2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.ColumnSelection;
35 import jalview.datamodel.DBRefEntry;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceFeature;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.FormatAdapter;
42 import jalview.io.SequenceAnnotationReport;
43 import jalview.schemes.AnnotationColourGradient;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.BuriedColourScheme;
46 import jalview.schemes.ClustalxColourScheme;
47 import jalview.schemes.HelixColourScheme;
48 import jalview.schemes.HydrophobicColourScheme;
49 import jalview.schemes.NucleotideColourScheme;
50 import jalview.schemes.PIDColourScheme;
51 import jalview.schemes.PurinePyrimidineColourScheme;
52 import jalview.schemes.StrandColourScheme;
53 import jalview.schemes.TaylorColourScheme;
54 import jalview.schemes.TurnColourScheme;
55 import jalview.schemes.UserColourScheme;
56 import jalview.schemes.ZappoColourScheme;
57 import jalview.util.DBRefUtils;
58 import jalview.util.GroupUrlLink;
59 import jalview.util.GroupUrlLink.UrlStringTooLongException;
60 import jalview.util.MessageManager;
61 import jalview.util.UrlLink;
63 import java.awt.Color;
64 import java.awt.event.ActionEvent;
65 import java.awt.event.ActionListener;
66 import java.util.ArrayList;
67 import java.util.Arrays;
68 import java.util.Collections;
69 import java.util.Hashtable;
70 import java.util.LinkedHashMap;
71 import java.util.List;
73 import java.util.TreeMap;
74 import java.util.Vector;
76 import javax.swing.ButtonGroup;
77 import javax.swing.JCheckBoxMenuItem;
78 import javax.swing.JColorChooser;
79 import javax.swing.JMenu;
80 import javax.swing.JMenuItem;
81 import javax.swing.JOptionPane;
82 import javax.swing.JPopupMenu;
83 import javax.swing.JRadioButtonMenuItem;
89 * @version $Revision: 1.118 $
91 public class PopupMenu extends JPopupMenu
93 JMenu groupMenu = new JMenu();
95 JMenuItem groupName = new JMenuItem();
97 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
113 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
115 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
117 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
119 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
121 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
123 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
125 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
127 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
131 JMenu sequenceMenu = new JMenu();
133 JMenuItem sequenceName = new JMenuItem();
135 JMenuItem sequenceDetails = new JMenuItem();
137 JMenuItem sequenceSelDetails = new JMenuItem();
139 JMenuItem makeReferenceSeq = new JMenuItem();
141 JMenuItem chooseAnnotations = new JMenuItem();
145 JMenuItem createGroupMenuItem = new JMenuItem();
147 JMenuItem unGroupMenuItem = new JMenuItem();
149 JMenuItem outline = new JMenuItem();
151 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
153 JMenu colourMenu = new JMenu();
155 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
157 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
159 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
161 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
163 JMenu editMenu = new JMenu();
165 JMenuItem cut = new JMenuItem();
167 JMenuItem copy = new JMenuItem();
169 JMenuItem upperCase = new JMenuItem();
171 JMenuItem lowerCase = new JMenuItem();
173 JMenuItem toggle = new JMenuItem();
175 JMenu pdbMenu = new JMenu();
177 JMenu outputMenu = new JMenu();
179 JMenu seqShowAnnotationsMenu = new JMenu();
181 JMenu seqHideAnnotationsMenu = new JMenu();
183 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
184 MessageManager.getString("label.add_reference_annotations"));
186 JMenu groupShowAnnotationsMenu = new JMenu();
188 JMenu groupHideAnnotationsMenu = new JMenu();
190 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
191 MessageManager.getString("label.add_reference_annotations"));
193 JMenuItem sequenceFeature = new JMenuItem();
195 JMenuItem textColour = new JMenuItem();
197 JMenu jMenu1 = new JMenu();
199 JMenuItem pdbStructureDialog = new JMenuItem();
201 JMenu rnaStructureMenu = new JMenu();
203 JMenuItem editSequence = new JMenuItem();
205 JMenu groupLinksMenu;
207 JMenuItem hideInsertions = new JMenuItem();
210 * Creates a new PopupMenu object.
