2 * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
3 * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.commands.*;
28 import jalview.datamodel.*;
29 import jalview.schemes.*;
30 import jalview.util.UrlLink;
31 import jalview.io.AppletFormatAdapter;
33 public class APopupMenu extends java.awt.PopupMenu implements
34 ActionListener, ItemListener
36 Menu groupMenu = new Menu();
38 MenuItem editGroupName = new MenuItem();
40 protected MenuItem clustalColour = new MenuItem();
42 protected MenuItem zappoColour = new MenuItem();
44 protected MenuItem taylorColour = new MenuItem();
46 protected MenuItem hydrophobicityColour = new MenuItem();
48 protected MenuItem helixColour = new MenuItem();
50 protected MenuItem strandColour = new MenuItem();
52 protected MenuItem turnColour = new MenuItem();
54 protected MenuItem buriedColour = new MenuItem();
56 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
58 protected MenuItem userDefinedColour = new MenuItem();
60 protected MenuItem PIDColour = new MenuItem();
62 protected MenuItem BLOSUM62Colour = new MenuItem();
64 MenuItem noColourmenuItem = new MenuItem();
66 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
68 final AlignmentPanel ap;
70 MenuItem unGroupMenuItem = new MenuItem();
72 MenuItem nucleotideMenuItem = new MenuItem();
74 Menu colourMenu = new Menu();
76 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
78 CheckboxMenuItem showText = new CheckboxMenuItem();
80 CheckboxMenuItem showColourText = new CheckboxMenuItem();
82 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
84 Menu editMenu = new Menu("Edit");
86 MenuItem copy = new MenuItem("Copy (Jalview Only)");
88 MenuItem cut = new MenuItem("Cut (Jalview Only)");
90 MenuItem toUpper = new MenuItem("To Upper Case");
92 MenuItem toLower = new MenuItem("To Lower Case");
94 MenuItem toggleCase = new MenuItem("Toggle Case");
96 Menu outputmenu = new Menu();
98 Menu seqMenu = new Menu();
100 MenuItem pdb = new MenuItem();
102 MenuItem hideSeqs = new MenuItem();
104 MenuItem repGroup = new MenuItem();
106 MenuItem sequenceName = new MenuItem("Edit Name/Description");
108 MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
110 MenuItem editSequence = new MenuItem("Edit Sequence");
114 MenuItem revealAll = new MenuItem();
116 Menu menu1 = new Menu();
118 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
120 // /////////////////////////////////////////////////////////
121 // If this is activated from the sequence panel, the user may want to
122 // edit or annotate a particular residue. Therefore display the residue menu
124 // If from the IDPanel, we must display the sequence menu
125 // ////////////////////////////////////////////////////////
133 } catch (Exception e)
138 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
140 MenuItem item = new MenuItem(
141 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
143 item.addActionListener(this);
144 outputmenu.add(item);
147 SequenceGroup sg = ap.av.getSelectionGroup();
149 if (sg != null && sg.getSize() > 0)
151 editGroupName.setLabel(sg.getName());
152 showText.setState(sg.getDisplayText());
153 showColourText.setState(sg.getColourText());
154 showBoxes.setState(sg.getDisplayBoxes());
155 displayNonconserved.setState(sg.getShowunconserved());
156 if (!ap.av.alignment.getGroups().contains(sg))
158 groupMenu.remove(unGroupMenuItem);
168 if (links != null && links.size() > 0)
170 Menu linkMenu = new Menu("Link");
172 for (int i = 0; i < links.size(); i++)
174 link = links.elementAt(i).toString();
175 UrlLink urlLink = new UrlLink(link);
176 if (!urlLink.isValid())
178 System.err.println(urlLink.getInvalidMessage());
181 final String target = urlLink.getTarget(); // link.substring(0,
182 // link.indexOf("|"));
183 final String label = urlLink.getLabel();
184 if (urlLink.isDynamic())
187 // collect matching db-refs
188 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(seq
189 .getDBRef(), new String[]
191 // collect id string too
192 String id = seq.getName();
193 String descr = seq.getDescription();
194 if (descr != null && descr.length() < 1)
200 for (int r = 0; r < dbr.length; r++)
202 if (id != null && dbr[r].getAccessionId().equals(id))
