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/>.
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;
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();
96 JMenuItem sequenceDetails = new JMenuItem();
98 JMenuItem sequenceSelDetails = new JMenuItem();
102 JMenuItem unGroupMenuItem = new JMenuItem();
104 JMenuItem outline = new JMenuItem();
106 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
108 JMenu colourMenu = new JMenu();
110 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
112 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
114 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
116 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
118 JMenu editMenu = new JMenu();
120 JMenuItem cut = new JMenuItem();
122 JMenuItem copy = new JMenuItem();
124 JMenuItem upperCase = new JMenuItem();
126 JMenuItem lowerCase = new JMenuItem();
128 JMenuItem toggle = new JMenuItem();
130 JMenu pdbMenu = new JMenu();
132 JMenuItem pdbFromFile = new JMenuItem();
134 JMenuItem enterPDB = new JMenuItem();
136 JMenuItem discoverPDB = new JMenuItem();
138 JMenu outputMenu = new JMenu();
140 JMenuItem sequenceFeature = new JMenuItem();
142 JMenuItem textColour = new JMenuItem();
144 JMenu jMenu1 = new JMenu();
146 JMenu structureMenu = new JMenu();
148 JMenu viewStructureMenu = new JMenu();
150 // JMenu colStructureMenu = new JMenu();
151 JMenuItem editSequence = new JMenuItem();
153 // JMenuItem annotationMenuItem = new JMenuItem();
155 JMenu groupLinksMenu;
158 * Creates a new PopupMenu object.
165 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
167 this(ap, seq, links, null);
177 public PopupMenu(final AlignmentPanel ap, final SequenceI seq,
178 Vector links, Vector groupLinks)
180 // /////////////////////////////////////////////////////////
181 // If this is activated from the sequence panel, the user may want to
182 // edit or annotate a particular residue. Therefore display the residue menu
184 // If from the IDPanel, we must display the sequence menu
185 // ////////////////////////////////////////////////////////
189 ButtonGroup colours = new ButtonGroup();
190 colours.add(noColourmenuItem);
191 colours.add(clustalColour);
192 colours.add(zappoColour);
193 colours.add(taylorColour);
194 colours.add(hydrophobicityColour);
195 colours.add(helixColour);
196 colours.add(strandColour);
197 colours.add(turnColour);
198 colours.add(buriedColour);
199 colours.add(abovePIDColour);
200 colours.add(userDefinedColour);
201 colours.add(PIDColour);
202 colours.add(BLOSUM62Colour);
203 colours.add(purinePyrimidineColour);
204 colours.add(RNAInteractionColour);
205 // colours.add(covariationColour);
207 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
209 JMenuItem item = new JMenuItem(
210 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
212 item.addActionListener(new java.awt.event.ActionListener()
214 public void actionPerformed(ActionEvent e)
216 outputText_actionPerformed(e);
220 outputMenu.add(item);
226 } catch (Exception e)
234 sequenceMenu.setText(sequence.getName());
236 if (seq.getDatasetSequence().getPDBId() != null
237 && seq.getDatasetSequence().getPDBId().size() > 0)
239 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
242 while (e.hasMoreElements())
244 final PDBEntry pdb = (PDBEntry) e.nextElement();
246 menuItem = new JMenuItem();
247 menuItem.setText(pdb.getId());
248 menuItem.addActionListener(new java.awt.event.ActionListener()
250 public void actionPerformed(ActionEvent e)
252 // TODO re JAL-860: optionally open dialog or provide a menu entry
253 // allowing user to open just one structure per sequence
254 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[]
255 { pdb })[0], null, ap);
256 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
260 viewStructureMenu.add(menuItem);
263 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
264 * menuItem.addActionListener(new java.awt.event.ActionListener() {
265 * public void actionPerformed(ActionEvent e) {
266 * colourByStructure(pdb.getId()); } });
267 * colStructureMenu.add(menuItem);
273 if (ap.av.getAlignment().isNucleotide() == false)
275 structureMenu.remove(viewStructureMenu);
277 // structureMenu.remove(colStructureMenu);
280 if (ap.av.getAlignment().isNucleotide() == true)
282 AlignmentAnnotation[] aa = ap.av.getAlignment()
283 .getAlignmentAnnotation();
284 for (int i = 0; i < aa.length; i++)
286 if (aa[i].getRNAStruc() != null)
288 final String rnastruc = aa[i].getRNAStruc();
289 final String structureLine = aa[i].label;
290 menuItem = new JMenuItem();
291 menuItem.setText("2D RNA " + structureLine);
292 menuItem.addActionListener(new java.awt.event.ActionListener()
295 public void actionPerformed(ActionEvent e)
297 //System.out.println("1:"+structureLine);
298 System.out.println("1:sname"+seq.getName());
299 System.out.println("2:seq"+seq);
301 //System.out.println("3:"+seq.getSequenceAsString());
302 System.out.println("3:strucseq"+rnastruc);
303 //System.out.println("4:struc"+seq.getRNA());
304 System.out.println("5:name"+seq.getName());
305 System.out.println("6:ap"+ap);
306 new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq
