2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
3 * Copyright (C) 2010 J Procter, AM Waterhouse, 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.*;
28 import jalview.analysis.*;
29 import jalview.commands.*;
30 import jalview.datamodel.*;
32 import jalview.schemes.*;
33 import jalview.util.GroupUrlLink;
34 import jalview.util.GroupUrlLink.UrlStringTooLongException;
35 import jalview.util.UrlLink;
41 * @version $Revision: 1.118 $
43 public class PopupMenu extends JPopupMenu
45 JMenu groupMenu = new JMenu();
47 JMenuItem groupName = new JMenuItem();
49 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
51 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
53 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
55 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
57 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
59 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
61 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
63 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
65 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
67 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
69 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
71 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
73 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
75 //protected JRadioButtonMenuItem covariationColour = new JRadioButtonMenuItem();
77 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
79 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
83 JMenu sequenceMenu = new JMenu();
85 JMenuItem sequenceName = new JMenuItem();
89 JMenuItem unGroupMenuItem = new JMenuItem();
91 JMenuItem outline = new JMenuItem();
93 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
95 JMenu colourMenu = new JMenu();
97 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
99 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
101 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
103 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
105 JMenu editMenu = new JMenu();
107 JMenuItem cut = new JMenuItem();
109 JMenuItem copy = new JMenuItem();
111 JMenuItem upperCase = new JMenuItem();
113 JMenuItem lowerCase = new JMenuItem();
115 JMenuItem toggle = new JMenuItem();
117 JMenu pdbMenu = new JMenu();
119 JMenuItem pdbFromFile = new JMenuItem();
121 JMenuItem enterPDB = new JMenuItem();
123 JMenuItem discoverPDB = new JMenuItem();
125 JMenu outputMenu = new JMenu();
127 JMenuItem sequenceFeature = new JMenuItem();
129 JMenuItem textColour = new JMenuItem();
131 JMenu jMenu1 = new JMenu();
133 JMenu structureMenu = new JMenu();
135 JMenu viewStructureMenu = new JMenu();
137 // JMenu colStructureMenu = new JMenu();
138 JMenuItem editSequence = new JMenuItem();
140 // JMenuItem annotationMenuItem = new JMenuItem();
142 JMenu groupLinksMenu;
145 * Creates a new PopupMenu object.
152 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
154 this(ap, seq, links, null);
164 public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links,
167 // /////////////////////////////////////////////////////////
168 // If this is activated from the sequence panel, the user may want to
169 // edit or annotate a particular residue. Therefore display the residue menu
171 // If from the IDPanel, we must display the sequence menu
172 // ////////////////////////////////////////////////////////
176 ButtonGroup colours = new ButtonGroup();
177 colours.add(noColourmenuItem);
178 colours.add(clustalColour);
179 colours.add(zappoColour);
180 colours.add(taylorColour);
181 colours.add(hydrophobicityColour);
182 colours.add(helixColour);
183 colours.add(strandColour);
184 colours.add(turnColour);
185 colours.add(buriedColour);
186 colours.add(abovePIDColour);
187 colours.add(userDefinedColour);
188 colours.add(PIDColour);
189 colours.add(BLOSUM62Colour);
190 colours.add(purinePyrimidineColour);
191 //colours.add(covariationColour);
193 for (int i = 0; i < jalview.io.FormatAdapter.WRITEABLE_FORMATS.length; i++)
195 JMenuItem item = new JMenuItem(
196 jalview.io.FormatAdapter.WRITEABLE_FORMATS[i]);
198 item.addActionListener(new java.awt.event.ActionListener()
200 public void actionPerformed(ActionEvent e)
202 outputText_actionPerformed(e);
206 outputMenu.add(item);
212 } catch (Exception e)
219 sequenceMenu.setText(sequence.getName());
222 if (seq.getDatasetSequence().getPDBId() != null
223 && seq.getDatasetSequence().getPDBId().size() > 0)
225 java.util.Enumeration e = seq.getDatasetSequence().getPDBId()
228 while (e.hasMoreElements())
230 final PDBEntry pdb = (PDBEntry) e.nextElement();
232 menuItem = new JMenuItem();
233 menuItem.setText(pdb.getId());
234 menuItem.addActionListener(new java.awt.event.ActionListener()
236 public void actionPerformed(ActionEvent e)
238 // TODO re JAL-860: optionally open dialog or provide a menu entry allowing user to open just one structure per sequence
239 new AppJmol(pdb, ap.av.collateForPDB(new PDBEntry[] { pdb })[0], null, ap);
240 // new PDBViewer(pdb, seqs2, null, ap, AppletFormatAdapter.FILE);
244 viewStructureMenu.add(menuItem);
