2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
3 * Copyright (C) 2014 The Jalview Authors
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/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
24 import java.awt.event.*;
26 import jalview.analysis.*;
27 import jalview.commands.*;
28 import jalview.datamodel.*;
29 import jalview.schemes.*;
30 import jalview.util.MessageManager;
31 import jalview.util.UrlLink;
32 import jalview.io.AppletFormatAdapter;
33 import jalview.io.SequenceAnnotationReport;
35 public class APopupMenu extends java.awt.PopupMenu implements
36 ActionListener, ItemListener
38 Menu groupMenu = new Menu();
40 MenuItem editGroupName = new MenuItem();
42 protected MenuItem clustalColour = new MenuItem();
44 protected MenuItem zappoColour = new MenuItem();
46 protected MenuItem taylorColour = new MenuItem();
48 protected MenuItem hydrophobicityColour = new MenuItem();
50 protected MenuItem helixColour = new MenuItem();
52 protected MenuItem strandColour = new MenuItem();
54 protected MenuItem turnColour = new MenuItem();
56 protected MenuItem buriedColour = new MenuItem();
58 protected CheckboxMenuItem abovePIDColour = new CheckboxMenuItem();
60 protected MenuItem userDefinedColour = new MenuItem();
62 protected MenuItem PIDColour = new MenuItem();
64 protected MenuItem BLOSUM62Colour = new MenuItem();
66 MenuItem noColourmenuItem = new MenuItem();
68 protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
70 final AlignmentPanel ap;
72 MenuItem unGroupMenuItem = new MenuItem();
74 MenuItem createGroupMenuItem = new MenuItem();
76 MenuItem nucleotideMenuItem = new MenuItem();
78 Menu colourMenu = new Menu();
80 CheckboxMenuItem showBoxes = new CheckboxMenuItem();
82 CheckboxMenuItem showText = new CheckboxMenuItem();
84 CheckboxMenuItem showColourText = new CheckboxMenuItem();
86 CheckboxMenuItem displayNonconserved = new CheckboxMenuItem();
88 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
90 MenuItem copy = new MenuItem(MessageManager.getString("label.jalview_copy"));
92 MenuItem cut = new MenuItem(MessageManager.getString("label.jalview_cut"));
94 MenuItem toUpper = new MenuItem(MessageManager.getString("label.to_upper_case"));
96 MenuItem toLower = new MenuItem(MessageManager.getString("label.to_lower_case"));
98 MenuItem toggleCase = new MenuItem(MessageManager.getString("label.toggle_case"));
100 Menu outputmenu = new Menu();
102 Menu seqMenu = new Menu();
104 MenuItem pdb = new MenuItem();
106 MenuItem hideSeqs = new MenuItem();
108 MenuItem repGroup = new MenuItem();
110 MenuItem sequenceName = new MenuItem(MessageManager.getString("label.edit_name_description"));
112 MenuItem sequenceFeature = new MenuItem(MessageManager.getString("label.create_sequence_feature"));
114 MenuItem editSequence = new MenuItem(MessageManager.getString("label.edit_sequence"));
116 MenuItem sequenceDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
118 MenuItem selSeqDetails = new MenuItem(MessageManager.getString("label.sequence_details") + "...");
122 MenuItem revealAll = new MenuItem();
124 MenuItem revealSeq = new MenuItem();
127 * index of sequence to be revealed
129 int revealSeq_index = -1;
131 Menu menu1 = new Menu();
133 public APopupMenu(AlignmentPanel apanel, final Sequence seq, Vector links)
135 // /////////////////////////////////////////////////////////
136 // If this is activated from the sequence panel, the user may want to
137 // edit or annotate a particular residue. Therefore display the residue menu
139 // If from the IDPanel, we must display the sequence menu
140 // ////////////////////////////////////////////////////////
148 } catch (Exception e)
153 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
155 MenuItem item = new MenuItem(
156 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
158 item.addActionListener(this);
159 outputmenu.add(item);
162 SequenceGroup sg = ap.av.getSelectionGroup();
164 if (sg != null && sg.getSize() > 0)
166 editGroupName.setLabel(MessageManager.formatMessage("label.name_param", new String[]{sg.getName()}));
