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 menuItem = new JMenuItem();
347 menuItem.setText(MessageManager.formatMessage(
348 "label.2d_rna_structure_line", new Object[]
350 menuItem.addActionListener(new java.awt.event.ActionListener()
353 public void actionPerformed(ActionEvent e)
355 new AppVarna(seq, aa, ap);
358 rnaStructureMenu.add(menuItem);
363 if (seq.getAnnotation() != null)
365 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
366 for (final AlignmentAnnotation aa : seqAnns)
368 if (aa.isValidStruc())
371 * valid sequence RNA secondary structure annotation
373 // TODO: make rnastrucF a bit more nice
374 menuItem = new JMenuItem();
375 menuItem.setText(MessageManager.formatMessage(
376 "label.2d_rna_sequence_name", new Object[]
378 menuItem.addActionListener(new java.awt.event.ActionListener()
381 public void actionPerformed(ActionEvent e)
383 // TODO: VARNA does'nt print gaps in the sequence
384 new AppVarna(seq, aa, ap);
387 rnaStructureMenu.add(menuItem);
393 menuItem = new JMenuItem(
394 MessageManager.getString("action.hide_sequences"));
395 menuItem.addActionListener(new java.awt.event.ActionListener()
398 public void actionPerformed(ActionEvent e)
400 hideSequences(false);
405 if (ap.av.getSelectionGroup() != null
406 && ap.av.getSelectionGroup().getSize() > 1)
408 menuItem = new JMenuItem(MessageManager.formatMessage(
409 "label.represent_group_with", new Object[]
411 menuItem.addActionListener(new java.awt.event.ActionListener()
414 public void actionPerformed(ActionEvent e)
419 sequenceMenu.add(menuItem);
422 if (ap.av.hasHiddenRows())
424 final int index = ap.av.getAlignment().findIndex(seq);
426 if (ap.av.adjustForHiddenSeqs(index)
427 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
429 menuItem = new JMenuItem(
430 MessageManager.getString("action.reveal_sequences"));
431 menuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 ap.av.showSequence(index);
437 if (ap.overviewPanel != null)
439 ap.overviewPanel.updateOverviewImage();
447 // for the case when no sequences are even visible
448 if (ap.av.hasHiddenRows())
451 menuItem = new JMenuItem(
452 MessageManager.getString("action.reveal_all"));
453 menuItem.addActionListener(new ActionListener()
456 public void actionPerformed(ActionEvent e)
458 ap.av.showAllHiddenSeqs();
459 if (ap.overviewPanel != null)
461 ap.overviewPanel.updateOverviewImage();
471 SequenceGroup sg = ap.av.getSelectionGroup();
472 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
473 .getGroups().contains(sg) : false;
475 if (sg != null && sg.getSize() > 0)
477 groupName.setText(MessageManager.formatMessage("label.name_param",
480 groupName.setText(MessageManager
481 .getString("label.edit_name_and_description_current_group"));
483 if (sg.cs instanceof ZappoColourScheme)
485 zappoColour.setSelected(true);
487 else if (sg.cs instanceof TaylorColourScheme)
489 taylorColour.setSelected(true);
491 else if (sg.cs instanceof PIDColourScheme)
493 PIDColour.setSelected(true);
495 else if (sg.cs instanceof Blosum62ColourScheme)
497 BLOSUM62Colour.setSelected(true);
499 else if (sg.cs instanceof UserColourScheme)
501 userDefinedColour.setSelected(true);
503 else if (sg.cs instanceof HydrophobicColourScheme)
505 hydrophobicityColour.setSelected(true);
507 else if (sg.cs instanceof HelixColourScheme)
509 helixColour.setSelected(true);
511 else if (sg.cs instanceof StrandColourScheme)
513 strandColour.setSelected(true);
515 else if (sg.cs instanceof TurnColourScheme)
517 turnColour.setSelected(true);
519 else if (sg.cs instanceof BuriedColourScheme)
521 buriedColour.setSelected(true);
523 else if (sg.cs instanceof ClustalxColourScheme)
525 clustalColour.setSelected(true);
527 else if (sg.cs instanceof PurinePyrimidineColourScheme)
529 purinePyrimidineColour.setSelected(true);
533 * else if (sg.cs instanceof CovariationColourScheme) {
534 * covariationColour.setSelected(true); }
538 noColourmenuItem.setSelected(true);
541 if (sg.cs != null && sg.cs.conservationApplied())
543 conservationMenuItem.setSelected(true);
545 displayNonconserved.setSelected(sg.getShowNonconserved());
546 showText.setSelected(sg.getDisplayText());
547 showColourText.setSelected(sg.getColourText());
548 showBoxes.setSelected(sg.getDisplayBoxes());
549 // add any groupURLs to the groupURL submenu and make it visible
550 if (groupLinks != null && groupLinks.size() > 0)
552 buildGroupURLMenu(sg, groupLinks);
554 // Add a 'show all structures' for the current selection
555 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
556 SequenceI sqass = null;
557 for (SequenceI sq : ap.av.getSequenceSelection())
559 Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
560 if (pes != null && pes.size() > 0)
562 reppdb.put(pes.get(0).getId(), pes.get(0));
563 for (PDBEntry pe : pes)
565 pdbe.put(pe.getId(), pe);
575 final PDBEntry[] pe = pdbe.values().toArray(
576 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
577 new PDBEntry[reppdb.size()]);
578 final JMenuItem gpdbview, rpdbview;
583 groupMenu.setVisible(false);
584 editMenu.setVisible(false);
589 createGroupMenuItem.setVisible(true);
590 unGroupMenuItem.setVisible(false);
591 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
595 createGroupMenuItem.setVisible(false);
596 unGroupMenuItem.setVisible(true);
597 jMenu1.setText(MessageManager.getString("action.edit_group"));
602 sequenceMenu.setVisible(false);
603 proteinStructureMenu.setVisible(false);
604 rnaStructureMenu.setVisible(false);
607 if (links != null && links.size() > 0)
610 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
611 Vector linkset = new Vector();
612 for (int i = 0; i < links.size(); i++)
614 String link = links.elementAt(i).toString();
615 UrlLink urlLink = null;
618 urlLink = new UrlLink(link);
619 } catch (Exception foo)
621 jalview.bin.Cache.log.error("Exception for URLLink '" + link
626 if (!urlLink.isValid())
628 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
631 final String label = urlLink.getLabel();
632 if (seq != null && urlLink.isDynamic())
635 // collect matching db-refs
636 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
637 seq.getDBRef(), new String[]
638 { urlLink.getTarget() });
639 // collect id string too
640 String id = seq.getName();
641 String descr = seq.getDescription();
642 if (descr != null && descr.length() < 1)
649 for (int r = 0; r < dbr.length; r++)
651 if (id != null && dbr[r].getAccessionId().equals(id))
653 // suppress duplicate link creation for the bare sequence ID
654 // string with this link
