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.gui.JalviewColourChooser.ColourChooserListener;
42 import jalview.io.FileFormatI;
43 import jalview.io.FileFormats;
44 import jalview.io.FormatAdapter;
45 import jalview.io.SequenceAnnotationReport;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.ColourSchemes;
49 import jalview.schemes.PIDColourScheme;
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;
55 import jalview.util.dialogrunner.RunResponse;
57 import java.awt.Color;
58 import java.awt.event.ActionEvent;
59 import java.awt.event.ActionListener;
60 import java.util.ArrayList;
61 import java.util.Arrays;
62 import java.util.BitSet;
63 import java.util.Collection;
64 import java.util.Collections;
65 import java.util.Hashtable;
66 import java.util.LinkedHashMap;
67 import java.util.List;
69 import java.util.SortedMap;
70 import java.util.TreeMap;
71 import java.util.Vector;
73 import javax.swing.JCheckBoxMenuItem;
74 import javax.swing.JMenu;
75 import javax.swing.JMenuItem;
76 import javax.swing.JPopupMenu;
82 * @version $Revision: 1.118 $
84 public class PopupMenu extends JPopupMenu implements ColourChangeListener
86 JMenu groupMenu = new JMenu();
88 JMenuItem groupName = new JMenuItem();
90 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
92 protected JMenuItem modifyPID = new JMenuItem();
94 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
96 protected JMenuItem modifyConservation = new JMenuItem();
100 JMenu sequenceMenu = new JMenu();
102 JMenuItem sequenceName = new JMenuItem();
104 JMenuItem sequenceDetails = new JMenuItem();
106 JMenuItem sequenceSelDetails = new JMenuItem();
108 JMenuItem makeReferenceSeq = new JMenuItem();
110 JMenuItem chooseAnnotations = new JMenuItem();
114 JMenuItem createGroupMenuItem = new JMenuItem();
116 JMenuItem unGroupMenuItem = new JMenuItem();
118 JMenuItem outline = new JMenuItem();
120 JMenu colourMenu = new JMenu();
122 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
124 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
126 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
128 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
130 JMenu editMenu = new JMenu();
132 JMenuItem cut = new JMenuItem();
134 JMenuItem copy = new JMenuItem();
136 JMenuItem upperCase = new JMenuItem();
138 JMenuItem lowerCase = new JMenuItem();
140 JMenuItem toggle = new JMenuItem();
142 JMenu pdbMenu = new JMenu();
144 JMenu outputMenu = new JMenu();
146 JMenu seqShowAnnotationsMenu = new JMenu();
148 JMenu seqHideAnnotationsMenu = new JMenu();
150 JMenuItem seqAddReferenceAnnotations = new JMenuItem(
151 MessageManager.getString("label.add_reference_annotations"));
153 JMenu groupShowAnnotationsMenu = new JMenu();
155 JMenu groupHideAnnotationsMenu = new JMenu();
157 JMenuItem groupAddReferenceAnnotations = new JMenuItem(
158 MessageManager.getString("label.add_reference_annotations"));
160 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()
238 : 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<>(), reppdb = new Hashtable<>();
467 SequenceI sqass = null;
468 for (SequenceI sq : alignPanel.av.getSequenceSelection())
470 Vector<PDBEntry> pes = sq.getDatasetSequence().getAllPDBEntries();
471 if (pes != null && pes.size() > 0)
473 reppdb.put(pes.get(0).getId(), pes.get(0));
474 for (PDBEntry pe : pes)
476 pdbe.put(pe.getId(), pe);
486 final PDBEntry[] pe = pdbe.values()
487 .toArray(new PDBEntry[pdbe.size()]),
488 pr = reppdb.values().toArray(new PDBEntry[reppdb.size()]);
489 final JMenuItem gpdbview, rpdbview;
494 groupMenu.setVisible(false);
495 editMenu.setVisible(false);
500 createGroupMenuItem.setVisible(true);
501 unGroupMenuItem.setVisible(false);
502 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
506 createGroupMenuItem.setVisible(false);
507 unGroupMenuItem.setVisible(true);
508 jMenu1.setText(MessageManager.getString("action.edit_group"));
513 sequenceMenu.setVisible(false);
514 pdbStructureDialog.setVisible(false);
515 rnaStructureMenu.setVisible(false);
518 addLinks(seq, features);
522 addFeatureDetails(features);
527 * Add a link to show feature details for each sequence feature
531 protected void addFeatureDetails(List<SequenceFeature> features)
533 if (features == null || features.isEmpty())
537 JMenu details = new JMenu(
538 MessageManager.getString("label.feature_details"));
541 for (final SequenceFeature sf : features)
543 int start = sf.getBegin();
544 int end = sf.getEnd();
548 desc = String.format("%s %d", sf.getType(), start);
552 desc = String.format("%s %d-%d", sf.getType(), start, end);
554 String tooltip = desc;
555 String description = sf.getDescription();
556 if (description != null)
558 description = StringUtils.stripHtmlTags(description);
559 if (description.length() > 12)
561 desc = desc + " " + description.substring(0, 12) + "..";
565 desc = desc + " " + description;
567 tooltip = tooltip + " " + description;
569 if (sf.getFeatureGroup() != null)
571 tooltip = tooltip + (" (" + sf.getFeatureGroup() + ")");
573 JMenuItem item = new JMenuItem(desc);
574 item.setToolTipText(tooltip);
575 item.addActionListener(new ActionListener()
578 public void actionPerformed(ActionEvent e)
580 showFeatureDetails(sf);
588 * Opens a panel showing a text report of feature dteails
592 protected void showFeatureDetails(SequenceFeature sf)
594 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
595 // it appears Java's CSS does not support border-collaps :-(
596 cap.addStylesheetRule("table { border-collapse: collapse;}");
597 cap.addStylesheetRule("table, td, th {border: 1px solid black;}");
598 cap.setText(sf.getDetailsReport());
600 Desktop.addInternalFrame(cap,
601 MessageManager.getString("label.feature_details"), 500, 500);
605 * Adds a 'Link' menu item with a sub-menu item for each hyperlink provided.
