2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 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.Conservation;
25 import jalview.commands.ChangeCaseCommand;
26 import jalview.commands.EditCommand;
27 import jalview.datamodel.AlignmentAnnotation;
28 import jalview.datamodel.Annotation;
29 import jalview.datamodel.DBRefEntry;
30 import jalview.datamodel.PDBEntry;
31 import jalview.datamodel.Sequence;
32 import jalview.datamodel.SequenceFeature;
33 import jalview.datamodel.SequenceGroup;
34 import jalview.datamodel.SequenceI;
35 import jalview.io.FormatAdapter;
36 import jalview.io.SequenceAnnotationReport;
37 import jalview.schemes.AnnotationColourGradient;
38 import jalview.schemes.Blosum62ColourScheme;
39 import jalview.schemes.BuriedColourScheme;
40 import jalview.schemes.ClustalxColourScheme;
41 import jalview.schemes.HelixColourScheme;
42 import jalview.schemes.HydrophobicColourScheme;
43 import jalview.schemes.NucleotideColourScheme;
44 import jalview.schemes.PIDColourScheme;
45 import jalview.schemes.PurinePyrimidineColourScheme;
46 import jalview.schemes.ResidueProperties;
47 import jalview.schemes.StrandColourScheme;
48 import jalview.schemes.TaylorColourScheme;
49 import jalview.schemes.TurnColourScheme;
50 import jalview.schemes.UserColourScheme;
51 import jalview.schemes.ZappoColourScheme;
52 import jalview.util.GroupUrlLink;
53 import jalview.util.GroupUrlLink.UrlStringTooLongException;
54 import jalview.util.MessageManager;
55 import jalview.util.UrlLink;
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.Hashtable;
62 import java.util.List;
63 import java.util.Vector;
65 import javax.swing.ButtonGroup;
66 import javax.swing.JCheckBoxMenuItem;
67 import javax.swing.JColorChooser;
68 import javax.swing.JMenu;
69 import javax.swing.JMenuItem;
70 import javax.swing.JOptionPane;
71 import javax.swing.JPopupMenu;
72 import javax.swing.JRadioButtonMenuItem;
78 * @version $Revision: 1.118 $
80 public class PopupMenu extends JPopupMenu
82 JMenu groupMenu = new JMenu();
84 JMenuItem groupName = new JMenuItem();
86 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
88 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
90 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
92 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
94 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
96 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
98 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
100 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
102 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
104 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
106 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
108 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
110 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
112 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
114 // protected JRadioButtonMenuItem covariationColour = new
115 // JRadioButtonMenuItem();
117 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
119 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
123 JMenu sequenceMenu = new JMenu();
125 JMenuItem sequenceName = new JMenuItem();
127 JMenuItem sequenceDetails = new JMenuItem();
129 JMenuItem sequenceSelDetails = new JMenuItem();
131 JMenuItem chooseAnnotations = new JMenuItem();
135 JMenuItem createGroupMenuItem = new JMenuItem();
137 JMenuItem unGroupMenuItem = new JMenuItem();
139 JMenuItem outline = new JMenuItem();
141 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
143 JMenu colourMenu = new JMenu();
145 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
147 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
149 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
151 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
153 JMenu editMenu = new JMenu();
155 JMenuItem cut = new JMenuItem();
157 JMenuItem copy = new JMenuItem();
159 JMenuItem upperCase = new JMenuItem();
161 JMenuItem lowerCase = new JMenuItem();
163 JMenuItem toggle = new JMenuItem();
165 JMenu pdbMenu = new JMenu();
167 JMenuItem pdbFromFile = new JMenuItem();
169 // JBPNote: Commented these out - Should add these services via the web
170 // services menu system.
171 // JMenuItem ContraFold = new JMenuItem();
173 // JMenuItem RNAFold = new JMenuItem();
175 JMenuItem enterPDB = new JMenuItem();
177 JMenuItem discoverPDB = new JMenuItem();
179 JMenu outputMenu = new JMenu();
181 JMenu showAnnotationsMenu = new JMenu();
183 JMenu hideAnnotationsMenu = new JMenu();
185 JMenuItem sequenceFeature = new JMenuItem();
187 JMenuItem textColour = new JMenuItem();
189 JMenu jMenu1 = new JMenu();
191 JMenu structureMenu = new JMenu();
193 JMenu viewStructureMenu = new JMenu();
195 // JMenu colStructureMenu = new JMenu();
196 JMenuItem editSequence = new JMenuItem();
198 // JMenuItem annotationMenuItem = new JMenuItem();
200 JMenu groupLinksMenu;
203 * Creates a new PopupMenu object.
