2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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/>.
22 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.commands.*;
28 import jalview.datamodel.*;
30 import jalview.schemes.*;
31 import jalview.util.GroupUrlLink;
32 import jalview.util.GroupUrlLink.UrlStringTooLongException;
33 import jalview.util.UrlLink;
39 * @version $Revision: 1.118 $
41 public class PopupMenu extends JPopupMenu
43 JMenu groupMenu = new JMenu();
45 JMenuItem groupName = new JMenuItem();
47 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
49 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
61 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
63 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
65 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
67 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
69 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
71 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
73 // protected JRadioButtonMenuItem covariationColour = new
74 // JRadioButtonMenuItem();
76 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
78 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
82 JMenu sequenceMenu = new JMenu();
84 JMenuItem sequenceName = new JMenuItem();
86 JMenuItem sequenceDetails = new JMenuItem();
88 JMenuItem sequenceSelDetails = new JMenuItem();
90 JMenuItem makeReferenceSeq = new JMenuItem();
94 JMenuItem unGroupMenuItem = new JMenuItem();
96 JMenuItem outline = new JMenuItem();
98 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
100 JMenu colourMenu = new JMenu();
102 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
104 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
106 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
108 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
110 JMenu editMenu = new JMenu();
112 JMenuItem cut = new JMenuItem();
114 JMenuItem copy = new JMenuItem();
116 JMenuItem upperCase = new JMenuItem();
118 JMenuItem lowerCase = new JMenuItem();
120 JMenuItem toggle = new JMenuItem();
122 JMenu pdbMenu = new JMenu();
124 JMenuItem pdbFromFile = new JMenuItem();
126 JMenuItem enterPDB = new JMenuItem();
128 JMenuItem discoverPDB = new JMenuItem();
130 JMenu outputMenu = new JMenu();
132 JMenuItem sequenceFeature = new JMenuItem();
134 JMenuItem textColour = new JMenuItem();
136 JMenu jMenu1 = new JMenu();
138 JMenu structureMenu = new JMenu();
140 JMenu viewStructureMenu = new JMenu();
142 // JMenu colStructureMenu = new JMenu();
143 JMenuItem editSequence = new JMenuItem();
145 // JMenuItem annotationMenuItem = new JMenuItem();
147 JMenu groupLinksMenu;
150 * Creates a new PopupMenu object.
157 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
159 this(ap, seq, links, null);
169 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
170 Vector links, Vector groupLinks)
172 // /////////////////////////////////////////////////////////
173 // If this is activated from the sequence panel, the user may want to
174 // edit or annotate a particular residue. Therefore display the residue menu
176 // If from the IDPanel, we must display the sequence menu
177 // ////////////////////////////////////////////////////////
181 ButtonGroup colours = new ButtonGroup();
182 colours.add(noColourmenuItem);
183 colours.add(clustalColour);
184 colours.add(zappoColour);
185 colours.add(taylorColour);
186 colours.add(hydrophobicityColour);
187 colours.add(helixColour);
188 colours.add(strandColour);
189 colours.add(turnColour);
190 colours.add(buriedColour);
191 colours.add(abovePIDColour);
192 colours.add(userDefinedColour);
193 colours.add(PIDColour);
194 colours.add(BLOSUM62Colour);
195 colours.add(purinePyrimidineColour);
196 // colours.add(covariationColour);
198 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
200 JMenuItem item = new JMenuItem(
201 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
203 item.addActionListener(new java.awt.event.ActionListener()
205 public void actionPerformed(ActionEvent e)
207 outputText_actionPerformed(e);
211 outputMenu.add(item);
217 } catch (Exception e)
225 sequenceMenu.setText(sequence.getName());
226 if (seq == ap.av.getAlignment().getSeqrep())
228 makeReferenceSeq.setText("Unmark representative");
230 makeReferenceSeq.setText("Mark as representative");
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
250 // allowing user to open just one structure per sequence
251 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
252 { pdb })[0], null, ap);
253 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
257 viewStructureMenu.add(menuItem);
260 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
261 * menuItem.addActionListener(new java.awt.event.ActionListener() {
262 * public void actionPerformed(ActionEvent e) {
263 * colourByStructure(pdb.getId()); } });
264 * colStructureMenu.add(menuItem);
270 if (ap.av.getAlignment().isNucleotide() == false)
272 structureMenu.remove(viewStructureMenu);
274 // structureMenu.remove(colStructureMenu);
276 if (ap.av.getAlignment().isNucleotide() == true)
278 AlignmentAnnotation[] aa = ap.av.getAlignment()
279 .getAlignmentAnnotation();
280 for (int i = 0; i < aa.length; i++)
282 if (aa[i].getRNAStruc() != null)
