2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
26 import java.awt.event.*;
30 import jalview.analysis.*;
31 import jalview.commands.*;
32 import jalview.datamodel.*;
34 import jalview.schemes.*;
35 import jalview.util.GroupUrlLink;
36 import jalview.util.GroupUrlLink.UrlStringTooLongException;
37 import jalview.util.MessageManager;
38 import jalview.util.UrlLink;
44 * @version $Revision: 1.118 $
46 public class PopupMenu extends JPopupMenu
48 JMenu groupMenu = new JMenu();
50 JMenuItem groupName = new JMenuItem();
52 protected JRadioButtonMenuItem clustalColour = new JRadioButtonMenuItem();
54 protected JRadioButtonMenuItem zappoColour = new JRadioButtonMenuItem();
56 protected JRadioButtonMenuItem taylorColour = new JRadioButtonMenuItem();
58 protected JRadioButtonMenuItem hydrophobicityColour = new JRadioButtonMenuItem();
60 protected JRadioButtonMenuItem helixColour = new JRadioButtonMenuItem();
62 protected JRadioButtonMenuItem strandColour = new JRadioButtonMenuItem();
64 protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
66 protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
68 protected JCheckBoxMenuItem abovePIDColour = new JCheckBoxMenuItem();
70 protected JRadioButtonMenuItem userDefinedColour = new JRadioButtonMenuItem();
72 protected JRadioButtonMenuItem PIDColour = new JRadioButtonMenuItem();
74 protected JRadioButtonMenuItem BLOSUM62Colour = new JRadioButtonMenuItem();
76 protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
77 protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
79 // protected JRadioButtonMenuItem covariationColour = new
80 // JRadioButtonMenuItem();
82 JRadioButtonMenuItem noColourmenuItem = new JRadioButtonMenuItem();
84 protected JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
88 JMenu sequenceMenu = new JMenu();
90 JMenuItem sequenceName = new JMenuItem();
92 JMenuItem sequenceDetails = new JMenuItem();
94 JMenuItem sequenceSelDetails = new JMenuItem();
97 JMenuItem createGroupMenuItem = new JMenuItem();
98 JMenuItem unGroupMenuItem = new JMenuItem();
100 JMenuItem outline = new JMenuItem();
102 JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();
104 JMenu colourMenu = new JMenu();
106 JCheckBoxMenuItem showBoxes = new JCheckBoxMenuItem();
108 JCheckBoxMenuItem showText = new JCheckBoxMenuItem();
110 JCheckBoxMenuItem showColourText = new JCheckBoxMenuItem();
112 JCheckBoxMenuItem displayNonconserved = new JCheckBoxMenuItem();
114 JMenu editMenu = new JMenu();
116 JMenuItem cut = new JMenuItem();
118 JMenuItem copy = new JMenuItem();
120 JMenuItem upperCase = new JMenuItem();
122 JMenuItem lowerCase = new JMenuItem();
124 JMenuItem toggle = new JMenuItem();
126 JMenu pdbMenu = new JMenu();
128 JMenuItem pdbFromFile = new JMenuItem();
129 // JBPNote: Commented these out - Should add these services via the web services menu system.
130 // JMenuItem ContraFold = new JMenuItem();
132 // JMenuItem RNAFold = 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(MessageManager.formatMessage("label.2d_rna_structure_line", new String[]{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(MessageManager.formatMessage("label.2d_rna_sequence_name", new String[]{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(MessageManager.getString("action.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(MessageManager.formatMessage("label.represent_group_with", new String[]{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(MessageManager.getString("action.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(MessageManager.getString("action.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();
418 boolean isDefinedGroup = (sg!=null) ? ap.av.getAlignment().getGroups().contains(sg) : false;
420 if (sg != null && sg.getSize() > 0)
422 groupName.setText(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
423 groupName.setText(MessageManager.getString("label.edit_name_and_description_current_group"));
425 if (sg.cs instanceof ZappoColourScheme)
427 zappoColour.setSelected(true);
429 else if (sg.cs instanceof TaylorColourScheme)
431 taylorColour.setSelected(true);
433 else if (sg.cs instanceof PIDColourScheme)
435 PIDColour.setSelected(true);
437 else if (sg.cs instanceof Blosum62ColourScheme)
439 BLOSUM62Colour.setSelected(true);
441 else if (sg.cs instanceof UserColourScheme)
443 userDefinedColour.setSelected(true);
445 else if (sg.cs instanceof HydrophobicColourScheme)
447 hydrophobicityColour.setSelected(true);
449 else if (sg.cs instanceof HelixColourScheme)
451 helixColour.setSelected(true);
453 else if (sg.cs instanceof StrandColourScheme)
455 strandColour.setSelected(true);
457 else if (sg.cs instanceof TurnColourScheme)
459 turnColour.setSelected(true);
461 else if (sg.cs instanceof BuriedColourScheme)
463 buriedColour.setSelected(true);
465 else if (sg.cs instanceof ClustalxColourScheme)
467 clustalColour.setSelected(true);
469 else if (sg.cs instanceof PurinePyrimidineColourScheme)
471 purinePyrimidineColour.setSelected(true);
476 * else if (sg.cs instanceof CovariationColourScheme) {
477 * covariationColour.setSelected(true); }
481 noColourmenuItem.setSelected(true);
484 if (sg.cs != null && sg.cs.conservationApplied())
486 conservationMenuItem.setSelected(true);
488 displayNonconserved.setSelected(sg.getShowNonconserved());
489 showText.setSelected(sg.getDisplayText());
490 showColourText.setSelected(sg.getColourText());
491 showBoxes.setSelected(sg.getDisplayBoxes());
492 // add any groupURLs to the groupURL submenu and make it visible
493 if (groupLinks != null && groupLinks.size() > 0)
495 buildGroupURLMenu(sg, groupLinks);
497 // Add a 'show all structures' for the current selection
498 Hashtable<String, PDBEntry> pdbe = new Hashtable<String, PDBEntry>(),reppdb=new Hashtable<String,PDBEntry>();
499 SequenceI sqass = null;
