2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
18 package jalview.appletgui;
23 import java.awt.event.*;
25 import jalview.analysis.*;
26 import jalview.commands.*;
27 import jalview.datamodel.*;
28 import jalview.schemes.*;
29 import jalview.util.UrlLink;
30 import jalview.io.AppletFormatAdapter;
31 import jalview.io.SequenceAnnotationReport;
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");
112 MenuItem sequenceDetails = new MenuItem("Sequence Details ...");
114 MenuItem selSeqDetails = new MenuItem("Sequence Details ...");
116 MenuItem makeReferenceSeq = new MenuItem();
120 MenuItem revealAll = new MenuItem();
122 MenuItem revealSeq = new MenuItem();
125 * index of sequence to be revealed
127 int revealSeq_index = -1;
129 Menu menu1 = new Menu();
131 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
133 // /////////////////////////////////////////////////////////
134 // If this is activated from the sequence panel, the user may want to
135 // edit or annotate a particular residue. Therefore display the residue menu
137 // If from the IDPanel, we must display the sequence menu
138 // ////////////////////////////////////////////////////////
146 } catch (Exception e)
151 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
153 MenuItem item = new MenuItem(
154 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
156 item.addActionListener(this);
157 outputmenu.add(item);
160 SequenceGroup sg = ap.av.getSelectionGroup();
162 if (sg != null && sg.getSize() > 0)
164 editGroupName.setLabel("Name: " + sg.getName());
165 showText.setState(sg.getDisplayText());
166 showColourText.setState(sg.getColourText());
167 showBoxes.setState(sg.getDisplayBoxes());
168 displayNonconserved.setState(sg.getShowNonconserved());
169 if (!ap.av.getAlignment().getGroups().contains(sg))
171 groupMenu.remove(unGroupMenuItem);
181 if (links != null && links.size() > 0)
183 Menu linkMenu = new Menu("Link");
185 for (int i = 0; i < links.size(); i++)
187 link = links.elementAt(i).toString();
188 UrlLink urlLink = new UrlLink(link);
189 if (!urlLink.isValid())
191 System.err.println(urlLink.getInvalidMessage());
194 final String target = urlLink.getTarget(); // link.substring(0,
195 // link.indexOf("|"));
196 final String label = urlLink.getLabel();
197 if (seq != null && urlLink.isDynamic())
200 // collect matching db-refs
201 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
202 seq.getDBRef(), new String[]
204 // collect id string too
205 String id = seq.getName();
206 String descr = seq.getDescription();
207 if (descr != null && descr.length() < 1)
213 for (int r = 0; r < dbr.length; r++)
215 if (id != null && dbr[r].getAccessionId().equals(id))
217 // suppress duplicate link creation for the bare sequence ID
218 // string with this link
221 // create Bare ID link for this RUL
222 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
226 for (int u = 0; u < urls.length; u += 2)
228 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
235 // create Bare ID link for this RUL
236 String[] urls = urlLink.makeUrls(id, true);
239 for (int u = 0; u < urls.length; u += 2)
241 addshowLink(linkMenu, label, urls[u + 1]);
244 // addshowLink(linkMenu, target, url_pref + id + url_suff);
246 // Now construct URLs from description but only try to do it for regex
248 if (descr != null && urlLink.getRegexReplace() != null)
250 // create link for this URL from description only if regex matches
251 String[] urls = urlLink.makeUrls(descr, true);
254 for (int u = 0; u < urls.length; u += 2)
256 addshowLink(linkMenu, label, urls[u + 1]);
263 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
268 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
269 * string and any matching database reference accessions String url_pref
270 * = link.substring(link.indexOf("|") + 1,
271 * link.indexOf("$SEQUENCE_ID$"));
273 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
274 * // collect matching db-refs DBRefEntry[] dbr =
275 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
276 * String[]{target}); // collect id string too String id =
277 * seq.getName(); if (id.indexOf("|") > -1) { id =
278 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
279 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