284 final String rnastruc = aa[i].getRNAStruc();
285 final String structureLine = aa[i].label;
286 menuItem = new JMenuItem();
287 menuItem.setText("2D RNA " + structureLine);
288 menuItem.addActionListener(new java.awt.event.ActionListener()
290 public void actionPerformed(ActionEvent e)
292 new AppVarna(structureLine, seq, seq.getSequenceAsString(),
293 rnastruc, seq.getName(), ap);
296 viewStructureMenu.add(menuItem);
300 // SequenceFeatures[] test = seq.getSequenceFeatures();
302 if (seq.getAnnotation() != null)
304 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
305 for (int i = 0; i < seqAnno.length; i++)
307 if (seqAnno[i].getRNAStruc() != null)
309 final String rnastruc = seqAnno[i].getRNAStruc();
311 // TODO: make rnastrucF a bit more nice
312 menuItem = new JMenuItem();
313 menuItem.setText("2D RNA - " + seq.getName());
314 menuItem.addActionListener(new java.awt.event.ActionListener()
316 public void actionPerformed(ActionEvent e)
318 // TODO: VARNA does'nt print gaps in the sequence
319 new AppVarna(seq.getName() + " structure", seq, seq
320 .getSequenceAsString(), rnastruc, seq.getName(),
324 viewStructureMenu.add(menuItem);
330 menuItem = new JMenuItem("Hide Sequences");
331 menuItem.addActionListener(new java.awt.event.ActionListener()
333 public void actionPerformed(ActionEvent e)
335 hideSequences(false);
340 if (ap.av.getSelectionGroup() != null
341 && ap.av.getSelectionGroup().getSize() > 1)
343 menuItem = new JMenuItem("Represent Group with " + seq.getName());
344 menuItem.addActionListener(new java.awt.event.ActionListener()
346 public void actionPerformed(ActionEvent e)
351 sequenceMenu.add(menuItem);
354 if (ap.av.hasHiddenRows())
356 final int index = ap.av.getAlignment().findIndex(seq);
358 if (ap.av.adjustForHiddenSeqs(index)
359 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
361 menuItem = new JMenuItem("Reveal Sequences");
362 menuItem.addActionListener(new ActionListener()
364 public void actionPerformed(ActionEvent e)
366 ap.av.showSequence(index);
367 if (ap.overviewPanel != null)
369 ap.overviewPanel.updateOverviewImage();
377 // for the case when no sequences are even visible
378 if (ap.av.hasHiddenRows())
381 menuItem = new JMenuItem("Reveal All");
382 menuItem.addActionListener(new ActionListener()
384 public void actionPerformed(ActionEvent e)
386 ap.av.showAllHiddenSeqs();
387 if (ap.overviewPanel != null)
389 ap.overviewPanel.updateOverviewImage();
399 SequenceGroup sg = ap.av.getSelectionGroup();
401 if (sg != null && sg.getSize() > 0)
403 groupName.setText("Name: " + sg.getName());
404 groupName.setText("Edit name and description of current group.");
406 if (sg.cs instanceof ZappoColourScheme)
408 zappoColour.setSelected(true);
410 else if (sg.cs instanceof TaylorColourScheme)
412 taylorColour.setSelected(true);
414 else if (sg.cs instanceof PIDColourScheme)
416 PIDColour.setSelected(true);
418 else if (sg.cs instanceof Blosum62ColourScheme)
420 BLOSUM62Colour.setSelected(true);
422 else if (sg.cs instanceof UserColourScheme)
424 userDefinedColour.setSelected(true);
426 else if (sg.cs instanceof HydrophobicColourScheme)
428 hydrophobicityColour.setSelected(true);
430 else if (sg.cs instanceof HelixColourScheme)
432 helixColour.setSelected(true);
434 else if (sg.cs instanceof StrandColourScheme)
436 strandColour.setSelected(true);
438 else if (sg.cs instanceof TurnColourScheme)
440 turnColour.setSelected(true);
442 else if (sg.cs instanceof BuriedColourScheme)
444 buriedColour.setSelected(true);
446 else if (sg.cs instanceof ClustalxColourScheme)
448 clustalColour.setSelected(true);
450 else if (sg.cs instanceof PurinePyrimidineColourScheme)
452 purinePyrimidineColour.setSelected(true);
455 * else if (sg.cs instanceof CovariationColourScheme) {
456 * covariationColour.setSelected(true); }
460 noColourmenuItem.setSelected(true);
463 if (sg.cs != null && sg.cs.conservationApplied())
465 conservationMenuItem.setSelected(true);
467 displayNonconserved.setSelected(sg.getShowNonconserved());
468 showText.setSelected(sg.getDisplayText());
469 showColourText.setSelected(sg.getColourText());
470 showBoxes.setSelected(sg.getDisplayBoxes());
471 // add any groupURLs to the groupURL submenu and make it visible
472 if (groupLinks != null && groupLinks.size() > 0)
474 buildGroupURLMenu(sg, groupLinks);
476 // Add a 'show all structures' for the current selection
477 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
478 SequenceI sqass = null;
479 for (SequenceI sq : ap.av.getSequenceSelection())
481 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
485 for (PDBEntry pe : pes)
487 pdbe.put(pe.getId(), pe);
497 final PDBEntry[] pe = pdbe.values().toArray(
498 new PDBEntry[pdbe.size()]);
499 final JMenuItem gpdbview;
500 if (pdbe.size() == 1)
502 structureMenu.add(gpdbview = new JMenuItem("View structure for "
503 + sqass.getDisplayId(false)));
507 structureMenu.add(gpdbview = new JMenuItem("View all "
508 + pdbe.size() + " structures."));
510 gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
511 gpdbview.addActionListener(new ActionListener()
515 public void actionPerformed(ActionEvent e)
517 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
524 groupMenu.setVisible(false);
525 editMenu.setVisible(false);
