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.MessageManager;
30 import jalview.util.UrlLink;
31 import jalview.io.AppletFormatAdapter;
32 import jalview.io.SequenceAnnotationReport;
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 createGroupMenuItem = new MenuItem();
75 MenuItem nucleotideMenuItem = new MenuItem();
77 Menu colourMenu = new Menu();
79 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
81 CheckboxMenuItem showText = new CheckboxMenuItem();
83 CheckboxMenuItem showColourText = new CheckboxMenuItem();
85 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
87 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
89 MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
91 MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
93 MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
95 MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
97 MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case"));
99 Menu outputmenu = new Menu();
101 Menu seqMenu = new Menu();
103 MenuItem pdb = new MenuItem();
105 MenuItem hideSeqs = new MenuItem();
107 MenuItem repGroup = new MenuItem();
109 MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
111 MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
113 MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
115 MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
117 MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
121 MenuItem revealAll = new MenuItem();
123 MenuItem revealSeq = new MenuItem();
126 * index of sequence to be revealed
128 int revealSeq_index = -1;
130 Menu menu1 = new Menu();
132 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
134 // /////////////////////////////////////////////////////////
135 // If this is activated from the sequence panel, the user may want to
136 // edit or annotate a particular residue. Therefore display the residue menu
138 // If from the IDPanel, we must display the sequence menu
139 // ////////////////////////////////////////////////////////
147 } catch (Exception e)
152 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
154 MenuItem item = new MenuItem(
155 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
157 item.addActionListener(this);
158 outputmenu.add(item);
161 SequenceGroup sg = ap.av.getSelectionGroup();
163 if (sg != null && sg.getSize() > 0)
165 editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
166 showText.setState(sg.getDisplayText());
167 showColourText.setState(sg.getColourText());
168 showBoxes.setState(sg.getDisplayBoxes());
169 displayNonconserved.setState(sg.getShowNonconserved());
170 if (!ap.av.getAlignment().getGroups().contains(sg))
172 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
173 groupMenu.remove(unGroupMenuItem);
175 menu1.setLabel(MessageManager.getString("action.edit_group"));
176 groupMenu.remove(createGroupMenuItem);
186 if (links != null && links.size() > 0)
188 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
190 for (int i = 0; i < links.size(); i++)
192 link = links.elementAt(i).toString();
193 UrlLink urlLink = new UrlLink(link);
194 if (!urlLink.isValid())
196 System.err.println(urlLink.getInvalidMessage());
199 final String target = urlLink.getTarget(); // link.substring(0,
200 // link.indexOf("|"));
201 final String label = urlLink.getLabel();
202 if (seq != null && urlLink.isDynamic())
205 // collect matching db-refs
206 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
207 seq.getDBRef(), new String[]
209 // collect id string too
210 String id = seq.getName();
211 String descr = seq.getDescription();
212 if (descr != null && descr.length() < 1)
218 for (int r = 0; r < dbr.length; r++)
220 if (id != null && dbr[r].getAccessionId().equals(id))
222 // suppress duplicate link creation for the bare sequence ID
223 // string with this link
226 // create Bare ID link for this RUL
227 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
231 for (int u = 0; u < urls.length; u += 2)
233 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
240 // create Bare ID link for this RUL
241 String[] urls = urlLink.makeUrls(id, true);
244 for (int u = 0; u < urls.length; u += 2)
246 addshowLink(linkMenu, label, urls[u + 1]);
249 // addshowLink(linkMenu, target, url_pref + id + url_suff);
251 // Now construct URLs from description but only try to do it for regex
253 if (descr != null && urlLink.getRegexReplace() != null)
255 // create link for this URL from description only if regex matches
256 String[] urls = urlLink.makeUrls(descr, true);
259 for (int u = 0; u < urls.length; u += 2)