606 * When seq is not null, these are links for the sequence id, which may be to
607 * external web sites for the sequence accession, and/or links embedded in
608 * non-positional features. When seq is null, only links embedded in the
609 * provided features are added.
614 void addLinks(final SequenceI seq, List<SequenceFeature> features)
616 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
618 List<String> nlinks = null;
621 nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
625 nlinks = new ArrayList<>();
628 if (features != null)
630 for (SequenceFeature sf : features)
632 if (sf.links != null)
634 for (String link : sf.links)
642 Map<String, List<String>> linkset = new LinkedHashMap<>();
644 for (String link : nlinks)
646 UrlLink urlLink = null;
649 urlLink = new UrlLink(link);
650 } catch (Exception foo)
652 Cache.log.error("Exception for URLLink '" + link + "'", foo);
656 if (!urlLink.isValid())
658 Cache.log.error(urlLink.getInvalidMessage());
662 urlLink.createLinksFromSeq(seq, linkset);
665 addshowLinks(linkMenu, linkset.values());
667 // only add link menu if it has entries
668 if (linkMenu.getItemCount() > 0)
670 if (sequence != null)
672 sequenceMenu.add(linkMenu);
682 * Add annotation types to 'Show annotations' and/or 'Hide annotations' menus.
683 * "All" is added first, followed by a separator. Then add any annotation
684 * types associated with the current selection. Separate menus are built for
685 * the selected sequence group (if any), and the selected sequence.
687 * Some annotation rows are always rendered together - these can be identified
688 * by a common graphGroup property > -1. Only one of each group will be marked
689 * as visible (to avoid duplication of the display). For such groups we add a
690 * composite type name, e.g.
692 * IUPredWS (Long), IUPredWS (Short)
696 protected void buildAnnotationTypesMenus(JMenu showMenu, JMenu hideMenu,
697 List<SequenceI> forSequences)
699 showMenu.removeAll();
700 hideMenu.removeAll();
702 final List<String> all = Arrays
704 { MessageManager.getString("label.all") });
705 addAnnotationTypeToShowHide(showMenu, forSequences, "", all, true,
707 addAnnotationTypeToShowHide(hideMenu, forSequences, "", all, true,
709 showMenu.addSeparator();
710 hideMenu.addSeparator();
712 final AlignmentAnnotation[] annotations = ap.getAlignment()
713 .getAlignmentAnnotation();
716 * Find shown/hidden annotations types, distinguished by source (calcId),
717 * and grouped by graphGroup. Using LinkedHashMap means we will retrieve in
718 * the insertion order, which is the order of the annotations on the
721 Map<String, List<List<String>>> shownTypes = new LinkedHashMap<>();
722 Map<String, List<List<String>>> hiddenTypes = new LinkedHashMap<>();
723 AlignmentAnnotationUtils.getShownHiddenTypes(shownTypes, hiddenTypes,
724 AlignmentAnnotationUtils.asList(annotations), forSequences);
726 for (String calcId : hiddenTypes.keySet())
728 for (List<String> type : hiddenTypes.get(calcId))
730 addAnnotationTypeToShowHide(showMenu, forSequences, calcId, type,
734 // grey out 'show annotations' if none are hidden
735 showMenu.setEnabled(!hiddenTypes.isEmpty());
737 for (String calcId : shownTypes.keySet())
739 for (List<String> type : shownTypes.get(calcId))
741 addAnnotationTypeToShowHide(hideMenu, forSequences, calcId, type,
745 // grey out 'hide annotations' if none are shown
746 hideMenu.setEnabled(!shownTypes.isEmpty());
750 * Returns a list of sequences - either the current selection group (if there
751 * is one), else the specified single sequence.
756 protected List<SequenceI> getSequenceScope(SequenceI seq)
758 List<SequenceI> forSequences = null;
759 final SequenceGroup selectionGroup = ap.av.getSelectionGroup();
760 if (selectionGroup != null && selectionGroup.getSize() > 0)
762 forSequences = selectionGroup.getSequences();
766 forSequences = seq == null ? Collections.<SequenceI> emptyList()
767 : Arrays.asList(seq);
773 * Add one annotation type to the 'Show Annotations' or 'Hide Annotations'
776 * @param showOrHideMenu
778 * @param forSequences
779 * the sequences whose annotations may be shown or hidden
784 * if true this is a special label meaning 'All'
785 * @param actionIsShow
786 * if true, the select menu item action is to show the annotation
789 protected void addAnnotationTypeToShowHide(JMenu showOrHideMenu,
790 final List<SequenceI> forSequences, String calcId,
791 final List<String> types, final boolean allTypes,
792 final boolean actionIsShow)
794 String label = types.toString(); // [a, b, c]
795 label = label.substring(1, label.length() - 1); // a, b, c
796 final JMenuItem item = new JMenuItem(label);
797 item.setToolTipText(calcId);
798 item.addActionListener(new ActionListener()
801 public void actionPerformed(ActionEvent e)
803 AlignmentUtils.showOrHideSequenceAnnotations(ap.getAlignment(),
804 types, forSequences, allTypes, actionIsShow);
808 showOrHideMenu.add(item);
811 private void buildGroupURLMenu(SequenceGroup sg, List<String> groupLinks)
814 // TODO: usability: thread off the generation of group url content so root
816 // sequence only URLs
817 // ID/regex match URLs
818 groupLinksMenu = new JMenu(
819 MessageManager.getString("action.group_link"));
820 // three types of url that might be created.
