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.FileFormatI;
42 import jalview.io.FileFormats;
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.StrandColourScheme;
55 import jalview.schemes.TaylorColourScheme;
56 import jalview.schemes.TurnColourScheme;
57 import jalview.schemes.UserColourScheme;
58 import jalview.schemes.ZappoColourScheme;
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.Arrays;
68 import java.util.Collection;
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.JPopupMenu;
83 import javax.swing.JRadioButtonMenuItem;
89 * @version $Revision: 1.118 $
91 public class PopupMenu extends JPopupMenu
93 JMenu groupMenu = new JMenu();
95 JMenuItem groupName = new JMenuItem();
97 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
115 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
117 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
119 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
121 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
123 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
125 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
127 protected JMenuItem modifyPID = new JMenuItem();
129 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
131 protected JMenuItem modifyConservation = new JMenuItem();
135 JMenu sequenceMenu = new JMenu();
137 JMenuItem sequenceName = new JMenuItem();
139 JMenuItem sequenceDetails = new JMenuItem();
141 JMenuItem sequenceSelDetails = new JMenuItem();
143 JMenuItem makeReferenceSeq = new JMenuItem();
145 JMenuItem chooseAnnotations = new JMenuItem();
149 JMenuItem createGroupMenuItem = new JMenuItem();
151 JMenuItem unGroupMenuItem = new JMenuItem();
153 JMenuItem outline = new JMenuItem();
155 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
157 JMenu colourMenu = new JMenu();
159 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
161 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
163 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
165 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
167 JMenu editMenu = new JMenu();
169 JMenuItem cut = new JMenuItem();
171 JMenuItem copy = new JMenuItem();
173 JMenuItem upperCase = new JMenuItem();
175 JMenuItem lowerCase = new JMenuItem();
177 JMenuItem toggle = new JMenuItem();
179 JMenu pdbMenu = new JMenu();
181 JMenu outputMenu = new JMenu();
183 JMenu seqShowAnnotationsMenu = new JMenu();
185 JMenu seqHideAnnotationsMenu = new JMenu();
187 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
188 MessageManager.getString("label.add_reference_annotations"));
190 JMenu groupShowAnnotationsMenu = new JMenu();
192 JMenu groupHideAnnotationsMenu = new JMenu();
194 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
195 MessageManager.getString("label.add_reference_annotations"));
197 JMenuItem sequenceFeature = new JMenuItem();
199 JMenuItem textColour = new JMenuItem();
201 JMenu jMenu1 = new JMenu();
203 JMenuItem pdbStructureDialog = new JMenuItem();
205 JMenu rnaStructureMenu = new JMenu();
207 JMenuItem editSequence = new JMenuItem();
209 JMenu groupLinksMenu;
211 JMenuItem hideInsertions = new JMenuItem();
214 * Creates a new PopupMenu object.
221 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
223 this(ap, seq, links, null);
233 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
234 List<String> links, List<String> groupLinks)
236 // /////////////////////////////////////////////////////////
237 // If this is activated from the sequence panel, the user may want to
238 // edit or annotate a particular residue. Therefore display the residue menu
240 // If from the IDPanel, we must display the sequence menu
241 // ////////////////////////////////////////////////////////
245 ButtonGroup colours = new ButtonGroup();
246 colours.add(noColourmenuItem);
247 colours.add(clustalColour);
248 colours.add(zappoColour);
249 colours.add(taylorColour);
250 colours.add(hydrophobicityColour);
251 colours.add(helixColour);
252 colours.add(strandColour);
253 colours.add(turnColour);
254 colours.add(buriedColour);
255 colours.add(userDefinedColour);
256 colours.add(PIDColour);
257 colours.add(BLOSUM62Colour);
258 colours.add(purinePyrimidineColour);
259 colours.add(RNAInteractionColour);
261 for (String ff : FileFormats.getInstance().getWritableFormats(true))
263 JMenuItem item = new JMenuItem(ff);
265 item.addActionListener(new 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 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 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 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 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);
543 if (sg.cs.conservationApplied())
545 conservationMenuItem.setSelected(true);
547 if (sg.cs.getThreshold() > 0)
549 abovePIDColour.setSelected(true);
552 modifyConservation.setEnabled(conservationMenuItem.isSelected());
553 modifyPID.setEnabled(abovePIDColour.isSelected());
554 displayNonconserved.setSelected(sg.getShowNonconserved());
555 showText.setSelected(sg.getDisplayText());
556 showColourText.setSelected(sg.getColourText());
557 showBoxes.setSelected(sg.getDisplayBoxes());
558 // add any groupURLs to the groupURL submenu and make it visible
559 if (groupLinks != null && groupLinks.size() > 0)
561 buildGroupURLMenu(sg, groupLinks);
563 // Add a 'show all structures' for the current selection
564 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
565 SequenceI sqass = null;
566 for (SequenceI sq : ap.av.getSequenceSelection())
568 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
569 if (pes != null && pes.size() > 0)
571 reppdb.put(pes.get(0).getId(), pes.get(0));
572 for (PDBEntry pe : pes)
574 pdbe.put(pe.getId(), pe);
584 final PDBEntry[] pe = pdbe.values().toArray(
585 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
586 new PDBEntry[reppdb.size()]);
587 final JMenuItem gpdbview, rpdbview;
592 groupMenu.setVisible(false);
593 editMenu.setVisible(false);
598 createGroupMenuItem.setVisible(true);
599 unGroupMenuItem.setVisible(false);
600 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
604 createGroupMenuItem.setVisible(false);
605 unGroupMenuItem.setVisible(true);
606 jMenu1.setText(MessageManager.getString("action.edit_group"));
611 sequenceMenu.setVisible(false);