217 public PopupMenu(final AlignmentPanel ap, Sequence seq, List<String> links)
219 this(ap, seq, links, null);
229 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
230 List<String> links, List<String> groupLinks)
232 // /////////////////////////////////////////////////////////
233 // If this is activated from the sequence panel, the user may want to
234 // edit or annotate a particular residue. Therefore display the residue menu
236 // If from the IDPanel, we must display the sequence menu
237 // ////////////////////////////////////////////////////////
241 ButtonGroup colours = new ButtonGroup();
242 colours.add(noColourmenuItem);
243 colours.add(clustalColour);
244 colours.add(zappoColour);
245 colours.add(taylorColour);
246 colours.add(hydrophobicityColour);
247 colours.add(helixColour);
248 colours.add(strandColour);
249 colours.add(turnColour);
250 colours.add(buriedColour);
251 colours.add(abovePIDColour);
252 colours.add(userDefinedColour);
253 colours.add(PIDColour);
254 colours.add(BLOSUM62Colour);
255 colours.add(purinePyrimidineColour);
256 colours.add(RNAInteractionColour);
258 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
260 JMenuItem item = new JMenuItem(
261 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
263 item.addActionListener(new java.awt.event.ActionListener()
266 public void actionPerformed(ActionEvent e)
268 outputText_actionPerformed(e);
272 outputMenu.add(item);
276 * Build menus for annotation types that may be shown or hidden, and for
277 * 'reference annotations' that may be added to the alignment. First for the
278 * currently selected sequence (if there is one):
280 final List<SequenceI> selectedSequence = (seq == null ? Collections
281 .<SequenceI> emptyList() : Arrays.asList(seq));
282 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
283 seqHideAnnotationsMenu, selectedSequence);
284 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
288 * And repeat for the current selection group (if there is one):
290 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
291 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
293 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
294 groupHideAnnotationsMenu, selectedGroup);
295 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
301 } catch (Exception e)
309 sequenceMenu.setText(sequence.getName());
310 if (seq == ap.av.getAlignment().getSeqrep())
312 makeReferenceSeq.setText(MessageManager
313 .getString("action.unmark_as_reference"));
317 makeReferenceSeq.setText(MessageManager
318 .getString("action.set_as_reference"));
321 if (!ap.av.getAlignment().isNucleotide())
323 remove(rnaStructureMenu);
327 int origCount = rnaStructureMenu.getItemCount();
329 * add menu items to 2D-render any alignment or sequence secondary
330 * structure annotation
332 AlignmentAnnotation[] aas = ap.av.getAlignment()
333 .getAlignmentAnnotation();
336 for (final AlignmentAnnotation aa : aas)
338 if (aa.isValidStruc() && aa.sequenceRef == null)
341 * valid alignment RNA secondary structure annotation
343 menuItem = new JMenuItem();
344 menuItem.setText(MessageManager.formatMessage(
345 "label.2d_rna_structure_line",
346 new Object[] { aa.label }));
347 menuItem.addActionListener(new java.awt.event.ActionListener()
350 public void actionPerformed(ActionEvent e)
352 new AppVarna(seq, aa, ap);
355 rnaStructureMenu.add(menuItem);
360 if (seq.getAnnotation() != null)
362 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
363 for (final AlignmentAnnotation aa : seqAnns)
365 if (aa.isValidStruc())
368 * valid sequence RNA secondary structure annotation
370 // TODO: make rnastrucF a bit more nice
371 menuItem = new JMenuItem();
372 menuItem.setText(MessageManager.formatMessage(
373 "label.2d_rna_sequence_name",
374 new Object[] { seq.getName() }));
375 menuItem.addActionListener(new java.awt.event.ActionListener()
378 public void actionPerformed(ActionEvent e)
380 // TODO: VARNA does'nt print gaps in the sequence
381 new AppVarna(seq, aa, ap);
384 rnaStructureMenu.add(menuItem);
388 if (rnaStructureMenu.getItemCount() == origCount)
390 remove(rnaStructureMenu);
394 menuItem = new JMenuItem(
395 MessageManager.getString("action.hide_sequences"));
396 menuItem.addActionListener(new java.awt.event.ActionListener()
399 public void actionPerformed(ActionEvent e)
401 hideSequences(false);
406 if (ap.av.getSelectionGroup() != null
407 && ap.av.getSelectionGroup().getSize() > 1)
409 menuItem = new JMenuItem(MessageManager.formatMessage(
410 "label.represent_group_with",
411 new Object[] { seq.getName() }));
412 menuItem.addActionListener(new java.awt.event.ActionListener()
415 public void actionPerformed(ActionEvent e)
420 sequenceMenu.add(menuItem);
423 if (ap.av.hasHiddenRows())
425 final int index = ap.av.getAlignment().findIndex(seq);
427 if (ap.av.adjustForHiddenSeqs(index)
428 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
430 menuItem = new JMenuItem(
431 MessageManager.getString("action.reveal_sequences"));
432 menuItem.addActionListener(new ActionListener()
435 public void actionPerformed(ActionEvent e)
437 ap.av.showSequence(index);
438 if (ap.overviewPanel != null)
440 ap.overviewPanel.updateOverviewImage();
448 // for the case when no sequences are even visible
449 if (ap.av.hasHiddenRows())
452 menuItem = new JMenuItem(
453 MessageManager.getString("action.reveal_all"));
454 menuItem.addActionListener(new ActionListener()
457 public void actionPerformed(ActionEvent e)
459 ap.av.showAllHiddenSeqs();
460 if (ap.overviewPanel != null)
462 ap.overviewPanel.updateOverviewImage();
472 SequenceGroup sg = ap.av.getSelectionGroup();
473 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
474 .getGroups().contains(sg) : false;
476 if (sg != null && sg.getSize() > 0)
478 groupName.setText(MessageManager
479 .getString("label.edit_name_and_description_current_group"));
481 if (sg.cs instanceof ZappoColourScheme)
483 zappoColour.setSelected(true);
485 else if (sg.cs instanceof TaylorColourScheme)
487 taylorColour.setSelected(true);
489 else if (sg.cs instanceof PIDColourScheme)
491 PIDColour.setSelected(true);
493 else if (sg.cs instanceof Blosum62ColourScheme)
495 BLOSUM62Colour.setSelected(true);
497 else if (sg.cs instanceof UserColourScheme)
499 userDefinedColour.setSelected(true);
501 else if (sg.cs instanceof HydrophobicColourScheme)
503 hydrophobicityColour.setSelected(true);
505 else if (sg.cs instanceof HelixColourScheme)
507 helixColour.setSelected(true);
509 else if (sg.cs instanceof StrandColourScheme)
511 strandColour.setSelected(true);
513 else if (sg.cs instanceof TurnColourScheme)
515 turnColour.setSelected(true);
