2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
23 import jalview.analysis.AAFrequency;
24 import jalview.analysis.AlignmentAnnotationUtils;
25 import jalview.analysis.AlignmentUtils;
26 import jalview.analysis.Conservation;
27 import jalview.bin.Cache;
28 import jalview.commands.ChangeCaseCommand;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.datamodel.AlignmentAnnotation;
32 import jalview.datamodel.AlignmentI;
33 import jalview.datamodel.Annotation;
34 import jalview.datamodel.DBRefEntry;
35 import jalview.datamodel.HiddenColumns;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.gui.ColourMenuHelper.ColourChangeListener;
41 import jalview.io.FileFormatI;
42 import jalview.io.FileFormats;
43 import jalview.io.FormatAdapter;
44 import jalview.io.SequenceAnnotationReport;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.ColourSchemeI;
47 import jalview.schemes.ColourSchemes;
48 import jalview.schemes.PIDColourScheme;
49 import jalview.schemes.ResidueColourScheme;
50 import jalview.util.GroupUrlLink;
51 import jalview.util.GroupUrlLink.UrlStringTooLongException;
52 import jalview.util.MessageManager;
53 import jalview.util.StringUtils;
54 import jalview.util.UrlLink;
56 import java.awt.Color;
57 import java.awt.event.ActionEvent;
58 import java.awt.event.ActionListener;
59 import java.util.ArrayList;
60 import java.util.Arrays;
61 import java.util.BitSet;
62 import java.util.Collection;
63 import java.util.Collections;
64 import java.util.Hashtable;
65 import java.util.LinkedHashMap;
66 import java.util.List;
68 import java.util.SortedMap;
69 import java.util.TreeMap;
70 import java.util.Vector;
72 import javax.swing.ButtonGroup;
73 import javax.swing.JCheckBoxMenuItem;
74 import javax.swing.JColorChooser;
75 import javax.swing.JMenu;
76 import javax.swing.JMenuItem;
77 import javax.swing.JPopupMenu;
78 import javax.swing.JRadioButtonMenuItem;
84 * @version $Revision: 1.118 $
86 public class PopupMenu extends JPopupMenu implements ColourChangeListener
88 JMenu groupMenu = new JMenu();
90 JMenuItem groupName = new JMenuItem();
92 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
94 protected JMenuItem modifyPID = new JMenuItem();
96 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
98 protected JRadioButtonMenuItem annotationColour;
100 protected JMenuItem modifyConservation = new JMenuItem();
104 JMenu sequenceMenu = new JMenu();
106 JMenuItem sequenceName = new JMenuItem();
108 JMenuItem sequenceDetails = new JMenuItem();
110 JMenuItem sequenceSelDetails = new JMenuItem();
112 JMenuItem makeReferenceSeq = new JMenuItem();
114 JMenuItem chooseAnnotations = new JMenuItem();
118 JMenuItem createGroupMenuItem = new JMenuItem();
120 JMenuItem unGroupMenuItem = new JMenuItem();
122 JMenuItem outline = new JMenuItem();
124 JMenu colourMenu = new JMenu();
126 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
128 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
130 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
132 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
134 JMenu editMenu = new JMenu();
136 JMenuItem cut = new JMenuItem();
138 JMenuItem copy = new JMenuItem();
140 JMenuItem upperCase = new JMenuItem();
142 JMenuItem lowerCase = new JMenuItem();
144 JMenuItem toggle = new JMenuItem();
146 JMenu pdbMenu = new JMenu();
148 JMenu outputMenu = new JMenu();
150 JMenu seqShowAnnotationsMenu = new JMenu();
152 JMenu seqHideAnnotationsMenu = new JMenu();
154 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
155 MessageManager.getString("label.add_reference_annotations"));
157 JMenu groupShowAnnotationsMenu = new JMenu();
159 JMenu groupHideAnnotationsMenu = new JMenu();
161 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
162 MessageManager.getString("label.add_reference_annotations"));
164 JMenuItem sequenceFeature = new JMenuItem();
166 JMenuItem textColour = new JMenuItem();
168 JMenu jMenu1 = new JMenu();
170 JMenuItem pdbStructureDialog = new JMenuItem();
172 JMenu rnaStructureMenu = new JMenu();
174 JMenuItem editSequence = new JMenuItem();
176 JMenu groupLinksMenu;
178 JMenuItem hideInsertions = new JMenuItem();
181 * Creates a new PopupMenu object.
