2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
23 import java.awt.event.*;
26 import javax.xml.parsers.ParserConfigurationException;
28 import org.xml.sax.SAXException;
30 import fr.orsay.lri.varna.exceptions.ExceptionFileFormatOrSyntax;
31 import fr.orsay.lri.varna.exceptions.ExceptionLoadingFailed;
32 import fr.orsay.lri.varna.exceptions.ExceptionPermissionDenied;
33 import fr.orsay.lri.varna.exceptions.ExceptionUnmatchedClosingParentheses;
36 import jalview.analysis.*;
37 import jalview.commands.*;
38 import jalview.datamodel.*;
40 import jalview.schemes.*;
41 import jalview.util.GroupUrlLink;
42 import jalview.util.GroupUrlLink.UrlStringTooLongException;
43 import jalview.util.UrlLink;
49 * @version $Revision: 1.118 $
51 public class PopupMenu extends JPopupMenu
53 JMenu groupMenu = new JMenu();
55 JMenuItem groupName = new JMenuItem();
57 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
61 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
63 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
65 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
67 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
69 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
71 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
73 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
75 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
77 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
79 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
81 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
82 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
84 // protected JRadioButtonMenuItem covariationColour = new
85 // JRadioButtonMenuItem();
87 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
89 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
93 JMenu sequenceMenu = new JMenu();
95 JMenuItem sequenceName = new JMenuItem();
99 JMenuItem unGroupMenuItem = new JMenuItem();
101 JMenuItem outline = new JMenuItem();
103 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
105 JMenu colourMenu = new JMenu();
107 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
109 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
111 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
113 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
115 JMenu editMenu = new JMenu();
117 JMenuItem cut = new JMenuItem();
119 JMenuItem copy = new JMenuItem();
121 JMenuItem upperCase = new JMenuItem();
123 JMenuItem lowerCase = new JMenuItem();
125 JMenuItem toggle = new JMenuItem();
127 JMenu pdbMenu = new JMenu();
129 JMenuItem pdbFromFile = new JMenuItem();
131 JMenuItem enterPDB = new JMenuItem();
133 JMenuItem discoverPDB = new JMenuItem();
135 JMenu outputMenu = new JMenu();
137 JMenuItem sequenceFeature = new JMenuItem();
139 JMenuItem textColour = new JMenuItem();
141 JMenu jMenu1 = new JMenu();
143 JMenu structureMenu = new JMenu();
145 JMenu viewStructureMenu = new JMenu();
147 // JMenu colStructureMenu = new JMenu();
148 JMenuItem editSequence = new JMenuItem();
150 // JMenuItem annotationMenuItem = new JMenuItem();
152 JMenu groupLinksMenu;
155 * Creates a new PopupMenu object.
162 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
164 this(ap, seq, links, null);
174 public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
177 // /////////////////////////////////////////////////////////
178 // If this is activated from the sequence panel, the user may want to
179 // edit or annotate a particular residue. Therefore display the residue menu
181 // If from the IDPanel, we must display the sequence menu
182 // ////////////////////////////////////////////////////////
186 ButtonGroup colours = new ButtonGroup();
187 colours.add(noColourmenuItem);
188 colours.add(clustalColour);
189 colours.add(zappoColour);
190 colours.add(taylorColour);
191 colours.add(hydrophobicityColour);
192 colours.add(helixColour);
193 colours.add(strandColour);
194 colours.add(turnColour);
195 colours.add(buriedColour);
196 colours.add(abovePIDColour);
197 colours.add(userDefinedColour);
198 colours.add(PIDColour);
199 colours.add(BLOSUM62Colour);
200 colours.add(purinePyrimidineColour);
201 colours.add(RNAInteractionColour);
202 // colours.add(covariationColour);
204 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
206 JMenuItem item = new JMenuItem(
207 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
209 item.addActionListener(new java.awt.event.ActionListener()
211 public void actionPerformed(ActionEvent e)
213 outputText_actionPerformed(e);
217 outputMenu.add(item);
223 } catch (Exception e)
231 sequenceMenu.setText(sequence.getName());
233 if (seq.getDatasetSequence().getPDBId() != null
234 && seq.getDatasetSequence().getPDBId().size() > 0)
236 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
239 while (e.hasMoreElements())
241 final PDBEntry pdb = (PDBEntry) e.nextElement();
243 menuItem = new JMenuItem();
244 menuItem.setText(pdb.getId());
245 menuItem.addActionListener(new java.awt.event.ActionListener()
247 public void actionPerformed(ActionEvent e)
249 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
250 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
251 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
