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;
35 import jalview.analysis.*;
36 import jalview.commands.*;
37 import jalview.datamodel.*;
39 import jalview.schemes.*;
40 import jalview.util.GroupUrlLink;
41 import jalview.util.GroupUrlLink.UrlStringTooLongException;
42 import jalview.util.UrlLink;
48 * @version $Revision: 1.118 $
50 public class PopupMenu extends JPopupMenu
52 JMenu groupMenu = new JMenu();
54 JMenuItem groupName = new JMenuItem();
56 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
60 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
62 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
64 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
66 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
68 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
70 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
72 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
74 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
76 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
78 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
80 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
81 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
83 // protected JRadioButtonMenuItem covariationColour = new
84 // JRadioButtonMenuItem();
86 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
88 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
92 JMenu sequenceMenu = new JMenu();
94 JMenuItem sequenceName = new JMenuItem();
98 JMenuItem unGroupMenuItem = new JMenuItem();
100 JMenuItem outline = new JMenuItem();
102 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
104 JMenu colourMenu = new JMenu();
106 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
108 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
110 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
112 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
114 JMenu editMenu = new JMenu();
116 JMenuItem cut = new JMenuItem();
118 JMenuItem copy = new JMenuItem();
120 JMenuItem upperCase = new JMenuItem();
122 JMenuItem lowerCase = new JMenuItem();
124 JMenuItem toggle = new JMenuItem();
126 JMenu pdbMenu = new JMenu();
128 JMenuItem pdbFromFile = new JMenuItem();
130 JMenuItem enterPDB = new JMenuItem();
132 JMenuItem discoverPDB = new JMenuItem();
134 JMenu outputMenu = new JMenu();
136 JMenuItem sequenceFeature = new JMenuItem();
138 JMenuItem textColour = new JMenuItem();
140 JMenu jMenu1 = new JMenu();
142 JMenu structureMenu = new JMenu();
144 JMenu viewStructureMenu = new JMenu();
146 // JMenu colStructureMenu = new JMenu();
147 JMenuItem editSequence = new JMenuItem();
149 // JMenuItem annotationMenuItem = new JMenuItem();
151 JMenu groupLinksMenu;
154 * Creates a new PopupMenu object.
161 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
163 this(ap, seq, links, null);
173 public PopupMenu(final AlignmentPanel ap, final SequenceI seq, Vector links,
176 // /////////////////////////////////////////////////////////
177 // If this is activated from the sequence panel, the user may want to
178 // edit or annotate a particular residue. Therefore display the residue menu
180 // If from the IDPanel, we must display the sequence menu
181 // ////////////////////////////////////////////////////////
185 ButtonGroup colours = new ButtonGroup();
186 colours.add(noColourmenuItem);
187 colours.add(clustalColour);
188 colours.add(zappoColour);
189 colours.add(taylorColour);
190 colours.add(hydrophobicityColour);
191 colours.add(helixColour);
192 colours.add(strandColour);
193 colours.add(turnColour);
194 colours.add(buriedColour);
195 colours.add(abovePIDColour);
196 colours.add(userDefinedColour);
197 colours.add(PIDColour);
198 colours.add(BLOSUM62Colour);
199 colours.add(purinePyrimidineColour);
200 colours.add(RNAInteractionColour);
201 // colours.add(covariationColour);
203 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
205 JMenuItem item = new JMenuItem(
206 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
208 item.addActionListener(new java.awt.event.ActionListener()
210 public void actionPerformed(ActionEvent e)
212 outputText_actionPerformed(e);
216 outputMenu.add(item);
222 } catch (Exception e)
230 sequenceMenu.setText(sequence.getName());
232 if (seq.getDatasetSequence().getPDBId() != null
233 && seq.getDatasetSequence().getPDBId().size() > 0)
235 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
238 while (e.hasMoreElements())
240 final PDBEntry pdb = (PDBEntry) e.nextElement();
242 menuItem = new JMenuItem();
243 menuItem.setText(pdb.getId());
244 menuItem.addActionListener(new java.awt.event.ActionListener()
246 public void actionPerformed(ActionEvent e)
248 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
249 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
250 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
254 viewStructureMenu.add(menuItem);
257 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
258 * menuItem.addActionListener(new java.awt.event.ActionListener() {
259 * public void actionPerformed(ActionEvent e) {