186 * non-positional features (for seq not null), or positional features
187 * at residue (for seq equal to null)
189 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
190 List<SequenceFeature> features)
192 this(ap, seq, features, null);
200 * the sequence under the cursor if in the Id panel, null if in the
203 * non-positional features if in the Id panel, features at the
204 * clicked residue if in the sequence panel
207 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
208 List<SequenceFeature> features, List<String> groupLinks)
210 // /////////////////////////////////////////////////////////
211 // If this is activated from the sequence panel, the user may want to
212 // edit or annotate a particular residue. Therefore display the residue menu
214 // If from the IDPanel, we must display the sequence menu
215 // ////////////////////////////////////////////////////////
216 this.ap = alignPanel;
219 for (String ff : FileFormats.getInstance().getWritableFormats(true))
221 JMenuItem item = new JMenuItem(ff);
223 item.addActionListener(new ActionListener()
226 public void actionPerformed(ActionEvent e)
228 outputText_actionPerformed(e);
232 outputMenu.add(item);
236 * Build menus for annotation types that may be shown or hidden, and for
237 * 'reference annotations' that may be added to the alignment. First for the
238 * currently selected sequence (if there is one):
240 final List<SequenceI> selectedSequence = (seq == null
241 ? Collections.<SequenceI> emptyList()
242 : Arrays.asList(seq));
243 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
244 seqHideAnnotationsMenu, selectedSequence);
245 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
249 * And repeat for the current selection group (if there is one):
251 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
252 ? Collections.<SequenceI> emptyList()
253 : alignPanel.av.getSelectionGroup().getSequences());
254 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
255 groupHideAnnotationsMenu, selectedGroup);
256 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
262 } catch (Exception e)
270 sequenceMenu.setText(sequence.getName());
271 if (seq == alignPanel.av.getAlignment().getSeqrep())
273 makeReferenceSeq.setText(
274 MessageManager.getString("action.unmark_as_reference"));
278 makeReferenceSeq.setText(
279 MessageManager.getString("action.set_as_reference"));
282 if (!alignPanel.av.getAlignment().isNucleotide())
284 remove(rnaStructureMenu);
288 int origCount = rnaStructureMenu.getItemCount();
290 * add menu items to 2D-render any alignment or sequence secondary
291 * structure annotation
293 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
294 .getAlignmentAnnotation();
297 for (final AlignmentAnnotation aa : aas)
299 if (aa.isValidStruc() && aa.sequenceRef == null)
302 * valid alignment RNA secondary structure annotation
304 menuItem = new JMenuItem();
305 menuItem.setText(MessageManager.formatMessage(
306 "label.2d_rna_structure_line", new Object[]
308 menuItem.addActionListener(new ActionListener()
311 public void actionPerformed(ActionEvent e)
313 new AppVarna(seq, aa, alignPanel);
316 rnaStructureMenu.add(menuItem);
321 if (seq.getAnnotation() != null)
323 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
324 for (final AlignmentAnnotation aa : seqAnns)
326 if (aa.isValidStruc())
329 * valid sequence RNA secondary structure annotation
331 // TODO: make rnastrucF a bit more nice
332 menuItem = new JMenuItem();
333 menuItem.setText(MessageManager.formatMessage(
334 "label.2d_rna_sequence_name", new Object[]
336 menuItem.addActionListener(new ActionListener()
339 public void actionPerformed(ActionEvent e)
341 // TODO: VARNA does'nt print gaps in the sequence
342 new AppVarna(seq, aa, alignPanel);
345 rnaStructureMenu.add(menuItem);
349 if (rnaStructureMenu.getItemCount() == origCount)
351 remove(rnaStructureMenu);
355 menuItem = new JMenuItem(
356 MessageManager.getString("action.hide_sequences"));
357 menuItem.addActionListener(new ActionListener()
360 public void actionPerformed(ActionEvent e)
362 hideSequences(false);
367 if (alignPanel.av.getSelectionGroup() != null
368 && alignPanel.av.getSelectionGroup().getSize() > 1)
370 menuItem = new JMenuItem(MessageManager
371 .formatMessage("label.represent_group_with", new Object[]
373 menuItem.addActionListener(new ActionListener()
376 public void actionPerformed(ActionEvent e)
381 sequenceMenu.add(menuItem);
384 if (alignPanel.av.hasHiddenRows())
386 final int index = alignPanel.av.getAlignment().findIndex(seq);
388 if (alignPanel.av.adjustForHiddenSeqs(index)
389 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
391 menuItem = new JMenuItem(
392 MessageManager.getString("action.reveal_sequences"));
393 menuItem.addActionListener(new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 alignPanel.av.showSequence(index);
399 if (alignPanel.overviewPanel != null)
401 alignPanel.overviewPanel.updateOverviewImage();
412 * - in the IdPanel (seq not null) if any sequence is hidden
413 * - in the IdPanel or SeqPanel if all sequences are hidden (seq is null)
415 if (alignPanel.av.hasHiddenRows())
417 boolean addOption = seq != null;
418 if (!addOption && alignPanel.av.getAlignment().getHeight() == 0)
424 menuItem = new JMenuItem(
425 MessageManager.getString("action.reveal_all"));
426 menuItem.addActionListener(new ActionListener()
429 public void actionPerformed(ActionEvent e)
431 alignPanel.av.showAllHiddenSeqs();
432 if (alignPanel.overviewPanel != null)
434 alignPanel.overviewPanel.updateOverviewImage();
442 SequenceGroup sg = alignPanel.av.getSelectionGroup();
443 boolean isDefinedGroup = (sg != null)
444 ? alignPanel.av.getAlignment().getGroups().contains(sg)
447 if (sg != null && sg.getSize() > 0)
449 groupName.setText(MessageManager
450 .getString("label.edit_name_and_description_current_group"));
452 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
454 conservationMenuItem.setEnabled(!sg.isNucleotide());
458 if (sg.cs.conservationApplied())
460 conservationMenuItem.setSelected(true);
462 if (sg.cs.getThreshold() > 0)
464 abovePIDColour.setSelected(true);
467 modifyConservation.setEnabled(conservationMenuItem.isSelected());
468 modifyPID.setEnabled(abovePIDColour.isSelected());
469 displayNonconserved.setSelected(sg.getShowNonconserved());
470 showText.setSelected(sg.getDisplayText());
471 showColourText.setSelected(sg.getColourText());
472 showBoxes.setSelected(sg.getDisplayBoxes());
473 // add any groupURLs to the groupURL submenu and make it visible
474 if (groupLinks != null && groupLinks.size() > 0)
476 buildGroupURLMenu(sg, groupLinks);
478 // Add a 'show all structures' for the current selection
479 Hashtable<String, PDBEntry> pdbe = new Hashtable<>(), reppdb = new Hashtable<>();
481 SequenceI sqass = null;
482 for (SequenceI sq : alignPanel.av.getSequenceSelection())
484 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
485 if (pes != null && pes.size() > 0)
487 reppdb.put(pes.get(0).getId(), pes.get(0));
488 for (PDBEntry pe : pes)
490 pdbe.put(pe.getId(), pe);
500 final PDBEntry[] pe = pdbe.values()
501 .toArray(new PDBEntry[pdbe.size()]),
502 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
503 final JMenuItem gpdbview, rpdbview;