821 JMenu[] linkMenus = new JMenu[] { null,
822 new JMenu(MessageManager.getString("action.ids")),
823 new JMenu(MessageManager.getString("action.sequences")),
824 new JMenu(MessageManager.getString("action.ids_sequences")) };
826 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
827 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
828 Hashtable<String, Object[]> commonDbrefs = new Hashtable<>();
829 for (int sq = 0; sq < seqs.length; sq++)
832 int start = seqs[sq].findPosition(sg.getStartRes()),
833 end = seqs[sq].findPosition(sg.getEndRes());
834 // just collect ids from dataset sequence
835 // TODO: check if IDs collected from selecton group intersects with the
836 // current selection, too
837 SequenceI sqi = seqs[sq];
838 while (sqi.getDatasetSequence() != null)
840 sqi = sqi.getDatasetSequence();
842 DBRefEntry[] dbr = sqi.getDBRefs();
843 if (dbr != null && dbr.length > 0)
845 for (int d = 0; d < dbr.length; d++)
847 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
848 Object[] sarray = commonDbrefs.get(src);
851 sarray = new Object[2];
852 sarray[0] = new int[] { 0 };
853 sarray[1] = new String[seqs.length];
855 commonDbrefs.put(src, sarray);
858 if (((String[]) sarray[1])[sq] == null)
860 if (!dbr[d].hasMap() || (dbr[d].getMap()
861 .locateMappedRange(start, end) != null))
863 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
864 ((int[]) sarray[0])[0]++;
870 // now create group links for all distinct ID/sequence sets.
871 boolean addMenu = false; // indicates if there are any group links to give
873 for (String link : groupLinks)
875 GroupUrlLink urlLink = null;
878 urlLink = new GroupUrlLink(link);
879 } catch (Exception foo)
881 Cache.log.error("Exception for GroupURLLink '" + link + "'", foo);
885 if (!urlLink.isValid())
887 Cache.log.error(urlLink.getInvalidMessage());
890 final String label = urlLink.getLabel();
891 boolean usingNames = false;
892 // Now see which parts of the group apply for this URL
893 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
894 Object[] idset = commonDbrefs.get(ltarget.toUpperCase());
895 String[] seqstr, ids; // input to makeUrl
898 int numinput = ((int[]) idset[0])[0];
899 String[] allids = ((String[]) idset[1]);
900 seqstr = new String[numinput];
901 ids = new String[numinput];
902 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
904 if (allids[sq] != null)
906 ids[idcount] = allids[sq];
907 seqstr[idcount++] = idandseqs[1][sq];
913 // just use the id/seq set
914 seqstr = idandseqs[1];
918 // and try and make the groupURL!
920 Object[] urlset = null;
923 urlset = urlLink.makeUrlStubs(ids, seqstr,
924 "FromJalview" + System.currentTimeMillis(), false);
925 } catch (UrlStringTooLongException e)
930 int type = urlLink.getGroupURLType() & 3;
931 // first two bits ofurlLink type bitfield are sequenceids and sequences
932 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
933 addshowLink(linkMenus[type],
934 label + (((type & 1) == 1)
935 ? ("(" + (usingNames ? "Names" : ltarget) + ")")
943 groupLinksMenu = new JMenu(
944 MessageManager.getString("action.group_link"));
945 for (int m = 0; m < linkMenus.length; m++)
947 if (linkMenus[m] != null
948 && linkMenus[m].getMenuComponentCount() > 0)
950 groupLinksMenu.add(linkMenus[m]);
954 groupMenu.add(groupLinksMenu);
958 private void addshowLinks(JMenu linkMenu,
959 Collection<List<String>> linkset)
961 for (List<String> linkstrset : linkset)
963 // split linkstr into label and url
964 addshowLink(linkMenu, linkstrset.get(1), linkstrset.get(3));
969 * add a show URL menu item to the given linkMenu
973 * - menu label string
977 private void addshowLink(JMenu linkMenu, String label, final String url)
979 JMenuItem item = new JMenuItem(label);
980 item.setToolTipText(MessageManager.formatMessage("label.open_url_param",
983 item.addActionListener(new ActionListener()
986 public void actionPerformed(ActionEvent e)
988 new Thread(new Runnable()
1005 * add a late bound groupURL item to the given linkMenu
1009 * - menu label string
1010 * @param urlgenerator
1011 * GroupURLLink used to generate URL
1013 * Object array returned from the makeUrlStubs function.
1015 private void addshowLink(JMenu linkMenu, String label,
1016 final GroupUrlLink urlgenerator, final Object[] urlstub)
1018 JMenuItem item = new JMenuItem(label);
1019 item.setToolTipText(MessageManager
1020 .formatMessage("label.open_url_seqs_param", new Object[]
1021 { urlgenerator.getUrl_prefix(),
1022 urlgenerator.getNumberInvolved(urlstub) }));
1023 // TODO: put in info about what is being sent.