247 * menuItem = new JMenuItem(); menuItem.setText(pdb.getId());
248 * menuItem.addActionListener(new java.awt.event.ActionListener() {
249 * public void actionPerformed(ActionEvent e) {
250 * colourByStructure(pdb.getId()); } });
251 * colStructureMenu.add(menuItem);
257 //JAN structureMenu.remove(viewStructureMenu);
258 // structureMenu.remove(colStructureMenu);
261 //if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S'){
262 //TODO: Something to check if it's an RNA
263 //like: if(seq.getAnnotation()[0].annotations[0].secondaryStructure == 'S')
264 final SequenceI seqI = seq.getDatasetSequence();
265 //ap.getAlignment().get
266 menuItem = new JMenuItem();
267 menuItem.setText("RNA structure");
268 menuItem.addActionListener(new java.awt.event.ActionListener()
270 public void actionPerformed(ActionEvent e)
272 System.out.println("Call Varna "+seqI.getSequenceAsString()+" "+seqI.getName());
273 new AppVarna(seqI.getSequenceAsString(),seqI.getName());
277 viewStructureMenu.add(menuItem);
281 menuItem = new JMenuItem("Hide Sequences");
282 menuItem.addActionListener(new java.awt.event.ActionListener()
284 public void actionPerformed(ActionEvent e)
286 hideSequences(false);
291 if (ap.av.getSelectionGroup() != null
292 && ap.av.getSelectionGroup().getSize() > 1)
294 menuItem = new JMenuItem("Represent Group with " + seq.getName());
295 menuItem.addActionListener(new java.awt.event.ActionListener()
297 public void actionPerformed(ActionEvent e)
302 sequenceMenu.add(menuItem);
305 if (ap.av.hasHiddenRows)
307 final int index = ap.av.alignment.findIndex(seq);
309 if (ap.av.adjustForHiddenSeqs(index)
310 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
312 menuItem = new JMenuItem("Reveal Sequences");
313 menuItem.addActionListener(new ActionListener()
315 public void actionPerformed(ActionEvent e)
317 ap.av.showSequence(index);
318 if (ap.overviewPanel != null)
320 ap.overviewPanel.updateOverviewImage();
327 menuItem = new JMenuItem("Reveal All");
328 menuItem.addActionListener(new ActionListener()
330 public void actionPerformed(ActionEvent e)
332 ap.av.showAllHiddenSeqs();
333 if (ap.overviewPanel != null)
335 ap.overviewPanel.updateOverviewImage();
345 SequenceGroup sg = ap.av.getSelectionGroup();
349 groupName.setText("Name: "+sg.getName());
350 groupName.setText("Edit name and description of current group.");
352 if (sg.cs instanceof ZappoColourScheme)
354 zappoColour.setSelected(true);
356 else if (sg.cs instanceof TaylorColourScheme)
358 taylorColour.setSelected(true);
360 else if (sg.cs instanceof PIDColourScheme)
362 PIDColour.setSelected(true);
364 else if (sg.cs instanceof Blosum62ColourScheme)
366 BLOSUM62Colour.setSelected(true);
368 else if (sg.cs instanceof UserColourScheme)
370 userDefinedColour.setSelected(true);
372 else if (sg.cs instanceof HydrophobicColourScheme)
374 hydrophobicityColour.setSelected(true);
376 else if (sg.cs instanceof HelixColourScheme)
378 helixColour.setSelected(true);
380 else if (sg.cs instanceof StrandColourScheme)
382 strandColour.setSelected(true);
384 else if (sg.cs instanceof TurnColourScheme)
386 turnColour.setSelected(true);
388 else if (sg.cs instanceof BuriedColourScheme)
390 buriedColour.setSelected(true);
392 else if (sg.cs instanceof ClustalxColourScheme)
394 clustalColour.setSelected(true);
396 else if (sg.cs instanceof PurinePyrimidineColourScheme)
398 purinePyrimidineColour.setSelected(true);
400 /* else if (sg.cs instanceof CovariationColourScheme)
402 covariationColour.setSelected(true);
406 noColourmenuItem.setSelected(true);
409 if (sg.cs != null && sg.cs.conservationApplied())
411 conservationMenuItem.setSelected(true);
413 displayNonconserved.setSelected(sg.getShowNonconserved());
414 showText.setSelected(sg.getDisplayText());
415 showColourText.setSelected(sg.getColourText());
416 showBoxes.setSelected(sg.getDisplayBoxes());
417 // add any groupURLs to the groupURL submenu and make it visible
418 if (groupLinks != null && groupLinks.size() > 0)
420 buildGroupURLMenu(sg, groupLinks);
422 // Add a 'show all structures' for the current selection
423 Hashtable<String, PDBEntry> pdbe=new Hashtable<String,PDBEntry>();
424 for (SequenceI sq: ap.av.getSequenceSelection())
426 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence().getPDBId();
428 for (PDBEntry pe: pes)
430 pdbe.put(pe.getId(), pe);
436 final PDBEntry[] pe = pdbe.values().toArray(new PDBEntry[pdbe.size()]);
437 final JMenuItem gpdbview;
438 structureMenu.add(gpdbview=new JMenuItem("View "+pdbe.size()+" structures."));
439 gpdbview.setToolTipText("Open a new Jmol view with all structures associated with the current selection and superimpose them using the alignment.");
440 gpdbview.addActionListener(new ActionListener()
444 public void actionPerformed(ActionEvent e)
446 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
453 groupMenu.setVisible(false);
454 editMenu.setVisible(false);
457 if (!ap.av.alignment.getGroups().contains(sg))
459 unGroupMenuItem.setVisible(false);
464 sequenceMenu.setVisible(false);
465 structureMenu.setVisible(false);
