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.FileFormat;
42 import jalview.io.FileFormatI;
43 import jalview.io.FormatAdapter;
44 import jalview.io.SequenceAnnotationReport;
45 import jalview.schemes.AnnotationColourGradient;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.BuriedColourScheme;
48 import jalview.schemes.ClustalxColourScheme;
49 import jalview.schemes.HelixColourScheme;
50 import jalview.schemes.HydrophobicColourScheme;
51 import jalview.schemes.NucleotideColourScheme;
52 import jalview.schemes.PIDColourScheme;
53 import jalview.schemes.PurinePyrimidineColourScheme;
54 import jalview.schemes.ResidueProperties;
55 import jalview.schemes.StrandColourScheme;
56 import jalview.schemes.TaylorColourScheme;
57 import jalview.schemes.TurnColourScheme;
58 import jalview.schemes.UserColourScheme;
59 import jalview.schemes.ZappoColourScheme;
60 import jalview.util.DBRefUtils;
61 import jalview.util.GroupUrlLink;
62 import jalview.util.GroupUrlLink.UrlStringTooLongException;
63 import jalview.util.MessageManager;
64 import jalview.util.UrlLink;
66 import java.awt.Color;
67 import java.awt.event.ActionEvent;
68 import java.awt.event.ActionListener;
69 import java.util.ArrayList;
70 import java.util.Arrays;
71 import java.util.Collections;
72 import java.util.Hashtable;
73 import java.util.LinkedHashMap;
74 import java.util.List;
76 import java.util.TreeMap;
77 import java.util.Vector;
79 import javax.swing.ButtonGroup;
80 import javax.swing.JCheckBoxMenuItem;
81 import javax.swing.JColorChooser;
82 import javax.swing.JMenu;
83 import javax.swing.JMenuItem;
84 import javax.swing.JOptionPane;
85 import javax.swing.JPopupMenu;
86 import javax.swing.JRadioButtonMenuItem;
92 * @version $Revision: 1.118 $
94 public class PopupMenu extends JPopupMenu
96 JMenu groupMenu = new JMenu();
98 JMenuItem groupName = new JMenuItem();
100 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
102 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
104 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
114 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
116 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
118 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
120 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
122 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
124 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
126 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
128 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
130 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
134 JMenu sequenceMenu = new JMenu();
136 JMenuItem sequenceName = new JMenuItem();
138 JMenuItem sequenceDetails = new JMenuItem();
140 JMenuItem sequenceSelDetails = new JMenuItem();
142 JMenuItem makeReferenceSeq = new JMenuItem();
144 JMenuItem chooseAnnotations = new JMenuItem();
148 JMenuItem createGroupMenuItem = new JMenuItem();
150 JMenuItem unGroupMenuItem = new JMenuItem();
152 JMenuItem outline = new JMenuItem();
154 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
156 JMenu colourMenu = new JMenu();
158 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
160 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
162 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
164 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
166 JMenu editMenu = new JMenu();
168 JMenuItem cut = new JMenuItem();
170 JMenuItem copy = new JMenuItem();
172 JMenuItem upperCase = new JMenuItem();
174 JMenuItem lowerCase = new JMenuItem();
176 JMenuItem toggle = new JMenuItem();
178 JMenu pdbMenu = new JMenu();
180 JMenu outputMenu = new JMenu();
182 JMenu seqShowAnnotationsMenu = new JMenu();
184 JMenu seqHideAnnotationsMenu = new JMenu();
186 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
187 MessageManager.getString("label.add_reference_annotations"));
189 JMenu groupShowAnnotationsMenu = new JMenu();
191 JMenu groupHideAnnotationsMenu = new JMenu();
193 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
194 MessageManager.getString("label.add_reference_annotations"));
196 JMenuItem sequenceFeature = new JMenuItem();
198 JMenuItem textColour = new JMenuItem();
200 JMenu jMenu1 = new JMenu();
202 JMenuItem pdbStructureDialog = new JMenuItem();
204 JMenu rnaStructureMenu = new JMenu();
206 JMenuItem editSequence = new JMenuItem();
208 JMenu groupLinksMenu;
210 JMenuItem hideInsertions = new JMenuItem();
213 * Creates a new PopupMenu object.
220 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
222 this(ap, seq, links, null);
232 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
233 List<String> links, List<String> groupLinks)
235 // /////////////////////////////////////////////////////////
236 // If this is activated from the sequence panel, the user may want to
237 // edit or annotate a particular residue. Therefore display the residue menu
239 // If from the IDPanel, we must display the sequence menu
240 // ////////////////////////////////////////////////////////
244 ButtonGroup colours = new ButtonGroup();
245 colours.add(noColourmenuItem);
246 colours.add(clustalColour);
247 colours.add(zappoColour);
248 colours.add(taylorColour);
249 colours.add(hydrophobicityColour);
250 colours.add(helixColour);
251 colours.add(strandColour);
252 colours.add(turnColour);
253 colours.add(buriedColour);
254 colours.add(abovePIDColour);
255 colours.add(userDefinedColour);
256 colours.add(PIDColour);
257 colours.add(BLOSUM62Colour);
258 colours.add(purinePyrimidineColour);
259 colours.add(RNAInteractionColour);
261 for (String ff : FileFormat.getWritableFormats())
263 JMenuItem item = new JMenuItem(ff);
265 item.addActionListener(new java.awt.event.ActionListener()
268 public void actionPerformed(ActionEvent e)
270 outputText_actionPerformed(e);
274 outputMenu.add(item);
278 * Build menus for annotation types that may be shown or hidden, and for
279 * 'reference annotations' that may be added to the alignment. First for the
280 * currently selected sequence (if there is one):
282 final List<SequenceI> selectedSequence = (seq == null ? Collections
283 .<SequenceI> emptyList() : Arrays.asList(seq));
284 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
285 seqHideAnnotationsMenu, selectedSequence);
286 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
290 * And repeat for the current selection group (if there is one):