308 //new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), seq.getName(), ap);
309 System.out.println("end");
312 viewStructureMenu.add(menuItem);
316 // SequenceFeatures[] test = seq.getSequenceFeatures();
318 if (seq.getAnnotation() != null)
320 AlignmentAnnotation seqAnno[] = seq.getAnnotation();
321 for (int i = 0; i < seqAnno.length; i++)
323 if (seqAnno[i].getRNAStruc() != null)
325 final String rnastruc = seqAnno[i].getRNAStruc();
327 // TODO: make rnastrucF a bit more nice
328 menuItem = new JMenuItem();
329 menuItem.setText("2D RNA - " + seq.getName());
330 menuItem.addActionListener(new java.awt.event.ActionListener()
332 public void actionPerformed(ActionEvent e)
334 // TODO: VARNA does'nt print gaps in the sequence
336 new AppVarna(seq.getName() + " structure", seq, seq
337 .getSequenceAsString(), rnastruc, seq.getName(),
341 viewStructureMenu.add(menuItem);
348 menuItem = new JMenuItem("Hide Sequences");
349 menuItem.addActionListener(new java.awt.event.ActionListener()
351 public void actionPerformed(ActionEvent e)
353 hideSequences(false);
358 if (ap.av.getSelectionGroup() != null
359 && ap.av.getSelectionGroup().getSize() > 1)
361 menuItem = new JMenuItem("Represent Group with " + seq.getName());
362 menuItem.addActionListener(new java.awt.event.ActionListener()
364 public void actionPerformed(ActionEvent e)
369 sequenceMenu.add(menuItem);
372 if (ap.av.hasHiddenRows())
374 final int index = ap.av.getAlignment().findIndex(seq);
376 if (ap.av.adjustForHiddenSeqs(index)
377 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
379 menuItem = new JMenuItem("Reveal Sequences");
380 menuItem.addActionListener(new ActionListener()
382 public void actionPerformed(ActionEvent e)
384 ap.av.showSequence(index);
385 if (ap.overviewPanel != null)
387 ap.overviewPanel.updateOverviewImage();
395 // for the case when no sequences are even visible
396 if (ap.av.hasHiddenRows())
399 menuItem = new JMenuItem("Reveal All");
400 menuItem.addActionListener(new ActionListener()
402 public void actionPerformed(ActionEvent e)
404 ap.av.showAllHiddenSeqs();
405 if (ap.overviewPanel != null)
407 ap.overviewPanel.updateOverviewImage();
417 SequenceGroup sg = ap.av.getSelectionGroup();
419 if (sg != null && sg.getSize() > 0)
421 groupName.setText("Name: " + sg.getName());
422 groupName.setText("Edit name and description of current group.");
424 if (sg.cs instanceof ZappoColourScheme)
426 zappoColour.setSelected(true);
428 else if (sg.cs instanceof TaylorColourScheme)
430 taylorColour.setSelected(true);
432 else if (sg.cs instanceof PIDColourScheme)
434 PIDColour.setSelected(true);
436 else if (sg.cs instanceof Blosum62ColourScheme)
438 BLOSUM62Colour.setSelected(true);
440 else if (sg.cs instanceof UserColourScheme)
442 userDefinedColour.setSelected(true);
444 else if (sg.cs instanceof HydrophobicColourScheme)
446 hydrophobicityColour.setSelected(true);
448 else if (sg.cs instanceof HelixColourScheme)
450 helixColour.setSelected(true);
452 else if (sg.cs instanceof StrandColourScheme)
454 strandColour.setSelected(true);
456 else if (sg.cs instanceof TurnColourScheme)
458 turnColour.setSelected(true);
460 else if (sg.cs instanceof BuriedColourScheme)
462 buriedColour.setSelected(true);
464 else if (sg.cs instanceof ClustalxColourScheme)
466 clustalColour.setSelected(true);
468 else if (sg.cs instanceof PurinePyrimidineColourScheme)
470 purinePyrimidineColour.setSelected(true);
473 else if (sg.cs instanceof RNAInteractionColourScheme)
475 RNAInteractionColour.setSelected(true);
478 * else if (sg.cs instanceof CovariationColourScheme) {
479 * covariationColour.setSelected(true); }
483 noColourmenuItem.setSelected(true);
486 if (sg.cs != null && sg.cs.conservationApplied())
488 conservationMenuItem.setSelected(true);
490 displayNonconserved.setSelected(sg.getShowNonconserved());
491 showText.setSelected(sg.getDisplayText());
492 showColourText.setSelected(sg.getColourText());
493 showBoxes.setSelected(sg.getDisplayBoxes());
494 // add any groupURLs to the groupURL submenu and make it visible
495 if (groupLinks != null && groupLinks.size() > 0)
497 buildGroupURLMenu(sg, groupLinks);
499 // Add a 'show all structures' for the current selection
500 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>();
501 SequenceI sqass = null;
502 for (SequenceI sq : ap.av.getSequenceSelection())
504 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
508 for (PDBEntry pe : pes)
510 pdbe.put(pe.getId(), pe);
520 final PDBEntry[] pe = pdbe.values().toArray(
521 new PDBEntry[pdbe.size()]);
522 final JMenuItem gpdbview;
523 if (pdbe.size() == 1)
525 structureMenu.add(gpdbview = new JMenuItem("View structure for "
526 + sqass.getDisplayId(false)));
530 structureMenu.add(gpdbview = new JMenuItem("View all "
531 + pdbe.size() + " structures."));
533 gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
534 gpdbview.addActionListener(new ActionListener()
538 public void actionPerformed(ActionEvent e)
540 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
547 groupMenu.setVisible(false);
548 editMenu.setVisible(false);
551 if (!ap.av.getAlignment().getGroups().contains(sg))
553 unGroupMenuItem.setVisible(false);
