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.AlignmentI;
29 import jalview.datamodel.AlignmentView;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.DBRefEntry;
32 import jalview.datamodel.PDBEntry;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceFeature;
35 import jalview.datamodel.SequenceGroup;
36 import jalview.datamodel.SequenceI;
37 import jalview.io.FormatAdapter;
38 import jalview.io.SequenceAnnotationReport;
39 import jalview.schemes.AnnotationColourGradient;
40 import jalview.schemes.Blosum62ColourScheme;
41 import jalview.schemes.BuriedColourScheme;
42 import jalview.schemes.ClustalxColourScheme;
43 import jalview.schemes.HelixColourScheme;
44 import jalview.schemes.HydrophobicColourScheme;
45 import jalview.schemes.NucleotideColourScheme;
46 import jalview.schemes.PIDColourScheme;
47 import jalview.schemes.PurinePyrimidineColourScheme;
48 import jalview.schemes.ResidueProperties;
49 import jalview.schemes.StrandColourScheme;
50 import jalview.schemes.TaylorColourScheme;
51 import jalview.schemes.TurnColourScheme;
52 import jalview.schemes.UserColourScheme;
53 import jalview.schemes.ZappoColourScheme;
54 import jalview.util.GroupUrlLink;
55 import jalview.util.GroupUrlLink.UrlStringTooLongException;
56 import jalview.util.MessageManager;
57 import jalview.util.UrlLink;
59 import java.awt.Color;
60 import java.awt.event.ActionEvent;
61 import java.awt.event.ActionListener;
62 import java.util.Hashtable;
63 import java.util.List;
64 import java.util.Vector;
66 import javax.swing.ButtonGroup;
67 import javax.swing.JCheckBoxMenuItem;
68 import javax.swing.JColorChooser;
69 import javax.swing.JMenu;
70 import javax.swing.JMenuItem;
71 import javax.swing.JOptionPane;
72 import javax.swing.JPopupMenu;
73 import javax.swing.JRadioButtonMenuItem;
79 * @version $Revision: 1.118 $
81 public class PopupMenu extends JPopupMenu
83 JMenu groupMenu = new JMenu();
85 JMenuItem groupName = new JMenuItem();
87 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
89 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
91 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
93 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
95 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
97 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
99 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
101 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
103 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
105 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
107 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
109 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
111 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
113 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
115 // protected JRadioButtonMenuItem covariationColour = new
116 // JRadioButtonMenuItem();
118 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
120 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
124 JMenu sequenceMenu = new JMenu();
126 JMenuItem sequenceName = new JMenuItem();
128 JMenuItem sequenceDetails = new JMenuItem();
130 JMenuItem sequenceSelDetails = new JMenuItem();
134 JMenuItem createGroupMenuItem = new JMenuItem();
136 JMenuItem unGroupMenuItem = new JMenuItem();
138 JMenuItem outline = new JMenuItem();
140 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
142 JMenu colourMenu = new JMenu();
144 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
146 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
148 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
150 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
152 JMenu editMenu = new JMenu();
154 JMenuItem cut = new JMenuItem();
156 JMenuItem copy = new JMenuItem();
158 JMenuItem upperCase = new JMenuItem();
160 JMenuItem lowerCase = new JMenuItem();
162 JMenuItem toggle = new JMenuItem();
164 JMenu pdbMenu = new JMenu();
166 JMenuItem pdbFromFile = new JMenuItem();
168 // JBPNote: Commented these out - Should add these services via the web
169 // services menu system.
170 // JMenuItem ContraFold = new JMenuItem();
172 // JMenuItem RNAFold = new JMenuItem();
174 JMenuItem enterPDB = new JMenuItem();
176 JMenuItem discoverPDB = new JMenuItem();
178 JMenu outputMenu = new JMenu();
180 JMenuItem sequenceFeature = new JMenuItem();
182 JMenuItem textColour = new JMenuItem();
184 JMenu jMenu1 = new JMenu();
186 JMenu structureMenu = new JMenu();
188 JMenu viewStructureMenu = new JMenu();
190 // JMenu colStructureMenu = new JMenu();
191 JMenuItem editSequence = new JMenuItem();
193 // JMenuItem annotationMenuItem = new JMenuItem();
195 JMenu groupLinksMenu;
198 * Creates a new PopupMenu object.
205 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
207 this(ap, seq, links, null);
217 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
218 Vector links, Vector groupLinks)
220 // /////////////////////////////////////////////////////////
221 // If this is activated from the sequence panel, the user may want to
222 // edit or annotate a particular residue. Therefore display the residue menu
224 // If from the IDPanel, we must display the sequence menu
225 // ////////////////////////////////////////////////////////
229 ButtonGroup colours = new ButtonGroup();
230 colours.add(noColourmenuItem);
231 colours.add(clustalColour);
232 colours.add(zappoColour);
233 colours.add(taylorColour);
234 colours.add(hydrophobicityColour);
235 colours.add(helixColour);
236 colours.add(strandColour);
237 colours.add(turnColour);
238 colours.add(buriedColour);
239 colours.add(abovePIDColour);
240 colours.add(userDefinedColour);
241 colours.add(PIDColour);
242 colours.add(BLOSUM62Colour);
243 colours.add(purinePyrimidineColour);
244 colours.add(RNAInteractionColour);
245 // colours.add(covariationColour);
247 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
249 JMenuItem item = new JMenuItem(
250 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
252 item.addActionListener(new java.awt.event.ActionListener()
254 public void actionPerformed(ActionEvent e)
256 outputText_actionPerformed(e);
260 outputMenu.add(item);
266 } catch (Exception e)
274 sequenceMenu.setText(sequence.getName());
276 if (seq.getDatasetSequence().getPDBId() != null
277 && seq.getDatasetSequence().getPDBId().size() > 0)
279 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
282 while (e.hasMoreElements())