612 pdbStructureDialog.setVisible(false);
613 rnaStructureMenu.setVisible(false);
616 if (links != null && links.size() > 0)
618 addFeatureLinks(seq, links);
623 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
628 void addFeatureLinks(final SequenceI seq, List<String> links)
630 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
631 Map<String, List<String>> linkset = new LinkedHashMap<String, List<String>>();
633 for (String link : links)
635 UrlLink urlLink = null;
638 urlLink = new UrlLink(link);
639 } catch (Exception foo)
641 Cache.log.error("Exception for URLLink '" + link + "'", foo);
645 if (!urlLink.isValid())
647 Cache.log.error(urlLink.getInvalidMessage());
651 urlLink.createLinksFromSeq(seq, linkset);
654 addshowLinks(linkMenu, linkset.values());
656 // disable link menu if there are no valid entries
657 if (linkMenu.getItemCount() > 0)
659 linkMenu.setEnabled(true);
663 linkMenu.setEnabled(false);
666 if (sequence != null)
668 sequenceMenu.add(linkMenu);
678 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
679 * "All" is added first, followed by a separator. Then add any annotation
680 * types associated with the current selection. Separate menus are built for
681 * the selected sequence group (if any), and the selected sequence.
683 * Some annotation rows are always rendered together - these can be identified
684 * by a common graphGroup property > -1. Only one of each group will be marked
685 * as visible (to avoid duplication of the display). For such groups we add a
686 * composite type name, e.g.
688 * IUPredWS (Long), IUPredWS (Short)
692 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
693 List<SequenceI> forSequences)
695 showMenu.removeAll();
696 hideMenu.removeAll();
698 final List<String> all = Arrays.asList(new String[] { MessageManager
699 .getString("label.all") });
700 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
701 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
703 showMenu.addSeparator();
704 hideMenu.addSeparator();
706 final AlignmentAnnotation[] annotations = ap.getAlignment()
707 .getAlignmentAnnotation();
710 * Find shown/hidden annotations types, distinguished by source (calcId),
711 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
712 * the insertion order, which is the order of the annotations on the
715 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
716 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
717 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
718 AlignmentAnnotationUtils.asList(annotations), forSequences);
720 for (String calcId : hiddenTypes.keySet())
722 for (List<String> type : hiddenTypes.get(calcId))
724 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
728 // grey out 'show annotations' if none are hidden
729 showMenu.setEnabled(!hiddenTypes.isEmpty());
731 for (String calcId : shownTypes.keySet())
733 for (List<String> type : shownTypes.get(calcId))
735 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
739 // grey out 'hide annotations' if none are shown
740 hideMenu.setEnabled(!shownTypes.isEmpty());
744 * Returns a list of sequences - either the current selection group (if there
745 * is one), else the specified single sequence.
750 protected List<SequenceI> getSequenceScope(SequenceI seq)
752 List<SequenceI> forSequences = null;
753 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
754 if (selectionGroup != null && selectionGroup.getSize() > 0)
756 forSequences = selectionGroup.getSequences();
760 forSequences = seq == null ? Collections.<SequenceI> emptyList()
761 : Arrays.asList(seq);
767 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
770 * @param showOrHideMenu
772 * @param forSequences
773 * the sequences whose annotations may be shown or hidden
778 * if true this is a special label meaning 'All'
779 * @param actionIsShow
780 * if true, the select menu item action is to show the annotation
783 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
784 final List<SequenceI> forSequences, String calcId,
785 final List<String> types, final boolean allTypes,
786 final boolean actionIsShow)
788 String label = types.toString(); // [a, b, c]
789 label = label.substring(1, label.length() - 1); // a, b, c
790 final JMenuItem item = new JMenuItem(label);
791 item.setToolTipText(calcId);
792 item.addActionListener(new ActionListener()
795 public void actionPerformed(ActionEvent e)
797 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
798 types, forSequences, allTypes, actionIsShow);
802 showOrHideMenu.add(item);
805 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
808 // TODO: usability: thread off the generation of group url content so root
810 // sequence only URLs
811 // ID/regex match URLs
812 groupLinksMenu = new JMenu(
813 MessageManager.getString("action.group_link"));
814 // three types of url that might be created.
815 JMenu[] linkMenus = new JMenu[] { null,
816 new JMenu(MessageManager.getString("action.ids")),
817 new JMenu(MessageManager.getString("action.sequences")),
818 new JMenu(MessageManager.getString("action.ids_sequences")) };
820 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
821 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
822 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
823 for (int sq = 0; sq < seqs.length; sq++)
826 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
827 .findPosition(sg.getEndRes());
828 // just collect ids from dataset sequence
829 // TODO: check if IDs collected from selecton group intersects with the
830 // current selection, too
831 SequenceI sqi = seqs[sq];
832 while (sqi.getDatasetSequence() != null)
834 sqi = sqi.getDatasetSequence();
836 DBRefEntry[] dbr = sqi.getDBRefs();
837 if (dbr != null && dbr.length > 0)
839 for (int d = 0; d < dbr.length; d++)
841 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
842 Object[] sarray = commonDbrefs.get(src);
845 sarray = new Object[2];
846 sarray[0] = new int[] { 0 };
847 sarray[1] = new String[seqs.length];
849 commonDbrefs.put(src, sarray);
852 if (((String[]) sarray[1])[sq] == null)
855 || (dbr[d].getMap().locateMappedRange(start, end) != null))
857 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
858 ((int[]) sarray[0])[0]++;
864 // now create group links for all distinct ID/sequence sets.
