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.ResidueProperties;
53 import jalview.schemes.StrandColourScheme;
54 import jalview.schemes.TaylorColourScheme;
55 import jalview.schemes.TurnColourScheme;
56 import jalview.schemes.UserColourScheme;
57 import jalview.schemes.ZappoColourScheme;
58 import jalview.util.DBRefUtils;
59 import jalview.util.GroupUrlLink;
60 import jalview.util.GroupUrlLink.UrlStringTooLongException;
61 import jalview.util.MessageManager;
62 import jalview.util.UrlLink;
64 import java.awt.Color;
65 import java.awt.event.ActionEvent;
66 import java.awt.event.ActionListener;
67 import java.util.ArrayList;
68 import java.util.Arrays;
69 import java.util.Collections;
70 import java.util.Hashtable;
71 import java.util.LinkedHashMap;
72 import java.util.List;
74 import java.util.TreeMap;
75 import java.util.Vector;
77 import javax.swing.ButtonGroup;
78 import javax.swing.JCheckBoxMenuItem;
79 import javax.swing.JColorChooser;
80 import javax.swing.JMenu;
81 import javax.swing.JMenuItem;
82 import javax.swing.JOptionPane;
83 import javax.swing.JPopupMenu;
84 import javax.swing.JRadioButtonMenuItem;
90 * @version $Revision: 1.118 $
92 public class PopupMenu extends JPopupMenu
94 JMenu groupMenu = new JMenu();
96 JMenuItem groupName = new JMenuItem();
98 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
114 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
116 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
118 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
126 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
128 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
132 JMenu sequenceMenu = new JMenu();
134 JMenuItem sequenceName = new JMenuItem();
136 JMenuItem sequenceDetails = new JMenuItem();
138 JMenuItem sequenceSelDetails = new JMenuItem();
140 JMenuItem makeReferenceSeq = new JMenuItem();
142 JMenuItem chooseAnnotations = new JMenuItem();
146 JMenuItem createGroupMenuItem = new JMenuItem();
148 JMenuItem unGroupMenuItem = new JMenuItem();
150 JMenuItem outline = new JMenuItem();
152 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
154 JMenu colourMenu = new JMenu();
156 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
158 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
160 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
162 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
164 JMenu editMenu = new JMenu();
166 JMenuItem cut = new JMenuItem();
168 JMenuItem copy = new JMenuItem();
170 JMenuItem upperCase = new JMenuItem();
172 JMenuItem lowerCase = new JMenuItem();
174 JMenuItem toggle = new JMenuItem();
176 JMenu pdbMenu = new JMenu();
178 JMenu outputMenu = new JMenu();
180 JMenu seqShowAnnotationsMenu = new JMenu();
182 JMenu seqHideAnnotationsMenu = new JMenu();
184 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
185 MessageManager.getString("label.add_reference_annotations"));
187 JMenu groupShowAnnotationsMenu = new JMenu();
189 JMenu groupHideAnnotationsMenu = new JMenu();
191 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
192 MessageManager.getString("label.add_reference_annotations"));
194 JMenuItem sequenceFeature = new JMenuItem();
196 JMenuItem textColour = new JMenuItem();
198 JMenu jMenu1 = new JMenu();
200 JMenuItem pdbStructureDialog = new JMenuItem();
202 JMenu rnaStructureMenu = new JMenu();
204 JMenuItem editSequence = new JMenuItem();
206 JMenu groupLinksMenu;
208 JMenuItem hideInsertions = new JMenuItem();
211 * Creates a new PopupMenu object.
218 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
220 this(ap, seq, links, null);
230 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
231 List<String> links, List<String> groupLinks)
233 // /////////////////////////////////////////////////////////
234 // If this is activated from the sequence panel, the user may want to
235 // edit or annotate a particular residue. Therefore display the residue menu
237 // If from the IDPanel, we must display the sequence menu
238 // ////////////////////////////////////////////////////////
242 ButtonGroup colours = new ButtonGroup();
243 colours.add(noColourmenuItem);
244 colours.add(clustalColour);
245 colours.add(zappoColour);
246 colours.add(taylorColour);
247 colours.add(hydrophobicityColour);
248 colours.add(helixColour);
249 colours.add(strandColour);
250 colours.add(turnColour);
251 colours.add(buriedColour);
252 colours.add(abovePIDColour);
253 colours.add(userDefinedColour);
254 colours.add(PIDColour);
255 colours.add(BLOSUM62Colour);
256 colours.add(purinePyrimidineColour);
257 colours.add(RNAInteractionColour);
259 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
261 JMenuItem item = new JMenuItem(
262 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
264 item.addActionListener(new java.awt.event.ActionListener()
267 public void actionPerformed(ActionEvent e)
269 outputText_actionPerformed(e);
273 outputMenu.add(item);
277 * Build menus for annotation types that may be shown or hidden, and for
278 * 'reference annotations' that may be added to the alignment. First for the
279 * currently selected sequence (if there is one):
281 final List<SequenceI> selectedSequence = (seq == null ? Collections
282 .<SequenceI> emptyList() : Arrays.asList(seq));
283 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
284 seqHideAnnotationsMenu, selectedSequence);
285 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
289 * And repeat for the current selection group (if there is one):
291 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
292 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
294 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
295 groupHideAnnotationsMenu, selectedGroup);
296 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
302 } catch (Exception e)
310 sequenceMenu.setText(sequence.getName());
311 if (seq == ap.av.getAlignment().getSeqrep())
313 makeReferenceSeq.setText(MessageManager
314 .getString("action.unmark_as_reference"));
318 makeReferenceSeq.setText(MessageManager
319 .getString("action.set_as_reference"));
322 if (!ap.av.getAlignment().isNucleotide())
324 remove(rnaStructureMenu);
328 int origCount = rnaStructureMenu.getItemCount();
330 * add menu items to 2D-render any alignment or sequence secondary
331 * structure annotation
333 AlignmentAnnotation[] aas = ap.av.getAlignment()
334 .getAlignmentAnnotation();
337 for (final AlignmentAnnotation aa : aas)
339 if (aa.isValidStruc() && aa.sequenceRef == null)
342 * valid alignment RNA secondary structure annotation
344 menuItem = new JMenuItem();
345 menuItem.setText(MessageManager.formatMessage(
346 "label.2d_rna_structure_line",