284 final PDBEntry pdb = (PDBEntry) e.nextElement();
286 menuItem = new JMenuItem();
287 menuItem.setText(pdb.getId());
288 menuItem.addActionListener(new java.awt.event.ActionListener()
290 public void actionPerformed(ActionEvent e)
292 // TODO re JAL-860: optionally open dialog or provide a menu entry
293 // allowing user to open just one structure per sequence
294 // new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
295 // { pdb })[0], null, ap);
296 new StructureViewer(ap.getStructureSelectionManager())
298 ap.av.collateForPDB(new PDBEntry[]
299 { pdb })[0], null, ap);
303 viewStructureMenu.add(menuItem);
306 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
307 * menuItem.addActionListener(new java.awt.event.ActionListener() {
308 * public void actionPerformed(ActionEvent e) {
309 * colourByStructure(pdb.getId()); } });
310 * colStructureMenu.add(menuItem);
316 if (ap.av.getAlignment().isNucleotide() == false)
318 structureMenu.remove(viewStructureMenu);
320 // structureMenu.remove(colStructureMenu);
323 if (ap.av.getAlignment().isNucleotide() == true)
325 AlignmentAnnotation[] aa = ap.av.getAlignment()
326 .getAlignmentAnnotation();
327 for (int i = 0; i < aa.length; i++)
329 if (aa[i].getRNAStruc() != null)
331 final String rnastruc = aa[i].getRNAStruc();
332 final String structureLine = aa[i].label;
333 menuItem = new JMenuItem();
334 menuItem.setText(MessageManager.formatMessage(
335 "label.2d_rna_structure_line", new String[]
337 menuItem.addActionListener(new java.awt.event.ActionListener()
340 public void actionPerformed(ActionEvent e)
342 // System.out.println("1:"+structureLine);
343 System.out.println("1:sname" + seq.getName());
344 System.out.println("2:seq" + seq);
346 // System.out.println("3:"+seq.getSequenceAsString());
347 System.out.println("3:strucseq" + rnastruc);
348 // System.out.println("4:struc"+seq.getRNA());
349 System.out.println("5:name" + seq.getName());
350 System.out.println("6:ap" + ap);
351 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
352 rnastruc, seq.getName(), ap);
353 // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(),
354 // seq.getName(), ap);
355 System.out.println("end");
358 viewStructureMenu.add(menuItem);
362 // SequenceFeatures[] test = seq.getSequenceFeatures();
364 if (seq.getAnnotation() != null)
366 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
367 for (int i = 0; i < seqAnno.length; i++)
369 if (seqAnno[i].getRNAStruc() != null)
371 final String rnastruc = seqAnno[i].getRNAStruc();
373 // TODO: make rnastrucF a bit more nice
374 menuItem = new JMenuItem();
375 menuItem.setText(MessageManager.formatMessage(
376 "label.2d_rna_sequence_name", new String[]
378 menuItem.addActionListener(new java.awt.event.ActionListener()
380 public void actionPerformed(ActionEvent e)
382 // TODO: VARNA does'nt print gaps in the sequence
384 new AppVarna(seq.getName() + " structure", seq, seq
385 .getSequenceAsString(), rnastruc, seq.getName(),
389 viewStructureMenu.add(menuItem);
396 menuItem = new JMenuItem(
397 MessageManager.getString("action.hide_sequences"));
398 menuItem.addActionListener(new java.awt.event.ActionListener()
400 public void actionPerformed(ActionEvent e)
402 hideSequences(false);
407 if (ap.av.getSelectionGroup() != null
408 && ap.av.getSelectionGroup().getSize() > 1)
410 menuItem = new JMenuItem(MessageManager.formatMessage(
411 "label.represent_group_with", new String[]
413 menuItem.addActionListener(new java.awt.event.ActionListener()
415 public void actionPerformed(ActionEvent e)
420 sequenceMenu.add(menuItem);
423 if (ap.av.hasHiddenRows())
425 final int index = ap.av.getAlignment().findIndex(seq);
427 if (ap.av.adjustForHiddenSeqs(index)
428 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
430 menuItem = new JMenuItem(
431 MessageManager.getString("action.reveal_sequences"));
432 menuItem.addActionListener(new ActionListener()
434 public void actionPerformed(ActionEvent e)
436 ap.av.showSequence(index);
437 if (ap.overviewPanel != null)
439 ap.overviewPanel.updateOverviewImage();
447 // for the case when no sequences are even visible
448 if (ap.av.hasHiddenRows())
451 menuItem = new JMenuItem(
452 MessageManager.getString("action.reveal_all"));
453 menuItem.addActionListener(new ActionListener()
455 public void actionPerformed(ActionEvent e)
457 ap.av.showAllHiddenSeqs();
458 if (ap.overviewPanel != null)
460 ap.overviewPanel.updateOverviewImage();
470 SequenceGroup sg = ap.av.getSelectionGroup();
471 boolean isDefinedGroup = (sg != null) ? ap.av.getAlignment()
472 .getGroups().contains(sg) : false;
474 if (sg != null && sg.getSize() > 0)
476 groupName.setText(MessageManager.formatMessage("label.name_param",
479 groupName.setText(MessageManager
480 .getString("label.edit_name_and_description_current_group"));
482 if (sg.cs instanceof ZappoColourScheme)
484 zappoColour.setSelected(true);
486 else if (sg.cs instanceof TaylorColourScheme)
488 taylorColour.setSelected(true);
490 else if (sg.cs instanceof PIDColourScheme)
492 PIDColour.setSelected(true);
494 else if (sg.cs instanceof Blosum62ColourScheme)
496 BLOSUM62Colour.setSelected(true);
498 else if (sg.cs instanceof UserColourScheme)
500 userDefinedColour.setSelected(true);
502 else if (sg.cs instanceof HydrophobicColourScheme)
504 hydrophobicityColour.setSelected(true);
506 else if (sg.cs instanceof HelixColourScheme)
508 helixColour.setSelected(true);
510 else if (sg.cs instanceof StrandColourScheme)
512 strandColour.setSelected(true);
514 else if (sg.cs instanceof TurnColourScheme)
516 turnColour.setSelected(true);
518 else if (sg.cs instanceof BuriedColourScheme)
520 buriedColour.setSelected(true);
522 else if (sg.cs instanceof ClustalxColourScheme)
524 clustalColour.setSelected(true);
526 else if (sg.cs instanceof PurinePyrimidineColourScheme)
528 purinePyrimidineColour.setSelected(true);
532 * else if (sg.cs instanceof CovariationColourScheme) {
533 * covariationColour.setSelected(true); }
537 noColourmenuItem.setSelected(true);
540 if (sg.cs != null && sg.cs.conservationApplied())
542 conservationMenuItem.setSelected(true);
544 displayNonconserved.setSelected(sg.getShowNonconserved());
545 showText.setSelected(sg.getDisplayText());
546 showColourText.setSelected(sg.getColourText());
547 showBoxes.setSelected(sg.getDisplayBoxes());
548 // add any groupURLs to the groupURL submenu and make it visible