657 // create Bare ID link for this RUL
658 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
662 for (int u = 0; u < urls.length; u += 2)
664 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
666 linkset.addElement(urls[u] + "|" + urls[u + 1]);
667 addshowLink(linkMenu, label + "|" + urls[u],
676 // create Bare ID link for this RUL
677 String[] urls = urlLink.makeUrls(id, true);
680 for (int u = 0; u < urls.length; u += 2)
682 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
684 linkset.addElement(urls[u] + "|" + urls[u + 1]);
685 addshowLink(linkMenu, label, urls[u + 1]);
690 // Create urls from description but only for URL links which are regex
692 if (descr != null && urlLink.getRegexReplace() != null)
694 // create link for this URL from description where regex matches
695 String[] urls = urlLink.makeUrls(descr, true);
698 for (int u = 0; u < urls.length; u += 2)
700 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
702 linkset.addElement(urls[u] + "|" + urls[u + 1]);
703 addshowLink(linkMenu, label, urls[u + 1]);
711 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
713 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
714 // Add a non-dynamic link
715 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
719 if (sequence != null)
721 sequenceMenu.add(linkMenu);
731 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
732 * "All" is added first, followed by a separator. Then add any annotation
733 * types associated with the current selection. Separate menus are built for
734 * the selected sequence group (if any), and the selected sequence.
736 * Some annotation rows are always rendered together - these can be identified
737 * by a common graphGroup property > -1. Only one of each group will be marked
738 * as visible (to avoid duplication of the display). For such groups we add a
739 * composite type name, e.g.
741 * IUPredWS (Long), IUPredWS (Short)
745 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
746 List<SequenceI> forSequences)
748 showMenu.removeAll();
749 hideMenu.removeAll();
751 final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
752 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
753 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
755 showMenu.addSeparator();
756 hideMenu.addSeparator();
758 final AlignmentAnnotation[] annotations = ap.getAlignment()
759 .getAlignmentAnnotation();
762 * Find shown/hidden annotations types, distinguished by source (calcId),
763 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
764 * the insertion order, which is the order of the annotations on the
767 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
768 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
769 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
771 AlignmentAnnotationUtils.asList(annotations),
774 for (String calcId : hiddenTypes.keySet())
776 for (List<String> type : hiddenTypes.get(calcId))
778 addAnnotationTypeToShowHide(showMenu, forSequences,
779 calcId, type, false, true);
782 // grey out 'show annotations' if none are hidden
783 showMenu.setEnabled(!hiddenTypes.isEmpty());
785 for (String calcId : shownTypes.keySet())
787 for (List<String> type : shownTypes.get(calcId))
789 addAnnotationTypeToShowHide(hideMenu, forSequences,
790 calcId, type, false, false);
793 // grey out 'hide annotations' if none are shown
794 hideMenu.setEnabled(!shownTypes.isEmpty());
798 * Returns a list of sequences - either the current selection group (if there
799 * is one), else the specified single sequence.
804 protected List<SequenceI> getSequenceScope(SequenceI seq)
806 List<SequenceI> forSequences = null;
807 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
808 if (selectionGroup != null && selectionGroup.getSize() > 0)
810 forSequences = selectionGroup.getSequences();
814 forSequences = seq == null ? Collections.<SequenceI> emptyList()
815 : Arrays.asList(seq);
821 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
824 * @param showOrHideMenu
826 * @param forSequences
827 * the sequences whose annotations may be shown or hidden
832 * if true this is a special label meaning 'All'
833 * @param actionIsShow
834 * if true, the select menu item action is to show the annotation
837 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
838 final List<SequenceI> forSequences, String calcId,
839 final List<String> types, final boolean allTypes,
840 final boolean actionIsShow)
842 String label = types.toString(); // [a, b, c]
843 label = label.substring(1, label.length() - 1); // a, b, c
844 final JMenuItem item = new JMenuItem(label);
845 item.setToolTipText(calcId);
846 item.addActionListener(new java.awt.event.ActionListener()
849 public void actionPerformed(ActionEvent e)
851 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
852 forSequences, allTypes, actionIsShow);
856 showOrHideMenu.add(item);
859 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
862 // TODO: usability: thread off the generation of group url content so root
864 // sequence only URLs
865 // ID/regex match URLs
866 groupLinksMenu = new JMenu(
867 MessageManager.getString("action.group_link"));
868 JMenu[] linkMenus = new JMenu[]
869 { null, new JMenu(MessageManager.getString("action.ids")),
870 new JMenu(MessageManager.getString("action.sequences")),
871 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
878 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
879 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
880 Hashtable commonDbrefs = new Hashtable();
881 for (int sq = 0; sq < seqs.length; sq++)
884 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
885 .findPosition(sg.getEndRes());
886 // just collect ids from dataset sequence
887 // TODO: check if IDs collected from selecton group intersects with the
888 // current selection, too
889 SequenceI sqi = seqs[sq];
890 while (sqi.getDatasetSequence() != null)
892 sqi = sqi.getDatasetSequence();
894 DBRefEntry[] dbr = sqi.getDBRef();
895 if (dbr != null && dbr.length > 0)
897 for (int d = 0; d < dbr.length; d++)
899 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
900 Object[] sarray = (Object[]) commonDbrefs.get(src);
903 sarray = new Object[2];
904 sarray[0] = new int[]
906 sarray[1] = new String[seqs.length];
908 commonDbrefs.put(src, sarray);
911 if (((String[]) sarray[1])[sq] == null)
914 || (dbr[d].getMap().locateMappedRange(start, end) != null))
916 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
917 ((int[]) sarray[0])[0]++;
923 // now create group links for all distinct ID/sequence sets.