517 else if (sg.cs instanceof BuriedColourScheme)
519 buriedColour.setSelected(true);
521 else if (sg.cs instanceof ClustalxColourScheme)
523 clustalColour.setSelected(true);
525 else if (sg.cs instanceof PurinePyrimidineColourScheme)
527 purinePyrimidineColour.setSelected(true);
531 * else if (sg.cs instanceof CovariationColourScheme) {
532 * covariationColour.setSelected(true); }
536 noColourmenuItem.setSelected(true);
539 if (sg.cs != null && sg.cs.conservationApplied())
541 conservationMenuItem.setSelected(true);
543 displayNonconserved.setSelected(sg.getShowNonconserved());
544 showText.setSelected(sg.getDisplayText());
545 showColourText.setSelected(sg.getColourText());
546 showBoxes.setSelected(sg.getDisplayBoxes());
547 // add any groupURLs to the groupURL submenu and make it visible
548 if (groupLinks != null && groupLinks.size() > 0)
550 buildGroupURLMenu(sg, groupLinks);
552 // Add a 'show all structures' for the current selection
553 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
554 SequenceI sqass = null;
555 for (SequenceI sq : ap.av.getSequenceSelection())
557 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
558 if (pes != null && pes.size() > 0)
560 reppdb.put(pes.get(0).getId(), pes.get(0));
561 for (PDBEntry pe : pes)
563 pdbe.put(pe.getId(), pe);
573 final PDBEntry[] pe = pdbe.values().toArray(
574 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
575 new PDBEntry[reppdb.size()]);
576 final JMenuItem gpdbview, rpdbview;
581 groupMenu.setVisible(false);
582 editMenu.setVisible(false);
587 createGroupMenuItem.setVisible(true);
588 unGroupMenuItem.setVisible(false);
589 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
593 createGroupMenuItem.setVisible(false);
594 unGroupMenuItem.setVisible(true);
595 jMenu1.setText(MessageManager.getString("action.edit_group"));
600 sequenceMenu.setVisible(false);
601 pdbStructureDialog.setVisible(false);
602 rnaStructureMenu.setVisible(false);
605 if (links != null && links.size() > 0)
607 addFeatureLinks(seq, links);
612 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
617 void addFeatureLinks(final SequenceI seq, List<String> links)
619 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
620 List<String> linkset = new ArrayList<String>();
621 for (String link : links)
623 UrlLink urlLink = null;
626 urlLink = new UrlLink(link);
627 } catch (Exception foo)
629 Cache.log.error("Exception for URLLink '" + link + "'", foo);
633 if (!urlLink.isValid())
635 Cache.log.error(urlLink.getInvalidMessage());
638 final String label = urlLink.getLabel();
639 if (seq != null && urlLink.isDynamic())
642 // collect matching db-refs
643 DBRefEntry[] dbr = DBRefUtils.selectRefs(seq.getDBRefs(),
644 new String[] { urlLink.getTarget() });
645 // collect id string too
646 String id = seq.getName();
647 String descr = seq.getDescription();
648 if (descr != null && descr.length() < 1)
655 for (int r = 0; r < dbr.length; r++)
657 if (id != null && dbr[r].getAccessionId().equals(id))
659 // suppress duplicate link creation for the bare sequence ID
660 // string with this link
663 // create Bare ID link for this URL
664 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(), true);
667 for (int u = 0; u < urls.length; u += 2)
669 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
671 linkset.add(urls[u] + "|" + urls[u + 1]);
672 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
680 // create Bare ID link for this URL
681 String[] urls = urlLink.makeUrls(id, true);
684 for (int u = 0; u < urls.length; u += 2)
686 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
688 linkset.add(urls[u] + "|" + urls[u + 1]);
689 addshowLink(linkMenu, label, urls[u + 1]);
694 // Create urls from description but only for URL links which are regex
696 if (descr != null && urlLink.getRegexReplace() != null)
698 // create link for this URL from description where regex matches
699 String[] urls = urlLink.makeUrls(descr, true);
702 for (int u = 0; u < urls.length; u += 2)
704 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
706 linkset.add(urls[u] + "|" + urls[u + 1]);
707 addshowLink(linkMenu, label, urls[u + 1]);
715 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
717 linkset.add(label + "|" + urlLink.getUrl_prefix());
718 // Add a non-dynamic link
719 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
723 if (sequence != null)
725 sequenceMenu.add(linkMenu);
734 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
735 * "All" is added first, followed by a separator. Then add any annotation
736 * types associated with the current selection. Separate menus are built for
737 * the selected sequence group (if any), and the selected sequence.
739 * Some annotation rows are always rendered together - these can be identified
740 * by a common graphGroup property > -1. Only one of each group will be marked
741 * as visible (to avoid duplication of the display). For such groups we add a
742 * composite type name, e.g.
744 * IUPredWS (Long), IUPredWS (Short)
748 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
749 List<SequenceI> forSequences)
751 showMenu.removeAll();
752 hideMenu.removeAll();
754 final List<String> all = Arrays.asList(new String[] { MessageManager
755 .getString("label.all") });
756 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
757 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
759 showMenu.addSeparator();
760 hideMenu.addSeparator();
762 final AlignmentAnnotation[] annotations = ap.getAlignment()
763 .getAlignmentAnnotation();
766 * Find shown/hidden annotations types, distinguished by source (calcId),
767 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
768 * the insertion order, which is the order of the annotations on the
771 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
772 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
773 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
774 AlignmentAnnotationUtils.asList(annotations), forSequences);
776 for (String calcId : hiddenTypes.keySet())
778 for (List<String> type : hiddenTypes.get(calcId))
780 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
784 // grey out 'show annotations' if none are hidden
785 showMenu.setEnabled(!hiddenTypes.isEmpty());
787 for (String calcId : shownTypes.keySet())
789 for (List<String> type : shownTypes.get(calcId))
791 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
795 // grey out 'hide annotations' if none are shown
796 hideMenu.setEnabled(!shownTypes.isEmpty());
800 * Returns a list of sequences - either the current selection group (if there
801 * is one), else the specified single sequence.