549 if (groupLinks != null && groupLinks.size() > 0)
551 buildGroupURLMenu(sg, groupLinks);
553 // Add a 'show all structures' for the current selection
554 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(), reppdb = new Hashtable<String, PDBEntry>();
555 SequenceI sqass = null;
556 for (SequenceI sq : ap.av.getSequenceSelection())
558 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
560 if (pes != null && pes.size() > 0)
562 reppdb.put(pes.get(0).getId(), pes.get(0));
563 for (PDBEntry pe : pes)
565 pdbe.put(pe.getId(), pe);
575 final PDBEntry[] pe = pdbe.values().toArray(
576 new PDBEntry[pdbe.size()]), pr = reppdb.values().toArray(
577 new PDBEntry[reppdb.size()]);
578 final JMenuItem gpdbview, rpdbview;
579 if (pdbe.size() == 1)
581 structureMenu.add(gpdbview = new JMenuItem(MessageManager
582 .formatMessage("label.view_structure_for", new String[]
583 { sqass.getDisplayId(false) })));
587 structureMenu.add(gpdbview = new JMenuItem(MessageManager
588 .formatMessage("label.view_all_structures", new String[]
589 { new Integer(pdbe.size()).toString() })));
591 gpdbview.setToolTipText(MessageManager
592 .getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
593 gpdbview.addActionListener(new ActionListener()
597 public void actionPerformed(ActionEvent e)
599 new StructureViewer(ap.getStructureSelectionManager())
600 .viewStructures(ap, pe, ap.av.collateForPDB(pe));
603 if (reppdb.size() > 1 && reppdb.size() < pdbe.size())
605 structureMenu.add(rpdbview = new JMenuItem(MessageManager
607 "label.view_all_representative_structures",
609 { new Integer(reppdb.size()).toString() })));
610 rpdbview.setToolTipText(MessageManager
611 .getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
612 rpdbview.addActionListener(new ActionListener()
616 public void actionPerformed(ActionEvent e)
618 new StructureViewer(ap.getStructureSelectionManager())
619 .viewStructures(ap, pr, ap.av.collateForPDB(pr));
627 groupMenu.setVisible(false);
628 editMenu.setVisible(false);
633 createGroupMenuItem.setVisible(true);
634 unGroupMenuItem.setVisible(false);
635 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
639 createGroupMenuItem.setVisible(false);
640 unGroupMenuItem.setVisible(true);
641 jMenu1.setText(MessageManager.getString("action.edit_group"));
646 sequenceMenu.setVisible(false);
647 structureMenu.setVisible(false);
650 if (links != null && links.size() > 0)
653 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
654 Vector linkset = new Vector();
655 for (int i = 0; i < links.size(); i++)
657 String link = links.elementAt(i).toString();
658 UrlLink urlLink = null;
661 urlLink = new UrlLink(link);
662 } catch (Exception foo)
664 jalview.bin.Cache.log.error("Exception for URLLink '" + link
669 if (!urlLink.isValid())
671 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
674 final String label = urlLink.getLabel();
675 if (seq != null && urlLink.isDynamic())
678 // collect matching db-refs
679 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
680 seq.getDBRef(), new String[]
681 { urlLink.getTarget() });
682 // collect id string too
683 String id = seq.getName();
684 String descr = seq.getDescription();
685 if (descr != null && descr.length() < 1)
692 for (int r = 0; r < dbr.length; r++)
694 if (id != null && dbr[r].getAccessionId().equals(id))
696 // suppress duplicate link creation for the bare sequence ID
697 // string with this link
700 // create Bare ID link for this RUL
701 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
705 for (int u = 0; u < urls.length; u += 2)
707 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
709 linkset.addElement(urls[u] + "|" + urls[u + 1]);
710 addshowLink(linkMenu, label + "|" + urls[u],
719 // create Bare ID link for this RUL
720 String[] urls = urlLink.makeUrls(id, true);
723 for (int u = 0; u < urls.length; u += 2)
725 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
727 linkset.addElement(urls[u] + "|" + urls[u + 1]);
728 addshowLink(linkMenu, label, urls[u + 1]);
733 // Create urls from description but only for URL links which are regex
735 if (descr != null && urlLink.getRegexReplace() != null)
737 // create link for this URL from description where regex matches
738 String[] urls = urlLink.makeUrls(descr, true);
741 for (int u = 0; u < urls.length; u += 2)
743 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
745 linkset.addElement(urls[u] + "|" + urls[u + 1]);
746 addshowLink(linkMenu, label, urls[u + 1]);
754 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
756 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
757 // Add a non-dynamic link
758 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
762 if (sequence != null)
764 sequenceMenu.add(linkMenu);
773 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
776 // TODO: usability: thread off the generation of group url content so root
778 // sequence only URLs
779 // ID/regex match URLs
780 groupLinksMenu = new JMenu(
781 MessageManager.getString("action.group_link"));
782 JMenu[] linkMenus = new JMenu[]
783 { null, new JMenu(MessageManager.getString("action.ids")),
784 new JMenu(MessageManager.getString("action.sequences")),
785 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three
792 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
793 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
794 Hashtable commonDbrefs = new Hashtable();
795 for (int sq = 0; sq < seqs.length; sq++)
798 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
799 .findPosition(sg.getEndRes());
800 // just collect ids from dataset sequence
801 // TODO: check if IDs collected from selecton group intersects with the
802 // current selection, too
803 SequenceI sqi = seqs[sq];
804 while (sqi.getDatasetSequence() != null)
806 sqi = sqi.getDatasetSequence();
808 DBRefEntry[] dbr = sqi.getDBRef();
809 if (dbr != null && dbr.length > 0)
811 for (int d = 0; d < dbr.length; d++)
813 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
814 Object[] sarray = (Object[]) commonDbrefs.get(src);
817 sarray = new Object[2];
818 sarray[0] = new int[]
820 sarray[1] = new String[seqs.length];
822 commonDbrefs.put(src, sarray);
825 if (((String[]) sarray[1])[sq] == null)
828 || (dbr[d].getMap().locateMappedRange(start, end) != null))
830 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
831 ((int[]) sarray[0])[0]++;
837 // now create group links for all distinct ID/sequence sets.