204 // suppress duplicate link creation for the bare sequence ID
205 // string with this link
208 // create Bare ID link for this RUL
209 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
213 for (int u = 0; u < urls.length; u += 2)
215 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
222 // create Bare ID link for this RUL
223 String[] urls = urlLink.makeUrls(id, true);
226 for (int u = 0; u < urls.length; u += 2)
228 addshowLink(linkMenu, label, urls[u + 1]);
231 // addshowLink(linkMenu, target, url_pref + id + url_suff);
233 // Now construct URLs from description but only try to do it for regex
235 if (descr != null && urlLink.getRegexReplace() != null)
237 // create link for this URL from description only if regex matches
238 String[] urls = urlLink.makeUrls(descr, true);
241 for (int u = 0; u < urls.length; u += 2)
243 addshowLink(linkMenu, label, urls[u + 1]);
250 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
255 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
256 * string and any matching database reference accessions String url_pref
257 * = link.substring(link.indexOf("|") + 1,
258 * link.indexOf("$SEQUENCE_ID$"));
260 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
261 * // collect matching db-refs DBRefEntry[] dbr =
262 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
263 * String[]{target}); // collect id string too String id =
264 * seq.getName(); if (id.indexOf("|") > -1) { id =
265 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
266 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
267 * suppress duplicate link creation for the bare sequence ID string with
268 * this link id = null; } addshowLink(linkMenu,
269 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
270 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
271 * create Bare ID link for this RUL addshowLink(linkMenu, target,
272 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
273 * link.substring(link.lastIndexOf("|")+1)); }
276 if (linkMenu.getItemCount() > 0)
280 seqMenu.add(linkMenu);
290 seqMenu.setLabel(seq.getName());
291 repGroup.setLabel("Represent Group with " + seq.getName());
298 if (!ap.av.hasHiddenRows)
305 * add a show URL menu item to the given linkMenu
309 * - menu label string
313 private void addshowLink(Menu linkMenu, final String target,
316 addshowLink(linkMenu, target, target, url);
320 * add a show URL menu item to the given linkMenu
324 * - URL target window
326 * - menu label string
330 private void addshowLink(Menu linkMenu, final String target,
331 final String label, final String url)
333 MenuItem item = new MenuItem(label);
334 item.addActionListener(new java.awt.event.ActionListener()
336 public void actionPerformed(ActionEvent e)
338 ap.alignFrame.showURL(url, target);
344 public void itemStateChanged(ItemEvent evt)
346 if (evt.getSource() == abovePIDColour)
348 abovePIDColour_itemStateChanged();
350 else if (evt.getSource() == showColourText)
352 showColourText_itemStateChanged();
354 else if (evt.getSource() == showText)
356 showText_itemStateChanged();
358 else if (evt.getSource() == showBoxes)
360 showBoxes_itemStateChanged();
362 else if (evt.getSource() == displayNonconserved)
364 this.showNonconserved_itemStateChanged();
368 public void actionPerformed(ActionEvent evt)
370 Object source = evt.getSource();
371 if (source == clustalColour)
373 clustalColour_actionPerformed();
375 else if (source == zappoColour)
377 zappoColour_actionPerformed();
379 else if (source == taylorColour)
381 taylorColour_actionPerformed();
383 else if (source == hydrophobicityColour)
385 hydrophobicityColour_actionPerformed();
387 else if (source == helixColour)
389 helixColour_actionPerformed();
391 else if (source == strandColour)
393 strandColour_actionPerformed();
395 else if (source == turnColour)
397 turnColour_actionPerformed();
399 else if (source == buriedColour)
401 buriedColour_actionPerformed();
403 else if (source == nucleotideMenuItem)
405 nucleotideMenuItem_actionPerformed();
408 else if (source == userDefinedColour)
410 userDefinedColour_actionPerformed();
412 else if (source == PIDColour)
414 PIDColour_actionPerformed();
416 else if (source == BLOSUM62Colour)