255 viewStructureMenu.add(menuItem);
258 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
259 * menuItem.addActionListener(new java.awt.event.ActionListener() {
260 * public void actionPerformed(ActionEvent e) {
261 * colourByStructure(pdb.getId()); } });
262 * colStructureMenu.add(menuItem);
268 if (ap.av.getAlignment().isNucleotide() == false)
270 structureMenu.remove(viewStructureMenu);
272 // structureMenu.remove(colStructureMenu);
275 if (ap.av.getAlignment().isNucleotide() == true)
277 AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
278 for (int i = 0; i < aa.length; i++)
280 if (aa[i].getRNAStruc() != null)
282 final String rnastruc = aa[i].getRNAStruc();
283 final String structureLine=aa[i].label;
284 menuItem = new JMenuItem();
285 menuItem.setText("2D RNA "+structureLine);
286 menuItem.addActionListener(new java.awt.event.ActionListener()
289 public void actionPerformed(ActionEvent e)
291 //System.out.println("1:"+structureLine);
292 System.out.println("1:sname"+seq.getName());
293 System.out.println("2:seq"+seq);
295 //System.out.println("3:"+seq.getSequenceAsString());
296 System.out.println("3:strucseq"+rnastruc);
297 //System.out.println("4:struc"+seq.getRNA());
298 System.out.println("5:name"+seq.getName());
299 System.out.println("6:ap"+ap);
300 new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
302 //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
303 System.out.println("end");
306 viewStructureMenu.add(menuItem);
310 // SequenceFeatures[] test = seq.getSequenceFeatures();
312 if (seq.getAnnotation() != null)
314 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
315 for (int i = 0; i < seqAnno.length; i++)
317 if (seqAnno[i].getRNAStruc() != null)
319 final String rnastruc = seqAnno[i].getRNAStruc();
321 // TODO: make rnastrucF a bit more nice
322 menuItem = new JMenuItem();
323 menuItem.setText("2D RNA - "+seq.getName());
324 menuItem.addActionListener(new java.awt.event.ActionListener()
326 public void actionPerformed(ActionEvent e)
328 // TODO: VARNA does'nt print gaps in the sequence
330 //new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(), seq.getName(), ap);
331 new AppVarna(seq.getName()+" structure",seq,seq.getSequenceAsString(), rnastruc, seq
335 viewStructureMenu.add(menuItem);
343 menuItem = new JMenuItem("Hide Sequences");
344 menuItem.addActionListener(new java.awt.event.ActionListener()
346 public void actionPerformed(ActionEvent e)
348 hideSequences(false);
353 if (ap.av.getSelectionGroup() != null
354 && ap.av.getSelectionGroup().getSize() > 1)
356 menuItem = new JMenuItem("Represent Group with " + seq.getName());
357 menuItem.addActionListener(new java.awt.event.ActionListener()
359 public void actionPerformed(ActionEvent e)
364 sequenceMenu.add(menuItem);
367 if (ap.av.hasHiddenRows())
369 final int index = ap.av.getAlignment().findIndex(seq);
371 if (ap.av.adjustForHiddenSeqs(index)
372 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
374 menuItem = new JMenuItem("Reveal Sequences");
375 menuItem.addActionListener(new ActionListener()
377 public void actionPerformed(ActionEvent e)
379 ap.av.showSequence(index);
380 if (ap.overviewPanel != null)
382 ap.overviewPanel.updateOverviewImage();
390 // for the case when no sequences are even visible
391 if (ap.av.hasHiddenRows()) {
393 menuItem = new JMenuItem("Reveal All");
394 menuItem.addActionListener(new ActionListener()
396 public void actionPerformed(ActionEvent e)
398 ap.av.showAllHiddenSeqs();
399 if (ap.overviewPanel != null)
401 ap.overviewPanel.updateOverviewImage();
411 SequenceGroup sg = ap.av.getSelectionGroup();
413 if (sg != null&& sg.getSize()>0)
415 groupName.setText("Name: "+sg.getName());
416 groupName.setText("Edit name and description of current group.");
418 if (sg.cs instanceof ZappoColourScheme)
420 zappoColour.setSelected(true);
422 else if (sg.cs instanceof TaylorColourScheme)
424 taylorColour.setSelected(true);
426 else if (sg.cs instanceof PIDColourScheme)
428 PIDColour.setSelected(true);
430 else if (sg.cs instanceof Blosum62ColourScheme)
432 BLOSUM62Colour.setSelected(true);
434 else if (sg.cs instanceof UserColourScheme)
436 userDefinedColour.setSelected(true);
438 else if (sg.cs instanceof HydrophobicColourScheme)
440 hydrophobicityColour.setSelected(true);
442 else if (sg.cs instanceof HelixColourScheme)
444 helixColour.setSelected(true);
446 else if (sg.cs instanceof StrandColourScheme)
448 strandColour.setSelected(true);
450 else if (sg.cs instanceof TurnColourScheme)
452 turnColour.setSelected(true);
454 else if (sg.cs instanceof BuriedColourScheme)
456 buriedColour.setSelected(true);
458 else if (sg.cs instanceof ClustalxColourScheme)
460 clustalColour.setSelected(true);
462 else if (sg.cs instanceof PurinePyrimidineColourScheme)
464 purinePyrimidineColour.setSelected(true);
467 else if (sg.cs instanceof RNAInteractionColourScheme)
469 RNAInteractionColour.setSelected(true);
472 * else if (sg.cs instanceof CovariationColourScheme) {
473 * covariationColour.setSelected(true); }
477 noColourmenuItem.setSelected(true);
480 if (sg.cs != null && sg.cs.conservationApplied())
482 conservationMenuItem.setSelected(true);
484 displayNonconserved.setSelected(sg.getShowNonconserved());