260 * colourByStructure(pdb.getId()); } });
261 * colStructureMenu.add(menuItem);
267 if (ap.av.getAlignment().isNucleotide() == false)
269 structureMenu.remove(viewStructureMenu);
271 // structureMenu.remove(colStructureMenu);
274 if (ap.av.getAlignment().isNucleotide() == true)
276 AlignmentAnnotation[] aa = ap.av.getAlignment().getAlignmentAnnotation();
277 for (int i = 0; i < aa.length; i++)
279 if (aa[i].getRNAStruc() != null)
281 final String rnastruc = aa[i].getRNAStruc();
282 final String structureLine=aa[i].label;
283 menuItem = new JMenuItem();
284 menuItem.setText("2D RNA "+structureLine);
285 menuItem.addActionListener(new java.awt.event.ActionListener()
288 public void actionPerformed(ActionEvent e)
290 //System.out.println("1:"+structureLine);
291 System.out.println("1:sname"+seq.getName());
292 System.out.println("2:seq"+seq);
294 //System.out.println("3:"+seq.getSequenceAsString());
295 System.out.println("3:strucseq"+rnastruc);
296 System.out.println("4:struc"+seq.getRNA());
297 System.out.println("5:name"+seq.getName());
298 System.out.println("6:ap"+ap);
299 new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
300 System.out.println("end");
303 viewStructureMenu.add(menuItem);
307 // SequenceFeatures[] test = seq.getSequenceFeatures();
309 if (seq.getAnnotation() != null)
311 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
312 for (int i = 0; i < seqAnno.length; i++)
314 if (seqAnno[i].getRNAStruc() != null)
316 final String rnastruc = seqAnno[i].getRNAStruc();
318 // TODO: make rnastrucF a bit more nice
319 menuItem = new JMenuItem();
320 menuItem.setText("2D RNA - "+seq.getName());
321 menuItem.addActionListener(new java.awt.event.ActionListener()
323 public void actionPerformed(ActionEvent e)
325 // TODO: VARNA does'nt print gaps in the sequence
327 new AppVarna(seq.getName()+" structure",seq,rnastruc,seq.getRNA(),
331 viewStructureMenu.add(menuItem);
339 menuItem = new JMenuItem("Hide Sequences");
340 menuItem.addActionListener(new java.awt.event.ActionListener()
342 public void actionPerformed(ActionEvent e)
344 hideSequences(false);
349 if (ap.av.getSelectionGroup() != null
350 && ap.av.getSelectionGroup().getSize() > 1)
352 menuItem = new JMenuItem("Represent Group with " + seq.getName());
353 menuItem.addActionListener(new java.awt.event.ActionListener()
355 public void actionPerformed(ActionEvent e)
360 sequenceMenu.add(menuItem);
363 if (ap.av.hasHiddenRows())
365 final int index = ap.av.getAlignment().findIndex(seq);
367 if (ap.av.adjustForHiddenSeqs(index)
368 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
370 menuItem = new JMenuItem("Reveal Sequences");
371 menuItem.addActionListener(new ActionListener()
373 public void actionPerformed(ActionEvent e)
375 ap.av.showSequence(index);
376 if (ap.overviewPanel != null)
378 ap.overviewPanel.updateOverviewImage();
386 // for the case when no sequences are even visible
387 if (ap.av.hasHiddenRows()) {
389 menuItem = new JMenuItem("Reveal All");
390 menuItem.addActionListener(new ActionListener()
392 public void actionPerformed(ActionEvent e)
394 ap.av.showAllHiddenSeqs();
395 if (ap.overviewPanel != null)
397 ap.overviewPanel.updateOverviewImage();
407 SequenceGroup sg = ap.av.getSelectionGroup();
409 if (sg != null&& sg.getSize()>0)
411 groupName.setText("Name: "+sg.getName());
412 groupName.setText("Edit name and description of current group.");
414 if (sg.cs instanceof ZappoColourScheme)
416 zappoColour.setSelected(true);
418 else if (sg.cs instanceof TaylorColourScheme)
420 taylorColour.setSelected(true);
422 else if (sg.cs instanceof PIDColourScheme)
424 PIDColour.setSelected(true);
426 else if (sg.cs instanceof Blosum62ColourScheme)
428 BLOSUM62Colour.setSelected(true);
430 else if (sg.cs instanceof UserColourScheme)
432 userDefinedColour.setSelected(true);
434 else if (sg.cs instanceof HydrophobicColourScheme)
436 hydrophobicityColour.setSelected(true);
438 else if (sg.cs instanceof HelixColourScheme)
440 helixColour.setSelected(true);
442 else if (sg.cs instanceof StrandColourScheme)
444 strandColour.setSelected(true);
446 else if (sg.cs instanceof TurnColourScheme)
448 turnColour.setSelected(true);
450 else if (sg.cs instanceof BuriedColourScheme)
452 buriedColour.setSelected(true);
454 else if (sg.cs instanceof ClustalxColourScheme)
456 clustalColour.setSelected(true);
458 else if (sg.cs instanceof PurinePyrimidineColourScheme)
460 purinePyrimidineColour.setSelected(true);
463 else if (sg.cs instanceof RNAInteractionColourScheme)
465 RNAInteractionColour.setSelected(true);
468 * else if (sg.cs instanceof CovariationColourScheme) {
469 * covariationColour.setSelected(true); }
473 noColourmenuItem.setSelected(true);
476 if (sg.cs != null && sg.cs.conservationApplied())
478 conservationMenuItem.setSelected(true);
480 displayNonconserved.setSelected(sg.getShowNonconserved());
481 showText.setSelected(sg.getDisplayText());
482 showColourText.setSelected(sg.getColourText());
483 showBoxes.setSelected(sg.getDisplayBoxes());
484 // add any groupURLs to the groupURL submenu and make it visible