292 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
293 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
295 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
296 groupHideAnnotationsMenu, selectedGroup);
297 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
303 } catch (Exception e)
311 sequenceMenu.setText(sequence.getName());
312 if (seq == ap.av.getAlignment().getSeqrep())
314 makeReferenceSeq.setText(MessageManager
315 .getString("action.unmark_as_reference"));
319 makeReferenceSeq.setText(MessageManager
320 .getString("action.set_as_reference"));
323 if (!ap.av.getAlignment().isNucleotide())
325 remove(rnaStructureMenu);
329 int origCount = rnaStructureMenu.getItemCount();
331 * add menu items to 2D-render any alignment or sequence secondary
332 * structure annotation
334 AlignmentAnnotation[] aas = ap.av.getAlignment()
335 .getAlignmentAnnotation();
338 for (final AlignmentAnnotation aa : aas)
340 if (aa.isValidStruc() && aa.sequenceRef == null)
343 * valid alignment RNA secondary structure annotation
345 menuItem = new JMenuItem();
346 menuItem.setText(MessageManager.formatMessage(
347 "label.2d_rna_structure_line",
348 new Object[] { aa.label }));
349 menuItem.addActionListener(new java.awt.event.ActionListener()
352 public void actionPerformed(ActionEvent e)
354 new AppVarna(seq, aa, ap);
357 rnaStructureMenu.add(menuItem);
362 if (seq.getAnnotation() != null)
364 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
365 for (final AlignmentAnnotation aa : seqAnns)
367 if (aa.isValidStruc())
370 * valid sequence RNA secondary structure annotation
372 // TODO: make rnastrucF a bit more nice
373 menuItem = new JMenuItem();
374 menuItem.setText(MessageManager.formatMessage(
375 "label.2d_rna_sequence_name",
376 new Object[] { seq.getName() }));
377 menuItem.addActionListener(new java.awt.event.ActionListener()
380 public void actionPerformed(ActionEvent e)
382 // TODO: VARNA does'nt print gaps in the sequence
383 new AppVarna(seq, aa, ap);
386 rnaStructureMenu.add(menuItem);
390 if (rnaStructureMenu.getItemCount() == origCount)
392 remove(rnaStructureMenu);
396 menuItem = new JMenuItem(
397 MessageManager.getString("action.hide_sequences"));
398 menuItem.addActionListener(new java.awt.event.ActionListener()
401 public void actionPerformed(ActionEvent e)
403 hideSequences(false);
408 if (ap.av.getSelectionGroup() != null
409 && ap.av.getSelectionGroup().getSize() > 1)
411 menuItem = new JMenuItem(MessageManager.formatMessage(
412 "label.represent_group_with",
413 new Object[] { seq.getName() }));
414 menuItem.addActionListener(new java.awt.event.ActionListener()
417 public void actionPerformed(ActionEvent e)
422 sequenceMenu.add(menuItem);
425 if (ap.av.hasHiddenRows())
427 final int index = ap.av.getAlignment().findIndex(seq);
429 if (ap.av.adjustForHiddenSeqs(index)
430 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
432 menuItem = new JMenuItem(
433 MessageManager.getString("action.reveal_sequences"));
434 menuItem.addActionListener(new ActionListener()
437 public void actionPerformed(ActionEvent e)
439 ap.av.showSequence(index);
440 if (ap.overviewPanel != null)
442 ap.overviewPanel.updateOverviewImage();
450 // for the case when no sequences are even visible
451 if (ap.av.hasHiddenRows())
454 menuItem = new JMenuItem(
455 MessageManager.getString("action.reveal_all"));
456 menuItem.addActionListener(new ActionListener()
459 public void actionPerformed(ActionEvent e)
461 ap.av.showAllHiddenSeqs();
462 if (ap.overviewPanel != null)
464 ap.overviewPanel.updateOverviewImage();
474 SequenceGroup sg = ap.av.getSelectionGroup();
475 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
476 .getGroups().contains(sg) : false;
478 if (sg != null && sg.getSize() > 0)
480 groupName.setText(MessageManager
481 .getString("label.edit_name_and_description_current_group"));
483 if (sg.cs instanceof ZappoColourScheme)
485 zappoColour.setSelected(true);
487 else if (sg.cs instanceof TaylorColourScheme)
489 taylorColour.setSelected(true);
491 else if (sg.cs instanceof PIDColourScheme)
493 PIDColour.setSelected(true);
495 else if (sg.cs instanceof Blosum62ColourScheme)
497 BLOSUM62Colour.setSelected(true);
499 else if (sg.cs instanceof UserColourScheme)
501 userDefinedColour.setSelected(true);
503 else if (sg.cs instanceof HydrophobicColourScheme)
505 hydrophobicityColour.setSelected(true);
507 else if (sg.cs instanceof HelixColourScheme)
509 helixColour.setSelected(true);
511 else if (sg.cs instanceof StrandColourScheme)
513 strandColour.setSelected(true);
515 else if (sg.cs instanceof TurnColourScheme)
517 turnColour.setSelected(true);
519 else if (sg.cs instanceof BuriedColourScheme)
521 buriedColour.setSelected(true);
523 else if (sg.cs instanceof ClustalxColourScheme)
525 clustalColour.setSelected(true);
527 else if (sg.cs instanceof PurinePyrimidineColourScheme)
529 purinePyrimidineColour.setSelected(true);
533 * else if (sg.cs instanceof CovariationColourScheme) {
534 * covariationColour.setSelected(true); }
538 noColourmenuItem.setSelected(true);
541 if (sg.cs != null && sg.cs.conservationApplied())
543 conservationMenuItem.setSelected(true);
545 displayNonconserved.setSelected(sg.getShowNonconserved());
546 showText.setSelected(sg.getDisplayText());
547 showColourText.setSelected(sg.getColourText());
548 showBoxes.setSelected(sg.getDisplayBoxes());
549 // add any groupURLs to the groupURL submenu and make it visible
550 if (groupLinks != null && groupLinks.size() > 0)
552 buildGroupURLMenu(sg, groupLinks);
554 // Add a 'show all structures' for the current selection
555 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
556 SequenceI sqass = null;
557 for (SequenceI sq : ap.av.getSequenceSelection())
559 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
560 if (pes != null && pes.size() > 0)
562 reppdb.put(pes.get(0).getId(), pes.get(0));
563 for (PDBEntry pe : pes)
565 pdbe.put(pe.getId(), pe);
575 final PDBEntry[] pe = pdbe.values().toArray(
576 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
577 new PDBEntry[reppdb.size()]);
578 final JMenuItem gpdbview, rpdbview;
583 groupMenu.setVisible(false);
584 editMenu.setVisible(false);
589 createGroupMenuItem.setVisible(true);
590 unGroupMenuItem.setVisible(false);