865 boolean addMenu = false; // indicates if there are any group links to give
867 for (String link : groupLinks)
869 GroupUrlLink urlLink = null;
872 urlLink = new GroupUrlLink(link);
873 } catch (Exception foo)
875 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
879 if (!urlLink.isValid())
881 Cache.log.error(urlLink.getInvalidMessage());
884 final String label = urlLink.getLabel();
885 boolean usingNames = false;
886 // Now see which parts of the group apply for this URL
887 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
888 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
889 String[] seqstr, ids; // input to makeUrl
892 int numinput = ((int[]) idset[0])[0];
893 String[] allids = ((String[]) idset[1]);
894 seqstr = new String[numinput];
895 ids = new String[numinput];
896 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
898 if (allids[sq] != null)
900 ids[idcount] = allids[sq];
901 seqstr[idcount++] = idandseqs[1][sq];
907 // just use the id/seq set
908 seqstr = idandseqs[1];
912 // and try and make the groupURL!
914 Object[] urlset = null;
917 urlset = urlLink.makeUrlStubs(ids, seqstr,
918 "FromJalview" + System.currentTimeMillis(), false);
919 } catch (UrlStringTooLongException e)
924 int type = urlLink.getGroupURLType() & 3;
925 // first two bits ofurlLink type bitfield are sequenceids and sequences
926 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
927 addshowLink(linkMenus[type], label
928 + (((type & 1) == 1) ? ("("
929 + (usingNames ? "Names" : ltarget) + ")") : ""),
936 groupLinksMenu = new JMenu(
937 MessageManager.getString("action.group_link"));
938 for (int m = 0; m < linkMenus.length; m++)
940 if (linkMenus[m] != null
941 && linkMenus[m].getMenuComponentCount() > 0)
943 groupLinksMenu.add(linkMenus[m]);
947 groupMenu.add(groupLinksMenu);
951 private void addshowLinks(JMenu linkMenu, Collection<List<String>> linkset)
953 for (List<String> linkstrset : linkset)
955 // split linkstr into label and url
956 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
961 * add a show URL menu item to the given linkMenu
965 * - menu label string
969 private void addshowLink(JMenu linkMenu, String label, final String url)
971 JMenuItem item = new JMenuItem(label);
972 item.setToolTipText(MessageManager.formatMessage(
973 "label.open_url_param", new Object[] { url }));
974 item.addActionListener(new ActionListener()
977 public void actionPerformed(ActionEvent e)
979 new Thread(new Runnable()
996 * add a late bound groupURL item to the given linkMenu
1000 * - menu label string
1001 * @param urlgenerator
1002 * GroupURLLink used to generate URL
1004 * Object array returned from the makeUrlStubs function.
1006 private void addshowLink(JMenu linkMenu, String label,
1007 final GroupUrlLink urlgenerator, final Object[] urlstub)
1009 JMenuItem item = new JMenuItem(label);
1010 item.setToolTipText(MessageManager.formatMessage(
1011 "label.open_url_seqs_param",
1012 new Object[] { urlgenerator.getUrl_prefix(),
1013 urlgenerator.getNumberInvolved(urlstub) }));
1014 // TODO: put in info about what is being sent.