485 if (groupLinks != null && groupLinks.size() > 0)
487 buildGroupURLMenu(sg, groupLinks);
489 // Add a 'show all structures' for the current selection
490 Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
491 SequenceI sqass=null;
492 for (SequenceI sq: ap.av.getSequenceSelection())
494 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
496 for (PDBEntry pe: pes)
498 pdbe.put(pe.getId(), pe);
508 final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
509 final JMenuItem gpdbview;
512 structureMenu.add(gpdbview=new JMenuItem("View structure for "+sqass.getDisplayId(false)));
514 structureMenu.add(gpdbview=new JMenuItem("View all "+pdbe.size()+" structures."));
516 gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
517 gpdbview.addActionListener(new ActionListener()
521 public void actionPerformed(ActionEvent e)
523 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
530 groupMenu.setVisible(false);
531 editMenu.setVisible(false);
534 if (!ap.av.getAlignment().getGroups().contains(sg))
536 unGroupMenuItem.setVisible(false);
541 sequenceMenu.setVisible(false);
542 structureMenu.setVisible(false);
545 if (links != null && links.size() > 0)
548 JMenu linkMenu = new JMenu("Link");
549 Vector linkset = new Vector();
550 for (int i = 0; i < links.size(); i++)
552 String link = links.elementAt(i).toString();
553 UrlLink urlLink = null;
556 urlLink = new UrlLink(link);
557 } catch (Exception foo)
559 jalview.bin.Cache.log.error("Exception for URLLink '" + link
564 if (!urlLink.isValid())
566 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
569 final String label = urlLink.getLabel();
570 if (seq!=null && urlLink.isDynamic())
573 // collect matching db-refs
574 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
575 seq.getDBRef(), new String[]
576 { urlLink.getTarget() });
577 // collect id string too
578 String id = seq.getName();
579 String descr = seq.getDescription();
580 if (descr != null && descr.length() < 1)
587 for (int r = 0; r < dbr.length; r++)
589 if (id != null && dbr[r].getAccessionId().equals(id))
591 // suppress duplicate link creation for the bare sequence ID
592 // string with this link
595 // create Bare ID link for this RUL
596 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
600 for (int u = 0; u < urls.length; u += 2)
602 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
604 linkset.addElement(urls[u] + "|" + urls[u + 1]);
605 addshowLink(linkMenu, label + "|" + urls[u],
614 // create Bare ID link for this RUL
615 String[] urls = urlLink.makeUrls(id, true);
618 for (int u = 0; u < urls.length; u += 2)
620 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
622 linkset.addElement(urls[u] + "|" + urls[u + 1]);
623 addshowLink(linkMenu, label, urls[u + 1]);
628 // Create urls from description but only for URL links which are regex
630 if (descr != null && urlLink.getRegexReplace() != null)
632 // create link for this URL from description where regex matches
633 String[] urls = urlLink.makeUrls(descr, true);
636 for (int u = 0; u < urls.length; u += 2)
638 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
640 linkset.addElement(urls[u] + "|" + urls[u + 1]);
641 addshowLink(linkMenu, label, urls[u + 1]);
649 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
651 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
652 // Add a non-dynamic link
653 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
657 if (sequence != null)
659 sequenceMenu.add(linkMenu);
668 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
671 // TODO: usability: thread off the generation of group url content so root
673 // sequence only URLs
674 // ID/regex match URLs
675 groupLinksMenu = new JMenu("Group Link");
676 JMenu[] linkMenus = new JMenu[]
677 { null, new JMenu("IDS"), new JMenu("Sequences"),
678 new JMenu("IDS and Sequences") }; // three types of url that might be
680 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
681 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
682 Hashtable commonDbrefs = new Hashtable();
683 for (int sq = 0; sq < seqs.length; sq++)
686 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
687 .findPosition(sg.getEndRes());
688 // just collect ids from dataset sequence
689 // TODO: check if IDs collected from selecton group intersects with the
690 // current selection, too
691 SequenceI sqi = seqs[sq];
692 while (sqi.getDatasetSequence() != null)
694 sqi = sqi.getDatasetSequence();
696 DBRefEntry[] dbr = sqi.getDBRef();
697 if (dbr != null && dbr.length > 0)
699 for (int d = 0; d < dbr.length; d++)
701 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
702 Object[] sarray = (Object[]) commonDbrefs.get(src);
705 sarray = new Object[2];
706 sarray[0] = new int[]
708 sarray[1] = new String[seqs.length];
710 commonDbrefs.put(src, sarray);
713 if (((String[]) sarray[1])[sq] == null)
716 || (dbr[d].getMap().locateMappedRange(start, end) != null))
718 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
719 ((int[]) sarray[0])[0]++;
725 // now create group links for all distinct ID/sequence sets.