591 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
595 createGroupMenuItem.setVisible(false);
596 unGroupMenuItem.setVisible(true);
597 jMenu1.setText(MessageManager.getString("action.edit_group"));
602 sequenceMenu.setVisible(false);
603 pdbStructureDialog.setVisible(false);
604 rnaStructureMenu.setVisible(false);
607 if (links != null && links.size() > 0)
609 addFeatureLinks(seq, links);
614 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
619 void addFeatureLinks(final SequenceI seq, List<String> links)
621 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
622 List<String> linkset = new ArrayList<String>();
623 for (String link : links)
625 UrlLink urlLink = null;
628 urlLink = new UrlLink(link);
629 } catch (Exception foo)
631 Cache.log.error("Exception for URLLink '" + link + "'", foo);
635 if (!urlLink.isValid())
637 Cache.log.error(urlLink.getInvalidMessage());
640 final String label = urlLink.getLabel();
641 if (seq != null && urlLink.isDynamic())
644 // collect matching db-refs
645 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
646 new String[] { urlLink.getTarget() });
647 // collect id string too
648 String id = seq.getName();
649 String descr = seq.getDescription();
650 if (descr != null && descr.length() < 1)
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 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
669 for (int u = 0; u < urls.length; u += 2)
671 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
673 linkset.add(urls[u] + "|" + urls[u + 1]);
674 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
682 // create Bare ID link for this URL
683 String[] urls = urlLink.makeUrls(id, true);
686 for (int u = 0; u < urls.length; u += 2)
688 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
690 linkset.add(urls[u] + "|" + urls[u + 1]);
691 addshowLink(linkMenu, label, urls[u + 1]);
696 // Create urls from description but only for URL links which are regex
698 if (descr != null && urlLink.getRegexReplace() != null)
700 // create link for this URL from description where regex matches
701 String[] urls = urlLink.makeUrls(descr, true);
704 for (int u = 0; u < urls.length; u += 2)
706 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
708 linkset.add(urls[u] + "|" + urls[u + 1]);
709 addshowLink(linkMenu, label, urls[u + 1]);
717 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
719 linkset.add(label + "|" + urlLink.getUrl_prefix());
720 // Add a non-dynamic link
721 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
725 if (sequence != null)
727 sequenceMenu.add(linkMenu);
736 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
737 * "All" is added first, followed by a separator. Then add any annotation
738 * types associated with the current selection. Separate menus are built for
739 * the selected sequence group (if any), and the selected sequence.
741 * Some annotation rows are always rendered together - these can be identified
742 * by a common graphGroup property > -1. Only one of each group will be marked
743 * as visible (to avoid duplication of the display). For such groups we add a
744 * composite type name, e.g.
746 * IUPredWS (Long), IUPredWS (Short)
750 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
751 List<SequenceI> forSequences)
753 showMenu.removeAll();
754 hideMenu.removeAll();
756 final List<String> all = Arrays.asList(new String[] { MessageManager
757 .getString("label.all") });
758 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
759 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
761 showMenu.addSeparator();
762 hideMenu.addSeparator();
764 final AlignmentAnnotation[] annotations = ap.getAlignment()
765 .getAlignmentAnnotation();
768 * Find shown/hidden annotations types, distinguished by source (calcId),
769 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
770 * the insertion order, which is the order of the annotations on the
773 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
774 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
775 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
776 AlignmentAnnotationUtils.asList(annotations), forSequences);
778 for (String calcId : hiddenTypes.keySet())
780 for (List<String> type : hiddenTypes.get(calcId))
782 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
786 // grey out 'show annotations' if none are hidden
787 showMenu.setEnabled(!hiddenTypes.isEmpty());
789 for (String calcId : shownTypes.keySet())
791 for (List<String> type : shownTypes.get(calcId))
793 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
797 // grey out 'hide annotations' if none are shown
798 hideMenu.setEnabled(!shownTypes.isEmpty());
802 * Returns a list of sequences - either the current selection group (if there
803 * is one), else the specified single sequence.
808 protected List<SequenceI> getSequenceScope(SequenceI seq)
810 List<SequenceI> forSequences = null;
811 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
812 if (selectionGroup != null && selectionGroup.getSize() > 0)
814 forSequences = selectionGroup.getSequences();
818 forSequences = seq == null ? Collections.<SequenceI> emptyList()
819 : Arrays.asList(seq);
825 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
828 * @param showOrHideMenu
830 * @param forSequences
831 * the sequences whose annotations may be shown or hidden
836 * if true this is a special label meaning 'All'
837 * @param actionIsShow
838 * if true, the select menu item action is to show the annotation
841 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
842 final List<SequenceI> forSequences, String calcId,
843 final List<String> types, final boolean allTypes,
844 final boolean actionIsShow)
846 String label = types.toString(); // [a, b, c]
847 label = label.substring(1, label.length() - 1); // a, b, c
848 final JMenuItem item = new JMenuItem(label);
849 item.setToolTipText(calcId);
850 item.addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
856 types, forSequences, allTypes, actionIsShow);
860 showOrHideMenu.add(item);
863 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
866 // TODO: usability: thread off the generation of group url content so root
868 // sequence only URLs
869 // ID/regex match URLs
870 groupLinksMenu = new JMenu(
871 MessageManager.getString("action.group_link"));
872 // three types of url that might be created.