1015 item.addActionListener(new ActionListener()
1018 public void actionPerformed(ActionEvent e)
1020 new Thread(new Runnable()
1028 showLink(urlgenerator.constructFrom(urlstub));
1029 } catch (UrlStringTooLongException e2)
1047 private void jbInit() throws Exception
1049 groupMenu.setText(MessageManager.getString("label.selection"));
1050 groupName.setText(MessageManager.getString("label.name"));
1051 groupName.addActionListener(new ActionListener()
1054 public void actionPerformed(ActionEvent e)
1056 groupName_actionPerformed();
1059 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1060 sequenceName.setText(MessageManager
1061 .getString("label.edit_name_description"));
1062 sequenceName.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 sequenceName_actionPerformed();
1070 chooseAnnotations.setText(MessageManager
1071 .getString("action.choose_annotations"));
1072 chooseAnnotations.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 chooseAnnotations_actionPerformed(e);
1080 sequenceDetails.setText(MessageManager
1081 .getString("label.sequence_details"));
1082 sequenceDetails.addActionListener(new ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 sequenceDetails_actionPerformed();
1090 sequenceSelDetails.setText(MessageManager
1091 .getString("label.sequence_details"));
1092 sequenceSelDetails.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 sequenceSelectionDetails_actionPerformed();
1100 PIDColour.setFocusPainted(false);
1102 .setText(MessageManager.getString("action.remove_group"));
1103 unGroupMenuItem.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 unGroupMenuItem_actionPerformed();
1111 createGroupMenuItem.setText(MessageManager
1112 .getString("action.create_group"));
1113 createGroupMenuItem.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 createGroupMenuItem_actionPerformed();
1122 outline.setText(MessageManager.getString("action.border_colour"));
1123 outline.addActionListener(new ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 outline_actionPerformed();
1132 .setText(MessageManager.getString("label.nucleotide"));
1133 nucleotideMenuItem.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 nucleotideMenuItem_actionPerformed();
1141 colourMenu.setText(MessageManager.getString("label.group_colour"));
1142 showBoxes.setText(MessageManager.getString("action.boxes"));
1143 showBoxes.setState(true);
1144 showBoxes.addActionListener(new ActionListener()
1147 public void actionPerformed(ActionEvent e)
1149 showBoxes_actionPerformed();
1152 showText.setText(MessageManager.getString("action.text"));
1153 showText.setState(true);
1154 showText.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 showText_actionPerformed();
1162 showColourText.setText(MessageManager.getString("label.colour_text"));
1163 showColourText.addActionListener(new ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 showColourText_actionPerformed();
1171 displayNonconserved.setText(MessageManager
1172 .getString("label.show_non_conversed"));
1173 displayNonconserved.setState(true);
1174 displayNonconserved.addActionListener(new ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 showNonconserved_actionPerformed();
1182 editMenu.setText(MessageManager.getString("action.edit"));
1183 cut.setText(MessageManager.getString("action.cut"));
1184 cut.addActionListener(new ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 cut_actionPerformed();
1192 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1193 upperCase.addActionListener(new ActionListener()
1196 public void actionPerformed(ActionEvent e)
1201 copy.setText(MessageManager.getString("action.copy"));
1202 copy.addActionListener(new ActionListener()
1205 public void actionPerformed(ActionEvent e)
1207 copy_actionPerformed();
1210 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1211 lowerCase.addActionListener(new ActionListener()
1214 public void actionPerformed(ActionEvent e)
1219 toggle.setText(MessageManager.getString("label.toggle_case"));
1220 toggle.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent e)
1228 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1230 seqShowAnnotationsMenu.setText(MessageManager
1231 .getString("label.show_annotations"));
1232 seqHideAnnotationsMenu.setText(MessageManager
1233 .getString("label.hide_annotations"));
1234 groupShowAnnotationsMenu.setText(MessageManager
1235 .getString("label.show_annotations"));
1236 groupHideAnnotationsMenu.setText(MessageManager
1237 .getString("label.hide_annotations"));
1238 sequenceFeature.setText(MessageManager
1239 .getString("label.create_sequence_feature"));
1240 sequenceFeature.addActionListener(new ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 sequenceFeature_actionPerformed();
1248 textColour.setText(MessageManager.getString("label.text_colour"));
1249 textColour.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent e)
1254 textColour_actionPerformed();
1257 jMenu1.setText(MessageManager.getString("label.group"));
1258 pdbStructureDialog.setText(MessageManager
1259 .getString("label.show_pdbstruct_dialog"));
1260 pdbStructureDialog.addActionListener(new ActionListener()
1263 public void actionPerformed(ActionEvent actionEvent)
1265 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1266 if (ap.av.getSelectionGroup() != null)
1268 selectedSeqs = ap.av.getSequenceSelection();
1270 new StructureChooser(selectedSeqs, sequence, ap);
1274 rnaStructureMenu.setText(MessageManager
1275 .getString("label.view_rna_structure"));
1277 // colStructureMenu.setText("Colour By Structure");
1278 editSequence.setText(MessageManager.getString("label.edit_sequence")
1280 editSequence.addActionListener(new ActionListener()
1283 public void actionPerformed(ActionEvent actionEvent)
1285 editSequence_actionPerformed(actionEvent);
1288 makeReferenceSeq.setText(MessageManager
1289 .getString("label.mark_as_representative"));
1290 makeReferenceSeq.addActionListener(new ActionListener()
1294 public void actionPerformed(ActionEvent actionEvent)
1296 makeReferenceSeq_actionPerformed(actionEvent);
1300 hideInsertions.setText(MessageManager
1301 .getString("label.hide_insertions"));
1302 hideInsertions.addActionListener(new ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 hideInsertions_actionPerformed(e);
1312 * annotationMenuItem.setText("By Annotation");
1313 * annotationMenuItem.addActionListener(new ActionListener() { public void
1314 * actionPerformed(ActionEvent actionEvent) {
1315 * annotationMenuItem_actionPerformed(actionEvent); } });
1317 groupMenu.add(sequenceSelDetails);
1320 add(rnaStructureMenu);
1321 add(pdbStructureDialog);
1322 if (sequence != null)
1324 add(hideInsertions);
1326 // annotations configuration panel suppressed for now
1327 // groupMenu.add(chooseAnnotations);
1330 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1331 * (if a selection group is in force).
