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.util.GroupUrlLink;
50 import jalview.util.GroupUrlLink.UrlStringTooLongException;
51 import jalview.util.MessageManager;
52 import jalview.util.StringUtils;
53 import jalview.util.UrlLink;
55 import java.awt.Color;
56 import java.awt.event.ActionEvent;
57 import java.awt.event.ActionListener;
58 import java.util.ArrayList;
59 import java.util.Arrays;
60 import java.util.BitSet;
61 import java.util.Collection;
62 import java.util.Collections;
63 import java.util.Hashtable;
64 import java.util.LinkedHashMap;
65 import java.util.List;
67 import java.util.SortedMap;
68 import java.util.TreeMap;
69 import java.util.Vector;
71 import javax.swing.JCheckBoxMenuItem;
72 import javax.swing.JColorChooser;
73 import javax.swing.JMenu;
74 import javax.swing.JMenuItem;
75 import javax.swing.JPopupMenu;
81 * @version $Revision: 1.118 $
83 public class PopupMenu extends JPopupMenu implements ColourChangeListener
85 JMenu groupMenu = new JMenu();
87 JMenuItem groupName = new JMenuItem();
89 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
91 protected JMenuItem modifyPID = new JMenuItem();
93 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
95 protected JMenuItem modifyConservation = new JMenuItem();
99 JMenu sequenceMenu = new JMenu();
101 JMenuItem sequenceName = new JMenuItem();
103 JMenuItem sequenceDetails = new JMenuItem();
105 JMenuItem sequenceSelDetails = new JMenuItem();
107 JMenuItem makeReferenceSeq = new JMenuItem();
109 JMenuItem chooseAnnotations = new JMenuItem();
113 JMenuItem createGroupMenuItem = new JMenuItem();
115 JMenuItem unGroupMenuItem = new JMenuItem();
117 JMenuItem outline = new JMenuItem();
119 JMenu colourMenu = new JMenu();
121 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
123 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
125 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
127 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
129 JMenu editMenu = new JMenu();
131 JMenuItem cut = new JMenuItem();
133 JMenuItem copy = new JMenuItem();
135 JMenuItem upperCase = new JMenuItem();
137 JMenuItem lowerCase = new JMenuItem();
139 JMenuItem toggle = new JMenuItem();
141 JMenu pdbMenu = new JMenu();
143 JMenu outputMenu = new JMenu();
145 JMenu seqShowAnnotationsMenu = new JMenu();
147 JMenu seqHideAnnotationsMenu = new JMenu();
149 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
150 MessageManager.getString("label.add_reference_annotations"));
152 JMenu groupShowAnnotationsMenu = new JMenu();
154 JMenu groupHideAnnotationsMenu = new JMenu();
156 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
157 MessageManager.getString("label.add_reference_annotations"));
159 JMenuItem sequenceFeature = new JMenuItem();
162 JMenuItem textColour = new JMenuItem();
164 JMenu jMenu1 = new JMenu();
166 JMenuItem pdbStructureDialog = new JMenuItem();
168 JMenu rnaStructureMenu = new JMenu();
170 JMenuItem editSequence = new JMenuItem();
172 JMenu groupLinksMenu;
174 JMenuItem hideInsertions = new JMenuItem();
177 * Creates a new PopupMenu object.
182 * non-positional features (for seq not null), or positional features
183 * at residue (for seq equal to null)
185 public PopupMenu(final AlignmentPanel ap, SequenceI seq,
186 List<SequenceFeature> features)
188 this(ap, seq, features, null);
196 * the sequence under the cursor if in the Id panel, null if in the
199 * non-positional features if in the Id panel, features at the
200 * clicked residue if in the sequence panel
203 public PopupMenu(final AlignmentPanel alignPanel, final SequenceI seq,
204 List<SequenceFeature> features, List<String> groupLinks)
206 // /////////////////////////////////////////////////////////
207 // If this is activated from the sequence panel, the user may want to
208 // edit or annotate a particular residue. Therefore display the residue menu
210 // If from the IDPanel, we must display the sequence menu
211 // ////////////////////////////////////////////////////////
212 this.ap = alignPanel;
215 for (String ff : FileFormats.getInstance().getWritableFormats(true))
217 JMenuItem item = new JMenuItem(ff);
219 item.addActionListener(new ActionListener()
222 public void actionPerformed(ActionEvent e)
224 outputText_actionPerformed(e);
228 outputMenu.add(item);
232 * Build menus for annotation types that may be shown or hidden, and for
233 * 'reference annotations' that may be added to the alignment. First for the
234 * currently selected sequence (if there is one):
236 final List<SequenceI> selectedSequence = (seq == null
237 ? Collections.<SequenceI> emptyList() : Arrays.asList(seq));
239 buildAnnotationTypesMenus(seqShowAnnotationsMenu,
240 seqHideAnnotationsMenu, selectedSequence);
241 configureReferenceAnnotationsMenu(seqAddReferenceAnnotations,
245 * And repeat for the current selection group (if there is one):
247 final List<SequenceI> selectedGroup = (alignPanel.av.getSelectionGroup() == null
248 ? Collections.<SequenceI> emptyList()
249 : alignPanel.av.getSelectionGroup().getSequences());
250 buildAnnotationTypesMenus(groupShowAnnotationsMenu,
251 groupHideAnnotationsMenu, selectedGroup);
252 configureReferenceAnnotationsMenu(groupAddReferenceAnnotations,
258 } catch (Exception e)
266 sequenceMenu.setText(sequence.getName());
267 if (seq == alignPanel.av.getAlignment().getSeqrep())
269 makeReferenceSeq.setText(
270 MessageManager.getString("action.unmark_as_reference"));
274 makeReferenceSeq.setText(
275 MessageManager.getString("action.set_as_reference"));
278 if (!alignPanel.av.getAlignment().isNucleotide())
280 remove(rnaStructureMenu);
284 int origCount = rnaStructureMenu.getItemCount();
286 * add menu items to 2D-render any alignment or sequence secondary
287 * structure annotation
289 AlignmentAnnotation[] aas = alignPanel.av.getAlignment()
290 .getAlignmentAnnotation();