418 BLOSUM62Colour_actionPerformed();
420 else if (source == noColourmenuItem)
422 noColourmenuItem_actionPerformed();
424 else if (source == conservationMenuItem)
426 conservationMenuItem_itemStateChanged();
428 else if (source == unGroupMenuItem)
430 unGroupMenuItem_actionPerformed();
433 else if (source == sequenceName)
437 else if (source == pdb)
441 else if (source == hideSeqs)
443 hideSequences(false);
445 else if (source == repGroup)
449 else if (source == revealAll)
451 ap.av.showAllHiddenSeqs();
454 else if (source == editGroupName)
456 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
457 getGroup().getDescription(), " Group Name",
458 "Group Description", ap.alignFrame,
459 "Edit Group Name / Description", 500, 100, true);
463 getGroup().setName(dialog.getName().replace(' ', '_'));
464 getGroup().setDescription(dialog.getDescription());
468 else if (source == copy)
470 ap.alignFrame.copy_actionPerformed();
472 else if (source == cut)
474 ap.alignFrame.cut_actionPerformed();
476 else if (source == editSequence)
478 SequenceGroup sg = ap.av.getSelectionGroup();
483 seq = (Sequence) sg.getSequenceAt(0);
485 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
486 sg.getStartRes(), sg.getEndRes() + 1), null,
487 "Edit Sequence ", null,
489 ap.alignFrame, "Edit Sequence", 500, 100, true);
493 EditCommand editCommand = new EditCommand("Edit Sequences",
494 EditCommand.REPLACE, dialog.getName().replace(' ',
495 ap.av.getGapCharacter()), sg
496 .getSequencesAsArray(ap.av.hiddenRepSequences),
497 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
499 ap.alignFrame.addHistoryItem(editCommand);
501 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
506 else if (source == toUpper || source == toLower || source == toggleCase)
508 SequenceGroup sg = ap.av.getSelectionGroup();
509 Vector regions = new Vector();
512 int start = sg.getStartRes();
513 int end = sg.getEndRes() + 1;
517 if (ap.av.hasHiddenColumns)
521 start = ap.av.colSel.adjustForHiddenColumns(start);
524 end = ap.av.colSel.getHiddenBoundaryRight(start);
527 end = sg.getEndRes() + 1;
529 if (end > sg.getEndRes())
531 end = sg.getEndRes() + 1;
535 regions.addElement(new int[]
538 if (ap.av.hasHiddenColumns)
540 start = ap.av.colSel.adjustForHiddenColumns(end);
541 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
543 } while (end < sg.getEndRes());
545 int[][] startEnd = new int[regions.size()][2];
546 for (int i = 0; i < regions.size(); i++)
548 startEnd[i] = (int[]) regions.elementAt(i);
554 if (source == toggleCase)
556 description = "Toggle Case";
557 caseChange = ChangeCaseCommand.TOGGLE_CASE;
559 else if (source == toUpper)
561 description = "To Upper Case";
562 caseChange = ChangeCaseCommand.TO_UPPER;
566 description = "To Lower Case";
567 caseChange = ChangeCaseCommand.TO_LOWER;
570 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
571 sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
574 ap.alignFrame.addHistoryItem(caseCommand);
576 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
581 else if (source == sequenceFeature)
583 SequenceGroup sg = ap.av.getSelectionGroup();
589 int gSize = sg.getSize();
590 SequenceI[] seqs = new SequenceI[gSize];
591 SequenceFeature[] features = new SequenceFeature[gSize];
593 for (int i = 0; i < gSize; i++)
595 seqs[i] = sg.getSequenceAt(i);
596 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
597 int end = sg.findEndRes(sg.getSequenceAt(i));
598 features[i] = new SequenceFeature(null, null, null, start, end,
602 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
605 ap.alignFrame.sequenceFeatures.setState(true);
606 ap.av.showSequenceFeatures(true);
607 ap.highlightSearchResults(null);
617 void outputText(ActionEvent e)
619 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
621 Frame frame = new Frame();
623 jalview.bin.JalviewLite.addFrame(frame, "Selection output - "
624 + e.getActionCommand(), 600, 500);
626 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(e
627 .getActionCommand(), new Alignment(ap.av
628 .getSelectionAsNewSequence()), ap.av.showJVSuffix));
634 EditNameDialog dialog = new EditNameDialog(seq.getName(), seq
635 .getDescription(), " Sequence Name",
636 "Sequence Description", ap.alignFrame,