468 if (links != null && links.size() > 0)
471 JMenu linkMenu = new JMenu("Link");
472 Vector linkset = new Vector();
473 for (int i = 0; i < links.size(); i++)
475 String link = links.elementAt(i).toString();
476 UrlLink urlLink = null;
479 urlLink = new UrlLink(link);
480 } catch (Exception foo)
482 jalview.bin.Cache.log.error("Exception for URLLink '" + link
487 if (!urlLink.isValid())
489 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
492 final String label = urlLink.getLabel();
493 if (urlLink.isDynamic())
496 // collect matching db-refs
497 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
498 seq.getDBRef(), new String[]
499 { urlLink.getTarget() });
500 // collect id string too
501 String id = seq.getName();
502 String descr = seq.getDescription();
503 if (descr != null && descr.length() < 1)
510 for (int r = 0; r < dbr.length; r++)
512 if (id != null && dbr[r].getAccessionId().equals(id))
514 // suppress duplicate link creation for the bare sequence ID
515 // string with this link
518 // create Bare ID link for this RUL
519 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
523 for (int u = 0; u < urls.length; u += 2)
525 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
527 linkset.addElement(urls[u] + "|" + urls[u + 1]);
528 addshowLink(linkMenu, label + "|" + urls[u],
537 // create Bare ID link for this RUL
538 String[] urls = urlLink.makeUrls(id, true);
541 for (int u = 0; u < urls.length; u += 2)
543 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
545 linkset.addElement(urls[u] + "|" + urls[u + 1]);
546 addshowLink(linkMenu, label, urls[u + 1]);
551 // Create urls from description but only for URL links which are regex
553 if (descr != null && urlLink.getRegexReplace() != null)
555 // create link for this URL from description where regex matches
556 String[] urls = urlLink.makeUrls(descr, true);
559 for (int u = 0; u < urls.length; u += 2)
561 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
563 linkset.addElement(urls[u] + "|" + urls[u + 1]);
564 addshowLink(linkMenu, label, urls[u + 1]);
572 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
574 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
575 // Add a non-dynamic link
576 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
580 if (sequence != null)
582 sequenceMenu.add(linkMenu);
591 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
594 // TODO: usability: thread off the generation of group url content so root
596 // sequence only URLs
597 // ID/regex match URLs
598 groupLinksMenu = new JMenu("Group Link");
599 JMenu[] linkMenus = new JMenu[]
600 { null, new JMenu("IDS"), new JMenu("Sequences"),
601 new JMenu("IDS and Sequences") }; // three types of url that might be
603 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
604 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
605 Hashtable commonDbrefs = new Hashtable();
606 for (int sq = 0; sq < seqs.length; sq++)
609 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
610 .findPosition(sg.getEndRes());
611 // just collect ids from dataset sequence
612 // TODO: check if IDs collected from selecton group intersects with the
613 // current selection, too
614 SequenceI sqi = seqs[sq];
615 while (sqi.getDatasetSequence() != null)
617 sqi = sqi.getDatasetSequence();
619 DBRefEntry[] dbr = sqi.getDBRef();
620 if (dbr != null && dbr.length > 0)
622 for (int d = 0; d < dbr.length; d++)
624 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
625 Object[] sarray = (Object[]) commonDbrefs.get(src);
628 sarray = new Object[2];
629 sarray[0] = new int[]
631 sarray[1] = new String[seqs.length];
633 commonDbrefs.put(src, sarray);
636 if (((String[]) sarray[1])[sq] == null)
639 || (dbr[d].getMap().locateMappedRange(start, end) != null))
641 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
642 ((int[]) sarray[0])[0]++;
648 // now create group links for all distinct ID/sequence sets.
649 boolean addMenu = false; // indicates if there are any group links to give
651 for (int i = 0; i < groupLinks.size(); i++)
653 String link = groupLinks.elementAt(i).toString();
654 GroupUrlLink urlLink = null;
657 urlLink = new GroupUrlLink(link);
658 } catch (Exception foo)
660 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
665 if (!urlLink.isValid())
667 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
670 final String label = urlLink.getLabel();
671 boolean usingNames = false;
672 // Now see which parts of the group apply for this URL
673 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
674 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
675 String[] seqstr, ids; // input to makeUrl
678 int numinput = ((int[]) idset[0])[0];
679 String[] allids = ((String[]) idset[1]);
680 seqstr = new String[numinput];
681 ids = new String[numinput];
682 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
684 if (allids[sq] != null)
686 ids[idcount] = allids[sq];
687 seqstr[idcount++] = idandseqs[1][sq];
693 // just use the id/seq set
694 seqstr = idandseqs[1];
698 // and try and make the groupURL!