293 for (final AlignmentAnnotation aa : aas)
295 if (aa.isValidStruc() && aa.sequenceRef == null)
298 * valid alignment RNA secondary structure annotation
300 menuItem = new JMenuItem();
301 menuItem.setText(MessageManager.formatMessage(
302 "label.2d_rna_structure_line", new Object[]
304 menuItem.addActionListener(new ActionListener()
307 public void actionPerformed(ActionEvent e)
309 new AppVarna(seq, aa, alignPanel);
312 rnaStructureMenu.add(menuItem);
317 if (seq.getAnnotation() != null)
319 AlignmentAnnotation seqAnns[] = seq.getAnnotation();
320 for (final AlignmentAnnotation aa : seqAnns)
322 if (aa.isValidStruc())
325 * valid sequence RNA secondary structure annotation
327 // TODO: make rnastrucF a bit more nice
328 menuItem = new JMenuItem();
329 menuItem.setText(MessageManager.formatMessage(
330 "label.2d_rna_sequence_name", new Object[]
332 menuItem.addActionListener(new ActionListener()
335 public void actionPerformed(ActionEvent e)
337 // TODO: VARNA does'nt print gaps in the sequence
338 new AppVarna(seq, aa, alignPanel);
341 rnaStructureMenu.add(menuItem);
345 if (rnaStructureMenu.getItemCount() == origCount)
347 remove(rnaStructureMenu);
351 menuItem = new JMenuItem(
352 MessageManager.getString("action.hide_sequences"));
353 menuItem.addActionListener(new ActionListener()
356 public void actionPerformed(ActionEvent e)
358 hideSequences(false);
363 if (alignPanel.av.getSelectionGroup() != null
364 && alignPanel.av.getSelectionGroup().getSize() > 1)
366 menuItem = new JMenuItem(MessageManager
367 .formatMessage("label.represent_group_with", new Object[]
369 menuItem.addActionListener(new ActionListener()
372 public void actionPerformed(ActionEvent e)
377 sequenceMenu.add(menuItem);
380 if (alignPanel.av.hasHiddenRows())
382 final int index = alignPanel.av.getAlignment().findIndex(seq);
384 if (alignPanel.av.adjustForHiddenSeqs(index)
385 - alignPanel.av.adjustForHiddenSeqs(index - 1) > 1)
387 menuItem = new JMenuItem(
388 MessageManager.getString("action.reveal_sequences"));
389 menuItem.addActionListener(new ActionListener()
392 public void actionPerformed(ActionEvent e)
394 alignPanel.av.showSequence(index);
395 if (alignPanel.overviewPanel != null)
397 alignPanel.overviewPanel.updateOverviewImage();
405 // for the case when no sequences are even visible
406 if (alignPanel.av.hasHiddenRows())
409 menuItem = new JMenuItem(
410 MessageManager.getString("action.reveal_all"));
411 menuItem.addActionListener(new ActionListener()
414 public void actionPerformed(ActionEvent e)
416 alignPanel.av.showAllHiddenSeqs();
417 if (alignPanel.overviewPanel != null)
419 alignPanel.overviewPanel.updateOverviewImage();
428 SequenceGroup sg = alignPanel.av.getSelectionGroup();
429 boolean isDefinedGroup = (sg != null)
430 ? alignPanel.av.getAlignment().getGroups().contains(sg)
433 if (sg != null && sg.getSize() > 0)
435 groupName.setText(MessageManager
436 .getString("label.edit_name_and_description_current_group"));
438 ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme());
440 conservationMenuItem.setEnabled(!sg.isNucleotide());
444 if (sg.cs.conservationApplied())
446 conservationMenuItem.setSelected(true);
448 if (sg.cs.getThreshold() > 0)
450 abovePIDColour.setSelected(true);
453 modifyConservation.setEnabled(conservationMenuItem.isSelected());
454 modifyPID.setEnabled(abovePIDColour.isSelected());
455 displayNonconserved.setSelected(sg.getShowNonconserved());
456 showText.setSelected(sg.getDisplayText());
457 showColourText.setSelected(sg.getColourText());
458 showBoxes.setSelected(sg.getDisplayBoxes());
459 // add any groupURLs to the groupURL submenu and make it visible
460 if (groupLinks != null && groupLinks.size() > 0)
462 buildGroupURLMenu(sg, groupLinks);
464 // Add a 'show all structures' for the current selection
465 Hashtable<String, PDBEntry> pdbe = new Hashtable<>();
466 Hashtable<String, PDBEntry> reppdb = new Hashtable<>();
468 SequenceI sqass = null;
469 for (SequenceI sq : alignPanel.av.getSequenceSelection())
471 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
472 if (pes != null && pes.size() > 0)
474 reppdb.put(pes.get(0).getId(), pes.get(0));
475 for (PDBEntry pe : pes)
477 pdbe.put(pe.getId(), pe);
487 final PDBEntry[] pe = pdbe.values()
488 .toArray(new PDBEntry[pdbe.size()]),
489 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
490 final JMenuItem gpdbview, rpdbview;
495 groupMenu.setVisible(false);
496 editMenu.setVisible(false);
501 createGroupMenuItem.setVisible(true);
502 unGroupMenuItem.setVisible(false);
503 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
507 createGroupMenuItem.setVisible(false);
508 unGroupMenuItem.setVisible(true);
509 jMenu1.setText(MessageManager.getString("action.edit_group"));
514 sequenceMenu.setVisible(false);
515 pdbStructureDialog.setVisible(false);
516 rnaStructureMenu.setVisible(false);
519 addLinks(seq, features);
523 addFeatureDetails(features);
528 * Add a link to show feature details for each sequence feature
532 protected void addFeatureDetails(List<SequenceFeature> features)
534 if (features == null || features.isEmpty())
538 JMenu details = new JMenu(
539 MessageManager.getString("label.feature_details"));
542 for (final SequenceFeature sf : features)
544 int start = sf.getBegin();
545 int end = sf.getEnd();
549 desc = String.format("%s %d", sf.getType(), start);
553 desc = String.format("%s %d-%d", sf.getType(), start, end);
555 String tooltip = desc;
556 String description = sf.getDescription();
557 if (description != null)
559 description = StringUtils.stripHtmlTags(description);
560 if (description.length() > 12)
562 desc = desc + " " + description.substring(0, 12) + "..";
566 desc = desc + " " + description;
568 tooltip = tooltip + " " + description;
570 if (sf.getFeatureGroup() != null)
