2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 ...");
118 MenuItem revealAll = new MenuItem();
120 MenuItem revealSeq = new MenuItem();
122 * index of sequence to be revealed
124 int revealSeq_index=-1;
125 Menu menu1 = new Menu();
127 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
129 // /////////////////////////////////////////////////////////
130 // If this is activated from the sequence panel, the user may want to
131 // edit or annotate a particular residue. Therefore display the residue menu
133 // If from the IDPanel, we must display the sequence menu
134 // ////////////////////////////////////////////////////////
142 } catch (Exception e)
147 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
149 MenuItem item = new MenuItem(
150 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
152 item.addActionListener(this);
153 outputmenu.add(item);
156 SequenceGroup sg = ap.av.getSelectionGroup();
158 if (sg != null && sg.getSize() > 0)
160 editGroupName.setLabel("Name: "+sg.getName());
161 showText.setState(sg.getDisplayText());
162 showColourText.setState(sg.getColourText());
163 showBoxes.setState(sg.getDisplayBoxes());
164 displayNonconserved.setState(sg.getShowNonconserved());
165 if (!ap.av.getAlignment().getGroups().contains(sg))
167 groupMenu.remove(unGroupMenuItem);
177 if (links != null && links.size() > 0)
179 Menu linkMenu = new Menu("Link");
181 for (int i = 0; i < links.size(); i++)
183 link = links.elementAt(i).toString();
184 UrlLink urlLink = new UrlLink(link);
185 if (!urlLink.isValid())
187 System.err.println(urlLink.getInvalidMessage());
190 final String target = urlLink.getTarget(); // link.substring(0,
191 // link.indexOf("|"));
192 final String label = urlLink.getLabel();
193 if (seq!=null && urlLink.isDynamic())
196 // collect matching db-refs
197 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
198 seq.getDBRef(), new String[]
200 // collect id string too
201 String id = seq.getName();
202 String descr = seq.getDescription();
203 if (descr != null && descr.length() < 1)
209 for (int r = 0; r < dbr.length; r++)
211 if (id != null && dbr[r].getAccessionId().equals(id))
213 // suppress duplicate link creation for the bare sequence ID
214 // string with this link
217 // create Bare ID link for this RUL
218 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
222 for (int u = 0; u < urls.length; u += 2)
224 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
231 // create Bare ID link for this RUL
232 String[] urls = urlLink.makeUrls(id, true);
235 for (int u = 0; u < urls.length; u += 2)
237 addshowLink(linkMenu, label, urls[u + 1]);
240 // addshowLink(linkMenu, target, url_pref + id + url_suff);
242 // Now construct URLs from description but only try to do it for regex
244 if (descr != null && urlLink.getRegexReplace() != null)
246 // create link for this URL from description only if regex matches
247 String[] urls = urlLink.makeUrls(descr, true);
250 for (int u = 0; u < urls.length; u += 2)
252 addshowLink(linkMenu, label, urls[u + 1]);
259 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
264 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
265 * string and any matching database reference accessions String url_pref
266 * = link.substring(link.indexOf("|") + 1,
267 * link.indexOf("$SEQUENCE_ID$"));
269 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
270 * // collect matching db-refs DBRefEntry[] dbr =
271 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
272 * String[]{target}); // collect id string too String id =
273 * seq.getName(); if (id.indexOf("|") > -1) { id =
274 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
275 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
276 * suppress duplicate link creation for the bare sequence ID string with
277 * this link id = null; } addshowLink(linkMenu,
278 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
279 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
280 * create Bare ID link for this RUL addshowLink(linkMenu, target,
281 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