924 boolean addMenu = false; // indicates if there are any group links to give
926 for (int i = 0; i < groupLinks.size(); i++)
928 String link = groupLinks.elementAt(i).toString();
929 GroupUrlLink urlLink = null;
932 urlLink = new GroupUrlLink(link);
933 } catch (Exception foo)
935 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
940 if (!urlLink.isValid())
942 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
945 final String label = urlLink.getLabel();
946 boolean usingNames = false;
947 // Now see which parts of the group apply for this URL
948 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
949 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
950 String[] seqstr, ids; // input to makeUrl
953 int numinput = ((int[]) idset[0])[0];
954 String[] allids = ((String[]) idset[1]);
955 seqstr = new String[numinput];
956 ids = new String[numinput];
957 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
959 if (allids[sq] != null)
961 ids[idcount] = allids[sq];
962 seqstr[idcount++] = idandseqs[1][sq];
968 // just use the id/seq set
969 seqstr = idandseqs[1];
973 // and try and make the groupURL!
975 Object[] urlset = null;
978 urlset = urlLink.makeUrlStubs(ids, seqstr,
979 "FromJalview" + System.currentTimeMillis(), false);
980 } catch (UrlStringTooLongException e)
985 int type = urlLink.getGroupURLType() & 3;
986 // first two bits ofurlLink type bitfield are sequenceids and sequences
987 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
988 addshowLink(linkMenus[type], label
989 + (((type & 1) == 1) ? ("("
990 + (usingNames ? "Names" : ltarget) + ")") : ""),
997 groupLinksMenu = new JMenu(
998 MessageManager.getString("action.group_link"));
999 for (int m = 0; m < linkMenus.length; m++)
1001 if (linkMenus[m] != null
1002 && linkMenus[m].getMenuComponentCount() > 0)
1004 groupLinksMenu.add(linkMenus[m]);
1008 groupMenu.add(groupLinksMenu);
1013 * add a show URL menu item to the given linkMenu
1017 * - menu label string
1021 private void addshowLink(JMenu linkMenu, String label, final String url)
1023 JMenuItem item = new JMenuItem(label);
1024 item.setToolTipText(MessageManager.formatMessage(
1025 "label.open_url_param", new Object[]
1027 item.addActionListener(new java.awt.event.ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 new Thread(new Runnable()
1049 * add a late bound groupURL item to the given linkMenu
1053 * - menu label string
1054 * @param urlgenerator
1055 * GroupURLLink used to generate URL
1057 * Object array returned from the makeUrlStubs function.
1059 private void addshowLink(JMenu linkMenu, String label,
1060 final GroupUrlLink urlgenerator, final Object[] urlstub)
1062 JMenuItem item = new JMenuItem(label);
1063 item.setToolTipText(MessageManager.formatMessage(
1064 "label.open_url_seqs_param",
1066 { urlgenerator.getUrl_prefix(),
1067 urlgenerator.getNumberInvolved(urlstub) }));
1068 // TODO: put in info about what is being sent.
1069 item.addActionListener(new java.awt.event.ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 new Thread(new Runnable()
1082 showLink(urlgenerator.constructFrom(urlstub));
1083 } catch (UrlStringTooLongException e)
1101 private void jbInit() throws Exception
1103 groupMenu.setText(MessageManager.getString("label.group"));
1104 groupMenu.setText(MessageManager.getString("label.selection"));
1105 groupName.setText(MessageManager.getString("label.name"));
1106 groupName.addActionListener(new java.awt.event.ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 groupName_actionPerformed();
1114 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1115 sequenceName.setText(MessageManager
1116 .getString("label.edit_name_description"));
1117 sequenceName.addActionListener(new java.awt.event.ActionListener()
1120 public void actionPerformed(ActionEvent e)
1122 sequenceName_actionPerformed();
1125 chooseAnnotations.setText(MessageManager
1126 .getString("label.choose_annotations") + "...");
1127 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1130 public void actionPerformed(ActionEvent e)
1132 chooseAnnotations_actionPerformed(e);
1135 sequenceDetails.setText(MessageManager
1136 .getString("label.sequence_details") + "...");
1137 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 sequenceDetails_actionPerformed();
1145 sequenceSelDetails.setText(MessageManager
1146 .getString("label.sequence_details") + "...");
1148 .addActionListener(new java.awt.event.ActionListener()
1151 public void actionPerformed(ActionEvent e)
1153 sequenceSelectionDetails_actionPerformed();
1156 PIDColour.setFocusPainted(false);
1158 .setText(MessageManager.getString("action.remove_group"));
1159 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1162 public void actionPerformed(ActionEvent e)
1164 unGroupMenuItem_actionPerformed();
1167 createGroupMenuItem.setText(MessageManager
1168 .getString("action.create_group"));
1170 .addActionListener(new java.awt.event.ActionListener()
1173 public void actionPerformed(ActionEvent e)
1175 createGroupMenuItem_actionPerformed();
1179 outline.setText(MessageManager.getString("action.border_colour"));
1180 outline.addActionListener(new java.awt.event.ActionListener()
1183 public void actionPerformed(ActionEvent e)
1185 outline_actionPerformed();
1189 .setText(MessageManager.getString("label.nucleotide"));
1190 nucleotideMenuItem.addActionListener(new ActionListener()
1193 public void actionPerformed(ActionEvent e)