1024 item.addActionListener(new ActionListener()
1027 public void actionPerformed(ActionEvent e)
1029 new Thread(new Runnable()
1037 showLink(urlgenerator.constructFrom(urlstub));
1038 } catch (UrlStringTooLongException e2)
1056 private void jbInit() throws Exception
1058 groupMenu.setText(MessageManager.getString("label.selection"));
1059 groupName.setText(MessageManager.getString("label.name"));
1060 groupName.addActionListener(new ActionListener()
1063 public void actionPerformed(ActionEvent e)
1065 groupName_actionPerformed();
1068 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1069 sequenceName.setText(
1070 MessageManager.getString("label.edit_name_description"));
1071 sequenceName.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 sequenceName_actionPerformed();
1080 .setText(MessageManager.getString("action.choose_annotations"));
1081 chooseAnnotations.addActionListener(new ActionListener()
1084 public void actionPerformed(ActionEvent e)
1086 chooseAnnotations_actionPerformed(e);
1090 .setText(MessageManager.getString("label.sequence_details"));
1091 sequenceDetails.addActionListener(new ActionListener()
1094 public void actionPerformed(ActionEvent e)
1096 sequenceDetails_actionPerformed();
1100 .setText(MessageManager.getString("label.sequence_details"));
1101 sequenceSelDetails.addActionListener(new ActionListener()
1104 public void actionPerformed(ActionEvent e)
1106 sequenceSelectionDetails_actionPerformed();
1111 .setText(MessageManager.getString("action.remove_group"));
1112 unGroupMenuItem.addActionListener(new ActionListener()
1115 public void actionPerformed(ActionEvent e)
1117 unGroupMenuItem_actionPerformed();
1121 .setText(MessageManager.getString("action.create_group"));
1122 createGroupMenuItem.addActionListener(new ActionListener()
1125 public void actionPerformed(ActionEvent e)
1127 createGroupMenuItem_actionPerformed();
1131 outline.setText(MessageManager.getString("action.border_colour"));
1132 outline.addActionListener(new ActionListener()
1135 public void actionPerformed(ActionEvent e)
1137 outline_actionPerformed();
1140 showBoxes.setText(MessageManager.getString("action.boxes"));
1141 showBoxes.setState(true);
1142 showBoxes.addActionListener(new ActionListener()
1145 public void actionPerformed(ActionEvent e)
1147 showBoxes_actionPerformed();
1150 showText.setText(MessageManager.getString("action.text"));
1151 showText.setState(true);
1152 showText.addActionListener(new ActionListener()
1155 public void actionPerformed(ActionEvent e)
1157 showText_actionPerformed();
1160 showColourText.setText(MessageManager.getString("label.colour_text"));
1161 showColourText.addActionListener(new ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 showColourText_actionPerformed();
1170 .setText(MessageManager.getString("label.show_non_conserved"));
1171 displayNonconserved.setState(true);
1172 displayNonconserved.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 showNonconserved_actionPerformed();
1180 editMenu.setText(MessageManager.getString("action.edit"));
1181 cut.setText(MessageManager.getString("action.cut"));
1182 cut.addActionListener(new ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 cut_actionPerformed();
1190 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1191 upperCase.addActionListener(new ActionListener()
1194 public void actionPerformed(ActionEvent e)
1199 copy.setText(MessageManager.getString("action.copy"));
1200 copy.addActionListener(new ActionListener()
1203 public void actionPerformed(ActionEvent e)
1205 copy_actionPerformed();
1208 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1209 lowerCase.addActionListener(new ActionListener()
1212 public void actionPerformed(ActionEvent e)
1217 toggle.setText(MessageManager.getString("label.toggle_case"));
1218 toggle.addActionListener(new ActionListener()
1221 public void actionPerformed(ActionEvent e)
1227 MessageManager.getString("label.out_to_textbox") + "...");
1228 seqShowAnnotationsMenu
1229 .setText(MessageManager.getString("label.show_annotations"));
1230 seqHideAnnotationsMenu
1231 .setText(MessageManager.getString("label.hide_annotations"));
1232 groupShowAnnotationsMenu
1233 .setText(MessageManager.getString("label.show_annotations"));
1234 groupHideAnnotationsMenu
1235 .setText(MessageManager.getString("label.hide_annotations"));
1236 sequenceFeature.setText(
1237 MessageManager.getString("label.create_sequence_feature"));
1238 sequenceFeature.addActionListener(new ActionListener()
1241 public void actionPerformed(ActionEvent e)
1243 sequenceFeature_actionPerformed();
1246 jMenu1.setText(MessageManager.getString("label.group"));
1247 pdbStructureDialog.setText(
1248 MessageManager.getString("label.show_pdbstruct_dialog"));
1249 pdbStructureDialog.addActionListener(new ActionListener()
1252 public void actionPerformed(ActionEvent actionEvent)
1254 SequenceI[] selectedSeqs = new SequenceI[] { sequence };
1255 if (ap.av.getSelectionGroup() != null)
1257 selectedSeqs = ap.av.getSequenceSelection();
1259 new StructureChooser(selectedSeqs, sequence, ap);
1264 .setText(MessageManager.getString("label.view_rna_structure"));
1266 // colStructureMenu.setText("Colour By Structure");
1267 editSequence.setText(
1268 MessageManager.getString("label.edit_sequence") + "...");
1269 editSequence.addActionListener(new ActionListener()
1272 public void actionPerformed(ActionEvent actionEvent)
1274 editSequence_actionPerformed();
1277 makeReferenceSeq.setText(
1278 MessageManager.getString("label.mark_as_representative"));
1279 makeReferenceSeq.addActionListener(new ActionListener()
1283 public void actionPerformed(ActionEvent actionEvent)
1285 makeReferenceSeq_actionPerformed(actionEvent);
1290 .setText(MessageManager.getString("label.hide_insertions"));
1291 hideInsertions.addActionListener(new ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 hideInsertions_actionPerformed(e);
1301 groupMenu.add(sequenceSelDetails);
1304 add(rnaStructureMenu);
1305 add(pdbStructureDialog);
1306 if (sequence != null)
1308 add(hideInsertions);
1310 // annotations configuration panel suppressed for now
1311 // groupMenu.add(chooseAnnotations);
1314 * Add show/hide annotations to the Sequence menu, and to the Selection menu
1315 * (if a selection group is in force).