210 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
212 this(ap, seq, links, null);
222 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
223 Vector links, Vector groupLinks)
225 // /////////////////////////////////////////////////////////
226 // If this is activated from the sequence panel, the user may want to
227 // edit or annotate a particular residue. Therefore display the residue menu
229 // If from the IDPanel, we must display the sequence menu
230 // ////////////////////////////////////////////////////////
234 ButtonGroup colours = new ButtonGroup();
235 colours.add(noColourmenuItem);
236 colours.add(clustalColour);
237 colours.add(zappoColour);
238 colours.add(taylorColour);
239 colours.add(hydrophobicityColour);
240 colours.add(helixColour);
241 colours.add(strandColour);
242 colours.add(turnColour);
243 colours.add(buriedColour);
244 colours.add(abovePIDColour);
245 colours.add(userDefinedColour);
246 colours.add(PIDColour);
247 colours.add(BLOSUM62Colour);
248 colours.add(purinePyrimidineColour);
249 colours.add(RNAInteractionColour);
250 // colours.add(covariationColour);
252 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
254 JMenuItem item = new JMenuItem(
255 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
257 item.addActionListener(new java.awt.event.ActionListener()
260 public void actionPerformed(ActionEvent e)
262 outputText_actionPerformed(e);
266 outputMenu.add(item);
269 buildAnnotationTypesMenu();
274 } catch (Exception e)
282 sequenceMenu.setText(sequence.getName());
284 if (seq.getDatasetSequence().getPDBId() != null
285 && seq.getDatasetSequence().getPDBId().size() > 0)
287 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
290 while (e.hasMoreElements())
292 final PDBEntry pdb = (PDBEntry) e.nextElement();
294 menuItem = new JMenuItem();
295 menuItem.setText(pdb.getId());
296 menuItem.addActionListener(new java.awt.event.ActionListener()
299 public void actionPerformed(ActionEvent e)
301 // TODO re JAL-860: optionally open dialog or provide a menu entry
302 // allowing user to open just one structure per sequence
303 // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
304 // { pdb })[0], null, ap);
305 new StructureViewer(ap.getStructureSelectionManager())
307 ap.av.collateForPDB(new PDBEntry[]
308 { pdb })[0], null, ap);
312 viewStructureMenu.add(menuItem);
315 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
316 * menuItem.addActionListener(new java.awt.event.ActionListener() {
317 * public void actionPerformed(ActionEvent e) {
318 * colourByStructure(pdb.getId()); } });
319 * colStructureMenu.add(menuItem);
325 if (ap.av.getAlignment().isNucleotide() == false)
327 structureMenu.remove(viewStructureMenu);
329 // structureMenu.remove(colStructureMenu);
332 if (ap.av.getAlignment().isNucleotide() == true)
334 AlignmentAnnotation[] aa = ap.av.getAlignment()
335 .getAlignmentAnnotation();
336 for (int i = 0; i < aa.length; i++)
338 if (aa[i].getRNAStruc() != null)
340 final String rnastruc = aa[i].getRNAStruc();
341 final String structureLine = aa[i].label;
342 menuItem = new JMenuItem();
343 menuItem.setText(MessageManager.formatMessage(
344 "label.2d_rna_structure_line", new String[]
346 menuItem.addActionListener(new java.awt.event.ActionListener()
350 public void actionPerformed(ActionEvent e)
352 // System.out.println("1:"+structureLine);
353 System.out.println("1:sname" + seq.getName());
354 System.out.println("2:seq" + seq);
356 // System.out.println("3:"+seq.getSequenceAsString());
357 System.out.println("3:strucseq" + rnastruc);
358 // System.out.println("4:struc"+seq.getRNA());
359 System.out.println("5:name" + seq.getName());
360 System.out.println("6:ap" + ap);
361 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
362 rnastruc, seq.getName(), ap);
363 // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
364 // seq.getName(), ap);
365 System.out.println("end");
368 viewStructureMenu.add(menuItem);
372 // SequenceFeatures[] test = seq.getSequenceFeatures();
374 if (seq.getAnnotation() != null)
376 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
377 for (int i = 0; i < seqAnno.length; i++)
379 if (seqAnno[i].getRNAStruc() != null)
381 final String rnastruc = seqAnno[i].getRNAStruc();
383 // TODO: make rnastrucF a bit more nice
384 menuItem = new JMenuItem();
385 menuItem.setText(MessageManager.formatMessage(
386 "label.2d_rna_sequence_name", new String[]
388 menuItem.addActionListener(new java.awt.event.ActionListener()
391 public void actionPerformed(ActionEvent e)
393 // TODO: VARNA does'nt print gaps in the sequence
395 new AppVarna(seq.getName() + " structure", seq, seq
396 .getSequenceAsString(), rnastruc, seq.getName(),
400 viewStructureMenu.add(menuItem);
407 menuItem = new JMenuItem(
408 MessageManager.getString("action.hide_sequences"));
409 menuItem.addActionListener(new java.awt.event.ActionListener()
412 public void actionPerformed(ActionEvent e)
414 hideSequences(false);
419 if (ap.av.getSelectionGroup() != null
420 && ap.av.getSelectionGroup().getSize() > 1)
422 menuItem = new JMenuItem(MessageManager.formatMessage(
423 "label.represent_group_with", new String[]
425 menuItem.addActionListener(new java.awt.event.ActionListener()
428 public void actionPerformed(ActionEvent e)
433 sequenceMenu.add(menuItem);
436 if (ap.av.hasHiddenRows())
438 final int index = ap.av.getAlignment().findIndex(seq);
440 if (ap.av.adjustForHiddenSeqs(index)
441 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
443 menuItem = new JMenuItem(
444 MessageManager.getString("action.reveal_sequences"));
445 menuItem.addActionListener(new ActionListener()
448 public void actionPerformed(ActionEvent e)
450 ap.av.showSequence(index);
451 if (ap.overviewPanel != null)
453 ap.overviewPanel.updateOverviewImage();
461 // for the case when no sequences are even visible
462 if (ap.av.hasHiddenRows())
465 menuItem = new JMenuItem(
466 MessageManager.getString("action.reveal_all"));
467 menuItem.addActionListener(new ActionListener()
470 public void actionPerformed(ActionEvent e)
472 ap.av.showAllHiddenSeqs();
473 if (ap.overviewPanel != null)
475 ap.overviewPanel.updateOverviewImage();
485 SequenceGroup sg = ap.av.getSelectionGroup();
486 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
487 .getGroups().contains(sg) : false;
489 if (sg != null && sg.getSize() > 0)
491 groupName.setText(MessageManager.formatMessage("label.name_param",
494 groupName.setText(MessageManager
495 .getString("label.edit_name_and_description_current_group"));
497 if (sg.cs instanceof ZappoColourScheme)
499 zappoColour.setSelected(true);
501 else if (sg.cs instanceof TaylorColourScheme)
503 taylorColour.setSelected(true);
505 else if (sg.cs instanceof PIDColourScheme)
507 PIDColour.setSelected(true);
509 else if (sg.cs instanceof Blosum62ColourScheme)
511 BLOSUM62Colour.setSelected(true);
513 else if (sg.cs instanceof UserColourScheme)
515 userDefinedColour.setSelected(true);