1195 nucleotideMenuItem_actionPerformed();
1198 colourMenu.setText(MessageManager.getString("label.group_colour"));
1199 showBoxes.setText(MessageManager.getString("action.boxes"));
1200 showBoxes.setState(true);
1201 showBoxes.addActionListener(new ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 showBoxes_actionPerformed();
1209 showText.setText(MessageManager.getString("action.text"));
1210 showText.setState(true);
1211 showText.addActionListener(new ActionListener()
1214 public void actionPerformed(ActionEvent e)
1216 showText_actionPerformed();
1219 showColourText.setText(MessageManager.getString("label.colour_text"));
1220 showColourText.addActionListener(new ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 showColourText_actionPerformed();
1228 displayNonconserved.setText(MessageManager
1229 .getString("label.show_non_conversed"));
1230 displayNonconserved.setState(true);
1231 displayNonconserved.addActionListener(new ActionListener()
1234 public void actionPerformed(ActionEvent e)
1236 showNonconserved_actionPerformed();
1239 editMenu.setText(MessageManager.getString("action.edit"));
1240 cut.setText(MessageManager.getString("action.cut"));
1241 cut.addActionListener(new ActionListener()
1244 public void actionPerformed(ActionEvent e)
1246 cut_actionPerformed();
1249 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1250 upperCase.addActionListener(new ActionListener()
1253 public void actionPerformed(ActionEvent e)
1258 copy.setText(MessageManager.getString("action.copy"));
1259 copy.addActionListener(new ActionListener()
1262 public void actionPerformed(ActionEvent e)
1264 copy_actionPerformed();
1267 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1268 lowerCase.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1276 toggle.setText(MessageManager.getString("label.toggle_case"));
1277 toggle.addActionListener(new ActionListener()
1280 public void actionPerformed(ActionEvent e)
1285 pdbMenu.setText(MessageManager
1286 .getString("label.associate_structure_with_sequence"));
1287 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1288 pdbFromFile.addActionListener(new ActionListener()
1291 public void actionPerformed(ActionEvent e)
1293 pdbFromFile_actionPerformed();
1297 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1298 enterPDB.addActionListener(new ActionListener()
1301 public void actionPerformed(ActionEvent e)
1303 enterPDB_actionPerformed();
1306 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1307 discoverPDB.addActionListener(new ActionListener()
1310 public void actionPerformed(ActionEvent e)
1312 discoverPDB_actionPerformed();
1315 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1317 seqShowAnnotationsMenu.setText(MessageManager
1318 .getString("label.show_annotations"));
1319 seqHideAnnotationsMenu.setText(MessageManager
1320 .getString("label.hide_annotations"));
1321 groupShowAnnotationsMenu.setText(MessageManager
1322 .getString("label.show_annotations"));
1323 groupHideAnnotationsMenu.setText(MessageManager
1324 .getString("label.hide_annotations"));
1325 sequenceFeature.setText(MessageManager
1326 .getString("label.create_sequence_feature"));
1327 sequenceFeature.addActionListener(new ActionListener()
1330 public void actionPerformed(ActionEvent e)
1332 sequenceFeature_actionPerformed();
1335 textColour.setText(MessageManager.getString("label.text_colour"));
1336 textColour.addActionListener(new ActionListener()
1339 public void actionPerformed(ActionEvent e)
1341 textColour_actionPerformed();
1344 jMenu1.setText(MessageManager.getString("label.group"));
1345 proteinStructureMenu.setText(MessageManager
1346 .getString("label.view_protein_structure"));
1347 proteinStructureMenu.addActionListener(new ActionListener()
1350 public void actionPerformed(ActionEvent actionEvent)
1352 SequenceI[] selectedSeqs = new SequenceI[]
1354 if (ap.av.getSelectionGroup() != null)
1356 selectedSeqs = ap.av.getSequenceSelection();
1358 new StructureChooser(selectedSeqs, sequence, ap);
1362 rnaStructureMenu.setText(MessageManager
1363 .getString("label.view_rna_structure"));
1365 // colStructureMenu.setText("Colour By Structure");
1366 editSequence.setText(MessageManager.getString("label.edit_sequence")
1368 editSequence.addActionListener(new ActionListener()
1371 public void actionPerformed(ActionEvent actionEvent)
1373 editSequence_actionPerformed(actionEvent);
1376 makeReferenceSeq.setText(MessageManager
1377 .getString("label.mark_as_representative"));
1378 makeReferenceSeq.addActionListener(new ActionListener()
1382 public void actionPerformed(ActionEvent actionEvent)
1384 makeReferenceSeq_actionPerformed(actionEvent);
1388 hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
1389 hideInsertions.addActionListener(new ActionListener()
1393 public void actionPerformed(ActionEvent e)
1395 hideInsertions_actionPerformed(e);
1399 * annotationMenuItem.setText("By Annotation");
1400 * annotationMenuItem.addActionListener(new ActionListener() { public void
1401 * actionPerformed(ActionEvent actionEvent) {
1402 * annotationMenuItem_actionPerformed(actionEvent); } });
1404 groupMenu.add(sequenceSelDetails);
1407 add(rnaStructureMenu);
1408 add(proteinStructureMenu);
1411 add(hideInsertions);
1413 // annotations configuration panel suppressed for now
1414 // groupMenu.add(chooseAnnotations);
1417 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1418 * (if a selection group is in force).
