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 structureMenu = new JMenuItem();
209 JMenu viewStructureMenu = 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 (seq.getDatasetSequence().getPDBId() != null
326 && seq.getDatasetSequence().getPDBId().size() > 0)
328 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
331 while (e.hasMoreElements())
333 final PDBEntry pdb = (PDBEntry) e.nextElement();
335 menuItem = new JMenuItem();
336 menuItem.setText(pdb.getId());
337 menuItem.addActionListener(new ActionListener()
340 public void actionPerformed(ActionEvent e)
342 // TODO re JAL-860: optionally open dialog or provide a menu entry
343 // allowing user to open just one structure per sequence
344 // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
345 // { pdb })[0], null, ap);
346 new StructureViewer(ap.getStructureSelectionManager())
348 ap.av.collateForPDB(new PDBEntry[]
349 { pdb })[0], null, ap);
352 viewStructureMenu.add(menuItem);
355 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
356 * menuItem.addActionListener(new java.awt.event.ActionListener() {
357 * public void actionPerformed(ActionEvent e) {
358 * colourByStructure(pdb.getId()); } });
359 * colStructureMenu.add(menuItem);
365 if (ap.av.getAlignment().isNucleotide() == false)
367 structureMenu.remove(viewStructureMenu);
370 if (ap.av.getAlignment().isNucleotide() == true)
372 AlignmentAnnotation[] aa = ap.av.getAlignment()
373 .getAlignmentAnnotation();
374 for (int i = 0; aa != null && i < aa.length; i++)
376 if (aa[i].isValidStruc() && aa[i].sequenceRef == null)
378 final String rnastruc = aa[i].getRNAStruc();
379 final String structureLine = aa[i].label + " (alignment)";
380 menuItem = new JMenuItem();
381 menuItem.setText(MessageManager.formatMessage(
382 "label.2d_rna_structure_line", new Object[]
384 menuItem.addActionListener(new java.awt.event.ActionListener()
387 public void actionPerformed(ActionEvent e)
389 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
390 rnastruc, seq.getName(), ap);
391 System.out.println("end");
394 viewStructureMenu.add(menuItem);
399 if (seq.getAnnotation() != null)
401 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
402 for (int i = 0; i < seqAnno.length; i++)
404 if (seqAnno[i].isValidStruc())
406 final String rnastruc = seqAnno[i].getRNAStruc();
408 // TODO: make rnastrucF a bit more nice
409 menuItem = new JMenuItem();
410 menuItem.setText(MessageManager.formatMessage(
411 "label.2d_rna_sequence_name", new Object[]
413 menuItem.addActionListener(new java.awt.event.ActionListener()
416 public void actionPerformed(ActionEvent e)
418 // TODO: VARNA does'nt print gaps in the sequence
420 new AppVarna(seq.getName() + " structure", seq, seq
421 .getSequenceAsString(), rnastruc, seq.getName(),
425 viewStructureMenu.add(menuItem);
431 menuItem = new JMenuItem(
432 MessageManager.getString("action.hide_sequences"));
433 menuItem.addActionListener(new java.awt.event.ActionListener()
436 public void actionPerformed(ActionEvent e)
438 hideSequences(false);
443 if (ap.av.getSelectionGroup() != null
444 && ap.av.getSelectionGroup().getSize() > 1)
446 menuItem = new JMenuItem(MessageManager.formatMessage(
447 "label.represent_group_with", new Object[]
449 menuItem.addActionListener(new java.awt.event.ActionListener()
452 public void actionPerformed(ActionEvent e)
457 sequenceMenu.add(menuItem);
460 if (ap.av.hasHiddenRows())
462 final int index = ap.av.getAlignment().findIndex(seq);
464 if (ap.av.adjustForHiddenSeqs(index)
465 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
467 menuItem = new JMenuItem(
468 MessageManager.getString("action.reveal_sequences"));
469 menuItem.addActionListener(new ActionListener()
472 public void actionPerformed(ActionEvent e)
474 ap.av.showSequence(index);
475 if (ap.overviewPanel != null)
477 ap.overviewPanel.updateOverviewImage();
485 // for the case when no sequences are even visible
486 if (ap.av.hasHiddenRows())
489 menuItem = new JMenuItem(
490 MessageManager.getString("action.reveal_all"));
491 menuItem.addActionListener(new ActionListener()
494 public void actionPerformed(ActionEvent e)
496 ap.av.showAllHiddenSeqs();
497 if (ap.overviewPanel != null)
499 ap.overviewPanel.updateOverviewImage();
509 SequenceGroup sg = ap.av.getSelectionGroup();
510 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
511 .getGroups().contains(sg) : false;
513 if (sg != null && sg.getSize() > 0)
515 groupName.setText(MessageManager.formatMessage("label.name_param",
518 groupName.setText(MessageManager
519 .getString("label.edit_name_and_description_current_group"));
521 if (sg.cs instanceof ZappoColourScheme)
523 zappoColour.setSelected(true);
525 else if (sg.cs instanceof TaylorColourScheme)
527 taylorColour.setSelected(true);
529 else if (sg.cs instanceof PIDColourScheme)
531 PIDColour.setSelected(true);
533 else if (sg.cs instanceof Blosum62ColourScheme)
535 BLOSUM62Colour.setSelected(true);
537 else if (sg.cs instanceof UserColourScheme)
539 userDefinedColour.setSelected(true);
541 else if (sg.cs instanceof HydrophobicColourScheme)
543 hydrophobicityColour.setSelected(true);
545 else if (sg.cs instanceof HelixColourScheme)
547 helixColour.setSelected(true);
549 else if (sg.cs instanceof StrandColourScheme)
551 strandColour.setSelected(true);
553 else if (sg.cs instanceof TurnColourScheme)
555 turnColour.setSelected(true);
557 else if (sg.cs instanceof BuriedColourScheme)
559 buriedColour.setSelected(true);
561 else if (sg.cs instanceof ClustalxColourScheme)
563 clustalColour.setSelected(true);
565 else if (sg.cs instanceof PurinePyrimidineColourScheme)
567 purinePyrimidineColour.setSelected(true);
571 * else if (sg.cs instanceof CovariationColourScheme) {
572 * covariationColour.setSelected(true); }
576 noColourmenuItem.setSelected(true);
579 if (sg.cs != null && sg.cs.conservationApplied())
581 conservationMenuItem.setSelected(true);
583 displayNonconserved.setSelected(sg.getShowNonconserved());