500 for (SequenceI sq : ap.av.getSequenceSelection())
502 Vector<PDBEntry> pes = (Vector<PDBEntry>) sq.getDatasetSequence()
506 reppdb.put(pes.get(0).getId(),pes.get(0));
507 for (PDBEntry pe : pes)
509 pdbe.put(pe.getId(), pe);
519 final PDBEntry[] pe = pdbe.values().toArray(
520 new PDBEntry[pdbe.size()]),pr = reppdb.values().toArray(
521 new PDBEntry[reppdb.size()]);
522 final JMenuItem gpdbview,rpdbview;
523 if (pdbe.size() == 1)
525 structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_structure_for", new String[]{sqass.getDisplayId(false)})));
529 structureMenu.add(gpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_structures", new String[]{new Integer(pdbe.size()).toString()})));
531 gpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_structures_associated_current_selection_superimpose_using_alignment"));
532 gpdbview.addActionListener(new ActionListener()
536 public void actionPerformed(ActionEvent e)
538 new AppJmol(ap, pe, ap.av.collateForPDB(pe));
541 if (reppdb.size()>1 && reppdb.size()<pdbe.size())
543 structureMenu.add(rpdbview = new JMenuItem(MessageManager.formatMessage("label.view_all_representative_structures", new String[]{new Integer(reppdb.size()).toString()})));
544 rpdbview.setToolTipText(MessageManager.getString("label.open_new_jmol_view_with_all_representative_structures_associated_current_selection_superimpose_using_alignment"));
545 rpdbview.addActionListener(new ActionListener()
549 public void actionPerformed(ActionEvent e)
551 new AppJmol(ap, pr, ap.av.collateForPDB(pr));
559 groupMenu.setVisible(false);
560 editMenu.setVisible(false);
565 createGroupMenuItem.setVisible(true);
566 unGroupMenuItem.setVisible(false);
567 jMenu1.setText(MessageManager.getString("action.edit_new_group"));
569 createGroupMenuItem.setVisible(false);
570 unGroupMenuItem.setVisible(true);
571 jMenu1.setText(MessageManager.getString("action.edit_group"));
576 sequenceMenu.setVisible(false);
577 structureMenu.setVisible(false);
580 if (links != null && links.size() > 0)
583 JMenu linkMenu = new JMenu(MessageManager.getString("action.link"));
584 Vector linkset = new Vector();
585 for (int i = 0; i < links.size(); i++)
587 String link = links.elementAt(i).toString();
588 UrlLink urlLink = null;
591 urlLink = new UrlLink(link);
592 } catch (Exception foo)
594 jalview.bin.Cache.log.error("Exception for URLLink '" + link
599 if (!urlLink.isValid())
601 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
604 final String label = urlLink.getLabel();
605 if (seq != null && urlLink.isDynamic())
608 // collect matching db-refs
609 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
610 seq.getDBRef(), new String[]
611 { urlLink.getTarget() });
612 // collect id string too
613 String id = seq.getName();
614 String descr = seq.getDescription();
615 if (descr != null && descr.length() < 1)
622 for (int r = 0; r < dbr.length; r++)
624 if (id != null && dbr[r].getAccessionId().equals(id))
626 // suppress duplicate link creation for the bare sequence ID
627 // string with this link
630 // create Bare ID link for this RUL
631 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
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],
649 // create Bare ID link for this RUL
650 String[] urls = urlLink.makeUrls(id, 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]);
663 // Create urls from description but only for URL links which are regex
665 if (descr != null && urlLink.getRegexReplace() != null)
667 // create link for this URL from description where regex matches
668 String[] urls = urlLink.makeUrls(descr, true);
671 for (int u = 0; u < urls.length; u += 2)
673 if (!linkset.contains(urls[u] + "|" + urls[u + 1]))
675 linkset.addElement(urls[u] + "|" + urls[u + 1]);
676 addshowLink(linkMenu, label, urls[u + 1]);
684 if (!linkset.contains(label + "|" + urlLink.getUrl_prefix()))
686 linkset.addElement(label + "|" + urlLink.getUrl_prefix());
687 // Add a non-dynamic link
688 addshowLink(linkMenu, label, urlLink.getUrl_prefix());
692 if (sequence != null)
694 sequenceMenu.add(linkMenu);
703 private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
706 // TODO: usability: thread off the generation of group url content so root
708 // sequence only URLs
709 // ID/regex match URLs
710 groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
711 JMenu[] linkMenus = new JMenu[]
712 { null, new JMenu(MessageManager.getString("action.ids")), new JMenu(MessageManager.getString("action.sequences")),
713 new JMenu(MessageManager.getString("action.ids_sequences")) }; // three types of url that might be
715 SequenceI[] seqs = ap.av.getSelectionAsNewSequence();
716 String[][] idandseqs = GroupUrlLink.formStrings(seqs);
717 Hashtable commonDbrefs = new Hashtable();
718 for (int sq = 0; sq < seqs.length; sq++)
721 int start = seqs[sq].findPosition(sg.getStartRes()), end = seqs[sq]
722 .findPosition(sg.getEndRes());
723 // just collect ids from dataset sequence
724 // TODO: check if IDs collected from selecton group intersects with the
725 // current selection, too
726 SequenceI sqi = seqs[sq];
727 while (sqi.getDatasetSequence() != null)
729 sqi = sqi.getDatasetSequence();
731 DBRefEntry[] dbr = sqi.getDBRef();
732 if (dbr != null && dbr.length > 0)
734 for (int d = 0; d < dbr.length; d++)
736 String src = dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
737 Object[] sarray = (Object[]) commonDbrefs.get(src);
740 sarray = new Object[2];
741 sarray[0] = new int[]
743 sarray[1] = new String[seqs.length];
745 commonDbrefs.put(src, sarray);
748 if (((String[]) sarray[1])[sq] == null)
751 || (dbr[d].getMap().locateMappedRange(start, end) != null))
753 ((String[]) sarray[1])[sq] = dbr[d].getAccessionId();
754 ((int[]) sarray[0])[0]++;
760 // now create group links for all distinct ID/sequence sets.