280 * suppress duplicate link creation for the bare sequence ID string with
281 * this link id = null; } addshowLink(linkMenu,
282 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
283 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
284 * create Bare ID link for this RUL addshowLink(linkMenu, target,
285 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
286 * link.substring(link.lastIndexOf("|")+1)); }
289 if (linkMenu.getItemCount() > 0)
293 seqMenu.add(linkMenu);
301 // TODO: add group link menu entry here
304 seqMenu.setLabel(seq.getName());
305 if (seq == ap.av.getAlignment().getSeqrep())
307 makeReferenceSeq.setLabel("Unmark representative");
309 makeReferenceSeq.setLabel("Mark as representative");
311 repGroup.setLabel("Represent Group with " + seq.getName());
318 if (!ap.av.hasHiddenRows())
325 final int index = ap.av.getAlignment().findIndex(seq);
327 if (ap.av.adjustForHiddenSeqs(index)
328 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
330 revealSeq_index = index;
340 * add a show URL menu item to the given linkMenu
344 * - menu label string
348 private void addshowLink(Menu linkMenu, final String target,
351 addshowLink(linkMenu, target, target, url);
355 * add a show URL menu item to the given linkMenu
359 * - URL target window
361 * - menu label string
365 private void addshowLink(Menu linkMenu, final String target,
366 final String label, final String url)
368 MenuItem item = new MenuItem(label);
369 item.addActionListener(new java.awt.event.ActionListener()
371 public void actionPerformed(ActionEvent e)
373 ap.alignFrame.showURL(url, target);
379 public void itemStateChanged(ItemEvent evt)
381 if (evt.getSource() == abovePIDColour)
383 abovePIDColour_itemStateChanged();
385 else if (evt.getSource() == showColourText)
387 showColourText_itemStateChanged();
389 else if (evt.getSource() == showText)
391 showText_itemStateChanged();
393 else if (evt.getSource() == showBoxes)
395 showBoxes_itemStateChanged();
397 else if (evt.getSource() == displayNonconserved)
399 this.showNonconserved_itemStateChanged();
403 public void actionPerformed(ActionEvent evt)
405 Object source = evt.getSource();
406 if (source == clustalColour)
408 clustalColour_actionPerformed();
410 else if (source == zappoColour)
412 zappoColour_actionPerformed();
414 else if (source == taylorColour)
416 taylorColour_actionPerformed();
418 else if (source == hydrophobicityColour)
420 hydrophobicityColour_actionPerformed();
422 else if (source == helixColour)
424 helixColour_actionPerformed();
426 else if (source == strandColour)
428 strandColour_actionPerformed();
430 else if (source == turnColour)
432 turnColour_actionPerformed();
434 else if (source == buriedColour)
436 buriedColour_actionPerformed();
438 else if (source == nucleotideMenuItem)
440 nucleotideMenuItem_actionPerformed();
443 else if (source == userDefinedColour)
445 userDefinedColour_actionPerformed();
447 else if (source == PIDColour)
449 PIDColour_actionPerformed();
451 else if (source == BLOSUM62Colour)
453 BLOSUM62Colour_actionPerformed();
455 else if (source == noColourmenuItem)
457 noColourmenuItem_actionPerformed();
459 else if (source == conservationMenuItem)
461 conservationMenuItem_itemStateChanged();
463 else if (source == unGroupMenuItem)
465 unGroupMenuItem_actionPerformed();
468 else if (source == sequenceName)
472 else if (source == sequenceDetails)
474 showSequenceDetails();
476 else if (source == selSeqDetails)
478 showSequenceSelectionDetails();
480 else if (source == pdb)
484 else if (source == hideSeqs)
486 hideSequences(false);
488 else if (source == repGroup)
492 else if (source == revealSeq)
494 ap.av.showSequence(revealSeq_index);
496 else if (source == revealAll)
498 ap.av.showAllHiddenSeqs();
501 else if (source == editGroupName)
503 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
504 getGroup().getDescription(), " Group Name",
505 "Group Description", ap.alignFrame,
506 "Edit Group Name / Description", 500, 100, true);
510 getGroup().setName(dialog.getName().replace(' ', '_'));
511 getGroup().setDescription(dialog.getDescription());
515 else if (source == copy)
517 ap.alignFrame.copy_actionPerformed();
519 else if (source == cut)
521 ap.alignFrame.cut_actionPerformed();