347 new Object[] { aa.label }));
348 menuItem.addActionListener(new java.awt.event.ActionListener()
351 public void actionPerformed(ActionEvent e)
353 new AppVarna(seq, aa, ap);
356 rnaStructureMenu.add(menuItem);
361 if (seq.getAnnotation() != null)
363 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
364 for (final AlignmentAnnotation aa : seqAnns)
366 if (aa.isValidStruc())
369 * valid sequence RNA secondary structure annotation
371 // TODO: make rnastrucF a bit more nice
372 menuItem = new JMenuItem();
373 menuItem.setText(MessageManager.formatMessage(
374 "label.2d_rna_sequence_name",
375 new Object[] { seq.getName() }));
376 menuItem.addActionListener(new java.awt.event.ActionListener()
379 public void actionPerformed(ActionEvent e)
381 // TODO: VARNA does'nt print gaps in the sequence
382 new AppVarna(seq, aa, ap);
385 rnaStructureMenu.add(menuItem);
389 if (rnaStructureMenu.getItemCount() == origCount)
391 remove(rnaStructureMenu);
395 menuItem = new JMenuItem(
396 MessageManager.getString("action.hide_sequences"));
397 menuItem.addActionListener(new java.awt.event.ActionListener()
400 public void actionPerformed(ActionEvent e)
402 hideSequences(false);
407 if (ap.av.getSelectionGroup() != null
408 && ap.av.getSelectionGroup().getSize() > 1)
410 menuItem = new JMenuItem(MessageManager.formatMessage(
411 "label.represent_group_with",
412 new Object[] { seq.getName() }));
413 menuItem.addActionListener(new java.awt.event.ActionListener()
416 public void actionPerformed(ActionEvent e)
421 sequenceMenu.add(menuItem);
424 if (ap.av.hasHiddenRows())
426 final int index = ap.av.getAlignment().findIndex(seq);
428 if (ap.av.adjustForHiddenSeqs(index)
429 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
431 menuItem = new JMenuItem(
432 MessageManager.getString("action.reveal_sequences"));
433 menuItem.addActionListener(new ActionListener()
436 public void actionPerformed(ActionEvent e)
438 ap.av.showSequence(index);
439 if (ap.overviewPanel != null)
441 ap.overviewPanel.updateOverviewImage();
449 // for the case when no sequences are even visible
450 if (ap.av.hasHiddenRows())
453 menuItem = new JMenuItem(
454 MessageManager.getString("action.reveal_all"));
455 menuItem.addActionListener(new ActionListener()
458 public void actionPerformed(ActionEvent e)
460 ap.av.showAllHiddenSeqs();
461 if (ap.overviewPanel != null)
463 ap.overviewPanel.updateOverviewImage();
473 SequenceGroup sg = ap.av.getSelectionGroup();
474 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
475 .getGroups().contains(sg) : false;
477 if (sg != null && sg.getSize() > 0)
479 groupName.setText(MessageManager.formatMessage("label.name_param",
480 new Object[] { sg.getName() }));
481 groupName.setText(MessageManager
482 .getString("label.edit_name_and_description_current_group"));
484 if (sg.cs instanceof ZappoColourScheme)
486 zappoColour.setSelected(true);
488 else if (sg.cs instanceof TaylorColourScheme)
490 taylorColour.setSelected(true);
492 else if (sg.cs instanceof PIDColourScheme)
494 PIDColour.setSelected(true);
496 else if (sg.cs instanceof Blosum62ColourScheme)
498 BLOSUM62Colour.setSelected(true);
500 else if (sg.cs instanceof UserColourScheme)
502 userDefinedColour.setSelected(true);
504 else if (sg.cs instanceof HydrophobicColourScheme)
506 hydrophobicityColour.setSelected(true);
508 else if (sg.cs instanceof HelixColourScheme)
510 helixColour.setSelected(true);
512 else if (sg.cs instanceof StrandColourScheme)
514 strandColour.setSelected(true);
516 else if (sg.cs instanceof TurnColourScheme)
518 turnColour.setSelected(true);
520 else if (sg.cs instanceof BuriedColourScheme)
522 buriedColour.setSelected(true);
524 else if (sg.cs instanceof ClustalxColourScheme)
526 clustalColour.setSelected(true);
528 else if (sg.cs instanceof PurinePyrimidineColourScheme)
530 purinePyrimidineColour.setSelected(true);
534 * else if (sg.cs instanceof CovariationColourScheme) {
535 * covariationColour.setSelected(true); }
539 noColourmenuItem.setSelected(true);
542 if (sg.cs != null && sg.cs.conservationApplied())
544 conservationMenuItem.setSelected(true);
546 displayNonconserved.setSelected(sg.getShowNonconserved());
547 showText.setSelected(sg.getDisplayText());
548 showColourText.setSelected(sg.getColourText());
549 showBoxes.setSelected(sg.getDisplayBoxes());
550 // add any groupURLs to the groupURL submenu and make it visible
551 if (groupLinks != null && groupLinks.size() > 0)
553 buildGroupURLMenu(sg, groupLinks);
555 // Add a 'show all structures' for the current selection
556 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
557 SequenceI sqass = null;
558 for (SequenceI sq : ap.av.getSequenceSelection())
560 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
561 if (pes != null && pes.size() > 0)
563 reppdb.put(pes.get(0).getId(), pes.get(0));
564 for (PDBEntry pe : pes)
566 pdbe.put(pe.getId(), pe);
576 final PDBEntry[] pe = pdbe.values().toArray(
577 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
578 new PDBEntry[reppdb.size()]);
579 final JMenuItem gpdbview, rpdbview;
584 groupMenu.setVisible(false);
585 editMenu.setVisible(false);
590 createGroupMenuItem.setVisible(true);
591 unGroupMenuItem.setVisible(false);
592 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
596 createGroupMenuItem.setVisible(false);
597 unGroupMenuItem.setVisible(true);
598 jMenu1.setText(MessageManager.getString("action.edit_group"));
603 sequenceMenu.setVisible(false);
604 pdbStructureDialog.setVisible(false);
605 rnaStructureMenu.setVisible(false);
608 if (links != null && links.size() > 0)
610 addFeatureLinks(seq, links);
615 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
620 void addFeatureLinks(final SequenceI seq, List<String> links)
622 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
623 List<String> linkset = new ArrayList<String>();
624 for (String link : links)
626 UrlLink urlLink = null;
629 urlLink = new UrlLink(link);
630 } catch (Exception foo)
632 Cache.log.error("Exception for URLLink '" + link + "'", foo);
636 if (!urlLink.isValid())
638 Cache.log.error(urlLink.getInvalidMessage());
641 final String label = urlLink.getLabel();
642 if (seq != null && urlLink.isDynamic())
645 // collect matching db-refs
646 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
647 new String[] { urlLink.getTarget() });
648 // collect id string too
649 String id = seq.getName();
650 String descr = seq.getDescription();
651 if (descr != null && descr.length() < 1)
658 for (int r = 0; r < dbr.length; r++)
660 if (id != null && dbr[r].getAccessionId().equals(id))
662 // suppress duplicate link creation for the bare sequence ID