700 Object[] urlset = null;
703 urlset = urlLink.makeUrlStubs(ids, seqstr,
704 "FromJalview" + System.currentTimeMillis(), false);
705 } catch (UrlStringTooLongException e)
710 int type = urlLink.getGroupURLType() & 3;
711 // System.out.println(urlLink.getGroupURLType()
712 // +" "+((String[])urlset[3])[0]);
713 // first two bits ofurlLink type bitfield are sequenceids and sequences
714 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
715 addshowLink(linkMenus[type], label
716 + (((type & 1) == 1) ? ("("
717 + (usingNames ? "Names" : ltarget) + ")") : ""),
724 groupLinksMenu = new JMenu("Group Links");
725 for (int m = 0; m < linkMenus.length; m++)
727 if (linkMenus[m] != null
728 && linkMenus[m].getMenuComponentCount() > 0)
730 groupLinksMenu.add(linkMenus[m]);
734 groupMenu.add(groupLinksMenu);
739 * add a show URL menu item to the given linkMenu
743 * - menu label string
747 private void addshowLink(JMenu linkMenu, String label, final String url)
749 JMenuItem item = new JMenuItem(label);
750 item.setToolTipText("open URL: " + url);
751 item.addActionListener(new java.awt.event.ActionListener()
753 public void actionPerformed(ActionEvent e)
755 new Thread(new Runnable()
771 * add a late bound groupURL item to the given linkMenu
775 * - menu label string
776 * @param urlgenerator
777 * GroupURLLink used to generate URL
779 * Object array returned from the makeUrlStubs function.
781 private void addshowLink(JMenu linkMenu, String label,
782 final GroupUrlLink urlgenerator, final Object[] urlstub)
784 JMenuItem item = new JMenuItem(label);
785 item.setToolTipText("open URL (" + urlgenerator.getUrl_prefix()
786 + "..) (" + urlgenerator.getNumberInvolved(urlstub) + " seqs)"); // TODO:
795 item.addActionListener(new java.awt.event.ActionListener()
797 public void actionPerformed(ActionEvent e)
799 new Thread(new Runnable()
806 showLink(urlgenerator.constructFrom(urlstub));
807 } catch (UrlStringTooLongException e)
825 private void jbInit() throws Exception
827 groupMenu.setText("Group");
828 groupMenu.setText("Selection");
829 groupName.setText("Name");
830 groupName.addActionListener(new java.awt.event.ActionListener()
832 public void actionPerformed(ActionEvent e)
834 groupName_actionPerformed();
837 sequenceMenu.setText("Sequence");
838 sequenceName.setText("Edit Name/Description");
839 sequenceName.addActionListener(new java.awt.event.ActionListener()
841 public void actionPerformed(ActionEvent e)
843 sequenceName_actionPerformed();
846 PIDColour.setFocusPainted(false);
847 unGroupMenuItem.setText("Remove Group");
848 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
850 public void actionPerformed(ActionEvent e)
852 unGroupMenuItem_actionPerformed();
856 outline.setText("Border colour");
857 outline.addActionListener(new java.awt.event.ActionListener()
859 public void actionPerformed(ActionEvent e)
861 outline_actionPerformed();
864 nucleotideMenuItem.setText("Nucleotide");
865 nucleotideMenuItem.addActionListener(new ActionListener()
867 public void actionPerformed(ActionEvent e)
869 nucleotideMenuItem_actionPerformed();
872 colourMenu.setText("Group Colour");
873 showBoxes.setText("Boxes");
874 showBoxes.setState(true);
875 showBoxes.addActionListener(new ActionListener()
877 public void actionPerformed(ActionEvent e)
879 showBoxes_actionPerformed();
882 showText.setText("Text");
883 showText.setState(true);
884 showText.addActionListener(new ActionListener()
886 public void actionPerformed(ActionEvent e)
888 showText_actionPerformed();
891 showColourText.setText("Colour Text");
892 showColourText.addActionListener(new ActionListener()
894 public void actionPerformed(ActionEvent e)
896 showColourText_actionPerformed();
899 displayNonconserved.setText("Show Nonconserved");
900 displayNonconserved.setState(true);
901 displayNonconserved.addActionListener(new ActionListener()
903 public void actionPerformed(ActionEvent e)
905 showNonconserved_actionPerformed();
908 editMenu.setText("Edit");
910 cut.addActionListener(new ActionListener()
912 public void actionPerformed(ActionEvent e)
914 cut_actionPerformed();
917 upperCase.setText("To Upper Case");
918 upperCase.addActionListener(new ActionListener()
920 public void actionPerformed(ActionEvent e)
925 copy.setText("Copy");
926 copy.addActionListener(new ActionListener()
928 public void actionPerformed(ActionEvent e)
930 copy_actionPerformed();
933 lowerCase.setText("To Lower Case");
934 lowerCase.addActionListener(new ActionListener()
936 public void actionPerformed(ActionEvent e)