167 showText.setState(sg.getDisplayText());
168 showColourText.setState(sg.getColourText());
169 showBoxes.setState(sg.getDisplayBoxes());
170 displayNonconserved.setState(sg.getShowNonconserved());
171 if (!ap.av.getAlignment().getGroups().contains(sg))
173 menu1.setLabel(MessageManager.getString("action.edit_new_group"));
174 groupMenu.remove(unGroupMenuItem);
176 menu1.setLabel(MessageManager.getString("action.edit_group"));
177 groupMenu.remove(createGroupMenuItem);
187 if (links != null && links.size() > 0)
189 Menu linkMenu = new Menu(MessageManager.getString("action.link"));
191 for (int i = 0; i < links.size(); i++)
193 link = links.elementAt(i).toString();
194 UrlLink urlLink = new UrlLink(link);
195 if (!urlLink.isValid())
197 System.err.println(urlLink.getInvalidMessage());
200 final String target = urlLink.getTarget(); // link.substring(0,
201 // link.indexOf("|"));
202 final String label = urlLink.getLabel();
203 if (seq != null && urlLink.isDynamic())
206 // collect matching db-refs
207 DBRefEntry[] dbr = jalview.util.DBRefUtils.selectRefs(
208 seq.getDBRef(), new String[]
210 // collect id string too
211 String id = seq.getName();
212 String descr = seq.getDescription();
213 if (descr != null && descr.length() < 1)
219 for (int r = 0; r < dbr.length; r++)
221 if (id != null && dbr[r].getAccessionId().equals(id))
223 // suppress duplicate link creation for the bare sequence ID
224 // string with this link
227 // create Bare ID link for this RUL
228 String[] urls = urlLink.makeUrls(dbr[r].getAccessionId(),
232 for (int u = 0; u < urls.length; u += 2)
234 addshowLink(linkMenu, label + "|" + urls[u], urls[u + 1]);
241 // create Bare ID link for this RUL
242 String[] urls = urlLink.makeUrls(id, true);
245 for (int u = 0; u < urls.length; u += 2)
247 addshowLink(linkMenu, label, urls[u + 1]);
250 // addshowLink(linkMenu, target, url_pref + id + url_suff);
252 // Now construct URLs from description but only try to do it for regex
254 if (descr != null && urlLink.getRegexReplace() != null)
256 // create link for this URL from description only if regex matches
257 String[] urls = urlLink.makeUrls(descr, true);
260 for (int u = 0; u < urls.length; u += 2)
262 addshowLink(linkMenu, label, urls[u + 1]);
269 addshowLink(linkMenu, target, urlLink.getUrl_prefix()); // link.substring(link.lastIndexOf("|")+1));
274 * if (link.indexOf("$SEQUENCE_ID$") > -1) { // Substitute SEQUENCE_ID
275 * string and any matching database reference accessions String url_pref
276 * = link.substring(link.indexOf("|") + 1,
277 * link.indexOf("$SEQUENCE_ID$"));
279 * String url_suff = link.substring(link.indexOf("$SEQUENCE_ID$") + 13);
280 * // collect matching db-refs DBRefEntry[] dbr =
281 * jalview.util.DBRefUtils.selectRefs(seq.getDBRef(), new
282 * String[]{target}); // collect id string too String id =
283 * seq.getName(); if (id.indexOf("|") > -1) { id =
284 * id.substring(id.lastIndexOf("|") + 1); } if (dbr!=null) { for (int
285 * r=0;r<dbr.length; r++) { if (dbr[r].getAccessionId().equals(id)) { //
286 * suppress duplicate link creation for the bare sequence ID string with
287 * this link id = null; } addshowLink(linkMenu,
288 * dbr[r].getSource()+"|"+dbr[r].getAccessionId(), target,
289 * url_pref+dbr[r].getAccessionId()+url_suff); } } if (id!=null) { //
290 * create Bare ID link for this RUL addshowLink(linkMenu, target,
291 * url_pref + id + url_suff); } } else { addshowLink(linkMenu, target,
292 * link.substring(link.lastIndexOf("|")+1)); }
295 if (linkMenu.getItemCount() > 0)
299 seqMenu.add(linkMenu);
307 // TODO: add group link menu entry here
310 seqMenu.setLabel(seq.getName());
311 repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{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 == createGroupMenuItem)
470 createGroupMenuItem_actionPerformed();
473 else if (source == sequenceName)
477 else if (source == sequenceDetails)
479 showSequenceDetails();
481 else if (source == selSeqDetails)
483 showSequenceSelectionDetails();
485 else if (source == pdb)
489 else if (source == hideSeqs)