663 // string with this link
666 // create Bare ID link for this URL
667 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
670 for (int u = 0; u < urls.length; u += 2)
672 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
674 linkset.add(urls[u] + "|" + urls[u + 1]);
675 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
683 // create Bare ID link for this URL
684 String[] urls = urlLink.makeUrls(id, true);
687 for (int u = 0; u < urls.length; u += 2)
689 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
691 linkset.add(urls[u] + "|" + urls[u + 1]);
692 addshowLink(linkMenu, label, urls[u + 1]);
697 // Create urls from description but only for URL links which are regex
699 if (descr != null && urlLink.getRegexReplace() != null)
701 // create link for this URL from description where regex matches
702 String[] urls = urlLink.makeUrls(descr, true);
705 for (int u = 0; u < urls.length; u += 2)
707 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
709 linkset.add(urls[u] + "|" + urls[u + 1]);
710 addshowLink(linkMenu, label, urls[u + 1]);
718 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
720 linkset.add(label + "|" + urlLink.getUrl_prefix());
721 // Add a non-dynamic link
722 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
726 if (sequence != null)
728 sequenceMenu.add(linkMenu);
737 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
738 * "All" is added first, followed by a separator. Then add any annotation
739 * types associated with the current selection. Separate menus are built for
740 * the selected sequence group (if any), and the selected sequence.
742 * Some annotation rows are always rendered together - these can be identified
743 * by a common graphGroup property > -1. Only one of each group will be marked
744 * as visible (to avoid duplication of the display). For such groups we add a
745 * composite type name, e.g.
747 * IUPredWS (Long), IUPredWS (Short)
751 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
752 List<SequenceI> forSequences)
754 showMenu.removeAll();
755 hideMenu.removeAll();
757 final List<String> all = Arrays.asList(new String[] { MessageManager
758 .getString("label.all") });
759 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
760 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
762 showMenu.addSeparator();
763 hideMenu.addSeparator();
765 final AlignmentAnnotation[] annotations = ap.getAlignment()
766 .getAlignmentAnnotation();
769 * Find shown/hidden annotations types, distinguished by source (calcId),
770 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
771 * the insertion order, which is the order of the annotations on the
774 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
775 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
776 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
777 AlignmentAnnotationUtils.asList(annotations), forSequences);
779 for (String calcId : hiddenTypes.keySet())
781 for (List<String> type : hiddenTypes.get(calcId))
783 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
787 // grey out 'show annotations' if none are hidden
788 showMenu.setEnabled(!hiddenTypes.isEmpty());
790 for (String calcId : shownTypes.keySet())
792 for (List<String> type : shownTypes.get(calcId))
794 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
798 // grey out 'hide annotations' if none are shown
799 hideMenu.setEnabled(!shownTypes.isEmpty());
803 * Returns a list of sequences - either the current selection group (if there
804 * is one), else the specified single sequence.
809 protected List<SequenceI> getSequenceScope(SequenceI seq)
811 List<SequenceI> forSequences = null;
812 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
813 if (selectionGroup != null && selectionGroup.getSize() > 0)
815 forSequences = selectionGroup.getSequences();
819 forSequences = seq == null ? Collections.<SequenceI> emptyList()
820 : Arrays.asList(seq);
826 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
829 * @param showOrHideMenu
831 * @param forSequences
832 * the sequences whose annotations may be shown or hidden
837 * if true this is a special label meaning 'All'
838 * @param actionIsShow
839 * if true, the select menu item action is to show the annotation
842 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
843 final List<SequenceI> forSequences, String calcId,
844 final List<String> types, final boolean allTypes,
845 final boolean actionIsShow)
847 String label = types.toString(); // [a, b, c]
848 label = label.substring(1, label.length() - 1); // a, b, c
849 final JMenuItem item = new JMenuItem(label);
850 item.setToolTipText(calcId);
851 item.addActionListener(new java.awt.event.ActionListener()
854 public void actionPerformed(ActionEvent e)
856 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
857 types, forSequences, allTypes, actionIsShow);
861 showOrHideMenu.add(item);
864 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
867 // TODO: usability: thread off the generation of group url content so root
869 // sequence only URLs
870 // ID/regex match URLs
871 groupLinksMenu = new JMenu(
872 MessageManager.getString("action.group_link"));
873 // three types of url that might be created.
874 JMenu[] linkMenus = new JMenu[] { null,
875 new JMenu(MessageManager.getString("action.ids")),
876 new JMenu(MessageManager.getString("action.sequences")),
877 new JMenu(MessageManager.getString("action.ids_sequences")) };
879 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
880 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
881 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
882 for (int sq = 0; sq < seqs.length; sq++)
885 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
886 .findPosition(sg.getEndRes());
887 // just collect ids from dataset sequence
888 // TODO: check if IDs collected from selecton group intersects with the
889 // current selection, too
890 SequenceI sqi = seqs[sq];
891 while (sqi.getDatasetSequence() != null)
893 sqi = sqi.getDatasetSequence();
895 DBRefEntry[] dbr = sqi.getDBRefs();
896 if (dbr != null && dbr.length > 0)
898 for (int d = 0; d < dbr.length; d++)
900 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
901 Object[] sarray = commonDbrefs.get(src);
904 sarray = new Object[2];
905 sarray[0] = new int[] { 0 };
906 sarray[1] = new String[seqs.length];
908 commonDbrefs.put(src, sarray);
911 if (((String[]) sarray[1])[sq] == null)
914 || (dbr[d].getMap().locateMappedRange(start, end) != null))
916 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
917 ((int[]) sarray[0])[0]++;
923 // now create group links for all distinct ID/sequence sets.