941 toggle.setText("Toggle Case");
942 toggle.addActionListener(new ActionListener()
944 public void actionPerformed(ActionEvent e)
949 pdbMenu.setText("Associate Structure with Sequence");
950 pdbFromFile.setText("From File");
951 pdbFromFile.addActionListener(new ActionListener()
953 public void actionPerformed(ActionEvent e)
955 pdbFromFile_actionPerformed();
958 enterPDB.setText("Enter PDB Id");
959 enterPDB.addActionListener(new ActionListener()
961 public void actionPerformed(ActionEvent e)
963 enterPDB_actionPerformed();
966 discoverPDB.setText("Discover PDB ids");
967 discoverPDB.addActionListener(new ActionListener()
969 public void actionPerformed(ActionEvent e)
971 discoverPDB_actionPerformed();
974 outputMenu.setText("Output to Textbox...");
975 sequenceFeature.setText("Create Sequence Feature");
976 sequenceFeature.addActionListener(new ActionListener()
978 public void actionPerformed(ActionEvent e)
980 sequenceFeature_actionPerformed();
983 textColour.setText("Text Colour");
984 textColour.addActionListener(new ActionListener()
986 public void actionPerformed(ActionEvent e)
988 textColour_actionPerformed();
991 jMenu1.setText("Group");
992 structureMenu.setText("Structure");
993 viewStructureMenu.setText("View Structure");
994 // colStructureMenu.setText("Colour By Structure");
995 editSequence.setText("Edit Sequence...");
996 editSequence.addActionListener(new ActionListener()
998 public void actionPerformed(ActionEvent actionEvent)
1000 editSequence_actionPerformed(actionEvent);
1004 * annotationMenuItem.setText("By Annotation");
1005 * annotationMenuItem.addActionListener(new ActionListener() { public void
1006 * actionPerformed(ActionEvent actionEvent) {
1007 * annotationMenuItem_actionPerformed(actionEvent); } });
1013 this.add(structureMenu);
1014 groupMenu.add(editMenu);
1015 groupMenu.add(outputMenu);
1016 groupMenu.add(sequenceFeature);
1017 groupMenu.add(jMenu1);
1018 sequenceMenu.add(sequenceName);
1019 colourMenu.add(textColour);
1020 colourMenu.add(noColourmenuItem);
1021 colourMenu.add(clustalColour);
1022 colourMenu.add(BLOSUM62Colour);
1023 colourMenu.add(PIDColour);
1024 colourMenu.add(zappoColour);
1025 colourMenu.add(taylorColour);
1026 colourMenu.add(hydrophobicityColour);
1027 colourMenu.add(helixColour);
1028 colourMenu.add(strandColour);
1029 colourMenu.add(turnColour);
1030 colourMenu.add(buriedColour);
1031 colourMenu.add(nucleotideMenuItem);
1032 colourMenu.add(purinePyrimidineColour);
1033 //colourMenu.add(covariationColour);
1034 colourMenu.add(userDefinedColour);
1036 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1038 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1039 .getUserColourSchemes().keys();
1041 while (userColours.hasMoreElements())
1043 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1044 item.addActionListener(new ActionListener()
1046 public void actionPerformed(ActionEvent evt)
1048 userDefinedColour_actionPerformed(evt);
1051 colourMenu.add(item);
1055 colourMenu.addSeparator();
1056 colourMenu.add(abovePIDColour);
1057 colourMenu.add(conservationMenuItem);
1058 // colourMenu.add(annotationMenuItem);
1061 editMenu.add(editSequence);
1062 editMenu.add(upperCase);
1063 editMenu.add(lowerCase);
1064 editMenu.add(toggle);
1065 pdbMenu.add(pdbFromFile);
1066 pdbMenu.add(enterPDB);
1067 pdbMenu.add(discoverPDB);
1068 jMenu1.add(groupName);
1069 jMenu1.add(unGroupMenuItem);
1070 jMenu1.add(colourMenu);
1071 jMenu1.add(showBoxes);
1072 jMenu1.add(showText);
1073 jMenu1.add(showColourText);
1074 jMenu1.add(outline);
1075 jMenu1.add(displayNonconserved);
1076 structureMenu.add(pdbMenu);
1077 structureMenu.add(viewStructureMenu);
1078 // structureMenu.add(colStructureMenu);
1079 noColourmenuItem.setText("None");
1080 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 noColourmenuItem_actionPerformed();
1088 clustalColour.setText("Clustalx colours");
1089 clustalColour.addActionListener(new java.awt.event.ActionListener()
1091 public void actionPerformed(ActionEvent e)
1093 clustalColour_actionPerformed();
1096 zappoColour.setText("Zappo");
1097 zappoColour.addActionListener(new java.awt.event.ActionListener()
1099 public void actionPerformed(ActionEvent e)
1101 zappoColour_actionPerformed();
1104 taylorColour.setText("Taylor");
1105 taylorColour.addActionListener(new java.awt.event.ActionListener()
1107 public void actionPerformed(ActionEvent e)
1109 taylorColour_actionPerformed();
1112 hydrophobicityColour.setText("Hydrophobicity");
1113 hydrophobicityColour