261 addshowLink(linkMenu, label, urls[u + 1]);
268 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
273 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
274 * string and any matching database reference accessions String url_pref
275 * = link.substring(link.indexOf("|") + 1,
276 * link.indexOf("$SEQUENCE_ID$"));
278 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
279 * // collect matching db-refs DBRefEntry[] dbr =
280 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
281 * String[]{target}); // collect id string too String id =
282 * seq.getName(); if (id.indexOf("|") > -1) { id =
283 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
284 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
285 * suppress duplicate link creation for the bare sequence ID string with
286 * this link id = null; } addshowLink(linkMenu,
287 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
288 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
289 * create Bare ID link for this RUL addshowLink(linkMenu, target,
290 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
291 * link.substring(link.lastIndexOf("|")+1)); }
294 if (linkMenu.getItemCount() > 0)
298 seqMenu.add(linkMenu);
306 // TODO: add group link menu entry here
309 seqMenu.setLabel(seq.getName());
310 repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{seq.getName()}));
317 if (!ap.av.hasHiddenRows())
324 final int index = ap.av.getAlignment().findIndex(seq);
326 if (ap.av.adjustForHiddenSeqs(index)
327 - ap.av.adjustForHiddenSeqs(index - 1) > 1)
329 revealSeq_index = index;
339 * add a show URL menu item to the given linkMenu
343 * - menu label string
347 private void addshowLink(Menu linkMenu, final String target,
350 addshowLink(linkMenu, target, target, url);
354 * add a show URL menu item to the given linkMenu
358 * - URL target window
360 * - menu label string
364 private void addshowLink(Menu linkMenu, final String target,
365 final String label, final String url)
367 MenuItem item = new MenuItem(label);
368 item.addActionListener(new java.awt.event.ActionListener()
370 public void actionPerformed(ActionEvent e)
372 ap.alignFrame.showURL(url, target);
378 public void itemStateChanged(ItemEvent evt)
380 if (evt.getSource() == abovePIDColour)
382 abovePIDColour_itemStateChanged();
384 else if (evt.getSource() == showColourText)
386 showColourText_itemStateChanged();
388 else if (evt.getSource() == showText)
390 showText_itemStateChanged();
392 else if (evt.getSource() == showBoxes)
394 showBoxes_itemStateChanged();
396 else if (evt.getSource() == displayNonconserved)
398 this.showNonconserved_itemStateChanged();
402 public void actionPerformed(ActionEvent evt)
404 Object source = evt.getSource();
405 if (source == clustalColour)
407 clustalColour_actionPerformed();
409 else if (source == zappoColour)
411 zappoColour_actionPerformed();
413 else if (source == taylorColour)
415 taylorColour_actionPerformed();
417 else if (source == hydrophobicityColour)
419 hydrophobicityColour_actionPerformed();
421 else if (source == helixColour)
423 helixColour_actionPerformed();
425 else if (source == strandColour)
427 strandColour_actionPerformed();
429 else if (source == turnColour)
431 turnColour_actionPerformed();
433 else if (source == buriedColour)
435 buriedColour_actionPerformed();
437 else if (source == nucleotideMenuItem)
439 nucleotideMenuItem_actionPerformed();
442 else if (source == userDefinedColour)
444 userDefinedColour_actionPerformed();
446 else if (source == PIDColour)
448 PIDColour_actionPerformed();
450 else if (source == BLOSUM62Colour)
452 BLOSUM62Colour_actionPerformed();
454 else if (source == noColourmenuItem)
456 noColourmenuItem_actionPerformed();
458 else if (source == conservationMenuItem)
460 conservationMenuItem_itemStateChanged();
462 else if (source == unGroupMenuItem)
464 unGroupMenuItem_actionPerformed();
467 else if (source == createGroupMenuItem)
469 createGroupMenuItem_actionPerformed();
472 else if (source == sequenceName)
476 else if (source == sequenceDetails)
478 showSequenceDetails();
480 else if (source == selSeqDetails)
482 showSequenceSelectionDetails();
484 else if (source == pdb)
488 else if (source == hideSeqs)
490 hideSequences(false);
492 else if (source == repGroup)
496 else if (source == revealSeq)
498 ap.av.showSequence(revealSeq_index);
500 else if (source == revealAll)
502 ap.av.showAllHiddenSeqs();
505 else if (source == editGroupName)
507 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
508 getGroup().getDescription(), " Group Name",