1333 sequenceMenu.add(seqShowAnnotationsMenu);
1334 sequenceMenu.add(seqHideAnnotationsMenu);
1335 sequenceMenu.add(seqAddReferenceAnnotations);
1336 groupMenu.add(groupShowAnnotationsMenu);
1337 groupMenu.add(groupHideAnnotationsMenu);
1338 groupMenu.add(groupAddReferenceAnnotations);
1339 groupMenu.add(editMenu);
1340 groupMenu.add(outputMenu);
1341 groupMenu.add(sequenceFeature);
1342 groupMenu.add(createGroupMenuItem);
1343 groupMenu.add(unGroupMenuItem);
1344 groupMenu.add(jMenu1);
1345 sequenceMenu.add(sequenceName);
1346 sequenceMenu.add(sequenceDetails);
1347 sequenceMenu.add(makeReferenceSeq);
1348 colourMenu.add(textColour);
1349 colourMenu.add(noColourmenuItem);
1350 colourMenu.add(clustalColour);
1351 colourMenu.add(BLOSUM62Colour);
1352 colourMenu.add(PIDColour);
1353 colourMenu.add(zappoColour);
1354 colourMenu.add(taylorColour);
1355 colourMenu.add(hydrophobicityColour);
1356 colourMenu.add(helixColour);
1357 colourMenu.add(strandColour);
1358 colourMenu.add(turnColour);
1359 colourMenu.add(buriedColour);
1360 colourMenu.add(nucleotideMenuItem);
1361 if (ap.getAlignment().isNucleotide())
1363 // JBPNote - commented since the colourscheme isn't functional
1364 colourMenu.add(purinePyrimidineColour);
1366 colourMenu.add(userDefinedColour);
1368 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1370 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1371 .getUserColourSchemes().keys();
1373 while (userColours.hasMoreElements())
1375 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1376 item.addActionListener(new ActionListener()
1379 public void actionPerformed(ActionEvent evt)
1381 userDefinedColour_actionPerformed(evt);
1384 colourMenu.add(item);
1388 colourMenu.addSeparator();
1389 colourMenu.add(conservationMenuItem);
1390 colourMenu.add(modifyConservation);
1391 colourMenu.add(abovePIDColour);
1392 colourMenu.add(modifyPID);
1395 editMenu.add(editSequence);
1396 editMenu.add(upperCase);
1397 editMenu.add(lowerCase);
1398 editMenu.add(toggle);
1399 // JBPNote: These shouldn't be added here - should appear in a generic
1400 // 'apply web service to this sequence menu'
1401 // pdbMenu.add(RNAFold);
1402 // pdbMenu.add(ContraFold);
1403 jMenu1.add(groupName);
1404 jMenu1.add(colourMenu);
1405 jMenu1.add(showBoxes);
1406 jMenu1.add(showText);
1407 jMenu1.add(showColourText);
1408 jMenu1.add(outline);
1409 jMenu1.add(displayNonconserved);
1410 noColourmenuItem.setText(MessageManager.getString("label.none"));
1411 noColourmenuItem.addActionListener(new ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 noColourmenuItem_actionPerformed();
1420 clustalColour.setText(MessageManager
1421 .getString("label.clustalx_colours"));
1422 clustalColour.addActionListener(new ActionListener()
1425 public void actionPerformed(ActionEvent e)
1427 clustalColour_actionPerformed();
1430 zappoColour.setText(MessageManager.getString("label.zappo"));
1431 zappoColour.addActionListener(new ActionListener()
1434 public void actionPerformed(ActionEvent e)
1436 zappoColour_actionPerformed();
1439 taylorColour.setText(MessageManager.getString("label.taylor"));
1440 taylorColour.addActionListener(new ActionListener()
1443 public void actionPerformed(ActionEvent e)
1445 taylorColour_actionPerformed();
1448 hydrophobicityColour.setText(MessageManager
1449 .getString("label.hydrophobicity"));
1450 hydrophobicityColour.addActionListener(new ActionListener()
1453 public void actionPerformed(ActionEvent e)
1455 hydrophobicityColour_actionPerformed();
1458 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1459 helixColour.addActionListener(new ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 helixColour_actionPerformed();
1467 strandColour.setText(MessageManager
1468 .getString("label.strand_propensity"));
1469 strandColour.addActionListener(new ActionListener()
1472 public void actionPerformed(ActionEvent e)
1474 strandColour_actionPerformed();
1477 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1478 turnColour.addActionListener(new ActionListener()
1481 public void actionPerformed(ActionEvent e)
1483 turnColour_actionPerformed();
1486 buriedColour.setText(MessageManager.getString("label.buried_index"));
1487 buriedColour.addActionListener(new ActionListener()
1490 public void actionPerformed(ActionEvent e)
1492 buriedColour_actionPerformed();
1495 userDefinedColour.setText(MessageManager
1496 .getString("action.user_defined"));
1497 userDefinedColour.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent e)
1502 userDefinedColour_actionPerformed(e);
1506 .setText(MessageManager.getString("label.percentage_identity"));
1507 PIDColour.addActionListener(new ActionListener()
1510 public void actionPerformed(ActionEvent e)
1512 PIDColour_actionPerformed();
1515 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1516 BLOSUM62Colour.addActionListener(new ActionListener()
1519 public void actionPerformed(ActionEvent e)
1521 BLOSUM62Colour_actionPerformed();
1524 purinePyrimidineColour.setText(MessageManager
1525 .getString("label.purine_pyrimidine"));
1526 purinePyrimidineColour.addActionListener(new ActionListener()
1529 public void actionPerformed(ActionEvent e)
1531 purinePyrimidineColour_actionPerformed();
1536 * covariationColour.addActionListener(new ActionListener() {
1537 * public void actionPerformed(ActionEvent e) {
1538 * covariationColour_actionPerformed(); } });
1540 abovePIDColour.setText(MessageManager
1541 .getString("label.above_identity_percentage"));
1542 abovePIDColour.addActionListener(new ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 abovePIDColour_actionPerformed();
1551 modifyPID.setText(MessageManager
1552 .getString("label.modify_identity_threshold"));
1553 modifyPID.addActionListener(new ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 modifyPID_actionPerformed();
1562 conservationMenuItem.setText(MessageManager
1563 .getString("label.conservation"));
1564 conservationMenuItem.addActionListener(new ActionListener()
1567 public void actionPerformed(ActionEvent e)
1569 conservationMenuItem_actionPerformed();
1573 modifyConservation.setText(MessageManager
1574 .getString("label.modify_conservation_threshold"));
1575 modifyConservation.addActionListener(new ActionListener()
1578 public void actionPerformed(ActionEvent e)
1580 modifyConservation_actionPerformed();
1585 protected void modifyConservation_actionPerformed()
1587 SequenceGroup sg = getGroup();
1590 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1591 SliderPanel.showConservationSlider();
1595 protected void modifyPID_actionPerformed()
1597 SequenceGroup sg = getGroup();
1600 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1602 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1603 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1605 SliderPanel.showPIDSlider();
1610 * Check for any annotations on the underlying dataset sequences (for the
1611 * current selection group) which are not 'on the alignment'.If any are found,
1612 * enable the option to add them to the alignment. The criteria for 'on the
1613 * alignment' is finding an alignment annotation on the alignment, matched on
1614 * calcId, label and sequenceRef.