528 if (!ap.av.getAlignment().getGroups().contains(sg))
530 unGroupMenuItem.setVisible(false);
535 sequenceMenu.setVisible(false);
536 structureMenu.setVisible(false);
539 if (links != null && links.size() > 0)
542 JMenu linkMenu = new JMenu("Link");
543 Vector linkset = new Vector();
544 for (int i = 0; i < links.size(); i++)
546 String link = links.elementAt(i).toString();
547 UrlLink urlLink = null;
550 urlLink = new UrlLink(link);
551 } catch (Exception foo)
553 jalview.bin.Cache.log.error("Exception for URLLink '" + link
558 if (!urlLink.isValid())
560 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
563 final String label = urlLink.getLabel();
564 if (seq != null && urlLink.isDynamic())
567 // collect matching db-refs
568 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
569 seq.getDBRef(), new String[]
570 { urlLink.getTarget() });
571 // collect id string too
572 String id = seq.getName();
573 String descr = seq.getDescription();
574 if (descr != null && descr.length() < 1)
581 for (int r = 0; r < dbr.length; r++)
583 if (id != null && dbr[r].getAccessionId().equals(id))
585 // suppress duplicate link creation for the bare sequence ID
586 // string with this link
589 // create Bare ID link for this RUL
590 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
594 for (int u = 0; u < urls.length; u += 2)
596 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
598 linkset.addElement(urls[u] + "|" + urls[u + 1]);
599 addshowLink(linkMenu, label + "|" + urls[u],
608 // create Bare ID link for this RUL
609 String[] urls = urlLink.makeUrls(id, true);
612 for (int u = 0; u < urls.length; u += 2)
614 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
616 linkset.addElement(urls[u] + "|" + urls[u + 1]);
617 addshowLink(linkMenu, label, urls[u + 1]);
622 // Create urls from description but only for URL links which are regex
624 if (descr != null && urlLink.getRegexReplace() != null)
626 // create link for this URL from description where regex matches
627 String[] urls = urlLink.makeUrls(descr, true);
630 for (int u = 0; u < urls.length; u += 2)
632 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
634 linkset.addElement(urls[u] + "|" + urls[u + 1]);
635 addshowLink(linkMenu, label, urls[u + 1]);
643 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
645 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
646 // Add a non-dynamic link
647 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
651 if (sequence != null)
653 sequenceMenu.add(linkMenu);
662 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
665 // TODO: usability: thread off the generation of group url content so root
667 // sequence only URLs
668 // ID/regex match URLs
669 groupLinksMenu = new JMenu("Group Link");
670 JMenu[] linkMenus = new JMenu[]
671 { null, new JMenu("IDS"), new JMenu("Sequences"),
672 new JMenu("IDS and Sequences") }; // three types of url that might be
674 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
675 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
676 Hashtable commonDbrefs = new Hashtable();
677 for (int sq = 0; sq < seqs.length; sq++)
680 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
681 .findPosition(sg.getEndRes());
682 // just collect ids from dataset sequence
683 // TODO: check if IDs collected from selecton group intersects with the
684 // current selection, too
685 SequenceI sqi = seqs[sq];
686 while (sqi.getDatasetSequence() != null)
688 sqi = sqi.getDatasetSequence();
690 DBRefEntry[] dbr = sqi.getDBRef();
691 if (dbr != null && dbr.length > 0)
693 for (int d = 0; d < dbr.length; d++)
695 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
696 Object[] sarray = (Object[]) commonDbrefs.get(src);
699 sarray = new Object[2];
700 sarray[0] = new int[]
702 sarray[1] = new String[seqs.length];
704 commonDbrefs.put(src, sarray);
707 if (((String[]) sarray[1])[sq] == null)
710 || (dbr[d].getMap().locateMappedRange(start, end) != null))
712 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
713 ((int[]) sarray[0])[0]++;
719 // now create group links for all distinct ID/sequence sets.
720 boolean addMenu = false; // indicates if there are any group links to give
722 for (int i = 0; i < groupLinks.size(); i++)
724 String link = groupLinks.elementAt(i).toString();
725 GroupUrlLink urlLink = null;
728 urlLink = new GroupUrlLink(link);
729 } catch (Exception foo)
731 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
736 if (!urlLink.isValid())
738 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
741 final String label = urlLink.getLabel();
742 boolean usingNames = false;
743 // Now see which parts of the group apply for this URL
744 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
745 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
746 String[] seqstr, ids; // input to makeUrl
749 int numinput = ((int[]) idset[0])[0];
750 String[] allids = ((String[]) idset[1]);
751 seqstr = new String[numinput];
752 ids = new String[numinput];
753 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
755 if (allids[sq] != null)
757 ids[idcount] = allids[sq];
758 seqstr[idcount++] = idandseqs[1][sq];
764 // just use the id/seq set
765 seqstr = idandseqs[1];
769 // and try and make the groupURL!