924 boolean addMenu = false; // indicates if there are any group links to give
926 for (String link : groupLinks)
928 GroupUrlLink urlLink = null;
931 urlLink = new GroupUrlLink(link);
932 } catch (Exception foo)
934 Cache.log.error("Exception for GroupURLLink '" + link
939 if (!urlLink.isValid())
941 Cache.log.error(urlLink.getInvalidMessage());
944 final String label = urlLink.getLabel();
945 boolean usingNames = false;
946 // Now see which parts of the group apply for this URL
947 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
948 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
949 String[] seqstr, ids; // input to makeUrl
952 int numinput = ((int[]) idset[0])[0];
953 String[] allids = ((String[]) idset[1]);
954 seqstr = new String[numinput];
955 ids = new String[numinput];
956 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
958 if (allids[sq] != null)
960 ids[idcount] = allids[sq];
961 seqstr[idcount++] = idandseqs[1][sq];
967 // just use the id/seq set
968 seqstr = idandseqs[1];
972 // and try and make the groupURL!
974 Object[] urlset = null;
977 urlset = urlLink.makeUrlStubs(ids, seqstr,
978 "FromJalview" + System.currentTimeMillis(), false);
979 } catch (UrlStringTooLongException e)
984 int type = urlLink.getGroupURLType() & 3;
985 // first two bits ofurlLink type bitfield are sequenceids and sequences
986 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
987 addshowLink(linkMenus[type], label
988 + (((type & 1) == 1) ? ("("
989 + (usingNames ? "Names" : ltarget) + ")") : ""),
996 groupLinksMenu = new JMenu(
997 MessageManager.getString("action.group_link"));
998 for (int m = 0; m < linkMenus.length; m++)
1000 if (linkMenus[m] != null
1001 && linkMenus[m].getMenuComponentCount() > 0)
1003 groupLinksMenu.add(linkMenus[m]);
1007 groupMenu.add(groupLinksMenu);
1012 * add a show URL menu item to the given linkMenu
1016 * - menu label string
1020 private void addshowLink(JMenu linkMenu, String label, final String url)
1022 JMenuItem item = new JMenuItem(label);
1023 item.setToolTipText(MessageManager.formatMessage(
1024 "label.open_url_param", new Object[] { url }));
1025 item.addActionListener(new java.awt.event.ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 new Thread(new Runnable()
1047 * add a late bound groupURL item to the given linkMenu
1051 * - menu label string
1052 * @param urlgenerator
1053 * GroupURLLink used to generate URL
1055 * Object array returned from the makeUrlStubs function.
1057 private void addshowLink(JMenu linkMenu, String label,
1058 final GroupUrlLink urlgenerator, final Object[] urlstub)
1060 JMenuItem item = new JMenuItem(label);
1061 item.setToolTipText(MessageManager.formatMessage(
1062 "label.open_url_seqs_param",
1063 new Object[] { urlgenerator.getUrl_prefix(),
1064 urlgenerator.getNumberInvolved(urlstub) }));
1065 // TODO: put in info about what is being sent.
1066 item.addActionListener(new ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 new Thread(new Runnable()
1079 showLink(urlgenerator.constructFrom(urlstub));
1080 } catch (UrlStringTooLongException e2)
1098 private void jbInit() throws Exception
1100 groupMenu.setText(MessageManager.getString("label.group"));
1101 groupMenu.setText(MessageManager.getString("label.selection"));
1102 groupName.setText(MessageManager.getString("label.name"));
1103 groupName.addActionListener(new java.awt.event.ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 groupName_actionPerformed();
1111 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1112 sequenceName.setText(MessageManager
1113 .getString("label.edit_name_description"));
1114 sequenceName.addActionListener(new java.awt.event.ActionListener()
1117 public void actionPerformed(ActionEvent e)
1119 sequenceName_actionPerformed();
1122 chooseAnnotations.setText(MessageManager
1123 .getString("action.choose_annotations"));
1124 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1127 public void actionPerformed(ActionEvent e)
1129 chooseAnnotations_actionPerformed(e);
1132 sequenceDetails.setText(MessageManager
1133 .getString("label.sequence_details"));
1134 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1137 public void actionPerformed(ActionEvent e)
1139 sequenceDetails_actionPerformed();
1142 sequenceSelDetails.setText(MessageManager
1143 .getString("label.sequence_details"));
1145 .addActionListener(new java.awt.event.ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 sequenceSelectionDetails_actionPerformed();
1153 PIDColour.setFocusPainted(false);
1155 .setText(MessageManager.getString("action.remove_group"));
1156 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 unGroupMenuItem_actionPerformed();
1164 createGroupMenuItem.setText(MessageManager
1165 .getString("action.create_group"));
1167 .addActionListener(new java.awt.event.ActionListener()
1170 public void actionPerformed(ActionEvent e)
1172 createGroupMenuItem_actionPerformed();
1176 outline.setText(MessageManager.getString("action.border_colour"));
1177 outline.addActionListener(new java.awt.event.ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 outline_actionPerformed();
1186 .setText(MessageManager.getString("label.nucleotide"));
1187 nucleotideMenuItem.addActionListener(new ActionListener()
1190 public void actionPerformed(ActionEvent e)
1192 nucleotideMenuItem_actionPerformed();
1195 colourMenu.setText(MessageManager.getString("label.group_colour"));
1196 showBoxes.setText(MessageManager.getString("action.boxes"));
1197 showBoxes.setState(true);
1198 showBoxes.addActionListener(new ActionListener()
1201 public void actionPerformed(ActionEvent e)
1203 showBoxes_actionPerformed();
1206 showText.setText(MessageManager.getString("action.text"));
1207 showText.setState(true);
1208 showText.addActionListener(new ActionListener()
1211 public void actionPerformed(ActionEvent e)
1213 showText_actionPerformed();