1616 * A tooltip is also constructed that displays the source (calcId) and type
1617 * (label) of the annotations that can be added.
1620 * @param forSequences
1622 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1623 List<SequenceI> forSequences)
1625 menuItem.setEnabled(false);
1628 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1629 * Using TreeMap means calcIds are shown in alphabetical order.
1631 Map<String, String> tipEntries = new TreeMap<String, String>();
1632 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1633 AlignmentI al = this.ap.av.getAlignment();
1634 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1635 tipEntries, candidates, al);
1636 if (!candidates.isEmpty())
1638 StringBuilder tooltip = new StringBuilder(64);
1639 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1642 * Found annotations that could be added. Enable the menu item, and
1643 * configure its tooltip and action.
1645 menuItem.setEnabled(true);
1646 for (String calcId : tipEntries.keySet())
1648 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1650 String tooltipText = JvSwingUtils.wrapTooltip(true,
1651 tooltip.toString());
1652 menuItem.setToolTipText(tooltipText);
1654 menuItem.addActionListener(new ActionListener()
1657 public void actionPerformed(ActionEvent e)
1659 addReferenceAnnotations_actionPerformed(candidates);
1666 * Add annotations to the sequences and to the alignment.
1669 * a map whose keys are sequences on the alignment, and values a list
1670 * of annotations to add to each sequence
1672 protected void addReferenceAnnotations_actionPerformed(
1673 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1675 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1676 final AlignmentI alignment = this.ap.getAlignment();
1677 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1682 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1684 if (!ap.av.getAlignment().hasSeqrep())
1686 // initialise the display flags so the user sees something happen
1687 ap.av.setDisplayReferenceSeq(true);
1688 ap.av.setColourByReferenceSeq(true);
1689 ap.av.getAlignment().setSeqrep(sequence);
1693 if (ap.av.getAlignment().getSeqrep() == sequence)
1695 ap.av.getAlignment().setSeqrep(null);
1699 ap.av.getAlignment().setSeqrep(sequence);
1705 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1707 if (sequence != null)
1709 ColumnSelection cs = ap.av.getColumnSelection();
1712 cs = new ColumnSelection();
1714 cs.hideInsertionsFor(sequence);
1715 ap.av.setColumnSelection(cs);
1720 protected void sequenceSelectionDetails_actionPerformed()
1722 createSequenceDetailsReport(ap.av.getSequenceSelection());
1725 protected void sequenceDetails_actionPerformed()
1727 createSequenceDetailsReport(new SequenceI[] { sequence });
1730 public void createSequenceDetailsReport(SequenceI[] sequences)
1732 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1733 StringBuilder contents = new StringBuilder(128);
1734 for (SequenceI seq : sequences)
1736 contents.append("<p><h2>"
1739 "label.create_sequence_details_report_annotation_for",
1740 new Object[] { seq.getDisplayId(true) })
1742 new SequenceAnnotationReport(null)
1743 .createSequenceAnnotationReport(
1748 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1749 .getSeqPanel().seqCanvas.fr.getMinMax()
1751 contents.append("</p>");
1753 cap.setText("<html>" + contents.toString() + "</html>");
1755 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1756 "label.sequence_details_for",
1757 (sequences.length == 1 ? new Object[] { sequences[0]
1758 .getDisplayId(true) } : new Object[] { MessageManager
1759 .getString("label.selection") })), 500, 400);
1763 protected void showNonconserved_actionPerformed()
1765 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1770 * call to refresh view after settings change
1774 ap.updateAnnotation();
1775 ap.paintAlignment(true);
1777 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1786 protected void clustalColour_actionPerformed()
1788 SequenceGroup sg = getGroup();
1789 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1799 protected void zappoColour_actionPerformed()
1801 getGroup().cs = new ZappoColourScheme();
