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/>.
18 package jalview.appletgui;
23 import java.awt.event.*;
25 import javax.swing.JRadioButtonMenuItem;
27 import jalview.analysis.*;
28 import jalview.commands.*;
29 import jalview.datamodel.*;
30 import jalview.schemes.*;
31 import jalview.util.UrlLink;
32 import jalview.io.AppletFormatAdapter;
34 public class APopupMenu extends java.awt.PopupMenu implements
35 ActionListener, ItemListener
37 Menu groupMenu = new Menu();
39 MenuItem editGroupName = new MenuItem();
41 protected MenuItem clustalColour = new MenuItem();
43 protected MenuItem zappoColour = new MenuItem();
45 protected MenuItem taylorColour = new MenuItem();
47 protected MenuItem hydrophobicityColour = new MenuItem();
49 protected MenuItem helixColour = new MenuItem();
51 protected MenuItem strandColour = new MenuItem();
53 protected MenuItem turnColour = new MenuItem();
55 protected MenuItem buriedColour = new MenuItem();
57 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
59 protected MenuItem userDefinedColour = new MenuItem();
61 protected MenuItem PIDColour = new MenuItem();
63 protected MenuItem BLOSUM62Colour = new MenuItem();
65 MenuItem noColourmenuItem = new MenuItem();
67 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
69 final AlignmentPanel ap;
71 MenuItem unGroupMenuItem = new MenuItem();
73 MenuItem nucleotideMenuItem = new MenuItem();
75 Menu colourMenu = new Menu();
77 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
79 CheckboxMenuItem showText = new CheckboxMenuItem();
81 CheckboxMenuItem showColourText = new CheckboxMenuItem();
83 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
85 Menu editMenu = new Menu("Edit");
87 MenuItem copy = new MenuItem("Copy (Jalview Only)");
89 MenuItem cut = new MenuItem("Cut (Jalview Only)");
91 MenuItem toUpper = new MenuItem("To Upper Case");
93 MenuItem toLower = new MenuItem("To Lower Case");
95 MenuItem toggleCase = new MenuItem("Toggle Case");
97 Menu outputmenu = new Menu();
99 Menu seqMenu = new Menu();
101 MenuItem pdb = new MenuItem();
103 MenuItem hideSeqs = new MenuItem();
105 MenuItem repGroup = new MenuItem();
107 MenuItem sequenceName = new MenuItem("Edit Name/Description");
109 MenuItem sequenceFeature = new MenuItem("Create Sequence Feature");
111 MenuItem editSequence = new MenuItem("Edit Sequence");
115 MenuItem revealAll = new MenuItem();
117 MenuItem revealSeq = new MenuItem();
119 * index of sequence to be revealed
121 int revealSeq_index=-1;
122 Menu menu1 = new Menu();
124 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
126 // /////////////////////////////////////////////////////////
127 // If this is activated from the sequence panel, the user may want to
128 // edit or annotate a particular residue. Therefore display the residue menu
130 // If from the IDPanel, we must display the sequence menu
131 // ////////////////////////////////////////////////////////
139 } catch (Exception e)
144 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
146 MenuItem item = new MenuItem(
147 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
149 item.addActionListener(this);
150 outputmenu.add(item);
153 SequenceGroup sg = ap.av.getSelectionGroup();
155 if (sg != null && sg.getSize() > 0)
157 editGroupName.setLabel("Name: "+sg.getName());
158 showText.setState(sg.getDisplayText());
159 showColourText.setState(sg.getColourText());
160 showBoxes.setState(sg.getDisplayBoxes());
161 displayNonconserved.setState(sg.getShowNonconserved());
162 if (!ap.av.alignment.getGroups().contains(sg))
164 groupMenu.remove(unGroupMenuItem);
174 if (links != null && links.size() > 0)
176 Menu linkMenu = new Menu("Link");