282 * link.substring(link.lastIndexOf("|")+1)); }
285 if (linkMenu.getItemCount() > 0)
289 seqMenu.add(linkMenu);
297 // TODO: add group link menu entry here
300 seqMenu.setLabel(seq.getName());
301 repGroup.setLabel("Represent Group with " + seq.getName());
308 if (!ap.av.hasHiddenRows())
313 final int index = ap.av.getAlignment().findIndex(seq);
315 if (ap.av.adjustForHiddenSeqs(index)
316 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
318 revealSeq_index=index;
326 * add a show URL menu item to the given linkMenu
330 * - menu label string
334 private void addshowLink(Menu linkMenu, final String target,
337 addshowLink(linkMenu, target, target, url);
341 * add a show URL menu item to the given linkMenu
345 * - URL target window
347 * - menu label string
351 private void addshowLink(Menu linkMenu, final String target,
352 final String label, final String url)
354 MenuItem item = new MenuItem(label);
355 item.addActionListener(new java.awt.event.ActionListener()
357 public void actionPerformed(ActionEvent e)
359 ap.alignFrame.showURL(url, target);
365 public void itemStateChanged(ItemEvent evt)
367 if (evt.getSource() == abovePIDColour)
369 abovePIDColour_itemStateChanged();
371 else if (evt.getSource() == showColourText)
373 showColourText_itemStateChanged();
375 else if (evt.getSource() == showText)
377 showText_itemStateChanged();
379 else if (evt.getSource() == showBoxes)
381 showBoxes_itemStateChanged();
383 else if (evt.getSource() == displayNonconserved)
385 this.showNonconserved_itemStateChanged();
389 public void actionPerformed(ActionEvent evt)
391 Object source = evt.getSource();
392 if (source == clustalColour)
394 clustalColour_actionPerformed();
396 else if (source == zappoColour)
398 zappoColour_actionPerformed();
400 else if (source == taylorColour)
402 taylorColour_actionPerformed();
404 else if (source == hydrophobicityColour)
406 hydrophobicityColour_actionPerformed();
408 else if (source == helixColour)
410 helixColour_actionPerformed();
412 else if (source == strandColour)
414 strandColour_actionPerformed();
416 else if (source == turnColour)
418 turnColour_actionPerformed();
420 else if (source == buriedColour)
422 buriedColour_actionPerformed();
424 else if (source == nucleotideMenuItem)
426 nucleotideMenuItem_actionPerformed();
429 else if (source == userDefinedColour)
431 userDefinedColour_actionPerformed();
433 else if (source == PIDColour)
435 PIDColour_actionPerformed();
437 else if (source == BLOSUM62Colour)
439 BLOSUM62Colour_actionPerformed();
441 else if (source == noColourmenuItem)
443 noColourmenuItem_actionPerformed();
445 else if (source == conservationMenuItem)
447 conservationMenuItem_itemStateChanged();
449 else if (source == unGroupMenuItem)
451 unGroupMenuItem_actionPerformed();
454 else if (source == sequenceName)
458 else if (source == sequenceDetails)
460 showSequenceDetails();
462 else if (source == selSeqDetails)
464 showSequenceSelectionDetails();
466 else if (source == pdb)
470 else if (source == hideSeqs)
472 hideSequences(false);
474 else if (source == repGroup)
478 else if (source == revealSeq)
480 ap.av.showSequence(revealSeq_index);
482 else if (source == revealAll)
484 ap.av.showAllHiddenSeqs();
487 else if (source == editGroupName)
489 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
490 getGroup().getDescription(), " Group Name",
491 "Group Description", ap.alignFrame,
492 "Edit Group Name / Description", 500, 100, true);
496 getGroup().setName(dialog.getName().replace(' ', '_'));
497 getGroup().setDescription(dialog.getDescription());
501 else if (source == copy)
503 ap.alignFrame.copy_actionPerformed();
505 else if (source == cut)
507 ap.alignFrame.cut_actionPerformed();
509 else if (source == editSequence)
511 SequenceGroup sg = ap.av.getSelectionGroup();
516 seq = (Sequence) sg.getSequenceAt(0);
518 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
519 sg.getStartRes(), sg.getEndRes() + 1), null,
520 "Edit Sequence ", null,
522 ap.alignFrame, "Edit Sequence", 500, 100, true);
526 EditCommand editCommand = new EditCommand("Edit Sequences",
527 EditCommand.REPLACE, dialog.getName().replace(' ',
