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 java.awt.Color;
24 import java.awt.event.ActionEvent;
25 import java.awt.event.ActionListener;
26 import java.util.Arrays;
27 import java.util.Collections;
28 import java.util.Hashtable;
29 import java.util.LinkedHashMap;
30 import java.util.List;
32 import java.util.TreeMap;
33 import java.util.Vector;
35 import javax.swing.ButtonGroup;
36 import javax.swing.JCheckBoxMenuItem;
37 import javax.swing.JColorChooser;
38 import javax.swing.JMenu;
39 import javax.swing.JMenuItem;
40 import javax.swing.JOptionPane;
41 import javax.swing.JPopupMenu;
42 import javax.swing.JRadioButtonMenuItem;
44 import jalview.analysis.AAFrequency;
45 import jalview.analysis.AlignmentAnnotationUtils;
46 import jalview.analysis.AlignmentUtils;
47 import jalview.analysis.Conservation;
48 import jalview.commands.ChangeCaseCommand;
49 import jalview.commands.EditCommand;
50 import jalview.commands.EditCommand.Action;
51 import jalview.datamodel.AlignmentAnnotation;
52 import jalview.datamodel.AlignmentI;
53 import jalview.datamodel.Annotation;
54 import jalview.datamodel.ColumnSelection;
55 import jalview.datamodel.DBRefEntry;
56 import jalview.datamodel.PDBEntry;
57 import jalview.datamodel.Sequence;
58 import jalview.datamodel.SequenceFeature;
59 import jalview.datamodel.SequenceGroup;
60 import jalview.datamodel.SequenceI;
61 import jalview.io.FormatAdapter;
62 import jalview.io.SequenceAnnotationReport;
63 import jalview.schemes.AnnotationColourGradient;
64 import jalview.schemes.Blosum62ColourScheme;
65 import jalview.schemes.BuriedColourScheme;
66 import jalview.schemes.ClustalxColourScheme;
67 import jalview.schemes.HelixColourScheme;
68 import jalview.schemes.HydrophobicColourScheme;
69 import jalview.schemes.NucleotideColourScheme;
70 import jalview.schemes.PIDColourScheme;
71 import jalview.schemes.PurinePyrimidineColourScheme;
72 import jalview.schemes.ResidueProperties;
73 import jalview.schemes.StrandColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.UserColourScheme;
77 import jalview.schemes.ZappoColourScheme;
78 import jalview.util.GroupUrlLink;
79 import jalview.util.GroupUrlLink.UrlStringTooLongException;
80 import jalview.util.MessageManager;
81 import jalview.util.UrlLink;
87 * @version $Revision: 1.118 $
89 public class PopupMenu extends JPopupMenu
91 private static final String ALL_ANNOTATIONS = "All";
93 private static final String COMMA = ",";
95 JMenu groupMenu = new JMenu();
97 JMenuItem groupName = new JMenuItem();
99 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
103 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
105 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
115 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
117 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
119 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
121 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
123 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
125 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
127 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
129 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
133 JMenu sequenceMenu = new JMenu();
135 JMenuItem sequenceName = new JMenuItem();
137 JMenuItem sequenceDetails = new JMenuItem();
139 JMenuItem sequenceSelDetails = new JMenuItem();
141 JMenuItem makeReferenceSeq = new JMenuItem();
143 JMenuItem chooseAnnotations = new JMenuItem();
147 JMenuItem createGroupMenuItem = new JMenuItem();
149 JMenuItem unGroupMenuItem = new JMenuItem();
151 JMenuItem outline = new JMenuItem();
153 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
155 JMenu colourMenu = new JMenu();
157 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
159 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
161 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
163 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
165 JMenu editMenu = new JMenu();
167 JMenuItem cut = new JMenuItem();
169 JMenuItem copy = new JMenuItem();
171 JMenuItem upperCase = new JMenuItem();
173 JMenuItem lowerCase = new JMenuItem();
175 JMenuItem toggle = new JMenuItem();
177 JMenu pdbMenu = new JMenu();
179 JMenuItem pdbFromFile = new JMenuItem();
181 JMenuItem enterPDB = new JMenuItem();
183 JMenuItem discoverPDB = new JMenuItem();
185 JMenu outputMenu = new JMenu();
187 JMenu seqShowAnnotationsMenu = new JMenu();
189 JMenu seqHideAnnotationsMenu = new JMenu();
191 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
192 MessageManager.getString("label.add_reference_annotations"));
194 JMenu groupShowAnnotationsMenu = new JMenu();
196 JMenu groupHideAnnotationsMenu = new JMenu();
198 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
199 MessageManager.getString("label.add_reference_annotations"));
201 JMenuItem sequenceFeature = new JMenuItem();
203 JMenuItem textColour = new JMenuItem();
205 JMenu jMenu1 = new JMenu();
207 JMenuItem proteinStructureMenu = new JMenuItem();
209 JMenu rnaStructureMenu = new JMenu();
211 JMenuItem editSequence = new JMenuItem();
213 JMenu groupLinksMenu;
215 JMenuItem hideInsertions = new JMenuItem();
218 * Creates a new PopupMenu object.