517 else if (sg.cs instanceof HydrophobicColourScheme)
519 hydrophobicityColour.setSelected(true);
521 else if (sg.cs instanceof HelixColourScheme)
523 helixColour.setSelected(true);
525 else if (sg.cs instanceof StrandColourScheme)
527 strandColour.setSelected(true);
529 else if (sg.cs instanceof TurnColourScheme)
531 turnColour.setSelected(true);
533 else if (sg.cs instanceof BuriedColourScheme)
535 buriedColour.setSelected(true);
537 else if (sg.cs instanceof ClustalxColourScheme)
539 clustalColour.setSelected(true);
541 else if (sg.cs instanceof PurinePyrimidineColourScheme)
543 purinePyrimidineColour.setSelected(true);
547 * else if (sg.cs instanceof CovariationColourScheme) {
548 * covariationColour.setSelected(true); }
552 noColourmenuItem.setSelected(true);
555 if (sg.cs != null && sg.cs.conservationApplied())
557 conservationMenuItem.setSelected(true);
559 displayNonconserved.setSelected(sg.getShowNonconserved());
560 showText.setSelected(sg.getDisplayText());
561 showColourText.setSelected(sg.getColourText());
562 showBoxes.setSelected(sg.getDisplayBoxes());
563 // add any groupURLs to the groupURL submenu and make it visible
564 if (groupLinks != null && groupLinks.size() > 0)
566 buildGroupURLMenu(sg, groupLinks);
568 // Add a 'show all structures' for the current selection
569 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
570 SequenceI sqass = null;
571 for (SequenceI sq : ap.av.getSequenceSelection())
573 Vector<PDBEntry> pes = sq.getDatasetSequence()
575 if (pes != null && pes.size() > 0)
577 reppdb.put(pes.get(0).getId(), pes.get(0));
578 for (PDBEntry pe : pes)
580 pdbe.put(pe.getId(), pe);
590 final PDBEntry[] pe = pdbe.values().toArray(
591 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
592 new PDBEntry[reppdb.size()]);
593 final JMenuItem gpdbview, rpdbview;
594 if (pdbe.size() == 1)
596 structureMenu.add(gpdbview = new JMenuItem(MessageManager
597 .formatMessage("label.view_structure_for", new String[]
598 { sqass.getDisplayId(false) })));
602 structureMenu.add(gpdbview = new JMenuItem(MessageManager
603 .formatMessage("label.view_all_structures", new String[]
604 { new Integer(pdbe.size()).toString() })));
606 gpdbview.setToolTipText(MessageManager
607 .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
608 gpdbview.addActionListener(new ActionListener()
612 public void actionPerformed(ActionEvent e)
614 new StructureViewer(ap.getStructureSelectionManager())
615 .viewStructures(ap, pe, ap.av.collateForPDB(pe));
618 if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
620 structureMenu.add(rpdbview = new JMenuItem(MessageManager
622 "label.view_all_representative_structures",
624 { new Integer(reppdb.size()).toString() })));
625 rpdbview.setToolTipText(MessageManager
626 .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
627 rpdbview.addActionListener(new ActionListener()
631 public void actionPerformed(ActionEvent e)
633 new StructureViewer(ap.getStructureSelectionManager())
634 .viewStructures(ap, pr, ap.av.collateForPDB(pr));
642 groupMenu.setVisible(false);
643 editMenu.setVisible(false);
648 createGroupMenuItem.setVisible(true);
649 unGroupMenuItem.setVisible(false);
650 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
654 createGroupMenuItem.setVisible(false);
655 unGroupMenuItem.setVisible(true);
656 jMenu1.setText(MessageManager.getString("action.edit_group"));
661 sequenceMenu.setVisible(false);
662 structureMenu.setVisible(false);
665 if (links != null && links.size() > 0)
668 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
669 Vector linkset = new Vector();
670 for (int i = 0; i < links.size(); i++)
672 String link = links.elementAt(i).toString();
673 UrlLink urlLink = null;
676 urlLink = new UrlLink(link);
677 } catch (Exception foo)
679 jalview.bin.Cache.log.error("Exception for URLLink '" + link
684 if (!urlLink.isValid())
686 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
689 final String label = urlLink.getLabel();
690 if (seq != null && urlLink.isDynamic())
693 // collect matching db-refs
694 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
695 seq.getDBRef(), new String[]
696 { urlLink.getTarget() });
697 // collect id string too
698 String id = seq.getName();
699 String descr = seq.getDescription();
700 if (descr != null && descr.length() < 1)
707 for (int r = 0; r < dbr.length; r++)
709 if (id != null && dbr[r].getAccessionId().equals(id))
711 // suppress duplicate link creation for the bare sequence ID
712 // string with this link
715 // create Bare ID link for this RUL
716 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
720 for (int u = 0; u < urls.length; u += 2)
722 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
724 linkset.addElement(urls[u] + "|" + urls[u + 1]);
725 addshowLink(linkMenu, label + "|" + urls[u],
734 // create Bare ID link for this RUL
735 String[] urls = urlLink.makeUrls(id, true);
738 for (int u = 0; u < urls.length; u += 2)
740 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
742 linkset.addElement(urls[u] + "|" + urls[u + 1]);
743 addshowLink(linkMenu, label, urls[u + 1]);
748 // Create urls from description but only for URL links which are regex
750 if (descr != null && urlLink.getRegexReplace() != null)
752 // create link for this URL from description where regex matches
753 String[] urls = urlLink.makeUrls(descr, true);
756 for (int u = 0; u < urls.length; u += 2)
758 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
760 linkset.addElement(urls[u] + "|" + urls[u + 1]);
761 addshowLink(linkMenu, label, urls[u + 1]);
769 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
771 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
772 // Add a non-dynamic link
773 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
777 if (sequence != null)
779 sequenceMenu.add(linkMenu);
789 * Find which sequence-specific annotation types are associated with the
790 * current selection, and add these as menu items (for show / hide annotation
793 protected void buildAnnotationTypesMenu()
795 List<String> found = new ArrayList<String>();
796 for (AlignmentAnnotation aa : ap.getAlignment()
797 .getAlignmentAnnotation())
799 if (aa.sequenceRef != null)
801 if (ap.av.getSelectionGroup().getSequences()
802 .contains(aa.sequenceRef))
804 final String label = aa.label;
805 if (!found.contains(label))
808 final JMenuItem showitem = new JMenuItem(label);
809 showitem.addActionListener(new java.awt.event.ActionListener()
812 public void actionPerformed(ActionEvent e)
814 showHideAnnotation_actionPerformed(label, true);
817 showAnnotationsMenu.add(showitem);
818 final JMenuItem hideitem = new JMenuItem(label);
819 hideitem.addActionListener(new java.awt.event.ActionListener()
822 public void actionPerformed(ActionEvent e)
824 showHideAnnotation_actionPerformed(label, false);
827 hideAnnotationsMenu.add(hideitem);
835 * Action on selecting an annotation type to show or hide for the selection.