485 showText.setSelected(sg.getDisplayText());
486 showColourText.setSelected(sg.getColourText());
487 showBoxes.setSelected(sg.getDisplayBoxes());
488 // add any groupURLs to the groupURL submenu and make it visible
489 if (groupLinks != null && groupLinks.size() > 0)
491 buildGroupURLMenu(sg, groupLinks);
493 // Add a 'show all structures' for the current selection
494 Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
495 SequenceI sqass=null;
496 for (SequenceI sq: ap.av.getSequenceSelection())
498 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
500 for (PDBEntry pe: pes)
502 pdbe.put(pe.getId(), pe);
512 final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
513 final JMenuItem gpdbview;
516 structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
518 structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
520 gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
521 gpdbview.addActionListener(new ActionListener()
525 public void actionPerformed(ActionEvent e)
527 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
534 groupMenu.setVisible(false);
535 editMenu.setVisible(false);
538 if (!ap.av.getAlignment().getGroups().contains(sg))
540 unGroupMenuItem.setVisible(false);
545 sequenceMenu.setVisible(false);
546 structureMenu.setVisible(false);
549 if (links != null && links.size() > 0)
552 JMenu linkMenu = new JMenu("Link");
553 Vector linkset = new Vector();
554 for (int i = 0; i < links.size(); i++)
556 String link = links.elementAt(i).toString();
557 UrlLink urlLink = null;
560 urlLink = new UrlLink(link);
561 } catch (Exception foo)
563 jalview.bin.Cache.log.error("Exception for URLLink '" + link
568 if (!urlLink.isValid())
570 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
573 final String label = urlLink.getLabel();
574 if (seq!=null && urlLink.isDynamic())
577 // collect matching db-refs
578 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
579 seq.getDBRef(), new String[]
580 { urlLink.getTarget() });
581 // collect id string too
582 String id = seq.getName();
583 String descr = seq.getDescription();
584 if (descr != null && descr.length() < 1)
591 for (int r = 0; r < dbr.length; r++)
593 if (id != null && dbr[r].getAccessionId().equals(id))
595 // suppress duplicate link creation for the bare sequence ID
596 // string with this link
599 // create Bare ID link for this RUL
600 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
604 for (int u = 0; u < urls.length; u += 2)
606 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
608 linkset.addElement(urls[u] + "|" + urls[u + 1]);
609 addshowLink(linkMenu, label + "|" + urls[u],
618 // create Bare ID link for this RUL
619 String[] urls = urlLink.makeUrls(id, true);
622 for (int u = 0; u < urls.length; u += 2)
624 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
626 linkset.addElement(urls[u] + "|" + urls[u + 1]);
627 addshowLink(linkMenu, label, urls[u + 1]);
632 // Create urls from description but only for URL links which are regex
634 if (descr != null && urlLink.getRegexReplace() != null)
636 // create link for this URL from description where regex matches
637 String[] urls = urlLink.makeUrls(descr, true);
640 for (int u = 0; u < urls.length; u += 2)
642 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
644 linkset.addElement(urls[u] + "|" + urls[u + 1]);
645 addshowLink(linkMenu, label, urls[u + 1]);
653 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
655 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
656 // Add a non-dynamic link
657 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
661 if (sequence != null)
663 sequenceMenu.add(linkMenu);
672 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
675 // TODO: usability: thread off the generation of group url content so root
677 // sequence only URLs
678 // ID/regex match URLs
679 groupLinksMenu = new JMenu("Group Link");
680 JMenu[] linkMenus = new JMenu[]
681 { null, new JMenu("IDS"), new JMenu("Sequences"),
682 new JMenu("IDS and Sequences") }; // three types of url that might be
684 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
685 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
686 Hashtable commonDbrefs = new Hashtable();
687 for (int sq = 0; sq < seqs.length; sq++)
690 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
691 .findPosition(sg.getEndRes());
692 // just collect ids from dataset sequence
693 // TODO: check if IDs collected from selecton group intersects with the
694 // current selection, too
695 SequenceI sqi = seqs[sq];
696 while (sqi.getDatasetSequence() != null)
698 sqi = sqi.getDatasetSequence();
700 DBRefEntry[] dbr = sqi.getDBRef();
701 if (dbr != null && dbr.length > 0)
703 for (int d = 0; d < dbr.length; d++)
705 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
706 Object[] sarray = (Object[]) commonDbrefs.get(src);
709 sarray = new Object[2];
710 sarray[0] = new int[]
712 sarray[1] = new String[seqs.length];
714 commonDbrefs.put(src, sarray);
717 if (((String[]) sarray[1])[sq] == null)
720 || (dbr[d].getMap().locateMappedRange(start, end) != null))
722 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
723 ((int[]) sarray[0])[0]++;
729 // now create group links for all distinct ID/sequence sets.