771 Object[] urlset = null;
774 urlset = urlLink.makeUrlStubs(ids, seqstr,
775 "FromJalview" + System.currentTimeMillis(), false);
776 } catch (UrlStringTooLongException e)
781 int type = urlLink.getGroupURLType() & 3;
782 // System.out.println(urlLink.getGroupURLType()
783 // +" "+((String[])urlset[3])[0]);
784 // first two bits ofurlLink type bitfield are sequenceids and sequences
785 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
786 addshowLink(linkMenus[type], label
787 + (((type & 1) == 1) ? ("("
788 + (usingNames ? "Names" : ltarget) + ")") : ""),
795 groupLinksMenu = new JMenu("Group Links");
796 for (int m = 0; m < linkMenus.length; m++)
798 if (linkMenus[m] != null
799 && linkMenus[m].getMenuComponentCount() > 0)
801 groupLinksMenu.add(linkMenus[m]);
805 groupMenu.add(groupLinksMenu);
810 * add a show URL menu item to the given linkMenu
814 * - menu label string
818 private void addshowLink(JMenu linkMenu, String label, final String url)
820 JMenuItem item = new JMenuItem(label);
821 item.setToolTipText("open URL: " + url);
822 item.addActionListener(new java.awt.event.ActionListener()
824 public void actionPerformed(ActionEvent e)
826 new Thread(new Runnable()
842 * add a late bound groupURL item to the given linkMenu
846 * - menu label string
847 * @param urlgenerator
848 * GroupURLLink used to generate URL
850 * Object array returned from the makeUrlStubs function.
852 private void addshowLink(JMenu linkMenu, String label,
853 final GroupUrlLink urlgenerator, final Object[] urlstub)
855 JMenuItem item = new JMenuItem(label);
856 item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
857 + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
866 item.addActionListener(new java.awt.event.ActionListener()
868 public void actionPerformed(ActionEvent e)
870 new Thread(new Runnable()
877 showLink(urlgenerator.constructFrom(urlstub));
878 } catch (UrlStringTooLongException e)
896 private void jbInit() throws Exception
898 groupMenu.setText("Group");
899 groupMenu.setText("Selection");
900 groupName.setText("Name");
901 groupName.addActionListener(new java.awt.event.ActionListener()
903 public void actionPerformed(ActionEvent e)
905 groupName_actionPerformed();
908 sequenceMenu.setText("Sequence");
909 sequenceName.setText("Edit Name/Description");
910 sequenceName.addActionListener(new java.awt.event.ActionListener()
912 public void actionPerformed(ActionEvent e)
914 sequenceName_actionPerformed();
917 sequenceDetails.setText("Sequence Details ...");
918 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
920 public void actionPerformed(ActionEvent e)
922 sequenceDetails_actionPerformed();
925 sequenceSelDetails.setText("Sequence Details ...");
927 .addActionListener(new java.awt.event.ActionListener()
929 public void actionPerformed(ActionEvent e)
931 sequenceSelectionDetails_actionPerformed();
934 PIDColour.setFocusPainted(false);
935 unGroupMenuItem.setText("Remove Group");
936 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
938 public void actionPerformed(ActionEvent e)
940 unGroupMenuItem_actionPerformed();
944 outline.setText("Border colour");
945 outline.addActionListener(new java.awt.event.ActionListener()
947 public void actionPerformed(ActionEvent e)
949 outline_actionPerformed();
952 nucleotideMenuItem.setText("Nucleotide");
953 nucleotideMenuItem.addActionListener(new ActionListener()
955 public void actionPerformed(ActionEvent e)
957 nucleotideMenuItem_actionPerformed();
960 colourMenu.setText("Group Colour");
961 showBoxes.setText("Boxes");
962 showBoxes.setState(true);
963 showBoxes.addActionListener(new ActionListener()
965 public void actionPerformed(ActionEvent e)
967 showBoxes_actionPerformed();
970 showText.setText("Text");
971 showText.setState(true);
972 showText.addActionListener(new ActionListener()
974 public void actionPerformed(ActionEvent e)
976 showText_actionPerformed();
979 showColourText.setText("Colour Text");
980 showColourText.addActionListener(new ActionListener()
982 public void actionPerformed(ActionEvent e)
984 showColourText_actionPerformed();
987 displayNonconserved.setText("Show Nonconserved");
988 displayNonconserved.setState(true);
989 displayNonconserved.addActionListener(new ActionListener()
991 public void actionPerformed(ActionEvent e)
993 showNonconserved_actionPerformed();
996 editMenu.setText("Edit");
998 cut.addActionListener(new ActionListener()
1000 public void actionPerformed(ActionEvent e)
1002 cut_actionPerformed();
1005 upperCase.setText("To Upper Case");
1006 upperCase.addActionListener(new ActionListener()
1008 public void actionPerformed(ActionEvent e)
1013 copy.setText("Copy");
1014 copy.addActionListener(new ActionListener()
1016 public void actionPerformed(ActionEvent e)
1018 copy_actionPerformed();
1021 lowerCase.setText("To Lower Case");
1022 lowerCase.addActionListener(new ActionListener()
1024 public void actionPerformed(ActionEvent e)
1029 toggle.setText("Toggle Case");
1030 toggle.addActionListener(new ActionListener()
1032 public void actionPerformed(ActionEvent e)
1037 pdbMenu.setText("Associate Structure with Sequence");
1038 pdbFromFile.setText("From File");
1039 pdbFromFile.addActionListener(new ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 pdbFromFile_actionPerformed();