584 showText.setSelected(sg.getDisplayText());
585 showColourText.setSelected(sg.getColourText());
586 showBoxes.setSelected(sg.getDisplayBoxes());
587 // add any groupURLs to the groupURL submenu and make it visible
588 if (groupLinks != null && groupLinks.size() > 0)
590 buildGroupURLMenu(sg, groupLinks);
592 // Add a 'show all structures' for the current selection
593 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
594 SequenceI sqass = null;
595 for (SequenceI sq : ap.av.getSequenceSelection())
597 Vector<PDBEntry> pes = sq.getDatasetSequence().getPDBId();
598 if (pes != null && pes.size() > 0)
600 reppdb.put(pes.get(0).getId(), pes.get(0));
601 for (PDBEntry pe : pes)
603 pdbe.put(pe.getId(), pe);
613 final PDBEntry[] pe = pdbe.values().toArray(
614 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
615 new PDBEntry[reppdb.size()]);
616 final JMenuItem gpdbview, rpdbview;
621 groupMenu.setVisible(false);
622 editMenu.setVisible(false);
627 createGroupMenuItem.setVisible(true);
628 unGroupMenuItem.setVisible(false);
629 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
633 createGroupMenuItem.setVisible(false);
634 unGroupMenuItem.setVisible(true);
635 jMenu1.setText(MessageManager.getString("action.edit_group"));
640 sequenceMenu.setVisible(false);
641 structureMenu.setVisible(false);
644 if (links != null && links.size() > 0)
647 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
648 Vector linkset = new Vector();
649 for (int i = 0; i < links.size(); i++)
651 String link = links.elementAt(i).toString();
652 UrlLink urlLink = null;
655 urlLink = new UrlLink(link);
656 } catch (Exception foo)
658 jalview.bin.Cache.log.error("Exception for URLLink '" + link
663 if (!urlLink.isValid())
665 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
668 final String label = urlLink.getLabel();
669 if (seq != null && urlLink.isDynamic())
672 // collect matching db-refs
673 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
674 seq.getDBRef(), new String[]
675 { urlLink.getTarget() });
676 // collect id string too
677 String id = seq.getName();
678 String descr = seq.getDescription();
679 if (descr != null && descr.length() < 1)
686 for (int r = 0; r < dbr.length; r++)
688 if (id != null && dbr[r].getAccessionId().equals(id))
690 // suppress duplicate link creation for the bare sequence ID
691 // string with this link
694 // create Bare ID link for this RUL
695 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
699 for (int u = 0; u < urls.length; u += 2)
701 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
703 linkset.addElement(urls[u] + "|" + urls[u + 1]);
704 addshowLink(linkMenu, label + "|" + urls[u],
713 // create Bare ID link for this RUL
714 String[] urls = urlLink.makeUrls(id, true);
717 for (int u = 0; u < urls.length; u += 2)
719 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
721 linkset.addElement(urls[u] + "|" + urls[u + 1]);
722 addshowLink(linkMenu, label, urls[u + 1]);
727 // Create urls from description but only for URL links which are regex
729 if (descr != null && urlLink.getRegexReplace() != null)
731 // create link for this URL from description where regex matches
732 String[] urls = urlLink.makeUrls(descr, true);
735 for (int u = 0; u < urls.length; u += 2)
737 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
739 linkset.addElement(urls[u] + "|" + urls[u + 1]);
740 addshowLink(linkMenu, label, urls[u + 1]);
748 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
750 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
751 // Add a non-dynamic link
752 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
756 if (sequence != null)
758 sequenceMenu.add(linkMenu);
768 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
769 * "All" is added first, followed by a separator. Then add any annotation
770 * types associated with the current selection. Separate menus are built for
771 * the selected sequence group (if any), and the selected sequence.
773 * Some annotation rows are always rendered together - these can be identified
774 * by a common graphGroup property > -1. Only one of each group will be marked
775 * as visible (to avoid duplication of the display). For such groups we add a
776 * composite type name, e.g.
778 * IUPredWS (Long), IUPredWS (Short)
782 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
783 List<SequenceI> forSequences)
785 showMenu.removeAll();
786 hideMenu.removeAll();
788 final List<String> all = Arrays.asList(ALL_ANNOTATIONS);
789 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true, true);
790 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
792 showMenu.addSeparator();
793 hideMenu.addSeparator();
795 final AlignmentAnnotation[] annotations = ap.getAlignment()
796 .getAlignmentAnnotation();
799 * Find shown/hidden annotations types, distinguished by source (calcId),
800 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
801 * the insertion order, which is the order of the annotations on the
804 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<String, List<List<String>>>();
805 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<String, List<List<String>>>();
806 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes,
808 AlignmentAnnotationUtils.asList(annotations),
811 for (String calcId : hiddenTypes.keySet())
813 for (List<String> type : hiddenTypes.get(calcId))
815 addAnnotationTypeToShowHide(showMenu, forSequences,
816 calcId, type, false, true);
819 // grey out 'show annotations' if none are hidden
820 showMenu.setEnabled(!hiddenTypes.isEmpty());
822 for (String calcId : shownTypes.keySet())
824 for (List<String> type : shownTypes.get(calcId))
826 addAnnotationTypeToShowHide(hideMenu, forSequences,
827 calcId, type, false, false);
830 // grey out 'hide annotations' if none are shown
831 hideMenu.setEnabled(!shownTypes.isEmpty());
835 * Returns a list of sequences - either the current selection group (if there
836 * is one), else the specified single sequence.