1216 showColourText.setText(MessageManager.getString("label.colour_text"));
1217 showColourText.addActionListener(new ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 showColourText_actionPerformed();
1225 displayNonconserved.setText(MessageManager
1226 .getString("label.show_non_conversed"));
1227 displayNonconserved.setState(true);
1228 displayNonconserved.addActionListener(new ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 showNonconserved_actionPerformed();
1236 editMenu.setText(MessageManager.getString("action.edit"));
1237 cut.setText(MessageManager.getString("action.cut"));
1238 cut.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 cut_actionPerformed();
1246 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1247 upperCase.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent e)
1255 copy.setText(MessageManager.getString("action.copy"));
1256 copy.addActionListener(new ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 copy_actionPerformed();
1264 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1265 lowerCase.addActionListener(new ActionListener()
1268 public void actionPerformed(ActionEvent e)
1273 toggle.setText(MessageManager.getString("label.toggle_case"));
1274 toggle.addActionListener(new ActionListener()
1277 public void actionPerformed(ActionEvent e)
1282 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1284 seqShowAnnotationsMenu.setText(MessageManager
1285 .getString("label.show_annotations"));
1286 seqHideAnnotationsMenu.setText(MessageManager
1287 .getString("label.hide_annotations"));
1288 groupShowAnnotationsMenu.setText(MessageManager
1289 .getString("label.show_annotations"));
1290 groupHideAnnotationsMenu.setText(MessageManager
1291 .getString("label.hide_annotations"));
1292 sequenceFeature.setText(MessageManager
1293 .getString("label.create_sequence_feature"));
1294 sequenceFeature.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent e)
1299 sequenceFeature_actionPerformed();
1302 textColour.setText(MessageManager.getString("label.text_colour"));
1303 textColour.addActionListener(new ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 textColour_actionPerformed();
1311 jMenu1.setText(MessageManager.getString("label.group"));
1312 pdbStructureDialog.setText(MessageManager
1313 .getString("label.show_pdbstruct_dialog"));
1314 pdbStructureDialog.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent actionEvent)
1319 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1320 if (ap.av.getSelectionGroup() != null)
1322 selectedSeqs = ap.av.getSequenceSelection();
1324 new StructureChooser(selectedSeqs, sequence, ap);
1328 rnaStructureMenu.setText(MessageManager
1329 .getString("label.view_rna_structure"));
1331 // colStructureMenu.setText("Colour By Structure");
1332 editSequence.setText(MessageManager.getString("label.edit_sequence")
1334 editSequence.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent actionEvent)
1339 editSequence_actionPerformed(actionEvent);
1342 makeReferenceSeq.setText(MessageManager
1343 .getString("label.mark_as_representative"));
1344 makeReferenceSeq.addActionListener(new ActionListener()
1348 public void actionPerformed(ActionEvent actionEvent)
1350 makeReferenceSeq_actionPerformed(actionEvent);
1354 hideInsertions.setText(MessageManager
1355 .getString("label.hide_insertions"));
1356 hideInsertions.addActionListener(new ActionListener()
1360 public void actionPerformed(ActionEvent e)
1362 hideInsertions_actionPerformed(e);
1366 * annotationMenuItem.setText("By Annotation");
1367 * annotationMenuItem.addActionListener(new ActionListener() { public void
1368 * actionPerformed(ActionEvent actionEvent) {
1369 * annotationMenuItem_actionPerformed(actionEvent); } });
1371 groupMenu.add(sequenceSelDetails);
1374 add(rnaStructureMenu);
1375 add(pdbStructureDialog);
1376 if (sequence != null)
1378 add(hideInsertions);
1380 // annotations configuration panel suppressed for now
1381 // groupMenu.add(chooseAnnotations);
1384 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1385 * (if a selection group is in force).
1387 sequenceMenu.add(seqShowAnnotationsMenu);
1388 sequenceMenu.add(seqHideAnnotationsMenu);
1389 sequenceMenu.add(seqAddReferenceAnnotations);
1390 groupMenu.add(groupShowAnnotationsMenu);
1391 groupMenu.add(groupHideAnnotationsMenu);
1392 groupMenu.add(groupAddReferenceAnnotations);
1393 groupMenu.add(editMenu);
1394 groupMenu.add(outputMenu);
1395 groupMenu.add(sequenceFeature);
1396 groupMenu.add(createGroupMenuItem);
1397 groupMenu.add(unGroupMenuItem);
1398 groupMenu.add(jMenu1);
1399 sequenceMenu.add(sequenceName);
1400 sequenceMenu.add(sequenceDetails);
1401 sequenceMenu.add(makeReferenceSeq);
1402 colourMenu.add(textColour);
1403 colourMenu.add(noColourmenuItem);
1404 colourMenu.add(clustalColour);
1405 colourMenu.add(BLOSUM62Colour);
1406 colourMenu.add(PIDColour);
1407 colourMenu.add(zappoColour);
1408 colourMenu.add(taylorColour);
1409 colourMenu.add(hydrophobicityColour);
1410 colourMenu.add(helixColour);
1411 colourMenu.add(strandColour);
1412 colourMenu.add(turnColour);
1413 colourMenu.add(buriedColour);
1414 colourMenu.add(nucleotideMenuItem);
1415 if (ap.getAlignment().isNucleotide())
1417 // JBPNote - commented since the colourscheme isn't functional
1418 colourMenu.add(purinePyrimidineColour);
1420 colourMenu.add(userDefinedColour);
1422 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1424 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1425 .getUserColourSchemes().keys();
1427 while (userColours.hasMoreElements())
1429 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1430 item.addActionListener(new ActionListener()
1433 public void actionPerformed(ActionEvent evt)
1435 userDefinedColour_actionPerformed(evt);
1438 colourMenu.add(item);
1442 colourMenu.addSeparator();
1443 colourMenu.add(abovePIDColour);
1444 colourMenu.add(conservationMenuItem);
1447 editMenu.add(editSequence);