558 sequenceMenu.setVisible(false);
559 structureMenu.setVisible(false);
562 if (links != null && links.size() > 0)
565 JMenu linkMenu = new JMenu("Link");
566 Vector linkset = new Vector();
567 for (int i = 0; i < links.size(); i++)
569 String link = links.elementAt(i).toString();
570 UrlLink urlLink = null;
573 urlLink = new UrlLink(link);
574 } catch (Exception foo)
576 jalview.bin.Cache.log.error("Exception for URLLink '" + link
581 if (!urlLink.isValid())
583 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
586 final String label = urlLink.getLabel();
587 if (seq != null && urlLink.isDynamic())
590 // collect matching db-refs
591 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
592 seq.getDBRef(), new String[]
593 { urlLink.getTarget() });
594 // collect id string too
595 String id = seq.getName();
596 String descr = seq.getDescription();
597 if (descr != null && descr.length() < 1)
604 for (int r = 0; r < dbr.length; r++)
606 if (id != null && dbr[r].getAccessionId().equals(id))
608 // suppress duplicate link creation for the bare sequence ID
609 // string with this link
612 // create Bare ID link for this RUL
613 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
617 for (int u = 0; u < urls.length; u += 2)
619 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
621 linkset.addElement(urls[u] + "|" + urls[u + 1]);
622 addshowLink(linkMenu, label + "|" + urls[u],
631 // create Bare ID link for this RUL
632 String[] urls = urlLink.makeUrls(id, true);
635 for (int u = 0; u < urls.length; u += 2)
637 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
639 linkset.addElement(urls[u] + "|" + urls[u + 1]);
640 addshowLink(linkMenu, label, urls[u + 1]);
645 // Create urls from description but only for URL links which are regex
647 if (descr != null && urlLink.getRegexReplace() != null)
649 // create link for this URL from description where regex matches
650 String[] urls = urlLink.makeUrls(descr, true);
653 for (int u = 0; u < urls.length; u += 2)
655 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
657 linkset.addElement(urls[u] + "|" + urls[u + 1]);
658 addshowLink(linkMenu, label, urls[u + 1]);
666 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
668 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
669 // Add a non-dynamic link
670 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
674 if (sequence != null)
676 sequenceMenu.add(linkMenu);
685 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
688 // TODO: usability: thread off the generation of group url content so root
690 // sequence only URLs
691 // ID/regex match URLs
692 groupLinksMenu = new JMenu("Group Link");
693 JMenu[] linkMenus = new JMenu[]
694 { null, new JMenu("IDS"), new JMenu("Sequences"),
695 new JMenu("IDS and Sequences") }; // three types of url that might be
697 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
698 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
699 Hashtable commonDbrefs = new Hashtable();
700 for (int sq = 0; sq < seqs.length; sq++)
703 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
704 .findPosition(sg.getEndRes());
705 // just collect ids from dataset sequence
706 // TODO: check if IDs collected from selecton group intersects with the
707 // current selection, too
708 SequenceI sqi = seqs[sq];
709 while (sqi.getDatasetSequence() != null)
711 sqi = sqi.getDatasetSequence();
713 DBRefEntry[] dbr = sqi.getDBRef();
714 if (dbr != null && dbr.length > 0)
716 for (int d = 0; d < dbr.length; d++)
718 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
719 Object[] sarray = (Object[]) commonDbrefs.get(src);
722 sarray = new Object[2];
723 sarray[0] = new int[]
725 sarray[1] = new String[seqs.length];
727 commonDbrefs.put(src, sarray);
730 if (((String[]) sarray[1])[sq] == null)
733 || (dbr[d].getMap().locateMappedRange(start, end) != null))
735 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
736 ((int[]) sarray[0])[0]++;
742 // now create group links for all distinct ID/sequence sets.
743 boolean addMenu = false; // indicates if there are any group links to give
745 for (int i = 0; i < groupLinks.size(); i++)
747 String link = groupLinks.elementAt(i).toString();
748 GroupUrlLink urlLink = null;
751 urlLink = new GroupUrlLink(link);
752 } catch (Exception foo)
754 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
759 if (!urlLink.isValid())
761 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
764 final String label = urlLink.getLabel();
765 boolean usingNames = false;
766 // Now see which parts of the group apply for this URL
767 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
768 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
769 String[] seqstr, ids; // input to makeUrl
772 int numinput = ((int[]) idset[0])[0];
773 String[] allids = ((String[]) idset[1]);
774 seqstr = new String[numinput];
775 ids = new String[numinput];
776 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
778 if (allids[sq] != null)
780 ids[idcount] = allids[sq];
781 seqstr[idcount++] = idandseqs[1][sq];
787 // just use the id/seq set
788 seqstr = idandseqs[1];
792 // and try and make the groupURL!