1420 sequenceMenu.add(seqShowAnnotationsMenu);
1421 sequenceMenu.add(seqHideAnnotationsMenu);
1422 sequenceMenu.add(seqAddReferenceAnnotations);
1423 groupMenu.add(groupShowAnnotationsMenu);
1424 groupMenu.add(groupHideAnnotationsMenu);
1425 groupMenu.add(groupAddReferenceAnnotations);
1426 groupMenu.add(editMenu);
1427 groupMenu.add(outputMenu);
1428 groupMenu.add(sequenceFeature);
1429 groupMenu.add(createGroupMenuItem);
1430 groupMenu.add(unGroupMenuItem);
1431 groupMenu.add(jMenu1);
1432 sequenceMenu.add(sequenceName);
1433 sequenceMenu.add(sequenceDetails);
1434 sequenceMenu.add(makeReferenceSeq);
1435 colourMenu.add(textColour);
1436 colourMenu.add(noColourmenuItem);
1437 colourMenu.add(clustalColour);
1438 colourMenu.add(BLOSUM62Colour);
1439 colourMenu.add(PIDColour);
1440 colourMenu.add(zappoColour);
1441 colourMenu.add(taylorColour);
1442 colourMenu.add(hydrophobicityColour);
1443 colourMenu.add(helixColour);
1444 colourMenu.add(strandColour);
1445 colourMenu.add(turnColour);
1446 colourMenu.add(buriedColour);
1447 colourMenu.add(nucleotideMenuItem);
1448 if (ap.getAlignment().isNucleotide())
1450 // JBPNote - commented since the colourscheme isn't functional
1451 colourMenu.add(purinePyrimidineColour);
1453 colourMenu.add(userDefinedColour);
1455 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1457 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1458 .getUserColourSchemes().keys();
1460 while (userColours.hasMoreElements())
1462 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1463 item.addActionListener(new ActionListener()
1466 public void actionPerformed(ActionEvent evt)
1468 userDefinedColour_actionPerformed(evt);
1471 colourMenu.add(item);
1475 colourMenu.addSeparator();
1476 colourMenu.add(abovePIDColour);
1477 colourMenu.add(conservationMenuItem);
1480 editMenu.add(editSequence);
1481 editMenu.add(upperCase);
1482 editMenu.add(lowerCase);
1483 editMenu.add(toggle);
1484 pdbMenu.add(pdbFromFile);
1485 // JBPNote: These shouldn't be added here - should appear in a generic
1486 // 'apply web service to this sequence menu'
1487 // pdbMenu.add(RNAFold);
1488 // pdbMenu.add(ContraFold);
1489 pdbMenu.add(enterPDB);
1490 pdbMenu.add(discoverPDB);
1491 jMenu1.add(groupName);
1492 jMenu1.add(colourMenu);
1493 jMenu1.add(showBoxes);
1494 jMenu1.add(showText);
1495 jMenu1.add(showColourText);
1496 jMenu1.add(outline);
1497 jMenu1.add(displayNonconserved);
1498 noColourmenuItem.setText(MessageManager.getString("label.none"));
1499 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1502 public void actionPerformed(ActionEvent e)
1504 noColourmenuItem_actionPerformed();
1508 clustalColour.setText(MessageManager
1509 .getString("label.clustalx_colours"));
1510 clustalColour.addActionListener(new java.awt.event.ActionListener()
1513 public void actionPerformed(ActionEvent e)
1515 clustalColour_actionPerformed();
1518 zappoColour.setText(MessageManager.getString("label.zappo"));
1519 zappoColour.addActionListener(new java.awt.event.ActionListener()
1522 public void actionPerformed(ActionEvent e)
1524 zappoColour_actionPerformed();
1527 taylorColour.setText(MessageManager.getString("label.taylor"));
1528 taylorColour.addActionListener(new java.awt.event.ActionListener()
1531 public void actionPerformed(ActionEvent e)
1533 taylorColour_actionPerformed();
1536 hydrophobicityColour.setText(MessageManager
1537 .getString("label.hydrophobicity"));
1538 hydrophobicityColour
1539 .addActionListener(new java.awt.event.ActionListener()
1542 public void actionPerformed(ActionEvent e)
1544 hydrophobicityColour_actionPerformed();
1547 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1548 helixColour.addActionListener(new java.awt.event.ActionListener()
1551 public void actionPerformed(ActionEvent e)
1553 helixColour_actionPerformed();
1556 strandColour.setText(MessageManager
1557 .getString("label.strand_propensity"));
1558 strandColour.addActionListener(new java.awt.event.ActionListener()
1561 public void actionPerformed(ActionEvent e)
1563 strandColour_actionPerformed();
1566 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1567 turnColour.addActionListener(new java.awt.event.ActionListener()
1570 public void actionPerformed(ActionEvent e)
1572 turnColour_actionPerformed();
1575 buriedColour.setText(MessageManager.getString("label.buried_index"));
1576 buriedColour.addActionListener(new java.awt.event.ActionListener()
1579 public void actionPerformed(ActionEvent e)
1581 buriedColour_actionPerformed();
1584 abovePIDColour.setText(MessageManager
1585 .getString("label.above_identity_percentage"));
1586 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1589 public void actionPerformed(ActionEvent e)
1591 abovePIDColour_actionPerformed();
1594 userDefinedColour.setText(MessageManager
1595 .getString("action.user_defined"));
1596 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1599 public void actionPerformed(ActionEvent e)
1601 userDefinedColour_actionPerformed(e);
1605 .setText(MessageManager.getString("label.percentage_identity"));
1606 PIDColour.addActionListener(new java.awt.event.ActionListener()
1609 public void actionPerformed(ActionEvent e)
1611 PIDColour_actionPerformed();
1614 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1615 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1618 public void actionPerformed(ActionEvent e)
1620 BLOSUM62Colour_actionPerformed();
1623 purinePyrimidineColour.setText(MessageManager
1624 .getString("label.purine_pyrimidine"));
1625 purinePyrimidineColour
1626 .addActionListener(new java.awt.event.ActionListener()
1629 public void actionPerformed(ActionEvent e)
1631 purinePyrimidineColour_actionPerformed();
1636 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1637 * public void actionPerformed(ActionEvent e) {
1638 * covariationColour_actionPerformed(); } });
1641 conservationMenuItem.setText(MessageManager
1642 .getString("label.conservation"));
1643 conservationMenuItem
1644 .addActionListener(new java.awt.event.ActionListener()
1647 public void actionPerformed(ActionEvent e)
1649 conservationMenuItem_actionPerformed();
1655 * Check for any annotations on the underlying dataset sequences (for the
1656 * current selection group) which are not 'on the alignment'.If any are found,
1657 * enable the option to add them to the alignment. The criteria for 'on the
1658 * alignment' is finding an alignment annotation on the alignment, matched on
1659 * calcId, label and sequenceRef.