1448 editMenu.add(upperCase);
1449 editMenu.add(lowerCase);
1450 editMenu.add(toggle);
1451 // JBPNote: These shouldn't be added here - should appear in a generic
1452 // 'apply web service to this sequence menu'
1453 // pdbMenu.add(RNAFold);
1454 // pdbMenu.add(ContraFold);
1455 jMenu1.add(groupName);
1456 jMenu1.add(colourMenu);
1457 jMenu1.add(showBoxes);
1458 jMenu1.add(showText);
1459 jMenu1.add(showColourText);
1460 jMenu1.add(outline);
1461 jMenu1.add(displayNonconserved);
1462 noColourmenuItem.setText(MessageManager.getString("label.none"));
1463 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1466 public void actionPerformed(ActionEvent e)
1468 noColourmenuItem_actionPerformed();
1472 clustalColour.setText(MessageManager
1473 .getString("label.clustalx_colours"));
1474 clustalColour.addActionListener(new java.awt.event.ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 clustalColour_actionPerformed();
1482 zappoColour.setText(MessageManager.getString("label.zappo"));
1483 zappoColour.addActionListener(new java.awt.event.ActionListener()
1486 public void actionPerformed(ActionEvent e)
1488 zappoColour_actionPerformed();
1491 taylorColour.setText(MessageManager.getString("label.taylor"));
1492 taylorColour.addActionListener(new java.awt.event.ActionListener()
1495 public void actionPerformed(ActionEvent e)
1497 taylorColour_actionPerformed();
1500 hydrophobicityColour.setText(MessageManager
1501 .getString("label.hydrophobicity"));
1502 hydrophobicityColour
1503 .addActionListener(new java.awt.event.ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 hydrophobicityColour_actionPerformed();
1511 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1512 helixColour.addActionListener(new java.awt.event.ActionListener()
1515 public void actionPerformed(ActionEvent e)
1517 helixColour_actionPerformed();
1520 strandColour.setText(MessageManager
1521 .getString("label.strand_propensity"));
1522 strandColour.addActionListener(new java.awt.event.ActionListener()
1525 public void actionPerformed(ActionEvent e)
1527 strandColour_actionPerformed();
1530 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1531 turnColour.addActionListener(new java.awt.event.ActionListener()
1534 public void actionPerformed(ActionEvent e)
1536 turnColour_actionPerformed();
1539 buriedColour.setText(MessageManager.getString("label.buried_index"));
1540 buriedColour.addActionListener(new java.awt.event.ActionListener()
1543 public void actionPerformed(ActionEvent e)
1545 buriedColour_actionPerformed();
1548 abovePIDColour.setText(MessageManager
1549 .getString("label.above_identity_percentage"));
1550 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1553 public void actionPerformed(ActionEvent e)
1555 abovePIDColour_actionPerformed();
1558 userDefinedColour.setText(MessageManager
1559 .getString("action.user_defined"));
1560 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1563 public void actionPerformed(ActionEvent e)
1565 userDefinedColour_actionPerformed(e);
1569 .setText(MessageManager.getString("label.percentage_identity"));
1570 PIDColour.addActionListener(new java.awt.event.ActionListener()
1573 public void actionPerformed(ActionEvent e)
1575 PIDColour_actionPerformed();
1578 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1579 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1582 public void actionPerformed(ActionEvent e)
1584 BLOSUM62Colour_actionPerformed();
1587 purinePyrimidineColour.setText(MessageManager
1588 .getString("label.purine_pyrimidine"));
1589 purinePyrimidineColour
1590 .addActionListener(new java.awt.event.ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 purinePyrimidineColour_actionPerformed();
1600 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1601 * public void actionPerformed(ActionEvent e) {
1602 * covariationColour_actionPerformed(); } });
1605 conservationMenuItem.setText(MessageManager
1606 .getString("label.conservation"));
1607 conservationMenuItem
1608 .addActionListener(new java.awt.event.ActionListener()
1611 public void actionPerformed(ActionEvent e)
1613 conservationMenuItem_actionPerformed();
1619 * Check for any annotations on the underlying dataset sequences (for the
1620 * current selection group) which are not 'on the alignment'.If any are found,
1621 * enable the option to add them to the alignment. The criteria for 'on the
1622 * alignment' is finding an alignment annotation on the alignment, matched on
1623 * calcId, label and sequenceRef.
1625 * A tooltip is also constructed that displays the source (calcId) and type
1626 * (label) of the annotations that can be added.
1629 * @param forSequences
1631 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1632 List<SequenceI> forSequences)
1634 menuItem.setEnabled(false);
1637 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1638 * Using TreeMap means calcIds are shown in alphabetical order.
1640 Map<String, String> tipEntries = new TreeMap<String, String>();
1641 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1642 AlignmentI al = this.ap.av.getAlignment();
1643 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1644 tipEntries, candidates, al);
1645 if (!candidates.isEmpty())
1647 StringBuilder tooltip = new StringBuilder(64);
1648 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1651 * Found annotations that could be added. Enable the menu item, and
1652 * configure its tooltip and action.
1654 menuItem.setEnabled(true);
1655 for (String calcId : tipEntries.keySet())
1657 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1659 String tooltipText = JvSwingUtils.wrapTooltip(true,
1660 tooltip.toString());
1661 menuItem.setToolTipText(tooltipText);
1663 menuItem.addActionListener(new ActionListener()
1666 public void actionPerformed(ActionEvent e)
1668 addReferenceAnnotations_actionPerformed(candidates);
1675 * Add annotations to the sequences and to the alignment.