794 Object[] urlset = null;
797 urlset = urlLink.makeUrlStubs(ids, seqstr,
798 "FromJalview" + System.currentTimeMillis(), false);
799 } catch (UrlStringTooLongException e)
804 int type = urlLink.getGroupURLType() & 3;
805 // System.out.println(urlLink.getGroupURLType()
806 // +" "+((String[])urlset[3])[0]);
807 // first two bits ofurlLink type bitfield are sequenceids and sequences
808 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
809 addshowLink(linkMenus[type], label
810 + (((type & 1) == 1) ? ("("
811 + (usingNames ? "Names" : ltarget) + ")") : ""),
818 groupLinksMenu = new JMenu("Group Links");
819 for (int m = 0; m < linkMenus.length; m++)
821 if (linkMenus[m] != null
822 && linkMenus[m].getMenuComponentCount() > 0)
824 groupLinksMenu.add(linkMenus[m]);
828 groupMenu.add(groupLinksMenu);
833 * add a show URL menu item to the given linkMenu
837 * - menu label string
841 private void addshowLink(JMenu linkMenu, String label, final String url)
843 JMenuItem item = new JMenuItem(label);
844 item.setToolTipText("open URL: " + url);
845 item.addActionListener(new java.awt.event.ActionListener()
847 public void actionPerformed(ActionEvent e)
849 new Thread(new Runnable()
865 * add a late bound groupURL item to the given linkMenu
869 * - menu label string
870 * @param urlgenerator
871 * GroupURLLink used to generate URL
873 * Object array returned from the makeUrlStubs function.
875 private void addshowLink(JMenu linkMenu, String label,
876 final GroupUrlLink urlgenerator, final Object[] urlstub)
878 JMenuItem item = new JMenuItem(label);
879 item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
880 + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
889 item.addActionListener(new java.awt.event.ActionListener()
891 public void actionPerformed(ActionEvent e)
893 new Thread(new Runnable()
900 showLink(urlgenerator.constructFrom(urlstub));
901 } catch (UrlStringTooLongException e)
919 private void jbInit() throws Exception
921 groupMenu.setText("Group");
922 groupMenu.setText("Selection");
923 groupName.setText("Name");
924 groupName.addActionListener(new java.awt.event.ActionListener()
926 public void actionPerformed(ActionEvent e)
928 groupName_actionPerformed();
931 sequenceMenu.setText("Sequence");
932 sequenceName.setText("Edit Name/Description");
933 sequenceName.addActionListener(new java.awt.event.ActionListener()
935 public void actionPerformed(ActionEvent e)
937 sequenceName_actionPerformed();
940 sequenceDetails.setText("Sequence Details ...");
941 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
943 public void actionPerformed(ActionEvent e)
945 sequenceDetails_actionPerformed();
948 sequenceSelDetails.setText("Sequence Details ...");
950 .addActionListener(new java.awt.event.ActionListener()
952 public void actionPerformed(ActionEvent e)
954 sequenceSelectionDetails_actionPerformed();
957 PIDColour.setFocusPainted(false);
958 unGroupMenuItem.setText("Remove Group");
959 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
961 public void actionPerformed(ActionEvent e)
963 unGroupMenuItem_actionPerformed();
967 outline.setText("Border colour");
968 outline.addActionListener(new java.awt.event.ActionListener()
970 public void actionPerformed(ActionEvent e)
972 outline_actionPerformed();
975 nucleotideMenuItem.setText("Nucleotide");
976 nucleotideMenuItem.addActionListener(new ActionListener()
978 public void actionPerformed(ActionEvent e)
980 nucleotideMenuItem_actionPerformed();
983 colourMenu.setText("Group Colour");
984 showBoxes.setText("Boxes");
985 showBoxes.setState(true);
986 showBoxes.addActionListener(new ActionListener()
988 public void actionPerformed(ActionEvent e)
990 showBoxes_actionPerformed();
993 showText.setText("Text");
994 showText.setState(true);
995 showText.addActionListener(new ActionListener()
997 public void actionPerformed(ActionEvent e)
999 showText_actionPerformed();
1002 showColourText.setText("Colour Text");
1003 showColourText.addActionListener(new ActionListener()
1005 public void actionPerformed(ActionEvent e)
1007 showColourText_actionPerformed();
1010 displayNonconserved.setText("Show Nonconserved");
1011 displayNonconserved.setState(true);
1012 displayNonconserved.addActionListener(new ActionListener()
1014 public void actionPerformed(ActionEvent e)
1016 showNonconserved_actionPerformed();
1019 editMenu.setText("Edit");
1021 cut.addActionListener(new ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 cut_actionPerformed();
1028 upperCase.setText("To Upper Case");
1029 upperCase.addActionListener(new ActionListener()
1031 public void actionPerformed(ActionEvent e)
1036 copy.setText("Copy");
1037 copy.addActionListener(new ActionListener()
1039 public void actionPerformed(ActionEvent e)
1041 copy_actionPerformed();
1044 lowerCase.setText("To Lower Case");
1045 lowerCase.addActionListener(new ActionListener()
1047 public void actionPerformed(ActionEvent e)
1052 toggle.setText("Toggle Case");
1053 toggle.addActionListener(new ActionListener()
1055 public void actionPerformed(ActionEvent e)
1060 pdbMenu.setText("Associate Structure with Sequence");