508 groupMenu.setVisible(false);
509 editMenu.setVisible(false);
514 createGroupMenuItem.setVisible(true);
515 unGroupMenuItem.setVisible(false);
516 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
520 createGroupMenuItem.setVisible(false);
521 unGroupMenuItem.setVisible(true);
522 jMenu1.setText(MessageManager.getString("action.edit_group"));
527 sequenceMenu.setVisible(false);
528 pdbStructureDialog.setVisible(false);
529 rnaStructureMenu.setVisible(false);
532 addLinks(seq, features);
536 addFeatureDetails(features);
541 * Add a link to show feature details for each sequence feature
545 protected void addFeatureDetails(List<SequenceFeature> features)
547 if (features == null || features.isEmpty())
551 JMenu details = new JMenu(
552 MessageManager.getString("label.feature_details"));
555 for (final SequenceFeature sf : features)
557 int start = sf.getBegin();
558 int end = sf.getEnd();
562 desc = String.format("%s %d", sf.getType(), start);
566 desc = String.format("%s %d-%d", sf.getType(), start, end);
568 String tooltip = desc;
569 String description = sf.getDescription();
570 if (description != null)
572 description = StringUtils.stripHtmlTags(description);
573 if (description.length() > 12)
575 desc = desc + " " + description.substring(0, 12) + "..";
579 desc = desc + " " + description;
581 tooltip = tooltip + " " + description;
583 if (sf.getFeatureGroup() != null)
585 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
587 JMenuItem item = new JMenuItem(desc);
588 item.setToolTipText(tooltip);
589 item.addActionListener(new ActionListener()
592 public void actionPerformed(ActionEvent e)
594 showFeatureDetails(sf);
602 * Opens a panel showing a text report of feature dteails
606 protected void showFeatureDetails(SequenceFeature sf)
608 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
609 // it appears Java's CSS does not support border-collaps :-(
610 cap.addStylesheetRule("table { border-collapse: collapse;}");
611 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
612 cap.setText(sf.getDetailsReport());
614 Desktop.addInternalFrame(cap,
615 MessageManager.getString("label.feature_details"), 500, 500);
619 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
620 * When seq is not null, these are links for the sequence id, which may be to
621 * external web sites for the sequence accession, and/or links embedded in
622 * non-positional features. When seq is null, only links embedded in the
623 * provided features are added.
628 void addLinks(final SequenceI seq, List<SequenceFeature> features)
630 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
632 List<String> nlinks = null;
635 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
639 nlinks = new ArrayList<>();
642 if (features != null)
644 for (SequenceFeature sf : features)
646 if (sf.links != null)
648 for (String link : sf.links)
656 Map<String, List<String>> linkset = new LinkedHashMap<>();
658 for (String link : nlinks)
660 UrlLink urlLink = null;
663 urlLink = new UrlLink(link);
664 } catch (Exception foo)
666 Cache.log.error("Exception for URLLink '" + link + "'", foo);
670 if (!urlLink.isValid())
672 Cache.log.error(urlLink.getInvalidMessage());
676 urlLink.createLinksFromSeq(seq, linkset);
679 addshowLinks(linkMenu, linkset.values());
681 // only add link menu if it has entries
682 if (linkMenu.getItemCount() > 0)
684 if (sequence != null)
686 sequenceMenu.add(linkMenu);
696 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
697 * "All" is added first, followed by a separator. Then add any annotation
698 * types associated with the current selection. Separate menus are built for
699 * the selected sequence group (if any), and the selected sequence.
701 * Some annotation rows are always rendered together - these can be identified
702 * by a common graphGroup property > -1. Only one of each group will be marked
703 * as visible (to avoid duplication of the display). For such groups we add a
704 * composite type name, e.g.
706 * IUPredWS (Long), IUPredWS (Short)
710 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
711 List<SequenceI> forSequences)
713 showMenu.removeAll();
714 hideMenu.removeAll();
716 final List<String> all = Arrays
718 { MessageManager.getString("label.all") });
719 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
721 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
723 showMenu.addSeparator();
724 hideMenu.addSeparator();
726 final AlignmentAnnotation[] annotations = ap.getAlignment()
727 .getAlignmentAnnotation();
730 * Find shown/hidden annotations types, distinguished by source (calcId),
731 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
732 * the insertion order, which is the order of the annotations on the
735 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
736 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
737 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
738 AlignmentAnnotationUtils.asList(annotations), forSequences);
740 for (String calcId : hiddenTypes.keySet())
742 for (List<String> type : hiddenTypes.get(calcId))
744 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
748 // grey out 'show annotations' if none are hidden
749 showMenu.setEnabled(!hiddenTypes.isEmpty());
751 for (String calcId : shownTypes.keySet())
753 for (List<String> type : shownTypes.get(calcId))
755 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
759 // grey out 'hide annotations' if none are shown
760 hideMenu.setEnabled(!shownTypes.isEmpty());
764 * Returns a list of sequences - either the current selection group (if there
765 * is one), else the specified single sequence.
770 protected List<SequenceI> getSequenceScope(SequenceI seq)
772 List<SequenceI> forSequences = null;
773 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
774 if (selectionGroup != null && selectionGroup.getSize() > 0)
776 forSequences = selectionGroup.getSequences();
780 forSequences = seq == null ? Collections.<SequenceI> emptyList()
781 : Arrays.asList(seq);
787 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
790 * @param showOrHideMenu
792 * @param forSequences
793 * the sequences whose annotations may be shown or hidden
798 * if true this is a special label meaning 'All'
799 * @param actionIsShow
800 * if true, the select menu item action is to show the annotation
803 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
804 final List<SequenceI> forSequences, String calcId,
805 final List<String> types, final boolean allTypes,
806 final boolean actionIsShow)
808 String label = types.toString(); // [a, b, c]
809 label = label.substring(1, label.length() - 1); // a, b, c
810 final JMenuItem item = new JMenuItem(label);
811 item.setToolTipText(calcId);
812 item.addActionListener(new ActionListener()
815 public void actionPerformed(ActionEvent e)
817 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
818 types, forSequences, allTypes, actionIsShow);
822 showOrHideMenu.add(item);
825 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
828 // TODO: usability: thread off the generation of group url content so root
830 // sequence only URLs
831 // ID/regex match URLs
832 groupLinksMenu = new JMenu(
833 MessageManager.getString("action.group_link"));
834 // three types of url that might be created.