873 JMenu[] linkMenus = new JMenu[] { null,
874 new JMenu(MessageManager.getString("action.ids")),
875 new JMenu(MessageManager.getString("action.sequences")),
876 new JMenu(MessageManager.getString("action.ids_sequences")) };
878 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
879 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
880 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
881 for (int sq = 0; sq < seqs.length; sq++)
884 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
885 .findPosition(sg.getEndRes());
886 // just collect ids from dataset sequence
887 // TODO: check if IDs collected from selecton group intersects with the
888 // current selection, too
889 SequenceI sqi = seqs[sq];
890 while (sqi.getDatasetSequence() != null)
892 sqi = sqi.getDatasetSequence();
894 DBRefEntry[] dbr = sqi.getDBRefs();
895 if (dbr != null && dbr.length > 0)
897 for (int d = 0; d < dbr.length; d++)
899 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
900 Object[] sarray = commonDbrefs.get(src);
903 sarray = new Object[2];
904 sarray[0] = new int[] { 0 };
905 sarray[1] = new String[seqs.length];
907 commonDbrefs.put(src, sarray);
910 if (((String[]) sarray[1])[sq] == null)
913 || (dbr[d].getMap().locateMappedRange(start, end) != null))
915 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
916 ((int[]) sarray[0])[0]++;
922 // now create group links for all distinct ID/sequence sets.
923 boolean addMenu = false; // indicates if there are any group links to give
925 for (String link : groupLinks)
927 GroupUrlLink urlLink = null;
930 urlLink = new GroupUrlLink(link);
931 } catch (Exception foo)
933 Cache.log.error("Exception for GroupURLLink '" + link
938 if (!urlLink.isValid())
940 Cache.log.error(urlLink.getInvalidMessage());
943 final String label = urlLink.getLabel();
944 boolean usingNames = false;
945 // Now see which parts of the group apply for this URL
946 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
947 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
948 String[] seqstr, ids; // input to makeUrl
951 int numinput = ((int[]) idset[0])[0];
952 String[] allids = ((String[]) idset[1]);
953 seqstr = new String[numinput];
954 ids = new String[numinput];
955 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
957 if (allids[sq] != null)
959 ids[idcount] = allids[sq];
960 seqstr[idcount++] = idandseqs[1][sq];
966 // just use the id/seq set
967 seqstr = idandseqs[1];
971 // and try and make the groupURL!
973 Object[] urlset = null;
976 urlset = urlLink.makeUrlStubs(ids, seqstr,
977 "FromJalview" + System.currentTimeMillis(), false);
978 } catch (UrlStringTooLongException e)
983 int type = urlLink.getGroupURLType() & 3;
984 // first two bits ofurlLink type bitfield are sequenceids and sequences
985 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
986 addshowLink(linkMenus[type], label
987 + (((type & 1) == 1) ? ("("
988 + (usingNames ? "Names" : ltarget) + ")") : ""),
995 groupLinksMenu = new JMenu(
996 MessageManager.getString("action.group_link"));
997 for (int m = 0; m < linkMenus.length; m++)
999 if (linkMenus[m] != null
1000 && linkMenus[m].getMenuComponentCount() > 0)
1002 groupLinksMenu.add(linkMenus[m]);
1006 groupMenu.add(groupLinksMenu);
1011 * add a show URL menu item to the given linkMenu
1015 * - menu label string
1019 private void addshowLink(JMenu linkMenu, String label, final String url)
1021 JMenuItem item = new JMenuItem(label);
1022 item.setToolTipText(MessageManager.formatMessage(
1023 "label.open_url_param", new Object[] { url }));
1024 item.addActionListener(new java.awt.event.ActionListener()
1027 public void actionPerformed(ActionEvent e)
1029 new Thread(new Runnable()
1046 * add a late bound groupURL item to the given linkMenu
1050 * - menu label string
1051 * @param urlgenerator
1052 * GroupURLLink used to generate URL
1054 * Object array returned from the makeUrlStubs function.
1056 private void addshowLink(JMenu linkMenu, String label,
1057 final GroupUrlLink urlgenerator, final Object[] urlstub)
1059 JMenuItem item = new JMenuItem(label);
1060 item.setToolTipText(MessageManager.formatMessage(
1061 "label.open_url_seqs_param",
1062 new Object[] { urlgenerator.getUrl_prefix(),
1063 urlgenerator.getNumberInvolved(urlstub) }));
1064 // TODO: put in info about what is being sent.
1065 item.addActionListener(new ActionListener()
1068 public void actionPerformed(ActionEvent e)
1070 new Thread(new Runnable()
1078 showLink(urlgenerator.constructFrom(urlstub));
1079 } catch (UrlStringTooLongException e2)
1097 private void jbInit() throws Exception
1099 groupMenu.setText(MessageManager.getString("label.selection"));
1100 groupName.setText(MessageManager.getString("label.name"));
1101 groupName.addActionListener(new java.awt.event.ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 groupName_actionPerformed();
1109 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1110 sequenceName.setText(MessageManager
1111 .getString("label.edit_name_description"));
1112 sequenceName.addActionListener(new java.awt.event.ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 sequenceName_actionPerformed();
1120 chooseAnnotations.setText(MessageManager
1121 .getString("action.choose_annotations"));
1122 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 chooseAnnotations_actionPerformed(e);
1130 sequenceDetails.setText(MessageManager
1131 .getString("label.sequence_details"));
1132 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 sequenceDetails_actionPerformed();
1140 sequenceSelDetails.setText(MessageManager
1141 .getString("label.sequence_details"));
1143 .addActionListener(new java.awt.event.ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 sequenceSelectionDetails_actionPerformed();
1151 PIDColour.setFocusPainted(false);
1153 .setText(MessageManager.getString("action.remove_group"));
1154 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 unGroupMenuItem_actionPerformed();
1162 createGroupMenuItem.setText(MessageManager
1163 .getString("action.create_group"));
1165 .addActionListener(new java.awt.event.ActionListener()
1168 public void actionPerformed(ActionEvent e)
1170 createGroupMenuItem_actionPerformed();
1174 outline.setText(MessageManager.getString("action.border_colour"));