761 boolean addMenu = false; // indicates if there are any group links to give
763 for (int i = 0; i < groupLinks.size(); i++)
765 String link = groupLinks.elementAt(i).toString();
766 GroupUrlLink urlLink = null;
769 urlLink = new GroupUrlLink(link);
770 } catch (Exception foo)
772 jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
777 if (!urlLink.isValid())
779 jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
782 final String label = urlLink.getLabel();
783 boolean usingNames = false;
784 // Now see which parts of the group apply for this URL
785 String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
786 Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
787 String[] seqstr, ids; // input to makeUrl
790 int numinput = ((int[]) idset[0])[0];
791 String[] allids = ((String[]) idset[1]);
792 seqstr = new String[numinput];
793 ids = new String[numinput];
794 for (int sq = 0, idcount = 0; sq < seqs.length; sq++)
796 if (allids[sq] != null)
798 ids[idcount] = allids[sq];
799 seqstr[idcount++] = idandseqs[1][sq];
805 // just use the id/seq set
806 seqstr = idandseqs[1];
810 // and try and make the groupURL!
812 Object[] urlset = null;
815 urlset = urlLink.makeUrlStubs(ids, seqstr,
816 "FromJalview" + System.currentTimeMillis(), false);
817 } catch (UrlStringTooLongException e)
822 int type = urlLink.getGroupURLType() & 3;
823 // System.out.println(urlLink.getGroupURLType()
824 // +" "+((String[])urlset[3])[0]);
825 // first two bits ofurlLink type bitfield are sequenceids and sequences
826 // TODO: FUTURE: ensure the groupURL menu structure can be generalised
827 addshowLink(linkMenus[type], label
828 + (((type & 1) == 1) ? ("("
829 + (usingNames ? "Names" : ltarget) + ")") : ""),
836 groupLinksMenu = new JMenu(MessageManager.getString("action.group_link"));
837 for (int m = 0; m < linkMenus.length; m++)
839 if (linkMenus[m] != null
840 && linkMenus[m].getMenuComponentCount() > 0)
842 groupLinksMenu.add(linkMenus[m]);
846 groupMenu.add(groupLinksMenu);
851 * add a show URL menu item to the given linkMenu
855 * - menu label string
859 private void addshowLink(JMenu linkMenu, String label, final String url)
861 JMenuItem item = new JMenuItem(label);
862 item.setToolTipText(MessageManager.formatMessage("label.open_url_param", new String[]{url}));
863 item.addActionListener(new java.awt.event.ActionListener()
865 public void actionPerformed(ActionEvent e)
867 new Thread(new Runnable()
883 * add a late bound groupURL item to the given linkMenu
887 * - menu label string
888 * @param urlgenerator
889 * GroupURLLink used to generate URL
891 * Object array returned from the makeUrlStubs function.
893 private void addshowLink(JMenu linkMenu, String label,
894 final GroupUrlLink urlgenerator, final Object[] urlstub)
896 JMenuItem item = new JMenuItem(label);
897 item.setToolTipText(MessageManager.formatMessage("label.open_url_seqs_param", new Object[]{urlgenerator.getUrl_prefix(),urlgenerator.getNumberInvolved(urlstub)}));
898 // TODO: put in info about what is being sent.
899 item.addActionListener(new java.awt.event.ActionListener()
901 public void actionPerformed(ActionEvent e)
903 new Thread(new Runnable()
910 showLink(urlgenerator.constructFrom(urlstub));
911 } catch (UrlStringTooLongException e)
929 private void jbInit() throws Exception
931 groupMenu.setText(MessageManager.getString("label.group"));
932 groupMenu.setText(MessageManager.getString("label.selection"));
933 groupName.setText(MessageManager.getString("label.name"));
934 groupName.addActionListener(new java.awt.event.ActionListener()
936 public void actionPerformed(ActionEvent e)
938 groupName_actionPerformed();
941 sequenceMenu.setText(MessageManager.getString("label.sequence"));
942 sequenceName.setText(MessageManager.getString("label.edit_name_description"));
943 sequenceName.addActionListener(new java.awt.event.ActionListener()
945 public void actionPerformed(ActionEvent e)
947 sequenceName_actionPerformed();
950 sequenceDetails.setText(MessageManager.getString("label.sequence_details") + "...");
951 sequenceDetails.addActionListener(new java.awt.event.ActionListener()
953 public void actionPerformed(ActionEvent e)
955 sequenceDetails_actionPerformed();
958 sequenceSelDetails.setText(MessageManager.getString("label.sequence_details") + "...");
960 .addActionListener(new java.awt.event.ActionListener()
962 public void actionPerformed(ActionEvent e)
964 sequenceSelectionDetails_actionPerformed();
967 PIDColour.setFocusPainted(false);
968 unGroupMenuItem.setText(MessageManager.getString("action.remove_group"));
969 unGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
971 public void actionPerformed(ActionEvent e)
973 unGroupMenuItem_actionPerformed();
976 createGroupMenuItem.setText(MessageManager.getString("action.create_group"));
977 createGroupMenuItem.addActionListener(new java.awt.event.ActionListener()
979 public void actionPerformed(ActionEvent e)
981 createGroupMenuItem_actionPerformed();
985 outline.setText(MessageManager.getString("action.border_colour"));
986 outline.addActionListener(new java.awt.event.ActionListener()
988 public void actionPerformed(ActionEvent e)
990 outline_actionPerformed();
993 nucleotideMenuItem.setText(MessageManager.getString("label.nucleotide"));
994 nucleotideMenuItem.addActionListener(new ActionListener()
996 public void actionPerformed(ActionEvent e)
998 nucleotideMenuItem_actionPerformed();