509 "Group Description", ap.alignFrame,
510 "Edit Group Name / Description", 500, 100, true);
514 getGroup().setName(dialog.getName().replace(' ', '_'));
515 getGroup().setDescription(dialog.getDescription());
519 else if (source == copy)
521 ap.alignFrame.copy_actionPerformed();
523 else if (source == cut)
525 ap.alignFrame.cut_actionPerformed();
527 else if (source == editSequence)
529 SequenceGroup sg = ap.av.getSelectionGroup();
534 seq = (Sequence) sg.getSequenceAt(0);
536 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
537 sg.getStartRes(), sg.getEndRes() + 1), null,
538 "Edit Sequence ", null,
540 ap.alignFrame, "Edit Sequence", 500, 100, true);
544 EditCommand editCommand = new EditCommand("Edit Sequences",
545 EditCommand.REPLACE, dialog.getName().replace(' ',
546 ap.av.getGapCharacter()),
547 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
548 sg.getStartRes(), sg.getEndRes() + 1,
549 ap.av.getAlignment());
551 ap.alignFrame.addHistoryItem(editCommand);
553 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
558 else if (source == toUpper || source == toLower || source == toggleCase)
560 SequenceGroup sg = ap.av.getSelectionGroup();
561 Vector regions = new Vector();
564 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
565 sg.getStartRes(), sg.getEndRes() + 1);
570 if (source == toggleCase)
572 description = "Toggle Case";
573 caseChange = ChangeCaseCommand.TOGGLE_CASE;
575 else if (source == toUpper)
577 description = "To Upper Case";
578 caseChange = ChangeCaseCommand.TO_UPPER;
582 description = "To Lower Case";
583 caseChange = ChangeCaseCommand.TO_LOWER;
586 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
587 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
588 startEnd, caseChange);
590 ap.alignFrame.addHistoryItem(caseCommand);
592 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
597 else if (source == sequenceFeature)
599 SequenceGroup sg = ap.av.getSelectionGroup();
605 int rsize = 0, gSize = sg.getSize();
606 SequenceI[] rseqs, seqs = new SequenceI[gSize];
607 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
609 for (int i = 0; i < gSize; i++)
611 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
612 int end = sg.findEndRes(sg.getSequenceAt(i));
615 seqs[rsize] = sg.getSequenceAt(i);
616 features[rsize] = new SequenceFeature(null, null, null, start,
621 rseqs = new SequenceI[rsize];
622 tfeatures = new SequenceFeature[rsize];
623 System.arraycopy(seqs, 0, rseqs, 0, rsize);
624 System.arraycopy(features, 0, tfeatures, 0, rsize);
625 features = tfeatures;
628 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
631 ap.alignFrame.sequenceFeatures.setState(true);
632 ap.av.showSequenceFeatures(true);
633 ap.highlightSearchResults(null);
643 void outputText(ActionEvent e)
645 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
647 Frame frame = new Frame();
649 jalview.bin.JalviewLite.addFrame(frame,
650 MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
651 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
652 // now returns a full copy of sequence data
653 // TODO consider using getSequenceSelection instead here
655 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
656 e.getActionCommand(),
657 new Alignment(ap.av.getSelectionAsNewSequence()),
658 ap.av.showJVSuffix));
662 protected void showSequenceSelectionDetails()
664 createSequenceDetailsReport(ap.av.getSequenceSelection());
667 protected void showSequenceDetails()
669 createSequenceDetailsReport(new SequenceI[]
673 public void createSequenceDetailsReport(SequenceI[] sequences)
676 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
678 StringBuffer contents = new StringBuffer();
679 for (SequenceI seq : sequences)
681 contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
682 new SequenceAnnotationReport(null)
683 .createSequenceAnnotationReport(
689 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
691 contents.append("</p>");
693 Frame frame = new Frame();
695 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
696 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
697 : "Selection"), 600, 500);
698 cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
703 EditNameDialog dialog = new EditNameDialog(seq.getName(),
704 seq.getDescription(), " Sequence Name",
705 "Sequence Description", ap.alignFrame,
706 "Edit Sequence Name / Description", 500, 100, true);
710 seq.setName(dialog.getName());
711 seq.setDescription(dialog.getDescription());
712 ap.paintAlignment(false);
718 if (seq.getPDBId() != null)