1175 outline.addActionListener(new java.awt.event.ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 outline_actionPerformed();
1184 .setText(MessageManager.getString("label.nucleotide"));
1185 nucleotideMenuItem.addActionListener(new ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 nucleotideMenuItem_actionPerformed();
1193 colourMenu.setText(MessageManager.getString("label.group_colour"));
1194 showBoxes.setText(MessageManager.getString("action.boxes"));
1195 showBoxes.setState(true);
1196 showBoxes.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 showBoxes_actionPerformed();
1204 showText.setText(MessageManager.getString("action.text"));
1205 showText.setState(true);
1206 showText.addActionListener(new ActionListener()
1209 public void actionPerformed(ActionEvent e)
1211 showText_actionPerformed();
1214 showColourText.setText(MessageManager.getString("label.colour_text"));
1215 showColourText.addActionListener(new ActionListener()
1218 public void actionPerformed(ActionEvent e)
1220 showColourText_actionPerformed();
1223 displayNonconserved.setText(MessageManager
1224 .getString("label.show_non_conversed"));
1225 displayNonconserved.setState(true);
1226 displayNonconserved.addActionListener(new ActionListener()
1229 public void actionPerformed(ActionEvent e)
1231 showNonconserved_actionPerformed();
1234 editMenu.setText(MessageManager.getString("action.edit"));
1235 cut.setText(MessageManager.getString("action.cut"));
1236 cut.addActionListener(new ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 cut_actionPerformed();
1244 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1245 upperCase.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent e)
1253 copy.setText(MessageManager.getString("action.copy"));
1254 copy.addActionListener(new ActionListener()
1257 public void actionPerformed(ActionEvent e)
1259 copy_actionPerformed();
1262 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1263 lowerCase.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1271 toggle.setText(MessageManager.getString("label.toggle_case"));
1272 toggle.addActionListener(new ActionListener()
1275 public void actionPerformed(ActionEvent e)
1280 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1282 seqShowAnnotationsMenu.setText(MessageManager
1283 .getString("label.show_annotations"));
1284 seqHideAnnotationsMenu.setText(MessageManager
1285 .getString("label.hide_annotations"));
1286 groupShowAnnotationsMenu.setText(MessageManager
1287 .getString("label.show_annotations"));
1288 groupHideAnnotationsMenu.setText(MessageManager
1289 .getString("label.hide_annotations"));
1290 sequenceFeature.setText(MessageManager
1291 .getString("label.create_sequence_feature"));
1292 sequenceFeature.addActionListener(new ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 sequenceFeature_actionPerformed();
1300 textColour.setText(MessageManager.getString("label.text_colour"));
1301 textColour.addActionListener(new ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 textColour_actionPerformed();
1309 jMenu1.setText(MessageManager.getString("label.group"));
1310 pdbStructureDialog.setText(MessageManager
1311 .getString("label.show_pdbstruct_dialog"));
1312 pdbStructureDialog.addActionListener(new ActionListener()
1315 public void actionPerformed(ActionEvent actionEvent)
1317 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1318 if (ap.av.getSelectionGroup() != null)
1320 selectedSeqs = ap.av.getSequenceSelection();
1322 new StructureChooser(selectedSeqs, sequence, ap);
1326 rnaStructureMenu.setText(MessageManager
1327 .getString("label.view_rna_structure"));
1329 // colStructureMenu.setText("Colour By Structure");
1330 editSequence.setText(MessageManager.getString("label.edit_sequence")
1332 editSequence.addActionListener(new ActionListener()
1335 public void actionPerformed(ActionEvent actionEvent)
1337 editSequence_actionPerformed(actionEvent);
1340 makeReferenceSeq.setText(MessageManager
1341 .getString("label.mark_as_representative"));
1342 makeReferenceSeq.addActionListener(new ActionListener()
1346 public void actionPerformed(ActionEvent actionEvent)
1348 makeReferenceSeq_actionPerformed(actionEvent);
1352 hideInsertions.setText(MessageManager
1353 .getString("label.hide_insertions"));
1354 hideInsertions.addActionListener(new ActionListener()
1358 public void actionPerformed(ActionEvent e)
1360 hideInsertions_actionPerformed(e);
1364 * annotationMenuItem.setText("By Annotation");
1365 * annotationMenuItem.addActionListener(new ActionListener() { public void
1366 * actionPerformed(ActionEvent actionEvent) {
1367 * annotationMenuItem_actionPerformed(actionEvent); } });
1369 groupMenu.add(sequenceSelDetails);
1372 add(rnaStructureMenu);
1373 add(pdbStructureDialog);
1374 if (sequence != null)
1376 add(hideInsertions);
1378 // annotations configuration panel suppressed for now
1379 // groupMenu.add(chooseAnnotations);
1382 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1383 * (if a selection group is in force).
1385 sequenceMenu.add(seqShowAnnotationsMenu);
1386 sequenceMenu.add(seqHideAnnotationsMenu);
1387 sequenceMenu.add(seqAddReferenceAnnotations);
1388 groupMenu.add(groupShowAnnotationsMenu);
1389 groupMenu.add(groupHideAnnotationsMenu);
1390 groupMenu.add(groupAddReferenceAnnotations);
1391 groupMenu.add(editMenu);
1392 groupMenu.add(outputMenu);
1393 groupMenu.add(sequenceFeature);
1394 groupMenu.add(createGroupMenuItem);
1395 groupMenu.add(unGroupMenuItem);
1396 groupMenu.add(jMenu1);
1397 sequenceMenu.add(sequenceName);
1398 sequenceMenu.add(sequenceDetails);
1399 sequenceMenu.add(makeReferenceSeq);
1400 colourMenu.add(textColour);
1401 colourMenu.add(noColourmenuItem);
1402 colourMenu.add(clustalColour);
1403 colourMenu.add(BLOSUM62Colour);
1404 colourMenu.add(PIDColour);
1405 colourMenu.add(zappoColour);
1406 colourMenu.add(taylorColour);
1407 colourMenu.add(hydrophobicityColour);
1408 colourMenu.add(helixColour);
1409 colourMenu.add(strandColour);
1410 colourMenu.add(turnColour);
1411 colourMenu.add(buriedColour);
1412 colourMenu.add(nucleotideMenuItem);
1413 if (ap.getAlignment().isNucleotide())
1415 // JBPNote - commented since the colourscheme isn't functional
1416 colourMenu.add(purinePyrimidineColour);
1418 colourMenu.add(userDefinedColour);
1420 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1422 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1423 .getUserColourSchemes().keys();