1001 colourMenu.setText(MessageManager.getString("label.group_colour"));
1002 showBoxes.setText(MessageManager.getString("action.boxes"));
1003 showBoxes.setState(true);
1004 showBoxes.addActionListener(new ActionListener()
1006 public void actionPerformed(ActionEvent e)
1008 showBoxes_actionPerformed();
1011 showText.setText(MessageManager.getString("action.text"));
1012 showText.setState(true);
1013 showText.addActionListener(new ActionListener()
1015 public void actionPerformed(ActionEvent e)
1017 showText_actionPerformed();
1020 showColourText.setText(MessageManager.getString("label.colour_text"));
1021 showColourText.addActionListener(new ActionListener()
1023 public void actionPerformed(ActionEvent e)
1025 showColourText_actionPerformed();
1028 displayNonconserved.setText(MessageManager.getString("label.show_non_conversed"));
1029 displayNonconserved.setState(true);
1030 displayNonconserved.addActionListener(new ActionListener()
1032 public void actionPerformed(ActionEvent e)
1034 showNonconserved_actionPerformed();
1037 editMenu.setText(MessageManager.getString("action.edit"));
1038 cut.setText(MessageManager.getString("action.cut"));
1039 cut.addActionListener(new ActionListener()
1041 public void actionPerformed(ActionEvent e)
1043 cut_actionPerformed();
1046 upperCase.setText(MessageManager.getString("label.to_upper_case"));
1047 upperCase.addActionListener(new ActionListener()
1049 public void actionPerformed(ActionEvent e)
1054 copy.setText(MessageManager.getString("action.copy"));
1055 copy.addActionListener(new ActionListener()
1057 public void actionPerformed(ActionEvent e)
1059 copy_actionPerformed();
1062 lowerCase.setText(MessageManager.getString("label.to_lower_case"));
1063 lowerCase.addActionListener(new ActionListener()
1065 public void actionPerformed(ActionEvent e)
1070 toggle.setText(MessageManager.getString("label.toggle_case"));
1071 toggle.addActionListener(new ActionListener()
1073 public void actionPerformed(ActionEvent e)
1078 pdbMenu.setText(MessageManager.getString("label.associate_structure_with_sequence"));
1079 pdbFromFile.setText(MessageManager.getString("label.from_file"));
1080 pdbFromFile.addActionListener(new ActionListener()
1082 public void actionPerformed(ActionEvent e)
1084 pdbFromFile_actionPerformed();
1087 // RNAFold.setText("From RNA Fold with predict2D");
1088 // RNAFold.addActionListener(new ActionListener()
1090 // public void actionPerformed(ActionEvent e)
1093 // RNAFold_actionPerformed();
1094 // } catch (Exception e1) {
1095 // // TODO Auto-generated catch block
1096 // e1.printStackTrace();
1100 // ContraFold.setText("From Contra Fold with predict2D");
1101 // ContraFold.addActionListener(new ActionListener()
1103 // public void actionPerformed(ActionEvent e)
1106 // ContraFold_actionPerformed();
1107 // } catch (Exception e1) {
1108 // // TODO Auto-generated catch block
1109 // e1.printStackTrace();
1113 enterPDB.setText(MessageManager.getString("label.enter_pdb_id"));
1114 enterPDB.addActionListener(new ActionListener()
1116 public void actionPerformed(ActionEvent e)
1118 enterPDB_actionPerformed();
1121 discoverPDB.setText(MessageManager.getString("label.discover_pdb_ids"));
1122 discoverPDB.addActionListener(new ActionListener()
1124 public void actionPerformed(ActionEvent e)
1126 discoverPDB_actionPerformed();
1129 outputMenu.setText(MessageManager.getString("label.out_to_textbox") + "...");
1130 sequenceFeature.setText(MessageManager.getString("label.create_sequence_feature"));
1131 sequenceFeature.addActionListener(new ActionListener()
1133 public void actionPerformed(ActionEvent e)
1135 sequenceFeature_actionPerformed();
1138 textColour.setText(MessageManager.getString("label.text_colour"));
1139 textColour.addActionListener(new ActionListener()
1141 public void actionPerformed(ActionEvent e)
1143 textColour_actionPerformed();
1146 jMenu1.setText(MessageManager.getString("label.group"));
1147 structureMenu.setText(MessageManager.getString("label.structure"));
1148 viewStructureMenu.setText(MessageManager.getString("label.view_structure"));
1149 // colStructureMenu.setText("Colour By Structure");
1150 editSequence.setText(MessageManager.getString("label.edit_sequence") + "...");
1151 editSequence.addActionListener(new ActionListener()
1153 public void actionPerformed(ActionEvent actionEvent)
1155 editSequence_actionPerformed(actionEvent);
1160 * annotationMenuItem.setText("By Annotation");
1161 * annotationMenuItem.addActionListener(new ActionListener() { public void
1162 * actionPerformed(ActionEvent actionEvent) {
1163 * annotationMenuItem_actionPerformed(actionEvent); } });
1165 groupMenu.add(sequenceSelDetails);
1168 this.add(structureMenu);
1169 groupMenu.add(editMenu);
1170 groupMenu.add(outputMenu);
1171 groupMenu.add(sequenceFeature);
1172 groupMenu.add(createGroupMenuItem);
1173 groupMenu.add(unGroupMenuItem);
1174 groupMenu.add(jMenu1);
1175 sequenceMenu.add(sequenceName);
1176 sequenceMenu.add(sequenceDetails);
1177 colourMenu.add(textColour);
1178 colourMenu.add(noColourmenuItem);
1179 colourMenu.add(clustalColour);
1180 colourMenu.add(BLOSUM62Colour);
1181 colourMenu.add(PIDColour);
1182 colourMenu.add(zappoColour);
1183 colourMenu.add(taylorColour);
1184 colourMenu.add(hydrophobicityColour);
1185 colourMenu.add(helixColour);
1186 colourMenu.add(strandColour);
1187 colourMenu.add(turnColour);
1188 colourMenu.add(buriedColour);
1189 colourMenu.add(nucleotideMenuItem);