1046 enterPDB.setText("Enter PDB Id");
1047 enterPDB.addActionListener(new ActionListener()
1049 public void actionPerformed(ActionEvent e)
1051 enterPDB_actionPerformed();
1054 discoverPDB.setText("Discover PDB ids");
1055 discoverPDB.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 discoverPDB_actionPerformed();
1062 outputMenu.setText("Output to Textbox...");
1063 sequenceFeature.setText("Create Sequence Feature");
1064 sequenceFeature.addActionListener(new ActionListener()
1066 public void actionPerformed(ActionEvent e)
1068 sequenceFeature_actionPerformed();
1071 textColour.setText("Text Colour");
1072 textColour.addActionListener(new ActionListener()
1074 public void actionPerformed(ActionEvent e)
1076 textColour_actionPerformed();
1079 jMenu1.setText("Group");
1080 structureMenu.setText("Structure");
1081 viewStructureMenu.setText("View Structure");
1082 // colStructureMenu.setText("Colour By Structure");
1083 editSequence.setText("Edit Sequence...");
1084 editSequence.addActionListener(new ActionListener()
1086 public void actionPerformed(ActionEvent actionEvent)
1088 editSequence_actionPerformed(actionEvent);
1091 makeReferenceSeq.setText("Mark as representative");
1092 makeReferenceSeq.addActionListener(new ActionListener()
1096 public void actionPerformed(ActionEvent actionEvent)
1098 makeReferenceSeq_actionPerformed(actionEvent);
1103 * annotationMenuItem.setText("By Annotation");
1104 * annotationMenuItem.addActionListener(new ActionListener() { public void
1105 * actionPerformed(ActionEvent actionEvent) {
1106 * annotationMenuItem_actionPerformed(actionEvent); } });
1108 groupMenu.add(sequenceSelDetails);
1111 this.add(structureMenu);
1112 groupMenu.add(editMenu);
1113 groupMenu.add(outputMenu);
1114 groupMenu.add(sequenceFeature);
1115 groupMenu.add(jMenu1);
1116 sequenceMenu.add(sequenceName);
1117 sequenceMenu.add(sequenceDetails);
1118 sequenceMenu.add(makeReferenceSeq);
1119 colourMenu.add(textColour);
1120 colourMenu.add(noColourmenuItem);
1121 colourMenu.add(clustalColour);
1122 colourMenu.add(BLOSUM62Colour);
1123 colourMenu.add(PIDColour);
1124 colourMenu.add(zappoColour);
1125 colourMenu.add(taylorColour);
1126 colourMenu.add(hydrophobicityColour);
1127 colourMenu.add(helixColour);
1128 colourMenu.add(strandColour);
1129 colourMenu.add(turnColour);
1130 colourMenu.add(buriedColour);
1131 colourMenu.add(nucleotideMenuItem);
1132 if (ap.getAlignment().isNucleotide())
1134 colourMenu.add(purinePyrimidineColour);
1136 // colourMenu.add(covariationColour);
1137 colourMenu.add(userDefinedColour);
1139 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1141 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1142 .getUserColourSchemes().keys();
1144 while (userColours.hasMoreElements())
1146 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1147 item.addActionListener(new ActionListener()
1149 public void actionPerformed(ActionEvent evt)
1151 userDefinedColour_actionPerformed(evt);
1154 colourMenu.add(item);
1158 colourMenu.addSeparator();
1159 colourMenu.add(abovePIDColour);
1160 colourMenu.add(conservationMenuItem);
1161 // colourMenu.add(annotationMenuItem);
1164 editMenu.add(editSequence);
1165 editMenu.add(upperCase);
1166 editMenu.add(lowerCase);
1167 editMenu.add(toggle);
1168 pdbMenu.add(pdbFromFile);
1169 pdbMenu.add(enterPDB);
1170 pdbMenu.add(discoverPDB);
1171 jMenu1.add(groupName);
1172 jMenu1.add(unGroupMenuItem);
1173 jMenu1.add(colourMenu);
1174 jMenu1.add(showBoxes);
1175 jMenu1.add(showText);
1176 jMenu1.add(showColourText);
1177 jMenu1.add(outline);
1178 jMenu1.add(displayNonconserved);
1179 structureMenu.add(pdbMenu);
1180 structureMenu.add(viewStructureMenu);
1181 // structureMenu.add(colStructureMenu);
1182 noColourmenuItem.setText("None");
1183 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1185 public void actionPerformed(ActionEvent e)
1187 noColourmenuItem_actionPerformed();
1191 clustalColour.setText("Clustalx colours");
1192 clustalColour.addActionListener(new java.awt.event.ActionListener()
1194 public void actionPerformed(ActionEvent e)
1196 clustalColour_actionPerformed();
1199 zappoColour.setText("Zappo");
1200 zappoColour.addActionListener(new java.awt.event.ActionListener()
1202 public void actionPerformed(ActionEvent e)
1204 zappoColour_actionPerformed();
1207 taylorColour.setText("Taylor");
1208 taylorColour.addActionListener(new java.awt.event.ActionListener()
1210 public void actionPerformed(ActionEvent e)
1212 taylorColour_actionPerformed();
1215 hydrophobicityColour.setText("Hydrophobicity");
1216 hydrophobicityColour
1217 .addActionListener(new java.awt.event.ActionListener()
1219 public void actionPerformed(ActionEvent e)
1221 hydrophobicityColour_actionPerformed();
1224 helixColour.setText("Helix propensity");
1225 helixColour.addActionListener(new java.awt.event.ActionListener()
1227 public void actionPerformed(ActionEvent e)
1229 helixColour_actionPerformed();
1232 strandColour.setText("Strand propensity");
1233 strandColour.addActionListener(new java.awt.event.ActionListener()
1235 public void actionPerformed(ActionEvent e)
1237 strandColour_actionPerformed();
1240 turnColour.setText("Turn propensity");