720 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
722 if (ap.av.applet.jmolAvailable)
723 new jalview.appletgui.AppletJmol(entry, new Sequence[]
724 { seq }, null, ap, AppletFormatAdapter.URL);
726 new MCview.AppletPDBViewer(entry, new Sequence[]
727 { seq }, null, ap, AppletFormatAdapter.URL);
732 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
733 cap.setText(MessageManager.getString("label.paste_pdb_file"));
734 cap.setPDBImport(seq);
735 Frame frame = new Frame();
737 jalview.bin.JalviewLite.addFrame(frame,
738 MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
742 private void jbInit() throws Exception
744 groupMenu.setLabel(MessageManager.getString("label.selection"));
745 sequenceFeature.addActionListener(this);
747 editGroupName.addActionListener(this);
748 unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
749 unGroupMenuItem.addActionListener(this);
751 createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
752 createGroupMenuItem.addActionListener(this);
754 nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
755 nucleotideMenuItem.addActionListener(this);
756 conservationMenuItem.addItemListener(this);
757 abovePIDColour.addItemListener(this);
758 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
759 showBoxes.setLabel(MessageManager.getString("label.boxes"));
760 showBoxes.setState(true);
761 showBoxes.addItemListener(this);
762 sequenceName.addActionListener(this);
763 sequenceDetails.addActionListener(this);
764 selSeqDetails.addActionListener(this);
765 displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
766 displayNonconserved.setState(false);
767 displayNonconserved.addItemListener(this);
768 showText.setLabel(MessageManager.getString("label.text"));
769 showText.addItemListener(this);
770 showColourText.setLabel(MessageManager.getString("label.colour_text"));
771 showColourText.addItemListener(this);
772 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
773 seqMenu.setLabel(MessageManager.getString("label.sequence"));
774 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
775 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
776 repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
777 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
778 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
779 menu1.setLabel(MessageManager.getString("label.group")+":");
785 // groupMenu.add(selSeqDetails);
786 groupMenu.add(editMenu);
787 groupMenu.add(outputmenu);
788 groupMenu.add(sequenceFeature);
789 groupMenu.add(createGroupMenuItem);
790 groupMenu.add(unGroupMenuItem);
791 groupMenu.add(menu1);
793 colourMenu.add(noColourmenuItem);
794 colourMenu.add(clustalColour);
795 colourMenu.add(BLOSUM62Colour);
796 colourMenu.add(PIDColour);
797 colourMenu.add(zappoColour);
798 colourMenu.add(taylorColour);
799 colourMenu.add(hydrophobicityColour);
800 colourMenu.add(helixColour);
801 colourMenu.add(strandColour);
802 colourMenu.add(turnColour);
803 colourMenu.add(buriedColour);
804 colourMenu.add(nucleotideMenuItem);
805 colourMenu.add(userDefinedColour);
806 colourMenu.addSeparator();
807 colourMenu.add(abovePIDColour);
808 colourMenu.add(conservationMenuItem);
810 noColourmenuItem.setLabel("None");
811 noColourmenuItem.addActionListener(this);
813 clustalColour.setLabel("Clustalx colours");
814 clustalColour.addActionListener(this);
815 zappoColour.setLabel("Zappo");
816 zappoColour.addActionListener(this);
817 taylorColour.setLabel("Taylor");
818 taylorColour.addActionListener(this);
819 hydrophobicityColour.setLabel("Hydrophobicity");
820 hydrophobicityColour.addActionListener(this);
821 helixColour.setLabel("Helix propensity");
822 helixColour.addActionListener(this);
823 strandColour.setLabel("Strand propensity");
824 strandColour.addActionListener(this);
825 turnColour.setLabel("Turn propensity");
826 turnColour.addActionListener(this);
827 buriedColour.setLabel("Buried Index");
828 buriedColour.addActionListener(this);
829 abovePIDColour.setLabel("Above % Identity");
831 userDefinedColour.setLabel("User Defined");
832 userDefinedColour.addActionListener(this);
833 PIDColour.setLabel("Percentage Identity");
834 PIDColour.addActionListener(this);
835 BLOSUM62Colour.setLabel("BLOSUM62");
836 BLOSUM62Colour.addActionListener(this);
837 conservationMenuItem.setLabel("Conservation");
840 copy.addActionListener(this);
842 cut.addActionListener(this);
844 editMenu.add(editSequence);
845 editSequence.addActionListener(this);
847 editMenu.add(toUpper);
848 toUpper.addActionListener(this);
849 editMenu.add(toLower);
850 toLower.addActionListener(this);