726 boolean addMenu = false; // indicates if there are any group links to give
728 for (int i = 0; i < groupLinks.size(); i++)
730 String link = groupLinks.elementAt(i).toString();
731 GroupUrlLink urlLink = null;
734 urlLink = new GroupUrlLink(link);
735 } catch (Exception foo)
737 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
742 if (!urlLink.isValid())
744 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
747 final String label = urlLink.getLabel();
748 boolean usingNames = false;
749 // Now see which parts of the group apply for this URL
750 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
751 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
752 String[] seqstr, ids; // input to makeUrl
755 int numinput = ((int[]) idset[0])[0];
756 String[] allids = ((String[]) idset[1]);
757 seqstr = new String[numinput];
758 ids = new String[numinput];
759 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
761 if (allids[sq] != null)
763 ids[idcount] = allids[sq];
764 seqstr[idcount++] = idandseqs[1][sq];
770 // just use the id/seq set
771 seqstr = idandseqs[1];
775 // and try and make the groupURL!
777 Object[] urlset = null;
780 urlset = urlLink.makeUrlStubs(ids, seqstr,
781 "FromJalview" + System.currentTimeMillis(), false);
782 } catch (UrlStringTooLongException e)
787 int type = urlLink.getGroupURLType() & 3;
788 // System.out.println(urlLink.getGroupURLType()
789 // +" "+((String[])urlset[3])[0]);
790 // first two bits ofurlLink type bitfield are sequenceids and sequences
791 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
792 addshowLink(linkMenus[type], label
793 + (((type & 1) == 1) ? ("("
794 + (usingNames ? "Names" : ltarget) + ")") : ""),
801 groupLinksMenu = new JMenu("Group Links");
802 for (int m = 0; m < linkMenus.length; m++)
804 if (linkMenus[m] != null
805 && linkMenus[m].getMenuComponentCount() > 0)
807 groupLinksMenu.add(linkMenus[m]);
811 groupMenu.add(groupLinksMenu);
816 * add a show URL menu item to the given linkMenu
820 * - menu label string
824 private void addshowLink(JMenu linkMenu, String label, final String url)
826 JMenuItem item = new JMenuItem(label);
827 item.setToolTipText("open URL: " + url);
828 item.addActionListener(new java.awt.event.ActionListener()
830 public void actionPerformed(ActionEvent e)
832 new Thread(new Runnable()
848 * add a late bound groupURL item to the given linkMenu
852 * - menu label string
853 * @param urlgenerator
854 * GroupURLLink used to generate URL
856 * Object array returned from the makeUrlStubs function.
858 private void addshowLink(JMenu linkMenu, String label,
859 final GroupUrlLink urlgenerator, final Object[] urlstub)
861 JMenuItem item = new JMenuItem(label);
862 item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
863 + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
872 item.addActionListener(new java.awt.event.ActionListener()
874 public void actionPerformed(ActionEvent e)
876 new Thread(new Runnable()
883 showLink(urlgenerator.constructFrom(urlstub));
884 } catch (UrlStringTooLongException e)
902 private void jbInit() throws Exception
904 groupMenu.setText("Group");
905 groupMenu.setText("Selection");
906 groupName.setText("Name");
907 groupName.addActionListener(new java.awt.event.ActionListener()
909 public void actionPerformed(ActionEvent e)
911 groupName_actionPerformed();
914 sequenceMenu.setText("Sequence");
915 sequenceName.setText("Edit Name/Description");
916 sequenceName.addActionListener(new java.awt.event.ActionListener()
918 public void actionPerformed(ActionEvent e)
920 sequenceName_actionPerformed();
923 PIDColour.setFocusPainted(false);
924 unGroupMenuItem.setText("Remove Group");
925 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
927 public void actionPerformed(ActionEvent e)
929 unGroupMenuItem_actionPerformed();
933 outline.setText("Border colour");
934 outline.addActionListener(new java.awt.event.ActionListener()
936 public void actionPerformed(ActionEvent e)
938 outline_actionPerformed();
941 nucleotideMenuItem.setText("Nucleotide");
942 nucleotideMenuItem.addActionListener(new ActionListener()
944 public void actionPerformed(ActionEvent e)
946 nucleotideMenuItem_actionPerformed();
949 colourMenu.setText("Group Colour");
950 showBoxes.setText("Boxes");
951 showBoxes.setState(true);
952 showBoxes.addActionListener(new ActionListener()
954 public void actionPerformed(ActionEvent e)
956 showBoxes_actionPerformed();
959 showText.setText("Text");
960 showText.setState(true);
961 showText.addActionListener(new ActionListener()
963 public void actionPerformed(ActionEvent e)
965 showText_actionPerformed();
968 showColourText.setText("Colour Text");
969 showColourText.addActionListener(new ActionListener()
971 public void actionPerformed(ActionEvent e)
973 showColourText_actionPerformed();
976 displayNonconserved.setText("Show Nonconserved");
977 displayNonconserved.setState(true);
978 displayNonconserved.addActionListener(new ActionListener()
980 public void actionPerformed(ActionEvent e)
982 showNonconserved_actionPerformed();
985 editMenu.setText("Edit");
987 cut.addActionListener(new ActionListener()
989 public void actionPerformed(ActionEvent e)
991 cut_actionPerformed();
994 upperCase.setText("To Upper Case");