841 protected List<SequenceI> getSequenceScope(SequenceI seq)
843 List<SequenceI> forSequences = null;
844 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
845 if (selectionGroup != null && selectionGroup.getSize() > 0)
847 forSequences = selectionGroup.getSequences();
851 forSequences = seq == null ? Collections.<SequenceI> emptyList()
852 : Arrays.asList(seq);
858 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
861 * @param showOrHideMenu
863 * @param forSequences
864 * the sequences whose annotations may be shown or hidden
869 * if true this is a special label meaning 'All'
870 * @param actionIsShow
871 * if true, the select menu item action is to show the annotation
874 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
875 final List<SequenceI> forSequences, String calcId,
876 final List<String> types, final boolean allTypes,
877 final boolean actionIsShow)
879 String label = types.toString(); // [a, b, c]
880 label = label.substring(1, label.length() - 1); // a, b, c
881 final JMenuItem item = new JMenuItem(label);
882 item.setToolTipText(calcId);
883 item.addActionListener(new java.awt.event.ActionListener()
886 public void actionPerformed(ActionEvent e)
888 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(), types,
889 forSequences, allTypes, actionIsShow);
893 showOrHideMenu.add(item);
896 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
899 // TODO: usability: thread off the generation of group url content so root
901 // sequence only URLs
902 // ID/regex match URLs
903 groupLinksMenu = new JMenu(
904 MessageManager.getString("action.group_link"));
905 JMenu[] linkMenus = new JMenu[]
906 { null, new JMenu(MessageManager.getString("action.ids")),
907 new JMenu(MessageManager.getString("action.sequences")),
908 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
915 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
916 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
917 Hashtable commonDbrefs = new Hashtable();
918 for (int sq = 0; sq < seqs.length; sq++)
921 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
922 .findPosition(sg.getEndRes());
923 // just collect ids from dataset sequence
924 // TODO: check if IDs collected from selecton group intersects with the
925 // current selection, too
926 SequenceI sqi = seqs[sq];
927 while (sqi.getDatasetSequence() != null)
929 sqi = sqi.getDatasetSequence();
931 DBRefEntry[] dbr = sqi.getDBRef();
932 if (dbr != null && dbr.length > 0)
934 for (int d = 0; d < dbr.length; d++)
936 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
937 Object[] sarray = (Object[]) commonDbrefs.get(src);
940 sarray = new Object[2];
941 sarray[0] = new int[]
943 sarray[1] = new String[seqs.length];
945 commonDbrefs.put(src, sarray);
948 if (((String[]) sarray[1])[sq] == null)
951 || (dbr[d].getMap().locateMappedRange(start, end) != null))
953 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
954 ((int[]) sarray[0])[0]++;
960 // now create group links for all distinct ID/sequence sets.
961 boolean addMenu = false; // indicates if there are any group links to give
963 for (int i = 0; i < groupLinks.size(); i++)
965 String link = groupLinks.elementAt(i).toString();
966 GroupUrlLink urlLink = null;
969 urlLink = new GroupUrlLink(link);
970 } catch (Exception foo)
972 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
977 if (!urlLink.isValid())
979 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
982 final String label = urlLink.getLabel();
983 boolean usingNames = false;
984 // Now see which parts of the group apply for this URL
985 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
986 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
987 String[] seqstr, ids; // input to makeUrl
990 int numinput = ((int[]) idset[0])[0];
991 String[] allids = ((String[]) idset[1]);
992 seqstr = new String[numinput];
993 ids = new String[numinput];
994 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
996 if (allids[sq] != null)
998 ids[idcount] = allids[sq];
999 seqstr[idcount++] = idandseqs[1][sq];
1005 // just use the id/seq set
1006 seqstr = idandseqs[1];
1010 // and try and make the groupURL!
1012 Object[] urlset = null;
1015 urlset = urlLink.makeUrlStubs(ids, seqstr,
1016 "FromJalview" + System.currentTimeMillis(), false);
1017 } catch (UrlStringTooLongException e)
1022 int type = urlLink.getGroupURLType() & 3;
1023 // first two bits ofurlLink type bitfield are sequenceids and sequences
1024 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
1025 addshowLink(linkMenus[type], label
1026 + (((type & 1) == 1) ? ("("
1027 + (usingNames ? "Names" : ltarget) + ")") : ""),
1034 groupLinksMenu = new JMenu(
1035 MessageManager.getString("action.group_link"));
1036 for (int m = 0; m < linkMenus.length; m++)
1038 if (linkMenus[m] != null
1039 && linkMenus[m].getMenuComponentCount() > 0)
1041 groupLinksMenu.add(linkMenus[m]);
1045 groupMenu.add(groupLinksMenu);
1050 * add a show URL menu item to the given linkMenu
1054 * - menu label string
1058 private void addshowLink(JMenu linkMenu, String label, final String url)
1060 JMenuItem item = new JMenuItem(label);
1061 item.setToolTipText(MessageManager.formatMessage(
1062 "label.open_url_param", new Object[]
1064 item.addActionListener(new java.awt.event.ActionListener()
1067 public void actionPerformed(ActionEvent e)
1069 new Thread(new Runnable()
1086 * add a late bound groupURL item to the given linkMenu
1090 * - menu label string
1091 * @param urlgenerator
1092 * GroupURLLink used to generate URL
1094 * Object array returned from the makeUrlStubs function.
1096 private void addshowLink(JMenu linkMenu, String label,
1097 final GroupUrlLink urlgenerator, final Object[] urlstub)
1099 JMenuItem item = new JMenuItem(label);
1100 item.setToolTipText(MessageManager.formatMessage(
1101 "label.open_url_seqs_param",
1103 { urlgenerator.getUrl_prefix(),
1104 urlgenerator.getNumberInvolved(urlstub) }));
1105 // TODO: put in info about what is being sent.