523 else if (source == editSequence)
525 SequenceGroup sg = ap.av.getSelectionGroup();
530 seq = (Sequence) sg.getSequenceAt(0);
532 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
533 sg.getStartRes(), sg.getEndRes() + 1), null,
534 "Edit Sequence ", null,
536 ap.alignFrame, "Edit Sequence", 500, 100, true);
540 EditCommand editCommand = new EditCommand("Edit Sequences",
541 EditCommand.REPLACE, dialog.getName().replace(' ',
542 ap.av.getGapCharacter()),
543 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
544 sg.getStartRes(), sg.getEndRes() + 1,
545 ap.av.getAlignment());
547 ap.alignFrame.addHistoryItem(editCommand);
549 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
554 else if (source == toUpper || source == toLower || source == toggleCase)
556 SequenceGroup sg = ap.av.getSelectionGroup();
557 Vector regions = new Vector();
560 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
561 sg.getStartRes(), sg.getEndRes() + 1);
566 if (source == toggleCase)
568 description = "Toggle Case";
569 caseChange = ChangeCaseCommand.TOGGLE_CASE;
571 else if (source == toUpper)
573 description = "To Upper Case";
574 caseChange = ChangeCaseCommand.TO_UPPER;
578 description = "To Lower Case";
579 caseChange = ChangeCaseCommand.TO_LOWER;
582 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
583 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
584 startEnd, caseChange);
586 ap.alignFrame.addHistoryItem(caseCommand);
588 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
593 else if (source == sequenceFeature)
595 SequenceGroup sg = ap.av.getSelectionGroup();
601 int rsize = 0, gSize = sg.getSize();
602 SequenceI[] rseqs, seqs = new SequenceI[gSize];
603 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
605 for (int i = 0; i < gSize; i++)
607 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
608 int end = sg.findEndRes(sg.getSequenceAt(i));
611 seqs[rsize] = sg.getSequenceAt(i);
612 features[rsize] = new SequenceFeature(null, null, null, start,
617 rseqs = new SequenceI[rsize];
618 tfeatures = new SequenceFeature[rsize];
619 System.arraycopy(seqs, 0, rseqs, 0, rsize);
620 System.arraycopy(features, 0, tfeatures, 0, rsize);
621 features = tfeatures;
624 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
627 ap.alignFrame.sequenceFeatures.setState(true);
628 ap.av.showSequenceFeatures(true);
629 ap.highlightSearchResults(null);
639 void outputText(ActionEvent e)
641 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
643 Frame frame = new Frame();
645 jalview.bin.JalviewLite.addFrame(frame,
646 "Selection output - " + e.getActionCommand(), 600, 500);
647 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
648 // now returns a full copy of sequence data
649 // TODO consider using getSequenceSelection instead here
651 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
652 e.getActionCommand(),
653 new Alignment(ap.av.getSelectionAsNewSequence()),
654 ap.av.showJVSuffix));
658 protected void showSequenceSelectionDetails()
660 createSequenceDetailsReport(ap.av.getSequenceSelection());
663 protected void showSequenceDetails()
665 createSequenceDetailsReport(new SequenceI[]
669 public void createSequenceDetailsReport(SequenceI[] sequences)
672 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
674 StringBuffer contents = new StringBuffer();
675 for (SequenceI seq : sequences)
677 contents.append("<p><h2>Annotation for " + seq.getDisplayId(true)
679 new SequenceAnnotationReport(null)
680 .createSequenceAnnotationReport(
686 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
688 contents.append("</p>");
690 Frame frame = new Frame();
692 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
693 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
694 : "Selection"), 600, 500);
695 cap.setText("<html>" + contents.toString() + "</html>");
700 EditNameDialog dialog = new EditNameDialog(seq.getName(),
701 seq.getDescription(), " Sequence Name",
702 "Sequence Description", ap.alignFrame,
703 "Edit Sequence Name / Description", 500, 100, true);
707 seq.setName(dialog.getName());
708 seq.setDescription(dialog.getDescription());
709 ap.paintAlignment(false);
715 if (seq.getPDBId() != null)
717 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