1317 sequenceMenu.add(seqShowAnnotationsMenu);
1318 sequenceMenu.add(seqHideAnnotationsMenu);
1319 sequenceMenu.add(seqAddReferenceAnnotations);
1320 groupMenu.add(groupShowAnnotationsMenu);
1321 groupMenu.add(groupHideAnnotationsMenu);
1322 groupMenu.add(groupAddReferenceAnnotations);
1323 groupMenu.add(editMenu);
1324 groupMenu.add(outputMenu);
1325 groupMenu.add(sequenceFeature);
1326 groupMenu.add(createGroupMenuItem);
1327 groupMenu.add(unGroupMenuItem);
1328 groupMenu.add(jMenu1);
1329 sequenceMenu.add(sequenceName);
1330 sequenceMenu.add(sequenceDetails);
1331 sequenceMenu.add(makeReferenceSeq);
1338 editMenu.add(editSequence);
1339 editMenu.add(upperCase);
1340 editMenu.add(lowerCase);
1341 editMenu.add(toggle);
1342 // JBPNote: These shouldn't be added here - should appear in a generic
1343 // 'apply web service to this sequence menu'
1344 // pdbMenu.add(RNAFold);
1345 // pdbMenu.add(ContraFold);
1346 jMenu1.add(groupName);
1347 jMenu1.add(colourMenu);
1348 jMenu1.add(showBoxes);
1349 jMenu1.add(showText);
1350 jMenu1.add(showColourText);
1351 jMenu1.add(outline);
1352 jMenu1.add(displayNonconserved);
1356 * Constructs the entries for the colour menu
1358 protected void initColourMenu()
1360 colourMenu.setText(MessageManager.getString("label.group_colour"));
1361 textColour.setText(MessageManager.getString("label.text_colour"));
1362 textColour.addActionListener(new ActionListener()
1365 public void actionPerformed(ActionEvent e)
1367 textColour_actionPerformed();
1371 abovePIDColour.setText(
1372 MessageManager.getString("label.above_identity_threshold"));
1373 abovePIDColour.addActionListener(new ActionListener()
1376 public void actionPerformed(ActionEvent e)
1378 abovePIDColour_actionPerformed(abovePIDColour.isSelected());
1383 MessageManager.getString("label.modify_identity_threshold"));
1384 modifyPID.addActionListener(new ActionListener()
1387 public void actionPerformed(ActionEvent e)
1389 modifyPID_actionPerformed();
1393 conservationMenuItem
1394 .setText(MessageManager.getString("action.by_conservation"));
1395 conservationMenuItem.addActionListener(new ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 conservationMenuItem_actionPerformed(
1401 conservationMenuItem.isSelected());
1405 modifyConservation.setText(MessageManager
1406 .getString("label.modify_conservation_threshold"));
1407 modifyConservation.addActionListener(new ActionListener()
1410 public void actionPerformed(ActionEvent e)
1412 modifyConservation_actionPerformed();
1418 * Builds the group colour sub-menu, including any user-defined colours which
1419 * were loaded at startup or during the Jalview session
1421 protected void buildColourMenu()
1423 SequenceGroup sg = ap.av.getSelectionGroup();
1427 * popup menu with no sequence group scope
1431 colourMenu.removeAll();
1432 colourMenu.add(textColour);
1433 colourMenu.addSeparator();
1435 ColourMenuHelper.addMenuItems(colourMenu, this, sg, false);
1437 colourMenu.addSeparator();
1438 colourMenu.add(conservationMenuItem);
1439 colourMenu.add(modifyConservation);
1440 colourMenu.add(abovePIDColour);
1441 colourMenu.add(modifyPID);
1444 protected void modifyConservation_actionPerformed()
1446 SequenceGroup sg = getGroup();
1449 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1450 SliderPanel.showConservationSlider();
1454 protected void modifyPID_actionPerformed()
1456 SequenceGroup sg = getGroup();
1459 // int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1461 // sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1462 SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup().getName());
1463 SliderPanel.showPIDSlider();
1468 * Check for any annotations on the underlying dataset sequences (for the
1469 * current selection group) which are not 'on the alignment'.If any are found,
1470 * enable the option to add them to the alignment. The criteria for 'on the
1471 * alignment' is finding an alignment annotation on the alignment, matched on
1472 * calcId, label and sequenceRef.
1474 * A tooltip is also constructed that displays the source (calcId) and type
1475 * (label) of the annotations that can be added.
