 sequenceMenu.add(makeReferenceSeq);
1408 colourMenu.add(textColour);
1409 colourMenu.add(noColourmenuItem);
1410 colourMenu.add(clustalColour);
1411 colourMenu.add(BLOSUM62Colour);
1412 colourMenu.add(PIDColour);
1413 colourMenu.add(zappoColour);
1414 colourMenu.add(taylorColour);
1415 colourMenu.add(hydrophobicityColour);
1416 colourMenu.add(helixColour);
1417 colourMenu.add(strandColour);
1418 colourMenu.add(turnColour);
1419 colourMenu.add(buriedColour);
1420 colourMenu.add(nucleotideMenuItem);
1421 if (ap.getAlignment().isNucleotide())
1423 // JBPNote - commented since the colourscheme isn't functional
1424 colourMenu.add(purinePyrimidineColour);
1426 colourMenu.add(userDefinedColour);
1428 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1430 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1431 .getUserColourSchemes().keys();
1433 while (userColours.hasMoreElements())
1435 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1436 item.addActionListener(new ActionListener()
1439 public void actionPerformed(ActionEvent evt)
1441 userDefinedColour_actionPerformed(evt);
1444 colourMenu.add(item);
1448 colourMenu.addSeparator();
1449 colourMenu.add(abovePIDColour);
1450 colourMenu.add(conservationMenuItem);
1453 editMenu.add(editSequence);
1454 editMenu.add(upperCase);
1455 editMenu.add(lowerCase);
1456 editMenu.add(toggle);
1457 // JBPNote: These shouldn't be added here - should appear in a generic
1458 // 'apply web service to this sequence menu'
1459 // pdbMenu.add(RNAFold);
1460 // pdbMenu.add(ContraFold);
1461 jMenu1.add(groupName);
1462 jMenu1.add(colourMenu);
1463 jMenu1.add(showBoxes);
1464 jMenu1.add(showText);
1465 jMenu1.add(showColourText);
1466 jMenu1.add(outline);
1467 jMenu1.add(displayNonconserved);
1468 noColourmenuItem.setText(MessageManager.getString("label.none"));
1469 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 noColourmenuItem_actionPerformed();
1478 clustalColour.setText(MessageManager
1479 .getString("label.clustalx_colours"));
1480 clustalColour.addActionListener(new java.awt.event.ActionListener()
1483 public void actionPerformed(ActionEvent e)
1485 clustalColour_actionPerformed();
1488 zappoColour.setText(MessageManager.getString("label.zappo"));
1489 zappoColour.addActionListener(new java.awt.event.ActionListener()
1492 public void actionPerformed(ActionEvent e)
1494 zappoColour_actionPerformed();
1497 taylorColour.setText(MessageManager.getString("label.taylor"));
1498 taylorColour.addActionListener(new java.awt.event.ActionListener()
1501 public void actionPerformed(ActionEvent e)
1503 taylorColour_actionPerformed();
1506 hydrophobicityColour.setText(MessageManager
1507 .getString("label.hydrophobicity"));
1508 hydrophobicityColour
1509 .addActionListener(new java.awt.event.ActionListener()
1512 public void actionPerformed(ActionEvent e)
1514 hydrophobicityColour_actionPerformed();
1517 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1518 helixColour.addActionListener(new java.awt.event.ActionListener()
1521 public void actionPerformed(ActionEvent e)
1523 helixColour_actionPerformed();
1526 strandColour.setText(MessageManager
1527 .getString("label.strand_propensity"));
1528 strandColour.addActionListener(new java.awt.event.ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 strandColour_actionPerformed();
1536 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1537 turnColour.addActionListener(new java.awt.event.ActionListener()
1540 public void actionPerformed(ActionEvent e)
1542 turnColour_actionPerformed();