1661 * A tooltip is also constructed that displays the source (calcId) and type
1662 * (label) of the annotations that can be added.
1665 * @param forSequences
1667 protected void configureReferenceAnnotationsMenu(
1668 JMenuItem menuItem, List<SequenceI> forSequences)
1670 menuItem.setEnabled(false);
1673 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1674 * Using TreeMap means calcIds are shown in alphabetical order.
1676 Map<String, String> tipEntries = new TreeMap<String, String>();
1677 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1678 AlignmentI al = this.ap.av.getAlignment();
1679 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1680 tipEntries, candidates, al);
1681 if (!candidates.isEmpty())
1683 StringBuilder tooltip = new StringBuilder(64);
1684 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1687 * Found annotations that could be added. Enable the menu item, and
1688 * configure its tooltip and action.
1690 menuItem.setEnabled(true);
1691 for (String calcId : tipEntries.keySet())
1693 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1695 String tooltipText = JvSwingUtils.wrapTooltip(true,
1696 tooltip.toString());
1697 menuItem.setToolTipText(tooltipText);
1699 menuItem.addActionListener(new ActionListener()
1702 public void actionPerformed(ActionEvent e)
1704 addReferenceAnnotations_actionPerformed(candidates);
1711 * Add annotations to the sequences and to the alignment.
1714 * a map whose keys are sequences on the alignment, and values a list
1715 * of annotations to add to each sequence
1717 protected void addReferenceAnnotations_actionPerformed(
1718 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1720 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1721 final AlignmentI alignment = this.ap.getAlignment();
1722 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1727 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1729 if (!ap.av.getAlignment().hasSeqrep())
1731 // initialise the display flags so the user sees something happen
1732 ap.av.setDisplayReferenceSeq(true);
1733 ap.av.setColourByReferenceSeq(true);
1734 ap.av.getAlignment().setSeqrep(sequence);
1738 if (ap.av.getAlignment().getSeqrep() == sequence)
1740 ap.av.getAlignment().setSeqrep(null);
1744 ap.av.getAlignment().setSeqrep(sequence);
1750 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1752 if (sequence != null)
1754 ColumnSelection cs = ap.av.getColumnSelection();
1757 cs = new ColumnSelection();
1759 cs.hideInsertionsFor(sequence);
1760 ap.av.setColumnSelection(cs);
1764 protected void sequenceSelectionDetails_actionPerformed()
1766 createSequenceDetailsReport(ap.av.getSequenceSelection());
1769 protected void sequenceDetails_actionPerformed()
1771 createSequenceDetailsReport(new SequenceI[]
1775 public void createSequenceDetailsReport(SequenceI[] sequences)
1777 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1778 StringBuffer contents = new StringBuffer();
1779 for (SequenceI seq : sequences)
1781 contents.append("<p><h2>"
1784 "label.create_sequence_details_report_annotation_for",
1786 { seq.getDisplayId(true) }) + "</h2></p><p>");
1787 new SequenceAnnotationReport(null)
1788 .createSequenceAnnotationReport(
1794 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1795 .getSeqPanel().seqCanvas.fr
1798 contents.append("</p>");
1800 cap.setText("<html>" + contents.toString() + "</html>");
1802 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1803 "label.sequence_details_for",
1804 (sequences.length == 1 ? new Object[]
1805 { sequences[0].getDisplayId(true) } : new Object[]
1806 { MessageManager.getString("label.selection") })), 500, 400);
1810 protected void showNonconserved_actionPerformed()
1812 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1817 * call to refresh view after settings change
1821 ap.updateAnnotation();
1822 ap.paintAlignment(true);
1824 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1833 protected void clustalColour_actionPerformed()
1835 SequenceGroup sg = getGroup();
1836 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1846 protected void zappoColour_actionPerformed()
1848 getGroup().cs = new ZappoColourScheme();
1858 protected void taylorColour_actionPerformed()
1860 getGroup().cs = new TaylorColourScheme();
1870 protected void hydrophobicityColour_actionPerformed()
1872 getGroup().cs = new HydrophobicColourScheme();
1882 protected void helixColour_actionPerformed()
1884 getGroup().cs = new HelixColourScheme();
1894 protected void strandColour_actionPerformed()
1896 getGroup().cs = new StrandColourScheme();
1906 protected void turnColour_actionPerformed()
1908 getGroup().cs = new TurnColourScheme();
1918 protected void buriedColour_actionPerformed()
1920 getGroup().cs = new BuriedColourScheme();
1930 public void nucleotideMenuItem_actionPerformed()
1932 getGroup().cs = new NucleotideColourScheme();
1936 protected void purinePyrimidineColour_actionPerformed()
1938 getGroup().cs = new PurinePyrimidineColourScheme();
1943 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1944 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1952 protected void abovePIDColour_actionPerformed()
1954 SequenceGroup sg = getGroup();
1960 if (abovePIDColour.isSelected())
1962 sg.cs.setConsensus(AAFrequency.calculate(
1963 sg.getSequences(ap.av.getHiddenRepSequences()),
1964 sg.getStartRes(), sg.getEndRes() + 1));
1966 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1969 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1971 SliderPanel.showPIDSlider();
1974 // remove PIDColouring
1976 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1988 protected void userDefinedColour_actionPerformed(ActionEvent e)
1990 SequenceGroup sg = getGroup();
1992 if (e.getSource().equals(userDefinedColour))
1994 new UserDefinedColours(ap, sg);
1998 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1999 .getUserColourSchemes().get(e.getActionCommand());
2007 * Open a panel where the user can choose which types of sequence annotation
2012 protected void chooseAnnotations_actionPerformed(ActionEvent e)
2014 // todo correct way to guard against opening a duplicate panel?