178 for (int i = 0; i < links.size(); i++)
180 link = links.elementAt(i).toString();
181 UrlLink urlLink = new UrlLink(link);
182 if (!urlLink.isValid())
184 System.err.println(urlLink.getInvalidMessage());
187 final String target = urlLink.getTarget(); // link.substring(0,
188 // link.indexOf("|"));
189 final String label = urlLink.getLabel();
190 if (urlLink.isDynamic())
193 // collect matching db-refs
194 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
195 seq.getDBRef(), new String[]
197 // collect id string too
198 String id = seq.getName();
199 String descr = seq.getDescription();
200 if (descr != null && descr.length() < 1)
206 for (int r = 0; r < dbr.length; r++)
208 if (id != null && dbr[r].getAccessionId().equals(id))
210 // suppress duplicate link creation for the bare sequence ID
211 // string with this link
214 // create Bare ID link for this RUL
215 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
219 for (int u = 0; u < urls.length; u += 2)
221 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
228 // create Bare ID link for this RUL
229 String[] urls = urlLink.makeUrls(id, true);
232 for (int u = 0; u < urls.length; u += 2)
234 addshowLink(linkMenu, label, urls[u + 1]);
237 // addshowLink(linkMenu, target, url_pref + id + url_suff);
239 // Now construct URLs from description but only try to do it for regex
241 if (descr != null && urlLink.getRegexReplace() != null)
243 // create link for this URL from description only if regex matches
244 String[] urls = urlLink.makeUrls(descr, true);
247 for (int u = 0; u < urls.length; u += 2)
249 addshowLink(linkMenu, label, urls[u + 1]);
256 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
261 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
262 * string and any matching database reference accessions String url_pref
263 * = link.substring(link.indexOf("|") + 1,
264 * link.indexOf("$SEQUENCE_ID$"));
266 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
267 * // collect matching db-refs DBRefEntry[] dbr =
268 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
269 * String[]{target}); // collect id string too String id =
270 * seq.getName(); if (id.indexOf("|") > -1) { id =
271 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
272 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
273 * suppress duplicate link creation for the bare sequence ID string with
274 * this link id = null; } addshowLink(linkMenu,
275 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
276 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
277 * create Bare ID link for this RUL addshowLink(linkMenu, target,
278 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
279 * link.substring(link.lastIndexOf("|")+1)); }
282 if (linkMenu.getItemCount() > 0)
286 seqMenu.add(linkMenu);
294 // TODO: add group link menu entry here
297 seqMenu.setLabel(seq.getName());
298 repGroup.setLabel("Represent Group with " + seq.getName());
305 if (!ap.av.hasHiddenRows)
310 final int index = ap.av.alignment.findIndex(seq);
312 if (ap.av.adjustForHiddenSeqs(index)
313 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
315 revealSeq_index=index;
323 * add a show URL menu item to the given linkMenu
327 * - menu label string
331 private void addshowLink(Menu linkMenu, final String target,
334 addshowLink(linkMenu, target, target, url);
338 * add a show URL menu item to the given linkMenu
342 * - URL target window
344 * - menu label string
348 private void addshowLink(Menu linkMenu, final String target,
349 final String label, final String url)
351 MenuItem item = new MenuItem(label);
352 item.addActionListener(new java.awt.event.ActionListener()