1811 protected void taylorColour_actionPerformed()
1813 getGroup().cs = new TaylorColourScheme();
1823 protected void hydrophobicityColour_actionPerformed()
1825 getGroup().cs = new HydrophobicColourScheme();
1835 protected void helixColour_actionPerformed()
1837 getGroup().cs = new HelixColourScheme();
1847 protected void strandColour_actionPerformed()
1849 getGroup().cs = new StrandColourScheme();
1859 protected void turnColour_actionPerformed()
1861 getGroup().cs = new TurnColourScheme();
1871 protected void buriedColour_actionPerformed()
1873 getGroup().cs = new BuriedColourScheme();
1883 public void nucleotideMenuItem_actionPerformed()
1885 getGroup().cs = new NucleotideColourScheme();
1889 protected void purinePyrimidineColour_actionPerformed()
1891 getGroup().cs = new PurinePyrimidineColourScheme();
1896 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1897 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1905 protected void abovePIDColour_actionPerformed()
1907 SequenceGroup sg = getGroup();
1913 boolean selected = abovePIDColour.isSelected();
1916 sg.cs.setConsensus(AAFrequency.calculate(
1917 sg.getSequences(ap.av.getHiddenRepSequences()),
1918 sg.getStartRes(), sg.getEndRes() + 1));
1920 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1923 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1925 SliderPanel.showPIDSlider();
1928 // remove PIDColouring
1930 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1931 SliderPanel.hidePIDSlider();
1933 modifyPID.setEnabled(selected);
1944 protected void userDefinedColour_actionPerformed(ActionEvent e)
1946 SequenceGroup sg = getGroup();
1948 if (e.getSource().equals(userDefinedColour))
1950 new UserDefinedColours(ap, sg);
1954 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1955 .getUserColourSchemes().get(e.getActionCommand());
1963 * Open a panel where the user can choose which types of sequence annotation
1968 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1970 // todo correct way to guard against opening a duplicate panel?
1971 new AnnotationChooser(ap);
1980 protected void PIDColour_actionPerformed()
1982 SequenceGroup sg = getGroup();
1983 sg.cs = new PIDColourScheme();
1984 sg.cs.setConsensus(AAFrequency.calculate(
1985 sg.getSequences(ap.av.getHiddenRepSequences()),
1986 sg.getStartRes(), sg.getEndRes() + 1));
1996 protected void BLOSUM62Colour_actionPerformed()
1998 SequenceGroup sg = getGroup();
2000 sg.cs = new Blosum62ColourScheme();
2002 sg.cs.setConsensus(AAFrequency.calculate(
2003 sg.getSequences(ap.av.getHiddenRepSequences()),
2004 sg.getStartRes(), sg.getEndRes() + 1));
2015 protected void noColourmenuItem_actionPerformed()
2017 getGroup().cs = null;
2027 protected void conservationMenuItem_actionPerformed()
2029 SequenceGroup sg = getGroup();
2035 boolean selected = conservationMenuItem.isSelected();
2038 // JBPNote: Conservation name shouldn't be i18n translated
2039 Conservation c = new Conservation("Group", sg.getSequences(ap.av
2040 .getHiddenRepSequences()), sg.getStartRes(),
2041 sg.getEndRes() + 1);
2044 c.verdict(false, ap.av.getConsPercGaps());
2046 sg.cs.setConservation(c);
2048 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2049 SliderPanel.showConservationSlider();
2052 // remove ConservationColouring
2054 sg.cs.setConservation(null);
2055 SliderPanel.hideConservationSlider();
2057 modifyConservation.setEnabled(selected);
2062 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2064 SequenceGroup sg = getGroup();
2070 AnnotationColourGradient acg = new AnnotationColourGradient(
2071 sequence.getAnnotation()[0], null,
2072 AnnotationColourGradient.NO_THRESHOLD);
2074 acg.setPredefinedColours(true);
2086 protected void groupName_actionPerformed()
2089 SequenceGroup sg = getGroup();
2090 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2091 sg.getDescription(), " "
2092 + MessageManager.getString("label.group_name") + " ",
2093 MessageManager.getString("label.group_description") + " ",
2094 MessageManager.getString("label.edit_group_name_description"),
2102 sg.setName(dialog.getName());
2103 sg.setDescription(dialog.getDescription());
2108 * Get selection group - adding it to the alignment if necessary.