572 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
574 JMenuItem item = new JMenuItem(desc);
575 item.setToolTipText(tooltip);
576 item.addActionListener(new ActionListener()
579 public void actionPerformed(ActionEvent e)
581 showFeatureDetails(sf);
589 * Opens a panel showing a text report of feature dteails
593 protected void showFeatureDetails(SequenceFeature sf)
595 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
596 // it appears Java's CSS does not support border-collaps :-(
597 cap.addStylesheetRule("table { border-collapse: collapse;}");
598 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
599 cap.setText(sf.getDetailsReport());
601 Desktop.addInternalFrame(cap,
602 MessageManager.getString("label.feature_details"), 500, 500);
606 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
607 * When seq is not null, these are links for the sequence id, which may be to
608 * external web sites for the sequence accession, and/or links embedded in
609 * non-positional features. When seq is null, only links embedded in the
610 * provided features are added.
615 void addLinks(final SequenceI seq, List<SequenceFeature> features)
617 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
619 List<String> nlinks = null;
622 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
626 nlinks = new ArrayList<>();
629 if (features != null)
631 for (SequenceFeature sf : features)
633 if (sf.links != null)
635 for (String link : sf.links)
643 Map<String, List<String>> linkset = new LinkedHashMap<>();
645 for (String link : nlinks)
647 UrlLink urlLink = null;
650 urlLink = new UrlLink(link);
651 } catch (Exception foo)
653 Cache.log.error("Exception for URLLink '" + link + "'", foo);
657 if (!urlLink.isValid())
659 Cache.log.error(urlLink.getInvalidMessage());
663 urlLink.createLinksFromSeq(seq, linkset);
666 addshowLinks(linkMenu, linkset.values());
668 // only add link menu if it has entries
669 if (linkMenu.getItemCount() > 0)
671 if (sequence != null)
673 sequenceMenu.add(linkMenu);
683 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
684 * "All" is added first, followed by a separator. Then add any annotation
685 * types associated with the current selection. Separate menus are built for
686 * the selected sequence group (if any), and the selected sequence.
688 * Some annotation rows are always rendered together - these can be identified
689 * by a common graphGroup property > -1. Only one of each group will be marked
690 * as visible (to avoid duplication of the display). For such groups we add a
691 * composite type name, e.g.
693 * IUPredWS (Long), IUPredWS (Short)
697 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
698 List<SequenceI> forSequences)
700 showMenu.removeAll();
701 hideMenu.removeAll();
703 final List<String> all = Arrays
705 { MessageManager.getString("label.all") });
706 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
708 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
710 showMenu.addSeparator();
711 hideMenu.addSeparator();
713 final AlignmentAnnotation[] annotations = ap.getAlignment()
714 .getAlignmentAnnotation();
717 * Find shown/hidden annotations types, distinguished by source (calcId),
718 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
719 * the insertion order, which is the order of the annotations on the
722 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
723 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
724 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
725 AlignmentAnnotationUtils.asList(annotations), forSequences);
727 for (String calcId : hiddenTypes.keySet())
729 for (List<String> type : hiddenTypes.get(calcId))
731 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
735 // grey out 'show annotations' if none are hidden
736 showMenu.setEnabled(!hiddenTypes.isEmpty());
738 for (String calcId : shownTypes.keySet())
740 for (List<String> type : shownTypes.get(calcId))
742 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
746 // grey out 'hide annotations' if none are shown
747 hideMenu.setEnabled(!shownTypes.isEmpty());
751 * Returns a list of sequences - either the current selection group (if there
752 * is one), else the specified single sequence.
757 protected List<SequenceI> getSequenceScope(SequenceI seq)
759 List<SequenceI> forSequences = null;
760 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
761 if (selectionGroup != null && selectionGroup.getSize() > 0)
763 forSequences = selectionGroup.getSequences();
767 forSequences = seq == null ? Collections.<SequenceI> emptyList()
768 : Arrays.asList(seq);
774 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
777 * @param showOrHideMenu
779 * @param forSequences
780 * the sequences whose annotations may be shown or hidden
785 * if true this is a special label meaning 'All'
786 * @param actionIsShow
787 * if true, the select menu item action is to show the annotation
790 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
791 final List<SequenceI> forSequences, String calcId,
792 final List<String> types, final boolean allTypes,
793 final boolean actionIsShow)
795 String label = types.toString(); // [a, b, c]
796 label = label.substring(1, label.length() - 1); // a, b, c
797 final JMenuItem item = new JMenuItem(label);
798 item.setToolTipText(calcId);
799 item.addActionListener(new ActionListener()
802 public void actionPerformed(ActionEvent e)
804 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
805 types, forSequences, allTypes, actionIsShow);
809 showOrHideMenu.add(item);
812 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
815 // TODO: usability: thread off the generation of group url content so root
817 // sequence only URLs
818 // ID/regex match URLs
819 groupLinksMenu = new JMenu(
820 MessageManager.getString("action.group_link"));
821 // three types of url that might be created.