1061 pdbFromFile.setText("From File");
1062 pdbFromFile.addActionListener(new ActionListener()
1064 public void actionPerformed(ActionEvent e)
1066 pdbFromFile_actionPerformed();
1069 enterPDB.setText("Enter PDB Id");
1070 enterPDB.addActionListener(new ActionListener()
1072 public void actionPerformed(ActionEvent e)
1074 enterPDB_actionPerformed();
1077 discoverPDB.setText("Discover PDB ids");
1078 discoverPDB.addActionListener(new ActionListener()
1080 public void actionPerformed(ActionEvent e)
1082 discoverPDB_actionPerformed();
1085 outputMenu.setText("Output to Textbox...");
1086 sequenceFeature.setText("Create Sequence Feature");
1087 sequenceFeature.addActionListener(new ActionListener()
1089 public void actionPerformed(ActionEvent e)
1091 sequenceFeature_actionPerformed();
1094 textColour.setText("Text Colour");
1095 textColour.addActionListener(new ActionListener()
1097 public void actionPerformed(ActionEvent e)
1099 textColour_actionPerformed();
1102 jMenu1.setText("Group");
1103 structureMenu.setText("Structure");
1104 viewStructureMenu.setText("View Structure");
1105 // colStructureMenu.setText("Colour By Structure");
1106 editSequence.setText("Edit Sequence...");
1107 editSequence.addActionListener(new ActionListener()
1109 public void actionPerformed(ActionEvent actionEvent)
1111 editSequence_actionPerformed(actionEvent);
1116 * annotationMenuItem.setText("By Annotation");
1117 * annotationMenuItem.addActionListener(new ActionListener() { public void
1118 * actionPerformed(ActionEvent actionEvent) {
1119 * annotationMenuItem_actionPerformed(actionEvent); } });
1121 groupMenu.add(sequenceSelDetails);
1124 this.add(structureMenu);
1125 groupMenu.add(editMenu);
1126 groupMenu.add(outputMenu);
1127 groupMenu.add(sequenceFeature);
1128 groupMenu.add(jMenu1);
1129 sequenceMenu.add(sequenceName);
1130 sequenceMenu.add(sequenceDetails);
1131 colourMenu.add(textColour);
1132 colourMenu.add(noColourmenuItem);
1133 colourMenu.add(clustalColour);
1134 colourMenu.add(BLOSUM62Colour);
1135 colourMenu.add(PIDColour);
1136 colourMenu.add(zappoColour);
1137 colourMenu.add(taylorColour);
1138 colourMenu.add(hydrophobicityColour);
1139 colourMenu.add(helixColour);
1140 colourMenu.add(strandColour);
1141 colourMenu.add(turnColour);
1142 colourMenu.add(buriedColour);
1143 colourMenu.add(nucleotideMenuItem);
1144 if (ap.getAlignment().isNucleotide()) {
1145 colourMenu.add(RNAInteractionColour);
1146 colourMenu.add(purinePyrimidineColour);
1148 // colourMenu.add(covariationColour);
1149 colourMenu.add(userDefinedColour);
1151 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1153 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1154 .getUserColourSchemes().keys();
1156 while (userColours.hasMoreElements())
1158 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1159 item.addActionListener(new ActionListener()
1161 public void actionPerformed(ActionEvent evt)
1163 userDefinedColour_actionPerformed(evt);
1166 colourMenu.add(item);
1170 colourMenu.addSeparator();
1171 colourMenu.add(abovePIDColour);
1172 colourMenu.add(conservationMenuItem);
1173 // colourMenu.add(annotationMenuItem);
1176 editMenu.add(editSequence);
1177 editMenu.add(upperCase);
1178 editMenu.add(lowerCase);
1179 editMenu.add(toggle);
1180 pdbMenu.add(pdbFromFile);
1181 pdbMenu.add(enterPDB);
1182 pdbMenu.add(discoverPDB);
1183 jMenu1.add(groupName);
1184 jMenu1.add(unGroupMenuItem);
1185 jMenu1.add(colourMenu);
1186 jMenu1.add(showBoxes);
1187 jMenu1.add(showText);
1188 jMenu1.add(showColourText);
1189 jMenu1.add(outline);
1190 jMenu1.add(displayNonconserved);
1191 structureMenu.add(pdbMenu);
1192 structureMenu.add(viewStructureMenu);
1193 // structureMenu.add(colStructureMenu);
1194 noColourmenuItem.setText("None");
1195 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1197 public void actionPerformed(ActionEvent e)
1199 noColourmenuItem_actionPerformed();
1203 clustalColour.setText("Clustalx colours");
1204 clustalColour.addActionListener(new java.awt.event.ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 clustalColour_actionPerformed();
1211 zappoColour.setText("Zappo");
1212 zappoColour.addActionListener(new java.awt.event.ActionListener()
1214 public void actionPerformed(ActionEvent e)
1216 zappoColour_actionPerformed();
1219 taylorColour.setText("Taylor");
1220 taylorColour.addActionListener(new java.awt.event.ActionListener()
1222 public void actionPerformed(ActionEvent e)
1224 taylorColour_actionPerformed();
1227 hydrophobicityColour.setText("Hydrophobicity");
1228 hydrophobicityColour
1229 .addActionListener(new java.awt.event.ActionListener()
1231 public void actionPerformed(ActionEvent e)
1233 hydrophobicityColour_actionPerformed();
1236 helixColour.setText("Helix propensity");
1237 helixColour.addActionListener(new java.awt.event.ActionListener()
1239 public void actionPerformed(ActionEvent e)
1241 helixColour_actionPerformed();
1244 strandColour.setText("Strand propensity");
1245 strandColour.addActionListener(new java.awt.event.ActionListener()
1247 public void actionPerformed(ActionEvent e)