838 boolean addMenu = false; // indicates if there are any group links to give
840 for (int i = 0; i < groupLinks.size(); i++)
842 String link = groupLinks.elementAt(i).toString();
843 GroupUrlLink urlLink = null;
846 urlLink = new GroupUrlLink(link);
847 } catch (Exception foo)
849 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
854 if (!urlLink.isValid())
856 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
859 final String label = urlLink.getLabel();
860 boolean usingNames = false;
861 // Now see which parts of the group apply for this URL
862 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
863 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
864 String[] seqstr, ids; // input to makeUrl
867 int numinput = ((int[]) idset[0])[0];
868 String[] allids = ((String[]) idset[1]);
869 seqstr = new String[numinput];
870 ids = new String[numinput];
871 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
873 if (allids[sq] != null)
875 ids[idcount] = allids[sq];
876 seqstr[idcount++] = idandseqs[1][sq];
882 // just use the id/seq set
883 seqstr = idandseqs[1];
887 // and try and make the groupURL!
889 Object[] urlset = null;
892 urlset = urlLink.makeUrlStubs(ids, seqstr,
893 "FromJalview" + System.currentTimeMillis(), false);
894 } catch (UrlStringTooLongException e)
899 int type = urlLink.getGroupURLType() & 3;
900 // System.out.println(urlLink.getGroupURLType()
901 // +" "+((String[])urlset[3])[0]);
902 // first two bits ofurlLink type bitfield are sequenceids and sequences
903 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
904 addshowLink(linkMenus[type], label
905 + (((type & 1) == 1) ? ("("
906 + (usingNames ? "Names" : ltarget) + ")") : ""),
913 groupLinksMenu = new JMenu(
914 MessageManager.getString("action.group_link"));
915 for (int m = 0; m < linkMenus.length; m++)
917 if (linkMenus[m] != null
918 && linkMenus[m].getMenuComponentCount() > 0)
920 groupLinksMenu.add(linkMenus[m]);
924 groupMenu.add(groupLinksMenu);
929 * add a show URL menu item to the given linkMenu
933 * - menu label string
937 private void addshowLink(JMenu linkMenu, String label, final String url)
939 JMenuItem item = new JMenuItem(label);
940 item.setToolTipText(MessageManager.formatMessage(
941 "label.open_url_param", new String[]
943 item.addActionListener(new java.awt.event.ActionListener()
945 public void actionPerformed(ActionEvent e)
947 new Thread(new Runnable()
963 * add a late bound groupURL item to the given linkMenu
967 * - menu label string
968 * @param urlgenerator
969 * GroupURLLink used to generate URL
971 * Object array returned from the makeUrlStubs function.
973 private void addshowLink(JMenu linkMenu, String label,
974 final GroupUrlLink urlgenerator, final Object[] urlstub)
976 JMenuItem item = new JMenuItem(label);
977 item.setToolTipText(MessageManager.formatMessage(
978 "label.open_url_seqs_param",
980 { urlgenerator.getUrl_prefix(),
981 urlgenerator.getNumberInvolved(urlstub) }));
982 // TODO: put in info about what is being sent.
983 item.addActionListener(new java.awt.event.ActionListener()
985 public void actionPerformed(ActionEvent e)
987 new Thread(new Runnable()
994 showLink(urlgenerator.constructFrom(urlstub));
995 } catch (UrlStringTooLongException e)
1013 private void jbInit() throws Exception
1015 groupMenu.setText(MessageManager.getString("label.group"));
1016 groupMenu.setText(MessageManager.getString("label.selection"));
1017 groupName.setText(MessageManager.getString("label.name"));
1018 groupName.addActionListener(new java.awt.event.ActionListener()
1020 public void actionPerformed(ActionEvent e)
1022 groupName_actionPerformed();
1025 sequenceMenu.setText(MessageManager.getString("label.sequence"));
1026 sequenceName.setText(MessageManager
1027 .getString("label.edit_name_description"));
1028 sequenceName.addActionListener(new java.awt.event.ActionListener()
1030 public void actionPerformed(ActionEvent e)
1032 sequenceName_actionPerformed();
1035 sequenceDetails.setText(MessageManager
1036 .getString("label.sequence_details") + "...");
1037 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 sequenceDetails_actionPerformed();
1044 sequenceSelDetails.setText(MessageManager
1045 .getString("label.sequence_details") + "...");
1047 .addActionListener(new java.awt.event.ActionListener()
1049 public void actionPerformed(ActionEvent e)
1051 sequenceSelectionDetails_actionPerformed();
1054 PIDColour.setFocusPainted(false);
1056 .setText(MessageManager.getString("action.remove_group"));
1057 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
1059 public void actionPerformed(ActionEvent e)
1061 unGroupMenuItem_actionPerformed();
1064 createGroupMenuItem.setText(MessageManager
1065 .getString("action.create_group"));
1067 .addActionListener(new java.awt.event.ActionListener()
1069 public void actionPerformed(ActionEvent e)
1071 createGroupMenuItem_actionPerformed();
1075 outline.setText(MessageManager.getString("action.border_colour"));
1076 outline.addActionListener(new java.awt.event.ActionListener()
1078 public void actionPerformed(ActionEvent e)
1080 outline_actionPerformed();
1084 .setText(MessageManager.getString("label.nucleotide"));
1085 nucleotideMenuItem.addActionListener(new ActionListener()
1087 public void actionPerformed(ActionEvent e)
1089 nucleotideMenuItem_actionPerformed();
1092 colourMenu.setText(MessageManager.getString("label.group_colour"));
1093 showBoxes.setText(MessageManager.getString("action.boxes"));
1094 showBoxes.setState(true);
1095 showBoxes.addActionListener(new ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 showBoxes_actionPerformed();
1102 showText.setText(MessageManager.getString("action.text"));
1103 showText.setState(true);
1104 showText.addActionListener(new ActionListener()
1106 public void actionPerformed(ActionEvent e)
1108 showText_actionPerformed();
1111 showColourText.setText(MessageManager.getString("label.colour_text"));
1112 showColourText.addActionListener(new ActionListener()