637 "Edit Sequence Name / Description", 500, 100, true);
641 seq.setName(dialog.getName());
642 seq.setDescription(dialog.getDescription());
643 ap.paintAlignment(false);
649 if (seq.getPDBId() != null)
651 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
653 if (ap.av.applet.jmolAvailable)
654 new jalview.appletgui.AppletJmol(entry, new Sequence[]
655 { seq }, null, ap, AppletFormatAdapter.URL);
657 new MCview.AppletPDBViewer(entry, new Sequence[]
658 { seq }, null, ap, AppletFormatAdapter.URL);
663 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
664 cap.setText("Paste your PDB file here.");
665 cap.setPDBImport(seq);
666 Frame frame = new Frame();
668 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
672 private void jbInit() throws Exception
674 groupMenu.setLabel("Group");
675 groupMenu.setLabel("Selection");
676 sequenceFeature.addActionListener(this);
678 editGroupName.addActionListener(this);
679 unGroupMenuItem.setLabel("Remove Group");
680 unGroupMenuItem.addActionListener(this);
682 nucleotideMenuItem.setLabel("Nucleotide");
683 nucleotideMenuItem.addActionListener(this);
684 conservationMenuItem.addItemListener(this);
685 abovePIDColour.addItemListener(this);
686 colourMenu.setLabel("Group Colour");
687 showBoxes.setLabel("Boxes");
688 showBoxes.setState(true);
689 showBoxes.addItemListener(this);
690 sequenceName.addActionListener(this);
691 displayNonconserved.setLabel("Show Nonconserved");
692 displayNonconserved.setState(false);
693 displayNonconserved.addItemListener(this);
694 showText.setLabel("Text");
695 showText.addItemListener(this);
696 showColourText.setLabel("Colour Text");
697 showColourText.addItemListener(this);
698 outputmenu.setLabel("Output to Textbox...");
699 seqMenu.setLabel("Sequence");
700 pdb.setLabel("View PDB Structure");
701 hideSeqs.setLabel("Hide Sequences");
702 repGroup.setLabel("Represent Group with");
703 revealAll.setLabel("Reveal All");
704 menu1.setLabel("Group");
709 groupMenu.add(editGroupName);
710 groupMenu.add(editMenu);
711 groupMenu.add(outputmenu);
712 groupMenu.add(sequenceFeature);
713 groupMenu.add(menu1);
715 colourMenu.add(noColourmenuItem);
716 colourMenu.add(clustalColour);
717 colourMenu.add(BLOSUM62Colour);
718 colourMenu.add(PIDColour);
719 colourMenu.add(zappoColour);
720 colourMenu.add(taylorColour);
721 colourMenu.add(hydrophobicityColour);
722 colourMenu.add(helixColour);
723 colourMenu.add(strandColour);
724 colourMenu.add(turnColour);
725 colourMenu.add(buriedColour);
726 colourMenu.add(nucleotideMenuItem);
727 colourMenu.add(userDefinedColour);
728 colourMenu.addSeparator();
729 colourMenu.add(abovePIDColour);
730 colourMenu.add(conservationMenuItem);
732 noColourmenuItem.setLabel("None");
733 noColourmenuItem.addActionListener(this);
735 clustalColour.setLabel("Clustalx colours");
736 clustalColour.addActionListener(this);
737 zappoColour.setLabel("Zappo");
738 zappoColour.addActionListener(this);
739 taylorColour.setLabel("Taylor");
740 taylorColour.addActionListener(this);
741 hydrophobicityColour.setLabel("Hydrophobicity");
742 hydrophobicityColour.addActionListener(this);
743 helixColour.setLabel("Helix propensity");
744 helixColour.addActionListener(this);
745 strandColour.setLabel("Strand propensity");
746 strandColour.addActionListener(this);
747 turnColour.setLabel("Turn propensity");
748 turnColour.addActionListener(this);
749 buriedColour.setLabel("Buried Index");
750 buriedColour.addActionListener(this);
751 abovePIDColour.setLabel("Above % Identity");
753 userDefinedColour.setLabel("User Defined");
754 userDefinedColour.addActionListener(this);
755 PIDColour.setLabel("Percentage Identity");
756 PIDColour.addActionListener(this);
757 BLOSUM62Colour.setLabel("BLOSUM62");
758 BLOSUM62Colour.addActionListener(this);
759 conservationMenuItem.setLabel("Conservation");
762 copy.addActionListener(this);
764 cut.addActionListener(this);
766 editMenu.add(editSequence);
767 editSequence.addActionListener(this);
769 editMenu.add(toUpper);
770 toUpper.addActionListener(this);
771 editMenu.add(toLower);
772 toLower.addActionListener(this);
773 editMenu.add(toggleCase);
774 seqMenu.add(sequenceName);
776 seqMenu.add(repGroup);