354 public void actionPerformed(ActionEvent e)
356 ap.alignFrame.showURL(url, target);
362 public void itemStateChanged(ItemEvent evt)
364 if (evt.getSource() == abovePIDColour)
366 abovePIDColour_itemStateChanged();
368 else if (evt.getSource() == showColourText)
370 showColourText_itemStateChanged();
372 else if (evt.getSource() == showText)
374 showText_itemStateChanged();
376 else if (evt.getSource() == showBoxes)
378 showBoxes_itemStateChanged();
380 else if (evt.getSource() == displayNonconserved)
382 this.showNonconserved_itemStateChanged();
386 public void actionPerformed(ActionEvent evt)
388 Object source = evt.getSource();
389 if (source == clustalColour)
391 clustalColour_actionPerformed();
393 else if (source == zappoColour)
395 zappoColour_actionPerformed();
397 else if (source == taylorColour)
399 taylorColour_actionPerformed();
401 else if (source == hydrophobicityColour)
403 hydrophobicityColour_actionPerformed();
405 else if (source == helixColour)
407 helixColour_actionPerformed();
409 else if (source == strandColour)
411 strandColour_actionPerformed();
413 else if (source == turnColour)
415 turnColour_actionPerformed();
417 else if (source == buriedColour)
419 buriedColour_actionPerformed();
421 else if (source == nucleotideMenuItem)
423 nucleotideMenuItem_actionPerformed();
426 else if (source == userDefinedColour)
428 userDefinedColour_actionPerformed();
430 else if (source == PIDColour)
432 PIDColour_actionPerformed();
434 else if (source == BLOSUM62Colour)
436 BLOSUM62Colour_actionPerformed();
438 else if (source == noColourmenuItem)
440 noColourmenuItem_actionPerformed();
442 else if (source == conservationMenuItem)
444 conservationMenuItem_itemStateChanged();
446 else if (source == unGroupMenuItem)
448 unGroupMenuItem_actionPerformed();
451 else if (source == sequenceName)
455 else if (source == pdb)
459 else if (source == hideSeqs)
461 hideSequences(false);
463 else if (source == repGroup)
467 else if (source == revealSeq)
469 ap.av.showSequence(revealSeq_index);
471 else if (source == revealAll)
473 ap.av.showAllHiddenSeqs();
476 else if (source == editGroupName)
478 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
479 getGroup().getDescription(), " Group Name",
480 "Group Description", ap.alignFrame,
481 "Edit Group Name / Description", 500, 100, true);
485 getGroup().setName(dialog.getName().replace(' ', '_'));
486 getGroup().setDescription(dialog.getDescription());
490 else if (source == copy)
492 ap.alignFrame.copy_actionPerformed();
494 else if (source == cut)
496 ap.alignFrame.cut_actionPerformed();
498 else if (source == editSequence)
500 SequenceGroup sg = ap.av.getSelectionGroup();
505 seq = (Sequence) sg.getSequenceAt(0);
507 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
508 sg.getStartRes(), sg.getEndRes() + 1), null,
509 "Edit Sequence ", null,
511 ap.alignFrame, "Edit Sequence", 500, 100, true);
515 EditCommand editCommand = new EditCommand("Edit Sequences",
516 EditCommand.REPLACE, dialog.getName().replace(' ',
517 ap.av.getGapCharacter()),
518 sg.getSequencesAsArray(ap.av.hiddenRepSequences),
519 sg.getStartRes(), sg.getEndRes() + 1, ap.av.alignment);
521 ap.alignFrame.addHistoryItem(editCommand);
523 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
528 else if (source == toUpper || source == toLower || source == toggleCase)
530 SequenceGroup sg = ap.av.getSelectionGroup();
531 Vector regions = new Vector();
534 int start = sg.getStartRes();
535 int end = sg.getEndRes() + 1;
539 if (ap.av.hasHiddenColumns)
543 start = ap.av.colSel.adjustForHiddenColumns(start);
546 end = ap.av.colSel.getHiddenBoundaryRight(start);
549 end = sg.getEndRes() + 1;