851 editMenu.add(toggleCase);
852 seqMenu.add(sequenceName);
853 // seqMenu.add(sequenceDetails);
855 if (!ap.av.applet.useXtrnalSviewer)
859 seqMenu.add(repGroup);
860 menu1.add(editGroupName);
861 menu1.add(colourMenu);
862 menu1.add(showBoxes);
864 menu1.add(showColourText);
865 menu1.add(displayNonconserved);
866 toggleCase.addActionListener(this);
867 pdb.addActionListener(this);
868 hideSeqs.addActionListener(this);
869 repGroup.addActionListener(this);
870 revealAll.addActionListener(this);
871 revealSeq.addActionListener(this);
876 ap.paintAlignment(true);
879 protected void clustalColour_actionPerformed()
881 SequenceGroup sg = getGroup();
882 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
886 protected void zappoColour_actionPerformed()
888 getGroup().cs = new ZappoColourScheme();
892 protected void taylorColour_actionPerformed()
894 getGroup().cs = new TaylorColourScheme();
898 protected void hydrophobicityColour_actionPerformed()
900 getGroup().cs = new HydrophobicColourScheme();
904 protected void helixColour_actionPerformed()
906 getGroup().cs = new HelixColourScheme();
910 protected void strandColour_actionPerformed()
912 getGroup().cs = new StrandColourScheme();
916 protected void turnColour_actionPerformed()
918 getGroup().cs = new TurnColourScheme();
922 protected void buriedColour_actionPerformed()
924 getGroup().cs = new BuriedColourScheme();
928 public void nucleotideMenuItem_actionPerformed()
930 getGroup().cs = new NucleotideColourScheme();
934 protected void abovePIDColour_itemStateChanged()
936 SequenceGroup sg = getGroup();
942 if (abovePIDColour.getState())
944 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
945 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
946 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
949 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
951 SliderPanel.showPIDSlider();
955 // remove PIDColouring
957 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
964 protected void userDefinedColour_actionPerformed()
966 new UserDefinedColours(ap, getGroup());
969 protected void PIDColour_actionPerformed()
971 SequenceGroup sg = getGroup();
972 sg.cs = new PIDColourScheme();
973 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
974 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
978 protected void BLOSUM62Colour_actionPerformed()
980 SequenceGroup sg = getGroup();
982 sg.cs = new Blosum62ColourScheme();
984 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
985 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
990 protected void noColourmenuItem_actionPerformed()
992 getGroup().cs = null;
996 protected void conservationMenuItem_itemStateChanged()
998 SequenceGroup sg = getGroup();
1004 if (conservationMenuItem.getState())
1007 sg.cs.setConservation(Conservation.calculateConservation("Group",
1008 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1009 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1010 .getWidth(), false, ap.av.getConsPercGaps(), false));
1011 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1012 SliderPanel.showConservationSlider();
1015 // remove ConservationColouring
1017 sg.cs.setConservation(null);
1023 SequenceGroup getGroup()
1025 SequenceGroup sg = ap.av.getSelectionGroup();
1027 // this method won't add a new group if it already exists
1030 ap.av.getAlignment().addGroup(sg);
1036 void unGroupMenuItem_actionPerformed()
1038 SequenceGroup sg = ap.av.getSelectionGroup();
1039 ap.av.getAlignment().deleteGroup(sg);
1040 ap.av.setSelectionGroup(null);
1041 ap.paintAlignment(true);
1044 void createGroupMenuItem_actionPerformed()
1046 getGroup(); // implicitly create group
1050 public void showColourText_itemStateChanged()
1052 getGroup().setColourText(showColourText.getState());
1056 public void showText_itemStateChanged()
1058 getGroup().setDisplayText(showText.getState());
1062 public void showNonconserved_itemStateChanged()
1064 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1068 public void showBoxes_itemStateChanged()
1070 getGroup().setDisplayBoxes(showBoxes.getState());
1074 void hideSequences(boolean representGroup)
1076 SequenceGroup sg = ap.av.getSelectionGroup();
1077 if (sg == null || sg.getSize() < 1)
1079 ap.av.hideSequence(new SequenceI[]
1084 ap.av.setSelectionGroup(null);
1088 ap.av.hideRepSequences(seq, sg);
1093 int gsize = sg.getSize();
1096 hseqs = new SequenceI[gsize];
1099 for (int i = 0; i < gsize; i++)
1101 hseqs[index++] = sg.getSequenceAt(i);
1104 ap.av.hideSequence(hseqs);
1105 ap.av.sendSelection();