822 JMenu[] linkMenus = new JMenu[] { null,
823 new JMenu(MessageManager.getString("action.ids")),
824 new JMenu(MessageManager.getString("action.sequences")),
825 new JMenu(MessageManager.getString("action.ids_sequences")) };
827 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
828 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
829 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
830 for (int sq = 0; sq < seqs.length; sq++)
833 int start = seqs[sq].findPosition(sg.getStartRes()),
834 end = seqs[sq].findPosition(sg.getEndRes());
835 // just collect ids from dataset sequence
836 // TODO: check if IDs collected from selecton group intersects with the
837 // current selection, too
838 SequenceI sqi = seqs[sq];
839 while (sqi.getDatasetSequence() != null)
841 sqi = sqi.getDatasetSequence();
843 DBRefEntry[] dbr = sqi.getDBRefs();
844 if (dbr != null && dbr.length > 0)
846 for (int d = 0; d < dbr.length; d++)
848 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
849 Object[] sarray = commonDbrefs.get(src);
852 sarray = new Object[2];
853 sarray[0] = new int[] { 0 };
854 sarray[1] = new String[seqs.length];
856 commonDbrefs.put(src, sarray);
859 if (((String[]) sarray[1])[sq] == null)
861 if (!dbr[d].hasMap() || (dbr[d].getMap()
862 .locateMappedRange(start, end) != null))
864 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
865 ((int[]) sarray[0])[0]++;
871 // now create group links for all distinct ID/sequence sets.
872 boolean addMenu = false; // indicates if there are any group links to give
874 for (String link : groupLinks)
876 GroupUrlLink urlLink = null;
879 urlLink = new GroupUrlLink(link);
880 } catch (Exception foo)
882 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
886 if (!urlLink.isValid())
888 Cache.log.error(urlLink.getInvalidMessage());
891 final String label = urlLink.getLabel();
892 boolean usingNames = false;
893 // Now see which parts of the group apply for this URL
894 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
895 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
896 String[] seqstr, ids; // input to makeUrl
899 int numinput = ((int[]) idset[0])[0];
900 String[] allids = ((String[]) idset[1]);
901 seqstr = new String[numinput];
902 ids = new String[numinput];
903 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
905 if (allids[sq] != null)
907 ids[idcount] = allids[sq];
908 seqstr[idcount++] = idandseqs[1][sq];
914 // just use the id/seq set
915 seqstr = idandseqs[1];
919 // and try and make the groupURL!
921 Object[] urlset = null;
924 urlset = urlLink.makeUrlStubs(ids, seqstr,
925 "FromJalview" + System.currentTimeMillis(), false);
926 } catch (UrlStringTooLongException e)
931 int type = urlLink.getGroupURLType() & 3;
932 // first two bits ofurlLink type bitfield are sequenceids and sequences
933 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
934 addshowLink(linkMenus[type],
935 label + (((type & 1) == 1)
936 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
944 groupLinksMenu = new JMenu(
945 MessageManager.getString("action.group_link"));
946 for (int m = 0; m < linkMenus.length; m++)
948 if (linkMenus[m] != null
949 && linkMenus[m].getMenuComponentCount() > 0)
951 groupLinksMenu.add(linkMenus[m]);
955 groupMenu.add(groupLinksMenu);
959 private void addshowLinks(JMenu linkMenu,
960 Collection<List<String>> linkset)
962 for (List<String> linkstrset : linkset)
964 // split linkstr into label and url
965 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
970 * add a show URL menu item to the given linkMenu
974 * - menu label string
978 private void addshowLink(JMenu linkMenu, String label, final String url)
980 JMenuItem item = new JMenuItem(label);
981 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
984 item.addActionListener(new ActionListener()
987 public void actionPerformed(ActionEvent e)
989 new Thread(new Runnable()
1006 * add a late bound groupURL item to the given linkMenu
1010 * - menu label string
1011 * @param urlgenerator
1012 * GroupURLLink used to generate URL
1014 * Object array returned from the makeUrlStubs function.
1016 private void addshowLink(JMenu linkMenu, String label,
1017 final GroupUrlLink urlgenerator, final Object[] urlstub)
1019 JMenuItem item = new JMenuItem(label);
1020 item.setToolTipText(MessageManager
1021 .formatMessage("label.open_url_seqs_param", new Object[]
1022 { urlgenerator.getUrl_prefix(),
1023 urlgenerator.getNumberInvolved(urlstub) }));
1024 // TODO: put in info about what is being sent.