1114 public void actionPerformed(ActionEvent e)
1116 showColourText_actionPerformed();
1119 displayNonconserved.setText(MessageManager
1120 .getString("label.show_non_conversed"));
1121 displayNonconserved.setState(true);
1122 displayNonconserved.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 showNonconserved_actionPerformed();
1129 editMenu.setText(MessageManager.getString("action.edit"));
1130 cut.setText(MessageManager.getString("action.cut"));
1131 cut.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 cut_actionPerformed();
1138 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1139 upperCase.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1146 copy.setText(MessageManager.getString("action.copy"));
1147 copy.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent e)
1151 copy_actionPerformed();
1154 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1155 lowerCase.addActionListener(new ActionListener()
1157 public void actionPerformed(ActionEvent e)
1162 toggle.setText(MessageManager.getString("label.toggle_case"));
1163 toggle.addActionListener(new ActionListener()
1165 public void actionPerformed(ActionEvent e)
1170 pdbMenu.setText(MessageManager
1171 .getString("label.associate_structure_with_sequence"));
1172 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1173 pdbFromFile.addActionListener(new ActionListener()
1175 public void actionPerformed(ActionEvent e)
1177 pdbFromFile_actionPerformed();
1180 // RNAFold.setText("From RNA Fold with predict2D");
1181 // RNAFold.addActionListener(new ActionListener()
1183 // public void actionPerformed(ActionEvent e)
1186 // RNAFold_actionPerformed();
1187 // } catch (Exception e1) {
1188 // // TODO Auto-generated catch block
1189 // e1.printStackTrace();
1193 // ContraFold.setText("From Contra Fold with predict2D");
1194 // ContraFold.addActionListener(new ActionListener()
1196 // public void actionPerformed(ActionEvent e)
1199 // ContraFold_actionPerformed();
1200 // } catch (Exception e1) {
1201 // // TODO Auto-generated catch block
1202 // e1.printStackTrace();
1206 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1207 enterPDB.addActionListener(new ActionListener()
1209 public void actionPerformed(ActionEvent e)
1211 enterPDB_actionPerformed();
1214 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1215 discoverPDB.addActionListener(new ActionListener()
1217 public void actionPerformed(ActionEvent e)
1219 discoverPDB_actionPerformed();
1222 outputMenu.setText(MessageManager.getString("label.out_to_textbox")
1224 sequenceFeature.setText(MessageManager
1225 .getString("label.create_sequence_feature"));
1226 sequenceFeature.addActionListener(new ActionListener()
1228 public void actionPerformed(ActionEvent e)
1230 sequenceFeature_actionPerformed();
1233 textColour.setText(MessageManager.getString("label.text_colour"));
1234 textColour.addActionListener(new ActionListener()
1236 public void actionPerformed(ActionEvent e)
1238 textColour_actionPerformed();
1241 jMenu1.setText(MessageManager.getString("label.group"));
1242 structureMenu.setText(MessageManager.getString("label.structure"));
1243 viewStructureMenu.setText(MessageManager
1244 .getString("label.view_structure"));
1245 // colStructureMenu.setText("Colour By Structure");
1246 editSequence.setText(MessageManager.getString("label.edit_sequence")
1248 editSequence.addActionListener(new ActionListener()
1250 public void actionPerformed(ActionEvent actionEvent)
1252 editSequence_actionPerformed(actionEvent);
1257 * annotationMenuItem.setText("By Annotation");
1258 * annotationMenuItem.addActionListener(new ActionListener() { public void
1259 * actionPerformed(ActionEvent actionEvent) {
1260 * annotationMenuItem_actionPerformed(actionEvent); } });
1262 groupMenu.add(sequenceSelDetails);
1265 this.add(structureMenu);
1266 groupMenu.add(editMenu);
1267 groupMenu.add(outputMenu);
1268 groupMenu.add(sequenceFeature);
1269 groupMenu.add(createGroupMenuItem);
1270 groupMenu.add(unGroupMenuItem);
1271 groupMenu.add(jMenu1);
1272 sequenceMenu.add(sequenceName);
1273 sequenceMenu.add(sequenceDetails);
1274 colourMenu.add(textColour);
1275 colourMenu.add(noColourmenuItem);
1276 colourMenu.add(clustalColour);
1277 colourMenu.add(BLOSUM62Colour);
1278 colourMenu.add(PIDColour);
1279 colourMenu.add(zappoColour);
1280 colourMenu.add(taylorColour);
1281 colourMenu.add(hydrophobicityColour);
1282 colourMenu.add(helixColour);
1283 colourMenu.add(strandColour);
1284 colourMenu.add(turnColour);
1285 colourMenu.add(buriedColour);
1286 colourMenu.add(nucleotideMenuItem);
1287 if (ap.getAlignment().isNucleotide())
1289 // JBPNote - commented since the colourscheme isn't functional
1290 // colourMenu.add(RNAInteractionColour);
1291 colourMenu.add(purinePyrimidineColour);
1293 // colourMenu.add(covariationColour);
1294 colourMenu.add(userDefinedColour);
1296 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1298 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1299 .getUserColourSchemes().keys();
1301 while (userColours.hasMoreElements())
1303 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1304 item.addActionListener(new ActionListener()
1306 public void actionPerformed(ActionEvent evt)
1308 userDefinedColour_actionPerformed(evt);
1311 colourMenu.add(item);
1315 colourMenu.addSeparator();
1316 colourMenu.add(abovePIDColour);
1317 colourMenu.add(conservationMenuItem);
1318 // colourMenu.add(annotationMenuItem);
1321 editMenu.add(editSequence);
1322 editMenu.add(upperCase);
1323 editMenu.add(lowerCase);
1324 editMenu.add(toggle);
1325 pdbMenu.add(pdbFromFile);
1326 // JBPNote: These shouldn't be added here - should appear in a generic
1327 // 'apply web service to this sequence menu'
1328 // pdbMenu.add(RNAFold);
1329 // pdbMenu.add(ContraFold);
1330 pdbMenu.add(enterPDB);
1331 pdbMenu.add(discoverPDB);
1332 jMenu1.add(groupName);
1333 jMenu1.add(colourMenu);
1334 jMenu1.add(showBoxes);
1335 jMenu1.add(showText);
1336 jMenu1.add(showColourText);