806 protected List<SequenceI> getSequenceScope(SequenceI seq)
808 List<SequenceI> forSequences = null;
809 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
810 if (selectionGroup != null && selectionGroup.getSize() > 0)
812 forSequences = selectionGroup.getSequences();
816 forSequences = seq == null ? Collections.<SequenceI> emptyList()
817 : Arrays.asList(seq);
823 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
826 * @param showOrHideMenu
828 * @param forSequences
829 * the sequences whose annotations may be shown or hidden
834 * if true this is a special label meaning 'All'
835 * @param actionIsShow
836 * if true, the select menu item action is to show the annotation
839 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
840 final List<SequenceI> forSequences, String calcId,
841 final List<String> types, final boolean allTypes,
842 final boolean actionIsShow)
844 String label = types.toString(); // [a, b, c]
845 label = label.substring(1, label.length() - 1); // a, b, c
846 final JMenuItem item = new JMenuItem(label);
847 item.setToolTipText(calcId);
848 item.addActionListener(new java.awt.event.ActionListener()
851 public void actionPerformed(ActionEvent e)
853 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
854 types, forSequences, allTypes, actionIsShow);
858 showOrHideMenu.add(item);
861 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
864 // TODO: usability: thread off the generation of group url content so root
866 // sequence only URLs
867 // ID/regex match URLs
868 groupLinksMenu = new JMenu(
869 MessageManager.getString("action.group_link"));
870 // three types of url that might be created.
871 JMenu[] linkMenus = new JMenu[] { null,
872 new JMenu(MessageManager.getString("action.ids")),
873 new JMenu(MessageManager.getString("action.sequences")),
874 new JMenu(MessageManager.getString("action.ids_sequences")) };
876 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
877 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
878 Hashtable<String, Object[]> commonDbrefs = new Hashtable<String, Object[]>();
879 for (int sq = 0; sq < seqs.length; sq++)
882 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
883 .findPosition(sg.getEndRes());
884 // just collect ids from dataset sequence
885 // TODO: check if IDs collected from selecton group intersects with the
886 // current selection, too
887 SequenceI sqi = seqs[sq];
888 while (sqi.getDatasetSequence() != null)
890 sqi = sqi.getDatasetSequence();
892 DBRefEntry[] dbr = sqi.getDBRefs();
893 if (dbr != null && dbr.length > 0)
895 for (int d = 0; d < dbr.length; d++)
897 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
898 Object[] sarray = commonDbrefs.get(src);
901 sarray = new Object[2];
902 sarray[0] = new int[] { 0 };
903 sarray[1] = new String[seqs.length];
905 commonDbrefs.put(src, sarray);
908 if (((String[]) sarray[1])[sq] == null)
911 || (dbr[d].getMap().locateMappedRange(start, end) != null))
913 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
914 ((int[]) sarray[0])[0]++;
920 // now create group links for all distinct ID/sequence sets.
921 boolean addMenu = false; // indicates if there are any group links to give
923 for (String link : groupLinks)
925 GroupUrlLink urlLink = null;
928 urlLink = new GroupUrlLink(link);
929 } catch (Exception foo)
931 Cache.log.error("Exception for GroupURLLink '" + link
936 if (!urlLink.isValid())
938 Cache.log.error(urlLink.getInvalidMessage());
941 final String label = urlLink.getLabel();
942 boolean usingNames = false;
943 // Now see which parts of the group apply for this URL
944 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
945 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
946 String[] seqstr, ids; // input to makeUrl
949 int numinput = ((int[]) idset[0])[0];
950 String[] allids = ((String[]) idset[1]);
951 seqstr = new String[numinput];
952 ids = new String[numinput];
953 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
955 if (allids[sq] != null)
957 ids[idcount] = allids[sq];
958 seqstr[idcount++] = idandseqs[1][sq];
964 // just use the id/seq set
965 seqstr = idandseqs[1];
969 // and try and make the groupURL!
971 Object[] urlset = null;
974 urlset = urlLink.makeUrlStubs(ids, seqstr,
975 "FromJalview" + System.currentTimeMillis(), false);
976 } catch (UrlStringTooLongException e)
981 int type = urlLink.getGroupURLType() & 3;
982 // first two bits ofurlLink type bitfield are sequenceids and sequences
983 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
984 addshowLink(linkMenus[type], label
985 + (((type & 1) == 1) ? ("("
986 + (usingNames ? "Names" : ltarget) + ")") : ""),
993 groupLinksMenu = new JMenu(
994 MessageManager.getString("action.group_link"));
995 for (int m = 0; m < linkMenus.length; m++)
997 if (linkMenus[m] != null
998 && linkMenus[m].getMenuComponentCount() > 0)
1000 groupLinksMenu.add(linkMenus[m]);
1004 groupMenu.add(groupLinksMenu);
1009 * add a show URL menu item to the given linkMenu
1013 * - menu label string
1017 private void addshowLink(JMenu linkMenu, String label, final String url)
1019 JMenuItem item = new JMenuItem(label);
1020 item.setToolTipText(MessageManager.formatMessage(
1021 "label.open_url_param", new Object[] { url }));
1022 item.addActionListener(new java.awt.event.ActionListener()
1025 public void actionPerformed(ActionEvent e)
1027 new Thread(new Runnable()
1044 * add a late bound groupURL item to the given linkMenu
1048 * - menu label string
1049 * @param urlgenerator
1050 * GroupURLLink used to generate URL
1052 * Object array returned from the makeUrlStubs function.
1054 private void addshowLink(JMenu linkMenu, String label,
1055 final GroupUrlLink urlgenerator, final Object[] urlstub)
1057 JMenuItem item = new JMenuItem(label);
1058 item.setToolTipText(MessageManager.formatMessage(
1059 "label.open_url_seqs_param",
1060 new Object[] { urlgenerator.getUrl_prefix(),
1061 urlgenerator.getNumberInvolved(urlstub) }));
1062 // TODO: put in info about what is being sent.