1025 item.addActionListener(new ActionListener()
1028 public void actionPerformed(ActionEvent e)
1030 new Thread(new Runnable()
1038 showLink(urlgenerator.constructFrom(urlstub));
1039 } catch (UrlStringTooLongException e2)
1057 private void jbInit() throws Exception
1059 groupMenu.setText(MessageManager.getString("label.selection"));
1060 groupName.setText(MessageManager.getString("label.name"));
1061 groupName.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 groupName_actionPerformed();
1069 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1070 sequenceName.setText(
1071 MessageManager.getString("label.edit_name_description"));
1072 sequenceName.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 sequenceName_actionPerformed();
1081 .setText(MessageManager.getString("action.choose_annotations"));
1082 chooseAnnotations.addActionListener(new ActionListener()
1085 public void actionPerformed(ActionEvent e)
1087 chooseAnnotations_actionPerformed(e);
1091 .setText(MessageManager.getString("label.sequence_details"));
1092 sequenceDetails.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent e)
1097 sequenceDetails_actionPerformed();
1101 .setText(MessageManager.getString("label.sequence_details"));
1102 sequenceSelDetails.addActionListener(new ActionListener()
1105 public void actionPerformed(ActionEvent e)
1107 sequenceSelectionDetails_actionPerformed();
1112 .setText(MessageManager.getString("action.remove_group"));
1113 unGroupMenuItem.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 unGroupMenuItem_actionPerformed();
1122 .setText(MessageManager.getString("action.create_group"));
1123 createGroupMenuItem.addActionListener(new ActionListener()
1126 public void actionPerformed(ActionEvent e)
1128 createGroupMenuItem_actionPerformed();
1132 outline.setText(MessageManager.getString("action.border_colour"));
1133 outline.addActionListener(new ActionListener()
1136 public void actionPerformed(ActionEvent e)
1138 outline_actionPerformed();
1141 showBoxes.setText(MessageManager.getString("action.boxes"));
1142 showBoxes.setState(true);
1143 showBoxes.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent e)
1148 showBoxes_actionPerformed();
1151 showText.setText(MessageManager.getString("action.text"));
1152 showText.setState(true);
1153 showText.addActionListener(new ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 showText_actionPerformed();
1161 showColourText.setText(MessageManager.getString("label.colour_text"));
1162 showColourText.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1167 showColourText_actionPerformed();
1171 .setText(MessageManager.getString("label.show_non_conserved"));
1172 displayNonconserved.setState(true);
1173 displayNonconserved.addActionListener(new ActionListener()
1176 public void actionPerformed(ActionEvent e)
1178 showNonconserved_actionPerformed();
1181 editMenu.setText(MessageManager.getString("action.edit"));
1182 cut.setText(MessageManager.getString("action.cut"));
1183 cut.addActionListener(new ActionListener()
1186 public void actionPerformed(ActionEvent e)
1188 cut_actionPerformed();
1191 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1192 upperCase.addActionListener(new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1200 copy.setText(MessageManager.getString("action.copy"));
1201 copy.addActionListener(new ActionListener()
1204 public void actionPerformed(ActionEvent e)
1206 copy_actionPerformed();
1209 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1210 lowerCase.addActionListener(new ActionListener()
1213 public void actionPerformed(ActionEvent e)
1218 toggle.setText(MessageManager.getString("label.toggle_case"));
1219 toggle.addActionListener(new ActionListener()
1222 public void actionPerformed(ActionEvent e)
1228 MessageManager.getString("label.out_to_textbox") + "...");
1229 seqShowAnnotationsMenu
1230 .setText(MessageManager.getString("label.show_annotations"));
1231 seqHideAnnotationsMenu
1232 .setText(MessageManager.getString("label.hide_annotations"));
1233 groupShowAnnotationsMenu
1234 .setText(MessageManager.getString("label.show_annotations"));
1235 groupHideAnnotationsMenu
1236 .setText(MessageManager.getString("label.hide_annotations"));
1237 sequenceFeature.setText(
1238 MessageManager.getString("label.create_sequence_feature"));
1239 sequenceFeature.addActionListener(new ActionListener()
1242 public void actionPerformed(ActionEvent e)
1244 sequenceFeature_actionPerformed();
1247 jMenu1.setText(MessageManager.getString("label.group"));
1248 pdbStructureDialog.setText(
1249 MessageManager.getString("label.show_pdbstruct_dialog"));
1250 pdbStructureDialog.addActionListener(new ActionListener()
1253 public void actionPerformed(ActionEvent actionEvent)
1255 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1256 if (ap.av.getSelectionGroup() != null)
1258 selectedSeqs = ap.av.getSequenceSelection();
1260 new StructureChooser(selectedSeqs, sequence, ap);
1265 .setText(MessageManager.getString("label.view_rna_structure"));
1267 // colStructureMenu.setText("Colour By Structure");
1268 editSequence.setText(
1269 MessageManager.getString("label.edit_sequence") + "...");
1270 editSequence.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent actionEvent)
1275 editSequence_actionPerformed(actionEvent);
1278 makeReferenceSeq.setText(
1279 MessageManager.getString("label.mark_as_representative"));
1280 makeReferenceSeq.addActionListener(new ActionListener()
1284 public void actionPerformed(ActionEvent actionEvent)
1286 makeReferenceSeq_actionPerformed(actionEvent);
1291 .setText(MessageManager.getString("label.hide_insertions"));
1292 hideInsertions.addActionListener(new ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 hideInsertions_actionPerformed(e);
1302 groupMenu.add(sequenceSelDetails);
1305 add(rnaStructureMenu);
1306 add(pdbStructureDialog);
1307 if (sequence != null)
1309 add(hideInsertions);
1311 // annotations configuration panel suppressed for now
1312 // groupMenu.add(chooseAnnotations);
1315 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1316 * (if a selection group is in force).