1106 item.addActionListener(new java.awt.event.ActionListener()
1109 public void actionPerformed(ActionEvent e)
1111 new Thread(new Runnable()
1119 showLink(urlgenerator.constructFrom(urlstub));
1120 } catch (UrlStringTooLongException e)
1138 private void jbInit() throws Exception
1140 groupMenu.setText(MessageManager.getString("label.group"));
1141 groupMenu.setText(MessageManager.getString("label.selection"));
1142 groupName.setText(MessageManager.getString("label.name"));
1143 groupName.addActionListener(new java.awt.event.ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 groupName_actionPerformed();
1151 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1152 sequenceName.setText(MessageManager
1153 .getString("label.edit_name_description"));
1154 sequenceName.addActionListener(new java.awt.event.ActionListener()
1157 public void actionPerformed(ActionEvent e)
1159 sequenceName_actionPerformed();
1162 chooseAnnotations.setText(MessageManager
1163 .getString("label.choose_annotations") + "...");
1164 chooseAnnotations.addActionListener(new java.awt.event.ActionListener()
1167 public void actionPerformed(ActionEvent e)
1169 chooseAnnotations_actionPerformed(e);
1172 sequenceDetails.setText(MessageManager
1173 .getString("label.sequence_details") + "...");
1174 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1177 public void actionPerformed(ActionEvent e)
1179 sequenceDetails_actionPerformed();
1182 sequenceSelDetails.setText(MessageManager
1183 .getString("label.sequence_details") + "...");
1185 .addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 sequenceSelectionDetails_actionPerformed();
1193 PIDColour.setFocusPainted(false);
1195 .setText(MessageManager.getString("action.remove_group"));
1196 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 unGroupMenuItem_actionPerformed();
1204 createGroupMenuItem.setText(MessageManager
1205 .getString("action.create_group"));
1207 .addActionListener(new java.awt.event.ActionListener()
1210 public void actionPerformed(ActionEvent e)
1212 createGroupMenuItem_actionPerformed();
1216 outline.setText(MessageManager.getString("action.border_colour"));
1217 outline.addActionListener(new java.awt.event.ActionListener()
1220 public void actionPerformed(ActionEvent e)
1222 outline_actionPerformed();
1226 .setText(MessageManager.getString("label.nucleotide"));
1227 nucleotideMenuItem.addActionListener(new ActionListener()
1230 public void actionPerformed(ActionEvent e)
1232 nucleotideMenuItem_actionPerformed();
1235 colourMenu.setText(MessageManager.getString("label.group_colour"));
1236 showBoxes.setText(MessageManager.getString("action.boxes"));
1237 showBoxes.setState(true);
1238 showBoxes.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 showBoxes_actionPerformed();
1246 showText.setText(MessageManager.getString("action.text"));
1247 showText.setState(true);
1248 showText.addActionListener(new ActionListener()
1251 public void actionPerformed(ActionEvent e)
1253 showText_actionPerformed();
1256 showColourText.setText(MessageManager.getString("label.colour_text"));
1257 showColourText.addActionListener(new ActionListener()
1260 public void actionPerformed(ActionEvent e)
1262 showColourText_actionPerformed();
1265 displayNonconserved.setText(MessageManager
1266 .getString("label.show_non_conversed"));
1267 displayNonconserved.setState(true);
1268 displayNonconserved.addActionListener(new ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 showNonconserved_actionPerformed();
1276 editMenu.setText(MessageManager.getString("action.edit"));
1277 cut.setText(MessageManager.getString("action.cut"));
1278 cut.addActionListener(new ActionListener()
1281 public void actionPerformed(ActionEvent e)
1283 cut_actionPerformed();
1286 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1287 upperCase.addActionListener(new ActionListener()
1290 public void actionPerformed(ActionEvent e)
1295 copy.setText(MessageManager.getString("action.copy"));
1296 copy.addActionListener(new ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 copy_actionPerformed();
1304 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1305 lowerCase.addActionListener(new ActionListener()
1308 public void actionPerformed(ActionEvent e)
1313 toggle.setText(MessageManager.getString("label.toggle_case"));
1314 toggle.addActionListener(new ActionListener()
1317 public void actionPerformed(ActionEvent e)
1322 pdbMenu.setText(MessageManager
1323 .getString("label.associate_structure_with_sequence"));
1324 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1325 pdbFromFile.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 pdbFromFile_actionPerformed();
1334 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1335 enterPDB.addActionListener(new ActionListener()
1338 public void actionPerformed(ActionEvent e)
1340 enterPDB_actionPerformed();
1343 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1344 discoverPDB.addActionListener(new ActionListener()
1347 public void actionPerformed(ActionEvent e)
1349 discoverPDB_actionPerformed();
1352 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1354 seqShowAnnotationsMenu.setText(MessageManager
1355 .getString("label.show_annotations"));
1356 seqHideAnnotationsMenu.setText(MessageManager
1357 .getString("label.hide_annotations"));
1358 groupShowAnnotationsMenu.setText(MessageManager
1359 .getString("label.show_annotations"));
1360 groupHideAnnotationsMenu.setText(MessageManager
1361 .getString("label.hide_annotations"));
1362 sequenceFeature.setText(MessageManager
1363 .getString("label.create_sequence_feature"));
1364 sequenceFeature.addActionListener(new ActionListener()
1367 public void actionPerformed(ActionEvent e)
1369 sequenceFeature_actionPerformed();
1372 textColour.setText(MessageManager.getString("label.text_colour"));
1373 textColour.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 textColour_actionPerformed();
1381 jMenu1.setText(MessageManager.getString("label.group"));
1382 structureMenu.setText(MessageManager.getString("label.view_structure"));
1383 structureMenu.addActionListener(new ActionListener()
1386 public void actionPerformed(ActionEvent actionEvent)
1388 SequenceI[] selectedSeqs = new SequenceI[]
1390 if (ap.av.getSelectionGroup() != null)
1392 selectedSeqs = ap.av.getSequenceSelection();
1394 new StructureChooser(selectedSeqs, sequence, ap);
1398 viewStructureMenu.setText(MessageManager
1399 .getString("label.view_structure"));
1400 // colStructureMenu.setText("Colour By Structure");
1401 editSequence.setText(MessageManager.getString("label.edit_sequence")
1403 editSequence.addActionListener(new ActionListener()
1406 public void actionPerformed(ActionEvent actionEvent)
1408 editSequence_actionPerformed(actionEvent);
1411 makeReferenceSeq.setText(MessageManager
1412 .getString("label.mark_as_representative"));
1413 makeReferenceSeq.addActionListener(new ActionListener()
1417 public void actionPerformed(ActionEvent actionEvent)
1419 makeReferenceSeq_actionPerformed(actionEvent);
1423 hideInsertions.setText(MessageManager.getString("label.hide_insertions"));
1424 hideInsertions.addActionListener(new ActionListener()
1428 public void actionPerformed(ActionEvent e)
1430 hideInsertions_actionPerformed(e);
1434 * annotationMenuItem.setText("By Annotation");
1435 * annotationMenuItem.addActionListener(new ActionListener() { public void
1436 * actionPerformed(ActionEvent actionEvent) {
1437 * annotationMenuItem_actionPerformed(actionEvent); } });
1439 groupMenu.add(sequenceSelDetails);
1445 add(hideInsertions);
1447 // annotations configuration panel suppressed for now
1448 // groupMenu.add(chooseAnnotations);
1451 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1452 * (if a selection group is in force).