995 upperCase.addActionListener(new ActionListener()
997 public void actionPerformed(ActionEvent e)
1002 copy.setText("Copy");
1003 copy.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 copy_actionPerformed();
1010 lowerCase.setText("To Lower Case");
1011 lowerCase.addActionListener(new ActionListener()
1013 public void actionPerformed(ActionEvent e)
1018 toggle.setText("Toggle Case");
1019 toggle.addActionListener(new ActionListener()
1021 public void actionPerformed(ActionEvent e)
1026 pdbMenu.setText("Associate Structure with Sequence");
1027 pdbFromFile.setText("From File");
1028 pdbFromFile.addActionListener(new ActionListener()
1030 public void actionPerformed(ActionEvent e)
1033 pdbFromFile_actionPerformed();
1034 } catch (ExceptionFileFormatOrSyntax e1) {
1035 // TODO Auto-generated catch block
1036 e1.printStackTrace();
1037 } catch (ParserConfigurationException e1) {
1038 // TODO Auto-generated catch block
1039 e1.printStackTrace();
1040 } catch (SAXException e1) {
1041 // TODO Auto-generated catch block
1042 e1.printStackTrace();
1043 } catch (ExceptionPermissionDenied e1) {
1044 // TODO Auto-generated catch block
1045 e1.printStackTrace();
1046 } catch (ExceptionLoadingFailed e1) {
1047 // TODO Auto-generated catch block
1048 e1.printStackTrace();
1049 } catch (InterruptedException e1) {
1050 // TODO Auto-generated catch block
1051 e1.printStackTrace();
1055 enterPDB.setText("Enter PDB Id");
1056 enterPDB.addActionListener(new ActionListener()
1058 public void actionPerformed(ActionEvent e)
1060 enterPDB_actionPerformed();
1063 discoverPDB.setText("Discover PDB ids");
1064 discoverPDB.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 discoverPDB_actionPerformed();
1071 outputMenu.setText("Output to Textbox...");
1072 sequenceFeature.setText("Create Sequence Feature");
1073 sequenceFeature.addActionListener(new ActionListener()
1075 public void actionPerformed(ActionEvent e)
1077 sequenceFeature_actionPerformed();
1080 textColour.setText("Text Colour");
1081 textColour.addActionListener(new ActionListener()
1083 public void actionPerformed(ActionEvent e)
1085 textColour_actionPerformed();
1088 jMenu1.setText("Group");
1089 structureMenu.setText("Structure");
1090 viewStructureMenu.setText("View Structure");
1091 // colStructureMenu.setText("Colour By Structure");
1092 editSequence.setText("Edit Sequence...");
1093 editSequence.addActionListener(new ActionListener()
1095 public void actionPerformed(ActionEvent actionEvent)
1097 editSequence_actionPerformed(actionEvent);
1101 * annotationMenuItem.setText("By Annotation");
1102 * annotationMenuItem.addActionListener(new ActionListener() { public void
1103 * actionPerformed(ActionEvent actionEvent) {
1104 * annotationMenuItem_actionPerformed(actionEvent); } });
1110 this.add(structureMenu);
1111 groupMenu.add(editMenu);
1112 groupMenu.add(outputMenu);
1113 groupMenu.add(sequenceFeature);
1114 groupMenu.add(jMenu1);
1115 sequenceMenu.add(sequenceName);
1116 colourMenu.add(textColour);
1117 colourMenu.add(noColourmenuItem);
1118 colourMenu.add(clustalColour);
1119 colourMenu.add(BLOSUM62Colour);
1120 colourMenu.add(PIDColour);
1121 colourMenu.add(zappoColour);
1122 colourMenu.add(taylorColour);
1123 colourMenu.add(hydrophobicityColour);
1124 colourMenu.add(helixColour);
1125 colourMenu.add(strandColour);
1126 colourMenu.add(turnColour);
1127 colourMenu.add(buriedColour);
1128 colourMenu.add(nucleotideMenuItem);
1129 colourMenu.add(RNAInteractionColour);
1130 if (ap.getAlignment().isNucleotide()) {
1131 colourMenu.add(purinePyrimidineColour);
1133 // colourMenu.add(covariationColour);
1134 colourMenu.add(userDefinedColour);
1136 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1138 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1139 .getUserColourSchemes().keys();
1141 while (userColours.hasMoreElements())
1143 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1144 item.addActionListener(new ActionListener()
1146 public void actionPerformed(ActionEvent evt)
1148 userDefinedColour_actionPerformed(evt);
1151 colourMenu.add(item);
1155 colourMenu.addSeparator();
1156 colourMenu.add(abovePIDColour);
1157 colourMenu.add(conservationMenuItem);
1158 // colourMenu.add(annotationMenuItem);
1161 editMenu.add(editSequence);
1162 editMenu.add(upperCase);
1163 editMenu.add(lowerCase);
1164 editMenu.add(toggle);
1165 pdbMenu.add(pdbFromFile);
1166 pdbMenu.add(enterPDB);
1167 pdbMenu.add(discoverPDB);
1168 jMenu1.add(groupName);
1169 jMenu1.add(unGroupMenuItem);
1170 jMenu1.add(colourMenu);
1171 jMenu1.add(showBoxes);
1172 jMenu1.add(showText);
1173 jMenu1.add(showColourText);
1174 jMenu1.add(outline);
1175 jMenu1.add(displayNonconserved);
1176 structureMenu.add(pdbMenu);
1177 structureMenu.add(viewStructureMenu);
1178 // structureMenu.add(colStructureMenu);
1179 noColourmenuItem.setText("None");
1180 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1182 public void actionPerformed(ActionEvent e)
1184 noColourmenuItem_actionPerformed();
1188 clustalColour.setText("Clustalx colours");
1189 clustalColour.addActionListener(new java.awt.event.ActionListener()
1191 public void actionPerformed(ActionEvent e)
1193 clustalColour_actionPerformed();