1063 item.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 new Thread(new Runnable()
1076 showLink(urlgenerator.constructFrom(urlstub));
1077 } catch (UrlStringTooLongException e2)
1095 private void jbInit() throws Exception
1097 groupMenu.setText(MessageManager.getString("label.selection"));
1098 groupName.setText(MessageManager.getString("label.name"));
1099 groupName.addActionListener(new java.awt.event.ActionListener()
1102 public void actionPerformed(ActionEvent e)
1104 groupName_actionPerformed();
1107 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1108 sequenceName.setText(MessageManager
1109 .getString("label.edit_name_description"));
1110 sequenceName.addActionListener(new java.awt.event.ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 sequenceName_actionPerformed();
1118 chooseAnnotations.setText(MessageManager
1119 .getString("action.choose_annotations"));
1120 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1123 public void actionPerformed(ActionEvent e)
1125 chooseAnnotations_actionPerformed(e);
1128 sequenceDetails.setText(MessageManager
1129 .getString("label.sequence_details"));
1130 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 sequenceDetails_actionPerformed();
1138 sequenceSelDetails.setText(MessageManager
1139 .getString("label.sequence_details"));
1141 .addActionListener(new java.awt.event.ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 sequenceSelectionDetails_actionPerformed();
1149 PIDColour.setFocusPainted(false);
1151 .setText(MessageManager.getString("action.remove_group"));
1152 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 unGroupMenuItem_actionPerformed();
1160 createGroupMenuItem.setText(MessageManager
1161 .getString("action.create_group"));
1163 .addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 createGroupMenuItem_actionPerformed();
1172 outline.setText(MessageManager.getString("action.border_colour"));
1173 outline.addActionListener(new java.awt.event.ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 outline_actionPerformed();
1182 .setText(MessageManager.getString("label.nucleotide"));
1183 nucleotideMenuItem.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 nucleotideMenuItem_actionPerformed();
1191 colourMenu.setText(MessageManager.getString("label.group_colour"));
1192 showBoxes.setText(MessageManager.getString("action.boxes"));
1193 showBoxes.setState(true);
1194 showBoxes.addActionListener(new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 showBoxes_actionPerformed();
1202 showText.setText(MessageManager.getString("action.text"));
1203 showText.setState(true);
1204 showText.addActionListener(new ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 showText_actionPerformed();
1212 showColourText.setText(MessageManager.getString("label.colour_text"));
1213 showColourText.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 showColourText_actionPerformed();
1221 displayNonconserved.setText(MessageManager
1222 .getString("label.show_non_conversed"));
1223 displayNonconserved.setState(true);
1224 displayNonconserved.addActionListener(new ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 showNonconserved_actionPerformed();
1232 editMenu.setText(MessageManager.getString("action.edit"));
1233 cut.setText(MessageManager.getString("action.cut"));
1234 cut.addActionListener(new ActionListener()
1237 public void actionPerformed(ActionEvent e)
1239 cut_actionPerformed();
1242 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1243 upperCase.addActionListener(new ActionListener()
1246 public void actionPerformed(ActionEvent e)
1251 copy.setText(MessageManager.getString("action.copy"));
1252 copy.addActionListener(new ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 copy_actionPerformed();
1260 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1261 lowerCase.addActionListener(new ActionListener()
1264 public void actionPerformed(ActionEvent e)
1269 toggle.setText(MessageManager.getString("label.toggle_case"));
1270 toggle.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1278 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1280 seqShowAnnotationsMenu.setText(MessageManager
1281 .getString("label.show_annotations"));
1282 seqHideAnnotationsMenu.setText(MessageManager
1283 .getString("label.hide_annotations"));
1284 groupShowAnnotationsMenu.setText(MessageManager
1285 .getString("label.show_annotations"));
1286 groupHideAnnotationsMenu.setText(MessageManager
1287 .getString("label.hide_annotations"));
1288 sequenceFeature.setText(MessageManager
1289 .getString("label.create_sequence_feature"));
1290 sequenceFeature.addActionListener(new ActionListener()
1293 public void actionPerformed(ActionEvent e)
1295 sequenceFeature_actionPerformed();
1298 textColour.setText(MessageManager.getString("label.text_colour"));
1299 textColour.addActionListener(new ActionListener()
1302 public void actionPerformed(ActionEvent e)
1304 textColour_actionPerformed();
1307 jMenu1.setText(MessageManager.getString("label.group"));
1308 pdbStructureDialog.setText(MessageManager
1309 .getString("label.show_pdbstruct_dialog"));
1310 pdbStructureDialog.addActionListener(new ActionListener()
1313 public void actionPerformed(ActionEvent actionEvent)
1315 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1316 if (ap.av.getSelectionGroup() != null)
1318 selectedSeqs = ap.av.getSequenceSelection();
1320 new StructureChooser(selectedSeqs, sequence, ap);
1324 rnaStructureMenu.setText(MessageManager
1325 .getString("label.view_rna_structure"));
1327 // colStructureMenu.setText("Colour By Structure");
1328 editSequence.setText(MessageManager.getString("label.edit_sequence")
1330 editSequence.addActionListener(new ActionListener()
1333 public void actionPerformed(ActionEvent actionEvent)
1335 editSequence_actionPerformed(actionEvent);
1338 makeReferenceSeq.setText(MessageManager
1339 .getString("label.mark_as_representative"));
1340 makeReferenceSeq.addActionListener(new ActionListener()
1344 public void actionPerformed(ActionEvent actionEvent)
1346 makeReferenceSeq_actionPerformed(actionEvent);
1350 hideInsertions.setText(MessageManager
1351 .getString("label.hide_insertions"));
1352 hideInsertions.addActionListener(new ActionListener()
1356 public void actionPerformed(ActionEvent e)
1358 hideInsertions_actionPerformed(e);
1362 * annotationMenuItem.setText("By Annotation");
1363 * annotationMenuItem.addActionListener(new ActionListener() { public void
1364 * actionPerformed(ActionEvent actionEvent) {
1365 * annotationMenuItem_actionPerformed(actionEvent); } });
1367 groupMenu.add(sequenceSelDetails);
1370 add(rnaStructureMenu);
1371 add(pdbStructureDialog);
1372 if (sequence != null)
1374 add(hideInsertions);
1376 // annotations configuration panel suppressed for now
1377 // groupMenu.add(chooseAnnotations);
1380 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1381 * (if a selection group is in force).