1190 if (ap.getAlignment().isNucleotide()) {
1191 // JBPNote - commented since the colourscheme isn't functional
1192 // colourMenu.add(RNAInteractionColour);
1193 colourMenu.add(purinePyrimidineColour);
1195 // colourMenu.add(covariationColour);
1196 colourMenu.add(userDefinedColour);
1198 if (jalview.gui.UserDefinedColours.getUserColourSchemes() != null)
1200 java.util.Enumeration userColours = jalview.gui.UserDefinedColours
1201 .getUserColourSchemes().keys();
1203 while (userColours.hasMoreElements())
1205 JMenuItem item = new JMenuItem(userColours.nextElement().toString());
1206 item.addActionListener(new ActionListener()
1208 public void actionPerformed(ActionEvent evt)
1210 userDefinedColour_actionPerformed(evt);
1213 colourMenu.add(item);
1217 colourMenu.addSeparator();
1218 colourMenu.add(abovePIDColour);
1219 colourMenu.add(conservationMenuItem);
1220 // colourMenu.add(annotationMenuItem);
1223 editMenu.add(editSequence);
1224 editMenu.add(upperCase);
1225 editMenu.add(lowerCase);
1226 editMenu.add(toggle);
1227 pdbMenu.add(pdbFromFile);
1228 // JBPNote: These shouldn't be added here - should appear in a generic 'apply web service to this sequence menu'
1229 // pdbMenu.add(RNAFold);
1230 // pdbMenu.add(ContraFold);
1231 pdbMenu.add(enterPDB);
1232 pdbMenu.add(discoverPDB);
1233 jMenu1.add(groupName);
1234 jMenu1.add(colourMenu);
1235 jMenu1.add(showBoxes);
1236 jMenu1.add(showText);
1237 jMenu1.add(showColourText);
1238 jMenu1.add(outline);
1239 jMenu1.add(displayNonconserved);
1240 structureMenu.add(pdbMenu);
1241 structureMenu.add(viewStructureMenu);
1242 // structureMenu.add(colStructureMenu);
1243 noColourmenuItem.setText(MessageManager.getString("label.none"));
1244 noColourmenuItem.addActionListener(new java.awt.event.ActionListener()
1246 public void actionPerformed(ActionEvent e)
1248 noColourmenuItem_actionPerformed();
1252 clustalColour.setText(MessageManager.getString("label.clustalx_colours"));
1253 clustalColour.addActionListener(new java.awt.event.ActionListener()
1255 public void actionPerformed(ActionEvent e)
1257 clustalColour_actionPerformed();
1260 zappoColour.setText(MessageManager.getString("label.zappo"));
1261 zappoColour.addActionListener(new java.awt.event.ActionListener()
1263 public void actionPerformed(ActionEvent e)
1265 zappoColour_actionPerformed();
1268 taylorColour.setText(MessageManager.getString("label.taylor"));
1269 taylorColour.addActionListener(new java.awt.event.ActionListener()
1271 public void actionPerformed(ActionEvent e)
1273 taylorColour_actionPerformed();
1276 hydrophobicityColour.setText(MessageManager.getString("label.hydrophobicity"));
1277 hydrophobicityColour
1278 .addActionListener(new java.awt.event.ActionListener()
1280 public void actionPerformed(ActionEvent e)
1282 hydrophobicityColour_actionPerformed();
1285 helixColour.setText(MessageManager.getString("label.helix_propensity"));
1286 helixColour.addActionListener(new java.awt.event.ActionListener()
1288 public void actionPerformed(ActionEvent e)
1290 helixColour_actionPerformed();
1293 strandColour.setText(MessageManager.getString("label.strand_propensity"));
1294 strandColour.addActionListener(new java.awt.event.ActionListener()
1296 public void actionPerformed(ActionEvent e)
1298 strandColour_actionPerformed();
1301 turnColour.setText(MessageManager.getString("label.turn_propensity"));
1302 turnColour.addActionListener(new java.awt.event.ActionListener()
1304 public void actionPerformed(ActionEvent e)
1306 turnColour_actionPerformed();
1309 buriedColour.setText(MessageManager.getString("label.buried_index"));
1310 buriedColour.addActionListener(new java.awt.event.ActionListener()
1312 public void actionPerformed(ActionEvent e)
1314 buriedColour_actionPerformed();
1317 abovePIDColour.setText(MessageManager.getString("label.above_identity_percentage"));
1318 abovePIDColour.addActionListener(new java.awt.event.ActionListener()
1320 public void actionPerformed(ActionEvent e)
1322 abovePIDColour_actionPerformed();
1325 userDefinedColour.setText(MessageManager.getString("action.user_defined"));
1326 userDefinedColour.addActionListener(new java.awt.event.ActionListener()
1328 public void actionPerformed(ActionEvent e)
1330 userDefinedColour_actionPerformed(e);
1333 PIDColour.setText(MessageManager.getString("label.percentage_identity"));
1334 PIDColour.addActionListener(new java.awt.event.ActionListener()
1336 public void actionPerformed(ActionEvent e)
1338 PIDColour_actionPerformed();
1341 BLOSUM62Colour.setText(MessageManager.getString("label.blosum62"));
1342 BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()
1344 public void actionPerformed(ActionEvent e)
1346 BLOSUM62Colour_actionPerformed();
1349 purinePyrimidineColour.setText(MessageManager.getString("label.purine_pyrimidine"));
1350 purinePyrimidineColour
1351 .addActionListener(new java.awt.event.ActionListener()
1353 public void actionPerformed(ActionEvent e)
1355 purinePyrimidineColour_actionPerformed();
1361 * covariationColour.addActionListener(new java.awt.event.ActionListener() {
1362 * public void actionPerformed(ActionEvent e) {
1363 * covariationColour_actionPerformed(); } });
1366 conservationMenuItem.setText(MessageManager.getString("label.conservation"));
1367 conservationMenuItem
1368 .addActionListener(new java.awt.event.ActionListener()
1370 public void actionPerformed(ActionEvent e)
1372 conservationMenuItem_actionPerformed();