1454 sequenceMenu.add(seqShowAnnotationsMenu);
1455 sequenceMenu.add(seqHideAnnotationsMenu);
1456 sequenceMenu.add(seqAddReferenceAnnotations);
1457 groupMenu.add(groupShowAnnotationsMenu);
1458 groupMenu.add(groupHideAnnotationsMenu);
1459 groupMenu.add(groupAddReferenceAnnotations);
1460 groupMenu.add(editMenu);
1461 groupMenu.add(outputMenu);
1462 groupMenu.add(sequenceFeature);
1463 groupMenu.add(createGroupMenuItem);
1464 groupMenu.add(unGroupMenuItem);
1465 groupMenu.add(jMenu1);
1466 sequenceMenu.add(sequenceName);
1467 sequenceMenu.add(sequenceDetails);
1468 sequenceMenu.add(makeReferenceSeq);
1469 colourMenu.add(textColour);
1470 colourMenu.add(noColourmenuItem);
1471 colourMenu.add(clustalColour);
1472 colourMenu.add(BLOSUM62Colour);
1473 colourMenu.add(PIDColour);
1474 colourMenu.add(zappoColour);
1475 colourMenu.add(taylorColour);
1476 colourMenu.add(hydrophobicityColour);
1477 colourMenu.add(helixColour);
1478 colourMenu.add(strandColour);
1479 colourMenu.add(turnColour);
1480 colourMenu.add(buriedColour);
1481 colourMenu.add(nucleotideMenuItem);
1482 if (ap.getAlignment().isNucleotide())
1484 // JBPNote - commented since the colourscheme isn't functional
1485 colourMenu.add(purinePyrimidineColour);
1487 colourMenu.add(userDefinedColour);
1489 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1491 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1492 .getUserColourSchemes().keys();
1494 while (userColours.hasMoreElements())
1496 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1497 item.addActionListener(new ActionListener()
1500 public void actionPerformed(ActionEvent evt)
1502 userDefinedColour_actionPerformed(evt);
1505 colourMenu.add(item);
1509 colourMenu.addSeparator();
1510 colourMenu.add(abovePIDColour);
1511 colourMenu.add(conservationMenuItem);
1514 editMenu.add(editSequence);
1515 editMenu.add(upperCase);
1516 editMenu.add(lowerCase);
1517 editMenu.add(toggle);
1518 pdbMenu.add(pdbFromFile);
1519 // JBPNote: These shouldn't be added here - should appear in a generic
1520 // 'apply web service to this sequence menu'
1521 // pdbMenu.add(RNAFold);
1522 // pdbMenu.add(ContraFold);
1523 pdbMenu.add(enterPDB);
1524 pdbMenu.add(discoverPDB);
1525 jMenu1.add(groupName);
1526 jMenu1.add(colourMenu);
1527 jMenu1.add(showBoxes);
1528 jMenu1.add(showText);
1529 jMenu1.add(showColourText);
1530 jMenu1.add(outline);
1531 jMenu1.add(displayNonconserved);
1532 noColourmenuItem.setText(MessageManager.getString("label.none"));
1533 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 noColourmenuItem_actionPerformed();
1542 clustalColour.setText(MessageManager
1543 .getString("label.clustalx_colours"));
1544 clustalColour.addActionListener(new java.awt.event.ActionListener()
1547 public void actionPerformed(ActionEvent e)
1549 clustalColour_actionPerformed();
1552 zappoColour.setText(MessageManager.getString("label.zappo"));
1553 zappoColour.addActionListener(new java.awt.event.ActionListener()
1556 public void actionPerformed(ActionEvent e)
1558 zappoColour_actionPerformed();
1561 taylorColour.setText(MessageManager.getString("label.taylor"));
1562 taylorColour.addActionListener(new java.awt.event.ActionListener()
1565 public void actionPerformed(ActionEvent e)
1567 taylorColour_actionPerformed();
1570 hydrophobicityColour.setText(MessageManager
1571 .getString("label.hydrophobicity"));
1572 hydrophobicityColour
1573 .addActionListener(new java.awt.event.ActionListener()
1576 public void actionPerformed(ActionEvent e)
1578 hydrophobicityColour_actionPerformed();
1581 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1582 helixColour.addActionListener(new java.awt.event.ActionListener()
1585 public void actionPerformed(ActionEvent e)
1587 helixColour_actionPerformed();
1590 strandColour.setText(MessageManager
1591 .getString("label.strand_propensity"));
1592 strandColour.addActionListener(new java.awt.event.ActionListener()
1595 public void actionPerformed(ActionEvent e)
1597 strandColour_actionPerformed();
1600 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1601 turnColour.addActionListener(new java.awt.event.ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 turnColour_actionPerformed();
1609 buriedColour.setText(MessageManager.getString("label.buried_index"));
1610 buriedColour.addActionListener(new java.awt.event.ActionListener()
1613 public void actionPerformed(ActionEvent e)
1615 buriedColour_actionPerformed();
1618 abovePIDColour.setText(MessageManager
1619 .getString("label.above_identity_percentage"));
1620 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1623 public void actionPerformed(ActionEvent e)
1625 abovePIDColour_actionPerformed();
1628 userDefinedColour.setText(MessageManager
1629 .getString("action.user_defined"));
1630 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1633 public void actionPerformed(ActionEvent e)
1635 userDefinedColour_actionPerformed(e);
1639 .setText(MessageManager.getString("label.percentage_identity"));
1640 PIDColour.addActionListener(new java.awt.event.ActionListener()
1643 public void actionPerformed(ActionEvent e)
1645 PIDColour_actionPerformed();
1648 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1649 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1652 public void actionPerformed(ActionEvent e)
1654 BLOSUM62Colour_actionPerformed();
1657 purinePyrimidineColour.setText(MessageManager
1658 .getString("label.purine_pyrimidine"));
1659 purinePyrimidineColour
1660 .addActionListener(new java.awt.event.ActionListener()
1663 public void actionPerformed(ActionEvent e)
1665 purinePyrimidineColour_actionPerformed();
1670 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1671 * public void actionPerformed(ActionEvent e) {
1672 * covariationColour_actionPerformed(); } });
1675 conservationMenuItem.setText(MessageManager
1676 .getString("label.conservation"));
1677 conservationMenuItem
1678 .addActionListener(new java.awt.event.ActionListener()
1681 public void actionPerformed(ActionEvent e)
1683 conservationMenuItem_actionPerformed();
1689 * Check for any annotations on the underlying dataset sequences (for the
1690 * current selection group) which are not 'on the alignment'.If any are found,
1691 * enable the option to add them to the alignment. The criteria for 'on the
1692 * alignment' is finding an alignment annotation on the alignment, matched on
1693 * calcId, label and sequenceRef.