1318 sequenceMenu.add(seqShowAnnotationsMenu);
1319 sequenceMenu.add(seqHideAnnotationsMenu);
1320 sequenceMenu.add(seqAddReferenceAnnotations);
1321 groupMenu.add(groupShowAnnotationsMenu);
1322 groupMenu.add(groupHideAnnotationsMenu);
1323 groupMenu.add(groupAddReferenceAnnotations);
1324 groupMenu.add(editMenu);
1325 groupMenu.add(outputMenu);
1326 groupMenu.add(sequenceFeature);
1327 groupMenu.add(createGroupMenuItem);
1328 groupMenu.add(unGroupMenuItem);
1329 groupMenu.add(jMenu1);
1330 sequenceMenu.add(sequenceName);
1331 sequenceMenu.add(sequenceDetails);
1332 sequenceMenu.add(makeReferenceSeq);
1339 editMenu.add(editSequence);
1340 editMenu.add(upperCase);
1341 editMenu.add(lowerCase);
1342 editMenu.add(toggle);
1343 // JBPNote: These shouldn't be added here - should appear in a generic
1344 // 'apply web service to this sequence menu'
1345 // pdbMenu.add(RNAFold);
1346 // pdbMenu.add(ContraFold);
1347 jMenu1.add(groupName);
1348 jMenu1.add(colourMenu);
1349 jMenu1.add(showBoxes);
1350 jMenu1.add(showText);
1351 jMenu1.add(showColourText);
1352 jMenu1.add(outline);
1353 jMenu1.add(displayNonconserved);
1357 * Constructs the entries for the colour menu
1359 protected void initColourMenu()
1361 colourMenu.setText(MessageManager.getString("label.group_colour"));
1362 textColour.setText(MessageManager.getString("label.text_colour"));
1363 textColour.addActionListener(new ActionListener()
1366 public void actionPerformed(ActionEvent e)
1368 textColour_actionPerformed();
1372 abovePIDColour.setText(
1373 MessageManager.getString("label.above_identity_threshold"));
1374 abovePIDColour.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent e)
1379 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1384 MessageManager.getString("label.modify_identity_threshold"));
1385 modifyPID.addActionListener(new ActionListener()
1388 public void actionPerformed(ActionEvent e)
1390 modifyPID_actionPerformed();
1394 conservationMenuItem
1395 .setText(MessageManager.getString("action.by_conservation"));
1396 conservationMenuItem.addActionListener(new ActionListener()
1399 public void actionPerformed(ActionEvent e)
1401 conservationMenuItem_actionPerformed(
1402 conservationMenuItem.isSelected());
1406 modifyConservation.setText(MessageManager
1407 .getString("label.modify_conservation_threshold"));
1408 modifyConservation.addActionListener(new ActionListener()
1411 public void actionPerformed(ActionEvent e)
1413 modifyConservation_actionPerformed();
1419 * Builds the group colour sub-menu, including any user-defined colours which
1420 * were loaded at startup or during the Jalview session
1422 protected void buildColourMenu()
1424 SequenceGroup sg = ap.av.getSelectionGroup();
1428 * popup menu with no sequence group scope
1432 colourMenu.removeAll();
1433 colourMenu.add(textColour);
1434 colourMenu.addSeparator();
1436 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1438 colourMenu.addSeparator();
1439 colourMenu.add(conservationMenuItem);
1440 colourMenu.add(modifyConservation);
1441 colourMenu.add(abovePIDColour);
1442 colourMenu.add(modifyPID);
1445 protected void modifyConservation_actionPerformed()
1447 SequenceGroup sg = getGroup();
1450 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1451 SliderPanel.showConservationSlider();
1455 protected void modifyPID_actionPerformed()
1457 SequenceGroup sg = getGroup();
1460 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1462 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1463 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1464 SliderPanel.showPIDSlider();
1469 * Check for any annotations on the underlying dataset sequences (for the
1470 * current selection group) which are not 'on the alignment'.If any are found,
1471 * enable the option to add them to the alignment. The criteria for 'on the
1472 * alignment' is finding an alignment annotation on the alignment, matched on
1473 * calcId, label and sequenceRef.
1475 * A tooltip is also constructed that displays the source (calcId) and type
1476 * (label) of the annotations that can be added.
1479 * @param forSequences
1481 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1482 List<SequenceI> forSequences)
1484 menuItem.setEnabled(false);
1487 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1488 * Using TreeMap means calcIds are shown in alphabetical order.
1490 SortedMap<String, String> tipEntries = new TreeMap<>();
1491 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1492 AlignmentI al = this.ap.av.getAlignment();
1493 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1495 if (!candidates.isEmpty())
1497 StringBuilder tooltip = new StringBuilder(64);
1498 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1501 * Found annotations that could be added. Enable the menu item, and
1502 * configure its tooltip and action.
1504 menuItem.setEnabled(true);
1505 for (String calcId : tipEntries.keySet())
1507 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1509 String tooltipText = JvSwingUtils.wrapTooltip(true,
1510 tooltip.toString());
1511 menuItem.setToolTipText(tooltipText);
1513 menuItem.addActionListener(new ActionListener()
1516 public void actionPerformed(ActionEvent e)
1518 addReferenceAnnotations_actionPerformed(candidates);
1525 * Add annotations to the sequences and to the alignment.