1377 protected void sequenceSelectionDetails_actionPerformed()
1379 createSequenceDetailsReport(ap.av.getSequenceSelection());
1382 protected void sequenceDetails_actionPerformed()
1384 createSequenceDetailsReport(new SequenceI[]
1388 public void createSequenceDetailsReport(SequenceI[] sequences)
1390 CutAndPasteHtmlTransfer cap = new CutAndPasteHtmlTransfer();
1391 StringBuffer contents = new StringBuffer();
1392 for (SequenceI seq : sequences)
1394 contents.append("<p><h2>" + MessageManager.formatMessage("label.create_sequence_details_report_annotation_for", new String[]{seq.getDisplayId(true)})
1396 new SequenceAnnotationReport(null)
1397 .createSequenceAnnotationReport(
1403 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
1405 contents.append("</p>");
1407 cap.setText("<html>" + contents.toString() + "</html>");
1409 Desktop.instance.addInternalFrame(cap, MessageManager.formatMessage("label.sequece_details_for", (sequences.length == 1 ? new String[]{sequences[0].getDisplayId(true)}: new String[]{MessageManager.getString("label.selection")}))
1414 protected void showNonconserved_actionPerformed()
1416 getGroup().setShowNonconserved(displayNonconserved.isSelected());
1421 * call to refresh view after settings change
1425 ap.updateAnnotation();
1426 ap.paintAlignment(true);
1428 PaintRefresher.Refresh(this, ap.av.getSequenceSetId());
1437 protected void clustalColour_actionPerformed()
1439 SequenceGroup sg = getGroup();
1440 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
1450 protected void zappoColour_actionPerformed()
1452 getGroup().cs = new ZappoColourScheme();
1462 protected void taylorColour_actionPerformed()
1464 getGroup().cs = new TaylorColourScheme();
1474 protected void hydrophobicityColour_actionPerformed()
1476 getGroup().cs = new HydrophobicColourScheme();
1486 protected void helixColour_actionPerformed()
1488 getGroup().cs = new HelixColourScheme();
1498 protected void strandColour_actionPerformed()
1500 getGroup().cs = new StrandColourScheme();
1510 protected void turnColour_actionPerformed()
1512 getGroup().cs = new TurnColourScheme();
1522 protected void buriedColour_actionPerformed()
1524 getGroup().cs = new BuriedColourScheme();
1534 public void nucleotideMenuItem_actionPerformed()
1536 getGroup().cs = new NucleotideColourScheme();
1540 protected void purinePyrimidineColour_actionPerformed()
1542 getGroup().cs = new PurinePyrimidineColourScheme();
1548 * protected void covariationColour_actionPerformed() { getGroup().cs = new
1549 * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
1557 protected void abovePIDColour_actionPerformed()
1559 SequenceGroup sg = getGroup();
1565 if (abovePIDColour.isSelected())
1567 sg.cs.setConsensus(AAFrequency.calculate(
1568 sg.getSequences(ap.av.getHiddenRepSequences()),
1569 sg.getStartRes(), sg.getEndRes() + 1));
1571 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
1574 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
1576 SliderPanel.showPIDSlider();
1579 // remove PIDColouring
1581 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
1593 protected void userDefinedColour_actionPerformed(ActionEvent e)
1595 SequenceGroup sg = getGroup();
1597 if (e.getSource().equals(userDefinedColour))
1599 new UserDefinedColours(ap, sg);
1603 UserColourScheme udc = (UserColourScheme) UserDefinedColours
1604 .getUserColourSchemes().get(e.getActionCommand());
1617 protected void PIDColour_actionPerformed()
1619 SequenceGroup sg = getGroup();
1620 sg.cs = new PIDColourScheme();
1621 sg.cs.setConsensus(AAFrequency.calculate(
1622 sg.getSequences(ap.av.getHiddenRepSequences()),
1623 sg.getStartRes(), sg.getEndRes() + 1));
1633 protected void BLOSUM62Colour_actionPerformed()
1635 SequenceGroup sg = getGroup();
1637 sg.cs = new Blosum62ColourScheme();
1639 sg.cs.setConsensus(AAFrequency.calculate(
1640 sg.getSequences(ap.av.getHiddenRepSequences()),
1641 sg.getStartRes(), sg.getEndRes() + 1));
1652 protected void noColourmenuItem_actionPerformed()
1654 getGroup().cs = null;
1664 protected void conservationMenuItem_actionPerformed()
1666 SequenceGroup sg = getGroup();
1672 if (conservationMenuItem.isSelected())
1674 // JBPNote: Conservation name shouldn't be i18n translated
1675 Conservation c = new Conservation("Group",
1676 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1677 .getHiddenRepSequences()), sg.getStartRes(),
1678 sg.getEndRes() + 1);
1681 c.verdict(false, ap.av.getConsPercGaps());
1683 sg.cs.setConservation(c);
1685 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1686 SliderPanel.showConservationSlider();
1689 // remove ConservationColouring
1691 sg.cs.setConservation(null);
1697 public void annotationMenuItem_actionPerformed(ActionEvent actionEvent)
1699 SequenceGroup sg = getGroup();
1705 AnnotationColourGradient acg = new AnnotationColourGradient(
1706 sequence.getAnnotation()[0], null,
1707 AnnotationColourGradient.NO_THRESHOLD);
1709 acg.setPredefinedColours(true);
1721 protected void groupName_actionPerformed()
1724 SequenceGroup sg = getGroup();
1725 EditNameDialog dialog = new EditNameDialog(sg.getName(),
1726 sg.getDescription(), " " + MessageManager.getString("label.group_name") + " ",
1727 MessageManager.getString("label.group_description") + " ", MessageManager.getString("label.edit_group_name_description"),
1735 sg.setName(dialog.getName());
1736 sg.setDescription(dialog.getDescription());
1741 * Get selection group - adding it to the alignment if necessary.