1695 * A tooltip is also constructed that displays the source (calcId) and type
1696 * (label) of the annotations that can be added.
1699 * @param forSequences
1701 protected void configureReferenceAnnotationsMenu(
1702 JMenuItem menuItem, List<SequenceI> forSequences)
1704 menuItem.setEnabled(false);
1707 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1708 * Using TreeMap means calcIds are shown in alphabetical order.
1710 Map<String, String> tipEntries = new TreeMap<String, String>();
1711 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<SequenceI, List<AlignmentAnnotation>>();
1712 AlignmentI al = this.ap.av.getAlignment();
1713 AlignmentUtils.findAddableReferenceAnnotations(forSequences,
1714 tipEntries, candidates, al);
1715 if (!candidates.isEmpty())
1717 StringBuilder tooltip = new StringBuilder(64);
1718 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1721 * Found annotations that could be added. Enable the menu item, and
1722 * configure its tooltip and action.
1724 menuItem.setEnabled(true);
1725 for (String calcId : tipEntries.keySet())
1727 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1729 String tooltipText = JvSwingUtils.wrapTooltip(true,
1730 tooltip.toString());
1731 menuItem.setToolTipText(tooltipText);
1733 menuItem.addActionListener(new ActionListener()
1736 public void actionPerformed(ActionEvent e)
1738 addReferenceAnnotations_actionPerformed(candidates);
1745 * Add annotations to the sequences and to the alignment.
1748 * a map whose keys are sequences on the alignment, and values a list
1749 * of annotations to add to each sequence
1751 protected void addReferenceAnnotations_actionPerformed(
1752 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1754 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1755 final AlignmentI alignment = this.ap.getAlignment();
1756 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1761 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1763 if (!ap.av.getAlignment().hasSeqrep())
1765 // initialise the display flags so the user sees something happen
1766 ap.av.setDisplayReferenceSeq(true);
1767 ap.av.setColourByReferenceSeq(true);
1768 ap.av.getAlignment().setSeqrep(sequence);
1772 if (ap.av.getAlignment().getSeqrep() == sequence)
1774 ap.av.getAlignment().setSeqrep(null);
1778 ap.av.getAlignment().setSeqrep(sequence);
1784 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1786 if (sequence != null)
1788 ColumnSelection cs = ap.av.getColumnSelection();
1791 cs = new ColumnSelection();
1793 cs.hideInsertionsFor(sequence);
1794 ap.av.setColumnSelection(cs);
1798 protected void sequenceSelectionDetails_actionPerformed()
1800 createSequenceDetailsReport(ap.av.getSequenceSelection());
1803 protected void sequenceDetails_actionPerformed()
1805 createSequenceDetailsReport(new SequenceI[]
1809 public void createSequenceDetailsReport(SequenceI[] sequences)
1811 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1812 StringBuffer contents = new StringBuffer();
1813 for (SequenceI seq : sequences)
1815 contents.append("<p><h2>"
1818 "label.create_sequence_details_report_annotation_for",
1820 { seq.getDisplayId(true) }) + "</h2></p><p>");
1821 new SequenceAnnotationReport(null)
1822 .createSequenceAnnotationReport(
1828 (ap.getSeqPanel().seqCanvas.fr != null) ? ap
1829 .getSeqPanel().seqCanvas.fr
1832 contents.append("</p>");
1834 cap.setText("<html>" + contents.toString() + "</html>");
1836 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
1837 "label.sequence_details_for",
1838 (sequences.length == 1 ? new Object[]
1839 { sequences[0].getDisplayId(true) } : new Object[]
1840 { MessageManager.getString("label.selection") })), 500, 400);
1844 protected void showNonconserved_actionPerformed()
1846 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1851 * call to refresh view after settings change
1855 ap.updateAnnotation();
1856 ap.paintAlignment(true);
1858 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1867 protected void clustalColour_actionPerformed()
1869 SequenceGroup sg = getGroup();
1870 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1880 protected void zappoColour_actionPerformed()
1882 getGroup().cs = new ZappoColourScheme();
1892 protected void taylorColour_actionPerformed()
1894 getGroup().cs = new TaylorColourScheme();
1904 protected void hydrophobicityColour_actionPerformed()
1906 getGroup().cs = new HydrophobicColourScheme();
1916 protected void helixColour_actionPerformed()
1918 getGroup().cs = new HelixColourScheme();
1928 protected void strandColour_actionPerformed()
1930 getGroup().cs = new StrandColourScheme();
1940 protected void turnColour_actionPerformed()
1942 getGroup().cs = new TurnColourScheme();
1952 protected void buriedColour_actionPerformed()
1954 getGroup().cs = new BuriedColourScheme();
1964 public void nucleotideMenuItem_actionPerformed()
1966 getGroup().cs = new NucleotideColourScheme();
1970 protected void purinePyrimidineColour_actionPerformed()
1972 getGroup().cs = new PurinePyrimidineColourScheme();
1977 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1978 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1986 protected void abovePIDColour_actionPerformed()
1988 SequenceGroup sg = getGroup();
1994 if (abovePIDColour.isSelected())
1996 sg.cs.setConsensus(AAFrequency.calculate(
1997 sg.getSequences(ap.av.getHiddenRepSequences()),
1998 sg.getStartRes(), sg.getEndRes() + 1));
2000 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
2003 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
2005 SliderPanel.showPIDSlider();
2008 // remove PIDColouring
2010 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
2022 protected void userDefinedColour_actionPerformed(ActionEvent e)
2024 SequenceGroup sg = getGroup();
2026 if (e.getSource().equals(userDefinedColour))
2028 new UserDefinedColours(ap, sg);
2032 UserColourScheme udc = (UserColourScheme) UserDefinedColours
2033 .getUserColourSchemes().get(e.getActionCommand());
2041 * Open a panel where the user can choose which types of sequence annotation
2046 protected void chooseAnnotations_actionPerformed(ActionEvent e)
2048 // todo correct way to guard against opening a duplicate panel?