835 JMenu[] linkMenus = new JMenu[] { null,
836 new JMenu(MessageManager.getString("action.ids")),
837 new JMenu(MessageManager.getString("action.sequences")),
838 new JMenu(MessageManager.getString("action.ids_sequences")) };
840 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
841 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
842 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
843 for (int sq = 0; sq < seqs.length; sq++)
846 int start = seqs[sq].findPosition(sg.getStartRes()),
847 end = seqs[sq].findPosition(sg.getEndRes());
848 // just collect ids from dataset sequence
849 // TODO: check if IDs collected from selecton group intersects with the
850 // current selection, too
851 SequenceI sqi = seqs[sq];
852 while (sqi.getDatasetSequence() != null)
854 sqi = sqi.getDatasetSequence();
856 DBRefEntry[] dbr = sqi.getDBRefs();
857 if (dbr != null && dbr.length > 0)
859 for (int d = 0; d < dbr.length; d++)
861 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
862 Object[] sarray = commonDbrefs.get(src);
865 sarray = new Object[2];
866 sarray[0] = new int[] { 0 };
867 sarray[1] = new String[seqs.length];
869 commonDbrefs.put(src, sarray);
872 if (((String[]) sarray[1])[sq] == null)
874 if (!dbr[d].hasMap() || (dbr[d].getMap()
875 .locateMappedRange(start, end) != null))
877 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
878 ((int[]) sarray[0])[0]++;
884 // now create group links for all distinct ID/sequence sets.
885 boolean addMenu = false; // indicates if there are any group links to give
887 for (String link : groupLinks)
889 GroupUrlLink urlLink = null;
892 urlLink = new GroupUrlLink(link);
893 } catch (Exception foo)
895 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
899 if (!urlLink.isValid())
901 Cache.log.error(urlLink.getInvalidMessage());
904 final String label = urlLink.getLabel();
905 boolean usingNames = false;
906 // Now see which parts of the group apply for this URL
907 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
908 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
909 String[] seqstr, ids; // input to makeUrl
912 int numinput = ((int[]) idset[0])[0];
913 String[] allids = ((String[]) idset[1]);
914 seqstr = new String[numinput];
915 ids = new String[numinput];
916 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
918 if (allids[sq] != null)
920 ids[idcount] = allids[sq];
921 seqstr[idcount++] = idandseqs[1][sq];
927 // just use the id/seq set
928 seqstr = idandseqs[1];
932 // and try and make the groupURL!
934 Object[] urlset = null;
937 urlset = urlLink.makeUrlStubs(ids, seqstr,
938 "FromJalview" + System.currentTimeMillis(), false);
939 } catch (UrlStringTooLongException e)
944 int type = urlLink.getGroupURLType() & 3;
945 // first two bits ofurlLink type bitfield are sequenceids and sequences
946 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
947 addshowLink(linkMenus[type],
948 label + (((type & 1) == 1)
949 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
957 groupLinksMenu = new JMenu(
958 MessageManager.getString("action.group_link"));
959 for (int m = 0; m < linkMenus.length; m++)
961 if (linkMenus[m] != null
962 && linkMenus[m].getMenuComponentCount() > 0)
964 groupLinksMenu.add(linkMenus[m]);
968 groupMenu.add(groupLinksMenu);
972 private void addshowLinks(JMenu linkMenu,
973 Collection<List<String>> linkset)
975 for (List<String> linkstrset : linkset)
977 // split linkstr into label and url
978 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
983 * add a show URL menu item to the given linkMenu
987 * - menu label string
991 private void addshowLink(JMenu linkMenu, String label, final String url)
993 JMenuItem item = new JMenuItem(label);
994 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
997 item.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 new Thread(new Runnable()
1019 * add a late bound groupURL item to the given linkMenu
1023 * - menu label string
1024 * @param urlgenerator
1025 * GroupURLLink used to generate URL
1027 * Object array returned from the makeUrlStubs function.
1029 private void addshowLink(JMenu linkMenu, String label,
1030 final GroupUrlLink urlgenerator, final Object[] urlstub)
1032 JMenuItem item = new JMenuItem(label);
1033 item.setToolTipText(MessageManager
1034 .formatMessage("label.open_url_seqs_param", new Object[]
1035 { urlgenerator.getUrl_prefix(),
1036 urlgenerator.getNumberInvolved(urlstub) }));
1037 // TODO: put in info about what is being sent.