551 if (end > sg.getEndRes())
553 end = sg.getEndRes() + 1;
557 regions.addElement(new int[]
560 if (ap.av.hasHiddenColumns)
562 start = ap.av.colSel.adjustForHiddenColumns(end);
563 start = ap.av.colSel.getHiddenBoundaryLeft(start) + 1;
565 } while (end < sg.getEndRes());
567 int[][] startEnd = new int[regions.size()][2];
568 for (int i = 0; i < regions.size(); i++)
570 startEnd[i] = (int[]) regions.elementAt(i);
576 if (source == toggleCase)
578 description = "Toggle Case";
579 caseChange = ChangeCaseCommand.TOGGLE_CASE;
581 else if (source == toUpper)
583 description = "To Upper Case";
584 caseChange = ChangeCaseCommand.TO_UPPER;
588 description = "To Lower Case";
589 caseChange = ChangeCaseCommand.TO_LOWER;
592 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
593 sg.getSequencesAsArray(ap.av.hiddenRepSequences), startEnd,
596 ap.alignFrame.addHistoryItem(caseCommand);
598 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
603 else if (source == sequenceFeature)
605 SequenceGroup sg = ap.av.getSelectionGroup();
611 int rsize = 0, gSize = sg.getSize();
612 SequenceI[] rseqs, seqs = new SequenceI[gSize];
613 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
615 for (int i = 0; i < gSize; i++)
617 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
618 int end = sg.findEndRes(sg.getSequenceAt(i));
621 seqs[rsize] = sg.getSequenceAt(i);
622 features[rsize] = new SequenceFeature(null, null, null, start,
627 rseqs = new SequenceI[rsize];
628 tfeatures = new SequenceFeature[rsize];
629 System.arraycopy(seqs, 0, rseqs, 0, rsize);
630 System.arraycopy(features, 0, tfeatures, 0, rsize);
631 features = tfeatures;
634 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
637 ap.alignFrame.sequenceFeatures.setState(true);
638 ap.av.showSequenceFeatures(true);
639 ap.highlightSearchResults(null);
649 void outputText(ActionEvent e)
651 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
653 Frame frame = new Frame();
655 jalview.bin.JalviewLite.addFrame(frame,
656 "Selection output - " + e.getActionCommand(), 600, 500);
658 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
659 e.getActionCommand(),
660 new Alignment(ap.av.getSelectionAsNewSequence()),
661 ap.av.showJVSuffix));
667 EditNameDialog dialog = new EditNameDialog(seq.getName(),
668 seq.getDescription(), " Sequence Name",
669 "Sequence Description", ap.alignFrame,
670 "Edit Sequence Name / Description", 500, 100, true);
674 seq.setName(dialog.getName());
675 seq.setDescription(dialog.getDescription());
676 ap.paintAlignment(false);
682 if (seq.getPDBId() != null)
684 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
686 if (ap.av.applet.jmolAvailable)
687 new jalview.appletgui.AppletJmol(entry, new Sequence[]
688 { seq }, null, ap, AppletFormatAdapter.URL);
690 new MCview.AppletPDBViewer(entry, new Sequence[]
691 { seq }, null, ap, AppletFormatAdapter.URL);
696 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
697 cap.setText("Paste your PDB file here.");
698 cap.setPDBImport(seq);
699 Frame frame = new Frame();
701 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file ", 400, 300);
705 private void jbInit() throws Exception
707 groupMenu.setLabel("Group");
708 groupMenu.setLabel("Selection");
709 sequenceFeature.addActionListener(this);
711 editGroupName.addActionListener(this);
712 unGroupMenuItem.setLabel("Remove Group");
713 unGroupMenuItem.addActionListener(this);
715 nucleotideMenuItem.setLabel("Nucleotide");
716 nucleotideMenuItem.addActionListener(this);
717 conservationMenuItem.addItemListener(this);
718 abovePIDColour.addItemListener(this);
719 colourMenu.setLabel("Group Colour");
720 showBoxes.setLabel("Boxes");