225 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
227 this(ap, seq, links, null);
237 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
238 Vector links, Vector groupLinks)
240 // /////////////////////////////////////////////////////////
241 // If this is activated from the sequence panel, the user may want to
242 // edit or annotate a particular residue. Therefore display the residue menu
244 // If from the IDPanel, we must display the sequence menu
245 // ////////////////////////////////////////////////////////
249 ButtonGroup colours = new ButtonGroup();
250 colours.add(noColourmenuItem);
251 colours.add(clustalColour);
252 colours.add(zappoColour);
253 colours.add(taylorColour);
254 colours.add(hydrophobicityColour);
255 colours.add(helixColour);
256 colours.add(strandColour);
257 colours.add(turnColour);
258 colours.add(buriedColour);
259 colours.add(abovePIDColour);
260 colours.add(userDefinedColour);
261 colours.add(PIDColour);
262 colours.add(BLOSUM62Colour);
263 colours.add(purinePyrimidineColour);
264 colours.add(RNAInteractionColour);
266 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
268 JMenuItem item = new JMenuItem(
269 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
271 item.addActionListener(new java.awt.event.ActionListener()
274 public void actionPerformed(ActionEvent e)
276 outputText_actionPerformed(e);
280 outputMenu.add(item);
284 * Build menus for annotation types that may be shown or hidden, and for
285 * 'reference annotations' that may be added to the alignment. First for the
286 * currently selected sequence (if there is one):
288 final List<SequenceI> selectedSequence = (seq == null ? Collections
289 .<SequenceI> emptyList() : Arrays.asList(seq));
290 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
291 seqHideAnnotationsMenu, selectedSequence);
292 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
296 * And repeat for the current selection group (if there is one):
298 final List<SequenceI> selectedGroup = (ap.av.getSelectionGroup() == null ? Collections
299 .<SequenceI> emptyList() : ap.av.getSelectionGroup()
301 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
302 groupHideAnnotationsMenu, selectedGroup);
303 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
309 } catch (Exception e)
317 sequenceMenu.setText(sequence.getName());
318 if (seq == ap.av.getAlignment().getSeqrep())
320 makeReferenceSeq.setText("Unmark representative");
322 makeReferenceSeq.setText("Mark as representative");
325 if (!ap.av.getAlignment().isNucleotide())
327 remove(rnaStructureMenu);
332 * add menu items to 2D-render any alignment or sequence secondary
333 * structure annotation
335 AlignmentAnnotation[] aas = ap.av.getAlignment()
336 .getAlignmentAnnotation();
339 for (final AlignmentAnnotation aa : aas)
341 if (aa.isValidStruc() && aa.sequenceRef == null)
344 * valid alignment RNA secondary structure annotation
346 final String structureLine = aa.label + " (alignment)";
347 menuItem = new JMenuItem();
348 menuItem.setText(MessageManager.formatMessage(
349 "label.2d_rna_structure_line", new Object[]
351 menuItem.addActionListener(new java.awt.event.ActionListener()
354 public void actionPerformed(ActionEvent e)
356 new AppVarna(structureLine, seq, aa, ap);
359 rnaStructureMenu.add(menuItem);
365 if (seq.getAnnotation() != null)
367 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
368 for (final AlignmentAnnotation aa : seqAnns)
370 if (aa.isValidStruc())
373 * valid sequence RNA secondary structure annotation
375 // TODO: make rnastrucF a bit more nice
376 menuItem = new JMenuItem();
377 menuItem.setText(MessageManager.formatMessage(
378 "label.2d_rna_sequence_name", new Object[]
380 menuItem.addActionListener(new java.awt.event.ActionListener()
383 public void actionPerformed(ActionEvent e)
385 // TODO: VARNA does'nt print gaps in the sequence
387 new AppVarna(seq.getName() + " structure", seq, aa,
391 rnaStructureMenu.add(menuItem);
397 menuItem = new JMenuItem(
398 MessageManager.getString("action.hide_sequences"));
399 menuItem.addActionListener(new java.awt.event.ActionListener()
402 public void actionPerformed(ActionEvent e)
404 hideSequences(false);
409 if (ap.av.getSelectionGroup() != null
410 && ap.av.getSelectionGroup().getSize() > 1)
412 menuItem = new JMenuItem(MessageManager.formatMessage(
413 "label.represent_group_with", new Object[]
415 menuItem.addActionListener(new java.awt.event.ActionListener()
418 public void actionPerformed(ActionEvent e)
423 sequenceMenu.add(menuItem);
426 if (ap.av.hasHiddenRows())
428 final int index = ap.av.getAlignment().findIndex(seq);
430 if (ap.av.adjustForHiddenSeqs(index)
431 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
433 menuItem = new JMenuItem(
434 MessageManager.getString("action.reveal_sequences"));
435 menuItem.addActionListener(new ActionListener()
438 public void actionPerformed(ActionEvent e)
440 ap.av.showSequence(index);
441 if (ap.overviewPanel != null)
443 ap.overviewPanel.updateOverviewImage();
451 // for the case when no sequences are even visible
452 if (ap.av.hasHiddenRows())
455 menuItem = new JMenuItem(
456 MessageManager.getString("action.reveal_all"));
457 menuItem.addActionListener(new ActionListener()
460 public void actionPerformed(ActionEvent e)
462 ap.av.showAllHiddenSeqs();
463 if (ap.overviewPanel != null)
465 ap.overviewPanel.updateOverviewImage();
475 SequenceGroup sg = ap.av.getSelectionGroup();
476 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
477 .getGroups().contains(sg) : false;
479 if (sg != null && sg.getSize() > 0)
481 groupName.setText(MessageManager.formatMessage("label.name_param",
484 groupName.setText(MessageManager
485 .getString("label.edit_name_and_description_current_group"));
487 if (sg.cs instanceof ZappoColourScheme)
489 zappoColour.setSelected(true);
491 else if (sg.cs instanceof TaylorColourScheme)
493 taylorColour.setSelected(true);
495 else if (sg.cs instanceof PIDColourScheme)
497 PIDColour.setSelected(true);
499 else if (sg.cs instanceof Blosum62ColourScheme)
501 BLOSUM62Colour.setSelected(true);
503 else if (sg.cs instanceof UserColourScheme)
505 userDefinedColour.setSelected(true);
507 else if (sg.cs instanceof HydrophobicColourScheme)
509 hydrophobicityColour.setSelected(true);
511 else if (sg.cs instanceof HelixColourScheme)
513 helixColour.setSelected(true);
515 else if (sg.cs instanceof StrandColourScheme)
517 strandColour.setSelected(true);
519 else if (sg.cs instanceof TurnColourScheme)
521 turnColour.setSelected(true);
523 else if (sg.cs instanceof BuriedColourScheme)
525 buriedColour.setSelected(true);
527 else if (sg.cs instanceof ClustalxColourScheme)
529 clustalColour.setSelected(true);
531 else if (sg.cs instanceof PurinePyrimidineColourScheme)
533 purinePyrimidineColour.setSelected(true);
537 * else if (sg.cs instanceof CovariationColourScheme) {
538 * covariationColour.setSelected(true); }
542 noColourmenuItem.setSelected(true);
545 if (sg.cs != null && sg.cs.conservationApplied())
547 conservationMenuItem.setSelected(true);
549 displayNonconserved.setSelected(sg.getShowNonconserved());
550 showText.setSelected(sg.getDisplayText());
551 showColourText.setSelected(sg.getColourText());
552 showBoxes.setSelected(sg.getDisplayBoxes());
553 // add any groupURLs to the groupURL submenu and make it visible
554 if (groupLinks != null && groupLinks.size() > 0)
556 buildGroupURLMenu(sg, groupLinks);