1743 * @return sequence group to operate on
1745 SequenceGroup getGroup()
1747 SequenceGroup sg = ap.av.getSelectionGroup();
1748 // this method won't add a new group if it already exists
1751 ap.av.getAlignment().addGroup(sg);
1763 void sequenceName_actionPerformed()
1765 EditNameDialog dialog = new EditNameDialog(sequence.getName(),
1766 sequence.getDescription(), " " + MessageManager.getString("label.sequence_name") + " ",
1767 MessageManager.getString("label.sequence_description") + " ", MessageManager.getString("label.edit_sequence_name_description"),
1775 if (dialog.getName() != null)
1777 if (dialog.getName().indexOf(" ") > -1)
1779 JOptionPane.showMessageDialog(ap,
1780 MessageManager.getString("label.spaces_converted_to_backslashes"),
1781 MessageManager.getString("label.no_spaces_allowed_sequence_name"),
1782 JOptionPane.WARNING_MESSAGE);
1785 sequence.setName(dialog.getName().replace(' ', '_'));
1786 ap.paintAlignment(false);
1789 sequence.setDescription(dialog.getDescription());
1791 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1802 void unGroupMenuItem_actionPerformed()
1804 SequenceGroup sg = ap.av.getSelectionGroup();
1805 ap.av.getAlignment().deleteGroup(sg);
1806 ap.av.setSelectionGroup(null);
1809 void createGroupMenuItem_actionPerformed()
1811 getGroup(); // implicitly creates group - note - should apply defaults / use standard alignment window logic for this
1821 protected void outline_actionPerformed()
1823 SequenceGroup sg = getGroup();
1824 Color col = JColorChooser.showDialog(this, MessageManager.getString("label.select_outline_colour"),
1829 sg.setOutlineColour(col);
1841 public void showBoxes_actionPerformed()
1843 getGroup().setDisplayBoxes(showBoxes.isSelected());
1853 public void showText_actionPerformed()
1855 getGroup().setDisplayText(showText.isSelected());
1865 public void showColourText_actionPerformed()
1867 getGroup().setColourText(showColourText.isSelected());
1871 public void showLink(String url)
1875 jalview.util.BrowserLauncher.openURL(url);
1876 } catch (Exception ex)
1879 .showInternalMessageDialog(
1881 MessageManager.getString("label.web_browser_not_found_unix"),
1882 MessageManager.getString("label.web_browser_not_found"), JOptionPane.WARNING_MESSAGE);
1884 ex.printStackTrace();
1888 void hideSequences(boolean representGroup)
1890 SequenceGroup sg = ap.av.getSelectionGroup();
1891 if (sg == null || sg.getSize() < 1)
1893 ap.av.hideSequence(new SequenceI[]
1898 ap.av.setSelectionGroup(null);
1902 ap.av.hideRepSequences(sequence, sg);
1907 int gsize = sg.getSize();
1910 hseqs = new SequenceI[gsize];
1913 for (int i = 0; i < gsize; i++)
1915 hseqs[index++] = sg.getSequenceAt(i);
1918 ap.av.hideSequence(hseqs);
1919 // refresh(); TODO: ? needed ?