1528 * a map whose keys are sequences on the alignment, and values a list
1529 * of annotations to add to each sequence
1531 protected void addReferenceAnnotations_actionPerformed(
1532 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1534 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1535 final AlignmentI alignment = this.ap.getAlignment();
1536 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1541 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1543 if (!ap.av.getAlignment().hasSeqrep())
1545 // initialise the display flags so the user sees something happen
1546 ap.av.setDisplayReferenceSeq(true);
1547 ap.av.setColourByReferenceSeq(true);
1548 ap.av.getAlignment().setSeqrep(sequence);
1552 if (ap.av.getAlignment().getSeqrep() == sequence)
1554 ap.av.getAlignment().setSeqrep(null);
1558 ap.av.getAlignment().setSeqrep(sequence);
1564 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1566 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1567 BitSet inserts = new BitSet();
1569 boolean markedPopup = false;
1570 // mark inserts in current selection
1571 if (ap.av.getSelectionGroup() != null)
1573 // mark just the columns in the selection group to be hidden
1574 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1575 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1577 // now clear columns without gaps
1578 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1584 inserts.and(sq.getInsertionsAsBits());
1586 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1587 ap.av.getSelectionGroup().getEndRes());
1590 // now mark for sequence under popup if we haven't already done it
1591 else if (!markedPopup && sequence != null)
1593 inserts.or(sequence.getInsertionsAsBits());
1595 // and set hidden columns accordingly
1596 hidden.hideColumns(inserts);
1601 protected void sequenceSelectionDetails_actionPerformed()
1603 createSequenceDetailsReport(ap.av.getSequenceSelection());
1606 protected void sequenceDetails_actionPerformed()
1608 createSequenceDetailsReport(new SequenceI[] { sequence });
1611 public void createSequenceDetailsReport(SequenceI[] sequences)
1613 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1614 StringBuilder contents = new StringBuilder(128);
1615 for (SequenceI seq : sequences)
1617 contents.append("<p><h2>" + MessageManager.formatMessage(
1618 "label.create_sequence_details_report_annotation_for",
1620 { seq.getDisplayId(true) }) + "</h2></p><p>");
1621 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1622 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1623 contents.append("</p>");
1625 cap.setText("<html>" + contents.toString() + "</html>");
1627 Desktop.addInternalFrame(cap,
1628 MessageManager.formatMessage("label.sequence_details_for",
1629 (sequences.length == 1 ? new Object[]
1630 { sequences[0].getDisplayId(true) }
1633 .getString("label.selection") })),
1638 protected void showNonconserved_actionPerformed()
1640 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1645 * call to refresh view after settings change
1649 ap.updateAnnotation();
1650 // removed paintAlignment(true) here:
1651 // updateAnnotation calls paintAlignment already, so don't need to call
1654 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1658 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1659 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1669 public void abovePIDColour_actionPerformed(boolean selected)
1671 SequenceGroup sg = getGroup();
1679 sg.cs.setConsensus(AAFrequency.calculate(
1680 sg.getSequences(ap.av.getHiddenRepSequences()),
1681 sg.getStartRes(), sg.getEndRes() + 1));
1683 int threshold = SliderPanel.setPIDSliderSource(ap,
1684 sg.getGroupColourScheme(), getGroup().getName());
1686 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1688 SliderPanel.showPIDSlider();
1691 // remove PIDColouring
1693 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1694 SliderPanel.hidePIDSlider();
1696 modifyPID.setEnabled(selected);
1702 * Open a panel where the user can choose which types of sequence annotation
1707 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1709 // todo correct way to guard against opening a duplicate panel?
1710 new AnnotationChooser(ap);
1719 public void conservationMenuItem_actionPerformed(boolean selected)
1721 SequenceGroup sg = getGroup();
1729 // JBPNote: Conservation name shouldn't be i18n translated
1730 Conservation c = new Conservation("Group",
1731 sg.getSequences(ap.av.getHiddenRepSequences()),
1732 sg.getStartRes(), sg.getEndRes() + 1);
1735 c.verdict(false, ap.av.getConsPercGaps());
1736 sg.cs.setConservation(c);
1738 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1740 SliderPanel.showConservationSlider();
1743 // remove ConservationColouring
1745 sg.cs.setConservation(null);
1746 SliderPanel.hideConservationSlider();
1748 modifyConservation.setEnabled(selected);
1759 protected void groupName_actionPerformed()
1762 SequenceGroup sg = getGroup();
1763 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1764 sg.getDescription(),
1765 " " + MessageManager.getString("label.group_name") + " ",
1766 MessageManager.getString("label.group_description") + " ",
1767 MessageManager.getString("label.edit_group_name_description"),
1775 sg.setName(dialog.getName());
1776 sg.setDescription(dialog.getDescription());
1781 * Get selection group - adding it to the alignment if necessary.
1783 * @return sequence group to operate on
1785 SequenceGroup getGroup()
1787 SequenceGroup sg = ap.av.getSelectionGroup();
1788 // this method won't add a new group if it already exists
1791 ap.av.getAlignment().addGroup(sg);
1803 void sequenceName_actionPerformed()
1805 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1806 sequence.getDescription(),
1807 " " + MessageManager.getString("label.sequence_name")
1809 MessageManager.getString("label.sequence_description") + " ",
1810 MessageManager.getString(
1811 "label.edit_sequence_name_description"),
1819 if (dialog.getName() != null)
1821 if (dialog.getName().indexOf(" ") > -1)
1823 JvOptionPane.showMessageDialog(ap,
1825 .getString("label.spaces_converted_to_backslashes"),
1827 .getString("label.no_spaces_allowed_sequence_name"),
1828 JvOptionPane.WARNING_MESSAGE);
1831 sequence.setName(dialog.getName().replace(' ', '_'));
1832 ap.paintAlignment(false, false);
1835 sequence.setDescription(dialog.getDescription());