1038 item.addActionListener(new ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 new Thread(new Runnable()
1051 showLink(urlgenerator.constructFrom(urlstub));
1052 } catch (UrlStringTooLongException e2)
1070 private void jbInit() throws Exception
1072 groupMenu.setText(MessageManager.getString("label.selection"));
1073 groupName.setText(MessageManager.getString("label.name"));
1074 groupName.addActionListener(new ActionListener()
1077 public void actionPerformed(ActionEvent e)
1079 groupName_actionPerformed();
1082 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1083 sequenceName.setText(
1084 MessageManager.getString("label.edit_name_description"));
1085 sequenceName.addActionListener(new ActionListener()
1088 public void actionPerformed(ActionEvent e)
1090 sequenceName_actionPerformed();
1094 .setText(MessageManager.getString("action.choose_annotations"));
1095 chooseAnnotations.addActionListener(new ActionListener()
1098 public void actionPerformed(ActionEvent e)
1100 chooseAnnotations_actionPerformed(e);
1104 .setText(MessageManager.getString("label.sequence_details"));
1105 sequenceDetails.addActionListener(new ActionListener()
1108 public void actionPerformed(ActionEvent e)
1110 sequenceDetails_actionPerformed();
1114 .setText(MessageManager.getString("label.sequence_details"));
1115 sequenceSelDetails.addActionListener(new ActionListener()
1118 public void actionPerformed(ActionEvent e)
1120 sequenceSelectionDetails_actionPerformed();
1125 .setText(MessageManager.getString("action.remove_group"));
1126 unGroupMenuItem.addActionListener(new ActionListener()
1129 public void actionPerformed(ActionEvent e)
1131 unGroupMenuItem_actionPerformed();
1135 .setText(MessageManager.getString("action.create_group"));
1136 createGroupMenuItem.addActionListener(new ActionListener()
1139 public void actionPerformed(ActionEvent e)
1141 createGroupMenuItem_actionPerformed();
1145 outline.setText(MessageManager.getString("action.border_colour"));
1146 outline.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent e)
1151 outline_actionPerformed();
1154 showBoxes.setText(MessageManager.getString("action.boxes"));
1155 showBoxes.setState(true);
1156 showBoxes.addActionListener(new ActionListener()
1159 public void actionPerformed(ActionEvent e)
1161 showBoxes_actionPerformed();
1164 showText.setText(MessageManager.getString("action.text"));
1165 showText.setState(true);
1166 showText.addActionListener(new ActionListener()
1169 public void actionPerformed(ActionEvent e)
1171 showText_actionPerformed();
1174 showColourText.setText(MessageManager.getString("label.colour_text"));
1175 showColourText.addActionListener(new ActionListener()
1178 public void actionPerformed(ActionEvent e)
1180 showColourText_actionPerformed();
1184 .setText(MessageManager.getString("label.show_non_conserved"));
1185 displayNonconserved.setState(true);
1186 displayNonconserved.addActionListener(new ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 showNonconserved_actionPerformed();
1194 editMenu.setText(MessageManager.getString("action.edit"));
1195 cut.setText(MessageManager.getString("action.cut"));
1196 cut.addActionListener(new ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 cut_actionPerformed();
1204 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1205 upperCase.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent e)
1213 copy.setText(MessageManager.getString("action.copy"));
1214 copy.addActionListener(new ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 copy_actionPerformed();
1222 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1223 lowerCase.addActionListener(new ActionListener()
1226 public void actionPerformed(ActionEvent e)
1231 toggle.setText(MessageManager.getString("label.toggle_case"));
1232 toggle.addActionListener(new ActionListener()
1235 public void actionPerformed(ActionEvent e)
1241 MessageManager.getString("label.out_to_textbox") + "...");
1242 seqShowAnnotationsMenu
1243 .setText(MessageManager.getString("label.show_annotations"));
1244 seqHideAnnotationsMenu
1245 .setText(MessageManager.getString("label.hide_annotations"));
1246 groupShowAnnotationsMenu
1247 .setText(MessageManager.getString("label.show_annotations"));
1248 groupHideAnnotationsMenu
1249 .setText(MessageManager.getString("label.hide_annotations"));
1250 sequenceFeature.setText(
1251 MessageManager.getString("label.create_sequence_feature"));
1252 sequenceFeature.addActionListener(new ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 sequenceFeature_actionPerformed();
1260 jMenu1.setText(MessageManager.getString("label.group"));
1261 pdbStructureDialog.setText(
1262 MessageManager.getString("label.show_pdbstruct_dialog"));
1263 pdbStructureDialog.addActionListener(new ActionListener()
1266 public void actionPerformed(ActionEvent actionEvent)
1268 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1269 if (ap.av.getSelectionGroup() != null)
1271 selectedSeqs = ap.av.getSequenceSelection();
1273 new StructureChooser(selectedSeqs, sequence, ap);
1278 .setText(MessageManager.getString("label.view_rna_structure"));
1280 // colStructureMenu.setText("Colour By Structure");
1281 editSequence.setText(
1282 MessageManager.getString("label.edit_sequence") + "...");
1283 editSequence.addActionListener(new ActionListener()
1286 public void actionPerformed(ActionEvent actionEvent)
1288 editSequence_actionPerformed(actionEvent);
1291 makeReferenceSeq.setText(
1292 MessageManager.getString("label.mark_as_representative"));
1293 makeReferenceSeq.addActionListener(new ActionListener()
1297 public void actionPerformed(ActionEvent actionEvent)
1299 makeReferenceSeq_actionPerformed(actionEvent);
1304 .setText(MessageManager.getString("label.hide_insertions"));
1305 hideInsertions.addActionListener(new ActionListener()
1309 public void actionPerformed(ActionEvent e)
1311 hideInsertions_actionPerformed(e);
1315 groupMenu.add(sequenceSelDetails);
1318 add(rnaStructureMenu);
1319 add(pdbStructureDialog);
1320 if (sequence != null)
1322 add(hideInsertions);
1324 // annotations configuration panel suppressed for now
1325 // groupMenu.add(chooseAnnotations);
1328 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1329 * (if a selection group is in force).