1196 zappoColour.setText("Zappo");
1197 zappoColour.addActionListener(new java.awt.event.ActionListener()
1199 public void actionPerformed(ActionEvent e)
1201 zappoColour_actionPerformed();
1204 taylorColour.setText("Taylor");
1205 taylorColour.addActionListener(new java.awt.event.ActionListener()
1207 public void actionPerformed(ActionEvent e)
1209 taylorColour_actionPerformed();
1212 hydrophobicityColour.setText("Hydrophobicity");
1213 hydrophobicityColour
1214 .addActionListener(new java.awt.event.ActionListener()
1216 public void actionPerformed(ActionEvent e)
1218 hydrophobicityColour_actionPerformed();
1221 helixColour.setText("Helix propensity");
1222 helixColour.addActionListener(new java.awt.event.ActionListener()
1224 public void actionPerformed(ActionEvent e)
1226 helixColour_actionPerformed();
1229 strandColour.setText("Strand propensity");
1230 strandColour.addActionListener(new java.awt.event.ActionListener()
1232 public void actionPerformed(ActionEvent e)
1234 strandColour_actionPerformed();
1237 turnColour.setText("Turn propensity");
1238 turnColour.addActionListener(new java.awt.event.ActionListener()
1240 public void actionPerformed(ActionEvent e)
1242 turnColour_actionPerformed();
1245 buriedColour.setText("Buried Index");
1246 buriedColour.addActionListener(new java.awt.event.ActionListener()
1248 public void actionPerformed(ActionEvent e)
1250 buriedColour_actionPerformed();
1253 abovePIDColour.setText("Above % Identity");
1254 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1256 public void actionPerformed(ActionEvent e)
1258 abovePIDColour_actionPerformed();
1261 userDefinedColour.setText("User Defined...");
1262 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1264 public void actionPerformed(ActionEvent e)
1266 userDefinedColour_actionPerformed(e);
1269 PIDColour.setText("Percentage Identity");
1270 PIDColour.addActionListener(new java.awt.event.ActionListener()
1272 public void actionPerformed(ActionEvent e)
1274 PIDColour_actionPerformed();
1277 BLOSUM62Colour.setText("BLOSUM62");
1278 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 BLOSUM62Colour_actionPerformed();
1285 purinePyrimidineColour.setText("Purine/Pyrimidine");
1286 purinePyrimidineColour
1287 .addActionListener(new java.awt.event.ActionListener()
1289 public void actionPerformed(ActionEvent e)
1291 purinePyrimidineColour_actionPerformed();
1295 RNAInteractionColour.setText("RNA Interaction type");
1296 RNAInteractionColour
1297 .addActionListener(new java.awt.event.ActionListener()
1299 public void actionPerformed(ActionEvent e)
1301 RNAInteractionColour_actionPerformed();
1305 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1306 * public void actionPerformed(ActionEvent e) {
1307 * covariationColour_actionPerformed(); } });
1310 conservationMenuItem.setText("Conservation");
1311 conservationMenuItem
1312 .addActionListener(new java.awt.event.ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 conservationMenuItem_actionPerformed();
1321 protected void showNonconserved_actionPerformed()
1323 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1328 * call to refresh view after settings change
1332 ap.updateAnnotation();
1333 ap.paintAlignment(true);
1335 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1344 protected void clustalColour_actionPerformed()
1346 SequenceGroup sg = getGroup();
1347 sg.cs = new ClustalxColourScheme(
1348 sg,ap.av.getHiddenRepSequences());
1358 protected void zappoColour_actionPerformed()
1360 getGroup().cs = new ZappoColourScheme();
1370 protected void taylorColour_actionPerformed()
1372 getGroup().cs = new TaylorColourScheme();
1382 protected void hydrophobicityColour_actionPerformed()
1384 getGroup().cs = new HydrophobicColourScheme();
1394 protected void helixColour_actionPerformed()
1396 getGroup().cs = new HelixColourScheme();
1406 protected void strandColour_actionPerformed()
1408 getGroup().cs = new StrandColourScheme();
1418 protected void turnColour_actionPerformed()
1420 getGroup().cs = new TurnColourScheme();
1430 protected void buriedColour_actionPerformed()
1432 getGroup().cs = new BuriedColourScheme();
1442 public void nucleotideMenuItem_actionPerformed()
1444 getGroup().cs = new NucleotideColourScheme();
1448 protected void purinePyrimidineColour_actionPerformed()
1450 getGroup().cs = new PurinePyrimidineColourScheme();
1454 protected void RNAInteractionColour_actionPerformed()
1456 getGroup().cs = new RNAInteractionColourScheme();
1460 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1461 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1469 protected void abovePIDColour_actionPerformed()
1471 SequenceGroup sg = getGroup();
1477 if (abovePIDColour.isSelected())
1479 sg.cs.setConsensus(AAFrequency.calculate(
1480 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1481 sg.getEndRes() + 1));
1483 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1486 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1488 SliderPanel.showPIDSlider();
1491 // remove PIDColouring
1493 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1505 protected void userDefinedColour_actionPerformed(ActionEvent e)
1507 SequenceGroup sg = getGroup();
1509 if (e.getActionCommand().equals("User Defined..."))