730 boolean addMenu = false; // indicates if there are any group links to give
732 for (int i = 0; i < groupLinks.size(); i++)
734 String link = groupLinks.elementAt(i).toString();
735 GroupUrlLink urlLink = null;
738 urlLink = new GroupUrlLink(link);
739 } catch (Exception foo)
741 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
746 if (!urlLink.isValid())
748 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
751 final String label = urlLink.getLabel();
752 boolean usingNames = false;
753 // Now see which parts of the group apply for this URL
754 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
755 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
756 String[] seqstr, ids; // input to makeUrl
759 int numinput = ((int[]) idset[0])[0];
760 String[] allids = ((String[]) idset[1]);
761 seqstr = new String[numinput];
762 ids = new String[numinput];
763 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
765 if (allids[sq] != null)
767 ids[idcount] = allids[sq];
768 seqstr[idcount++] = idandseqs[1][sq];
774 // just use the id/seq set
775 seqstr = idandseqs[1];
779 // and try and make the groupURL!
781 Object[] urlset = null;
784 urlset = urlLink.makeUrlStubs(ids, seqstr,
785 "FromJalview" + System.currentTimeMillis(), false);
786 } catch (UrlStringTooLongException e)
791 int type = urlLink.getGroupURLType() & 3;
792 // System.out.println(urlLink.getGroupURLType()
793 // +" "+((String[])urlset[3])[0]);
794 // first two bits ofurlLink type bitfield are sequenceids and sequences
795 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
796 addshowLink(linkMenus[type], label
797 + (((type & 1) == 1) ? ("("
798 + (usingNames ? "Names" : ltarget) + ")") : ""),
805 groupLinksMenu = new JMenu("Group Links");
806 for (int m = 0; m < linkMenus.length; m++)
808 if (linkMenus[m] != null
809 && linkMenus[m].getMenuComponentCount() > 0)
811 groupLinksMenu.add(linkMenus[m]);
815 groupMenu.add(groupLinksMenu);
820 * add a show URL menu item to the given linkMenu
824 * - menu label string
828 private void addshowLink(JMenu linkMenu, String label, final String url)
830 JMenuItem item = new JMenuItem(label);
831 item.setToolTipText("open URL: " + url);
832 item.addActionListener(new java.awt.event.ActionListener()
834 public void actionPerformed(ActionEvent e)
836 new Thread(new Runnable()
852 * add a late bound groupURL item to the given linkMenu
856 * - menu label string
857 * @param urlgenerator
858 * GroupURLLink used to generate URL
860 * Object array returned from the makeUrlStubs function.
862 private void addshowLink(JMenu linkMenu, String label,
863 final GroupUrlLink urlgenerator, final Object[] urlstub)
865 JMenuItem item = new JMenuItem(label);
866 item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
867 + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
876 item.addActionListener(new java.awt.event.ActionListener()
878 public void actionPerformed(ActionEvent e)
880 new Thread(new Runnable()
887 showLink(urlgenerator.constructFrom(urlstub));
888 } catch (UrlStringTooLongException e)
906 private void jbInit() throws Exception
908 groupMenu.setText("Group");
909 groupMenu.setText("Selection");
910 groupName.setText("Name");
911 groupName.addActionListener(new java.awt.event.ActionListener()
913 public void actionPerformed(ActionEvent e)
915 groupName_actionPerformed();
918 sequenceMenu.setText("Sequence");
919 sequenceName.setText("Edit Name/Description");
920 sequenceName.addActionListener(new java.awt.event.ActionListener()
922 public void actionPerformed(ActionEvent e)
924 sequenceName_actionPerformed();
927 PIDColour.setFocusPainted(false);
928 unGroupMenuItem.setText("Remove Group");
929 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
931 public void actionPerformed(ActionEvent e)
933 unGroupMenuItem_actionPerformed();
937 outline.setText("Border colour");
938 outline.addActionListener(new java.awt.event.ActionListener()
940 public void actionPerformed(ActionEvent e)
942 outline_actionPerformed();
945 nucleotideMenuItem.setText("Nucleotide");
946 nucleotideMenuItem.addActionListener(new ActionListener()
948 public void actionPerformed(ActionEvent e)
950 nucleotideMenuItem_actionPerformed();
953 colourMenu.setText("Group Colour");
954 showBoxes.setText("Boxes");
955 showBoxes.setState(true);
956 showBoxes.addActionListener(new ActionListener()
958 public void actionPerformed(ActionEvent e)
960 showBoxes_actionPerformed();
963 showText.setText("Text");
964 showText.setState(true);
965 showText.addActionListener(new ActionListener()
967 public void actionPerformed(ActionEvent e)
969 showText_actionPerformed();
972 showColourText.setText("Colour Text");
973 showColourText.addActionListener(new ActionListener()
975 public void actionPerformed(ActionEvent e)
977 showColourText_actionPerformed();
980 displayNonconserved.setText("Show Nonconserved");
981 displayNonconserved.setState(true);
982 displayNonconserved.addActionListener(new ActionListener()
984 public void actionPerformed(ActionEvent e)
986 showNonconserved_actionPerformed();
989 editMenu.setText("Edit");
991 cut.addActionListener(new ActionListener()
993 public void actionPerformed(ActionEvent e)
995 cut_actionPerformed();