1331 sequenceMenu.add(seqShowAnnotationsMenu);
1332 sequenceMenu.add(seqHideAnnotationsMenu);
1333 sequenceMenu.add(seqAddReferenceAnnotations);
1334 groupMenu.add(groupShowAnnotationsMenu);
1335 groupMenu.add(groupHideAnnotationsMenu);
1336 groupMenu.add(groupAddReferenceAnnotations);
1337 groupMenu.add(editMenu);
1338 groupMenu.add(outputMenu);
1339 groupMenu.add(sequenceFeature);
1340 groupMenu.add(createGroupMenuItem);
1341 groupMenu.add(unGroupMenuItem);
1342 groupMenu.add(jMenu1);
1343 sequenceMenu.add(sequenceName);
1344 sequenceMenu.add(sequenceDetails);
1345 sequenceMenu.add(makeReferenceSeq);
1352 editMenu.add(editSequence);
1353 editMenu.add(upperCase);
1354 editMenu.add(lowerCase);
1355 editMenu.add(toggle);
1356 // JBPNote: These shouldn't be added here - should appear in a generic
1357 // 'apply web service to this sequence menu'
1358 // pdbMenu.add(RNAFold);
1359 // pdbMenu.add(ContraFold);
1360 jMenu1.add(groupName);
1361 jMenu1.add(colourMenu);
1362 jMenu1.add(showBoxes);
1363 jMenu1.add(showText);
1364 jMenu1.add(showColourText);
1365 jMenu1.add(outline);
1366 jMenu1.add(displayNonconserved);
1370 * Constructs the entries for the colour menu
1372 protected void initColourMenu()
1374 colourMenu.setText(MessageManager.getString("label.group_colour"));
1375 textColour.setText(MessageManager.getString("label.text_colour"));
1376 textColour.addActionListener(new ActionListener()
1379 public void actionPerformed(ActionEvent e)
1381 textColour_actionPerformed();
1385 abovePIDColour.setText(
1386 MessageManager.getString("label.above_identity_threshold"));
1387 abovePIDColour.addActionListener(new ActionListener()
1390 public void actionPerformed(ActionEvent e)
1392 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1397 MessageManager.getString("label.modify_identity_threshold"));
1398 modifyPID.addActionListener(new ActionListener()
1401 public void actionPerformed(ActionEvent e)
1403 modifyPID_actionPerformed();
1407 conservationMenuItem
1408 .setText(MessageManager.getString("action.by_conservation"));
1409 conservationMenuItem.addActionListener(new ActionListener()
1412 public void actionPerformed(ActionEvent e)
1414 conservationMenuItem_actionPerformed(
1415 conservationMenuItem.isSelected());
1419 annotationColour = new JRadioButtonMenuItem(
1420 MessageManager.getString("action.by_annotation"));
1421 annotationColour.setName(ResidueColourScheme.ANNOTATION_COLOUR);
1422 annotationColour.setEnabled(false);
1423 annotationColour.setToolTipText(
1424 MessageManager.getString("label.by_annotation_tooltip"));
1426 modifyConservation.setText(MessageManager
1427 .getString("label.modify_conservation_threshold"));
1428 modifyConservation.addActionListener(new ActionListener()
1431 public void actionPerformed(ActionEvent e)
1433 modifyConservation_actionPerformed();
1439 * Builds the group colour sub-menu, including any user-defined colours which
1440 * were loaded at startup or during the Jalview session
1442 protected void buildColourMenu()
1444 SequenceGroup sg = ap.av.getSelectionGroup();
1448 * popup menu with no sequence group scope
1452 colourMenu.removeAll();
1453 colourMenu.add(textColour);
1454 colourMenu.addSeparator();
1456 ButtonGroup bg = ColourMenuHelper.addMenuItems(colourMenu, this, sg,
1458 bg.add(annotationColour);
1459 colourMenu.add(annotationColour);
1461 colourMenu.addSeparator();
1462 colourMenu.add(conservationMenuItem);
1463 colourMenu.add(modifyConservation);
1464 colourMenu.add(abovePIDColour);
1465 colourMenu.add(modifyPID);
1468 protected void modifyConservation_actionPerformed()
1470 SequenceGroup sg = getGroup();
1473 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1474 SliderPanel.showConservationSlider();
1478 protected void modifyPID_actionPerformed()
1480 SequenceGroup sg = getGroup();
1483 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1485 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1486 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1487 SliderPanel.showPIDSlider();
1492 * Check for any annotations on the underlying dataset sequences (for the
1493 * current selection group) which are not 'on the alignment'.If any are found,
1494 * enable the option to add them to the alignment. The criteria for 'on the
1495 * alignment' is finding an alignment annotation on the alignment, matched on
1496 * calcId, label and sequenceRef.
1498 * A tooltip is also constructed that displays the source (calcId) and type
1499 * (label) of the annotations that can be added.
1502 * @param forSequences
1504 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1505 List<SequenceI> forSequences)
1507 menuItem.setEnabled(false);
1510 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1511 * Using TreeMap means calcIds are shown in alphabetical order.
1513 SortedMap<String, String> tipEntries = new TreeMap<>();
1514 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1515 AlignmentI al = this.ap.av.getAlignment();
1516 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1518 if (!candidates.isEmpty())
1520 StringBuilder tooltip = new StringBuilder(64);
1521 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1524 * Found annotations that could be added. Enable the menu item, and
1525 * configure its tooltip and action.
1527 menuItem.setEnabled(true);
1528 for (String calcId : tipEntries.keySet())
1530 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1532 String tooltipText = JvSwingUtils.wrapTooltip(true,
1533 tooltip.toString());
1534 menuItem.setToolTipText(tooltipText);
1536 menuItem.addActionListener(new ActionListener()
1539 public void actionPerformed(ActionEvent e)
1541 addReferenceAnnotations_actionPerformed(candidates);
1548 * Add annotations to the sequences and to the alignment.