777 menu1.add(unGroupMenuItem);
778 menu1.add(colourMenu);
779 menu1.add(showBoxes);
781 menu1.add(showColourText);
782 menu1.add(displayNonconserved);
783 toggleCase.addActionListener(this);
784 pdb.addActionListener(this);
785 hideSeqs.addActionListener(this);
786 repGroup.addActionListener(this);
787 revealAll.addActionListener(this);
792 ap.paintAlignment(true);
795 protected void clustalColour_actionPerformed()
797 SequenceGroup sg = getGroup();
798 sg.cs = new ClustalxColourScheme(sg
799 .getSequences(ap.av.hiddenRepSequences), ap.av.alignment
804 protected void zappoColour_actionPerformed()
806 getGroup().cs = new ZappoColourScheme();
810 protected void taylorColour_actionPerformed()
812 getGroup().cs = new TaylorColourScheme();
816 protected void hydrophobicityColour_actionPerformed()
818 getGroup().cs = new HydrophobicColourScheme();
822 protected void helixColour_actionPerformed()
824 getGroup().cs = new HelixColourScheme();
828 protected void strandColour_actionPerformed()
830 getGroup().cs = new StrandColourScheme();
834 protected void turnColour_actionPerformed()
836 getGroup().cs = new TurnColourScheme();
840 protected void buriedColour_actionPerformed()
842 getGroup().cs = new BuriedColourScheme();
846 public void nucleotideMenuItem_actionPerformed()
848 getGroup().cs = new NucleotideColourScheme();
852 protected void abovePIDColour_itemStateChanged()
854 SequenceGroup sg = getGroup();
860 if (abovePIDColour.getState())
862 sg.cs.setConsensus(AAFrequency.calculate(sg
863 .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
865 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
868 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
870 SliderPanel.showPIDSlider();
874 // remove PIDColouring
876 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
883 protected void userDefinedColour_actionPerformed()
885 new UserDefinedColours(ap, getGroup());
888 protected void PIDColour_actionPerformed()
890 SequenceGroup sg = getGroup();
891 sg.cs = new PIDColourScheme();
892 sg.cs.setConsensus(AAFrequency.calculate(sg
893 .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
898 protected void BLOSUM62Colour_actionPerformed()
900 SequenceGroup sg = getGroup();
902 sg.cs = new Blosum62ColourScheme();
904 sg.cs.setConsensus(AAFrequency.calculate(sg
905 .getSequences(ap.av.hiddenRepSequences), 0, ap.av.alignment
911 protected void noColourmenuItem_actionPerformed()
913 getGroup().cs = null;
917 protected void conservationMenuItem_itemStateChanged()
919 SequenceGroup sg = getGroup();
925 if (conservationMenuItem.getState())
928 Conservation c = new Conservation("Group",
929 ResidueProperties.propHash, 3, sg
930 .getSequences(ap.av.hiddenRepSequences), 0,
931 ap.av.alignment.getWidth());
934 c.verdict(false, ap.av.ConsPercGaps);
936 sg.cs.setConservation(c);
938 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
939 SliderPanel.showConservationSlider();
942 // remove ConservationColouring
944 sg.cs.setConservation(null);
950 SequenceGroup getGroup()
952 SequenceGroup sg = ap.av.getSelectionGroup();
954 // this method won't add a new group if it already exists
957 ap.av.alignment.addGroup(sg);
963 void unGroupMenuItem_actionPerformed()
965 SequenceGroup sg = ap.av.getSelectionGroup();
966 ap.av.alignment.deleteGroup(sg);
967 ap.av.setSelectionGroup(null);
968 ap.paintAlignment(true);
971 public void showColourText_itemStateChanged()
973 getGroup().setColourText(showColourText.getState());
977 public void showText_itemStateChanged()
979 getGroup().setDisplayText(showText.getState());
983 public void showNonconserved_itemStateChanged()
985 getGroup().setShowunconserved(this.displayNonconserved.getState());
989 public void showBoxes_itemStateChanged()
991 getGroup().setDisplayBoxes(showBoxes.getState());
995 void hideSequences(boolean representGroup)
997 SequenceGroup sg = ap.av.getSelectionGroup();
998 if (sg == null || sg.getSize() < 1)
1000 ap.av.hideSequence(new SequenceI[]
1005 ap.av.setSelectionGroup(null);
1009 ap.av.hideRepSequences(seq, sg);
1014 int gsize = sg.getSize();
1017 hseqs = new SequenceI[gsize];
1020 for (int i = 0; i < gsize; i++)
1022 hseqs[index++] = sg.getSequenceAt(i);
1025 ap.av.hideSequence(hseqs);