1337 jMenu1.add(outline);
1338 jMenu1.add(displayNonconserved);
1339 structureMenu.add(pdbMenu);
1340 structureMenu.add(viewStructureMenu);
1341 // structureMenu.add(colStructureMenu);
1342 noColourmenuItem.setText(MessageManager.getString("label.none"));
1343 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1345 public void actionPerformed(ActionEvent e)
1347 noColourmenuItem_actionPerformed();
1351 clustalColour.setText(MessageManager
1352 .getString("label.clustalx_colours"));
1353 clustalColour.addActionListener(new java.awt.event.ActionListener()
1355 public void actionPerformed(ActionEvent e)
1357 clustalColour_actionPerformed();
1360 zappoColour.setText(MessageManager.getString("label.zappo"));
1361 zappoColour.addActionListener(new java.awt.event.ActionListener()
1363 public void actionPerformed(ActionEvent e)
1365 zappoColour_actionPerformed();
1368 taylorColour.setText(MessageManager.getString("label.taylor"));
1369 taylorColour.addActionListener(new java.awt.event.ActionListener()
1371 public void actionPerformed(ActionEvent e)
1373 taylorColour_actionPerformed();
1376 hydrophobicityColour.setText(MessageManager
1377 .getString("label.hydrophobicity"));
1378 hydrophobicityColour
1379 .addActionListener(new java.awt.event.ActionListener()
1381 public void actionPerformed(ActionEvent e)
1383 hydrophobicityColour_actionPerformed();
1386 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1387 helixColour.addActionListener(new java.awt.event.ActionListener()
1389 public void actionPerformed(ActionEvent e)
1391 helixColour_actionPerformed();
1394 strandColour.setText(MessageManager
1395 .getString("label.strand_propensity"));
1396 strandColour.addActionListener(new java.awt.event.ActionListener()
1398 public void actionPerformed(ActionEvent e)
1400 strandColour_actionPerformed();
1403 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1404 turnColour.addActionListener(new java.awt.event.ActionListener()
1406 public void actionPerformed(ActionEvent e)
1408 turnColour_actionPerformed();
1411 buriedColour.setText(MessageManager.getString("label.buried_index"));
1412 buriedColour.addActionListener(new java.awt.event.ActionListener()
1414 public void actionPerformed(ActionEvent e)
1416 buriedColour_actionPerformed();
1419 abovePIDColour.setText(MessageManager
1420 .getString("label.above_identity_percentage"));
1421 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1423 public void actionPerformed(ActionEvent e)
1425 abovePIDColour_actionPerformed();
1428 userDefinedColour.setText(MessageManager
1429 .getString("action.user_defined"));
1430 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1432 public void actionPerformed(ActionEvent e)
1434 userDefinedColour_actionPerformed(e);
1438 .setText(MessageManager.getString("label.percentage_identity"));
1439 PIDColour.addActionListener(new java.awt.event.ActionListener()
1441 public void actionPerformed(ActionEvent e)
1443 PIDColour_actionPerformed();
1446 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1447 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1449 public void actionPerformed(ActionEvent e)
1451 BLOSUM62Colour_actionPerformed();
1454 purinePyrimidineColour.setText(MessageManager
1455 .getString("label.purine_pyrimidine"));
1456 purinePyrimidineColour
1457 .addActionListener(new java.awt.event.ActionListener()
1459 public void actionPerformed(ActionEvent e)
1461 purinePyrimidineColour_actionPerformed();
1466 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1467 * public void actionPerformed(ActionEvent e) {
1468 * covariationColour_actionPerformed(); } });
1471 conservationMenuItem.setText(MessageManager
1472 .getString("label.conservation"));
1473 conservationMenuItem
1474 .addActionListener(new java.awt.event.ActionListener()
1476 public void actionPerformed(ActionEvent e)
1478 conservationMenuItem_actionPerformed();
1483 protected void sequenceSelectionDetails_actionPerformed()
1485 createSequenceDetailsReport(ap.av.getSequenceSelection());
1488 protected void sequenceDetails_actionPerformed()
1490 createSequenceDetailsReport(new SequenceI[]
1494 public void createSequenceDetailsReport(SequenceI[] sequences)
1496 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1497 StringBuffer contents = new StringBuffer();
1498 for (SequenceI seq : sequences)
1500 contents.append("<p><h2>"
1503 "label.create_sequence_details_report_annotation_for",
1505 { seq.getDisplayId(true) }) + "</h2></p><p>");
1506 new SequenceAnnotationReport(null)
1507 .createSequenceAnnotationReport(
1513 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1515 contents.append("</p>");
1517 cap.setText("<html>" + contents.toString() + "</html>");
1519 Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage(
1520 "label.sequece_details_for",
1521 (sequences.length == 1 ? new String[]
1522 { sequences[0].getDisplayId(true) } : new String[]
1523 { MessageManager.getString("label.selection") })), 500, 400);
1527 protected void showNonconserved_actionPerformed()
1529 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1534 * call to refresh view after settings change
1538 ap.updateAnnotation();
1539 ap.paintAlignment(true);
1541 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1550 protected void clustalColour_actionPerformed()
1552 SequenceGroup sg = getGroup();
1553 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1563 protected void zappoColour_actionPerformed()
1565 getGroup().cs = new ZappoColourScheme();
1575 protected void taylorColour_actionPerformed()
1577 getGroup().cs = new TaylorColourScheme();
1587 protected void hydrophobicityColour_actionPerformed()
1589 getGroup().cs = new HydrophobicColourScheme();
1599 protected void helixColour_actionPerformed()
1601 getGroup().cs = new HelixColourScheme();
1611 protected void strandColour_actionPerformed()
1613 getGroup().cs = new StrandColourScheme();
1623 protected void turnColour_actionPerformed()
1625 getGroup().cs = new TurnColourScheme();
1635 protected void buriedColour_actionPerformed()