840 protected void showHideAnnotation_actionPerformed(String type,
843 for (AlignmentAnnotation aa : ap.getAlignment()
844 .getAlignmentAnnotation())
846 if (aa.sequenceRef != null && type.equals(aa.label))
848 if (ap.av.getSelectionGroup().getSequences()
849 .contains(aa.sequenceRef))
858 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
861 // TODO: usability: thread off the generation of group url content so root
863 // sequence only URLs
864 // ID/regex match URLs
865 groupLinksMenu = new JMenu(
866 MessageManager.getString("action.group_link"));
867 JMenu[] linkMenus = new JMenu[]
868 { null, new JMenu(MessageManager.getString("action.ids")),
869 new JMenu(MessageManager.getString("action.sequences")),
870 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
877 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
878 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
879 Hashtable commonDbrefs = new Hashtable();
880 for (int sq = 0; sq < seqs.length; sq++)
883 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
884 .findPosition(sg.getEndRes());
885 // just collect ids from dataset sequence
886 // TODO: check if IDs collected from selecton group intersects with the
887 // current selection, too
888 SequenceI sqi = seqs[sq];
889 while (sqi.getDatasetSequence() != null)
891 sqi = sqi.getDatasetSequence();
893 DBRefEntry[] dbr = sqi.getDBRef();
894 if (dbr != null && dbr.length > 0)
896 for (int d = 0; d < dbr.length; d++)
898 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
899 Object[] sarray = (Object[]) commonDbrefs.get(src);
902 sarray = new Object[2];
903 sarray[0] = new int[]
905 sarray[1] = new String[seqs.length];
907 commonDbrefs.put(src, sarray);
910 if (((String[]) sarray[1])[sq] == null)
913 || (dbr[d].getMap().locateMappedRange(start, end) != null))
915 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
916 ((int[]) sarray[0])[0]++;
922 // now create group links for all distinct ID/sequence sets.
923 boolean addMenu = false; // indicates if there are any group links to give
925 for (int i = 0; i < groupLinks.size(); i++)
927 String link = groupLinks.elementAt(i).toString();
928 GroupUrlLink urlLink = null;
931 urlLink = new GroupUrlLink(link);
932 } catch (Exception foo)
934 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
939 if (!urlLink.isValid())
941 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
944 final String label = urlLink.getLabel();
945 boolean usingNames = false;
946 // Now see which parts of the group apply for this URL
947 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
948 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
949 String[] seqstr, ids; // input to makeUrl
952 int numinput = ((int[]) idset[0])[0];
953 String[] allids = ((String[]) idset[1]);
954 seqstr = new String[numinput];
955 ids = new String[numinput];
956 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
958 if (allids[sq] != null)
960 ids[idcount] = allids[sq];
961 seqstr[idcount++] = idandseqs[1][sq];
967 // just use the id/seq set
968 seqstr = idandseqs[1];
972 // and try and make the groupURL!
974 Object[] urlset = null;
977 urlset = urlLink.makeUrlStubs(ids, seqstr,
978 "FromJalview" + System.currentTimeMillis(), false);
979 } catch (UrlStringTooLongException e)
984 int type = urlLink.getGroupURLType() & 3;
985 // System.out.println(urlLink.getGroupURLType()
986 // +" "+((String[])urlset[3])[0]);
987 // first two bits ofurlLink type bitfield are sequenceids and sequences
988 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
989 addshowLink(linkMenus[type], label
990 + (((type & 1) == 1) ? ("("
991 + (usingNames ? "Names" : ltarget) + ")") : ""),
998 groupLinksMenu = new JMenu(
999 MessageManager.getString("action.group_link"));
1000 for (int m = 0; m < linkMenus.length; m++)
1002 if (linkMenus[m] != null
1003 && linkMenus[m].getMenuComponentCount() > 0)
1005 groupLinksMenu.add(linkMenus[m]);
1009 groupMenu.add(groupLinksMenu);
1014 * add a show URL menu item to the given linkMenu
1018 * - menu label string
1022 private void addshowLink(JMenu linkMenu, String label, final String url)
1024 JMenuItem item = new JMenuItem(label);
1025 item.setToolTipText(MessageManager.formatMessage(
1026 "label.open_url_param", new String[]
1028 item.addActionListener(new java.awt.event.ActionListener()
1031 public void actionPerformed(ActionEvent e)
1033 new Thread(new Runnable()
1050 * add a late bound groupURL item to the given linkMenu
1054 * - menu label string
1055 * @param urlgenerator
1056 * GroupURLLink used to generate URL
1058 * Object array returned from the makeUrlStubs function.
1060 private void addshowLink(JMenu linkMenu, String label,
1061 final GroupUrlLink urlgenerator, final Object[] urlstub)
1063 JMenuItem item = new JMenuItem(label);
1064 item.setToolTipText(MessageManager.formatMessage(
1065 "label.open_url_seqs_param",
1067 { urlgenerator.getUrl_prefix(),
1068 urlgenerator.getNumberInvolved(urlstub) }));
1069 // TODO: put in info about what is being sent.