998 upperCase.setText("To Upper Case");
999 upperCase.addActionListener(new ActionListener()
1001 public void actionPerformed(ActionEvent e)
1006 copy.setText("Copy");
1007 copy.addActionListener(new ActionListener()
1009 public void actionPerformed(ActionEvent e)
1011 copy_actionPerformed();
1014 lowerCase.setText("To Lower Case");
1015 lowerCase.addActionListener(new ActionListener()
1017 public void actionPerformed(ActionEvent e)
1022 toggle.setText("Toggle Case");
1023 toggle.addActionListener(new ActionListener()
1025 public void actionPerformed(ActionEvent e)
1030 pdbMenu.setText("Associate Structure with Sequence");
1031 pdbFromFile.setText("From File");
1032 pdbFromFile.addActionListener(new ActionListener()
1034 public void actionPerformed(ActionEvent e)
1037 pdbFromFile_actionPerformed();
1038 } catch (ExceptionFileFormatOrSyntax e1) {
1039 // TODO Auto-generated catch block
1040 e1.printStackTrace();
1041 } catch (ParserConfigurationException e1) {
1042 // TODO Auto-generated catch block
1043 e1.printStackTrace();
1044 } catch (SAXException e1) {
1045 // TODO Auto-generated catch block
1046 e1.printStackTrace();
1047 } catch (ExceptionPermissionDenied e1) {
1048 // TODO Auto-generated catch block
1049 e1.printStackTrace();
1050 } catch (ExceptionLoadingFailed e1) {
1051 // TODO Auto-generated catch block
1052 e1.printStackTrace();
1053 } catch (InterruptedException e1) {
1054 // TODO Auto-generated catch block
1055 e1.printStackTrace();
1056 } catch (ExceptionUnmatchedClosingParentheses e1) {
1057 // TODO Auto-generated catch block
1058 e1.printStackTrace();
1062 enterPDB.setText("Enter PDB Id");
1063 enterPDB.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1067 enterPDB_actionPerformed();
1070 discoverPDB.setText("Discover PDB ids");
1071 discoverPDB.addActionListener(new ActionListener()
1073 public void actionPerformed(ActionEvent e)
1075 discoverPDB_actionPerformed();
1078 outputMenu.setText("Output to Textbox...");
1079 sequenceFeature.setText("Create Sequence Feature");
1080 sequenceFeature.addActionListener(new ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 sequenceFeature_actionPerformed();
1087 textColour.setText("Text Colour");
1088 textColour.addActionListener(new ActionListener()
1090 public void actionPerformed(ActionEvent e)
1092 textColour_actionPerformed();
1095 jMenu1.setText("Group");
1096 structureMenu.setText("Structure");
1097 viewStructureMenu.setText("View Structure");
1098 // colStructureMenu.setText("Colour By Structure");
1099 editSequence.setText("Edit Sequence...");
1100 editSequence.addActionListener(new ActionListener()
1102 public void actionPerformed(ActionEvent actionEvent)
1104 editSequence_actionPerformed(actionEvent);
1108 * annotationMenuItem.setText("By Annotation");
1109 * annotationMenuItem.addActionListener(new ActionListener() { public void
1110 * actionPerformed(ActionEvent actionEvent) {
1111 * annotationMenuItem_actionPerformed(actionEvent); } });
1117 this.add(structureMenu);
1118 groupMenu.add(editMenu);
1119 groupMenu.add(outputMenu);
1120 groupMenu.add(sequenceFeature);
1121 groupMenu.add(jMenu1);
1122 sequenceMenu.add(sequenceName);
1123 colourMenu.add(textColour);
1124 colourMenu.add(noColourmenuItem);
1125 colourMenu.add(clustalColour);
1126 colourMenu.add(BLOSUM62Colour);
1127 colourMenu.add(PIDColour);
1128 colourMenu.add(zappoColour);
1129 colourMenu.add(taylorColour);
1130 colourMenu.add(hydrophobicityColour);
1131 colourMenu.add(helixColour);
1132 colourMenu.add(strandColour);
1133 colourMenu.add(turnColour);
1134 colourMenu.add(buriedColour);
1135 colourMenu.add(nucleotideMenuItem);
1136 colourMenu.add(RNAInteractionColour);
1137 if (ap.getAlignment().isNucleotide()) {
1138 colourMenu.add(purinePyrimidineColour);
1140 // colourMenu.add(covariationColour);
1141 colourMenu.add(userDefinedColour);
1143 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1145 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1146 .getUserColourSchemes().keys();
1148 while (userColours.hasMoreElements())
1150 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1151 item.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent evt)
1155 userDefinedColour_actionPerformed(evt);
1158 colourMenu.add(item);
1162 colourMenu.addSeparator();
1163 colourMenu.add(abovePIDColour);
1164 colourMenu.add(conservationMenuItem);
1165 // colourMenu.add(annotationMenuItem);
1168 editMenu.add(editSequence);
1169 editMenu.add(upperCase);
1170 editMenu.add(lowerCase);
1171 editMenu.add(toggle);
1172 pdbMenu.add(pdbFromFile);
1173 pdbMenu.add(enterPDB);
1174 pdbMenu.add(discoverPDB);
1175 jMenu1.add(groupName);
1176 jMenu1.add(unGroupMenuItem);
1177 jMenu1.add(colourMenu);
1178 jMenu1.add(showBoxes);
1179 jMenu1.add(showText);
1180 jMenu1.add(showColourText);
1181 jMenu1.add(outline);
1182 jMenu1.add(displayNonconserved);
1183 structureMenu.add(pdbMenu);
1184 structureMenu.add(viewStructureMenu);
1185 // structureMenu.add(colStructureMenu);
1186 noColourmenuItem.setText("None");
1187 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1189 public void actionPerformed(ActionEvent e)
1191 noColourmenuItem_actionPerformed();
1195 clustalColour.setText("Clustalx colours");