1551 * a map whose keys are sequences on the alignment, and values a list
1552 * of annotations to add to each sequence
1554 protected void addReferenceAnnotations_actionPerformed(
1555 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1557 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1558 final AlignmentI alignment = this.ap.getAlignment();
1559 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1564 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1566 if (!ap.av.getAlignment().hasSeqrep())
1568 // initialise the display flags so the user sees something happen
1569 ap.av.setDisplayReferenceSeq(true);
1570 ap.av.setColourByReferenceSeq(true);
1571 ap.av.getAlignment().setSeqrep(sequence);
1575 if (ap.av.getAlignment().getSeqrep() == sequence)
1577 ap.av.getAlignment().setSeqrep(null);
1581 ap.av.getAlignment().setSeqrep(sequence);
1587 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1589 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1590 BitSet inserts = new BitSet();
1592 boolean markedPopup = false;
1593 // mark inserts in current selection
1594 if (ap.av.getSelectionGroup() != null)
1596 // mark just the columns in the selection group to be hidden
1597 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1598 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1600 // now clear columns without gaps
1601 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1607 inserts.and(sq.getInsertionsAsBits());
1609 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1610 ap.av.getSelectionGroup().getEndRes());
1613 // now mark for sequence under popup if we haven't already done it
1614 else if (!markedPopup && sequence != null)
1616 inserts.or(sequence.getInsertionsAsBits());
1618 // and set hidden columns accordingly
1619 hidden.hideColumns(inserts);
1624 protected void sequenceSelectionDetails_actionPerformed()
1626 createSequenceDetailsReport(ap.av.getSequenceSelection());
1629 protected void sequenceDetails_actionPerformed()
1631 createSequenceDetailsReport(new SequenceI[] { sequence });
1634 public void createSequenceDetailsReport(SequenceI[] sequences)
1636 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1637 StringBuilder contents = new StringBuilder(128);
1638 for (SequenceI seq : sequences)
1640 contents.append("<p><h2>" + MessageManager.formatMessage(
1641 "label.create_sequence_details_report_annotation_for",
1643 { seq.getDisplayId(true) }) + "</h2></p><p>");
1644 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1645 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1646 contents.append("</p>");
1648 cap.setText("<html>" + contents.toString() + "</html>");
1650 Desktop.addInternalFrame(cap,
1651 MessageManager.formatMessage("label.sequence_details_for",
1652 (sequences.length == 1 ? new Object[]
1653 { sequences[0].getDisplayId(true) }
1656 .getString("label.selection") })),
1661 protected void showNonconserved_actionPerformed()
1663 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1668 * call to refresh view after settings change
1672 ap.updateAnnotation();
1673 // removed paintAlignment(true) here:
1674 // updateAnnotation calls paintAlignment already, so don't need to call
1677 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1681 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1682 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1692 public void abovePIDColour_actionPerformed(boolean selected)
1694 SequenceGroup sg = getGroup();
1702 sg.cs.setConsensus(AAFrequency.calculate(
1703 sg.getSequences(ap.av.getHiddenRepSequences()),
1704 sg.getStartRes(), sg.getEndRes() + 1));
1706 int threshold = SliderPanel.setPIDSliderSource(ap,
1707 sg.getGroupColourScheme(), getGroup().getName());
1709 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1711 SliderPanel.showPIDSlider();
1714 // remove PIDColouring
1716 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1717 SliderPanel.hidePIDSlider();
1719 modifyPID.setEnabled(selected);
1725 * Open a panel where the user can choose which types of sequence annotation
1730 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1732 // todo correct way to guard against opening a duplicate panel?
1733 new AnnotationChooser(ap);
1742 public void conservationMenuItem_actionPerformed(boolean selected)
1744 SequenceGroup sg = getGroup();
1752 // JBPNote: Conservation name shouldn't be i18n translated
1753 Conservation c = new Conservation("Group",
1754 sg.getSequences(ap.av.getHiddenRepSequences()),
1755 sg.getStartRes(), sg.getEndRes() + 1);
1758 c.verdict(false, ap.av.getConsPercGaps());
1759 sg.cs.setConservation(c);
1761 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1763 SliderPanel.showConservationSlider();
1766 // remove ConservationColouring
1768 sg.cs.setConservation(null);
1769 SliderPanel.hideConservationSlider();
1771 modifyConservation.setEnabled(selected);
1782 protected void groupName_actionPerformed()
1785 SequenceGroup sg = getGroup();
1786 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1787 sg.getDescription(),
1788 " " + MessageManager.getString("label.group_name") + " ",
1789 MessageManager.getString("label.group_description") + " ",
1790 MessageManager.getString("label.edit_group_name_description"),
1798 sg.setName(dialog.getName());
1799 sg.setDescription(dialog.getDescription());
1804 * Get selection group - adding it to the alignment if necessary.