1070 item.addActionListener(new java.awt.event.ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 new Thread(new Runnable()
1083 showLink(urlgenerator.constructFrom(urlstub));
1084 } catch (UrlStringTooLongException e)
1102 private void jbInit() throws Exception
1104 groupMenu.setText(MessageManager.getString("label.group"));
1105 groupMenu.setText(MessageManager.getString("label.selection"));
1106 groupName.setText(MessageManager.getString("label.name"));
1107 groupName.addActionListener(new java.awt.event.ActionListener()
1110 public void actionPerformed(ActionEvent e)
1112 groupName_actionPerformed();
1115 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1116 sequenceName.setText(MessageManager
1117 .getString("label.edit_name_description"));
1118 sequenceName.addActionListener(new java.awt.event.ActionListener()
1121 public void actionPerformed(ActionEvent e)
1123 sequenceName_actionPerformed();
1126 chooseAnnotations.setText(MessageManager
1127 .getString("label.choose_annotations") + "...");
1129 .addActionListener(new java.awt.event.ActionListener()
1132 public void actionPerformed(ActionEvent e)
1134 chooseAnnotations_actionPerformed(e);
1137 sequenceDetails.setText(MessageManager
1138 .getString("label.sequence_details") + "...");
1139 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1142 public void actionPerformed(ActionEvent e)
1144 sequenceDetails_actionPerformed();
1147 sequenceSelDetails.setText(MessageManager
1148 .getString("label.sequence_details") + "...");
1150 .addActionListener(new java.awt.event.ActionListener()
1153 public void actionPerformed(ActionEvent e)
1155 sequenceSelectionDetails_actionPerformed();
1158 PIDColour.setFocusPainted(false);
1160 .setText(MessageManager.getString("action.remove_group"));
1161 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 unGroupMenuItem_actionPerformed();
1169 createGroupMenuItem.setText(MessageManager
1170 .getString("action.create_group"));
1172 .addActionListener(new java.awt.event.ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 createGroupMenuItem_actionPerformed();
1181 outline.setText(MessageManager.getString("action.border_colour"));
1182 outline.addActionListener(new java.awt.event.ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 outline_actionPerformed();
1191 .setText(MessageManager.getString("label.nucleotide"));
1192 nucleotideMenuItem.addActionListener(new ActionListener()
1195 public void actionPerformed(ActionEvent e)
1197 nucleotideMenuItem_actionPerformed();
1200 colourMenu.setText(MessageManager.getString("label.group_colour"));
1201 showBoxes.setText(MessageManager.getString("action.boxes"));
1202 showBoxes.setState(true);
1203 showBoxes.addActionListener(new ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 showBoxes_actionPerformed();
1211 showText.setText(MessageManager.getString("action.text"));
1212 showText.setState(true);
1213 showText.addActionListener(new ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 showText_actionPerformed();
1221 showColourText.setText(MessageManager.getString("label.colour_text"));
1222 showColourText.addActionListener(new ActionListener()
1225 public void actionPerformed(ActionEvent e)
1227 showColourText_actionPerformed();
1230 displayNonconserved.setText(MessageManager
1231 .getString("label.show_non_conversed"));
1232 displayNonconserved.setState(true);
1233 displayNonconserved.addActionListener(new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 showNonconserved_actionPerformed();
1241 editMenu.setText(MessageManager.getString("action.edit"));
1242 cut.setText(MessageManager.getString("action.cut"));
1243 cut.addActionListener(new ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 cut_actionPerformed();
1251 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1252 upperCase.addActionListener(new ActionListener()
1255 public void actionPerformed(ActionEvent e)
1260 copy.setText(MessageManager.getString("action.copy"));
1261 copy.addActionListener(new ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 copy_actionPerformed();
1269 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1270 lowerCase.addActionListener(new ActionListener()
1273 public void actionPerformed(ActionEvent e)
1278 toggle.setText(MessageManager.getString("label.toggle_case"));
1279 toggle.addActionListener(new ActionListener()
1282 public void actionPerformed(ActionEvent e)
1287 pdbMenu.setText(MessageManager
1288 .getString("label.associate_structure_with_sequence"));
1289 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1290 pdbFromFile.addActionListener(new ActionListener()
1293 public void actionPerformed(ActionEvent e)
1295 pdbFromFile_actionPerformed();
1298 // RNAFold.setText("From RNA Fold with predict2D");
1299 // RNAFold.addActionListener(new ActionListener()
1301 // public void actionPerformed(ActionEvent e)
1304 // RNAFold_actionPerformed();
1305 // } catch (Exception e1) {
1306 // // TODO Auto-generated catch block
1307 // e1.printStackTrace();
1311 // ContraFold.setText("From Contra Fold with predict2D");
1312 // ContraFold.addActionListener(new ActionListener()
1314 // public void actionPerformed(ActionEvent e)
1317 // ContraFold_actionPerformed();
1318 // } catch (Exception e1) {
1319 // // TODO Auto-generated catch block
1320 // e1.printStackTrace();
1324 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1325 enterPDB.addActionListener(new ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 enterPDB_actionPerformed();
1333 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1334 discoverPDB.addActionListener(new ActionListener()
1337 public void actionPerformed(ActionEvent e)
1339 discoverPDB_actionPerformed();
1342 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1344 showAnnotationsMenu.setText(MessageManager
1345 .getString("label.show_annotations"));
1346 hideAnnotationsMenu.setText(MessageManager
1347 .getString("label.hide_annotations"));
1348 sequenceFeature.setText(MessageManager
1349 .getString("label.create_sequence_feature"));
1350 sequenceFeature.addActionListener(new ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 sequenceFeature_actionPerformed();
1358 textColour.setText(MessageManager.getString("label.text_colour"));
1359 textColour.addActionListener(new ActionListener()
1362 public void actionPerformed(ActionEvent e)
1364 textColour_actionPerformed();
1367 jMenu1.setText(MessageManager.getString("label.group"));
1368 structureMenu.setText(MessageManager.getString("label.structure"));
1369 viewStructureMenu.setText(MessageManager
1370 .getString("label.view_structure"));
1371 // colStructureMenu.setText("Colour By Structure");
1372 editSequence.setText(MessageManager.getString("label.edit_sequence")
1374 editSequence.addActionListener(new ActionListener()
1377 public void actionPerformed(ActionEvent actionEvent)
1379 editSequence_actionPerformed(actionEvent);
1384 * annotationMenuItem.setText("By Annotation");
1385 * annotationMenuItem.addActionListener(new ActionListener() { public void
1386 * actionPerformed(ActionEvent actionEvent) {
1387 * annotationMenuItem_actionPerformed(actionEvent); } });
1389 groupMenu.add(sequenceSelDetails);
1392 this.add(structureMenu);
1393 groupMenu.add(chooseAnnotations);