528 ap.av.getGapCharacter()),
529 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
530 sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());
532 ap.alignFrame.addHistoryItem(editCommand);
534 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
539 else if (source == toUpper || source == toLower || source == toggleCase)
541 SequenceGroup sg = ap.av.getSelectionGroup();
542 Vector regions = new Vector();
545 int[][] startEnd = ap.av.getVisibleRegionBoundaries(sg.getStartRes(),
551 if (source == toggleCase)
553 description = "Toggle Case";
554 caseChange = ChangeCaseCommand.TOGGLE_CASE;
556 else if (source == toUpper)
558 description = "To Upper Case";
559 caseChange = ChangeCaseCommand.TO_UPPER;
563 description = "To Lower Case";
564 caseChange = ChangeCaseCommand.TO_LOWER;
567 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
568 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), startEnd,
571 ap.alignFrame.addHistoryItem(caseCommand);
573 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
578 else if (source == sequenceFeature)
580 SequenceGroup sg = ap.av.getSelectionGroup();
586 int rsize = 0, gSize = sg.getSize();
587 SequenceI[] rseqs, seqs = new SequenceI[gSize];
588 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
590 for (int i = 0; i < gSize; i++)
592 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
593 int end = sg.findEndRes(sg.getSequenceAt(i));
596 seqs[rsize] = sg.getSequenceAt(i);
597 features[rsize] = new SequenceFeature(null, null, null, start,
602 rseqs = new SequenceI[rsize];
603 tfeatures = new SequenceFeature[rsize];
604 System.arraycopy(seqs, 0, rseqs, 0, rsize);
605 System.arraycopy(features, 0, tfeatures, 0, rsize);
606 features = tfeatures;
609 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
612 ap.alignFrame.sequenceFeatures.setState(true);
613 ap.av.showSequenceFeatures(true);
614 ap.highlightSearchResults(null);
625 void outputText(ActionEvent e)
627 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
629 Frame frame = new Frame();
631 jalview.bin.JalviewLite.addFrame(frame,
632 "Selection output - " + e.getActionCommand(), 600, 500);
633 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
634 // TODO consider using getSequenceSelection instead here
636 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
637 e.getActionCommand(),
638 new Alignment(ap.av.getSelectionAsNewSequence()),
639 ap.av.showJVSuffix));
642 protected void showSequenceSelectionDetails()
644 createSequenceDetailsReport(ap.av.getSequenceSelection());
647 protected void showSequenceDetails()
649 createSequenceDetailsReport(new SequenceI[]{seq});
651 public void createSequenceDetailsReport(SequenceI[] sequences)
654 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
656 StringBuffer contents = new StringBuffer();
657 for (SequenceI seq:sequences)
659 contents.append("<p><h2>Annotation for "+seq.getDisplayId(true)+"</h2></p><p>");
660 new SequenceAnnotationReport(null)
661 .createSequenceAnnotationReport(
666 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
668 contents.append("</p>");
670 Frame frame = new Frame();
672 jalview.bin.JalviewLite.addFrame(frame,
673 "Sequence Details for " + (sequences.length==1 ? sequences[0].getDisplayId(true) : "Selection")
675 cap.setText("<html>" + contents.toString() + "</html>");
680 EditNameDialog dialog = new EditNameDialog(seq.getName(),
681 seq.getDescription(), " Sequence Name",
682 "Sequence Description", ap.alignFrame,
683 "Edit Sequence Name / Description", 500, 100, true);
687 seq.setName(dialog.getName());
688 seq.setDescription(dialog.getDescription());
689 ap.paintAlignment(false);
695 if (seq.getPDBId() != null)
697 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
699 if (ap.av.applet.jmolAvailable)
700 new jalview.appletgui.AppletJmol(entry, new Sequence[]
701 { seq }, null, ap, AppletFormatAdapter.URL);
703 new MCview.AppletPDBViewer(entry, new Sequence[]
704 { seq }, null, ap, AppletFormatAdapter.URL);
709 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
710 cap.setText("Paste your PDB file here.");