1425 while (userColours.hasMoreElements())
1427 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1428 item.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent evt)
1433 userDefinedColour_actionPerformed(evt);
1436 colourMenu.add(item);
1440 colourMenu.addSeparator();
1441 colourMenu.add(abovePIDColour);
1442 colourMenu.add(conservationMenuItem);
1445 editMenu.add(editSequence);
1446 editMenu.add(upperCase);
1447 editMenu.add(lowerCase);
1448 editMenu.add(toggle);
1449 // JBPNote: These shouldn't be added here - should appear in a generic
1450 // 'apply web service to this sequence menu'
1451 // pdbMenu.add(RNAFold);
1452 // pdbMenu.add(ContraFold);
1453 jMenu1.add(groupName);
1454 jMenu1.add(colourMenu);
1455 jMenu1.add(showBoxes);
1456 jMenu1.add(showText);
1457 jMenu1.add(showColourText);
1458 jMenu1.add(outline);
1459 jMenu1.add(displayNonconserved);
1460 noColourmenuItem.setText(MessageManager.getString("label.none"));
1461 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1464 public void actionPerformed(ActionEvent e)
1466 noColourmenuItem_actionPerformed();
1470 clustalColour.setText(MessageManager
1471 .getString("label.clustalx_colours"));
1472 clustalColour.addActionListener(new java.awt.event.ActionListener()
1475 public void actionPerformed(ActionEvent e)
1477 clustalColour_actionPerformed();
1480 zappoColour.setText(MessageManager.getString("label.zappo"));
1481 zappoColour.addActionListener(new java.awt.event.ActionListener()
1484 public void actionPerformed(ActionEvent e)
1486 zappoColour_actionPerformed();
1489 taylorColour.setText(MessageManager.getString("label.taylor"));
1490 taylorColour.addActionListener(new java.awt.event.ActionListener()
1493 public void actionPerformed(ActionEvent e)
1495 taylorColour_actionPerformed();
1498 hydrophobicityColour.setText(MessageManager
1499 .getString("label.hydrophobicity"));
1500 hydrophobicityColour
1501 .addActionListener(new java.awt.event.ActionListener()
1504 public void actionPerformed(ActionEvent e)
1506 hydrophobicityColour_actionPerformed();
1509 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1510 helixColour.addActionListener(new java.awt.event.ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 helixColour_actionPerformed();
1518 strandColour.setText(MessageManager
1519 .getString("label.strand_propensity"));
1520 strandColour.addActionListener(new java.awt.event.ActionListener()
1523 public void actionPerformed(ActionEvent e)
1525 strandColour_actionPerformed();
1528 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1529 turnColour.addActionListener(new java.awt.event.ActionListener()
1532 public void actionPerformed(ActionEvent e)
1534 turnColour_actionPerformed();
1537 buriedColour.setText(MessageManager.getString("label.buried_index"));
1538 buriedColour.addActionListener(new java.awt.event.ActionListener()
1541 public void actionPerformed(ActionEvent e)
1543 buriedColour_actionPerformed();
1546 abovePIDColour.setText(MessageManager
1547 .getString("label.above_identity_percentage"));
1548 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1551 public void actionPerformed(ActionEvent e)
1553 abovePIDColour_actionPerformed();
1556 userDefinedColour.setText(MessageManager
1557 .getString("action.user_defined"));
1558 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 userDefinedColour_actionPerformed(e);
1567 .setText(MessageManager.getString("label.percentage_identity"));
1568 PIDColour.addActionListener(new java.awt.event.ActionListener()
1571 public void actionPerformed(ActionEvent e)
1573 PIDColour_actionPerformed();
1576 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1577 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1580 public void actionPerformed(ActionEvent e)
1582 BLOSUM62Colour_actionPerformed();
1585 purinePyrimidineColour.setText(MessageManager
1586 .getString("label.purine_pyrimidine"));
1587 purinePyrimidineColour
1588 .addActionListener(new java.awt.event.ActionListener()
1591 public void actionPerformed(ActionEvent e)
1593 purinePyrimidineColour_actionPerformed();
1598 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1599 * public void actionPerformed(ActionEvent e) {
1600 * covariationColour_actionPerformed(); } });
1603 conservationMenuItem.setText(MessageManager
1604 .getString("label.conservation"));
1605 conservationMenuItem
1606 .addActionListener(new java.awt.event.ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 conservationMenuItem_actionPerformed();
1617 * Check for any annotations on the underlying dataset sequences (for the
1618 * current selection group) which are not 'on the alignment'.If any are found,
1619 * enable the option to add them to the alignment. The criteria for 'on the
1620 * alignment' is finding an alignment annotation on the alignment, matched on
1621 * calcId, label and sequenceRef.
1623 * A tooltip is also constructed that displays the source (calcId) and type
1624 * (label) of the annotations that can be added.
1627 * @param forSequences
1629 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1630 List<SequenceI> forSequences)
1632 menuItem.setEnabled(false);
1635 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1636 * Using TreeMap means calcIds are shown in alphabetical order.
1638 Map<String, String> tipEntries = new TreeMap<String, String>();
1639 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1640 AlignmentI al = this.ap.av.getAlignment();
1641 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1642 tipEntries, candidates, al);
1643 if (!candidates.isEmpty())
1645 StringBuilder tooltip = new StringBuilder(64);
1646 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1649 * Found annotations that could be added. Enable the menu item, and
1650 * configure its tooltip and action.
1652 menuItem.setEnabled(true);
1653 for (String calcId : tipEntries.keySet())
1655 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1657 String tooltipText = JvSwingUtils.wrapTooltip(true,
1658 tooltip.toString());
1659 menuItem.setToolTipText(tooltipText);
1661 menuItem.addActionListener(new ActionListener()
1664 public void actionPerformed(ActionEvent e)
1666 addReferenceAnnotations_actionPerformed(candidates);
1673 * Add annotations to the sequences and to the alignment.