1545 buriedColour.setText(MessageManager.getString("label.buried_index"));
1546 buriedColour.addActionListener(new java.awt.event.ActionListener()
1549 public void actionPerformed(ActionEvent e)
1551 buriedColour_actionPerformed();
1554 abovePIDColour.setText(MessageManager
1555 .getString("label.above_identity_percentage"));
1556 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1559 public void actionPerformed(ActionEvent e)
1561 abovePIDColour_actionPerformed();
1564 userDefinedColour.setText(MessageManager
1565 .getString("action.user_defined"));
1566 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 userDefinedColour_actionPerformed(e);
1575 .setText(MessageManager.getString("label.percentage_identity"));
1576 PIDColour.addActionListener(new java.awt.event.ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 PIDColour_actionPerformed();
1584 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1585 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1588 public void actionPerformed(ActionEvent e)
1590 BLOSUM62Colour_actionPerformed();
1593 purinePyrimidineColour.setText(MessageManager
1594 .getString("label.purine_pyrimidine"));
1595 purinePyrimidineColour
1596 .addActionListener(new java.awt.event.ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 purinePyrimidineColour_actionPerformed();
1606 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1607 * public void actionPerformed(ActionEvent e) {
1608 * covariationColour_actionPerformed(); } });
1611 conservationMenuItem.setText(MessageManager
1612 .getString("label.conservation"));
1613 conservationMenuItem
1614 .addActionListener(new java.awt.event.ActionListener()
1617 public void actionPerformed(ActionEvent e)
1619 conservationMenuItem_actionPerformed();
1625 * Check for any annotations on the underlying dataset sequences (for the
1626 * current selection group) which are not 'on the alignment'.If any are found,
1627 * enable the option to add them to the alignment. The criteria for 'on the
1628 * alignment' is finding an alignment annotation on the alignment, matched on
1629 * calcId, label and sequenceRef.
1631 * A tooltip is also constructed that displays the source (calcId) and type
1632 * (label) of the annotations that can be added.
1635 * @param forSequences
1637 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1638 List<SequenceI> forSequences)
1640 menuItem.setEnabled(false);
1643 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1644 * Using TreeMap means calcIds are shown in alphabetical order.
1646 Map<String, String> tipEntries = new TreeMap<String, String>();
1647 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1648 AlignmentI al = this.ap.av.getAlignment();
1649 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1650 tipEntries, candidates, al);
1651 if (!candidates.isEmpty())
1653 StringBuilder tooltip = new StringBuilder(64);
1654 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1657 * Found annotations that could be added. Enable the menu item, and
1658 * configure its tooltip and action.
1660 menuItem.setEnabled(true);
1661 for (String calcId : tipEntries.keySet())
1663 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1665 String tooltipText = JvSwingUtils.wrapTooltip(true,
1666 tooltip.toString());
1667 menuItem.setToolTipText(tooltipText);
1669 menuItem.addActionListener(new ActionListener()
1672 public void actionPerformed(ActionEvent e)
1674 addReferenceAnnotations_actionPerformed(candidates);
1681 * Add annotations to the sequences and to the alignment.