558 // Add a 'show all structures' for the current selection
559 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
560 SequenceI sqass = null;
561 for (SequenceI sq : ap.av.getSequenceSelection())
563 Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
564 if (pes != null && pes.size() > 0)
566 reppdb.put(pes.get(0).getId(), pes.get(0));
567 for (PDBEntry pe : pes)
569 pdbe.put(pe.getId(), pe);
579 final PDBEntry[] pe = pdbe.values().toArray(
580 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
581 new PDBEntry[reppdb.size()]);
582 final JMenuItem gpdbview, rpdbview;
587 groupMenu.setVisible(false);
588 editMenu.setVisible(false);
593 createGroupMenuItem.setVisible(true);
594 unGroupMenuItem.setVisible(false);
595 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
599 createGroupMenuItem.setVisible(false);
600 unGroupMenuItem.setVisible(true);
601 jMenu1.setText(MessageManager.getString("action.edit_group"));
606 sequenceMenu.setVisible(false);
607 proteinStructureMenu.setVisible(false);
608 rnaStructureMenu.setVisible(false);
611 if (links != null && links.size() > 0)
614 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
615 Vector linkset = new Vector();
616 for (int i = 0; i < links.size(); i++)
618 String link = links.elementAt(i).toString();
619 UrlLink urlLink = null;
622 urlLink = new UrlLink(link);
623 } catch (Exception foo)
625 jalview.bin.Cache.log.error("Exception for URLLink '" + link
630 if (!urlLink.isValid())
632 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
635 final String label = urlLink.getLabel();
636 if (seq != null && urlLink.isDynamic())
639 // collect matching db-refs
640 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
641 seq.getDBRef(), new String[]
642 { urlLink.getTarget() });
643 // collect id string too
644 String id = seq.getName();
645 String descr = seq.getDescription();
646 if (descr != null && descr.length() < 1)
653 for (int r = 0; r < dbr.length; r++)
655 if (id != null && dbr[r].getAccessionId().equals(id))
657 // suppress duplicate link creation for the bare sequence ID
658 // string with this link
661 // create Bare ID link for this RUL
662 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
666 for (int u = 0; u < urls.length; u += 2)
668 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
670 linkset.addElement(urls[u] + "|" + urls[u + 1]);
671 addshowLink(linkMenu, label + "|" + urls[u],
680 // create Bare ID link for this RUL
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.addElement(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.addElement(urls[u] + "|" + urls[u + 1]);
707 addshowLink(linkMenu, label, urls[u + 1]);
715 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
717 linkset.addElement(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);
735 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
736 * "All" is added first, followed by a separator. Then add any annotation
737 * types associated with the current selection. Separate menus are built for
738 * the selected sequence group (if any), and the selected sequence.
740 * Some annotation rows are always rendered together - these can be identified
741 * by a common graphGroup property > -1. Only one of each group will be marked
742 * as visible (to avoid duplication of the display). For such groups we add a
743 * composite type name, e.g.
745 * IUPredWS (Long), IUPredWS (Short)
749 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
750 List<SequenceI> forSequences)
752 showMenu.removeAll();
753 hideMenu.removeAll();
755 final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
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,
775 AlignmentAnnotationUtils.asList(annotations),
778 for (String calcId : hiddenTypes.keySet())
780 for (List<String> type : hiddenTypes.get(calcId))
782 addAnnotationTypeToShowHide(showMenu, forSequences,
783 calcId, type, false, true);
786 // grey out 'show annotations' if none are hidden
787 showMenu.setEnabled(!hiddenTypes.isEmpty());
789 for (String calcId : shownTypes.keySet())
791 for (List<String> type : shownTypes.get(calcId))
793 addAnnotationTypeToShowHide(hideMenu, forSequences,
794 calcId, type, false, false);
797 // grey out 'hide annotations' if none are shown
798 hideMenu.setEnabled(!shownTypes.isEmpty());
802 * Returns a list of sequences - either the current selection group (if there
803 * is one), else the specified single sequence.
808 protected List<SequenceI> getSequenceScope(SequenceI seq)
810 List<SequenceI> forSequences = null;
811 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
812 if (selectionGroup != null && selectionGroup.getSize() > 0)
814 forSequences = selectionGroup.getSequences();
818 forSequences = seq == null ? Collections.<SequenceI> emptyList()
819 : Arrays.asList(seq);
825 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
828 * @param showOrHideMenu
830 * @param forSequences
831 * the sequences whose annotations may be shown or hidden
836 * if true this is a special label meaning 'All'
837 * @param actionIsShow
838 * if true, the select menu item action is to show the annotation
841 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
842 final List<SequenceI> forSequences, String calcId,
843 final List<String> types, final boolean allTypes,
844 final boolean actionIsShow)
846 String label = types.toString(); // [a, b, c]
847 label = label.substring(1, label.length() - 1); // a, b, c
848 final JMenuItem item = new JMenuItem(label);
849 item.setToolTipText(calcId);
850 item.addActionListener(new java.awt.event.ActionListener()
853 public void actionPerformed(ActionEvent e)
855 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
856 forSequences, allTypes, actionIsShow);
860 showOrHideMenu.add(item);
863 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
866 // TODO: usability: thread off the generation of group url content so root
868 // sequence only URLs
869 // ID/regex match URLs
870 groupLinksMenu = new JMenu(
871 MessageManager.getString("action.group_link"));
872 JMenu[] linkMenus = new JMenu[]
873 { null, new JMenu(MessageManager.getString("action.ids")),
874 new JMenu(MessageManager.getString("action.sequences")),
875 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
882 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
883 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
884 Hashtable commonDbrefs = new Hashtable();
885 for (int sq = 0; sq < seqs.length; sq++)
888 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
889 .findPosition(sg.getEndRes());
890 // just collect ids from dataset sequence
891 // TODO: check if IDs collected from selecton group intersects with the
892 // current selection, too
893 SequenceI sqi = seqs[sq];
894 while (sqi.getDatasetSequence() != null)
896 sqi = sqi.getDatasetSequence();
898 DBRefEntry[] dbr = sqi.getDBRef();
899 if (dbr != null && dbr.length > 0)
901 for (int d = 0; d < dbr.length; d++)
903 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
904 Object[] sarray = (Object[]) commonDbrefs.get(src);
907 sarray = new Object[2];
908 sarray[0] = new int[]
910 sarray[1] = new String[seqs.length];
912 commonDbrefs.put(src, sarray);
915 if (((String[]) sarray[1])[sq] == null)
918 || (dbr[d].getMap().locateMappedRange(start, end) != null))
920 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
921 ((int[]) sarray[0])[0]++;
927 // now create group links for all distinct ID/sequence sets.