1241 turnColour.addActionListener(new java.awt.event.ActionListener()
1243 public void actionPerformed(ActionEvent e)
1245 turnColour_actionPerformed();
1248 buriedColour.setText("Buried Index");
1249 buriedColour.addActionListener(new java.awt.event.ActionListener()
1251 public void actionPerformed(ActionEvent e)
1253 buriedColour_actionPerformed();
1256 abovePIDColour.setText("Above % Identity");
1257 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1259 public void actionPerformed(ActionEvent e)
1261 abovePIDColour_actionPerformed();
1264 userDefinedColour.setText("User Defined...");
1265 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1267 public void actionPerformed(ActionEvent e)
1269 userDefinedColour_actionPerformed(e);
1272 PIDColour.setText("Percentage Identity");
1273 PIDColour.addActionListener(new java.awt.event.ActionListener()
1275 public void actionPerformed(ActionEvent e)
1277 PIDColour_actionPerformed();
1280 BLOSUM62Colour.setText("BLOSUM62");
1281 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1283 public void actionPerformed(ActionEvent e)
1285 BLOSUM62Colour_actionPerformed();
1288 purinePyrimidineColour.setText("Purine/Pyrimidine");
1289 purinePyrimidineColour
1290 .addActionListener(new java.awt.event.ActionListener()
1292 public void actionPerformed(ActionEvent e)
1294 purinePyrimidineColour_actionPerformed();
1298 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1299 * public void actionPerformed(ActionEvent e) {
1300 * covariationColour_actionPerformed(); } });
1303 conservationMenuItem.setText("Conservation");
1304 conservationMenuItem
1305 .addActionListener(new java.awt.event.ActionListener()
1307 public void actionPerformed(ActionEvent e)
1309 conservationMenuItem_actionPerformed();
1314 protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent)
1316 if (!ap.av.getAlignment().hasSeqrep())
1318 // initialise the display flags so the user sees something happen
1319 ap.av.setDisplayReferenceSeq(true);
1320 ap.av.setColourByReferenceSeq(true);
1321 ap.av.getAlignment().setSeqrep(sequence);
1325 if (ap.av.getAlignment().getSeqrep() == sequence)
1327 ap.av.getAlignment().setSeqrep(null);
1331 ap.av.getAlignment().setSeqrep(sequence);
1337 protected void sequenceSelectionDetails_actionPerformed()
1339 createSequenceDetailsReport(ap.av.getSequenceSelection());
1342 protected void sequenceDetails_actionPerformed()
1344 createSequenceDetailsReport(new SequenceI[]
1348 public void createSequenceDetailsReport(SequenceI[] sequences)
1350 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1351 StringBuffer contents = new StringBuffer();
1352 for (SequenceI seq : sequences)
1354 contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1356 new SequenceAnnotationReport(null)
1357 .createSequenceAnnotationReport(
1363 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1365 contents.append("</p>");
1367 cap.setText("<html>" + contents.toString() + "</html>");
1369 Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1370 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1371 : "Selection"), 500, 400);
1375 protected void showNonconserved_actionPerformed()
1377 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1382 * call to refresh view after settings change
1386 ap.updateAnnotation();
1387 ap.paintAlignment(true);
1389 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1398 protected void clustalColour_actionPerformed()
1400 SequenceGroup sg = getGroup();
1401 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1411 protected void zappoColour_actionPerformed()
1413 getGroup().cs = new ZappoColourScheme();
1423 protected void taylorColour_actionPerformed()
1425 getGroup().cs = new TaylorColourScheme();
1435 protected void hydrophobicityColour_actionPerformed()
1437 getGroup().cs = new HydrophobicColourScheme();
1447 protected void helixColour_actionPerformed()
1449 getGroup().cs = new HelixColourScheme();
1459 protected void strandColour_actionPerformed()
1461 getGroup().cs = new StrandColourScheme();
1471 protected void turnColour_actionPerformed()
1473 getGroup().cs = new TurnColourScheme();
1483 protected void buriedColour_actionPerformed()
1485 getGroup().cs = new BuriedColourScheme();
1495 public void nucleotideMenuItem_actionPerformed()
1497 getGroup().cs = new NucleotideColourScheme();
1501 protected void purinePyrimidineColour_actionPerformed()
1503 getGroup().cs = new PurinePyrimidineColourScheme();
1508 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1509 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1517 protected void abovePIDColour_actionPerformed()
1519 SequenceGroup sg = getGroup();
1525 if (abovePIDColour.isSelected())
1527 sg.cs.setConsensus(AAFrequency.calculate(
1528 sg.getSequences(ap.av.getHiddenRepSequences()),
1529 sg.getStartRes(), sg.getEndRes() + 1));
1531 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1534 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1536 SliderPanel.showPIDSlider();
1539 // remove PIDColouring
1541 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1553 protected void userDefinedColour_actionPerformed(ActionEvent e)
1555 SequenceGroup sg = getGroup();
1557 if (e.getActionCommand().equals("User Defined..."))