1511 new UserDefinedColours(ap, sg);
1515 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1516 .getUserColourSchemes().get(e.getActionCommand());
1529 protected void PIDColour_actionPerformed()
1531 SequenceGroup sg = getGroup();
1532 sg.cs = new PIDColourScheme();
1533 sg.cs.setConsensus(AAFrequency.calculate(
1534 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1535 sg.getEndRes() + 1));
1545 protected void BLOSUM62Colour_actionPerformed()
1547 SequenceGroup sg = getGroup();
1549 sg.cs = new Blosum62ColourScheme();
1551 sg.cs.setConsensus(AAFrequency.calculate(
1552 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1553 sg.getEndRes() + 1));
1564 protected void noColourmenuItem_actionPerformed()
1566 getGroup().cs = null;
1576 protected void conservationMenuItem_actionPerformed()
1578 SequenceGroup sg = getGroup();
1584 if (conservationMenuItem.isSelected())
1586 Conservation c = new Conservation("Group",
1587 ResidueProperties.propHash, 3,
1588 sg.getSequences(ap.av.getHiddenRepSequences()), sg.getStartRes(),
1589 sg.getEndRes() + 1);
1592 c.verdict(false, ap.av.getConsPercGaps());
1594 sg.cs.setConservation(c);
1596 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1597 SliderPanel.showConservationSlider();
1600 // remove ConservationColouring
1602 sg.cs.setConservation(null);
1608 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1610 SequenceGroup sg = getGroup();
1616 AnnotationColourGradient acg = new AnnotationColourGradient(
1617 sequence.getAnnotation()[0], null,
1618 AnnotationColourGradient.NO_THRESHOLD);
1620 acg.predefinedColours = true;
1632 protected void groupName_actionPerformed()
1635 SequenceGroup sg = getGroup();
1636 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1637 sg.getDescription(), " Group Name ",
1638 "Group Description ", "Edit Group Name/Description",
1646 sg.setName(dialog.getName());
1647 sg.setDescription(dialog.getDescription());
1652 * Get selection group - adding it to the alignment if necessary.
1654 * @return sequence group to operate on
1656 SequenceGroup getGroup()
1658 SequenceGroup sg = ap.av.getSelectionGroup();
1659 // this method won't add a new group if it already exists
1662 ap.av.getAlignment().addGroup(sg);
1674 void sequenceName_actionPerformed()
1676 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1677 sequence.getDescription(), " Sequence Name ",
1678 "Sequence Description ", "Edit Sequence Name/Description",
1686 if (dialog.getName() != null)
1688 if (dialog.getName().indexOf(" ") > -1)
1690 JOptionPane.showMessageDialog(ap,
1691 "Spaces have been converted to \"_\"",
1692 "No spaces allowed in Sequence Name",
1693 JOptionPane.WARNING_MESSAGE);
1696 sequence.setName(dialog.getName().replace(' ', '_'));
1697 ap.paintAlignment(false);
1700 sequence.setDescription(dialog.getDescription());
1702 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1713 void unGroupMenuItem_actionPerformed()
1715 SequenceGroup sg = ap.av.getSelectionGroup();
1716 ap.av.getAlignment().deleteGroup(sg);
1717 ap.av.setSelectionGroup(null);
1727 protected void outline_actionPerformed()
1729 SequenceGroup sg = getGroup();
1730 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1735 sg.setOutlineColour(col);
1747 public void showBoxes_actionPerformed()
1749 getGroup().setDisplayBoxes(showBoxes.isSelected());
1759 public void showText_actionPerformed()
1761 getGroup().setDisplayText(showText.isSelected());
1771 public void showColourText_actionPerformed()
1773 getGroup().setColourText(showColourText.isSelected());
1777 public void showLink(String url)
1781 jalview.util.BrowserLauncher.openURL(url);
1782 } catch (Exception ex)
1785 .showInternalMessageDialog(
1787 "Unixers: Couldn't find default web browser."
1788 + "\nAdd the full path to your browser in Preferences.",
1789 "Web browser not found", JOptionPane.WARNING_MESSAGE);
1791 ex.printStackTrace();
1795 void hideSequences(boolean representGroup)
1797 SequenceGroup sg = ap.av.getSelectionGroup();
1798 if (sg == null || sg.getSize() < 1)
1800 ap.av.hideSequence(new SequenceI[]
1805 ap.av.setSelectionGroup(null);
1809 ap.av.hideRepSequences(sequence, sg);
1814 int gsize = sg.getSize();
1817 hseqs = new SequenceI[gsize];
1820 for (int i = 0; i < gsize; i++)
1822 hseqs[index++] = sg.getSequenceAt(i);
1825 ap.av.hideSequence(hseqs);
1826 // refresh(); TODO: ? needed ?