1249 strandColour_actionPerformed();
1252 turnColour.setText("Turn propensity");
1253 turnColour.addActionListener(new java.awt.event.ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 turnColour_actionPerformed();
1260 buriedColour.setText("Buried Index");
1261 buriedColour.addActionListener(new java.awt.event.ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 buriedColour_actionPerformed();
1268 abovePIDColour.setText("Above % Identity");
1269 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 abovePIDColour_actionPerformed();
1276 userDefinedColour.setText("User Defined...");
1277 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1279 public void actionPerformed(ActionEvent e)
1281 userDefinedColour_actionPerformed(e);
1284 PIDColour.setText("Percentage Identity");
1285 PIDColour.addActionListener(new java.awt.event.ActionListener()
1287 public void actionPerformed(ActionEvent e)
1289 PIDColour_actionPerformed();
1292 BLOSUM62Colour.setText("BLOSUM62");
1293 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1295 public void actionPerformed(ActionEvent e)
1297 BLOSUM62Colour_actionPerformed();
1300 purinePyrimidineColour.setText("Purine/Pyrimidine");
1301 purinePyrimidineColour
1302 .addActionListener(new java.awt.event.ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 purinePyrimidineColour_actionPerformed();
1310 RNAInteractionColour.setText("RNA Interaction type");
1311 RNAInteractionColour
1312 .addActionListener(new java.awt.event.ActionListener()
1314 public void actionPerformed(ActionEvent e)
1316 RNAInteractionColour_actionPerformed();
1320 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1321 * public void actionPerformed(ActionEvent e) {
1322 * covariationColour_actionPerformed(); } });
1325 conservationMenuItem.setText("Conservation");
1326 conservationMenuItem
1327 .addActionListener(new java.awt.event.ActionListener()
1329 public void actionPerformed(ActionEvent e)
1331 conservationMenuItem_actionPerformed();
1336 protected void sequenceSelectionDetails_actionPerformed()
1338 createSequenceDetailsReport(ap.av.getSequenceSelection());
1341 protected void sequenceDetails_actionPerformed()
1343 createSequenceDetailsReport(new SequenceI[]
1347 public void createSequenceDetailsReport(SequenceI[] sequences)
1349 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1350 StringBuffer contents = new StringBuffer();
1351 for (SequenceI seq : sequences)
1353 contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
1355 new SequenceAnnotationReport(null)
1356 .createSequenceAnnotationReport(
1362 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1364 contents.append("</p>");
1366 cap.setText("<html>" + contents.toString() + "</html>");
1368 Desktop.instance.addInternalFrame(cap, "Sequence Details for "
1369 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
1370 : "Selection"), 500, 400);
1374 protected void showNonconserved_actionPerformed()
1376 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1381 * call to refresh view after settings change
1385 ap.updateAnnotation();
1386 ap.paintAlignment(true);
1388 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1397 protected void clustalColour_actionPerformed()
1399 SequenceGroup sg = getGroup();
1400 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1410 protected void zappoColour_actionPerformed()
1412 getGroup().cs = new ZappoColourScheme();
1422 protected void taylorColour_actionPerformed()
1424 getGroup().cs = new TaylorColourScheme();
1434 protected void hydrophobicityColour_actionPerformed()
1436 getGroup().cs = new HydrophobicColourScheme();
1446 protected void helixColour_actionPerformed()
1448 getGroup().cs = new HelixColourScheme();
1458 protected void strandColour_actionPerformed()
1460 getGroup().cs = new StrandColourScheme();
1470 protected void turnColour_actionPerformed()
1472 getGroup().cs = new TurnColourScheme();
1482 protected void buriedColour_actionPerformed()
1484 getGroup().cs = new BuriedColourScheme();
1494 public void nucleotideMenuItem_actionPerformed()
1496 getGroup().cs = new NucleotideColourScheme();
1500 protected void purinePyrimidineColour_actionPerformed()
1502 getGroup().cs = new PurinePyrimidineColourScheme();
1506 protected void RNAInteractionColour_actionPerformed()
1508 getGroup().cs = new RNAInteractionColourScheme();
1512 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1513 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1521 protected void abovePIDColour_actionPerformed()
1523 SequenceGroup sg = getGroup();
1529 if (abovePIDColour.isSelected())
1531 sg.cs.setConsensus(AAFrequency.calculate(
1532 sg.getSequences(ap.av.getHiddenRepSequences()),
1533 sg.getStartRes(), sg.getEndRes() + 1));
1535 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1538 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1540 SliderPanel.showPIDSlider();
1543 // remove PIDColouring
1545 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1557 protected void userDefinedColour_actionPerformed(ActionEvent e)
1559 SequenceGroup sg = getGroup();
1561 if (e.getActionCommand().equals("User Defined..."))