1383 sequenceMenu.add(seqShowAnnotationsMenu);
1384 sequenceMenu.add(seqHideAnnotationsMenu);
1385 sequenceMenu.add(seqAddReferenceAnnotations);
1386 groupMenu.add(groupShowAnnotationsMenu);
1387 groupMenu.add(groupHideAnnotationsMenu);
1388 groupMenu.add(groupAddReferenceAnnotations);
1389 groupMenu.add(editMenu);
1390 groupMenu.add(outputMenu);
1391 groupMenu.add(sequenceFeature);
1392 groupMenu.add(createGroupMenuItem);
1393 groupMenu.add(unGroupMenuItem);
1394 groupMenu.add(jMenu1);
1395 sequenceMenu.add(sequenceName);
1396 sequenceMenu.add(sequenceDetails);
1397 sequenceMenu.add(makeReferenceSeq);
1398 colourMenu.add(textColour);
1399 colourMenu.add(noColourmenuItem);
1400 colourMenu.add(clustalColour);
1401 colourMenu.add(BLOSUM62Colour);
1402 colourMenu.add(PIDColour);
1403 colourMenu.add(zappoColour);
1404 colourMenu.add(taylorColour);
1405 colourMenu.add(hydrophobicityColour);
1406 colourMenu.add(helixColour);
1407 colourMenu.add(strandColour);
1408 colourMenu.add(turnColour);
1409 colourMenu.add(buriedColour);
1410 colourMenu.add(nucleotideMenuItem);
1411 if (ap.getAlignment().isNucleotide())
1413 // JBPNote - commented since the colourscheme isn't functional
1414 colourMenu.add(purinePyrimidineColour);
1416 colourMenu.add(userDefinedColour);
1418 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1420 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1421 .getUserColourSchemes().keys();
1423 while (userColours.hasMoreElements())
1425 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1426 item.addActionListener(new ActionListener()
1429 public void actionPerformed(ActionEvent evt)
1431 userDefinedColour_actionPerformed(evt);
1434 colourMenu.add(item);
1438 colourMenu.addSeparator();
1439 colourMenu.add(abovePIDColour);
1440 colourMenu.add(conservationMenuItem);
1443 editMenu.add(editSequence);
1444 editMenu.add(upperCase);
1445 editMenu.add(lowerCase);
1446 editMenu.add(toggle);
1447 // JBPNote: These shouldn't be added here - should appear in a generic
1448 // 'apply web service to this sequence menu'
1449 // pdbMenu.add(RNAFold);
1450 // pdbMenu.add(ContraFold);
1451 jMenu1.add(groupName);
1452 jMenu1.add(colourMenu);
1453 jMenu1.add(showBoxes);
1454 jMenu1.add(showText);
1455 jMenu1.add(showColourText);
1456 jMenu1.add(outline);
1457 jMenu1.add(displayNonconserved);
1458 noColourmenuItem.setText(MessageManager.getString("label.none"));
1459 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1462 public void actionPerformed(ActionEvent e)
1464 noColourmenuItem_actionPerformed();
1468 clustalColour.setText(MessageManager
1469 .getString("label.clustalx_colours"));
1470 clustalColour.addActionListener(new java.awt.event.ActionListener()
1473 public void actionPerformed(ActionEvent e)
1475 clustalColour_actionPerformed();
1478 zappoColour.setText(MessageManager.getString("label.zappo"));
1479 zappoColour.addActionListener(new java.awt.event.ActionListener()
1482 public void actionPerformed(ActionEvent e)
1484 zappoColour_actionPerformed();
1487 taylorColour.setText(MessageManager.getString("label.taylor"));
1488 taylorColour.addActionListener(new java.awt.event.ActionListener()
1491 public void actionPerformed(ActionEvent e)
1493 taylorColour_actionPerformed();
1496 hydrophobicityColour.setText(MessageManager
1497 .getString("label.hydrophobicity"));
1498 hydrophobicityColour
1499 .addActionListener(new java.awt.event.ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 hydrophobicityColour_actionPerformed();
1507 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1508 helixColour.addActionListener(new java.awt.event.ActionListener()
1511 public void actionPerformed(ActionEvent e)
1513 helixColour_actionPerformed();
1516 strandColour.setText(MessageManager
1517 .getString("label.strand_propensity"));
1518 strandColour.addActionListener(new java.awt.event.ActionListener()
1521 public void actionPerformed(ActionEvent e)
1523 strandColour_actionPerformed();
1526 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1527 turnColour.addActionListener(new java.awt.event.ActionListener()
1530 public void actionPerformed(ActionEvent e)
1532 turnColour_actionPerformed();
1535 buriedColour.setText(MessageManager.getString("label.buried_index"));
1536 buriedColour.addActionListener(new java.awt.event.ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 buriedColour_actionPerformed();
1544 abovePIDColour.setText(MessageManager
1545 .getString("label.above_identity_percentage"));
1546 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1549 public void actionPerformed(ActionEvent e)
1551 abovePIDColour_actionPerformed();
1554 userDefinedColour.setText(MessageManager
1555 .getString("action.user_defined"));
1556 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1559 public void actionPerformed(ActionEvent e)
1561 userDefinedColour_actionPerformed(e);
1565 .setText(MessageManager.getString("label.percentage_identity"));
1566 PIDColour.addActionListener(new java.awt.event.ActionListener()
1569 public void actionPerformed(ActionEvent e)
1571 PIDColour_actionPerformed();
1574 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1575 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1578 public void actionPerformed(ActionEvent e)
1580 BLOSUM62Colour_actionPerformed();
1583 purinePyrimidineColour.setText(MessageManager
1584 .getString("label.purine_pyrimidine"));
1585 purinePyrimidineColour
1586 .addActionListener(new java.awt.event.ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 purinePyrimidineColour_actionPerformed();
1596 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1597 * public void actionPerformed(ActionEvent e) {
1598 * covariationColour_actionPerformed(); } });
1601 conservationMenuItem.setText(MessageManager
1602 .getString("label.conservation"));
1603 conservationMenuItem
1604 .addActionListener(new java.awt.event.ActionListener()
1607 public void actionPerformed(ActionEvent e)
1609 conservationMenuItem_actionPerformed();
1615 * Check for any annotations on the underlying dataset sequences (for the
1616 * current selection group) which are not 'on the alignment'.If any are found,
1617 * enable the option to add them to the alignment. The criteria for 'on the