1827 ap.av.sendSelection();
1830 public void copy_actionPerformed()
1832 ap.alignFrame.copy_actionPerformed(null);
1835 public void cut_actionPerformed()
1837 ap.alignFrame.cut_actionPerformed(null);
1840 void changeCase(ActionEvent e)
1842 Object source = e.getSource();
1843 SequenceGroup sg = ap.av.getSelectionGroup();
1847 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1848 sg.getEndRes() + 1);
1853 if (source == toggle)
1855 description = "Toggle Case";
1856 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1858 else if (source == upperCase)
1860 description = "To Upper Case";
1861 caseChange = ChangeCaseCommand.TO_UPPER;
1865 description = "To Lower Case";
1866 caseChange = ChangeCaseCommand.TO_LOWER;
1869 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1870 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
1873 ap.alignFrame.addHistoryItem(caseCommand);
1875 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1881 public void outputText_actionPerformed(ActionEvent e)
1883 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1884 cap.setForInput(null);
1885 Desktop.addInternalFrame(cap,
1886 "Alignment output - " + e.getActionCommand(), 600, 500);
1888 String[] omitHidden = null;
1890 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1891 // or we simply trust the user wants
1892 // wysiwig behaviour
1893 SequenceGroup sg = ap.av.getSelectionGroup();
1894 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1895 omitHidden = ap.av.getViewAsString(true);
1896 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1897 AlignmentAnnotation[] nala = ap.av.getAlignment().getAlignmentAnnotation();
1900 for (int i = 0; i < nala.length; i++)
1902 AlignmentAnnotation na = nala[i];
1903 oal.addAnnotation(na);
1906 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1907 oal, omitHidden, csel, sg));
1911 public void pdbFromFile_actionPerformed() throws ExceptionFileFormatOrSyntax, ParserConfigurationException, SAXException, ExceptionPermissionDenied, ExceptionLoadingFailed, InterruptedException
1913 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1914 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1915 chooser.setFileView(new jalview.io.JalviewFileView());
1916 chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1917 chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1919 int value = chooser.showOpenDialog(null);
1921 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1923 String choice = chooser.getSelectedFile().getPath();
1924 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1925 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1930 public void enterPDB_actionPerformed()
1932 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1933 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1935 if (id != null && id.length() > 0)
1937 PDBEntry entry = new PDBEntry();
1938 entry.setId(id.toUpperCase());
1939 sequence.getDatasetSequence().addPDBId(entry);
1943 public void discoverPDB_actionPerformed()
1946 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
1948 : ap.av.getSequenceSelection());
1949 Thread discpdb = new Thread(new Runnable()
1954 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1955 .fetchDBRefs(false);
1962 public void sequenceFeature_actionPerformed()
1964 SequenceGroup sg = ap.av.getSelectionGroup();
1970 int rsize = 0, gSize = sg.getSize();
1971 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1972 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1974 for (int i = 0; i < gSize; i++)
1976 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1977 int end = sg.findEndRes(sg.getSequenceAt(i));
1980 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1981 features[rsize] = new SequenceFeature(null, null, null, start, end,
1986 rseqs = new SequenceI[rsize];
1987 tfeatures = new SequenceFeature[rsize];
1988 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1989 System.arraycopy(features, 0, tfeatures, 0, rsize);
1990 features = tfeatures;
1992 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1993 features, true, ap))
1995 ap.alignFrame.setShowSeqFeatures(true);
1996 ap.highlightSearchResults(null);
2000 public void textColour_actionPerformed()
2002 SequenceGroup sg = getGroup();
2005 new TextColourChooser().chooseColour(ap, sg);
2009 public void colourByStructure(String pdbid)
2011 Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
2014 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2015 "Coloured by " + pdbid, anots);
2017 ap.av.getAlignment().addAnnotation(an);
2018 an.createSequenceMapping(sequence, 0, true);
2019 // an.adjustForAlignment();
2020 ap.av.getAlignment().setAnnotationIndex(an, 0);
2022 ap.adjustAnnotationHeight();
2024 sequence.addAlignmentAnnotation(an);
2028 public void editSequence_actionPerformed(ActionEvent actionEvent)
2030 SequenceGroup sg = ap.av.getSelectionGroup();
2034 if (sequence == null)
2035 sequence = (Sequence) sg.getSequenceAt(0);
2037 EditNameDialog dialog = new EditNameDialog(
2038 sequence.getSequenceAsString(sg.getStartRes(),
2039 sg.getEndRes() + 1), null, "Edit Sequence ", null,
2040 "Edit Sequence", ap.alignFrame);
2044 EditCommand editCommand = new EditCommand("Edit Sequences",
2045 EditCommand.REPLACE, dialog.getName().replace(' ',
2046 ap.av.getGapCharacter()),
2047 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2048 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2050 ap.alignFrame.addHistoryItem(editCommand);
2052 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()