1684 * a map whose keys are sequences on the alignment, and values a list
1685 * of annotations to add to each sequence
1687 protected void addReferenceAnnotations_actionPerformed(
1688 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1690 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1691 final AlignmentI alignment = this.ap.getAlignment();
1692 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1697 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1699 if (!ap.av.getAlignment().hasSeqrep())
1701 // initialise the display flags so the user sees something happen
1702 ap.av.setDisplayReferenceSeq(true);
1703 ap.av.setColourByReferenceSeq(true);
1704 ap.av.getAlignment().setSeqrep(sequence);
1708 if (ap.av.getAlignment().getSeqrep() == sequence)
1710 ap.av.getAlignment().setSeqrep(null);
1714 ap.av.getAlignment().setSeqrep(sequence);
1720 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1722 if (sequence != null)
1724 ColumnSelection cs = ap.av.getColumnSelection();
1727 cs = new ColumnSelection();
1729 cs.hideInsertionsFor(sequence);
1730 ap.av.setColumnSelection(cs);
1735 protected void sequenceSelectionDetails_actionPerformed()
1737 createSequenceDetailsReport(ap.av.getSequenceSelection());
1740 protected void sequenceDetails_actionPerformed()
1742 createSequenceDetailsReport(new SequenceI[] { sequence });
1745 public void createSequenceDetailsReport(SequenceI[] sequences)
1747 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1748 StringBuffer contents = new StringBuffer();
1749 for (SequenceI seq : sequences)
1751 contents.append("<p><h2>"
1754 "label.create_sequence_details_report_annotation_for",
1755 new Object[] { seq.getDisplayId(true) })
1757 new SequenceAnnotationReport(null)
1758 .createSequenceAnnotationReport(
1764 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1765 .getSeqPanel().seqCanvas.fr.getMinMax()
1767 contents.append("</p>");
1769 cap.setText("<html>" + contents.toString() + "</html>");
1771 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1772 "label.sequence_details_for",
1773 (sequences.length == 1 ? new Object[] { sequences[0]
1774 .getDisplayId(true) } : new Object[] { MessageManager
1775 .getString("label.selection") })), 500, 400);
1779 protected void showNonconserved_actionPerformed()
1781 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1786 * call to refresh view after settings change
1790 ap.updateAnnotation();
1791 ap.paintAlignment(true);
1793 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1802 protected void clustalColour_actionPerformed()
1804 SequenceGroup sg = getGroup();
1805 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1815 protected void zappoColour_actionPerformed()
1817 getGroup().cs = new ZappoColourScheme();
1827 protected void taylorColour_actionPerformed()
1829 getGroup().cs = new TaylorColourScheme();
1839 protected void hydrophobicityColour_actionPerformed()
1841 getGroup().cs = new HydrophobicColourScheme();
1851 protected void helixColour_actionPerformed()
1853 getGroup().cs = new HelixColourScheme();
1863 protected void strandColour_actionPerformed()
1865 getGroup().cs = new StrandColourScheme();
1875 protected void turnColour_actionPerformed()
1877 getGroup().cs = new TurnColourScheme();
1887 protected void buriedColour_actionPerformed()
1889 getGroup().cs = new BuriedColourScheme();
1899 public void nucleotideMenuItem_actionPerformed()
1901 getGroup().cs = new NucleotideColourScheme();
1905 protected void purinePyrimidineColour_actionPerformed()
1907 getGroup().cs = new PurinePyrimidineColourScheme();
1912 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1913 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1921 protected void abovePIDColour_actionPerformed()
1923 SequenceGroup sg = getGroup();
1929 if (abovePIDColour.isSelected())
1931 sg.cs.setConsensus(AAFrequency.calculate(
1932 sg.getSequences(ap.av.getHiddenRepSequences()),
1933 sg.getStartRes(), sg.getEndRes() + 1));
1935 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1938 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1940 SliderPanel.showPIDSlider();
1943 // remove PIDColouring
1945 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1957 protected void userDefinedColour_actionPerformed(ActionEvent e)
1959 SequenceGroup sg = getGroup();
1961 if (e.getSource().equals(userDefinedColour))
1963 new UserDefinedColours(ap, sg);
1967 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1968 .getUserColourSchemes().get(e.getActionCommand());
1976 * Open a panel where the user can choose which types of sequence annotation
1981 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1983 // todo correct way to guard against opening a duplicate panel?