1559 new UserDefinedColours(ap, sg);
1563 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1564 .getUserColourSchemes().get(e.getActionCommand());
1577 protected void PIDColour_actionPerformed()
1579 SequenceGroup sg = getGroup();
1580 sg.cs = new PIDColourScheme();
1581 sg.cs.setConsensus(AAFrequency.calculate(
1582 sg.getSequences(ap.av.getHiddenRepSequences()),
1583 sg.getStartRes(), sg.getEndRes() + 1));
1593 protected void BLOSUM62Colour_actionPerformed()
1595 SequenceGroup sg = getGroup();
1597 sg.cs = new Blosum62ColourScheme();
1599 sg.cs.setConsensus(AAFrequency.calculate(
1600 sg.getSequences(ap.av.getHiddenRepSequences()),
1601 sg.getStartRes(), sg.getEndRes() + 1));
1612 protected void noColourmenuItem_actionPerformed()
1614 getGroup().cs = null;
1624 protected void conservationMenuItem_actionPerformed()
1626 SequenceGroup sg = getGroup();
1632 if (conservationMenuItem.isSelected())
1634 Conservation c = new Conservation("Group",
1635 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1636 .getHiddenRepSequences()), sg.getStartRes(),
1637 sg.getEndRes() + 1);
1640 c.verdict(false, ap.av.getConsPercGaps());
1642 sg.cs.setConservation(c);
1644 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1645 SliderPanel.showConservationSlider();
1648 // remove ConservationColouring
1650 sg.cs.setConservation(null);
1656 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1658 SequenceGroup sg = getGroup();
1664 AnnotationColourGradient acg = new AnnotationColourGradient(
1665 sequence.getAnnotation()[0], null,
1666 AnnotationColourGradient.NO_THRESHOLD);
1668 acg.predefinedColours = true;
1680 protected void groupName_actionPerformed()
1683 SequenceGroup sg = getGroup();
1684 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1685 sg.getDescription(), " Group Name ",
1686 "Group Description ", "Edit Group Name/Description",
1694 sg.setName(dialog.getName());
1695 sg.setDescription(dialog.getDescription());
1700 * Get selection group - adding it to the alignment if necessary.
1702 * @return sequence group to operate on
1704 SequenceGroup getGroup()
1706 SequenceGroup sg = ap.av.getSelectionGroup();
1707 // this method won't add a new group if it already exists
1710 ap.av.getAlignment().addGroup(sg);
1722 void sequenceName_actionPerformed()
1724 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1725 sequence.getDescription(), " Sequence Name ",
1726 "Sequence Description ", "Edit Sequence Name/Description",
1734 if (dialog.getName() != null)
1736 if (dialog.getName().indexOf(" ") > -1)
1738 JOptionPane.showMessageDialog(ap,
1739 "Spaces have been converted to \"_\"",
1740 "No spaces allowed in Sequence Name",
1741 JOptionPane.WARNING_MESSAGE);
1744 sequence.setName(dialog.getName().replace(' ', '_'));
1745 ap.paintAlignment(false);
1748 sequence.setDescription(dialog.getDescription());
1750 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1761 void unGroupMenuItem_actionPerformed()
1763 SequenceGroup sg = ap.av.getSelectionGroup();
1764 ap.av.getAlignment().deleteGroup(sg);
1765 ap.av.setSelectionGroup(null);
1775 protected void outline_actionPerformed()
1777 SequenceGroup sg = getGroup();
1778 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1783 sg.setOutlineColour(col);
1795 public void showBoxes_actionPerformed()
1797 getGroup().setDisplayBoxes(showBoxes.isSelected());
1807 public void showText_actionPerformed()
1809 getGroup().setDisplayText(showText.isSelected());
1819 public void showColourText_actionPerformed()
1821 getGroup().setColourText(showColourText.isSelected());
1825 public void showLink(String url)
1829 jalview.util.BrowserLauncher.openURL(url);
1830 } catch (Exception ex)
1833 .showInternalMessageDialog(
1835 "Unixers: Couldn't find default web browser."
1836 + "\nAdd the full path to your browser in Preferences.",
1837 "Web browser not found", JOptionPane.WARNING_MESSAGE);
1839 ex.printStackTrace();
1843 void hideSequences(boolean representGroup)
1845 SequenceGroup sg = ap.av.getSelectionGroup();
1846 if (sg == null || sg.getSize() < 1)
1848 ap.av.hideSequence(new SequenceI[]
1853 ap.av.setSelectionGroup(null);
1857 ap.av.hideRepSequences(sequence, sg);
1862 int gsize = sg.getSize();
1865 hseqs = new SequenceI[gsize];
1868 for (int i = 0; i < gsize; i++)
1870 hseqs[index++] = sg.getSequenceAt(i);
1873 ap.av.hideSequence(hseqs);
1874 // refresh(); TODO: ? needed ?