1618 * alignment' is finding an alignment annotation on the alignment, matched on
1619 * calcId, label and sequenceRef.
1621 * A tooltip is also constructed that displays the source (calcId) and type
1622 * (label) of the annotations that can be added.
1625 * @param forSequences
1627 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1628 List<SequenceI> forSequences)
1630 menuItem.setEnabled(false);
1633 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1634 * Using TreeMap means calcIds are shown in alphabetical order.
1636 Map<String, String> tipEntries = new TreeMap<String, String>();
1637 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1638 AlignmentI al = this.ap.av.getAlignment();
1639 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1640 tipEntries, candidates, al);
1641 if (!candidates.isEmpty())
1643 StringBuilder tooltip = new StringBuilder(64);
1644 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1647 * Found annotations that could be added. Enable the menu item, and
1648 * configure its tooltip and action.
1650 menuItem.setEnabled(true);
1651 for (String calcId : tipEntries.keySet())
1653 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1655 String tooltipText = JvSwingUtils.wrapTooltip(true,
1656 tooltip.toString());
1657 menuItem.setToolTipText(tooltipText);
1659 menuItem.addActionListener(new ActionListener()
1662 public void actionPerformed(ActionEvent e)
1664 addReferenceAnnotations_actionPerformed(candidates);
1671 * Add annotations to the sequences and to the alignment.
1674 * a map whose keys are sequences on the alignment, and values a list
1675 * of annotations to add to each sequence
1677 protected void addReferenceAnnotations_actionPerformed(
1678 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1680 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1681 final AlignmentI alignment = this.ap.getAlignment();
1682 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1687 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1689 if (!ap.av.getAlignment().hasSeqrep())
1691 // initialise the display flags so the user sees something happen
1692 ap.av.setDisplayReferenceSeq(true);
1693 ap.av.setColourByReferenceSeq(true);
1694 ap.av.getAlignment().setSeqrep(sequence);
1698 if (ap.av.getAlignment().getSeqrep() == sequence)
1700 ap.av.getAlignment().setSeqrep(null);
1704 ap.av.getAlignment().setSeqrep(sequence);
1710 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1712 if (sequence != null)
1714 ColumnSelection cs = ap.av.getColumnSelection();
1717 cs = new ColumnSelection();
1719 cs.hideInsertionsFor(sequence);
1720 ap.av.setColumnSelection(cs);
1725 protected void sequenceSelectionDetails_actionPerformed()
1727 createSequenceDetailsReport(ap.av.getSequenceSelection());
1730 protected void sequenceDetails_actionPerformed()
1732 createSequenceDetailsReport(new SequenceI[] { sequence });
1735 public void createSequenceDetailsReport(SequenceI[] sequences)
1737 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1738 StringBuffer contents = new StringBuffer();
1739 for (SequenceI seq : sequences)
1741 contents.append("<p><h2>"
1744 "label.create_sequence_details_report_annotation_for",
1745 new Object[] { seq.getDisplayId(true) })
1747 new SequenceAnnotationReport(null)
1748 .createSequenceAnnotationReport(
1754 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1755 .getSeqPanel().seqCanvas.fr.getMinMax()
1757 contents.append("</p>");
1759 cap.setText("<html>" + contents.toString() + "</html>");
1761 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1762 "label.sequence_details_for",
1763 (sequences.length == 1 ? new Object[] { sequences[0]
1764 .getDisplayId(true) } : new Object[] { MessageManager
1765 .getString("label.selection") })), 500, 400);
1769 protected void showNonconserved_actionPerformed()
1771 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1776 * call to refresh view after settings change
1780 ap.updateAnnotation();
1781 ap.paintAlignment(true);
1783 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1792 protected void clustalColour_actionPerformed()
1794 SequenceGroup sg = getGroup();
1795 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1805 protected void zappoColour_actionPerformed()
1807 getGroup().cs = new ZappoColourScheme();
1817 protected void taylorColour_actionPerformed()
1819 getGroup().cs = new TaylorColourScheme();
1829 protected void hydrophobicityColour_actionPerformed()
1831 getGroup().cs = new HydrophobicColourScheme();
1841 protected void helixColour_actionPerformed()
1843 getGroup().cs = new HelixColourScheme();
1853 protected void strandColour_actionPerformed()
1855 getGroup().cs = new StrandColourScheme();
1865 protected void turnColour_actionPerformed()
1867 getGroup().cs = new TurnColourScheme();
1877 protected void buriedColour_actionPerformed()
1879 getGroup().cs = new BuriedColourScheme();
1889 public void nucleotideMenuItem_actionPerformed()
1891 getGroup().cs = new NucleotideColourScheme();
1895 protected void purinePyrimidineColour_actionPerformed()
1897 getGroup().cs = new PurinePyrimidineColourScheme();
1902 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1903 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1911 protected void abovePIDColour_actionPerformed()
1913 SequenceGroup sg = getGroup();
1919 if (abovePIDColour.isSelected())
1921 sg.cs.setConsensus(AAFrequency.calculate(
1922 sg.getSequences(ap.av.getHiddenRepSequences()),
1923 sg.getStartRes(), sg.getEndRes() + 1));
1925 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1928 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1930 SliderPanel.showPIDSlider();
1933 // remove PIDColouring
1935 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1947 protected void userDefinedColour_actionPerformed(ActionEvent e)
1949 SequenceGroup sg = getGroup();
1951 if (e.getSource().equals(userDefinedColour))
1953 new UserDefinedColours(ap, sg);
1957 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1958 .getUserColourSchemes().get(e.getActionCommand());
1966 * Open a panel where the user can choose which types of sequence annotation
1971 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1973 // todo correct way to guard against opening a duplicate panel?