1114 .addActionListener(new java.awt.event.ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 hydrophobicityColour_actionPerformed();
1121 helixColour.setText("Helix propensity");
1122 helixColour.addActionListener(new java.awt.event.ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 helixColour_actionPerformed();
1129 strandColour.setText("Strand propensity");
1130 strandColour.addActionListener(new java.awt.event.ActionListener()
1132 public void actionPerformed(ActionEvent e)
1134 strandColour_actionPerformed();
1137 turnColour.setText("Turn propensity");
1138 turnColour.addActionListener(new java.awt.event.ActionListener()
1140 public void actionPerformed(ActionEvent e)
1142 turnColour_actionPerformed();
1145 buriedColour.setText("Buried Index");
1146 buriedColour.addActionListener(new java.awt.event.ActionListener()
1148 public void actionPerformed(ActionEvent e)
1150 buriedColour_actionPerformed();
1153 abovePIDColour.setText("Above % Identity");
1154 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1156 public void actionPerformed(ActionEvent e)
1158 abovePIDColour_actionPerformed();
1161 userDefinedColour.setText("User Defined...");
1162 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1164 public void actionPerformed(ActionEvent e)
1166 userDefinedColour_actionPerformed(e);
1169 PIDColour.setText("Percentage Identity");
1170 PIDColour.addActionListener(new java.awt.event.ActionListener()
1172 public void actionPerformed(ActionEvent e)
1174 PIDColour_actionPerformed();
1177 BLOSUM62Colour.setText("BLOSUM62");
1178 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1180 public void actionPerformed(ActionEvent e)
1182 BLOSUM62Colour_actionPerformed();
1185 purinePyrimidineColour.setText("Purine/Pyrimidine");
1186 purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
1188 public void actionPerformed(ActionEvent e)
1190 purinePyrimidineColour_actionPerformed();
1194 covariationColour.addActionListener(new java.awt.event.ActionListener()
1196 public void actionPerformed(ActionEvent e)
1198 covariationColour_actionPerformed();
1202 conservationMenuItem.setText("Conservation");
1203 conservationMenuItem
1204 .addActionListener(new java.awt.event.ActionListener()
1206 public void actionPerformed(ActionEvent e)
1208 conservationMenuItem_actionPerformed();
1213 protected void showNonconserved_actionPerformed()
1215 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1220 * call to refresh view after settings change
1224 ap.updateAnnotation();
1225 ap.paintAlignment(true);
1227 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1236 protected void clustalColour_actionPerformed()
1238 SequenceGroup sg = getGroup();
1239 sg.cs = new ClustalxColourScheme(
1240 sg.getSequences(ap.av.hiddenRepSequences),
1241 ap.av.alignment.getWidth());
1251 protected void zappoColour_actionPerformed()
1253 getGroup().cs = new ZappoColourScheme();
1263 protected void taylorColour_actionPerformed()
1265 getGroup().cs = new TaylorColourScheme();
1275 protected void hydrophobicityColour_actionPerformed()
1277 getGroup().cs = new HydrophobicColourScheme();
1287 protected void helixColour_actionPerformed()
1289 getGroup().cs = new HelixColourScheme();
1299 protected void strandColour_actionPerformed()
1301 getGroup().cs = new StrandColourScheme();
1311 protected void turnColour_actionPerformed()
1313 getGroup().cs = new TurnColourScheme();
1323 protected void buriedColour_actionPerformed()
1325 getGroup().cs = new BuriedColourScheme();
1335 public void nucleotideMenuItem_actionPerformed()
1337 getGroup().cs = new NucleotideColourScheme();
1341 protected void purinePyrimidineColour_actionPerformed()
1343 getGroup().cs = new PurinePyrimidineColourScheme();
1347 protected void covariationColour_actionPerformed()
1349 getGroup().cs = new CovariationColourScheme(sequence.getAnnotation()[0]);
1359 protected void abovePIDColour_actionPerformed()
1361 SequenceGroup sg = getGroup();
1367 if (abovePIDColour.isSelected())
1369 sg.cs.setConsensus(AAFrequency.calculate(
1370 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1371 sg.getEndRes() + 1));
1373 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1376 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1378 SliderPanel.showPIDSlider();
1381 // remove PIDColouring
1383 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1395 protected void userDefinedColour_actionPerformed(ActionEvent e)
1397 SequenceGroup sg = getGroup();
1399 if (e.getActionCommand().equals("User Defined..."))