721 showBoxes.setState(true);
722 showBoxes.addItemListener(this);
723 sequenceName.addActionListener(this);
724 displayNonconserved.setLabel("Show Nonconserved");
725 displayNonconserved.setState(false);
726 displayNonconserved.addItemListener(this);
727 showText.setLabel("Text");
728 showText.addItemListener(this);
729 showColourText.setLabel("Colour Text");
730 showColourText.addItemListener(this);
731 outputmenu.setLabel("Output to Textbox...");
732 seqMenu.setLabel("Sequence");
733 pdb.setLabel("View PDB Structure");
734 hideSeqs.setLabel("Hide Sequences");
735 repGroup.setLabel("Represent Group with");
736 revealAll.setLabel("Reveal All");
737 revealSeq.setLabel("Reveal Sequences");
738 menu1.setLabel("Group");
744 groupMenu.add(editGroupName);
745 groupMenu.add(editMenu);
746 groupMenu.add(outputmenu);
747 groupMenu.add(sequenceFeature);
748 groupMenu.add(menu1);
750 colourMenu.add(noColourmenuItem);
751 colourMenu.add(clustalColour);
752 colourMenu.add(BLOSUM62Colour);
753 colourMenu.add(PIDColour);
754 colourMenu.add(zappoColour);
755 colourMenu.add(taylorColour);
756 colourMenu.add(hydrophobicityColour);
757 colourMenu.add(helixColour);
758 colourMenu.add(strandColour);
759 colourMenu.add(turnColour);
760 colourMenu.add(buriedColour);
761 colourMenu.add(nucleotideMenuItem);
762 colourMenu.add(userDefinedColour);
763 colourMenu.addSeparator();
764 colourMenu.add(abovePIDColour);
765 colourMenu.add(conservationMenuItem);
767 noColourmenuItem.setLabel("None");
768 noColourmenuItem.addActionListener(this);
770 clustalColour.setLabel("Clustalx colours");
771 clustalColour.addActionListener(this);
772 zappoColour.setLabel("Zappo");
773 zappoColour.addActionListener(this);
774 taylorColour.setLabel("Taylor");
775 taylorColour.addActionListener(this);
776 hydrophobicityColour.setLabel("Hydrophobicity");
777 hydrophobicityColour.addActionListener(this);
778 helixColour.setLabel("Helix propensity");
779 helixColour.addActionListener(this);
780 strandColour.setLabel("Strand propensity");
781 strandColour.addActionListener(this);
782 turnColour.setLabel("Turn propensity");
783 turnColour.addActionListener(this);
784 buriedColour.setLabel("Buried Index");
785 buriedColour.addActionListener(this);
786 abovePIDColour.setLabel("Above % Identity");
788 userDefinedColour.setLabel("User Defined");
789 userDefinedColour.addActionListener(this);
790 PIDColour.setLabel("Percentage Identity");
791 PIDColour.addActionListener(this);
792 BLOSUM62Colour.setLabel("BLOSUM62");
793 BLOSUM62Colour.addActionListener(this);
794 conservationMenuItem.setLabel("Conservation");
797 copy.addActionListener(this);
799 cut.addActionListener(this);
801 editMenu.add(editSequence);
802 editSequence.addActionListener(this);
804 editMenu.add(toUpper);
805 toUpper.addActionListener(this);
806 editMenu.add(toLower);
807 toLower.addActionListener(this);
808 editMenu.add(toggleCase);
809 seqMenu.add(sequenceName);
810 if (!ap.av.applet.useXtrnalSviewer)
814 seqMenu.add(repGroup);
815 menu1.add(unGroupMenuItem);
816 menu1.add(colourMenu);
817 menu1.add(showBoxes);
819 menu1.add(showColourText);
820 menu1.add(displayNonconserved);
821 toggleCase.addActionListener(this);
822 pdb.addActionListener(this);
823 hideSeqs.addActionListener(this);
824 repGroup.addActionListener(this);
825 revealAll.addActionListener(this);
826 revealSeq.addActionListener(this);
831 ap.paintAlignment(true);
834 protected void clustalColour_actionPerformed()
836 SequenceGroup sg = getGroup();
837 sg.cs = new ClustalxColourScheme(
838 sg.getSequences(ap.av.hiddenRepSequences),
839 ap.av.alignment.getWidth());
843 protected void zappoColour_actionPerformed()
845 getGroup().cs = new ZappoColourScheme();