1984 new AnnotationChooser(ap);
1993 protected void PIDColour_actionPerformed()
1995 SequenceGroup sg = getGroup();
1996 sg.cs = new PIDColourScheme();
1997 sg.cs.setConsensus(AAFrequency.calculate(
1998 sg.getSequences(ap.av.getHiddenRepSequences()),
1999 sg.getStartRes(), sg.getEndRes() + 1));
2009 protected void BLOSUM62Colour_actionPerformed()
2011 SequenceGroup sg = getGroup();
2013 sg.cs = new Blosum62ColourScheme();
2015 sg.cs.setConsensus(AAFrequency.calculate(
2016 sg.getSequences(ap.av.getHiddenRepSequences()),
2017 sg.getStartRes(), sg.getEndRes() + 1));
2028 protected void noColourmenuItem_actionPerformed()
2030 getGroup().cs = null;
2040 protected void conservationMenuItem_actionPerformed()
2042 SequenceGroup sg = getGroup();
2048 if (conservationMenuItem.isSelected())
2050 // JBPNote: Conservation name shouldn't be i18n translated
2051 Conservation c = new Conservation("Group", sg.getSequences(ap.av
2052 .getHiddenRepSequences()), sg.getStartRes(),
2053 sg.getEndRes() + 1);
2056 c.verdict(false, ap.av.getConsPercGaps());
2058 sg.cs.setConservation(c);
2060 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2061 SliderPanel.showConservationSlider();
2064 // remove ConservationColouring
2066 sg.cs.setConservation(null);
2072 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2074 SequenceGroup sg = getGroup();
2080 AnnotationColourGradient acg = new AnnotationColourGradient(
2081 sequence.getAnnotation()[0], null,
2082 AnnotationColourGradient.NO_THRESHOLD);
2084 acg.setPredefinedColours(true);
2096 protected void groupName_actionPerformed()
2099 SequenceGroup sg = getGroup();
2100 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2101 sg.getDescription(), " "
2102 + MessageManager.getString("label.group_name") + " ",
2103 MessageManager.getString("label.group_description") + " ",
2104 MessageManager.getString("label.edit_group_name_description"),
2112 sg.setName(dialog.getName());
2113 sg.setDescription(dialog.getDescription());
2118 * Get selection group - adding it to the alignment if necessary.
2120 * @return sequence group to operate on
2122 SequenceGroup getGroup()
2124 SequenceGroup sg = ap.av.getSelectionGroup();
2125 // this method won't add a new group if it already exists
2128 ap.av.getAlignment().addGroup(sg);
2140 void sequenceName_actionPerformed()
2142 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2143 sequence.getDescription(),
2144 " " + MessageManager.getString("label.sequence_name")
2146 MessageManager.getString("label.sequence_description") + " ",
2148 .getString("label.edit_sequence_name_description"),
2156 if (dialog.getName() != null)
2158 if (dialog.getName().indexOf(" ") > -1)
2164 .getString("label.spaces_converted_to_backslashes"),
2166 .getString("label.no_spaces_allowed_sequence_name"),
2167 JOptionPane.WARNING_MESSAGE);
2170 sequence.setName(dialog.getName().replace(' ', '_'));
2171 ap.paintAlignment(false);
2174 sequence.setDescription(dialog.getDescription());
2176 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2187 void unGroupMenuItem_actionPerformed()
2189 SequenceGroup sg = ap.av.getSelectionGroup();
2190 ap.av.getAlignment().deleteGroup(sg);
2191 ap.av.setSelectionGroup(null);
2195 void createGroupMenuItem_actionPerformed()
2197 getGroup(); // implicitly creates group - note - should apply defaults / use
2198 // standard alignment window logic for this
2208 protected void outline_actionPerformed()
2210 SequenceGroup sg = getGroup();
2211 Color col = JColorChooser.showDialog(this,
2212 MessageManager.getString("label.select_outline_colour"),
2217 sg.setOutlineColour(col);
2229 public void showBoxes_actionPerformed()
2231 getGroup().setDisplayBoxes(showBoxes.isSelected());
2241 public void showText_actionPerformed()
2243 getGroup().setDisplayText(showText.isSelected());
2253 public void showColourText_actionPerformed()
2255 getGroup().setColourText(showColourText.isSelected());
2259 public void showLink(String url)
2263 jalview.util.BrowserLauncher.openURL(url);
2264 } catch (Exception ex)
2266 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2267 MessageManager.getString("label.web_browser_not_found_unix"),
2268 MessageManager.getString("label.web_browser_not_found"),