928 boolean addMenu = false; // indicates if there are any group links to give
930 for (int i = 0; i < groupLinks.size(); i++)
932 String link = groupLinks.elementAt(i).toString();
933 GroupUrlLink urlLink = null;
936 urlLink = new GroupUrlLink(link);
937 } catch (Exception foo)
939 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
944 if (!urlLink.isValid())
946 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
949 final String label = urlLink.getLabel();
950 boolean usingNames = false;
951 // Now see which parts of the group apply for this URL
952 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
953 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
954 String[] seqstr, ids; // input to makeUrl
957 int numinput = ((int[]) idset[0])[0];
958 String[] allids = ((String[]) idset[1]);
959 seqstr = new String[numinput];
960 ids = new String[numinput];
961 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
963 if (allids[sq] != null)
965 ids[idcount] = allids[sq];
966 seqstr[idcount++] = idandseqs[1][sq];
972 // just use the id/seq set
973 seqstr = idandseqs[1];
977 // and try and make the groupURL!
979 Object[] urlset = null;
982 urlset = urlLink.makeUrlStubs(ids, seqstr,
983 "FromJalview" + System.currentTimeMillis(), false);
984 } catch (UrlStringTooLongException e)
989 int type = urlLink.getGroupURLType() & 3;
990 // first two bits ofurlLink type bitfield are sequenceids and sequences
991 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
992 addshowLink(linkMenus[type], label
993 + (((type & 1) == 1) ? ("("
994 + (usingNames ? "Names" : ltarget) + ")") : ""),
1001 groupLinksMenu = new JMenu(
1002 MessageManager.getString("action.group_link"));
1003 for (int m = 0; m < linkMenus.length; m++)
1005 if (linkMenus[m] != null
1006 && linkMenus[m].getMenuComponentCount() > 0)
1008 groupLinksMenu.add(linkMenus[m]);
1012 groupMenu.add(groupLinksMenu);
1017 * add a show URL menu item to the given linkMenu
1021 * - menu label string
1025 private void addshowLink(JMenu linkMenu, String label, final String url)
1027 JMenuItem item = new JMenuItem(label);
1028 item.setToolTipText(MessageManager.formatMessage(
1029 "label.open_url_param", new Object[]
1031 item.addActionListener(new java.awt.event.ActionListener()
1034 public void actionPerformed(ActionEvent e)
1036 new Thread(new Runnable()
1053 * add a late bound groupURL item to the given linkMenu
1057 * - menu label string
1058 * @param urlgenerator
1059 * GroupURLLink used to generate URL
1061 * Object array returned from the makeUrlStubs function.
1063 private void addshowLink(JMenu linkMenu, String label,
1064 final GroupUrlLink urlgenerator, final Object[] urlstub)
1066 JMenuItem item = new JMenuItem(label);
1067 item.setToolTipText(MessageManager.formatMessage(
1068 "label.open_url_seqs_param",
1070 { urlgenerator.getUrl_prefix(),
1071 urlgenerator.getNumberInvolved(urlstub) }));
1072 // TODO: put in info about what is being sent.
1073 item.addActionListener(new java.awt.event.ActionListener()
1076 public void actionPerformed(ActionEvent e)
1078 new Thread(new Runnable()
1086 showLink(urlgenerator.constructFrom(urlstub));
1087 } catch (UrlStringTooLongException e)
1105 private void jbInit() throws Exception
1107 groupMenu.setText(MessageManager.getString("label.group"));
1108 groupMenu.setText(MessageManager.getString("label.selection"));
1109 groupName.setText(MessageManager.getString("label.name"));
1110 groupName.addActionListener(new java.awt.event.ActionListener()
1113 public void actionPerformed(ActionEvent e)
1115 groupName_actionPerformed();
1118 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1119 sequenceName.setText(MessageManager
1120 .getString("label.edit_name_description"));
1121 sequenceName.addActionListener(new java.awt.event.ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 sequenceName_actionPerformed();
1129 chooseAnnotations.setText(MessageManager
1130 .getString("label.choose_annotations") + "...");
1131 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1134 public void actionPerformed(ActionEvent e)
1136 chooseAnnotations_actionPerformed(e);
1139 sequenceDetails.setText(MessageManager
1140 .getString("label.sequence_details") + "...");
1141 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1144 public void actionPerformed(ActionEvent e)
1146 sequenceDetails_actionPerformed();
1149 sequenceSelDetails.setText(MessageManager
1150 .getString("label.sequence_details") + "...");
1152 .addActionListener(new java.awt.event.ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 sequenceSelectionDetails_actionPerformed();
1160 PIDColour.setFocusPainted(false);
1162 .setText(MessageManager.getString("action.remove_group"));
1163 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1166 public void actionPerformed(ActionEvent e)
1168 unGroupMenuItem_actionPerformed();
1171 createGroupMenuItem.setText(MessageManager
1172 .getString("action.create_group"));
1174 .addActionListener(new java.awt.event.ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 createGroupMenuItem_actionPerformed();
1183 outline.setText(MessageManager.getString("action.border_colour"));
1184 outline.addActionListener(new java.awt.event.ActionListener()
1187 public void actionPerformed(ActionEvent e)
1189 outline_actionPerformed();
1193 .setText(MessageManager.getString("label.nucleotide"));
1194 nucleotideMenuItem.addActionListener(new ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 nucleotideMenuItem_actionPerformed();
1202 colourMenu.setText(MessageManager.getString("label.group_colour"));
1203 showBoxes.setText(MessageManager.getString("action.boxes"));
1204 showBoxes.setState(true);
1205 showBoxes.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent e)
1210 showBoxes_actionPerformed();
1213 showText.setText(MessageManager.getString("action.text"));
1214 showText.setState(true);
1215 showText.addActionListener(new ActionListener()
1218 public void actionPerformed(ActionEvent e)
1220 showText_actionPerformed();
1223 showColourText.setText(MessageManager.getString("label.colour_text"));
1224 showColourText.addActionListener(new ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 showColourText_actionPerformed();