1394 groupMenu.add(showAnnotationsMenu);
1395 groupMenu.add(hideAnnotationsMenu);
1396 groupMenu.add(editMenu);
1397 groupMenu.add(outputMenu);
1398 groupMenu.add(sequenceFeature);
1399 groupMenu.add(createGroupMenuItem);
1400 groupMenu.add(unGroupMenuItem);
1401 groupMenu.add(jMenu1);
1402 sequenceMenu.add(sequenceName);
1403 sequenceMenu.add(sequenceDetails);
1404 colourMenu.add(textColour);
1405 colourMenu.add(noColourmenuItem);
1406 colourMenu.add(clustalColour);
1407 colourMenu.add(BLOSUM62Colour);
1408 colourMenu.add(PIDColour);
1409 colourMenu.add(zappoColour);
1410 colourMenu.add(taylorColour);
1411 colourMenu.add(hydrophobicityColour);
1412 colourMenu.add(helixColour);
1413 colourMenu.add(strandColour);
1414 colourMenu.add(turnColour);
1415 colourMenu.add(buriedColour);
1416 colourMenu.add(nucleotideMenuItem);
1417 if (ap.getAlignment().isNucleotide())
1419 // JBPNote - commented since the colourscheme isn't functional
1420 // colourMenu.add(RNAInteractionColour);
1421 colourMenu.add(purinePyrimidineColour);
1423 // colourMenu.add(covariationColour);
1424 colourMenu.add(userDefinedColour);
1426 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1428 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1429 .getUserColourSchemes().keys();
1431 while (userColours.hasMoreElements())
1433 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1434 item.addActionListener(new ActionListener()
1437 public void actionPerformed(ActionEvent evt)
1439 userDefinedColour_actionPerformed(evt);
1442 colourMenu.add(item);
1446 colourMenu.addSeparator();
1447 colourMenu.add(abovePIDColour);
1448 colourMenu.add(conservationMenuItem);
1449 // colourMenu.add(annotationMenuItem);
1452 editMenu.add(editSequence);
1453 editMenu.add(upperCase);
1454 editMenu.add(lowerCase);
1455 editMenu.add(toggle);
1456 pdbMenu.add(pdbFromFile);
1457 // JBPNote: These shouldn't be added here - should appear in a generic
1458 // 'apply web service to this sequence menu'
1459 // pdbMenu.add(RNAFold);
1460 // pdbMenu.add(ContraFold);
1461 pdbMenu.add(enterPDB);
1462 pdbMenu.add(discoverPDB);
1463 jMenu1.add(groupName);
1464 jMenu1.add(colourMenu);
1465 jMenu1.add(showBoxes);
1466 jMenu1.add(showText);
1467 jMenu1.add(showColourText);
1468 jMenu1.add(outline);
1469 jMenu1.add(displayNonconserved);
1470 structureMenu.add(pdbMenu);
1471 structureMenu.add(viewStructureMenu);
1472 // structureMenu.add(colStructureMenu);
1473 noColourmenuItem.setText(MessageManager.getString("label.none"));
1474 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1477 public void actionPerformed(ActionEvent e)
1479 noColourmenuItem_actionPerformed();
1483 clustalColour.setText(MessageManager
1484 .getString("label.clustalx_colours"));
1485 clustalColour.addActionListener(new java.awt.event.ActionListener()
1488 public void actionPerformed(ActionEvent e)
1490 clustalColour_actionPerformed();
1493 zappoColour.setText(MessageManager.getString("label.zappo"));
1494 zappoColour.addActionListener(new java.awt.event.ActionListener()
1497 public void actionPerformed(ActionEvent e)
1499 zappoColour_actionPerformed();
1502 taylorColour.setText(MessageManager.getString("label.taylor"));
1503 taylorColour.addActionListener(new java.awt.event.ActionListener()
1506 public void actionPerformed(ActionEvent e)
1508 taylorColour_actionPerformed();
1511 hydrophobicityColour.setText(MessageManager
1512 .getString("label.hydrophobicity"));
1513 hydrophobicityColour
1514 .addActionListener(new java.awt.event.ActionListener()
1517 public void actionPerformed(ActionEvent e)
1519 hydrophobicityColour_actionPerformed();
1522 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1523 helixColour.addActionListener(new java.awt.event.ActionListener()
1526 public void actionPerformed(ActionEvent e)
1528 helixColour_actionPerformed();
1531 strandColour.setText(MessageManager
1532 .getString("label.strand_propensity"));
1533 strandColour.addActionListener(new java.awt.event.ActionListener()
1536 public void actionPerformed(ActionEvent e)
1538 strandColour_actionPerformed();
1541 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1542 turnColour.addActionListener(new java.awt.event.ActionListener()
1545 public void actionPerformed(ActionEvent e)
1547 turnColour_actionPerformed();
1550 buriedColour.setText(MessageManager.getString("label.buried_index"));
1551 buriedColour.addActionListener(new java.awt.event.ActionListener()
1554 public void actionPerformed(ActionEvent e)
1556 buriedColour_actionPerformed();
1559 abovePIDColour.setText(MessageManager
1560 .getString("label.above_identity_percentage"));
1561 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1564 public void actionPerformed(ActionEvent e)
1566 abovePIDColour_actionPerformed();
1569 userDefinedColour.setText(MessageManager
1570 .getString("action.user_defined"));
1571 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1574 public void actionPerformed(ActionEvent e)
1576 userDefinedColour_actionPerformed(e);
1580 .setText(MessageManager.getString("label.percentage_identity"));
1581 PIDColour.addActionListener(new java.awt.event.ActionListener()
1584 public void actionPerformed(ActionEvent e)
1586 PIDColour_actionPerformed();
1589 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1590 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1593 public void actionPerformed(ActionEvent e)
1595 BLOSUM62Colour_actionPerformed();
1598 purinePyrimidineColour.setText(MessageManager
1599 .getString("label.purine_pyrimidine"));
1600 purinePyrimidineColour
1601 .addActionListener(new java.awt.event.ActionListener()
1604 public void actionPerformed(ActionEvent e)
1606 purinePyrimidineColour_actionPerformed();
1611 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1612 * public void actionPerformed(ActionEvent e) {
1613 * covariationColour_actionPerformed(); } });
1616 conservationMenuItem.setText(MessageManager
1617 .getString("label.conservation"));
1618 conservationMenuItem
1619 .addActionListener(new java.awt.event.ActionListener()
1622 public void actionPerformed(ActionEvent e)
1624 conservationMenuItem_actionPerformed();
1629 protected void sequenceSelectionDetails_actionPerformed()
1631 createSequenceDetailsReport(ap.av.getSequenceSelection());
1634 protected void sequenceDetails_actionPerformed()
1636 createSequenceDetailsReport(new SequenceI[]
1640 public void createSequenceDetailsReport(SequenceI[] sequences)
1642 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1643 StringBuffer contents = new StringBuffer();
1644 for (SequenceI seq : sequences)
1646 contents.append("<p><h2>"
1649 "label.create_sequence_details_report_annotation_for",
1651 { seq.getDisplayId(true) }) + "</h2></p><p>");
1652 new SequenceAnnotationReport(null)
1653 .createSequenceAnnotationReport(
1659 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1661 contents.append("</p>");
1663 cap.setText("<html>" + contents.toString() + "</html>");
1665 Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
1666 "label.sequece_details_for",
1667 (sequences.length == 1 ? new String[]
1668 { sequences[0].getDisplayId(true) } : new String[]
1669 { MessageManager.getString("label.selection") })), 500, 400);
1673 protected void showNonconserved_actionPerformed()