1401 new UserDefinedColours(ap, sg);
1405 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1406 .getUserColourSchemes().get(e.getActionCommand());
1419 protected void PIDColour_actionPerformed()
1421 SequenceGroup sg = getGroup();
1422 sg.cs = new PIDColourScheme();
1423 sg.cs.setConsensus(AAFrequency.calculate(
1424 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1425 sg.getEndRes() + 1));
1435 protected void BLOSUM62Colour_actionPerformed()
1437 SequenceGroup sg = getGroup();
1439 sg.cs = new Blosum62ColourScheme();
1441 sg.cs.setConsensus(AAFrequency.calculate(
1442 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1443 sg.getEndRes() + 1));
1454 protected void noColourmenuItem_actionPerformed()
1456 getGroup().cs = null;
1466 protected void conservationMenuItem_actionPerformed()
1468 SequenceGroup sg = getGroup();
1474 if (conservationMenuItem.isSelected())
1476 Conservation c = new Conservation("Group",
1477 ResidueProperties.propHash, 3,
1478 sg.getSequences(ap.av.hiddenRepSequences), sg.getStartRes(),
1479 sg.getEndRes() + 1);
1482 c.verdict(false, ap.av.ConsPercGaps);
1484 sg.cs.setConservation(c);
1486 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1487 SliderPanel.showConservationSlider();
1490 // remove ConservationColouring
1492 sg.cs.setConservation(null);
1498 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1500 SequenceGroup sg = getGroup();
1506 AnnotationColourGradient acg = new AnnotationColourGradient(
1507 sequence.getAnnotation()[0], null,
1508 AnnotationColourGradient.NO_THRESHOLD);
1510 acg.predefinedColours = true;
1522 protected void groupName_actionPerformed()
1525 SequenceGroup sg = getGroup();
1526 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1527 sg.getDescription(), " Group Name ",
1528 "Group Description ", "Edit Group Name/Description",
1536 sg.setName(dialog.getName());
1537 sg.setDescription(dialog.getDescription());
1542 * Get selection group - adding it to the alignment if necessary.
1544 * @return sequence group to operate on
1546 SequenceGroup getGroup()
1548 SequenceGroup sg = ap.av.getSelectionGroup();
1549 // this method won't add a new group if it already exists
1552 ap.av.alignment.addGroup(sg);
1564 void sequenceName_actionPerformed()
1566 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1567 sequence.getDescription(), " Sequence Name ",
1568 "Sequence Description ", "Edit Sequence Name/Description",
1576 if (dialog.getName() != null)
1578 if (dialog.getName().indexOf(" ") > -1)
1580 JOptionPane.showMessageDialog(ap,
1581 "Spaces have been converted to \"_\"",
1582 "No spaces allowed in Sequence Name",
1583 JOptionPane.WARNING_MESSAGE);
1586 sequence.setName(dialog.getName().replace(' ', '_'));
1587 ap.paintAlignment(false);
1590 sequence.setDescription(dialog.getDescription());
1592 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1603 void unGroupMenuItem_actionPerformed()
1605 SequenceGroup sg = ap.av.getSelectionGroup();
1606 ap.av.alignment.deleteGroup(sg);
1607 ap.av.setSelectionGroup(null);
1617 protected void outline_actionPerformed()
1619 SequenceGroup sg = getGroup();
1620 Color col = JColorChooser.showDialog(this, "Select Outline Colour",
1625 sg.setOutlineColour(col);
1637 public void showBoxes_actionPerformed()
1639 getGroup().setDisplayBoxes(showBoxes.isSelected());
1649 public void showText_actionPerformed()
1651 getGroup().setDisplayText(showText.isSelected());
1661 public void showColourText_actionPerformed()
1663 getGroup().setColourText(showColourText.isSelected());
1667 public void showLink(String url)
1671 jalview.util.BrowserLauncher.openURL(url);
1672 } catch (Exception ex)
1675 .showInternalMessageDialog(
1677 "Unixers: Couldn't find default web browser."
1678 + "\nAdd the full path to your browser in Preferences.",
1679 "Web browser not found", JOptionPane.WARNING_MESSAGE);
1681 ex.printStackTrace();
1685 void hideSequences(boolean representGroup)
1687 SequenceGroup sg = ap.av.getSelectionGroup();
1688 if (sg == null || sg.getSize() < 1)
1690 ap.av.hideSequence(new SequenceI[]
1695 ap.av.setSelectionGroup(null);
1699 ap.av.hideRepSequences(sequence, sg);
1704 int gsize = sg.getSize();
1707 hseqs = new SequenceI[gsize];
1710 for (int i = 0; i < gsize; i++)
1712 hseqs[index++] = sg.getSequenceAt(i);
1715 ap.av.hideSequence(hseqs);
1716 // refresh(); TODO: ? needed ?