1232 displayNonconserved.setText(MessageManager
1233 .getString("label.show_non_conversed"));
1234 displayNonconserved.setState(true);
1235 displayNonconserved.addActionListener(new ActionListener()
1238 public void actionPerformed(ActionEvent e)
1240 showNonconserved_actionPerformed();
1243 editMenu.setText(MessageManager.getString("action.edit"));
1244 cut.setText(MessageManager.getString("action.cut"));
1245 cut.addActionListener(new ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 cut_actionPerformed();
1253 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1254 upperCase.addActionListener(new ActionListener()
1257 public void actionPerformed(ActionEvent e)
1262 copy.setText(MessageManager.getString("action.copy"));
1263 copy.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent e)
1268 copy_actionPerformed();
1271 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1272 lowerCase.addActionListener(new ActionListener()
1275 public void actionPerformed(ActionEvent e)
1280 toggle.setText(MessageManager.getString("label.toggle_case"));
1281 toggle.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent e)
1289 pdbMenu.setText(MessageManager
1290 .getString("label.associate_structure_with_sequence"));
1291 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1292 pdbFromFile.addActionListener(new ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 pdbFromFile_actionPerformed();
1301 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1302 enterPDB.addActionListener(new ActionListener()
1305 public void actionPerformed(ActionEvent e)
1307 enterPDB_actionPerformed();
1310 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1311 discoverPDB.addActionListener(new ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 discoverPDB_actionPerformed();
1319 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1321 seqShowAnnotationsMenu.setText(MessageManager
1322 .getString("label.show_annotations"));
1323 seqHideAnnotationsMenu.setText(MessageManager
1324 .getString("label.hide_annotations"));
1325 groupShowAnnotationsMenu.setText(MessageManager
1326 .getString("label.show_annotations"));
1327 groupHideAnnotationsMenu.setText(MessageManager
1328 .getString("label.hide_annotations"));
1329 sequenceFeature.setText(MessageManager
1330 .getString("label.create_sequence_feature"));
1331 sequenceFeature.addActionListener(new ActionListener()
1334 public void actionPerformed(ActionEvent e)
1336 sequenceFeature_actionPerformed();
1339 textColour.setText(MessageManager.getString("label.text_colour"));
1340 textColour.addActionListener(new ActionListener()
1343 public void actionPerformed(ActionEvent e)
1345 textColour_actionPerformed();
1348 jMenu1.setText(MessageManager.getString("label.group"));
1349 proteinStructureMenu.setText(MessageManager
1350 .getString("label.view_protein_structure"));
1351 proteinStructureMenu.addActionListener(new ActionListener()
1354 public void actionPerformed(ActionEvent actionEvent)
1356 SequenceI[] selectedSeqs = new SequenceI[]
1358 if (ap.av.getSelectionGroup() != null)
1360 selectedSeqs = ap.av.getSequenceSelection();
1362 new StructureChooser(selectedSeqs, sequence, ap);
1366 rnaStructureMenu.setText(MessageManager
1367 .getString("label.view_rna_structure"));
1369 // colStructureMenu.setText("Colour By Structure");
1370 editSequence.setText(MessageManager.getString("label.edit_sequence")
1372 editSequence.addActionListener(new ActionListener()
1375 public void actionPerformed(ActionEvent actionEvent)
1377 editSequence_actionPerformed(actionEvent);
1380 makeReferenceSeq.setText(MessageManager
1381 .getString("label.mark_as_representative"));
1382 makeReferenceSeq.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent actionEvent)
1388 makeReferenceSeq_actionPerformed(actionEvent);
1392 hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
1393 hideInsertions.addActionListener(new ActionListener()
1397 public void actionPerformed(ActionEvent e)
1399 hideInsertions_actionPerformed(e);
1403 * annotationMenuItem.setText("By Annotation");
1404 * annotationMenuItem.addActionListener(new ActionListener() { public void
1405 * actionPerformed(ActionEvent actionEvent) {
1406 * annotationMenuItem_actionPerformed(actionEvent); } });
1408 groupMenu.add(sequenceSelDetails);
1411 add(rnaStructureMenu);
1412 add(proteinStructureMenu);
1415 add(hideInsertions);
1417 // annotations configuration panel suppressed for now
1418 // groupMenu.add(chooseAnnotations);
1421 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1422 * (if a selection group is in force).
1424 sequenceMenu.add(seqShowAnnotationsMenu);
1425 sequenceMenu.add(seqHideAnnotationsMenu);
1426 sequenceMenu.add(seqAddReferenceAnnotations);
1427 groupMenu.add(groupShowAnnotationsMenu);
1428 groupMenu.add(groupHideAnnotationsMenu);
1429 groupMenu.add(groupAddReferenceAnnotations);
1430 groupMenu.add(editMenu);
1431 groupMenu.add(outputMenu);
1432 groupMenu.add(sequenceFeature);
1433 groupMenu.add(createGroupMenuItem);
1434 groupMenu.add(unGroupMenuItem);
1435 groupMenu.add(jMenu1);
1436 sequenceMenu.add(sequenceName);
1437 sequenceMenu.add(sequenceDetails);
1438 sequenceMenu.add(makeReferenceSeq);
1439 colourMenu.add(textColour);
1440 colourMenu.add(noColourmenuItem);
1441 colourMenu.add(clustalColour);
1442 colourMenu.add(BLOSUM62Colour);
1443 colourMenu.add(PIDColour);
1444 colourMenu.add(zappoColour);
1445 colourMenu.add(taylorColour);
1446 colourMenu.add(hydrophobicityColour);
1447 colourMenu.add(helixColour);
1448 colourMenu.add(strandColour);
1449 colourMenu.add(turnColour);
1450 colourMenu.add(buriedColour);
1451 colourMenu.add(nucleotideMenuItem);
1452 if (ap.getAlignment().isNucleotide())
1454 // JBPNote - commented since the colourscheme isn't functional
1455 colourMenu.add(purinePyrimidineColour);
1457 colourMenu.add(userDefinedColour);
1459 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1461 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1462 .getUserColourSchemes().keys();
1464 while (userColours.hasMoreElements())
1466 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1467 item.addActionListener(new ActionListener()