1196 clustalColour.addActionListener(new java.awt.event.ActionListener()
1198 public void actionPerformed(ActionEvent e)
1200 clustalColour_actionPerformed();
1203 zappoColour.setText("Zappo");
1204 zappoColour.addActionListener(new java.awt.event.ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 zappoColour_actionPerformed();
1211 taylorColour.setText("Taylor");
1212 taylorColour.addActionListener(new java.awt.event.ActionListener()
1214 public void actionPerformed(ActionEvent e)
1216 taylorColour_actionPerformed();
1219 hydrophobicityColour.setText("Hydrophobicity");
1220 hydrophobicityColour
1221 .addActionListener(new java.awt.event.ActionListener()
1223 public void actionPerformed(ActionEvent e)
1225 hydrophobicityColour_actionPerformed();
1228 helixColour.setText("Helix propensity");
1229 helixColour.addActionListener(new java.awt.event.ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 helixColour_actionPerformed();
1236 strandColour.setText("Strand propensity");
1237 strandColour.addActionListener(new java.awt.event.ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 strandColour_actionPerformed();
1244 turnColour.setText("Turn propensity");
1245 turnColour.addActionListener(new java.awt.event.ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 turnColour_actionPerformed();
1252 buriedColour.setText("Buried Index");
1253 buriedColour.addActionListener(new java.awt.event.ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 buriedColour_actionPerformed();
1260 abovePIDColour.setText("Above % Identity");
1261 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 abovePIDColour_actionPerformed();
1268 userDefinedColour.setText("User Defined...");
1269 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 userDefinedColour_actionPerformed(e);
1276 PIDColour.setText("Percentage Identity");
1277 PIDColour.addActionListener(new java.awt.event.ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 PIDColour_actionPerformed();
1284 BLOSUM62Colour.setText("BLOSUM62");
1285 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 BLOSUM62Colour_actionPerformed();
1292 purinePyrimidineColour.setText("Purine/Pyrimidine");
1293 purinePyrimidineColour
1294 .addActionListener(new java.awt.event.ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 purinePyrimidineColour_actionPerformed();
1302 RNAInteractionColour.setText("RNA Interaction type");
1303 RNAInteractionColour
1304 .addActionListener(new java.awt.event.ActionListener()
1306 public void actionPerformed(ActionEvent e)
1308 RNAInteractionColour_actionPerformed();
1312 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1313 * public void actionPerformed(ActionEvent e) {
1314 * covariationColour_actionPerformed(); } });
1317 conservationMenuItem.setText("Conservation");
1318 conservationMenuItem
1319 .addActionListener(new java.awt.event.ActionListener()
1321 public void actionPerformed(ActionEvent e)
1323 conservationMenuItem_actionPerformed();
1328 protected void showNonconserved_actionPerformed()
1330 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1335 * call to refresh view after settings change
1339 ap.updateAnnotation();
1340 ap.paintAlignment(true);
1342 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1351 protected void clustalColour_actionPerformed()
1353 SequenceGroup sg = getGroup();
1354 sg.cs = new ClustalxColourScheme(
1355 sg,ap.av.getHiddenRepSequences());
1365 protected void zappoColour_actionPerformed()
1367 getGroup().cs = new ZappoColourScheme();
1377 protected void taylorColour_actionPerformed()
1379 getGroup().cs = new TaylorColourScheme();
1389 protected void hydrophobicityColour_actionPerformed()
1391 getGroup().cs = new HydrophobicColourScheme();
1401 protected void helixColour_actionPerformed()
1403 getGroup().cs = new HelixColourScheme();
1413 protected void strandColour_actionPerformed()
1415 getGroup().cs = new StrandColourScheme();
1425 protected void turnColour_actionPerformed()
1427 getGroup().cs = new TurnColourScheme();
1437 protected void buriedColour_actionPerformed()
1439 getGroup().cs = new BuriedColourScheme();
1449 public void nucleotideMenuItem_actionPerformed()
1451 getGroup().cs = new NucleotideColourScheme();
1455 protected void purinePyrimidineColour_actionPerformed()
1457 getGroup().cs = new PurinePyrimidineColourScheme();
1461 protected void RNAInteractionColour_actionPerformed()
1463 getGroup().cs = new RNAInteractionColourScheme();
1467 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1468 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1476 protected void abovePIDColour_actionPerformed()
1478 SequenceGroup sg = getGroup();
1484 if (abovePIDColour.isSelected())
1486 sg.cs.setConsensus(AAFrequency.calculate(
1487 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1488 sg.getEndRes() + 1));
1490 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1493 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1495 SliderPanel.showPIDSlider();
1498 // remove PIDColouring
1500 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1512 protected void userDefinedColour_actionPerformed(ActionEvent e)
1514 SequenceGroup sg = getGroup();
1516 if (e.getActionCommand().equals("User Defined..."))