2269 JOptionPane.WARNING_MESSAGE);
2271 ex.printStackTrace();
2275 void hideSequences(boolean representGroup)
2277 ap.av.hideSequences(sequence, representGroup);
2280 public void copy_actionPerformed()
2282 ap.alignFrame.copy_actionPerformed(null);
2285 public void cut_actionPerformed()
2287 ap.alignFrame.cut_actionPerformed(null);
2290 void changeCase(ActionEvent e)
2292 Object source = e.getSource();
2293 SequenceGroup sg = ap.av.getSelectionGroup();
2297 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2298 sg.getStartRes(), sg.getEndRes() + 1);
2303 if (source == toggle)
2305 description = MessageManager.getString("label.toggle_case");
2306 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2308 else if (source == upperCase)
2310 description = MessageManager.getString("label.to_upper_case");
2311 caseChange = ChangeCaseCommand.TO_UPPER;
2315 description = MessageManager.getString("label.to_lower_case");
2316 caseChange = ChangeCaseCommand.TO_LOWER;
2319 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2320 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2321 startEnd, caseChange);
2323 ap.alignFrame.addHistoryItem(caseCommand);
2325 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2331 public void outputText_actionPerformed(ActionEvent e)
2333 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2334 cap.setForInput(null);
2335 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2336 "label.alignment_output_command",
2337 new Object[] { e.getActionCommand() }), 600, 500);
2339 String[] omitHidden = null;
2341 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2342 // or we simply trust the user wants
2343 // wysiwig behaviour
2345 cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
2349 public void sequenceFeature_actionPerformed()
2351 SequenceGroup sg = ap.av.getSelectionGroup();
2357 int rsize = 0, gSize = sg.getSize();
2358 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2359 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2361 for (int i = 0; i < gSize; i++)
2363 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2364 int end = sg.findEndRes(sg.getSequenceAt(i));
2367 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2368 features[rsize] = new SequenceFeature(null, null, null, start, end,
2373 rseqs = new SequenceI[rsize];
2374 tfeatures = new SequenceFeature[rsize];
2375 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2376 System.arraycopy(features, 0, tfeatures, 0, rsize);
2377 features = tfeatures;
2379 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2380 features, true, ap))
2382 ap.alignFrame.setShowSeqFeatures(true);
2383 ap.highlightSearchResults(null);
2387 public void textColour_actionPerformed()
2389 SequenceGroup sg = getGroup();
2392 new TextColourChooser().chooseColour(ap, sg);
2396 public void colourByStructure(String pdbid)
2398 Annotation[] anots = ap.av.getStructureSelectionManager()
2399 .colourSequenceFromStructure(sequence, pdbid);
2401 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2402 "Coloured by " + pdbid, anots);
2404 ap.av.getAlignment().addAnnotation(an);
2405 an.createSequenceMapping(sequence, 0, true);
2406 // an.adjustForAlignment();
2407 ap.av.getAlignment().setAnnotationIndex(an, 0);
2409 ap.adjustAnnotationHeight();
2411 sequence.addAlignmentAnnotation(an);
2415 public void editSequence_actionPerformed(ActionEvent actionEvent)
2417 SequenceGroup sg = ap.av.getSelectionGroup();
2421 if (sequence == null)
2423 sequence = sg.getSequenceAt(0);
2426 EditNameDialog dialog = new EditNameDialog(
2427 sequence.getSequenceAsString(sg.getStartRes(),
2428 sg.getEndRes() + 1), null,
2429 MessageManager.getString("label.edit_sequence"), null,
2430 MessageManager.getString("label.edit_sequence"),
2435 EditCommand editCommand = new EditCommand(
2436 MessageManager.getString("label.edit_sequences"),
2437 Action.REPLACE, dialog.getName().replace(' ',
2438 ap.av.getGapCharacter()),
2439 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2440 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2442 ap.alignFrame.addHistoryItem(editCommand);
2444 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()