1470 public void actionPerformed(ActionEvent evt)
1472 userDefinedColour_actionPerformed(evt);
1475 colourMenu.add(item);
1479 colourMenu.addSeparator();
1480 colourMenu.add(abovePIDColour);
1481 colourMenu.add(conservationMenuItem);
1484 editMenu.add(editSequence);
1485 editMenu.add(upperCase);
1486 editMenu.add(lowerCase);
1487 editMenu.add(toggle);
1488 pdbMenu.add(pdbFromFile);
1489 // JBPNote: These shouldn't be added here - should appear in a generic
1490 // 'apply web service to this sequence menu'
1491 // pdbMenu.add(RNAFold);
1492 // pdbMenu.add(ContraFold);
1493 pdbMenu.add(enterPDB);
1494 pdbMenu.add(discoverPDB);
1495 jMenu1.add(groupName);
1496 jMenu1.add(colourMenu);
1497 jMenu1.add(showBoxes);
1498 jMenu1.add(showText);
1499 jMenu1.add(showColourText);
1500 jMenu1.add(outline);
1501 jMenu1.add(displayNonconserved);
1502 noColourmenuItem.setText(MessageManager.getString("label.none"));
1503 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 noColourmenuItem_actionPerformed();
1512 clustalColour.setText(MessageManager
1513 .getString("label.clustalx_colours"));
1514 clustalColour.addActionListener(new java.awt.event.ActionListener()
1517 public void actionPerformed(ActionEvent e)
1519 clustalColour_actionPerformed();
1522 zappoColour.setText(MessageManager.getString("label.zappo"));
1523 zappoColour.addActionListener(new java.awt.event.ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 zappoColour_actionPerformed();
1531 taylorColour.setText(MessageManager.getString("label.taylor"));
1532 taylorColour.addActionListener(new java.awt.event.ActionListener()
1535 public void actionPerformed(ActionEvent e)
1537 taylorColour_actionPerformed();
1540 hydrophobicityColour.setText(MessageManager
1541 .getString("label.hydrophobicity"));
1542 hydrophobicityColour
1543 .addActionListener(new java.awt.event.ActionListener()
1546 public void actionPerformed(ActionEvent e)
1548 hydrophobicityColour_actionPerformed();
1551 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1552 helixColour.addActionListener(new java.awt.event.ActionListener()
1555 public void actionPerformed(ActionEvent e)
1557 helixColour_actionPerformed();
1560 strandColour.setText(MessageManager
1561 .getString("label.strand_propensity"));
1562 strandColour.addActionListener(new java.awt.event.ActionListener()
1565 public void actionPerformed(ActionEvent e)
1567 strandColour_actionPerformed();
1570 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1571 turnColour.addActionListener(new java.awt.event.ActionListener()
1574 public void actionPerformed(ActionEvent e)
1576 turnColour_actionPerformed();
1579 buriedColour.setText(MessageManager.getString("label.buried_index"));
1580 buriedColour.addActionListener(new java.awt.event.ActionListener()
1583 public void actionPerformed(ActionEvent e)
1585 buriedColour_actionPerformed();
1588 abovePIDColour.setText(MessageManager
1589 .getString("label.above_identity_percentage"));
1590 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 abovePIDColour_actionPerformed();
1598 userDefinedColour.setText(MessageManager
1599 .getString("action.user_defined"));
1600 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1603 public void actionPerformed(ActionEvent e)
1605 userDefinedColour_actionPerformed(e);
1609 .setText(MessageManager.getString("label.percentage_identity"));
1610 PIDColour.addActionListener(new java.awt.event.ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 PIDColour_actionPerformed();
1618 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1619 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 BLOSUM62Colour_actionPerformed();
1627 purinePyrimidineColour.setText(MessageManager
1628 .getString("label.purine_pyrimidine"));
1629 purinePyrimidineColour
1630 .addActionListener(new java.awt.event.ActionListener()
1633 public void actionPerformed(ActionEvent e)
1635 purinePyrimidineColour_actionPerformed();
1640 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1641 * public void actionPerformed(ActionEvent e) {
1642 * covariationColour_actionPerformed(); } });
1645 conservationMenuItem.setText(MessageManager
1646 .getString("label.conservation"));
1647 conservationMenuItem
1648 .addActionListener(new java.awt.event.ActionListener()
1651 public void actionPerformed(ActionEvent e)
1653 conservationMenuItem_actionPerformed();
1659 * Check for any annotations on the underlying dataset sequences (for the
1660 * current selection group) which are not 'on the alignment'.If any are found,
1661 * enable the option to add them to the alignment. The criteria for 'on the
1662 * alignment' is finding an alignment annotation on the alignment, matched on
1663 * calcId, label and sequenceRef.
1665 * A tooltip is also constructed that displays the source (calcId) and type
1666 * (label) of the annotations that can be added.
1669 * @param forSequences
1671 protected void configureReferenceAnnotationsMenu(
1672 JMenuItem menuItem, List<SequenceI> forSequences)
1674 menuItem.setEnabled(false);
1677 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1678 * Using TreeMap means calcIds are shown in alphabetical order.
1680 Map<String, String> tipEntries = new TreeMap<String, String>();
1681 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1682 AlignmentI al = this.ap.av.getAlignment();
1683 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1684 tipEntries, candidates, al);
1685 if (!candidates.isEmpty())
1687 StringBuilder tooltip = new StringBuilder(64);
1688 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1691 * Found annotations that could be added. Enable the menu item, and
1692 * configure its tooltip and action.
1694 menuItem.setEnabled(true);
1695 for (String calcId : tipEntries.keySet())
1697 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1699 String tooltipText = JvSwingUtils.wrapTooltip(true,
1700 tooltip.toString());
1701 menuItem.setToolTipText(tooltipText);
1703 menuItem.addActionListener(new ActionListener()
1706 public void actionPerformed(ActionEvent e)
1708 addReferenceAnnotations_actionPerformed(candidates);
1715 * Add annotations to the sequences and to the alignment.