711 cap.setPDBImport(seq);
712 Frame frame = new Frame();
714 jalview.bin.JalviewLite.addFrame(frame, "Paste PDB file for sequence "+seq.getName(), 400, 300);
718 private void jbInit() throws Exception
720 groupMenu.setLabel("Group");
721 groupMenu.setLabel("Selection");
722 sequenceFeature.addActionListener(this);
724 editGroupName.addActionListener(this);
725 unGroupMenuItem.setLabel("Remove Group");
726 unGroupMenuItem.addActionListener(this);
728 nucleotideMenuItem.setLabel("Nucleotide");
729 nucleotideMenuItem.addActionListener(this);
730 conservationMenuItem.addItemListener(this);
731 abovePIDColour.addItemListener(this);
732 colourMenu.setLabel("Group Colour");
733 showBoxes.setLabel("Boxes");
734 showBoxes.setState(true);
735 showBoxes.addItemListener(this);
736 sequenceName.addActionListener(this);
737 sequenceDetails.addActionListener(this);
738 selSeqDetails.addActionListener(this);
739 displayNonconserved.setLabel("Show Nonconserved");
740 displayNonconserved.setState(false);
741 displayNonconserved.addItemListener(this);
742 showText.setLabel("Text");
743 showText.addItemListener(this);
744 showColourText.setLabel("Colour Text");
745 showColourText.addItemListener(this);
746 outputmenu.setLabel("Output to Textbox...");
747 seqMenu.setLabel("Sequence");
748 pdb.setLabel("View PDB Structure");
749 hideSeqs.setLabel("Hide Sequences");
750 repGroup.setLabel("Represent Group with");
751 revealAll.setLabel("Reveal All");
752 revealSeq.setLabel("Reveal Sequences");
753 menu1.setLabel("Group");
759 // groupMenu.add(selSeqDetails);
760 groupMenu.add(editGroupName);
761 groupMenu.add(editMenu);
762 groupMenu.add(outputmenu);
763 groupMenu.add(sequenceFeature);
764 groupMenu.add(menu1);
766 colourMenu.add(noColourmenuItem);
767 colourMenu.add(clustalColour);
768 colourMenu.add(BLOSUM62Colour);
769 colourMenu.add(PIDColour);
770 colourMenu.add(zappoColour);
771 colourMenu.add(taylorColour);
772 colourMenu.add(hydrophobicityColour);
773 colourMenu.add(helixColour);
774 colourMenu.add(strandColour);
775 colourMenu.add(turnColour);
776 colourMenu.add(buriedColour);
777 colourMenu.add(nucleotideMenuItem);
778 colourMenu.add(userDefinedColour);
779 colourMenu.addSeparator();
780 colourMenu.add(abovePIDColour);
781 colourMenu.add(conservationMenuItem);
783 noColourmenuItem.setLabel("None");
784 noColourmenuItem.addActionListener(this);
786 clustalColour.setLabel("Clustalx colours");
787 clustalColour.addActionListener(this);
788 zappoColour.setLabel("Zappo");
789 zappoColour.addActionListener(this);
790 taylorColour.setLabel("Taylor");
791 taylorColour.addActionListener(this);
792 hydrophobicityColour.setLabel("Hydrophobicity");
793 hydrophobicityColour.addActionListener(this);
794 helixColour.setLabel("Helix propensity");
795 helixColour.addActionListener(this);
796 strandColour.setLabel("Strand propensity");
797 strandColour.addActionListener(this);
798 turnColour.setLabel("Turn propensity");
799 turnColour.addActionListener(this);
800 buriedColour.setLabel("Buried Index");
801 buriedColour.addActionListener(this);
802 abovePIDColour.setLabel("Above % Identity");
804 userDefinedColour.setLabel("User Defined");
805 userDefinedColour.addActionListener(this);
806 PIDColour.setLabel("Percentage Identity");
807 PIDColour.addActionListener(this);
808 BLOSUM62Colour.setLabel("BLOSUM62");
809 BLOSUM62Colour.addActionListener(this);
810 conservationMenuItem.setLabel("Conservation");
813 copy.addActionListener(this);
815 cut.addActionListener(this);
817 editMenu.add(editSequence);
818 editSequence.addActionListener(this);
820 editMenu.add(toUpper);
821 toUpper.addActionListener(this);
822 editMenu.add(toLower);
823 toLower.addActionListener(this);
824 editMenu.add(toggleCase);
825 seqMenu.add(sequenceName);
826 // seqMenu.add(sequenceDetails);
828 if (!ap.av.applet.useXtrnalSviewer)
832 seqMenu.add(repGroup);
833 menu1.add(unGroupMenuItem);
834 menu1.add(colourMenu);
835 menu1.add(showBoxes);
837 menu1.add(showColourText);
838 menu1.add(displayNonconserved);
839 toggleCase.addActionListener(this);
840 pdb.addActionListener(this);
841 hideSeqs.addActionListener(this);