719 if (ap.av.applet.jmolAvailable)
720 new jalview.appletgui.AppletJmol(entry, new Sequence[]
721 { seq }, null, ap, AppletFormatAdapter.URL);
723 new MCview.AppletPDBViewer(entry, new Sequence[]
724 { seq }, null, ap, AppletFormatAdapter.URL);
729 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
730 cap.setText("Paste your PDB file here.");
731 cap.setPDBImport(seq);
732 Frame frame = new Frame();
734 jalview.bin.JalviewLite.addFrame(frame,
735 "Paste PDB file for sequence " + seq.getName(), 400, 300);
739 private void jbInit() throws Exception
741 groupMenu.setLabel("Group");
742 groupMenu.setLabel("Selection");
743 sequenceFeature.addActionListener(this);
745 editGroupName.addActionListener(this);
746 unGroupMenuItem.setLabel("Remove Group");
747 unGroupMenuItem.addActionListener(this);
749 nucleotideMenuItem.setLabel("Nucleotide");
750 nucleotideMenuItem.addActionListener(this);
751 conservationMenuItem.addItemListener(this);
752 abovePIDColour.addItemListener(this);
753 colourMenu.setLabel("Group Colour");
754 showBoxes.setLabel("Boxes");
755 showBoxes.setState(true);
756 showBoxes.addItemListener(this);
757 sequenceName.addActionListener(this);
758 sequenceDetails.addActionListener(this);
759 selSeqDetails.addActionListener(this);
760 displayNonconserved.setLabel("Show Nonconserved");
761 displayNonconserved.setState(false);
762 displayNonconserved.addItemListener(this);
763 showText.setLabel("Text");
764 showText.addItemListener(this);
765 showColourText.setLabel("Colour Text");
766 showColourText.addItemListener(this);
767 outputmenu.setLabel("Output to Textbox...");
768 seqMenu.setLabel("Sequence");
769 pdb.setLabel("View PDB Structure");
770 hideSeqs.setLabel("Hide Sequences");
771 repGroup.setLabel("Represent Group with");
772 revealAll.setLabel("Reveal All");
773 revealSeq.setLabel("Reveal Sequences");
774 menu1.setLabel("Group");
780 // groupMenu.add(selSeqDetails);
781 groupMenu.add(editGroupName);
782 groupMenu.add(editMenu);
783 groupMenu.add(outputmenu);
784 groupMenu.add(sequenceFeature);
785 groupMenu.add(menu1);
787 colourMenu.add(noColourmenuItem);
788 colourMenu.add(clustalColour);
789 colourMenu.add(BLOSUM62Colour);
790 colourMenu.add(PIDColour);
791 colourMenu.add(zappoColour);
792 colourMenu.add(taylorColour);
793 colourMenu.add(hydrophobicityColour);
794 colourMenu.add(helixColour);
795 colourMenu.add(strandColour);
796 colourMenu.add(turnColour);
797 colourMenu.add(buriedColour);
798 colourMenu.add(nucleotideMenuItem);
799 colourMenu.add(userDefinedColour);
800 colourMenu.addSeparator();
801 colourMenu.add(abovePIDColour);
802 colourMenu.add(conservationMenuItem);
804 noColourmenuItem.setLabel("None");
805 noColourmenuItem.addActionListener(this);
807 clustalColour.setLabel("Clustalx colours");
808 clustalColour.addActionListener(this);
809 zappoColour.setLabel("Zappo");
810 zappoColour.addActionListener(this);
811 taylorColour.setLabel("Taylor");
812 taylorColour.addActionListener(this);
813 hydrophobicityColour.setLabel("Hydrophobicity");
814 hydrophobicityColour.addActionListener(this);
815 helixColour.setLabel("Helix propensity");
816 helixColour.addActionListener(this);
817 strandColour.setLabel("Strand propensity");
818 strandColour.addActionListener(this);
819 turnColour.setLabel("Turn propensity");
820 turnColour.addActionListener(this);
821 buriedColour.setLabel("Buried Index");
822 buriedColour.addActionListener(this);
823 abovePIDColour.setLabel("Above % Identity");
825 userDefinedColour.setLabel("User Defined");
826 userDefinedColour.addActionListener(this);
827 PIDColour.setLabel("Percentage Identity");
828 PIDColour.addActionListener(this);
829 BLOSUM62Colour.setLabel("BLOSUM62");
830 BLOSUM62Colour.addActionListener(this);
831 conservationMenuItem.setLabel("Conservation");
834 copy.addActionListener(this);
836 cut.addActionListener(this);
838 editMenu.add(editSequence);
839 editSequence.addActionListener(this);
841 editMenu.add(toUpper);
842 toUpper.addActionListener(this);
843 editMenu.add(toLower);
844 toLower.addActionListener(this);
845 editMenu.add(toggleCase);
846 seqMenu.add(sequenceName);
847 // seqMenu.add(sequenceDetails);
849 if (!ap.av.applet.useXtrnalSviewer)
853 seqMenu.add(repGroup);
854 menu1.add(unGroupMenuItem);