2015 new AnnotationChooser(ap);
2024 protected void PIDColour_actionPerformed()
2026 SequenceGroup sg = getGroup();
2027 sg.cs = new PIDColourScheme();
2028 sg.cs.setConsensus(AAFrequency.calculate(
2029 sg.getSequences(ap.av.getHiddenRepSequences()),
2030 sg.getStartRes(), sg.getEndRes() + 1));
2040 protected void BLOSUM62Colour_actionPerformed()
2042 SequenceGroup sg = getGroup();
2044 sg.cs = new Blosum62ColourScheme();
2046 sg.cs.setConsensus(AAFrequency.calculate(
2047 sg.getSequences(ap.av.getHiddenRepSequences()),
2048 sg.getStartRes(), sg.getEndRes() + 1));
2059 protected void noColourmenuItem_actionPerformed()
2061 getGroup().cs = null;
2071 protected void conservationMenuItem_actionPerformed()
2073 SequenceGroup sg = getGroup();
2079 if (conservationMenuItem.isSelected())
2081 // JBPNote: Conservation name shouldn't be i18n translated
2082 Conservation c = new Conservation("Group",
2083 ResidueProperties.propHash, 3, sg.getSequences(ap.av
2084 .getHiddenRepSequences()), sg.getStartRes(),
2085 sg.getEndRes() + 1);
2088 c.verdict(false, ap.av.getConsPercGaps());
2090 sg.cs.setConservation(c);
2092 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2093 SliderPanel.showConservationSlider();
2096 // remove ConservationColouring
2098 sg.cs.setConservation(null);
2104 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2106 SequenceGroup sg = getGroup();
2112 AnnotationColourGradient acg = new AnnotationColourGradient(
2113 sequence.getAnnotation()[0], null,
2114 AnnotationColourGradient.NO_THRESHOLD);
2116 acg.setPredefinedColours(true);
2128 protected void groupName_actionPerformed()
2131 SequenceGroup sg = getGroup();
2132 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2133 sg.getDescription(), " "
2134 + MessageManager.getString("label.group_name") + " ",
2135 MessageManager.getString("label.group_description") + " ",
2136 MessageManager.getString("label.edit_group_name_description"),
2144 sg.setName(dialog.getName());
2145 sg.setDescription(dialog.getDescription());
2150 * Get selection group - adding it to the alignment if necessary.
2152 * @return sequence group to operate on
2154 SequenceGroup getGroup()
2156 SequenceGroup sg = ap.av.getSelectionGroup();
2157 // this method won't add a new group if it already exists
2160 ap.av.getAlignment().addGroup(sg);
2172 void sequenceName_actionPerformed()
2174 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2175 sequence.getDescription(),
2176 " " + MessageManager.getString("label.sequence_name")
2178 MessageManager.getString("label.sequence_description") + " ",
2180 .getString("label.edit_sequence_name_description"),
2188 if (dialog.getName() != null)
2190 if (dialog.getName().indexOf(" ") > -1)
2196 .getString("label.spaces_converted_to_backslashes"),
2198 .getString("label.no_spaces_allowed_sequence_name"),
2199 JOptionPane.WARNING_MESSAGE);
2202 sequence.setName(dialog.getName().replace(' ', '_'));
2203 ap.paintAlignment(false);
2206 sequence.setDescription(dialog.getDescription());
2208 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2219 void unGroupMenuItem_actionPerformed()
2221 SequenceGroup sg = ap.av.getSelectionGroup();
2222 ap.av.getAlignment().deleteGroup(sg);
2223 ap.av.setSelectionGroup(null);
2227 void createGroupMenuItem_actionPerformed()
2229 getGroup(); // implicitly creates group - note - should apply defaults / use
2230 // standard alignment window logic for this
2240 protected void outline_actionPerformed()
2242 SequenceGroup sg = getGroup();
2243 Color col = JColorChooser.showDialog(this,
2244 MessageManager.getString("label.select_outline_colour"),
2249 sg.setOutlineColour(col);
2261 public void showBoxes_actionPerformed()
2263 getGroup().setDisplayBoxes(showBoxes.isSelected());
2273 public void showText_actionPerformed()
2275 getGroup().setDisplayText(showText.isSelected());
2285 public void showColourText_actionPerformed()
2287 getGroup().setColourText(showColourText.isSelected());
2291 public void showLink(String url)
2295 jalview.util.BrowserLauncher.openURL(url);
2296 } catch (Exception ex)
2298 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2299 MessageManager.getString("label.web_browser_not_found_unix"),
2300 MessageManager.getString("label.web_browser_not_found"),
2301 JOptionPane.WARNING_MESSAGE);
2303 ex.printStackTrace();
2307 void hideSequences(boolean representGroup)
2309 SequenceGroup sg = ap.av.getSelectionGroup();
2310 if (sg == null || sg.getSize() < 1)
2312 ap.av.hideSequence(new SequenceI[]
2317 ap.av.setSelectionGroup(null);
2321 ap.av.hideRepSequences(sequence, sg);
2326 int gsize = sg.getSize();
2327 SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
2329 ap.av.hideSequence(hseqs);
2330 // refresh(); TODO: ? needed ?