1518 new UserDefinedColours(ap, sg);
1522 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1523 .getUserColourSchemes().get(e.getActionCommand());
1536 protected void PIDColour_actionPerformed()
1538 SequenceGroup sg = getGroup();
1539 sg.cs = new PIDColourScheme();
1540 sg.cs.setConsensus(AAFrequency.calculate(
1541 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1542 sg.getEndRes() + 1));
1552 protected void BLOSUM62Colour_actionPerformed()
1554 SequenceGroup sg = getGroup();
1556 sg.cs = new Blosum62ColourScheme();
1558 sg.cs.setConsensus(AAFrequency.calculate(
1559 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1560 sg.getEndRes() + 1));
1571 protected void noColourmenuItem_actionPerformed()
1573 getGroup().cs = null;
1583 protected void conservationMenuItem_actionPerformed()
1585 SequenceGroup sg = getGroup();
1591 if (conservationMenuItem.isSelected())
1593 Conservation c = new Conservation("Group",
1594 ResidueProperties.propHash, 3,
1595 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1596 sg.getEndRes() + 1);
1599 c.verdict(false, ap.av.getConsPercGaps());
1601 sg.cs.setConservation(c);
1603 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1604 SliderPanel.showConservationSlider();
1607 // remove ConservationColouring
1609 sg.cs.setConservation(null);
1615 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1617 SequenceGroup sg = getGroup();
1623 AnnotationColourGradient acg = new AnnotationColourGradient(
1624 sequence.getAnnotation()[0], null,
1625 AnnotationColourGradient.NO_THRESHOLD);
1627 acg.predefinedColours = true;
1639 protected void groupName_actionPerformed()
1642 SequenceGroup sg = getGroup();
1643 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1644 sg.getDescription(), " Group Name ",
1645 "Group Description ", "Edit Group Name/Description",
1653 sg.setName(dialog.getName());
1654 sg.setDescription(dialog.getDescription());
1659 * Get selection group - adding it to the alignment if necessary.
1661 * @return sequence group to operate on
1663 SequenceGroup getGroup()
1665 SequenceGroup sg = ap.av.getSelectionGroup();
1666 // this method won't add a new group if it already exists
1669 ap.av.getAlignment().addGroup(sg);
1681 void sequenceName_actionPerformed()
1683 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1684 sequence.getDescription(), " Sequence Name ",
1685 "Sequence Description ", "Edit Sequence Name/Description",
1693 if (dialog.getName() != null)
1695 if (dialog.getName().indexOf(" ") > -1)
1697 JOptionPane.showMessageDialog(ap,
1698 "Spaces have been converted to \"_\"",
1699 "No spaces allowed in Sequence Name",
1700 JOptionPane.WARNING_MESSAGE);
1703 sequence.setName(dialog.getName().replace(' ', '_'));
1704 ap.paintAlignment(false);
1707 sequence.setDescription(dialog.getDescription());
1709 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1720 void unGroupMenuItem_actionPerformed()
1722 SequenceGroup sg = ap.av.getSelectionGroup();
1723 ap.av.getAlignment().deleteGroup(sg);
1724 ap.av.setSelectionGroup(null);
1734 protected void outline_actionPerformed()
1736 SequenceGroup sg = getGroup();
1737 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1742 sg.setOutlineColour(col);
1754 public void showBoxes_actionPerformed()
1756 getGroup().setDisplayBoxes(showBoxes.isSelected());
1766 public void showText_actionPerformed()
1768 getGroup().setDisplayText(showText.isSelected());
1778 public void showColourText_actionPerformed()
1780 getGroup().setColourText(showColourText.isSelected());
1784 public void showLink(String url)
1788 jalview.util.BrowserLauncher.openURL(url);
1789 } catch (Exception ex)
1792 .showInternalMessageDialog(
1794 "Unixers: Couldn't find default web browser."