1478 * @param forSequences
1480 protected void configureReferenceAnnotationsMenu(JMenuItem menuItem,
1481 List<SequenceI> forSequences)
1483 menuItem.setEnabled(false);
1486 * Temporary store to hold distinct calcId / type pairs for the tooltip.
1487 * Using TreeMap means calcIds are shown in alphabetical order.
1489 SortedMap<String, String> tipEntries = new TreeMap<>();
1490 final Map<SequenceI, List<AlignmentAnnotation>> candidates = new LinkedHashMap<>();
1491 AlignmentI al = this.ap.av.getAlignment();
1492 AlignmentUtils.findAddableReferenceAnnotations(forSequences, tipEntries,
1494 if (!candidates.isEmpty())
1496 StringBuilder tooltip = new StringBuilder(64);
1497 tooltip.append(MessageManager.getString("label.add_annotations_for"));
1500 * Found annotations that could be added. Enable the menu item, and
1501 * configure its tooltip and action.
1503 menuItem.setEnabled(true);
1504 for (String calcId : tipEntries.keySet())
1506 tooltip.append("<br/>" + calcId + "/" + tipEntries.get(calcId));
1508 String tooltipText = JvSwingUtils.wrapTooltip(true,
1509 tooltip.toString());
1510 menuItem.setToolTipText(tooltipText);
1512 menuItem.addActionListener(new ActionListener()
1515 public void actionPerformed(ActionEvent e)
1517 addReferenceAnnotations_actionPerformed(candidates);
1524 * Add annotations to the sequences and to the alignment.
1527 * a map whose keys are sequences on the alignment, and values a list
1528 * of annotations to add to each sequence
1530 protected void addReferenceAnnotations_actionPerformed(
1531 Map<SequenceI, List<AlignmentAnnotation>> candidates)
1533 final SequenceGroup selectionGroup = this.ap.av.getSelectionGroup();
1534 final AlignmentI alignment = this.ap.getAlignment();
1535 AlignmentUtils.addReferenceAnnotations(candidates, alignment,
1540 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1542 if (!ap.av.getAlignment().hasSeqrep())
1544 // initialise the display flags so the user sees something happen
1545 ap.av.setDisplayReferenceSeq(true);
1546 ap.av.setColourByReferenceSeq(true);
1547 ap.av.getAlignment().setSeqrep(sequence);
1551 if (ap.av.getAlignment().getSeqrep() == sequence)
1553 ap.av.getAlignment().setSeqrep(null);
1557 ap.av.getAlignment().setSeqrep(sequence);
1563 protected void hideInsertions_actionPerformed(ActionEvent actionEvent)
1565 HiddenColumns hidden = ap.av.getAlignment().getHiddenColumns();
1566 BitSet inserts = new BitSet();
1568 boolean markedPopup = false;
1569 // mark inserts in current selection
1570 if (ap.av.getSelectionGroup() != null)
1572 // mark just the columns in the selection group to be hidden
1573 inserts.set(ap.av.getSelectionGroup().getStartRes(),
1574 ap.av.getSelectionGroup().getEndRes() + 1); // TODO why +1?
1576 // now clear columns without gaps
1577 for (SequenceI sq : ap.av.getSelectionGroup().getSequences())
1583 inserts.and(sq.getInsertionsAsBits());
1585 hidden.clearAndHideColumns(inserts, ap.av.getSelectionGroup().getStartRes(),
1586 ap.av.getSelectionGroup().getEndRes());
1589 // now mark for sequence under popup if we haven't already done it
1590 else if (!markedPopup && sequence != null)
1592 inserts.or(sequence.getInsertionsAsBits());
1594 // and set hidden columns accordingly
1595 hidden.hideColumns(inserts);
1600 protected void sequenceSelectionDetails_actionPerformed()
1602 createSequenceDetailsReport(ap.av.getSequenceSelection());
1605 protected void sequenceDetails_actionPerformed()
1607 createSequenceDetailsReport(new SequenceI[] { sequence });
1610 public void createSequenceDetailsReport(SequenceI[] sequences)
1612 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1613 StringBuilder contents = new StringBuilder(128);
1614 for (SequenceI seq : sequences)
1616 contents.append("<p><h2>" + MessageManager.formatMessage(
1617 "label.create_sequence_details_report_annotation_for",
1619 { seq.getDisplayId(true) }) + "</h2></p><p>");
1620 new SequenceAnnotationReport(null).createSequenceAnnotationReport(
1621 contents, seq, true, true, ap.getSeqPanel().seqCanvas.fr);
1622 contents.append("</p>");
1624 cap.setText("<html>" + contents.toString() + "</html>");
1626 Desktop.addInternalFrame(cap,
1627 MessageManager.formatMessage("label.sequence_details_for",
1628 (sequences.length == 1 ? new Object[]
1629 { sequences[0].getDisplayId(true) }
1632 .getString("label.selection") })),
1637 protected void showNonconserved_actionPerformed()
1639 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1644 * call to refresh view after settings change
1648 ap.updateAnnotation();
1649 // removed paintAlignment(true) here:
1650 // updateAnnotation calls paintAlignment already, so don't need to call
1653 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1657 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1658 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1668 public void abovePIDColour_actionPerformed(boolean selected)
1670 SequenceGroup sg = getGroup();
1678 sg.cs.setConsensus(AAFrequency.calculate(
1679 sg.getSequences(ap.av.getHiddenRepSequences()),
1680 sg.getStartRes(), sg.getEndRes() + 1));
1682 int threshold = SliderPanel.setPIDSliderSource(ap,
1683 sg.getGroupColourScheme(), getGroup().getName());
1685 sg.cs.setThreshold(threshold, ap.av.isIgnoreGapsConsensus());
1687 SliderPanel.showPIDSlider();
1690 // remove PIDColouring
1692 sg.cs.setThreshold(0, ap.av.isIgnoreGapsConsensus());
1693 SliderPanel.hidePIDSlider();
1695 modifyPID.setEnabled(selected);
1701 * Open a panel where the user can choose which types of sequence annotation
1706 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1708 // todo correct way to guard against opening a duplicate panel?