1678 * a map whose keys are sequences on the alignment, and values a list
1679 * of annotations to add to each sequence
1681 protected void addReferenceAnnotations_actionPerformed(
1682 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1684 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1685 final AlignmentI alignment = this.ap.getAlignment();
1686 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1691 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1693 if (!ap.av.getAlignment().hasSeqrep())
1695 // initialise the display flags so the user sees something happen
1696 ap.av.setDisplayReferenceSeq(true);
1697 ap.av.setColourByReferenceSeq(true);
1698 ap.av.getAlignment().setSeqrep(sequence);
1702 if (ap.av.getAlignment().getSeqrep() == sequence)
1704 ap.av.getAlignment().setSeqrep(null);
1708 ap.av.getAlignment().setSeqrep(sequence);
1714 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1716 if (sequence != null)
1718 ColumnSelection cs = ap.av.getColumnSelection();
1721 cs = new ColumnSelection();
1723 cs.hideInsertionsFor(sequence);
1724 ap.av.setColumnSelection(cs);
1729 protected void sequenceSelectionDetails_actionPerformed()
1731 createSequenceDetailsReport(ap.av.getSequenceSelection());
1734 protected void sequenceDetails_actionPerformed()
1736 createSequenceDetailsReport(new SequenceI[] { sequence });
1739 public void createSequenceDetailsReport(SequenceI[] sequences)
1741 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1742 StringBuffer contents = new StringBuffer();
1743 for (SequenceI seq : sequences)
1745 contents.append("<p><h2>"
1748 "label.create_sequence_details_report_annotation_for",
1749 new Object[] { seq.getDisplayId(true) })
1751 new SequenceAnnotationReport(null)
1752 .createSequenceAnnotationReport(
1758 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1759 .getSeqPanel().seqCanvas.fr.getMinMax()
1761 contents.append("</p>");
1763 cap.setText("<html>" + contents.toString() + "</html>");
1765 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1766 "label.sequence_details_for",
1767 (sequences.length == 1 ? new Object[] { sequences[0]
1768 .getDisplayId(true) } : new Object[] { MessageManager
1769 .getString("label.selection") })), 500, 400);
1773 protected void showNonconserved_actionPerformed()
1775 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1780 * call to refresh view after settings change
1784 ap.updateAnnotation();
1785 ap.paintAlignment(true);
1787 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1796 protected void clustalColour_actionPerformed()
1798 SequenceGroup sg = getGroup();
1799 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1809 protected void zappoColour_actionPerformed()
1811 getGroup().cs = new ZappoColourScheme();
1821 protected void taylorColour_actionPerformed()
1823 getGroup().cs = new TaylorColourScheme();
1833 protected void hydrophobicityColour_actionPerformed()
1835 getGroup().cs = new HydrophobicColourScheme();
1845 protected void helixColour_actionPerformed()
1847 getGroup().cs = new HelixColourScheme();
1857 protected void strandColour_actionPerformed()
1859 getGroup().cs = new StrandColourScheme();
1869 protected void turnColour_actionPerformed()
1871 getGroup().cs = new TurnColourScheme();
1881 protected void buriedColour_actionPerformed()
1883 getGroup().cs = new BuriedColourScheme();
1893 public void nucleotideMenuItem_actionPerformed()
1895 getGroup().cs = new NucleotideColourScheme();
1899 protected void purinePyrimidineColour_actionPerformed()
1901 getGroup().cs = new PurinePyrimidineColourScheme();
1906 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1907 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1915 protected void abovePIDColour_actionPerformed()
1917 SequenceGroup sg = getGroup();
1923 if (abovePIDColour.isSelected())
1925 sg.cs.setConsensus(AAFrequency.calculate(
1926 sg.getSequences(ap.av.getHiddenRepSequences()),
1927 sg.getStartRes(), sg.getEndRes() + 1));
1929 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1932 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1934 SliderPanel.showPIDSlider();
1937 // remove PIDColouring
1939 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1951 protected void userDefinedColour_actionPerformed(ActionEvent e)
1953 SequenceGroup sg = getGroup();
1955 if (e.getSource().equals(userDefinedColour))
1957 new UserDefinedColours(ap, sg);
1961 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1962 .getUserColourSchemes().get(e.getActionCommand());
1970 * Open a panel where the user can choose which types of sequence annotation
1975 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1977 // todo correct way to guard against opening a duplicate panel?
1978 new AnnotationChooser(ap);
1987 protected void PIDColour_actionPerformed()
1989 SequenceGroup sg = getGroup();
1990 sg.cs = new PIDColourScheme();
1991 sg.cs.setConsensus(AAFrequency.calculate(
1992 sg.getSequences(ap.av.getHiddenRepSequences()),
1993 sg.getStartRes(), sg.getEndRes() + 1));
2003 protected void BLOSUM62Colour_actionPerformed()
2005 SequenceGroup sg = getGroup();
2007 sg.cs = new Blosum62ColourScheme();
2009 sg.cs.setConsensus(AAFrequency.calculate(
2010 sg.getSequences(ap.av.getHiddenRepSequences()),
2011 sg.getStartRes(), sg.getEndRes() + 1));
2022 protected void noColourmenuItem_actionPerformed()
2024 getGroup().cs = null;
2034 protected void conservationMenuItem_actionPerformed()
2036 SequenceGroup sg = getGroup();
2042 if (conservationMenuItem.isSelected())
2044 // JBPNote: Conservation name shouldn't be i18n translated
2045 Conservation c = new Conservation("Group",
2046 ResidueProperties.propHash, 3, sg.getSequences(ap.av
2047 .getHiddenRepSequences()), sg.getStartRes(),
2048 sg.getEndRes() + 1);
2051 c.verdict(false, ap.av.getConsPercGaps());
2053 sg.cs.setConservation(c);
2055 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2056 SliderPanel.showConservationSlider();
2059 // remove ConservationColouring
2061 sg.cs.setConservation(null);
2067 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2069 SequenceGroup sg = getGroup();
2075 AnnotationColourGradient acg = new AnnotationColourGradient(
2076 sequence.getAnnotation()[0], null,
2077 AnnotationColourGradient.NO_THRESHOLD);
2079 acg.setPredefinedColours(true);
2091 protected void groupName_actionPerformed()
2094 SequenceGroup sg = getGroup();
2095 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2096 sg.getDescription(), " "
2097 + MessageManager.getString("label.group_name") + " ",
2098 MessageManager.getString("label.group_description") + " ",
2099 MessageManager.getString("label.edit_group_name_description"),
2107 sg.setName(dialog.getName());
2108 sg.setDescription(dialog.getDescription());
2113 * Get selection group - adding it to the alignment if necessary.