1717 ap.av.sendSelection();
1720 public void copy_actionPerformed()
1722 ap.alignFrame.copy_actionPerformed(null);
1725 public void cut_actionPerformed()
1727 ap.alignFrame.cut_actionPerformed(null);
1730 void changeCase(ActionEvent e)
1732 Object source = e.getSource();
1733 SequenceGroup sg = ap.av.getSelectionGroup();
1737 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1738 sg.getEndRes() + 1);
1743 if (source == toggle)
1745 description = "Toggle Case";
1746 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1748 else if (source == upperCase)
1750 description = "To Upper Case";
1751 caseChange = ChangeCaseCommand.TO_UPPER;
1755 description = "To Lower Case";
1756 caseChange = ChangeCaseCommand.TO_LOWER;
1759 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1760 sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
1763 ap.alignFrame.addHistoryItem(caseCommand);
1765 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1771 public void outputText_actionPerformed(ActionEvent e)
1773 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1774 cap.setForInput(null);
1775 Desktop.addInternalFrame(cap,
1776 "Alignment output - " + e.getActionCommand(), 600, 500);
1778 String[] omitHidden = null;
1780 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1781 // or we simply trust the user wants
1782 // wysiwig behaviour
1783 SequenceGroup sg = ap.av.getSelectionGroup();
1784 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1785 omitHidden = ap.av.getViewAsString(true);
1786 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1787 AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
1790 for (int i = 0; i < nala.length; i++)
1792 AlignmentAnnotation na = nala[i];
1793 oal.addAnnotation(na);
1796 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
1797 oal, omitHidden, csel, sg));
1801 public void pdbFromFile_actionPerformed()
1803 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
1804 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
1805 chooser.setFileView(new jalview.io.JalviewFileView());
1806 chooser.setDialogTitle("Select a PDB file for "+sequence.getDisplayId(false));
1807 chooser.setToolTipText("Load a PDB file and associate it with sequence '"+sequence.getDisplayId(false)+"'");
1809 int value = chooser.showOpenDialog(null);
1811 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
1813 String choice = chooser.getSelectedFile().getPath();
1814 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
1815 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, jalview.io.AppletFormatAdapter.FILE, sequence, true);
1820 public void enterPDB_actionPerformed()
1822 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
1823 "Enter PDB Id", "Enter PDB Id", JOptionPane.QUESTION_MESSAGE);
1825 if (id != null && id.length() > 0)
1827 PDBEntry entry = new PDBEntry();
1828 entry.setId(id.toUpperCase());
1829 sequence.getDatasetSequence().addPDBId(entry);
1833 public void discoverPDB_actionPerformed()
1836 final SequenceI[] sequences = ((ap.av.selectionGroup == null) ? new Sequence[]
1838 : ap.av.selectionGroup.getSequencesInOrder(ap.av.alignment));
1839 Thread discpdb = new Thread(new Runnable()
1844 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
1845 .fetchDBRefs(false);
1852 public void sequenceFeature_actionPerformed()
1854 SequenceGroup sg = ap.av.getSelectionGroup();
1860 int rsize = 0, gSize = sg.getSize();
1861 SequenceI[] rseqs, seqs = new SequenceI[gSize];
1862 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
1864 for (int i = 0; i < gSize; i++)
1866 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
1867 int end = sg.findEndRes(sg.getSequenceAt(i));
1870 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
1871 features[rsize] = new SequenceFeature(null, null, null, start, end,
1876 rseqs = new SequenceI[rsize];
1877 tfeatures = new SequenceFeature[rsize];
1878 System.arraycopy(seqs, 0, rseqs, 0, rsize);
1879 System.arraycopy(features, 0, tfeatures, 0, rsize);
1880 features = tfeatures;
1882 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
1883 features, true, ap))
1885 ap.alignFrame.setShowSeqFeatures(true);
1886 ap.highlightSearchResults(null);
1890 public void textColour_actionPerformed()
1892 SequenceGroup sg = getGroup();
1895 new TextColourChooser().chooseColour(ap, sg);
1899 public void colourByStructure(String pdbid)
1901 Annotation[] anots = ap.av.getStructureSelectionManager().colourSequenceFromStructure(
1904 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
1905 "Coloured by " + pdbid, anots);
1907 ap.av.alignment.addAnnotation(an);
1908 an.createSequenceMapping(sequence, 0, true);
1909 // an.adjustForAlignment();
1910 ap.av.alignment.setAnnotationIndex(an, 0);
1912 ap.adjustAnnotationHeight();
1914 sequence.addAlignmentAnnotation(an);
1918 public void editSequence_actionPerformed(ActionEvent actionEvent)
1920 SequenceGroup sg = ap.av.getSelectionGroup();
1924 if (sequence == null)
1925 sequence = (Sequence) sg.getSequenceAt(0);
1927 EditNameDialog dialog = new EditNameDialog(
1928 sequence.getSequenceAsString(sg.getStartRes(),
1929 sg.getEndRes() + 1), null, "Edit Sequence ", null,
1930 "Edit Sequence", ap.alignFrame);
1934 EditCommand editCommand = new EditCommand("Edit Sequences",
1935 EditCommand.REPLACE, dialog.getName().replace(' ',
1936 ap.av.getGapCharacter()),
1937 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
1938 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
1940 ap.alignFrame.addHistoryItem(editCommand);
1942 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()