1709 new AnnotationChooser(ap);
1718 public void conservationMenuItem_actionPerformed(boolean selected)
1720 SequenceGroup sg = getGroup();
1728 // JBPNote: Conservation name shouldn't be i18n translated
1729 Conservation c = new Conservation("Group",
1730 sg.getSequences(ap.av.getHiddenRepSequences()),
1731 sg.getStartRes(), sg.getEndRes() + 1);
1734 c.verdict(false, ap.av.getConsPercGaps());
1735 sg.cs.setConservation(c);
1737 SliderPanel.setConservationSlider(ap, sg.getGroupColourScheme(),
1739 SliderPanel.showConservationSlider();
1742 // remove ConservationColouring
1744 sg.cs.setConservation(null);
1745 SliderPanel.hideConservationSlider();
1747 modifyConservation.setEnabled(selected);
1753 * Shows a dialog where group name and description may be edited
1755 protected void groupName_actionPerformed()
1757 SequenceGroup sg = getGroup();
1758 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1759 sg.getDescription(),
1760 MessageManager.getString("label.group_name"),
1761 MessageManager.getString("label.group_description"));
1762 dialog.showDialog(ap.alignFrame,
1763 MessageManager.getString("label.edit_group_name_description"),
1764 new RunResponse(JvOptionPane.OK_OPTION)
1769 sg.setName(dialog.getName());
1770 sg.setDescription(dialog.getDescription());
1777 * Get selection group - adding it to the alignment if necessary.
1779 * @return sequence group to operate on
1781 SequenceGroup getGroup()
1783 SequenceGroup sg = ap.av.getSelectionGroup();
1784 // this method won't add a new group if it already exists
1787 ap.av.getAlignment().addGroup(sg);
1794 * Shows a dialog where sequence name and description may be edited
1796 void sequenceName_actionPerformed()
1798 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1799 sequence.getDescription(),
1800 MessageManager.getString("label.sequence_name"),
1801 MessageManager.getString("label.sequence_description"));
1802 dialog.showDialog(ap.alignFrame,
1803 MessageManager.getString(
1804 "label.edit_sequence_name_description"),
1805 new RunResponse(JvOptionPane.OK_OPTION)
1810 if (dialog.getName() != null)
1812 if (dialog.getName().indexOf(" ") > -1)
1814 JvOptionPane.showMessageDialog(ap,
1815 MessageManager.getString(
1816 "label.spaces_converted_to_underscores"),
1817 MessageManager.getString(
1818 "label.no_spaces_allowed_sequence_name"),
1819 JvOptionPane.WARNING_MESSAGE);
1821 sequence.setName(dialog.getName().replace(' ', '_'));
1822 ap.paintAlignment(false, false);
1824 sequence.setDescription(dialog.getDescription());
1825 ap.av.firePropertyChange("alignment", null,
1826 ap.av.getAlignment().getSequences());
1837 void unGroupMenuItem_actionPerformed()
1839 SequenceGroup sg = ap.av.getSelectionGroup();
1840 ap.av.getAlignment().deleteGroup(sg);
1841 ap.av.setSelectionGroup(null);
1845 void createGroupMenuItem_actionPerformed()
1847 getGroup(); // implicitly creates group - note - should apply defaults / use
1848 // standard alignment window logic for this
1853 * Offers a colour chooser and sets the selected colour as the group outline
1855 protected void outline_actionPerformed()
1857 String title = MessageManager
1858 .getString("label.select_outline_colour");
1859 ColourChooserListener listener = new ColourChooserListener()
1862 public void colourSelected(Color c)
1864 getGroup().setOutlineColour(c);
1868 JalviewColourChooser.showColourChooser(Desktop.getDesktop(),
1869 title, Color.BLUE, listener);
1878 public void showBoxes_actionPerformed()
1880 getGroup().setDisplayBoxes(showBoxes.isSelected());
1890 public void showText_actionPerformed()
1892 getGroup().setDisplayText(showText.isSelected());
1902 public void showColourText_actionPerformed()
1904 getGroup().setColourText(showColourText.isSelected());
1908 public void showLink(String url)
1912 jalview.util.BrowserLauncher.openURL(url);
1913 } catch (Exception ex)
1915 JvOptionPane.showInternalMessageDialog(Desktop.desktop,
1916 MessageManager.getString("label.web_browser_not_found_unix"),
1917 MessageManager.getString("label.web_browser_not_found"),
1918 JvOptionPane.WARNING_MESSAGE);
1920 ex.printStackTrace();
1924 void hideSequences(boolean representGroup)
1926 ap.av.hideSequences(sequence, representGroup);
1929 public void copy_actionPerformed()
1931 ap.alignFrame.copy_actionPerformed(null);
1934 public void cut_actionPerformed()
1936 ap.alignFrame.cut_actionPerformed(null);
1939 void changeCase(ActionEvent e)
1941 Object source = e.getSource();
1942 SequenceGroup sg = ap.av.getSelectionGroup();
1946 List<int[]> startEnd = ap.av.getVisibleRegionBoundaries(
1947 sg.getStartRes(), sg.getEndRes() + 1);
1952 if (source == toggle)
1954 description = MessageManager.getString("label.toggle_case");