1563 new UserDefinedColours(ap, sg);
1567 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1568 .getUserColourSchemes().get(e.getActionCommand());
1581 protected void PIDColour_actionPerformed()
1583 SequenceGroup sg = getGroup();
1584 sg.cs = new PIDColourScheme();
1585 sg.cs.setConsensus(AAFrequency.calculate(
1586 sg.getSequences(ap.av.getHiddenRepSequences()),
1587 sg.getStartRes(), sg.getEndRes() + 1));
1597 protected void BLOSUM62Colour_actionPerformed()
1599 SequenceGroup sg = getGroup();
1601 sg.cs = new Blosum62ColourScheme();
1603 sg.cs.setConsensus(AAFrequency.calculate(
1604 sg.getSequences(ap.av.getHiddenRepSequences()),
1605 sg.getStartRes(), sg.getEndRes() + 1));
1616 protected void noColourmenuItem_actionPerformed()
1618 getGroup().cs = null;
1628 protected void conservationMenuItem_actionPerformed()
1630 SequenceGroup sg = getGroup();
1636 if (conservationMenuItem.isSelected())
1638 Conservation c = new Conservation("Group",
1639 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1640 .getHiddenRepSequences()), sg.getStartRes(),
1641 sg.getEndRes() + 1);
1644 c.verdict(false, ap.av.getConsPercGaps());
1646 sg.cs.setConservation(c);
1648 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1649 SliderPanel.showConservationSlider();
1652 // remove ConservationColouring
1654 sg.cs.setConservation(null);
1660 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1662 SequenceGroup sg = getGroup();
1668 AnnotationColourGradient acg = new AnnotationColourGradient(
1669 sequence.getAnnotation()[0], null,
1670 AnnotationColourGradient.NO_THRESHOLD);
1672 acg.predefinedColours = true;
1684 protected void groupName_actionPerformed()
1687 SequenceGroup sg = getGroup();
1688 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1689 sg.getDescription(), " Group Name ",
1690 "Group Description ", "Edit Group Name/Description",
1698 sg.setName(dialog.getName());
1699 sg.setDescription(dialog.getDescription());
1704 * Get selection group - adding it to the alignment if necessary.
1706 * @return sequence group to operate on
1708 SequenceGroup getGroup()
1710 SequenceGroup sg = ap.av.getSelectionGroup();
1711 // this method won't add a new group if it already exists
1714 ap.av.getAlignment().addGroup(sg);
1726 void sequenceName_actionPerformed()
1728 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1729 sequence.getDescription(), " Sequence Name ",
1730 "Sequence Description ", "Edit Sequence Name/Description",
1738 if (dialog.getName() != null)
1740 if (dialog.getName().indexOf(" ") > -1)
1742 JOptionPane.showMessageDialog(ap,
1743 "Spaces have been converted to \"_\"",
1744 "No spaces allowed in Sequence Name",
1745 JOptionPane.WARNING_MESSAGE);
1748 sequence.setName(dialog.getName().replace(' ', '_'));
1749 ap.paintAlignment(false);
1752 sequence.setDescription(dialog.getDescription());
1754 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1765 void unGroupMenuItem_actionPerformed()
1767 SequenceGroup sg = ap.av.getSelectionGroup();
1768 ap.av.getAlignment().deleteGroup(sg);
1769 ap.av.setSelectionGroup(null);
1779 protected void outline_actionPerformed()
1781 SequenceGroup sg = getGroup();
1782 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1787 sg.setOutlineColour(col);
1799 public void showBoxes_actionPerformed()
1801 getGroup().setDisplayBoxes(showBoxes.isSelected());
1811 public void showText_actionPerformed()
1813 getGroup().setDisplayText(showText.isSelected());
1823 public void showColourText_actionPerformed()
1825 getGroup().setColourText(showColourText.isSelected());
1829 public void showLink(String url)
1833 jalview.util.BrowserLauncher.openURL(url);
1834 } catch (Exception ex)
1837 .showInternalMessageDialog(
1839 "Unixers: Couldn't find default web browser."
1840 + "\nAdd the full path to your browser in Preferences.",
1841 "Web browser not found", JOptionPane.WARNING_MESSAGE);
1843 ex.printStackTrace();
1847 void hideSequences(boolean representGroup)
1849 SequenceGroup sg = ap.av.getSelectionGroup();
1850 if (sg == null || sg.getSize() < 1)
1852 ap.av.hideSequence(new SequenceI[]
1857 ap.av.setSelectionGroup(null);
1861 ap.av.hideRepSequences(sequence, sg);
1866 int gsize = sg.getSize();
1869 hseqs = new SequenceI[gsize];
1872 for (int i = 0; i < gsize; i++)
1874 hseqs[index++] = sg.getSequenceAt(i);
1877 ap.av.hideSequence(hseqs);
1878 // refresh(); TODO: ? needed ?