1676 * a map whose keys are sequences on the alignment, and values a list
1677 * of annotations to add to each sequence
1679 protected void addReferenceAnnotations_actionPerformed(
1680 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1682 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1683 final AlignmentI alignment = this.ap.getAlignment();
1684 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1689 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1691 if (!ap.av.getAlignment().hasSeqrep())
1693 // initialise the display flags so the user sees something happen
1694 ap.av.setDisplayReferenceSeq(true);
1695 ap.av.setColourByReferenceSeq(true);
1696 ap.av.getAlignment().setSeqrep(sequence);
1700 if (ap.av.getAlignment().getSeqrep() == sequence)
1702 ap.av.getAlignment().setSeqrep(null);
1706 ap.av.getAlignment().setSeqrep(sequence);
1712 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1714 if (sequence != null)
1716 ColumnSelection cs = ap.av.getColumnSelection();
1719 cs = new ColumnSelection();
1721 cs.hideInsertionsFor(sequence);
1722 ap.av.setColumnSelection(cs);
1727 protected void sequenceSelectionDetails_actionPerformed()
1729 createSequenceDetailsReport(ap.av.getSequenceSelection());
1732 protected void sequenceDetails_actionPerformed()
1734 createSequenceDetailsReport(new SequenceI[] { sequence });
1737 public void createSequenceDetailsReport(SequenceI[] sequences)
1739 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1740 StringBuffer contents = new StringBuffer();
1741 for (SequenceI seq : sequences)
1743 contents.append("<p><h2>"
1746 "label.create_sequence_details_report_annotation_for",
1747 new Object[] { seq.getDisplayId(true) })
1749 new SequenceAnnotationReport(null)
1750 .createSequenceAnnotationReport(
1756 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1757 .getSeqPanel().seqCanvas.fr.getMinMax()
1759 contents.append("</p>");
1761 cap.setText("<html>" + contents.toString() + "</html>");
1763 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1764 "label.sequence_details_for",
1765 (sequences.length == 1 ? new Object[] { sequences[0]
1766 .getDisplayId(true) } : new Object[] { MessageManager
1767 .getString("label.selection") })), 500, 400);
1771 protected void showNonconserved_actionPerformed()
1773 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1778 * call to refresh view after settings change
1782 ap.updateAnnotation();
1783 ap.paintAlignment(true);
1785 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1794 protected void clustalColour_actionPerformed()
1796 SequenceGroup sg = getGroup();
1797 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1807 protected void zappoColour_actionPerformed()
1809 getGroup().cs = new ZappoColourScheme();
1819 protected void taylorColour_actionPerformed()
1821 getGroup().cs = new TaylorColourScheme();
1831 protected void hydrophobicityColour_actionPerformed()
1833 getGroup().cs = new HydrophobicColourScheme();
1843 protected void helixColour_actionPerformed()
1845 getGroup().cs = new HelixColourScheme();
1855 protected void strandColour_actionPerformed()
1857 getGroup().cs = new StrandColourScheme();
1867 protected void turnColour_actionPerformed()
1869 getGroup().cs = new TurnColourScheme();
1879 protected void buriedColour_actionPerformed()
1881 getGroup().cs = new BuriedColourScheme();
1891 public void nucleotideMenuItem_actionPerformed()
1893 getGroup().cs = new NucleotideColourScheme();
1897 protected void purinePyrimidineColour_actionPerformed()
1899 getGroup().cs = new PurinePyrimidineColourScheme();
1904 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1905 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1913 protected void abovePIDColour_actionPerformed()
1915 SequenceGroup sg = getGroup();
1921 if (abovePIDColour.isSelected())
1923 sg.cs.setConsensus(AAFrequency.calculate(
1924 sg.getSequences(ap.av.getHiddenRepSequences()),
1925 sg.getStartRes(), sg.getEndRes() + 1));
1927 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1930 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1932 SliderPanel.showPIDSlider();
1935 // remove PIDColouring
1937 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1949 protected void userDefinedColour_actionPerformed(ActionEvent e)
1951 SequenceGroup sg = getGroup();
1953 if (e.getSource().equals(userDefinedColour))
1955 new UserDefinedColours(ap, sg);
1959 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1960 .getUserColourSchemes().get(e.getActionCommand());
1968 * Open a panel where the user can choose which types of sequence annotation
1973 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1975 // todo correct way to guard against opening a duplicate panel?
1976 new AnnotationChooser(ap);
1985 protected void PIDColour_actionPerformed()
1987 SequenceGroup sg = getGroup();
1988 sg.cs = new PIDColourScheme();
1989 sg.cs.setConsensus(AAFrequency.calculate(
1990 sg.getSequences(ap.av.getHiddenRepSequences()),
1991 sg.getStartRes(), sg.getEndRes() + 1));
2001 protected void BLOSUM62Colour_actionPerformed()
2003 SequenceGroup sg = getGroup();
2005 sg.cs = new Blosum62ColourScheme();
2007 sg.cs.setConsensus(AAFrequency.calculate(
2008 sg.getSequences(ap.av.getHiddenRepSequences()),
2009 sg.getStartRes(), sg.getEndRes() + 1));
2020 protected void noColourmenuItem_actionPerformed()
2022 getGroup().cs = null;
2032 protected void conservationMenuItem_actionPerformed()
2034 SequenceGroup sg = getGroup();
2040 if (conservationMenuItem.isSelected())
2042 // JBPNote: Conservation name shouldn't be i18n translated
2043 Conservation c = new Conservation("Group",
2044 ResidueProperties.propHash, 3, sg.getSequences(ap.av
2045 .getHiddenRepSequences()), sg.getStartRes(),
2046 sg.getEndRes() + 1);
2049 c.verdict(false, ap.av.getConsPercGaps());
2051 sg.cs.setConservation(c);
2053 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2054 SliderPanel.showConservationSlider();
2057 // remove ConservationColouring
2059 sg.cs.setConservation(null);
2065 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2067 SequenceGroup sg = getGroup();
2073 AnnotationColourGradient acg = new AnnotationColourGradient(
2074 sequence.getAnnotation()[0], null,
2075 AnnotationColourGradient.NO_THRESHOLD);
2077 acg.setPredefinedColours(true);
2089 protected void groupName_actionPerformed()
2092 SequenceGroup sg = getGroup();
2093 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2094 sg.getDescription(), " "
2095 + MessageManager.getString("label.group_name") + " ",
2096 MessageManager.getString("label.group_description") + " ",
2097 MessageManager.getString("label.edit_group_name_description"),
2105 sg.setName(dialog.getName());
2106 sg.setDescription(dialog.getDescription());
2111 * Get selection group - adding it to the alignment if necessary.