2049 new AnnotationChooser(ap);
2058 protected void PIDColour_actionPerformed()
2060 SequenceGroup sg = getGroup();
2061 sg.cs = new PIDColourScheme();
2062 sg.cs.setConsensus(AAFrequency.calculate(
2063 sg.getSequences(ap.av.getHiddenRepSequences()),
2064 sg.getStartRes(), sg.getEndRes() + 1));
2074 protected void BLOSUM62Colour_actionPerformed()
2076 SequenceGroup sg = getGroup();
2078 sg.cs = new Blosum62ColourScheme();
2080 sg.cs.setConsensus(AAFrequency.calculate(
2081 sg.getSequences(ap.av.getHiddenRepSequences()),
2082 sg.getStartRes(), sg.getEndRes() + 1));
2093 protected void noColourmenuItem_actionPerformed()
2095 getGroup().cs = null;
2105 protected void conservationMenuItem_actionPerformed()
2107 SequenceGroup sg = getGroup();
2113 if (conservationMenuItem.isSelected())
2115 // JBPNote: Conservation name shouldn't be i18n translated
2116 Conservation c = new Conservation("Group",
2117 ResidueProperties.propHash, 3, sg.getSequences(ap.av
2118 .getHiddenRepSequences()), sg.getStartRes(),
2119 sg.getEndRes() + 1);
2122 c.verdict(false, ap.av.getConsPercGaps());
2124 sg.cs.setConservation(c);
2126 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
2127 SliderPanel.showConservationSlider();
2130 // remove ConservationColouring
2132 sg.cs.setConservation(null);
2138 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
2140 SequenceGroup sg = getGroup();
2146 AnnotationColourGradient acg = new AnnotationColourGradient(
2147 sequence.getAnnotation()[0], null,
2148 AnnotationColourGradient.NO_THRESHOLD);
2150 acg.setPredefinedColours(true);
2162 protected void groupName_actionPerformed()
2165 SequenceGroup sg = getGroup();
2166 EditNameDialog dialog = new EditNameDialog(sg.getName(),
2167 sg.getDescription(), " "
2168 + MessageManager.getString("label.group_name") + " ",
2169 MessageManager.getString("label.group_description") + " ",
2170 MessageManager.getString("label.edit_group_name_description"),
2178 sg.setName(dialog.getName());
2179 sg.setDescription(dialog.getDescription());
2184 * Get selection group - adding it to the alignment if necessary.
2186 * @return sequence group to operate on
2188 SequenceGroup getGroup()
2190 SequenceGroup sg = ap.av.getSelectionGroup();
2191 // this method won't add a new group if it already exists
2194 ap.av.getAlignment().addGroup(sg);
2206 void sequenceName_actionPerformed()
2208 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2209 sequence.getDescription(),
2210 " " + MessageManager.getString("label.sequence_name")
2212 MessageManager.getString("label.sequence_description") + " ",
2214 .getString("label.edit_sequence_name_description"),
2222 if (dialog.getName() != null)
2224 if (dialog.getName().indexOf(" ") > -1)
2230 .getString("label.spaces_converted_to_backslashes"),
2232 .getString("label.no_spaces_allowed_sequence_name"),
2233 JOptionPane.WARNING_MESSAGE);
2236 sequence.setName(dialog.getName().replace(' ', '_'));
2237 ap.paintAlignment(false);
2240 sequence.setDescription(dialog.getDescription());
2242 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2253 void unGroupMenuItem_actionPerformed()
2255 SequenceGroup sg = ap.av.getSelectionGroup();
2256 ap.av.getAlignment().deleteGroup(sg);
2257 ap.av.setSelectionGroup(null);
2261 void createGroupMenuItem_actionPerformed()
2263 getGroup(); // implicitly creates group - note - should apply defaults / use
2264 // standard alignment window logic for this
2274 protected void outline_actionPerformed()
2276 SequenceGroup sg = getGroup();
2277 Color col = JColorChooser.showDialog(this,
2278 MessageManager.getString("label.select_outline_colour"),
2283 sg.setOutlineColour(col);
2295 public void showBoxes_actionPerformed()
2297 getGroup().setDisplayBoxes(showBoxes.isSelected());
2307 public void showText_actionPerformed()
2309 getGroup().setDisplayText(showText.isSelected());
2319 public void showColourText_actionPerformed()
2321 getGroup().setColourText(showColourText.isSelected());
2325 public void showLink(String url)
2329 jalview.util.BrowserLauncher.openURL(url);
2330 } catch (Exception ex)
2332 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2333 MessageManager.getString("label.web_browser_not_found_unix"),
2334 MessageManager.getString("label.web_browser_not_found"),
2335 JOptionPane.WARNING_MESSAGE);
2337 ex.printStackTrace();
2341 void hideSequences(boolean representGroup)
2343 SequenceGroup sg = ap.av.getSelectionGroup();
2344 if (sg == null || sg.getSize() < 1)
2346 ap.av.hideSequence(new SequenceI[]
2351 ap.av.setSelectionGroup(null);
2355 ap.av.hideRepSequences(sequence, sg);
2360 int gsize = sg.getSize();
2361 SequenceI[] hseqs = sg.getSequences().toArray(new SequenceI[gsize]);
2363 ap.av.hideSequence(hseqs);
2364 // refresh(); TODO: ? needed ?