1920 ap.av.sendSelection();
1923 public void copy_actionPerformed()
1925 ap.alignFrame.copy_actionPerformed(null);
1928 public void cut_actionPerformed()
1930 ap.alignFrame.cut_actionPerformed(null);
1933 void changeCase(ActionEvent e)
1935 Object source = e.getSource();
1936 SequenceGroup sg = ap.av.getSelectionGroup();
1940 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
1941 sg.getEndRes() + 1);
1946 if (source == toggle)
1948 description = MessageManager.getString("label.toggle_case");
1949 caseChange = ChangeCaseCommand.TOGGLE_CASE;
1951 else if (source == upperCase)
1953 description = MessageManager.getString("label.to_upper_case");
1954 caseChange = ChangeCaseCommand.TO_UPPER;
1958 description = MessageManager.getString("label.to_lower_case");
1959 caseChange = ChangeCaseCommand.TO_LOWER;
1962 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
1963 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
1964 startEnd, caseChange);
1966 ap.alignFrame.addHistoryItem(caseCommand);
1968 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
1974 public void outputText_actionPerformed(ActionEvent e)
1976 CutAndPasteTransfer cap = new CutAndPasteTransfer();
1977 cap.setForInput(null);
1978 Desktop.addInternalFrame(cap,
1979 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}), 600, 500);
1981 String[] omitHidden = null;
1983 System.out.println("PROMPT USER HERE"); // TODO: decide if a prompt happens
1984 // or we simply trust the user wants
1985 // wysiwig behaviour
1986 SequenceGroup sg = ap.av.getSelectionGroup();
1987 ColumnSelection csel = new ColumnSelection(ap.av.getColumnSelection());
1988 omitHidden = ap.av.getViewAsString(true);
1989 Alignment oal = new Alignment(ap.av.getSequenceSelection());
1990 AlignmentAnnotation[] nala = ap.av.getAlignment()
1991 .getAlignmentAnnotation();
1994 for (int i = 0; i < nala.length; i++)
1996 AlignmentAnnotation na = nala[i];
1997 oal.addAnnotation(na);
2000 cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
2001 oal, omitHidden, csel, sg));
2005 public void pdbFromFile_actionPerformed()
2007 jalview.io.JalviewFileChooser chooser = new jalview.io.JalviewFileChooser(
2008 jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
2009 chooser.setFileView(new jalview.io.JalviewFileView());
2010 chooser.setDialogTitle(MessageManager.formatMessage("label.select_pdb_file_for", new String[]{sequence.getDisplayId(false)}));
2011 chooser.setToolTipText(MessageManager.formatMessage("label.load_pdb_file_associate_with_sequence", new String[]{new Integer(sequence.getDisplayId(false)).toString()}));
2013 int value = chooser.showOpenDialog(null);
2015 if (value == jalview.io.JalviewFileChooser.APPROVE_OPTION)
2017 String choice = chooser.getSelectedFile().getPath();
2018 jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);
2019 new AssociatePdbFileWithSeq().associatePdbWithSeq(choice,
2020 jalview.io.AppletFormatAdapter.FILE, sequence, true);
2024 // JBNote: commented out - these won't be instantiated here...!
2025 // public void RNAFold_actionPerformed() throws Exception
2027 // Predict2D P2D = new Predict2D();
2028 // P2D.getStructure2DFromRNAFold("toto");
2031 // public void ContraFold_actionPerformed() throws Exception
2033 // Predict2D P2D = new Predict2D();
2034 // P2D.getStructure2DFromContraFold("toto");
2036 public void enterPDB_actionPerformed()
2038 String id = JOptionPane.showInternalInputDialog(Desktop.desktop,
2039 MessageManager.getString("label.enter_pdb_id"), MessageManager.getString("label.enter_pdb_id"), JOptionPane.QUESTION_MESSAGE);
2041 if (id != null && id.length() > 0)
2043 PDBEntry entry = new PDBEntry();
2044 entry.setId(id.toUpperCase());
2045 sequence.getDatasetSequence().addPDBId(entry);
2049 public void discoverPDB_actionPerformed()
2052 final SequenceI[] sequences = ((ap.av.getSelectionGroup() == null) ? new SequenceI[]
2054 : ap.av.getSequenceSelection());
2055 Thread discpdb = new Thread(new Runnable()
2060 new jalview.ws.DBRefFetcher(sequences, ap.alignFrame)
2061 .fetchDBRefs(false);
2068 public void sequenceFeature_actionPerformed()
2070 SequenceGroup sg = ap.av.getSelectionGroup();
2076 int rsize = 0, gSize = sg.getSize();
2077 SequenceI[] rseqs, seqs = new SequenceI[gSize];
2078 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
2080 for (int i = 0; i < gSize; i++)
2082 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
2083 int end = sg.findEndRes(sg.getSequenceAt(i));
2086 seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence();
2087 features[rsize] = new SequenceFeature(null, null, null, start, end,
2092 rseqs = new SequenceI[rsize];
2093 tfeatures = new SequenceFeature[rsize];
2094 System.arraycopy(seqs, 0, rseqs, 0, rsize);
2095 System.arraycopy(features, 0, tfeatures, 0, rsize);
2096 features = tfeatures;
2098 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
2099 features, true, ap))
2101 ap.alignFrame.setShowSeqFeatures(true);
2102 ap.highlightSearchResults(null);
2106 public void textColour_actionPerformed()
2108 SequenceGroup sg = getGroup();
2111 new TextColourChooser().chooseColour(ap, sg);
2115 public void colourByStructure(String pdbid)
2117 Annotation[] anots = ap.av.getStructureSelectionManager()
2118 .colourSequenceFromStructure(sequence, pdbid);
2120 AlignmentAnnotation an = new AlignmentAnnotation("Structure",
2121 "Coloured by " + pdbid, anots);
2123 ap.av.getAlignment().addAnnotation(an);
2124 an.createSequenceMapping(sequence, 0, true);
2125 // an.adjustForAlignment();
2126 ap.av.getAlignment().setAnnotationIndex(an, 0);
2128 ap.adjustAnnotationHeight();
2130 sequence.addAlignmentAnnotation(an);
2134 public void editSequence_actionPerformed(ActionEvent actionEvent)
2136 SequenceGroup sg = ap.av.getSelectionGroup();
2140 if (sequence == null)
2141 sequence = (Sequence) sg.getSequenceAt(0);
2143 EditNameDialog dialog = new EditNameDialog(
2144 sequence.getSequenceAsString(sg.getStartRes(),
2145 sg.getEndRes() + 1), null, MessageManager.getString("label.edit_sequence"), null,
2146 MessageManager.getString("label.edit_sequence"), ap.alignFrame);
2150 EditCommand editCommand = new EditCommand(MessageManager.getString("label.edit_sequences"),
2151 EditCommand.REPLACE, dialog.getName().replace(' ',
2152 ap.av.getGapCharacter()),
2153 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
2154 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
2156 ap.alignFrame.addHistoryItem(editCommand);
2158 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()