2331 ap.av.sendSelection();
2334 public void copy_actionPerformed()
2336 ap.alignFrame.copy_actionPerformed(null);
2339 public void cut_actionPerformed()
2341 ap.alignFrame.cut_actionPerformed(null);
2344 void changeCase(ActionEvent e)
2346 Object source = e.getSource();
2347 SequenceGroup sg = ap.av.getSelectionGroup();
2351 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2353 sg.getEndRes() + 1);
2358 if (source == toggle)
2360 description = MessageManager.getString("label.toggle_case");
2361 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2363 else if (source == upperCase)
2365 description = MessageManager.getString("label.to_upper_case");
2366 caseChange = ChangeCaseCommand.TO_UPPER;
2370 description = MessageManager.getString("label.to_lower_case");
2371 caseChange = ChangeCaseCommand.TO_LOWER;
2374 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2375 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2376 startEnd, caseChange);
2378 ap.alignFrame.addHistoryItem(caseCommand);
2380 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2386 public void outputText_actionPerformed(ActionEvent e)
2388 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2389 cap.setForInput(null);
2390 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2391 "label.alignment_output_command", new Object[]
2392 { e.getActionCommand() }), 600, 500);
2394 String[] omitHidden = null;
2396 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2397 // or we simply trust the user wants
2398 // wysiwig behaviour
2400 cap.setText(new FormatAdapter(ap).formatSequences(e.getActionCommand(),
2404 public void pdbFromFile_actionPerformed()
2406 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2407 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2408 chooser.setFileView(new jalview.io.JalviewFileView());
2409 chooser.setDialogTitle(MessageManager.formatMessage(
2410 "label.select_pdb_file_for", new Object[]
2411 { sequence.getDisplayId(false) }));
2412 chooser.setToolTipText(MessageManager.formatMessage(
2413 "label.load_pdb_file_associate_with_sequence", new Object[]
2414 { sequence.getDisplayId(false) }));
2416 int value = chooser.showOpenDialog(null);
2418 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2420 String choice = chooser.getSelectedFile().getPath();
2421 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2422 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2423 jalview.io.AppletFormatAdapter.FILE, sequence, true,
2430 public void enterPDB_actionPerformed()
2432 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2433 MessageManager.getString("label.enter_pdb_id"),
2434 MessageManager.getString("label.enter_pdb_id"),
2435 JOptionPane.QUESTION_MESSAGE);
2437 if (id != null && id.length() > 0)
2439 PDBEntry entry = new PDBEntry();
2440 entry.setId(id.toUpperCase());
2441 sequence.getDatasetSequence().addPDBId(entry);
2445 public void discoverPDB_actionPerformed()
2448 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2450 : ap.av.getSequenceSelection());
2451 Thread discpdb = new Thread(new Runnable()
2457 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2458 .fetchDBRefs(false);
2465 public void sequenceFeature_actionPerformed()
2467 SequenceGroup sg = ap.av.getSelectionGroup();
2473 int rsize = 0, gSize = sg.getSize();
2474 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2475 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2477 for (int i = 0; i < gSize; i++)
2479 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2480 int end = sg.findEndRes(sg.getSequenceAt(i));
2483 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2484 features[rsize] = new SequenceFeature(null, null, null, start, end,
2489 rseqs = new SequenceI[rsize];
2490 tfeatures = new SequenceFeature[rsize];
2491 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2492 System.arraycopy(features, 0, tfeatures, 0, rsize);
2493 features = tfeatures;
2495 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2496 features, true, ap))
2498 ap.alignFrame.setShowSeqFeatures(true);
2499 ap.highlightSearchResults(null);
2503 public void textColour_actionPerformed()
2505 SequenceGroup sg = getGroup();
2508 new TextColourChooser().chooseColour(ap, sg);
2512 public void colourByStructure(String pdbid)
2514 Annotation[] anots = ap.av.getStructureSelectionManager()
2515 .colourSequenceFromStructure(sequence, pdbid);
2517 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2518 "Coloured by " + pdbid, anots);
2520 ap.av.getAlignment().addAnnotation(an);
2521 an.createSequenceMapping(sequence, 0, true);
2522 // an.adjustForAlignment();
2523 ap.av.getAlignment().setAnnotationIndex(an, 0);
2525 ap.adjustAnnotationHeight();
2527 sequence.addAlignmentAnnotation(an);
2531 public void editSequence_actionPerformed(ActionEvent actionEvent)
2533 SequenceGroup sg = ap.av.getSelectionGroup();
2537 if (sequence == null)
2539 sequence = sg.getSequenceAt(0);
2542 EditNameDialog dialog = new EditNameDialog(
2543 sequence.getSequenceAsString(sg.getStartRes(),
2544 sg.getEndRes() + 1), null,
2545 MessageManager.getString("label.edit_sequence"), null,
2546 MessageManager.getString("label.edit_sequence"),
2551 EditCommand editCommand = new EditCommand(
2552 MessageManager.getString("label.edit_sequences"),
2553 Action.REPLACE, dialog.getName().replace(' ',
2554 ap.av.getGapCharacter()),
2555 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2556 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2558 ap.alignFrame.addHistoryItem(editCommand);
2560 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()