1875 ap.av.sendSelection();
1878 public void copy_actionPerformed()
1880 ap.alignFrame.copy_actionPerformed(null);
1883 public void cut_actionPerformed()
1885 ap.alignFrame.cut_actionPerformed(null);
1888 void changeCase(ActionEvent e)
1890 Object source = e.getSource();
1891 SequenceGroup sg = ap.av.getSelectionGroup();
1895 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1896 sg.getEndRes() + 1);
1901 if (source == toggle)
1903 description = "Toggle Case";
1904 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1906 else if (source == upperCase)
1908 description = "To Upper Case";
1909 caseChange = ChangeCaseCommand.TO_UPPER;
1913 description = "To Lower Case";
1914 caseChange = ChangeCaseCommand.TO_LOWER;
1917 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1918 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1919 startEnd, caseChange);
1921 ap.alignFrame.addHistoryItem(caseCommand);
1923 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1929 public void outputText_actionPerformed(ActionEvent e)
1931 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1932 cap.setForInput(null);
1933 Desktop.addInternalFrame(cap,
1934 "Alignment output - " + e.getActionCommand(), 600, 500);
1936 String[] omitHidden = null;
1938 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1939 // or we simply trust the user wants
1940 // wysiwig behaviour
1941 SequenceGroup sg = ap.av.getSelectionGroup();
1942 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1943 omitHidden = ap.av.getViewAsString(true);
1944 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1945 AlignmentAnnotation[] nala = ap.av.getAlignment()
1946 .getAlignmentAnnotation();
1949 for (int i = 0; i < nala.length; i++)
1951 AlignmentAnnotation na = nala[i];
1952 oal.addAnnotation(na);
1955 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1956 oal, omitHidden, csel, sg));
1960 public void pdbFromFile_actionPerformed()
1962 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1963 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1964 chooser.setFileView(new jalview.io.JalviewFileView());
1965 chooser.setDialogTitle("Select a PDB file for "
1966 + sequence.getDisplayId(false));
1967 chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1968 + sequence.getDisplayId(false) + "'");
1970 int value = chooser.showOpenDialog(null);
1972 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1974 String choice = chooser.getSelectedFile().getPath();
1975 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1976 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1977 jalview.io.AppletFormatAdapter.FILE, sequence, true);
1982 public void enterPDB_actionPerformed()
1984 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1985 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1987 if (id != null && id.length() > 0)
1989 PDBEntry entry = new PDBEntry();
1990 entry.setId(id.toUpperCase());
1991 sequence.getDatasetSequence().addPDBId(entry);
1995 public void discoverPDB_actionPerformed()
1998 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2000 : ap.av.getSequenceSelection());
2001 Thread discpdb = new Thread(new Runnable()
2006 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2007 .fetchDBRefs(false);
2014 public void sequenceFeature_actionPerformed()
2016 SequenceGroup sg = ap.av.getSelectionGroup();
2022 int rsize = 0, gSize = sg.getSize();
2023 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2024 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2026 for (int i = 0; i < gSize; i++)
2028 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2029 int end = sg.findEndRes(sg.getSequenceAt(i));
2032 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2033 features[rsize] = new SequenceFeature(null, null, null, start, end,
2038 rseqs = new SequenceI[rsize];
2039 tfeatures = new SequenceFeature[rsize];
2040 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2041 System.arraycopy(features, 0, tfeatures, 0, rsize);
2042 features = tfeatures;
2044 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2045 features, true, ap))
2047 ap.alignFrame.setShowSeqFeatures(true);
2048 ap.highlightSearchResults(null);
2052 public void textColour_actionPerformed()
2054 SequenceGroup sg = getGroup();
2057 new TextColourChooser().chooseColour(ap, sg);
2061 public void colourByStructure(String pdbid)
2063 Annotation[] anots = ap.av.getStructureSelectionManager()
2064 .colourSequenceFromStructure(sequence, pdbid);
2066 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2067 "Coloured by " + pdbid, anots);
2069 ap.av.getAlignment().addAnnotation(an);
2070 an.createSequenceMapping(sequence, 0, true);
2071 // an.adjustForAlignment();
2072 ap.av.getAlignment().setAnnotationIndex(an, 0);
2074 ap.adjustAnnotationHeight();
2076 sequence.addAlignmentAnnotation(an);
2080 public void editSequence_actionPerformed(ActionEvent actionEvent)
2082 SequenceGroup sg = ap.av.getSelectionGroup();
2086 if (sequence == null)
2087 sequence = (Sequence) sg.getSequenceAt(0);
2089 EditNameDialog dialog = new EditNameDialog(
2090 sequence.getSequenceAsString(sg.getStartRes(),
2091 sg.getEndRes() + 1), null, "Edit Sequence ", null,
2092 "Edit Sequence", ap.alignFrame);
2096 EditCommand editCommand = new EditCommand("Edit Sequences",
2097 EditCommand.REPLACE, dialog.getName().replace(' ',
2098 ap.av.getGapCharacter()),
2099 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2100 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2102 ap.alignFrame.addHistoryItem(editCommand);
2104 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()