849 protected void taylorColour_actionPerformed()
851 getGroup().cs = new TaylorColourScheme();
855 protected void hydrophobicityColour_actionPerformed()
857 getGroup().cs = new HydrophobicColourScheme();
861 protected void helixColour_actionPerformed()
863 getGroup().cs = new HelixColourScheme();
867 protected void strandColour_actionPerformed()
869 getGroup().cs = new StrandColourScheme();
873 protected void turnColour_actionPerformed()
875 getGroup().cs = new TurnColourScheme();
879 protected void buriedColour_actionPerformed()
881 getGroup().cs = new BuriedColourScheme();
885 public void nucleotideMenuItem_actionPerformed()
887 getGroup().cs = new NucleotideColourScheme();
891 protected void abovePIDColour_itemStateChanged()
893 SequenceGroup sg = getGroup();
899 if (abovePIDColour.getState())
901 sg.cs.setConsensus(AAFrequency.calculate(
902 sg.getSequences(ap.av.hiddenRepSequences), 0,
903 ap.av.alignment.getWidth()));
904 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
907 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
909 SliderPanel.showPIDSlider();
913 // remove PIDColouring
915 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
922 protected void userDefinedColour_actionPerformed()
924 new UserDefinedColours(ap, getGroup());
927 protected void PIDColour_actionPerformed()
929 SequenceGroup sg = getGroup();
930 sg.cs = new PIDColourScheme();
931 sg.cs.setConsensus(AAFrequency.calculate(
932 sg.getSequences(ap.av.hiddenRepSequences), 0,
933 ap.av.alignment.getWidth()));
937 protected void BLOSUM62Colour_actionPerformed()
939 SequenceGroup sg = getGroup();
941 sg.cs = new Blosum62ColourScheme();
943 sg.cs.setConsensus(AAFrequency.calculate(
944 sg.getSequences(ap.av.hiddenRepSequences), 0,
945 ap.av.alignment.getWidth()));
950 protected void noColourmenuItem_actionPerformed()
952 getGroup().cs = null;
956 protected void conservationMenuItem_itemStateChanged()
958 SequenceGroup sg = getGroup();
964 if (conservationMenuItem.getState())
967 Conservation c = new Conservation("Group",
968 ResidueProperties.propHash, 3,
969 sg.getSequences(ap.av.hiddenRepSequences), 0,
970 ap.av.alignment.getWidth());
973 c.verdict(false, ap.av.ConsPercGaps);
975 sg.cs.setConservation(c);
977 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
978 SliderPanel.showConservationSlider();
981 // remove ConservationColouring
983 sg.cs.setConservation(null);
989 SequenceGroup getGroup()
991 SequenceGroup sg = ap.av.getSelectionGroup();
993 // this method won't add a new group if it already exists
996 ap.av.alignment.addGroup(sg);
1002 void unGroupMenuItem_actionPerformed()
1004 SequenceGroup sg = ap.av.getSelectionGroup();
1005 ap.av.alignment.deleteGroup(sg);
1006 ap.av.setSelectionGroup(null);
1007 ap.paintAlignment(true);
1010 public void showColourText_itemStateChanged()
1012 getGroup().setColourText(showColourText.getState());
1016 public void showText_itemStateChanged()
1018 getGroup().setDisplayText(showText.getState());
1022 public void showNonconserved_itemStateChanged()
1024 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1028 public void showBoxes_itemStateChanged()
1030 getGroup().setDisplayBoxes(showBoxes.getState());
1034 void hideSequences(boolean representGroup)
1036 SequenceGroup sg = ap.av.getSelectionGroup();
1037 if (sg == null || sg.getSize() < 1)
1039 ap.av.hideSequence(new SequenceI[]
1044 ap.av.setSelectionGroup(null);
1048 ap.av.hideRepSequences(seq, sg);
1053 int gsize = sg.getSize();
1056 hseqs = new SequenceI[gsize];
1059 for (int i = 0; i < gsize; i++)
1061 hseqs[index++] = sg.getSequenceAt(i);
1064 ap.av.hideSequence(hseqs);
1065 ap.av.sendSelection();