2113 * @return sequence group to operate on
2115 SequenceGroup getGroup()
2117 SequenceGroup sg = ap.av.getSelectionGroup();
2118 // this method won't add a new group if it already exists
2121 ap.av.getAlignment().addGroup(sg);
2133 void sequenceName_actionPerformed()
2135 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2136 sequence.getDescription(),
2137 " " + MessageManager.getString("label.sequence_name")
2139 MessageManager.getString("label.sequence_description") + " ",
2141 .getString("label.edit_sequence_name_description"),
2149 if (dialog.getName() != null)
2151 if (dialog.getName().indexOf(" ") > -1)
2157 .getString("label.spaces_converted_to_backslashes"),
2159 .getString("label.no_spaces_allowed_sequence_name"),
2160 JOptionPane.WARNING_MESSAGE);
2163 sequence.setName(dialog.getName().replace(' ', '_'));
2164 ap.paintAlignment(false);
2167 sequence.setDescription(dialog.getDescription());
2169 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2180 void unGroupMenuItem_actionPerformed()
2182 SequenceGroup sg = ap.av.getSelectionGroup();
2183 ap.av.getAlignment().deleteGroup(sg);
2184 ap.av.setSelectionGroup(null);
2188 void createGroupMenuItem_actionPerformed()
2190 getGroup(); // implicitly creates group - note - should apply defaults / use
2191 // standard alignment window logic for this
2201 protected void outline_actionPerformed()
2203 SequenceGroup sg = getGroup();
2204 Color col = JColorChooser.showDialog(this,
2205 MessageManager.getString("label.select_outline_colour"),
2210 sg.setOutlineColour(col);
2222 public void showBoxes_actionPerformed()
2224 getGroup().setDisplayBoxes(showBoxes.isSelected());
2234 public void showText_actionPerformed()
2236 getGroup().setDisplayText(showText.isSelected());
2246 public void showColourText_actionPerformed()
2248 getGroup().setColourText(showColourText.isSelected());
2252 public void showLink(String url)
2256 jalview.util.BrowserLauncher.openURL(url);
2257 } catch (Exception ex)
2259 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2260 MessageManager.getString("label.web_browser_not_found_unix"),
2261 MessageManager.getString("label.web_browser_not_found"),
2262 JOptionPane.WARNING_MESSAGE);
2264 ex.printStackTrace();
2268 void hideSequences(boolean representGroup)
2270 ap.av.hideSequences(sequence, representGroup);
2273 public void copy_actionPerformed()
2275 ap.alignFrame.copy_actionPerformed(null);
2278 public void cut_actionPerformed()
2280 ap.alignFrame.cut_actionPerformed(null);
2283 void changeCase(ActionEvent e)
2285 Object source = e.getSource();
2286 SequenceGroup sg = ap.av.getSelectionGroup();
2290 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2291 sg.getStartRes(), sg.getEndRes() + 1);
2296 if (source == toggle)
2298 description = MessageManager.getString("label.toggle_case");
2299 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2301 else if (source == upperCase)
2303 description = MessageManager.getString("label.to_upper_case");
2304 caseChange = ChangeCaseCommand.TO_UPPER;
2308 description = MessageManager.getString("label.to_lower_case");
2309 caseChange = ChangeCaseCommand.TO_LOWER;
2312 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2313 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2314 startEnd, caseChange);
2316 ap.alignFrame.addHistoryItem(caseCommand);
2318 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2324 public void outputText_actionPerformed(ActionEvent e)
2326 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2327 cap.setForInput(null);
2328 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2329 "label.alignment_output_command",
2330 new Object[] { e.getActionCommand() }), 600, 500);
2332 String[] omitHidden = null;
2334 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2335 // or we simply trust the user wants
2336 // wysiwig behaviour
2338 FileFormatI fileFormat = FileFormat.forName(e.getActionCommand());
2339 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2342 public void sequenceFeature_actionPerformed()
2344 SequenceGroup sg = ap.av.getSelectionGroup();
2350 int rsize = 0, gSize = sg.getSize();
2351 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2352 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2354 for (int i = 0; i < gSize; i++)
2356 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2357 int end = sg.findEndRes(sg.getSequenceAt(i));
2360 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2361 features[rsize] = new SequenceFeature(null, null, null, start, end,
2366 rseqs = new SequenceI[rsize];
2367 tfeatures = new SequenceFeature[rsize];
2368 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2369 System.arraycopy(features, 0, tfeatures, 0, rsize);
2370 features = tfeatures;
2372 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2373 features, true, ap))
2375 ap.alignFrame.setShowSeqFeatures(true);
2376 ap.highlightSearchResults(null);
2380 public void textColour_actionPerformed()
2382 SequenceGroup sg = getGroup();
2385 new TextColourChooser().chooseColour(ap, sg);
2389 public void colourByStructure(String pdbid)
2391 Annotation[] anots = ap.av.getStructureSelectionManager()
2392 .colourSequenceFromStructure(sequence, pdbid);
2394 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2395 "Coloured by " + pdbid, anots);
2397 ap.av.getAlignment().addAnnotation(an);
2398 an.createSequenceMapping(sequence, 0, true);
2399 // an.adjustForAlignment();
2400 ap.av.getAlignment().setAnnotationIndex(an, 0);
2402 ap.adjustAnnotationHeight();
2404 sequence.addAlignmentAnnotation(an);
2408 public void editSequence_actionPerformed(ActionEvent actionEvent)
2410 SequenceGroup sg = ap.av.getSelectionGroup();
2414 if (sequence == null)
2416 sequence = sg.getSequenceAt(0);
2419 EditNameDialog dialog = new EditNameDialog(
2420 sequence.getSequenceAsString(sg.getStartRes(),
2421 sg.getEndRes() + 1), null,
2422 MessageManager.getString("label.edit_sequence"), null,
2423 MessageManager.getString("label.edit_sequence"),
2428 EditCommand editCommand = new EditCommand(
2429 MessageManager.getString("label.edit_sequences"),
2430 Action.REPLACE, dialog.getName().replace(' ',
2431 ap.av.getGapCharacter()),
2432 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2433 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2435 ap.alignFrame.addHistoryItem(editCommand);
2437 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()