1795 + "\nAdd the full path to your browser in Preferences.",
1796 "Web browser not found", JOptionPane.WARNING_MESSAGE);
1798 ex.printStackTrace();
1802 void hideSequences(boolean representGroup)
1804 SequenceGroup sg = ap.av.getSelectionGroup();
1805 if (sg == null || sg.getSize() < 1)
1807 ap.av.hideSequence(new SequenceI[]
1812 ap.av.setSelectionGroup(null);
1816 ap.av.hideRepSequences(sequence, sg);
1821 int gsize = sg.getSize();
1824 hseqs = new SequenceI[gsize];
1827 for (int i = 0; i < gsize; i++)
1829 hseqs[index++] = sg.getSequenceAt(i);
1832 ap.av.hideSequence(hseqs);
1833 // refresh(); TODO: ? needed ?
1834 ap.av.sendSelection();
1837 public void copy_actionPerformed()
1839 ap.alignFrame.copy_actionPerformed(null);
1842 public void cut_actionPerformed()
1844 ap.alignFrame.cut_actionPerformed(null);
1847 void changeCase(ActionEvent e)
1849 Object source = e.getSource();
1850 SequenceGroup sg = ap.av.getSelectionGroup();
1854 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1855 sg.getEndRes() + 1);
1860 if (source == toggle)
1862 description = "Toggle Case";
1863 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1865 else if (source == upperCase)
1867 description = "To Upper Case";
1868 caseChange = ChangeCaseCommand.TO_UPPER;
1872 description = "To Lower Case";
1873 caseChange = ChangeCaseCommand.TO_LOWER;
1876 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1877 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
1880 ap.alignFrame.addHistoryItem(caseCommand);
1882 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1888 public void outputText_actionPerformed(ActionEvent e)
1890 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1891 cap.setForInput(null);
1892 Desktop.addInternalFrame(cap,
1893 "Alignment output - " + e.getActionCommand(), 600, 500);
1895 String[] omitHidden = null;
1897 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1898 // or we simply trust the user wants
1899 // wysiwig behaviour
1900 SequenceGroup sg = ap.av.getSelectionGroup();
1901 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1902 omitHidden = ap.av.getViewAsString(true);
1903 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1904 AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation();
1907 for (int i = 0; i < nala.length; i++)
1909 AlignmentAnnotation na = nala[i];
1910 oal.addAnnotation(na);
1913 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1914 oal, omitHidden, csel, sg));
1918 public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException, ExceptionUnmatchedClosingParentheses
1920 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1921 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1922 chooser.setFileView(new jalview.io.JalviewFileView());
1923 chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1924 chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1926 int value = chooser.showOpenDialog(null);
1928 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1930 String choice = chooser.getSelectedFile().getPath();
1931 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1932 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1937 public void enterPDB_actionPerformed()
1939 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1940 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1942 if (id != null && id.length() > 0)
1944 PDBEntry entry = new PDBEntry();
1945 entry.setId(id.toUpperCase());
1946 sequence.getDatasetSequence().addPDBId(entry);
1950 public void discoverPDB_actionPerformed()
1953 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
1955 : ap.av.getSequenceSelection());
1956 Thread discpdb = new Thread(new Runnable()
1961 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1962 .fetchDBRefs(false);
1969 public void sequenceFeature_actionPerformed()
1971 SequenceGroup sg = ap.av.getSelectionGroup();
1977 int rsize = 0, gSize = sg.getSize();
1978 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1979 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1981 for (int i = 0; i < gSize; i++)
1983 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1984 int end = sg.findEndRes(sg.getSequenceAt(i));
1987 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1988 features[rsize] = new SequenceFeature(null, null, null, start, end,
1993 rseqs = new SequenceI[rsize];
1994 tfeatures = new SequenceFeature[rsize];
1995 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1996 System.arraycopy(features, 0, tfeatures, 0, rsize);
1997 features = tfeatures;
1999 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2000 features, true, ap))
2002 ap.alignFrame.setShowSeqFeatures(true);
2003 ap.highlightSearchResults(null);
2007 public void textColour_actionPerformed()
2009 SequenceGroup sg = getGroup();
2012 new TextColourChooser().chooseColour(ap, sg);
2016 public void colourByStructure(String pdbid)
2018 Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
2021 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2022 "Coloured by " + pdbid, anots);
2024 ap.av.getAlignment().addAnnotation(an);
2025 an.createSequenceMapping(sequence, 0, true);
2026 // an.adjustForAlignment();
2027 ap.av.getAlignment().setAnnotationIndex(an, 0);
2029 ap.adjustAnnotationHeight();
2031 sequence.addAlignmentAnnotation(an);
2035 public void editSequence_actionPerformed(ActionEvent actionEvent)
2037 SequenceGroup sg = ap.av.getSelectionGroup();
2041 if (sequence == null)
2042 sequence = (Sequence) sg.getSequenceAt(0);
2044 EditNameDialog dialog = new EditNameDialog(
2045 sequence.getSequenceAsString(sg.getStartRes(),
2046 sg.getEndRes() + 1), null, "Edit Sequence ", null,
2047 "Edit Sequence", ap.alignFrame);
2051 EditCommand editCommand = new EditCommand("Edit Sequences",
2052 EditCommand.REPLACE, dialog.getName().replace(' ',
2053 ap.av.getGapCharacter()),
2054 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2055 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2057 ap.alignFrame.addHistoryItem(editCommand);
2059 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()