1675 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1680 * call to refresh view after settings change
1684 ap.updateAnnotation();
1685 ap.paintAlignment(true);
1687 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1696 protected void clustalColour_actionPerformed()
1698 SequenceGroup sg = getGroup();
1699 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1709 protected void zappoColour_actionPerformed()
1711 getGroup().cs = new ZappoColourScheme();
1721 protected void taylorColour_actionPerformed()
1723 getGroup().cs = new TaylorColourScheme();
1733 protected void hydrophobicityColour_actionPerformed()
1735 getGroup().cs = new HydrophobicColourScheme();
1745 protected void helixColour_actionPerformed()
1747 getGroup().cs = new HelixColourScheme();
1757 protected void strandColour_actionPerformed()
1759 getGroup().cs = new StrandColourScheme();
1769 protected void turnColour_actionPerformed()
1771 getGroup().cs = new TurnColourScheme();
1781 protected void buriedColour_actionPerformed()
1783 getGroup().cs = new BuriedColourScheme();
1793 public void nucleotideMenuItem_actionPerformed()
1795 getGroup().cs = new NucleotideColourScheme();
1799 protected void purinePyrimidineColour_actionPerformed()
1801 getGroup().cs = new PurinePyrimidineColourScheme();
1806 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1807 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1815 protected void abovePIDColour_actionPerformed()
1817 SequenceGroup sg = getGroup();
1823 if (abovePIDColour.isSelected())
1825 sg.cs.setConsensus(AAFrequency.calculate(
1826 sg.getSequences(ap.av.getHiddenRepSequences()),
1827 sg.getStartRes(), sg.getEndRes() + 1));
1829 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1832 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1834 SliderPanel.showPIDSlider();
1837 // remove PIDColouring
1839 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1851 protected void userDefinedColour_actionPerformed(ActionEvent e)
1853 SequenceGroup sg = getGroup();
1855 if (e.getSource().equals(userDefinedColour))
1857 new UserDefinedColours(ap, sg);
1861 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1862 .getUserColourSchemes().get(e.getActionCommand());
1870 * Open a panel where the user can choose which types of sequence annotation
1875 protected void chooseAnnotations_actionPerformed(ActionEvent e)
1877 // todo correct way to guard against opening a duplicate panel?
1878 new AnnotationChooser(ap);
1886 protected void PIDColour_actionPerformed()
1888 SequenceGroup sg = getGroup();
1889 sg.cs = new PIDColourScheme();
1890 sg.cs.setConsensus(AAFrequency.calculate(
1891 sg.getSequences(ap.av.getHiddenRepSequences()),
1892 sg.getStartRes(), sg.getEndRes() + 1));
1902 protected void BLOSUM62Colour_actionPerformed()
1904 SequenceGroup sg = getGroup();
1906 sg.cs = new Blosum62ColourScheme();
1908 sg.cs.setConsensus(AAFrequency.calculate(
1909 sg.getSequences(ap.av.getHiddenRepSequences()),
1910 sg.getStartRes(), sg.getEndRes() + 1));
1921 protected void noColourmenuItem_actionPerformed()
1923 getGroup().cs = null;
1933 protected void conservationMenuItem_actionPerformed()
1935 SequenceGroup sg = getGroup();
1941 if (conservationMenuItem.isSelected())
1943 // JBPNote: Conservation name shouldn't be i18n translated
1944 Conservation c = new Conservation("Group",
1945 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1946 .getHiddenRepSequences()), sg.getStartRes(),
1947 sg.getEndRes() + 1);
1950 c.verdict(false, ap.av.getConsPercGaps());
1952 sg.cs.setConservation(c);
1954 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1955 SliderPanel.showConservationSlider();
1958 // remove ConservationColouring
1960 sg.cs.setConservation(null);
1966 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1968 SequenceGroup sg = getGroup();
1974 AnnotationColourGradient acg = new AnnotationColourGradient(
1975 sequence.getAnnotation()[0], null,
1976 AnnotationColourGradient.NO_THRESHOLD);
1978 acg.setPredefinedColours(true);
1990 protected void groupName_actionPerformed()
1993 SequenceGroup sg = getGroup();
1994 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1995 sg.getDescription(), " "
1996 + MessageManager.getString("label.group_name") + " ",
1997 MessageManager.getString("label.group_description") + " ",
1998 MessageManager.getString("label.edit_group_name_description"),
2006 sg.setName(dialog.getName());
2007 sg.setDescription(dialog.getDescription());
2012 * Get selection group - adding it to the alignment if necessary.
2014 * @return sequence group to operate on
2016 SequenceGroup getGroup()
2018 SequenceGroup sg = ap.av.getSelectionGroup();
2019 // this method won't add a new group if it already exists
2022 ap.av.getAlignment().addGroup(sg);
2034 void sequenceName_actionPerformed()
2036 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
2037 sequence.getDescription(),
2038 " " + MessageManager.getString("label.sequence_name")
2040 MessageManager.getString("label.sequence_description") + " ",
2042 .getString("label.edit_sequence_name_description"),
2050 if (dialog.getName() != null)
2052 if (dialog.getName().indexOf(" ") > -1)
2058 .getString("label.spaces_converted_to_backslashes"),
2060 .getString("label.no_spaces_allowed_sequence_name"),
2061 JOptionPane.WARNING_MESSAGE);
2064 sequence.setName(dialog.getName().replace(' ', '_'));
2065 ap.paintAlignment(false);
2068 sequence.setDescription(dialog.getDescription());
2070 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2081 void unGroupMenuItem_actionPerformed()
2083 SequenceGroup sg = ap.av.getSelectionGroup();
2084 ap.av.getAlignment().deleteGroup(sg);
2085 ap.av.setSelectionGroup(null);
2089 void createGroupMenuItem_actionPerformed()
2091 getGroup(); // implicitly creates group - note - should apply defaults / use
2092 // standard alignment window logic for this
2102 protected void outline_actionPerformed()
2104 SequenceGroup sg = getGroup();
2105 Color col = JColorChooser.showDialog(this,
2106 MessageManager.getString("label.select_outline_colour"),
2111 sg.setOutlineColour(col);
2123 public void showBoxes_actionPerformed()
2125 getGroup().setDisplayBoxes(showBoxes.isSelected());
2135 public void showText_actionPerformed()
2137 getGroup().setDisplayText(showText.isSelected());
2147 public void showColourText_actionPerformed()
2149 getGroup().setColourText(showColourText.isSelected());
2153 public void showLink(String url)
2157 jalview.util.BrowserLauncher.openURL(url);
2158 } catch (Exception ex)
2160 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2161 MessageManager.getString("label.web_browser_not_found_unix"),
2162 MessageManager.getString("label.web_browser_not_found"),
2163 JOptionPane.WARNING_MESSAGE);
2165 ex.printStackTrace();
2169 void hideSequences(boolean representGroup)
2171 SequenceGroup sg = ap.av.getSelectionGroup();
2172 if (sg == null || sg.getSize() < 1)
2174 ap.av.hideSequence(new SequenceI[]
2179 ap.av.setSelectionGroup(null);
2183 ap.av.hideRepSequences(sequence, sg);
2188 int gsize = sg.getSize();
2191 hseqs = new SequenceI[gsize];
2194 for (int i = 0; i < gsize; i++)
2196 hseqs[index++] = sg.getSequenceAt(i);
2199 ap.av.hideSequence(hseqs);
2200 // refresh(); TODO: ? needed ?