2115 * @return sequence group to operate on
2117 SequenceGroup getGroup()
2119 SequenceGroup sg = ap.av.getSelectionGroup();
2120 // this method won't add a new group if it already exists
2123 ap.av.getAlignment().addGroup(sg);
2135 void sequenceName_actionPerformed()
2137 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2138 sequence.getDescription(),
2139 " " + MessageManager.getString("label.sequence_name")
2141 MessageManager.getString("label.sequence_description") + " ",
2143 .getString("label.edit_sequence_name_description"),
2151 if (dialog.getName() != null)
2153 if (dialog.getName().indexOf(" ") > -1)
2159 .getString("label.spaces_converted_to_backslashes"),
2161 .getString("label.no_spaces_allowed_sequence_name"),
2162 JOptionPane.WARNING_MESSAGE);
2165 sequence.setName(dialog.getName().replace(' ', '_'));
2166 ap.paintAlignment(false);
2169 sequence.setDescription(dialog.getDescription());
2171 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2182 void unGroupMenuItem_actionPerformed()
2184 SequenceGroup sg = ap.av.getSelectionGroup();
2185 ap.av.getAlignment().deleteGroup(sg);
2186 ap.av.setSelectionGroup(null);
2190 void createGroupMenuItem_actionPerformed()
2192 getGroup(); // implicitly creates group - note - should apply defaults / use
2193 // standard alignment window logic for this
2203 protected void outline_actionPerformed()
2205 SequenceGroup sg = getGroup();
2206 Color col = JColorChooser.showDialog(this,
2207 MessageManager.getString("label.select_outline_colour"),
2212 sg.setOutlineColour(col);
2224 public void showBoxes_actionPerformed()
2226 getGroup().setDisplayBoxes(showBoxes.isSelected());
2236 public void showText_actionPerformed()
2238 getGroup().setDisplayText(showText.isSelected());
2248 public void showColourText_actionPerformed()
2250 getGroup().setColourText(showColourText.isSelected());
2254 public void showLink(String url)
2258 jalview.util.BrowserLauncher.openURL(url);
2259 } catch (Exception ex)
2261 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2262 MessageManager.getString("label.web_browser_not_found_unix"),
2263 MessageManager.getString("label.web_browser_not_found"),
2264 JOptionPane.WARNING_MESSAGE);
2266 ex.printStackTrace();
2270 void hideSequences(boolean representGroup)
2272 ap.av.hideSequences(sequence, representGroup);
2275 public void copy_actionPerformed()
2277 ap.alignFrame.copy_actionPerformed(null);
2280 public void cut_actionPerformed()
2282 ap.alignFrame.cut_actionPerformed(null);
2285 void changeCase(ActionEvent e)
2287 Object source = e.getSource();
2288 SequenceGroup sg = ap.av.getSelectionGroup();
2292 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2293 sg.getStartRes(), sg.getEndRes() + 1);
2298 if (source == toggle)
2300 description = MessageManager.getString("label.toggle_case");
2301 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2303 else if (source == upperCase)
2305 description = MessageManager.getString("label.to_upper_case");
2306 caseChange = ChangeCaseCommand.TO_UPPER;
2310 description = MessageManager.getString("label.to_lower_case");
2311 caseChange = ChangeCaseCommand.TO_LOWER;
2314 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2315 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2316 startEnd, caseChange);
2318 ap.alignFrame.addHistoryItem(caseCommand);
2320 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2326 public void outputText_actionPerformed(ActionEvent e)
2328 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2329 cap.setForInput(null);
2330 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2331 "label.alignment_output_command",
2332 new Object[] { e.getActionCommand() }), 600, 500);
2334 String[] omitHidden = null;
2336 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2337 // or we simply trust the user wants
2338 // wysiwig behaviour
2340 cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
2344 public void sequenceFeature_actionPerformed()
2346 SequenceGroup sg = ap.av.getSelectionGroup();
2352 int rsize = 0, gSize = sg.getSize();
2353 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2354 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2356 for (int i = 0; i < gSize; i++)
2358 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2359 int end = sg.findEndRes(sg.getSequenceAt(i));
2362 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2363 features[rsize] = new SequenceFeature(null, null, null, start, end,
2368 rseqs = new SequenceI[rsize];
2369 tfeatures = new SequenceFeature[rsize];
2370 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2371 System.arraycopy(features, 0, tfeatures, 0, rsize);
2372 features = tfeatures;
2374 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2375 features, true, ap))
2377 ap.alignFrame.setShowSeqFeatures(true);
2378 ap.highlightSearchResults(null);
2382 public void textColour_actionPerformed()
2384 SequenceGroup sg = getGroup();
2387 new TextColourChooser().chooseColour(ap, sg);
2391 public void colourByStructure(String pdbid)
2393 Annotation[] anots = ap.av.getStructureSelectionManager()
2394 .colourSequenceFromStructure(sequence, pdbid);
2396 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2397 "Coloured by " + pdbid, anots);
2399 ap.av.getAlignment().addAnnotation(an);
2400 an.createSequenceMapping(sequence, 0, true);
2401 // an.adjustForAlignment();
2402 ap.av.getAlignment().setAnnotationIndex(an, 0);
2404 ap.adjustAnnotationHeight();
2406 sequence.addAlignmentAnnotation(an);
2410 public void editSequence_actionPerformed(ActionEvent actionEvent)
2412 SequenceGroup sg = ap.av.getSelectionGroup();
2416 if (sequence == null)
2418 sequence = sg.getSequenceAt(0);
2421 EditNameDialog dialog = new EditNameDialog(
2422 sequence.getSequenceAsString(sg.getStartRes(),
2423 sg.getEndRes() + 1), null,
2424 MessageManager.getString("label.edit_sequence"), null,
2425 MessageManager.getString("label.edit_sequence"),
2430 EditCommand editCommand = new EditCommand(
2431 MessageManager.getString("label.edit_sequences"),
2432 Action.REPLACE, dialog.getName().replace(' ',
2433 ap.av.getGapCharacter()),
2434 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2435 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2437 ap.alignFrame.addHistoryItem(editCommand);
2439 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()