1955 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1957 else if (source == upperCase)
1959 description = MessageManager.getString("label.to_upper_case");
1960 caseChange = ChangeCaseCommand.TO_UPPER;
1964 description = MessageManager.getString("label.to_lower_case");
1965 caseChange = ChangeCaseCommand.TO_LOWER;
1968 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1969 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1970 startEnd, caseChange);
1972 ap.alignFrame.addHistoryItem(caseCommand);
1974 ap.av.firePropertyChange("alignment", null,
1975 ap.av.getAlignment().getSequences());
1980 public void outputText_actionPerformed(ActionEvent e)
1982 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1983 cap.setForInput(null);
1984 Desktop.addInternalFrame(cap, MessageManager
1985 .formatMessage("label.alignment_output_command", new Object[]
1986 { e.getActionCommand() }), 600, 500);
1988 String[] omitHidden = null;
1990 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1991 // or we simply trust the user wants
1992 // wysiwig behaviour
1994 FileFormatI fileFormat = FileFormats.getInstance()
1995 .forName(e.getActionCommand());
1997 new FormatAdapter(ap).formatSequences(fileFormat, ap, true));
2000 public void sequenceFeature_actionPerformed()
2002 SequenceGroup sg = ap.av.getSelectionGroup();
2008 List<SequenceI> seqs = new ArrayList<>();
2009 List<SequenceFeature> features = new ArrayList<>();
2012 * assemble dataset sequences, and template new sequence features,
2013 * for the amend features dialog
2015 int gSize = sg.getSize();
2016 for (int i = 0; i < gSize; i++)
2018 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2019 int end = sg.findEndRes(sg.getSequenceAt(i));
2022 seqs.add(sg.getSequenceAt(i).getDatasetSequence());
2023 features.add(new SequenceFeature(null, null, start, end, null));
2028 * an entirely gapped region will generate empty lists of sequence / features
2030 if (!seqs.isEmpty())
2032 new FeatureEditor(ap).createFeatures(seqs, features, new Runnable()
2036 ap.alignFrame.setShowSeqFeatures(true);
2037 ap.av.setSearchResults(null); // clear highlighting
2038 ap.repaint(); // draw new/amended features
2044 public void textColour_actionPerformed()
2046 SequenceGroup sg = getGroup();
2049 new TextColourChooser().chooseColour(ap, sg);
2053 public void colourByStructure(String pdbid)
2055 Annotation[] anots = ap.av.getStructureSelectionManager()
2056 .colourSequenceFromStructure(sequence, pdbid);
2058 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2059 "Coloured by " + pdbid, anots);
2061 ap.av.getAlignment().addAnnotation(an);
2062 an.createSequenceMapping(sequence, 0, true);
2063 // an.adjustForAlignment();
2064 ap.av.getAlignment().setAnnotationIndex(an, 0);
2066 ap.adjustAnnotationHeight();
2068 sequence.addAlignmentAnnotation(an);
2073 * Shows a dialog where sequence characters may be edited. Any changes are
2074 * applied, and added as an available 'Undo' item in the edit commands
2077 public void editSequence_actionPerformed()
2079 SequenceGroup sg = ap.av.getSelectionGroup();
2083 if (sequence == null)
2085 sequence = sg.getSequenceAt(0);
2088 EditNameDialog dialog = new EditNameDialog(
2089 sequence.getSequenceAsString(sg.getStartRes(),
2090 sg.getEndRes() + 1),
2091 null, MessageManager.getString("label.edit_sequence"), null);
2092 dialog.showDialog(ap.alignFrame,
2093 MessageManager.getString("label.edit_sequence"),
2094 new RunResponse(JvOptionPane.OK_OPTION)
2099 EditCommand editCommand = new EditCommand(
2100 MessageManager.getString("label.edit_sequences"),
2102 dialog.getName().replace(' ',
2103 ap.av.getGapCharacter()),
2104 sg.getSequencesAsArray(
2105 ap.av.getHiddenRepSequences()),
2106 sg.getStartRes(), sg.getEndRes() + 1,
2107 ap.av.getAlignment());
2108 ap.alignFrame.addHistoryItem(editCommand);
2109 ap.av.firePropertyChange("alignment", null,
2110 ap.av.getAlignment().getSequences());
2117 * Action on user selecting an item from the colour menu (that does not have
2118 * its bespoke action handler)
2123 public void changeColour_actionPerformed(String colourSchemeName)
2125 SequenceGroup sg = getGroup();
2127 * switch to the chosen colour scheme (or null for None)
2129 ColourSchemeI colourScheme = ColourSchemes.getInstance()
2130 .getColourScheme(colourSchemeName, sg,
2131 ap.av.getHiddenRepSequences());
2132 sg.setColourScheme(colourScheme);
2133 if (colourScheme instanceof Blosum62ColourScheme
2134 || colourScheme instanceof PIDColourScheme)
2136 sg.cs.setConsensus(AAFrequency.calculate(
2137 sg.getSequences(ap.av.getHiddenRepSequences()),
2138 sg.getStartRes(), sg.getEndRes() + 1));