1718 * a map whose keys are sequences on the alignment, and values a list
1719 * of annotations to add to each sequence
1721 protected void addReferenceAnnotations_actionPerformed(
1722 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1724 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1725 final AlignmentI alignment = this.ap.getAlignment();
1726 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1731 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1733 if (!ap.av.getAlignment().hasSeqrep())
1735 // initialise the display flags so the user sees something happen
1736 ap.av.setDisplayReferenceSeq(true);
1737 ap.av.setColourByReferenceSeq(true);
1738 ap.av.getAlignment().setSeqrep(sequence);
1742 if (ap.av.getAlignment().getSeqrep() == sequence)
1744 ap.av.getAlignment().setSeqrep(null);
1748 ap.av.getAlignment().setSeqrep(sequence);
1754 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1756 if (sequence != null)
1758 ColumnSelection cs = ap.av.getColumnSelection();
1761 cs = new ColumnSelection();
1763 cs.hideInsertionsFor(sequence);
1764 ap.av.setColumnSelection(cs);
1768 protected void sequenceSelectionDetails_actionPerformed()
1770 createSequenceDetailsReport(ap.av.getSequenceSelection());
1773 protected void sequenceDetails_actionPerformed()
1775 createSequenceDetailsReport(new SequenceI[]
1779 public void createSequenceDetailsReport(SequenceI[] sequences)
1781 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1782 StringBuffer contents = new StringBuffer();
1783 for (SequenceI seq : sequences)
1785 contents.append("<p><h2>"
1788 "label.create_sequence_details_report_annotation_for",
1790 { seq.getDisplayId(true) }) + "</h2></p><p>");
1791 new SequenceAnnotationReport(null)
1792 .createSequenceAnnotationReport(
1798 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1799 .getSeqPanel().seqCanvas.fr
1802 contents.append("</p>");
1804 cap.setText("<html>" + contents.toString() + "</html>");
1806 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1807 "label.sequence_details_for",
1808 (sequences.length == 1 ? new Object[]
1809 { sequences[0].getDisplayId(true) } : new Object[]
1810 { MessageManager.getString("label.selection") })), 500, 400);
1814 protected void showNonconserved_actionPerformed()
1816 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1821 * call to refresh view after settings change
1825 ap.updateAnnotation();
1826 ap.paintAlignment(true);
1828 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1837 protected void clustalColour_actionPerformed()
1839 SequenceGroup sg = getGroup();
1840 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1850 protected void zappoColour_actionPerformed()
1852 getGroup().cs = new ZappoColourScheme();
1862 protected void taylorColour_actionPerformed()
1864 getGroup().cs = new TaylorColourScheme();
1874 protected void hydrophobicityColour_actionPerformed()
1876 getGroup().cs = new HydrophobicColourScheme();
1886 protected void helixColour_actionPerformed()
1888 getGroup().cs = new HelixColourScheme();
1898 protected void strandColour_actionPerformed()
1900 getGroup().cs = new StrandColourScheme();
1910 protected void turnColour_actionPerformed()
1912 getGroup().cs = new TurnColourScheme();
1922 protected void buriedColour_actionPerformed()
1924 getGroup().cs = new BuriedColourScheme();
1934 public void nucleotideMenuItem_actionPerformed()
1936 getGroup().cs = new NucleotideColourScheme();
1940 protected void purinePyrimidineColour_actionPerformed()
1942 getGroup().cs = new PurinePyrimidineColourScheme();
1947 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1948 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1956 protected void abovePIDColour_actionPerformed()
1958 SequenceGroup sg = getGroup();
1964 if (abovePIDColour.isSelected())
1966 sg.cs.setConsensus(AAFrequency.calculate(
1967 sg.getSequences(ap.av.getHiddenRepSequences()),
1968 sg.getStartRes(), sg.getEndRes() + 1));
1970 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1973 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1975 SliderPanel.showPIDSlider();
1978 // remove PIDColouring
1980 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1992 protected void userDefinedColour_actionPerformed(ActionEvent e)
1994 SequenceGroup sg = getGroup();
1996 if (e.getSource().equals(userDefinedColour))
1998 new UserDefinedColours(ap, sg);
2002 UserColourScheme udc = (UserColourScheme) UserDefinedColours
2003 .getUserColourSchemes().get(e.getActionCommand());
2011 * Open a panel where the user can choose which types of sequence annotation
2016 protected void chooseAnnotations_actionPerformed(ActionEvent e)
2018 // todo correct way to guard against opening a duplicate panel?
2019 new AnnotationChooser(ap);
2028 protected void PIDColour_actionPerformed()
2030 SequenceGroup sg = getGroup();
2031 sg.cs = new PIDColourScheme();
2032 sg.cs.setConsensus(AAFrequency.calculate(
2033 sg.getSequences(ap.av.getHiddenRepSequences()),
2034 sg.getStartRes(), sg.getEndRes() + 1));
2044 protected void BLOSUM62Colour_actionPerformed()
2046 SequenceGroup sg = getGroup();
2048 sg.cs = new Blosum62ColourScheme();
2050 sg.cs.setConsensus(AAFrequency.calculate(
2051 sg.getSequences(ap.av.getHiddenRepSequences()),
2052 sg.getStartRes(), sg.getEndRes() + 1));
2063 protected void noColourmenuItem_actionPerformed()
2065 getGroup().cs = null;
2075 protected void conservationMenuItem_actionPerformed()
2077 SequenceGroup sg = getGroup();
2083 if (conservationMenuItem.isSelected())
2085 // JBPNote: Conservation name shouldn't be i18n translated
2086 Conservation c = new Conservation("Group",
2087 ResidueProperties.propHash, 3, sg.getSequences(ap.av
2088 .getHiddenRepSequences()), sg.getStartRes(),
2089 sg.getEndRes() + 1);
2092 c.verdict(false, ap.av.getConsPercGaps());
2094 sg.cs.setConservation(c);
2096 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2097 SliderPanel.showConservationSlider();
2100 // remove ConservationColouring
2102 sg.cs.setConservation(null);
2108 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2110 SequenceGroup sg = getGroup();
2116 AnnotationColourGradient acg = new AnnotationColourGradient(
2117 sequence.getAnnotation()[0], null,
2118 AnnotationColourGradient.NO_THRESHOLD);
2120 acg.setPredefinedColours(true);
2132 protected void groupName_actionPerformed()
2135 SequenceGroup sg = getGroup();
2136 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2137 sg.getDescription(), " "
2138 + MessageManager.getString("label.group_name") + " ",
2139 MessageManager.getString("label.group_description") + " ",
2140 MessageManager.getString("label.edit_group_name_description"),
2148 sg.setName(dialog.getName());
2149 sg.setDescription(dialog.getDescription());
2154 * Get selection group - adding it to the alignment if necessary.