2201 ap.av.sendSelection();
2204 public void copy_actionPerformed()
2206 ap.alignFrame.copy_actionPerformed(null);
2209 public void cut_actionPerformed()
2211 ap.alignFrame.cut_actionPerformed(null);
2214 void changeCase(ActionEvent e)
2216 Object source = e.getSource();
2217 SequenceGroup sg = ap.av.getSelectionGroup();
2221 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
2222 sg.getEndRes() + 1);
2227 if (source == toggle)
2229 description = MessageManager.getString("label.toggle_case");
2230 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2232 else if (source == upperCase)
2234 description = MessageManager.getString("label.to_upper_case");
2235 caseChange = ChangeCaseCommand.TO_UPPER;
2239 description = MessageManager.getString("label.to_lower_case");
2240 caseChange = ChangeCaseCommand.TO_LOWER;
2243 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2244 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2245 startEnd, caseChange);
2247 ap.alignFrame.addHistoryItem(caseCommand);
2249 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2255 public void outputText_actionPerformed(ActionEvent e)
2257 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2258 cap.setForInput(null);
2259 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2260 "label.alignment_output_command", new String[]
2261 { e.getActionCommand() }), 600, 500);
2263 String[] omitHidden = null;
2265 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2266 // or we simply trust the user wants
2267 // wysiwig behaviour
2269 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(), ap.av, true));
2272 public void pdbFromFile_actionPerformed()
2274 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2275 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2276 chooser.setFileView(new jalview.io.JalviewFileView());
2277 chooser.setDialogTitle(MessageManager.formatMessage(
2278 "label.select_pdb_file_for", new String[]
2279 { sequence.getDisplayId(false) }));
2280 chooser.setToolTipText(MessageManager.formatMessage(
2281 "label.load_pdb_file_associate_with_sequence", new String[]
2282 { sequence.getDisplayId(false) }));
2284 int value = chooser.showOpenDialog(null);
2286 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2288 String choice = chooser.getSelectedFile().getPath();
2289 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2290 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2291 jalview.io.AppletFormatAdapter.FILE, sequence, true);
2296 // JBNote: commented out - these won't be instantiated here...!
2297 // public void RNAFold_actionPerformed() throws Exception
2299 // Predict2D P2D = new Predict2D();
2300 // P2D.getStructure2DFromRNAFold("toto");
2303 // public void ContraFold_actionPerformed() throws Exception
2305 // Predict2D P2D = new Predict2D();
2306 // P2D.getStructure2DFromContraFold("toto");
2308 public void enterPDB_actionPerformed()
2310 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2311 MessageManager.getString("label.enter_pdb_id"),
2312 MessageManager.getString("label.enter_pdb_id"),
2313 JOptionPane.QUESTION_MESSAGE);
2315 if (id != null && id.length() > 0)
2317 PDBEntry entry = new PDBEntry();
2318 entry.setId(id.toUpperCase());
2319 sequence.getDatasetSequence().addPDBId(entry);
2323 public void discoverPDB_actionPerformed()
2326 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2328 : ap.av.getSequenceSelection());
2329 Thread discpdb = new Thread(new Runnable()
2335 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2336 .fetchDBRefs(false);
2343 public void sequenceFeature_actionPerformed()
2345 SequenceGroup sg = ap.av.getSelectionGroup();
2351 int rsize = 0, gSize = sg.getSize();
2352 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2353 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2355 for (int i = 0; i < gSize; i++)
2357 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2358 int end = sg.findEndRes(sg.getSequenceAt(i));
2361 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2362 features[rsize] = new SequenceFeature(null, null, null, start, end,
2367 rseqs = new SequenceI[rsize];
2368 tfeatures = new SequenceFeature[rsize];
2369 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2370 System.arraycopy(features, 0, tfeatures, 0, rsize);
2371 features = tfeatures;
2373 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2374 features, true, ap))
2376 ap.alignFrame.setShowSeqFeatures(true);
2377 ap.highlightSearchResults(null);
2381 public void textColour_actionPerformed()
2383 SequenceGroup sg = getGroup();
2386 new TextColourChooser().chooseColour(ap, sg);
2390 public void colourByStructure(String pdbid)
2392 Annotation[] anots = ap.av.getStructureSelectionManager()
2393 .colourSequenceFromStructure(sequence, pdbid);
2395 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2396 "Coloured by " + pdbid, anots);
2398 ap.av.getAlignment().addAnnotation(an);
2399 an.createSequenceMapping(sequence, 0, true);
2400 // an.adjustForAlignment();
2401 ap.av.getAlignment().setAnnotationIndex(an, 0);
2403 ap.adjustAnnotationHeight();
2405 sequence.addAlignmentAnnotation(an);
2409 public void editSequence_actionPerformed(ActionEvent actionEvent)
2411 SequenceGroup sg = ap.av.getSelectionGroup();
2415 if (sequence == null)
2416 sequence = sg.getSequenceAt(0);
2418 EditNameDialog dialog = new EditNameDialog(
2419 sequence.getSequenceAsString(sg.getStartRes(),
2420 sg.getEndRes() + 1), null,
2421 MessageManager.getString("label.edit_sequence"), null,
2422 MessageManager.getString("label.edit_sequence"),
2427 EditCommand editCommand = new EditCommand(
2428 MessageManager.getString("label.edit_sequences"),
2429 EditCommand.REPLACE, dialog.getName().replace(' ',
2430 ap.av.getGapCharacter()),
2431 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2432 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2434 ap.alignFrame.addHistoryItem(editCommand);
2436 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()