1837 ap.av.firePropertyChange("alignment", null,
1838 ap.av.getAlignment().getSequences());
1848 void unGroupMenuItem_actionPerformed()
1850 SequenceGroup sg = ap.av.getSelectionGroup();
1851 ap.av.getAlignment().deleteGroup(sg);
1852 ap.av.setSelectionGroup(null);
1856 void createGroupMenuItem_actionPerformed()
1858 getGroup(); // implicitly creates group - note - should apply defaults / use
1859 // standard alignment window logic for this
1869 protected void outline_actionPerformed()
1871 SequenceGroup sg = getGroup();
1872 Color col = JColorChooser.showDialog(this,
1873 MessageManager.getString("label.select_outline_colour"),
1878 sg.setOutlineColour(col);
1890 public void showBoxes_actionPerformed()
1892 getGroup().setDisplayBoxes(showBoxes.isSelected());
1902 public void showText_actionPerformed()
1904 getGroup().setDisplayText(showText.isSelected());
1914 public void showColourText_actionPerformed()
1916 getGroup().setColourText(showColourText.isSelected());
1920 public void showLink(String url)
1924 jalview.util.BrowserLauncher.openURL(url);
1925 } catch (Exception ex)
1927 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1928 MessageManager.getString("label.web_browser_not_found_unix"),
1929 MessageManager.getString("label.web_browser_not_found"),
1930 JvOptionPane.WARNING_MESSAGE);
1932 ex.printStackTrace();
1936 void hideSequences(boolean representGroup)
1938 ap.av.hideSequences(sequence, representGroup);
1941 public void copy_actionPerformed()
1943 ap.alignFrame.copy_actionPerformed(null);
1946 public void cut_actionPerformed()
1948 ap.alignFrame.cut_actionPerformed(null);
1951 void changeCase(ActionEvent e)
1953 Object source = e.getSource();
1954 SequenceGroup sg = ap.av.getSelectionGroup();
1958 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1959 sg.getStartRes(), sg.getEndRes() + 1);
1964 if (source == toggle)
1966 description = MessageManager.getString("label.toggle_case");
1967 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1969 else if (source == upperCase)
1971 description = MessageManager.getString("label.to_upper_case");
1972 caseChange = ChangeCaseCommand.TO_UPPER;
1976 description = MessageManager.getString("label.to_lower_case");
1977 caseChange = ChangeCaseCommand.TO_LOWER;
1980 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1981 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1982 startEnd, caseChange);
1984 ap.alignFrame.addHistoryItem(caseCommand);
1986 ap.av.firePropertyChange("alignment", null,
1987 ap.av.getAlignment().getSequences());
1992 public void outputText_actionPerformed(ActionEvent e)
1994 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1995 cap.setForInput(null);
1996 Desktop.addInternalFrame(cap, MessageManager
1997 .formatMessage("label.alignment_output_command", new Object[]
1998 { e.getActionCommand() }), 600, 500);
2000 String[] omitHidden = null;
2002 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2003 // or we simply trust the user wants
2004 // wysiwig behaviour
2006 FileFormatI fileFormat = FileFormats.getInstance()
2007 .forName(e.getActionCommand());
2009 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2012 public void sequenceFeature_actionPerformed()
2014 SequenceGroup sg = ap.av.getSelectionGroup();
2020 List<SequenceI> seqs = new ArrayList<>();
2021 List<SequenceFeature> features = new ArrayList<>();
2024 * assemble dataset sequences, and template new sequence features,
2025 * for the amend features dialog
2027 int gSize = sg.getSize();
2028 for (int i = 0; i < gSize; i++)
2030 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2031 int end = sg.findEndRes(sg.getSequenceAt(i));
2034 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2035 features.add(new SequenceFeature(null, null, start, end, null));
2040 * an entirely gapped region will generate empty lists of sequence / features
2042 if (!seqs.isEmpty())
2044 if (ap.getSeqPanel().seqCanvas.getFeatureRenderer()
2045 .amendFeatures(seqs, features, true, ap))
2047 ap.alignFrame.setShowSeqFeatures(true);
2048 ap.av.setSearchResults(null); // clear highlighting
2049 ap.repaint(); // draw new/amended features
2054 public void textColour_actionPerformed()
2056 SequenceGroup sg = getGroup();
2059 new TextColourChooser().chooseColour(ap, sg);
2063 public void colourByStructure(String pdbid)
2065 Annotation[] anots = ap.av.getStructureSelectionManager()
2066 .colourSequenceFromStructure(sequence, pdbid);
2068 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2069 "Coloured by " + pdbid, anots);
2071 ap.av.getAlignment().addAnnotation(an);
2072 an.createSequenceMapping(sequence, 0, true);
2073 // an.adjustForAlignment();
2074 ap.av.getAlignment().setAnnotationIndex(an, 0);
2076 ap.adjustAnnotationHeight();
2078 sequence.addAlignmentAnnotation(an);
2082 public void editSequence_actionPerformed(ActionEvent actionEvent)
2084 SequenceGroup sg = ap.av.getSelectionGroup();
2088 if (sequence == null)
2090 sequence = sg.getSequenceAt(0);
2093 EditNameDialog dialog = new EditNameDialog(
2094 sequence.getSequenceAsString(sg.getStartRes(),
2095 sg.getEndRes() + 1),
2096 null, MessageManager.getString("label.edit_sequence"), null,
2097 MessageManager.getString("label.edit_sequence"),
2102 EditCommand editCommand = new EditCommand(
2103 MessageManager.getString("label.edit_sequences"),
2105 dialog.getName().replace(' ', ap.av.getGapCharacter()),
2106 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2107 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2109 ap.alignFrame.addHistoryItem(editCommand);
2111 ap.av.firePropertyChange("alignment", null,
2112 ap.av.getAlignment().getSequences());
2118 * Action on user selecting an item from the colour menu (that does not have
2119 * its bespoke action handler)
2124 public void changeColour_actionPerformed(String colourSchemeName)
2126 SequenceGroup sg = getGroup();
2128 * switch to the chosen colour scheme (or null for None)
2130 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2131 .getColourScheme(colourSchemeName, sg,
2132 ap.av.getHiddenRepSequences());
2133 sg.setColourScheme(colourScheme);
2134 if (colourScheme instanceof Blosum62ColourScheme
2135 || colourScheme instanceof PIDColourScheme)
2137 sg.cs.setConsensus(AAFrequency.calculate(
2138 sg.getSequences(ap.av.getHiddenRepSequences()),
2139 sg.getStartRes(), sg.getEndRes() + 1));