1637 getGroup().cs = new BuriedColourScheme();
1647 public void nucleotideMenuItem_actionPerformed()
1649 getGroup().cs = new NucleotideColourScheme();
1653 protected void purinePyrimidineColour_actionPerformed()
1655 getGroup().cs = new PurinePyrimidineColourScheme();
1660 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1661 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1669 protected void abovePIDColour_actionPerformed()
1671 SequenceGroup sg = getGroup();
1677 if (abovePIDColour.isSelected())
1679 sg.cs.setConsensus(AAFrequency.calculate(
1680 sg.getSequences(ap.av.getHiddenRepSequences()),
1681 sg.getStartRes(), sg.getEndRes() + 1));
1683 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1686 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1688 SliderPanel.showPIDSlider();
1691 // remove PIDColouring
1693 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1705 protected void userDefinedColour_actionPerformed(ActionEvent e)
1707 SequenceGroup sg = getGroup();
1709 if (e.getSource().equals(userDefinedColour))
1711 new UserDefinedColours(ap, sg);
1715 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1716 .getUserColourSchemes().get(e.getActionCommand());
1729 protected void PIDColour_actionPerformed()
1731 SequenceGroup sg = getGroup();
1732 sg.cs = new PIDColourScheme();
1733 sg.cs.setConsensus(AAFrequency.calculate(
1734 sg.getSequences(ap.av.getHiddenRepSequences()),
1735 sg.getStartRes(), sg.getEndRes() + 1));
1745 protected void BLOSUM62Colour_actionPerformed()
1747 SequenceGroup sg = getGroup();
1749 sg.cs = new Blosum62ColourScheme();
1751 sg.cs.setConsensus(AAFrequency.calculate(
1752 sg.getSequences(ap.av.getHiddenRepSequences()),
1753 sg.getStartRes(), sg.getEndRes() + 1));
1764 protected void noColourmenuItem_actionPerformed()
1766 getGroup().cs = null;
1776 protected void conservationMenuItem_actionPerformed()
1778 SequenceGroup sg = getGroup();
1784 if (conservationMenuItem.isSelected())
1786 // JBPNote: Conservation name shouldn't be i18n translated
1787 Conservation c = new Conservation("Group",
1788 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1789 .getHiddenRepSequences()), sg.getStartRes(),
1790 sg.getEndRes() + 1);
1793 c.verdict(false, ap.av.getConsPercGaps());
1795 sg.cs.setConservation(c);
1797 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1798 SliderPanel.showConservationSlider();
1801 // remove ConservationColouring
1803 sg.cs.setConservation(null);
1809 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1811 SequenceGroup sg = getGroup();
1817 AnnotationColourGradient acg = new AnnotationColourGradient(
1818 sequence.getAnnotation()[0], null,
1819 AnnotationColourGradient.NO_THRESHOLD);
1821 acg.setPredefinedColours(true);
1833 protected void groupName_actionPerformed()
1836 SequenceGroup sg = getGroup();
1837 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1838 sg.getDescription(), " "
1839 + MessageManager.getString("label.group_name") + " ",
1840 MessageManager.getString("label.group_description") + " ",
1841 MessageManager.getString("label.edit_group_name_description"),
1849 sg.setName(dialog.getName());
1850 sg.setDescription(dialog.getDescription());
1855 * Get selection group - adding it to the alignment if necessary.
1857 * @return sequence group to operate on
1859 SequenceGroup getGroup()
1861 SequenceGroup sg = ap.av.getSelectionGroup();
1862 // this method won't add a new group if it already exists
1865 ap.av.getAlignment().addGroup(sg);
1877 void sequenceName_actionPerformed()
1879 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1880 sequence.getDescription(),
1881 " " + MessageManager.getString("label.sequence_name")
1883 MessageManager.getString("label.sequence_description") + " ",
1885 .getString("label.edit_sequence_name_description"),
1893 if (dialog.getName() != null)
1895 if (dialog.getName().indexOf(" ") > -1)
1901 .getString("label.spaces_converted_to_backslashes"),
1903 .getString("label.no_spaces_allowed_sequence_name"),
1904 JOptionPane.WARNING_MESSAGE);
1907 sequence.setName(dialog.getName().replace(' ', '_'));
1908 ap.paintAlignment(false);
1911 sequence.setDescription(dialog.getDescription());
1913 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1924 void unGroupMenuItem_actionPerformed()
1926 SequenceGroup sg = ap.av.getSelectionGroup();
1927 ap.av.getAlignment().deleteGroup(sg);
1928 ap.av.setSelectionGroup(null);
1932 void createGroupMenuItem_actionPerformed()
1934 getGroup(); // implicitly creates group - note - should apply defaults / use
1935 // standard alignment window logic for this
1945 protected void outline_actionPerformed()
1947 SequenceGroup sg = getGroup();
1948 Color col = JColorChooser.showDialog(this,
1949 MessageManager.getString("label.select_outline_colour"),
1954 sg.setOutlineColour(col);
1966 public void showBoxes_actionPerformed()
1968 getGroup().setDisplayBoxes(showBoxes.isSelected());
1978 public void showText_actionPerformed()
1980 getGroup().setDisplayText(showText.isSelected());
1990 public void showColourText_actionPerformed()
1992 getGroup().setColourText(showColourText.isSelected());
1996 public void showLink(String url)
2000 jalview.util.BrowserLauncher.openURL(url);
2001 } catch (Exception ex)
2003 JOptionPane.showInternalMessageDialog(Desktop.desktop,
2004 MessageManager.getString("label.web_browser_not_found_unix"),
2005 MessageManager.getString("label.web_browser_not_found"),
2006 JOptionPane.WARNING_MESSAGE);
2008 ex.printStackTrace();
2012 void hideSequences(boolean representGroup)
2014 SequenceGroup sg = ap.av.getSelectionGroup();
2015 if (sg == null || sg.getSize() < 1)
2017 ap.av.hideSequence(new SequenceI[]
2022 ap.av.setSelectionGroup(null);
2026 ap.av.hideRepSequences(sequence, sg);
2031 int gsize = sg.getSize();
2034 hseqs = new SequenceI[gsize];
2037 for (int i = 0; i < gsize; i++)
2039 hseqs[index++] = sg.getSequenceAt(i);
2042 ap.av.hideSequence(hseqs);
2043 // refresh(); TODO: ? needed ?