842 repGroup.addActionListener(this);
843 revealAll.addActionListener(this);
844 revealSeq.addActionListener(this);
849 ap.paintAlignment(true);
852 protected void clustalColour_actionPerformed()
854 SequenceGroup sg = getGroup();
855 sg.cs = new ClustalxColourScheme(
856 sg,ap.av.getHiddenRepSequences());
860 protected void zappoColour_actionPerformed()
862 getGroup().cs = new ZappoColourScheme();
866 protected void taylorColour_actionPerformed()
868 getGroup().cs = new TaylorColourScheme();
872 protected void hydrophobicityColour_actionPerformed()
874 getGroup().cs = new HydrophobicColourScheme();
878 protected void helixColour_actionPerformed()
880 getGroup().cs = new HelixColourScheme();
884 protected void strandColour_actionPerformed()
886 getGroup().cs = new StrandColourScheme();
890 protected void turnColour_actionPerformed()
892 getGroup().cs = new TurnColourScheme();
896 protected void buriedColour_actionPerformed()
898 getGroup().cs = new BuriedColourScheme();
902 public void nucleotideMenuItem_actionPerformed()
904 getGroup().cs = new NucleotideColourScheme();
908 protected void abovePIDColour_itemStateChanged()
910 SequenceGroup sg = getGroup();
916 if (abovePIDColour.getState())
918 sg.cs.setConsensus(AAFrequency.calculate(
919 sg.getSequences(ap.av.getHiddenRepSequences()), 0,
920 ap.av.getAlignment().getWidth()));
921 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
924 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
926 SliderPanel.showPIDSlider();
930 // remove PIDColouring
932 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
939 protected void userDefinedColour_actionPerformed()
941 new UserDefinedColours(ap, getGroup());
944 protected void PIDColour_actionPerformed()
946 SequenceGroup sg = getGroup();
947 sg.cs = new PIDColourScheme();
948 sg.cs.setConsensus(AAFrequency.calculate(
949 sg.getSequences(ap.av.getHiddenRepSequences()), 0,
950 ap.av.getAlignment().getWidth()));
954 protected void BLOSUM62Colour_actionPerformed()
956 SequenceGroup sg = getGroup();
958 sg.cs = new Blosum62ColourScheme();
960 sg.cs.setConsensus(AAFrequency.calculate(
961 sg.getSequences(ap.av.getHiddenRepSequences()), 0,
962 ap.av.getAlignment().getWidth()));
967 protected void noColourmenuItem_actionPerformed()
969 getGroup().cs = null;
973 protected void conservationMenuItem_itemStateChanged()
975 SequenceGroup sg = getGroup();
981 if (conservationMenuItem.getState())
984 sg.cs.setConservation(Conservation.calculateConservation("Group",
985 ResidueProperties.propHash, 3,
986 sg.getSequences(ap.av.getHiddenRepSequences()), 0,
987 ap.av.getAlignment().getWidth(),
988 false, ap.av.getConsPercGaps(),false));
989 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
990 SliderPanel.showConservationSlider();
993 // remove ConservationColouring
995 sg.cs.setConservation(null);
1001 SequenceGroup getGroup()
1003 SequenceGroup sg = ap.av.getSelectionGroup();
1005 // this method won't add a new group if it already exists
1008 ap.av.getAlignment().addGroup(sg);
1014 void unGroupMenuItem_actionPerformed()
1016 SequenceGroup sg = ap.av.getSelectionGroup();
1017 ap.av.getAlignment().deleteGroup(sg);
1018 ap.av.setSelectionGroup(null);
1019 ap.paintAlignment(true);
1022 public void showColourText_itemStateChanged()
1024 getGroup().setColourText(showColourText.getState());
1028 public void showText_itemStateChanged()
1030 getGroup().setDisplayText(showText.getState());
1034 public void showNonconserved_itemStateChanged()
1036 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1040 public void showBoxes_itemStateChanged()
1042 getGroup().setDisplayBoxes(showBoxes.getState());
1046 void hideSequences(boolean representGroup)
1048 SequenceGroup sg = ap.av.getSelectionGroup();
1049 if (sg == null || sg.getSize() < 1)
1051 ap.av.hideSequence(new SequenceI[]
1056 ap.av.setSelectionGroup(null);
1060 ap.av.hideRepSequences(seq, sg);
1065 int gsize = sg.getSize();
1068 hseqs = new SequenceI[gsize];
1071 for (int i = 0; i < gsize; i++)
1073 hseqs[index++] = sg.getSequenceAt(i);
1076 ap.av.hideSequence(hseqs);
1077 ap.av.sendSelection();