855 menu1.add(colourMenu);
856 menu1.add(showBoxes);
858 menu1.add(showColourText);
859 menu1.add(displayNonconserved);
860 toggleCase.addActionListener(this);
861 pdb.addActionListener(this);
862 hideSeqs.addActionListener(this);
863 repGroup.addActionListener(this);
864 revealAll.addActionListener(this);
865 revealSeq.addActionListener(this);
870 ap.paintAlignment(true);
873 protected void clustalColour_actionPerformed()
875 SequenceGroup sg = getGroup();
876 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
880 protected void zappoColour_actionPerformed()
882 getGroup().cs = new ZappoColourScheme();
886 protected void taylorColour_actionPerformed()
888 getGroup().cs = new TaylorColourScheme();
892 protected void hydrophobicityColour_actionPerformed()
894 getGroup().cs = new HydrophobicColourScheme();
898 protected void helixColour_actionPerformed()
900 getGroup().cs = new HelixColourScheme();
904 protected void strandColour_actionPerformed()
906 getGroup().cs = new StrandColourScheme();
910 protected void turnColour_actionPerformed()
912 getGroup().cs = new TurnColourScheme();
916 protected void buriedColour_actionPerformed()
918 getGroup().cs = new BuriedColourScheme();
922 public void nucleotideMenuItem_actionPerformed()
924 getGroup().cs = new NucleotideColourScheme();
928 protected void abovePIDColour_itemStateChanged()
930 SequenceGroup sg = getGroup();
936 if (abovePIDColour.getState())
938 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
939 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
940 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
943 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
945 SliderPanel.showPIDSlider();
949 // remove PIDColouring
951 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
958 protected void userDefinedColour_actionPerformed()
960 new UserDefinedColours(ap, getGroup());
963 protected void PIDColour_actionPerformed()
965 SequenceGroup sg = getGroup();
966 sg.cs = new PIDColourScheme();
967 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
968 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
972 protected void BLOSUM62Colour_actionPerformed()
974 SequenceGroup sg = getGroup();
976 sg.cs = new Blosum62ColourScheme();
978 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
979 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
984 protected void noColourmenuItem_actionPerformed()
986 getGroup().cs = null;
990 protected void conservationMenuItem_itemStateChanged()
992 SequenceGroup sg = getGroup();
998 if (conservationMenuItem.getState())
1001 sg.cs.setConservation(Conservation.calculateConservation("Group",
1002 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1003 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1004 .getWidth(), false, ap.av.getConsPercGaps(), false));
1005 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1006 SliderPanel.showConservationSlider();
1009 // remove ConservationColouring
1011 sg.cs.setConservation(null);
1017 SequenceGroup getGroup()
1019 SequenceGroup sg = ap.av.getSelectionGroup();
1021 // this method won't add a new group if it already exists
1024 ap.av.getAlignment().addGroup(sg);
1030 void unGroupMenuItem_actionPerformed()
1032 SequenceGroup sg = ap.av.getSelectionGroup();
1033 ap.av.getAlignment().deleteGroup(sg);
1034 ap.av.setSelectionGroup(null);
1035 ap.paintAlignment(true);
1038 public void showColourText_itemStateChanged()
1040 getGroup().setColourText(showColourText.getState());
1044 public void showText_itemStateChanged()
1046 getGroup().setDisplayText(showText.getState());
1050 public void showNonconserved_itemStateChanged()
1052 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1056 public void showBoxes_itemStateChanged()
1058 getGroup().setDisplayBoxes(showBoxes.getState());
1062 void hideSequences(boolean representGroup)
1064 SequenceGroup sg = ap.av.getSelectionGroup();
1065 if (sg == null || sg.getSize() < 1)
1067 ap.av.hideSequence(new SequenceI[]
1072 ap.av.setSelectionGroup(null);
1076 ap.av.hideRepSequences(seq, sg);
1081 int gsize = sg.getSize();
1084 hseqs = new SequenceI[gsize];
1087 for (int i = 0; i < gsize; i++)
1089 hseqs[index++] = sg.getSequenceAt(i);
1092 ap.av.hideSequence(hseqs);
1093 ap.av.sendSelection();