1806 * @return sequence group to operate on
1808 SequenceGroup getGroup()
1810 SequenceGroup sg = ap.av.getSelectionGroup();
1811 // this method won't add a new group if it already exists
1814 ap.av.getAlignment().addGroup(sg);
1826 void sequenceName_actionPerformed()
1828 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1829 sequence.getDescription(),
1830 " " + MessageManager.getString("label.sequence_name")
1832 MessageManager.getString("label.sequence_description") + " ",
1833 MessageManager.getString(
1834 "label.edit_sequence_name_description"),
1842 if (dialog.getName() != null)
1844 if (dialog.getName().indexOf(" ") > -1)
1846 JvOptionPane.showMessageDialog(ap,
1848 .getString("label.spaces_converted_to_backslashes"),
1850 .getString("label.no_spaces_allowed_sequence_name"),
1851 JvOptionPane.WARNING_MESSAGE);
1854 sequence.setName(dialog.getName().replace(' ', '_'));
1855 ap.paintAlignment(false, false);
1858 sequence.setDescription(dialog.getDescription());
1860 ap.av.firePropertyChange("alignment", null,
1861 ap.av.getAlignment().getSequences());
1871 void unGroupMenuItem_actionPerformed()
1873 SequenceGroup sg = ap.av.getSelectionGroup();
1874 ap.av.getAlignment().deleteGroup(sg);
1875 ap.av.setSelectionGroup(null);
1879 void createGroupMenuItem_actionPerformed()
1881 getGroup(); // implicitly creates group - note - should apply defaults / use
1882 // standard alignment window logic for this
1892 protected void outline_actionPerformed()
1894 SequenceGroup sg = getGroup();
1895 Color col = JColorChooser.showDialog(this,
1896 MessageManager.getString("label.select_outline_colour"),
1901 sg.setOutlineColour(col);
1913 public void showBoxes_actionPerformed()
1915 getGroup().setDisplayBoxes(showBoxes.isSelected());
1925 public void showText_actionPerformed()
1927 getGroup().setDisplayText(showText.isSelected());
1937 public void showColourText_actionPerformed()
1939 getGroup().setColourText(showColourText.isSelected());
1943 public void showLink(String url)
1947 jalview.util.BrowserLauncher.openURL(url);
1948 } catch (Exception ex)
1950 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1951 MessageManager.getString("label.web_browser_not_found_unix"),
1952 MessageManager.getString("label.web_browser_not_found"),
1953 JvOptionPane.WARNING_MESSAGE);
1955 ex.printStackTrace();
1959 void hideSequences(boolean representGroup)
1961 ap.av.hideSequences(sequence, representGroup);
1964 public void copy_actionPerformed()
1966 ap.alignFrame.copy_actionPerformed(null);
1969 public void cut_actionPerformed()
1971 ap.alignFrame.cut_actionPerformed(null);
1974 void changeCase(ActionEvent e)
1976 Object source = e.getSource();
1977 SequenceGroup sg = ap.av.getSelectionGroup();
1981 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1982 sg.getStartRes(), sg.getEndRes() + 1);
1987 if (source == toggle)
1989 description = MessageManager.getString("label.toggle_case");
1990 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1992 else if (source == upperCase)
1994 description = MessageManager.getString("label.to_upper_case");
1995 caseChange = ChangeCaseCommand.TO_UPPER;
1999 description = MessageManager.getString("label.to_lower_case");
2000 caseChange = ChangeCaseCommand.TO_LOWER;
2003 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2004 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2005 startEnd, caseChange);
2007 ap.alignFrame.addHistoryItem(caseCommand);
2009 ap.av.firePropertyChange("alignment", null,
2010 ap.av.getAlignment().getSequences());
2015 public void outputText_actionPerformed(ActionEvent e)
2017 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2018 cap.setForInput(null);
2019 Desktop.addInternalFrame(cap, MessageManager
2020 .formatMessage("label.alignment_output_command", new Object[]
2021 { e.getActionCommand() }), 600, 500);
2023 String[] omitHidden = null;
2025 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2026 // or we simply trust the user wants
2027 // wysiwig behaviour
2029 FileFormatI fileFormat = FileFormats.getInstance()
2030 .forName(e.getActionCommand());
2032 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2035 public void sequenceFeature_actionPerformed()
2037 SequenceGroup sg = ap.av.getSelectionGroup();
2043 List<SequenceI> seqs = new ArrayList<>();
2044 List<SequenceFeature> features = new ArrayList<>();
2047 * assemble dataset sequences, and template new sequence features,
2048 * for the amend features dialog
2050 int gSize = sg.getSize();
2051 for (int i = 0; i < gSize; i++)
2053 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2054 int end = sg.findEndRes(sg.getSequenceAt(i));
2057 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2058 features.add(new SequenceFeature(null, null, start, end, null));
2063 * an entirely gapped region will generate empty lists of sequence / features
2065 if (!seqs.isEmpty())
2067 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2068 .amendFeatures(seqs, features, true, ap))
2070 ap.alignFrame.setShowSeqFeatures(true);
2071 ap.av.setSearchResults(null); // clear highlighting
2072 ap.repaint(); // draw new/amended features
2077 public void textColour_actionPerformed()
2079 SequenceGroup sg = getGroup();
2082 new TextColourChooser().chooseColour(ap, sg);
2086 public void colourByStructure(String pdbid)
2088 Annotation[] anots = ap.av.getStructureSelectionManager()
2089 .colourSequenceFromStructure(sequence, pdbid);
2091 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2092 "Coloured by " + pdbid, anots);
2094 ap.av.getAlignment().addAnnotation(an);
2095 an.createSequenceMapping(sequence, 0, true);
2096 // an.adjustForAlignment();
2097 ap.av.getAlignment().setAnnotationIndex(an, 0);
2099 ap.adjustAnnotationHeight();
2101 sequence.addAlignmentAnnotation(an);
2105 public void editSequence_actionPerformed(ActionEvent actionEvent)
2107 SequenceGroup sg = ap.av.getSelectionGroup();
2111 if (sequence == null)
2113 sequence = sg.getSequenceAt(0);
2116 EditNameDialog dialog = new EditNameDialog(
2117 sequence.getSequenceAsString(sg.getStartRes(),
2118 sg.getEndRes() + 1),
2119 null, MessageManager.getString("label.edit_sequence"), null,
2120 MessageManager.getString("label.edit_sequence"),
2125 EditCommand editCommand = new EditCommand(
2126 MessageManager.getString("label.edit_sequences"),
2128 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2129 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2130 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2132 ap.alignFrame.addHistoryItem(editCommand);
2134 ap.av.firePropertyChange("alignment", null,
2135 ap.av.getAlignment().getSequences());
2141 * Action on user selecting an item from the colour menu (that does not have
2142 * its bespoke action handler)
2147 public void changeColour_actionPerformed(String colourSchemeName)
2149 SequenceGroup sg = getGroup();
2151 * switch to the chosen colour scheme (or null for None)
2153 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2154 .getColourScheme(colourSchemeName, ap.av, sg,
2155 ap.av.getHiddenRepSequences());
2156 sg.setColourScheme(colourScheme);
2157 if (colourScheme instanceof Blosum62ColourScheme
2158 || colourScheme instanceof PIDColourScheme)
2160 sg.cs.setConsensus(AAFrequency.calculate(
2161 sg.getSequences(ap.av.getHiddenRepSequences()),
2162 sg.getStartRes(), sg.getEndRes() + 1));