1879 ap.av.sendSelection();
1882 public void copy_actionPerformed()
1884 ap.alignFrame.copy_actionPerformed(null);
1887 public void cut_actionPerformed()
1889 ap.alignFrame.cut_actionPerformed(null);
1892 void changeCase(ActionEvent e)
1894 Object source = e.getSource();
1895 SequenceGroup sg = ap.av.getSelectionGroup();
1899 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1900 sg.getEndRes() + 1);
1905 if (source == toggle)
1907 description = "Toggle Case";
1908 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1910 else if (source == upperCase)
1912 description = "To Upper Case";
1913 caseChange = ChangeCaseCommand.TO_UPPER;
1917 description = "To Lower Case";
1918 caseChange = ChangeCaseCommand.TO_LOWER;
1921 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1922 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1923 startEnd, caseChange);
1925 ap.alignFrame.addHistoryItem(caseCommand);
1927 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1933 public void outputText_actionPerformed(ActionEvent e)
1935 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1936 cap.setForInput(null);
1937 Desktop.addInternalFrame(cap,
1938 "Alignment output - " + e.getActionCommand(), 600, 500);
1940 String[] omitHidden = null;
1942 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1943 // or we simply trust the user wants
1944 // wysiwig behaviour
1945 SequenceGroup sg = ap.av.getSelectionGroup();
1946 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1947 omitHidden = ap.av.getViewAsString(true);
1948 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1949 AlignmentAnnotation[] nala = ap.av.getAlignment()
1950 .getAlignmentAnnotation();
1953 for (int i = 0; i < nala.length; i++)
1955 AlignmentAnnotation na = nala[i];
1956 oal.addAnnotation(na);
1959 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1960 oal, omitHidden, csel, sg));
1964 public void pdbFromFile_actionPerformed()
1966 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1967 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1968 chooser.setFileView(new jalview.io.JalviewFileView());
1969 chooser.setDialogTitle("Select a PDB file for "
1970 + sequence.getDisplayId(false));
1971 chooser.setToolTipText("Load a PDB file and associate it with sequence '"
1972 + sequence.getDisplayId(false) + "'");
1974 int value = chooser.showOpenDialog(null);
1976 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1978 String choice = chooser.getSelectedFile().getPath();
1979 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1980 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
1981 jalview.io.AppletFormatAdapter.FILE, sequence, true);
1986 public void enterPDB_actionPerformed()
1988 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1989 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1991 if (id != null && id.length() > 0)
1993 PDBEntry entry = new PDBEntry();
1994 entry.setId(id.toUpperCase());
1995 sequence.getDatasetSequence().addPDBId(entry);
1999 public void discoverPDB_actionPerformed()
2002 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2004 : ap.av.getSequenceSelection());
2005 Thread discpdb = new Thread(new Runnable()
2010 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2011 .fetchDBRefs(false);
2018 public void sequenceFeature_actionPerformed()
2020 SequenceGroup sg = ap.av.getSelectionGroup();
2026 int rsize = 0, gSize = sg.getSize();
2027 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2028 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2030 for (int i = 0; i < gSize; i++)
2032 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2033 int end = sg.findEndRes(sg.getSequenceAt(i));
2036 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2037 features[rsize] = new SequenceFeature(null, null, null, start, end,
2042 rseqs = new SequenceI[rsize];
2043 tfeatures = new SequenceFeature[rsize];
2044 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2045 System.arraycopy(features, 0, tfeatures, 0, rsize);
2046 features = tfeatures;
2048 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2049 features, true, ap))
2051 ap.alignFrame.setShowSeqFeatures(true);
2052 ap.highlightSearchResults(null);
2056 public void textColour_actionPerformed()
2058 SequenceGroup sg = getGroup();
2061 new TextColourChooser().chooseColour(ap, sg);
2065 public void colourByStructure(String pdbid)
2067 Annotation[] anots = ap.av.getStructureSelectionManager()
2068 .colourSequenceFromStructure(sequence, pdbid);
2070 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2071 "Coloured by " + pdbid, anots);
2073 ap.av.getAlignment().addAnnotation(an);
2074 an.createSequenceMapping(sequence, 0, true);
2075 // an.adjustForAlignment();
2076 ap.av.getAlignment().setAnnotationIndex(an, 0);
2078 ap.adjustAnnotationHeight();
2080 sequence.addAlignmentAnnotation(an);
2084 public void editSequence_actionPerformed(ActionEvent actionEvent)
2086 SequenceGroup sg = ap.av.getSelectionGroup();
2090 if (sequence == null)
2091 sequence = (Sequence) sg.getSequenceAt(0);
2093 EditNameDialog dialog = new EditNameDialog(
2094 sequence.getSequenceAsString(sg.getStartRes(),
2095 sg.getEndRes() + 1), null, "Edit Sequence ", null,
2096 "Edit Sequence", ap.alignFrame);
2100 EditCommand editCommand = new EditCommand("Edit Sequences",
2101 EditCommand.REPLACE, dialog.getName().replace(' ',
2102 ap.av.getGapCharacter()),
2103 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2104 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2106 ap.alignFrame.addHistoryItem(editCommand);
2108 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()