1974 new AnnotationChooser(ap);
1983 protected void PIDColour_actionPerformed()
1985 SequenceGroup sg = getGroup();
1986 sg.cs = new PIDColourScheme();
1987 sg.cs.setConsensus(AAFrequency.calculate(
1988 sg.getSequences(ap.av.getHiddenRepSequences()),
1989 sg.getStartRes(), sg.getEndRes() + 1));
1999 protected void BLOSUM62Colour_actionPerformed()
2001 SequenceGroup sg = getGroup();
2003 sg.cs = new Blosum62ColourScheme();
2005 sg.cs.setConsensus(AAFrequency.calculate(
2006 sg.getSequences(ap.av.getHiddenRepSequences()),
2007 sg.getStartRes(), sg.getEndRes() + 1));
2018 protected void noColourmenuItem_actionPerformed()
2020 getGroup().cs = null;
2030 protected void conservationMenuItem_actionPerformed()
2032 SequenceGroup sg = getGroup();
2038 if (conservationMenuItem.isSelected())
2040 // JBPNote: Conservation name shouldn't be i18n translated
2041 Conservation c = new Conservation("Group", 3, sg.getSequences(ap.av
2042 .getHiddenRepSequences()), sg.getStartRes(),
2043 sg.getEndRes() + 1);
2046 c.verdict(false, ap.av.getConsPercGaps());
2048 sg.cs.setConservation(c);
2050 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2051 SliderPanel.showConservationSlider();
2054 // remove ConservationColouring
2056 sg.cs.setConservation(null);
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 JOptionPane.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 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2257 MessageManager.getString("label.web_browser_not_found_unix"),
2258 MessageManager.getString("label.web_browser_not_found"),
2259 JOptionPane.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 cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
2339 public void sequenceFeature_actionPerformed()
2341 SequenceGroup sg = ap.av.getSelectionGroup();
2347 int rsize = 0, gSize = sg.getSize();
2348 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2349 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2351 for (int i = 0; i < gSize; i++)
2353 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2354 int end = sg.findEndRes(sg.getSequenceAt(i));
2357 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2358 features[rsize] = new SequenceFeature(null, null, null, start, end,
2363 rseqs = new SequenceI[rsize];
2364 tfeatures = new SequenceFeature[rsize];
2365 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2366 System.arraycopy(features, 0, tfeatures, 0, rsize);
2367 features = tfeatures;
2369 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2370 features, true, ap))
2372 ap.alignFrame.setShowSeqFeatures(true);
2373 ap.highlightSearchResults(null);
2377 public void textColour_actionPerformed()
2379 SequenceGroup sg = getGroup();
2382 new TextColourChooser().chooseColour(ap, sg);
2386 public void colourByStructure(String pdbid)
2388 Annotation[] anots = ap.av.getStructureSelectionManager()
2389 .colourSequenceFromStructure(sequence, pdbid);
2391 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2392 "Coloured by " + pdbid, anots);
2394 ap.av.getAlignment().addAnnotation(an);
2395 an.createSequenceMapping(sequence, 0, true);
2396 // an.adjustForAlignment();
2397 ap.av.getAlignment().setAnnotationIndex(an, 0);
2399 ap.adjustAnnotationHeight();
2401 sequence.addAlignmentAnnotation(an);
2405 public void editSequence_actionPerformed(ActionEvent actionEvent)
2407 SequenceGroup sg = ap.av.getSelectionGroup();
2411 if (sequence == null)
2413 sequence = sg.getSequenceAt(0);
2416 EditNameDialog dialog = new EditNameDialog(
2417 sequence.getSequenceAsString(sg.getStartRes(),
2418 sg.getEndRes() + 1), null,
2419 MessageManager.getString("label.edit_sequence"), null,
2420 MessageManager.getString("label.edit_sequence"),
2425 EditCommand editCommand = new EditCommand(
2426 MessageManager.getString("label.edit_sequences"),
2427 Action.REPLACE, dialog.getName().replace(' ',
2428 ap.av.getGapCharacter()),
2429 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2430 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2432 ap.alignFrame.addHistoryItem(editCommand);
2434 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()