2044 ap.av.sendSelection();
2047 public void copy_actionPerformed()
2049 ap.alignFrame.copy_actionPerformed(null);
2052 public void cut_actionPerformed()
2054 ap.alignFrame.cut_actionPerformed(null);
2057 void changeCase(ActionEvent e)
2059 Object source = e.getSource();
2060 SequenceGroup sg = ap.av.getSelectionGroup();
2064 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
2065 sg.getEndRes() + 1);
2070 if (source == toggle)
2072 description = MessageManager.getString("label.toggle_case");
2073 caseChange = ChangeCaseCommand.TOGGLE_CASE;
2075 else if (source == upperCase)
2077 description = MessageManager.getString("label.to_upper_case");
2078 caseChange = ChangeCaseCommand.TO_UPPER;
2082 description = MessageManager.getString("label.to_lower_case");
2083 caseChange = ChangeCaseCommand.TO_LOWER;
2086 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
2087 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2088 startEnd, caseChange);
2090 ap.alignFrame.addHistoryItem(caseCommand);
2092 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
2098 public void outputText_actionPerformed(ActionEvent e)
2100 CutAndPasteTransfer cap = new CutAndPasteTransfer();
2101 cap.setForInput(null);
2102 Desktop.addInternalFrame(cap, MessageManager.formatMessage(
2103 "label.alignment_output_command", new String[]
2104 { e.getActionCommand() }), 600, 500);
2106 String[] omitHidden = null;
2108 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
2109 // or we simply trust the user wants
2110 // wysiwig behaviour
2112 AlignmentView selvew = ap.av.getAlignmentView(true, false);
2113 AlignmentI aselview = selvew.getVisibleAlignment(ap.av
2114 .getGapCharacter());
2115 List<AlignmentAnnotation> ala = (ap.av
2116 .getVisibleAlignmentAnnotation(true));
2119 for (AlignmentAnnotation aa : ala)
2121 aselview.addAnnotation(aa);
2124 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2125 aselview, null, null, null));
2128 public void pdbFromFile_actionPerformed()
2130 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2131 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2132 chooser.setFileView(new jalview.io.JalviewFileView());
2133 chooser.setDialogTitle(MessageManager.formatMessage(
2134 "label.select_pdb_file_for", new String[]
2135 { sequence.getDisplayId(false) }));
2136 chooser.setToolTipText(MessageManager.formatMessage(
2137 "label.load_pdb_file_associate_with_sequence", new String[]
2138 { sequence.getDisplayId(false) }));
2140 int value = chooser.showOpenDialog(null);
2142 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2144 String choice = chooser.getSelectedFile().getPath();
2145 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2146 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2147 jalview.io.AppletFormatAdapter.FILE, sequence, true);
2152 // JBNote: commented out - these won't be instantiated here...!
2153 // public void RNAFold_actionPerformed() throws Exception
2155 // Predict2D P2D = new Predict2D();
2156 // P2D.getStructure2DFromRNAFold("toto");
2159 // public void ContraFold_actionPerformed() throws Exception
2161 // Predict2D P2D = new Predict2D();
2162 // P2D.getStructure2DFromContraFold("toto");
2164 public void enterPDB_actionPerformed()
2166 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2167 MessageManager.getString("label.enter_pdb_id"),
2168 MessageManager.getString("label.enter_pdb_id"),
2169 JOptionPane.QUESTION_MESSAGE);
2171 if (id != null && id.length() > 0)
2173 PDBEntry entry = new PDBEntry();
2174 entry.setId(id.toUpperCase());
2175 sequence.getDatasetSequence().addPDBId(entry);
2179 public void discoverPDB_actionPerformed()
2182 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2184 : ap.av.getSequenceSelection());
2185 Thread discpdb = new Thread(new Runnable()
2190 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2191 .fetchDBRefs(false);
2198 public void sequenceFeature_actionPerformed()
2200 SequenceGroup sg = ap.av.getSelectionGroup();
2206 int rsize = 0, gSize = sg.getSize();
2207 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2208 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2210 for (int i = 0; i < gSize; i++)
2212 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2213 int end = sg.findEndRes(sg.getSequenceAt(i));
2216 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2217 features[rsize] = new SequenceFeature(null, null, null, start, end,
2222 rseqs = new SequenceI[rsize];
2223 tfeatures = new SequenceFeature[rsize];
2224 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2225 System.arraycopy(features, 0, tfeatures, 0, rsize);
2226 features = tfeatures;
2228 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2229 features, true, ap))
2231 ap.alignFrame.setShowSeqFeatures(true);
2232 ap.highlightSearchResults(null);
2236 public void textColour_actionPerformed()
2238 SequenceGroup sg = getGroup();
2241 new TextColourChooser().chooseColour(ap, sg);
2245 public void colourByStructure(String pdbid)
2247 Annotation[] anots = ap.av.getStructureSelectionManager()
2248 .colourSequenceFromStructure(sequence, pdbid);
2250 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2251 "Coloured by " + pdbid, anots);
2253 ap.av.getAlignment().addAnnotation(an);
2254 an.createSequenceMapping(sequence, 0, true);
2255 // an.adjustForAlignment();
2256 ap.av.getAlignment().setAnnotationIndex(an, 0);
2258 ap.adjustAnnotationHeight();
2260 sequence.addAlignmentAnnotation(an);
2264 public void editSequence_actionPerformed(ActionEvent actionEvent)
2266 SequenceGroup sg = ap.av.getSelectionGroup();
2270 if (sequence == null)
2271 sequence = (Sequence) sg.getSequenceAt(0);
2273 EditNameDialog dialog = new EditNameDialog(
2274 sequence.getSequenceAsString(sg.getStartRes(),
2275 sg.getEndRes() + 1), null,
2276 MessageManager.getString("label.edit_sequence"), null,
2277 MessageManager.getString("label.edit_sequence"),
2282 EditCommand editCommand = new EditCommand(
2283 MessageManager.getString("label.edit_sequences"),
2284 EditCommand.REPLACE, dialog.getName().replace(' ',
2285 ap.av.getGapCharacter()),
2286 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2287 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2289 ap.alignFrame.addHistoryItem(editCommand);
2291 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()