2156 * @return sequence group to operate on
2158 SequenceGroup getGroup()
2160 SequenceGroup sg = ap.av.getSelectionGroup();
2161 // this method won't add a new group if it already exists
2164 ap.av.getAlignment().addGroup(sg);
2176 void sequenceName_actionPerformed()
2178 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2179 sequence.getDescription(),
2180 " " + MessageManager.getString("label.sequence_name")
2182 MessageManager.getString("label.sequence_description") + " ",
2184 .getString("label.edit_sequence_name_description"),
2192 if (dialog.getName() != null)
2194 if (dialog.getName().indexOf(" ") > -1)
2200 .getString("label.spaces_converted_to_backslashes"),
2202 .getString("label.no_spaces_allowed_sequence_name"),
2203 JOptionPane.WARNING_MESSAGE);
2206 sequence.setName(dialog.getName().replace(' ', '_'));
2207 ap.paintAlignment(false);
2210 sequence.setDescription(dialog.getDescription());
2212 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2223 void unGroupMenuItem_actionPerformed()
2225 SequenceGroup sg = ap.av.getSelectionGroup();
2226 ap.av.getAlignment().deleteGroup(sg);
2227 ap.av.setSelectionGroup(null);
2231 void createGroupMenuItem_actionPerformed()
2233 getGroup(); // implicitly creates group - note - should apply defaults / use
2234 // standard alignment window logic for this
2244 protected void outline_actionPerformed()
2246 SequenceGroup sg = getGroup();
2247 Color col = JColorChooser.showDialog(this,
2248 MessageManager.getString("label.select_outline_colour"),
2253 sg.setOutlineColour(col);
2265 public void showBoxes_actionPerformed()
2267 getGroup().setDisplayBoxes(showBoxes.isSelected());
2277 public void showText_actionPerformed()
2279 getGroup().setDisplayText(showText.isSelected());
2289 public void showColourText_actionPerformed()
2291 getGroup().setColourText(showColourText.isSelected());
2295 public void showLink(String url)
2299 jalview.util.BrowserLauncher.openURL(url);
2300 } catch (Exception ex)
2302 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2303 MessageManager.getString("label.web_browser_not_found_unix"),
2304 MessageManager.getString("label.web_browser_not_found"),
2305 JOptionPane.WARNING_MESSAGE);
2307 ex.printStackTrace();
2311 void hideSequences(boolean representGroup)
2313 SequenceGroup sg = ap.av.getSelectionGroup();
2314 if (sg == null || sg.getSize() < 1)
2316 ap.av.hideSequence(new SequenceI[]
2321 ap.av.setSelectionGroup(null);
2325 ap.av.hideRepSequences(sequence, sg);
2330 int gsize = sg.getSize();
2331 SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
2333 ap.av.hideSequence(hseqs);
2334 // refresh(); TODO: ? needed ?
2335 ap.av.sendSelection();
2338 public void copy_actionPerformed()
2340 ap.alignFrame.copy_actionPerformed(null);
2343 public void cut_actionPerformed()
2345 ap.alignFrame.cut_actionPerformed(null);
2348 void changeCase(ActionEvent e)
2350 Object source = e.getSource();
2351 SequenceGroup sg = ap.av.getSelectionGroup();
2355 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2357 sg.getEndRes() + 1);
2362 if (source == toggle)
2364 description = MessageManager.getString("label.toggle_case");
2365 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2367 else if (source == upperCase)
2369 description = MessageManager.getString("label.to_upper_case");
2370 caseChange = ChangeCaseCommand.TO_UPPER;
2374 description = MessageManager.getString("label.to_lower_case");
2375 caseChange = ChangeCaseCommand.TO_LOWER;
2378 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2379 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2380 startEnd, caseChange);
2382 ap.alignFrame.addHistoryItem(caseCommand);
2384 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2390 public void outputText_actionPerformed(ActionEvent e)
2392 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2393 cap.setForInput(null);
2394 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2395 "label.alignment_output_command", new Object[]
2396 { e.getActionCommand() }), 600, 500);
2398 String[] omitHidden = null;
2400 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2401 // or we simply trust the user wants
2402 // wysiwig behaviour
2404 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2408 public void pdbFromFile_actionPerformed()
2410 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2411 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2412 chooser.setFileView(new jalview.io.JalviewFileView());
2413 chooser.setDialogTitle(MessageManager.formatMessage(
2414 "label.select_pdb_file_for", new Object[]
2415 { sequence.getDisplayId(false) }));
2416 chooser.setToolTipText(MessageManager.formatMessage(
2417 "label.load_pdb_file_associate_with_sequence", new Object[]
2418 { sequence.getDisplayId(false) }));
2420 int value = chooser.showOpenDialog(null);
2422 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2424 String choice = chooser.getSelectedFile().getPath();
2425 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2426 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2427 jalview.io.AppletFormatAdapter.FILE, sequence, true,
2434 public void enterPDB_actionPerformed()
2436 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2437 MessageManager.getString("label.enter_pdb_id"),
2438 MessageManager.getString("label.enter_pdb_id"),
2439 JOptionPane.QUESTION_MESSAGE);
2441 if (id != null && id.length() > 0)
2443 PDBEntry entry = new PDBEntry();
2444 entry.setId(id.toUpperCase());
2445 sequence.getDatasetSequence().addPDBId(entry);
2449 public void discoverPDB_actionPerformed()
2452 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2454 : ap.av.getSequenceSelection());
2455 Thread discpdb = new Thread(new Runnable()
2461 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2462 .fetchDBRefs(false);
2469 public void sequenceFeature_actionPerformed()
2471 SequenceGroup sg = ap.av.getSelectionGroup();
2477 int rsize = 0, gSize = sg.getSize();
2478 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2479 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2481 for (int i = 0; i < gSize; i++)
2483 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2484 int end = sg.findEndRes(sg.getSequenceAt(i));
2487 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2488 features[rsize] = new SequenceFeature(null, null, null, start, end,
2493 rseqs = new SequenceI[rsize];
2494 tfeatures = new SequenceFeature[rsize];
2495 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2496 System.arraycopy(features, 0, tfeatures, 0, rsize);
2497 features = tfeatures;
2499 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2500 features, true, ap))
2502 ap.alignFrame.setShowSeqFeatures(true);
2503 ap.highlightSearchResults(null);
2507 public void textColour_actionPerformed()
2509 SequenceGroup sg = getGroup();
2512 new TextColourChooser().chooseColour(ap, sg);
2516 public void colourByStructure(String pdbid)
2518 Annotation[] anots = ap.av.getStructureSelectionManager()
2519 .colourSequenceFromStructure(sequence, pdbid);
2521 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2522 "Coloured by " + pdbid, anots);
2524 ap.av.getAlignment().addAnnotation(an);
2525 an.createSequenceMapping(sequence, 0, true);
2526 // an.adjustForAlignment();
2527 ap.av.getAlignment().setAnnotationIndex(an, 0);
2529 ap.adjustAnnotationHeight();
2531 sequence.addAlignmentAnnotation(an);
2535 public void editSequence_actionPerformed(ActionEvent actionEvent)
2537 SequenceGroup sg = ap.av.getSelectionGroup();
2541 if (sequence == null)
2543 sequence = sg.getSequenceAt(0);
2546 EditNameDialog dialog = new EditNameDialog(
2547 sequence.getSequenceAsString(sg.getStartRes(),
2548 sg.getEndRes() + 1), null,
2549 MessageManager.getString("label.edit_sequence"), null,
2550 MessageManager.getString("label.edit_sequence"),
2555 EditCommand editCommand = new EditCommand(
2556 MessageManager.getString("label.edit_sequences"),
2557 Action.REPLACE, dialog.getName().replace(' ',
2558 ap.av.getGapCharacter()),
2559 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2560 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2562 ap.alignFrame.addHistoryItem(editCommand);
2564 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()