2110 * @return sequence group to operate on
2112 SequenceGroup getGroup()
2114 SequenceGroup sg = ap.av.getSelectionGroup();
2115 // this method won't add a new group if it already exists
2118 ap.av.getAlignment().addGroup(sg);
2130 void sequenceName_actionPerformed()
2132 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2133 sequence.getDescription(),
2134 " " + MessageManager.getString("label.sequence_name")
2136 MessageManager.getString("label.sequence_description") + " ",
2138 .getString("label.edit_sequence_name_description"),
2146 if (dialog.getName() != null)
2148 if (dialog.getName().indexOf(" ") > -1)
2154 .getString("label.spaces_converted_to_backslashes"),
2156 .getString("label.no_spaces_allowed_sequence_name"),
2157 JvOptionPane.WARNING_MESSAGE);
2160 sequence.setName(dialog.getName().replace(' ', '_'));
2161 ap.paintAlignment(false);
2164 sequence.setDescription(dialog.getDescription());
2166 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2177 void unGroupMenuItem_actionPerformed()
2179 SequenceGroup sg = ap.av.getSelectionGroup();
2180 ap.av.getAlignment().deleteGroup(sg);
2181 ap.av.setSelectionGroup(null);
2185 void createGroupMenuItem_actionPerformed()
2187 getGroup(); // implicitly creates group - note - should apply defaults / use
2188 // standard alignment window logic for this
2198 protected void outline_actionPerformed()
2200 SequenceGroup sg = getGroup();
2201 Color col = JColorChooser.showDialog(this,
2202 MessageManager.getString("label.select_outline_colour"),
2207 sg.setOutlineColour(col);
2219 public void showBoxes_actionPerformed()
2221 getGroup().setDisplayBoxes(showBoxes.isSelected());
2231 public void showText_actionPerformed()
2233 getGroup().setDisplayText(showText.isSelected());
2243 public void showColourText_actionPerformed()
2245 getGroup().setColourText(showColourText.isSelected());
2249 public void showLink(String url)
2253 jalview.util.BrowserLauncher.openURL(url);
2254 } catch (Exception ex)
2256 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
2257 MessageManager.getString("label.web_browser_not_found_unix"),
2258 MessageManager.getString("label.web_browser_not_found"),
2259 JvOptionPane.WARNING_MESSAGE);
2261 ex.printStackTrace();
2265 void hideSequences(boolean representGroup)
2267 ap.av.hideSequences(sequence, representGroup);
2270 public void copy_actionPerformed()
2272 ap.alignFrame.copy_actionPerformed(null);
2275 public void cut_actionPerformed()
2277 ap.alignFrame.cut_actionPerformed(null);
2280 void changeCase(ActionEvent e)
2282 Object source = e.getSource();
2283 SequenceGroup sg = ap.av.getSelectionGroup();
2287 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2288 sg.getStartRes(), sg.getEndRes() + 1);
2293 if (source == toggle)
2295 description = MessageManager.getString("label.toggle_case");
2296 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2298 else if (source == upperCase)
2300 description = MessageManager.getString("label.to_upper_case");
2301 caseChange = ChangeCaseCommand.TO_UPPER;
2305 description = MessageManager.getString("label.to_lower_case");
2306 caseChange = ChangeCaseCommand.TO_LOWER;
2309 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2310 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2311 startEnd, caseChange);
2313 ap.alignFrame.addHistoryItem(caseCommand);
2315 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2321 public void outputText_actionPerformed(ActionEvent e)
2323 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2324 cap.setForInput(null);
2325 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2326 "label.alignment_output_command",
2327 new Object[] { e.getActionCommand() }), 600, 500);
2329 String[] omitHidden = null;
2331 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2332 // or we simply trust the user wants
2333 // wysiwig behaviour
2335 FileFormatI fileFormat = FileFormats.getInstance().forName(
2336 e.getActionCommand());
2337 cap.setText(new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2340 public void sequenceFeature_actionPerformed()
2342 SequenceGroup sg = ap.av.getSelectionGroup();
2348 int rsize = 0, gSize = sg.getSize();
2349 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2350 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2352 for (int i = 0; i < gSize; i++)
2354 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2355 int end = sg.findEndRes(sg.getSequenceAt(i));
2358 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2359 features[rsize] = new SequenceFeature(null, null, null, start, end,
2364 rseqs = new SequenceI[rsize];
2365 tfeatures = new SequenceFeature[rsize];
2366 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2367 System.arraycopy(features, 0, tfeatures, 0, rsize);
2368 features = tfeatures;
2370 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2371 features, true, ap))
2373 ap.alignFrame.setShowSeqFeatures(true);
2374 ap.highlightSearchResults(null);
2378 public void textColour_actionPerformed()
2380 SequenceGroup sg = getGroup();
2383 new TextColourChooser().chooseColour(ap, sg);
2387 public void colourByStructure(String pdbid)
2389 Annotation[] anots = ap.av.getStructureSelectionManager()
2390 .colourSequenceFromStructure(sequence, pdbid);
2392 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2393 "Coloured by " + pdbid, anots);
2395 ap.av.getAlignment().addAnnotation(an);
2396 an.createSequenceMapping(sequence, 0, true);
2397 // an.adjustForAlignment();
2398 ap.av.getAlignment().setAnnotationIndex(an, 0);
2400 ap.adjustAnnotationHeight();
2402 sequence.addAlignmentAnnotation(an);
2406 public void editSequence_actionPerformed(ActionEvent actionEvent)
2408 SequenceGroup sg = ap.av.getSelectionGroup();
2412 if (sequence == null)
2414 sequence = sg.getSequenceAt(0);
2417 EditNameDialog dialog = new EditNameDialog(
2418 sequence.getSequenceAsString(sg.getStartRes(),
2419 sg.getEndRes() + 1), null,
2420 MessageManager.getString("label.edit_sequence"), null,
2421 MessageManager.getString("label.edit_sequence"),
2426 EditCommand editCommand = new EditCommand(
2427 MessageManager.getString("label.edit_sequences"),
2428 Action.REPLACE, dialog.getName().replace(' ',
2429 ap.av.getGapCharacter()),
2430 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2431 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2433 ap.alignFrame.addHistoryItem(editCommand);
2435 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()