2365 ap.av.sendSelection();
2368 public void copy_actionPerformed()
2370 ap.alignFrame.copy_actionPerformed(null);
2373 public void cut_actionPerformed()
2375 ap.alignFrame.cut_actionPerformed(null);
2378 void changeCase(ActionEvent e)
2380 Object source = e.getSource();
2381 SequenceGroup sg = ap.av.getSelectionGroup();
2385 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
2387 sg.getEndRes() + 1);
2392 if (source == toggle)
2394 description = MessageManager.getString("label.toggle_case");
2395 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2397 else if (source == upperCase)
2399 description = MessageManager.getString("label.to_upper_case");
2400 caseChange = ChangeCaseCommand.TO_UPPER;
2404 description = MessageManager.getString("label.to_lower_case");
2405 caseChange = ChangeCaseCommand.TO_LOWER;
2408 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2409 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2410 startEnd, caseChange);
2412 ap.alignFrame.addHistoryItem(caseCommand);
2414 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2420 public void outputText_actionPerformed(ActionEvent e)
2422 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2423 cap.setForInput(null);
2424 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2425 "label.alignment_output_command", new Object[]
2426 { e.getActionCommand() }), 600, 500);
2428 String[] omitHidden = null;
2430 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2431 // or we simply trust the user wants
2432 // wysiwig behaviour
2434 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2438 public void pdbFromFile_actionPerformed()
2440 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2441 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2442 chooser.setFileView(new jalview.io.JalviewFileView());
2443 chooser.setDialogTitle(MessageManager.formatMessage(
2444 "label.select_pdb_file_for", new Object[]
2445 { sequence.getDisplayId(false) }));
2446 chooser.setToolTipText(MessageManager.formatMessage(
2447 "label.load_pdb_file_associate_with_sequence", new Object[]
2448 { sequence.getDisplayId(false) }));
2450 int value = chooser.showOpenDialog(null);
2452 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2454 String choice = chooser.getSelectedFile().getPath();
2455 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2456 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2457 jalview.io.AppletFormatAdapter.FILE, sequence, true,
2464 public void enterPDB_actionPerformed()
2466 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2467 MessageManager.getString("label.enter_pdb_id"),
2468 MessageManager.getString("label.enter_pdb_id"),
2469 JOptionPane.QUESTION_MESSAGE);
2471 if (id != null && id.length() > 0)
2473 PDBEntry entry = new PDBEntry();
2474 entry.setId(id.toUpperCase());
2475 sequence.getDatasetSequence().addPDBId(entry);
2479 public void discoverPDB_actionPerformed()
2482 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2484 : ap.av.getSequenceSelection());
2485 Thread discpdb = new Thread(new Runnable()
2491 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2492 .fetchDBRefs(false);
2499 public void sequenceFeature_actionPerformed()
2501 SequenceGroup sg = ap.av.getSelectionGroup();
2507 int rsize = 0, gSize = sg.getSize();
2508 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2509 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2511 for (int i = 0; i < gSize; i++)
2513 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2514 int end = sg.findEndRes(sg.getSequenceAt(i));
2517 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2518 features[rsize] = new SequenceFeature(null, null, null, start, end,
2523 rseqs = new SequenceI[rsize];
2524 tfeatures = new SequenceFeature[rsize];
2525 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2526 System.arraycopy(features, 0, tfeatures, 0, rsize);
2527 features = tfeatures;
2529 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2530 features, true, ap))
2532 ap.alignFrame.setShowSeqFeatures(true);
2533 ap.highlightSearchResults(null);
2537 public void textColour_actionPerformed()
2539 SequenceGroup sg = getGroup();
2542 new TextColourChooser().chooseColour(ap, sg);
2546 public void colourByStructure(String pdbid)
2548 Annotation[] anots = ap.av.getStructureSelectionManager()
2549 .colourSequenceFromStructure(sequence, pdbid);
2551 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2552 "Coloured by " + pdbid, anots);
2554 ap.av.getAlignment().addAnnotation(an);
2555 an.createSequenceMapping(sequence, 0, true);
2556 // an.adjustForAlignment();
2557 ap.av.getAlignment().setAnnotationIndex(an, 0);
2559 ap.adjustAnnotationHeight();
2561 sequence.addAlignmentAnnotation(an);
2565 public void editSequence_actionPerformed(ActionEvent actionEvent)
2567 SequenceGroup sg = ap.av.getSelectionGroup();
2571 if (sequence == null)
2573 sequence = sg.getSequenceAt(0);
2576 EditNameDialog dialog = new EditNameDialog(
2577 sequence.getSequenceAsString(sg.getStartRes(),
2578 sg.getEndRes() + 1), null,
2579 MessageManager.getString("label.edit_sequence"), null,
2580 MessageManager.getString("label.edit_sequence"),
2585 EditCommand editCommand = new EditCommand(
2586 MessageManager.getString("label.edit_sequences"),
2587 Action.REPLACE, dialog.getName().replace(' ',
2588 ap.av.getGapCharacter()),
2589 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2590 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2592 ap.alignFrame.addHistoryItem(editCommand);
2594 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()