491 hideSequences(false);
493 else if (source == repGroup)
497 else if (source == revealSeq)
499 ap.av.showSequence(revealSeq_index);
501 else if (source == revealAll)
503 ap.av.showAllHiddenSeqs();
506 else if (source == editGroupName)
508 EditNameDialog dialog = new EditNameDialog(getGroup().getName(),
509 getGroup().getDescription(), " Group Name",
510 "Group Description", ap.alignFrame,
511 "Edit Group Name / Description", 500, 100, true);
515 getGroup().setName(dialog.getName().replace(' ', '_'));
516 getGroup().setDescription(dialog.getDescription());
520 else if (source == copy)
522 ap.alignFrame.copy_actionPerformed();
524 else if (source == cut)
526 ap.alignFrame.cut_actionPerformed();
528 else if (source == editSequence)
530 SequenceGroup sg = ap.av.getSelectionGroup();
535 seq = (Sequence) sg.getSequenceAt(0);
537 EditNameDialog dialog = new EditNameDialog(seq.getSequenceAsString(
538 sg.getStartRes(), sg.getEndRes() + 1), null,
539 "Edit Sequence ", null,
541 ap.alignFrame, "Edit Sequence", 500, 100, true);
545 EditCommand editCommand = new EditCommand("Edit Sequences",
546 EditCommand.REPLACE, dialog.getName().replace(' ',
547 ap.av.getGapCharacter()),
548 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
549 sg.getStartRes(), sg.getEndRes() + 1,
550 ap.av.getAlignment());
552 ap.alignFrame.addHistoryItem(editCommand);
554 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
559 else if (source == toUpper || source == toLower || source == toggleCase)
561 SequenceGroup sg = ap.av.getSelectionGroup();
562 Vector regions = new Vector();
565 int[][] startEnd = ap.av.getVisibleRegionBoundaries(
566 sg.getStartRes(), sg.getEndRes() + 1);
571 if (source == toggleCase)
573 description = "Toggle Case";
574 caseChange = ChangeCaseCommand.TOGGLE_CASE;
576 else if (source == toUpper)
578 description = "To Upper Case";
579 caseChange = ChangeCaseCommand.TO_UPPER;
583 description = "To Lower Case";
584 caseChange = ChangeCaseCommand.TO_LOWER;
587 ChangeCaseCommand caseCommand = new ChangeCaseCommand(description,
588 sg.getSequencesAsArray(ap.av.getHiddenRepSequences()),
589 startEnd, caseChange);
591 ap.alignFrame.addHistoryItem(caseCommand);
593 ap.av.firePropertyChange("alignment", null, ap.av.getAlignment()
598 else if (source == sequenceFeature)
600 SequenceGroup sg = ap.av.getSelectionGroup();
606 int rsize = 0, gSize = sg.getSize();
607 SequenceI[] rseqs, seqs = new SequenceI[gSize];
608 SequenceFeature[] tfeatures, features = new SequenceFeature[gSize];
610 for (int i = 0; i < gSize; i++)
612 int start = sg.getSequenceAt(i).findPosition(sg.getStartRes());
613 int end = sg.findEndRes(sg.getSequenceAt(i));
616 seqs[rsize] = sg.getSequenceAt(i);
617 features[rsize] = new SequenceFeature(null, null, null, start,
622 rseqs = new SequenceI[rsize];
623 tfeatures = new SequenceFeature[rsize];
624 System.arraycopy(seqs, 0, rseqs, 0, rsize);
625 System.arraycopy(features, 0, tfeatures, 0, rsize);
626 features = tfeatures;
629 if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs,
632 ap.alignFrame.sequenceFeatures.setState(true);
633 ap.av.showSequenceFeatures(true);
634 ap.highlightSearchResults(null);
644 void outputText(ActionEvent e)
646 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
648 Frame frame = new Frame();
650 jalview.bin.JalviewLite.addFrame(frame,
651 MessageManager.formatMessage("label.selection_output_command", new String[]{e.getActionCommand()}),600, 500);
652 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method
653 // now returns a full copy of sequence data
654 // TODO consider using getSequenceSelection instead here
656 cap.setText(new jalview.io.AppletFormatAdapter().formatSequences(
657 e.getActionCommand(),
658 new Alignment(ap.av.getSelectionAsNewSequence()),
659 ap.av.showJVSuffix));
663 protected void showSequenceSelectionDetails()
665 createSequenceDetailsReport(ap.av.getSequenceSelection());
668 protected void showSequenceDetails()
670 createSequenceDetailsReport(new SequenceI[]
674 public void createSequenceDetailsReport(SequenceI[] sequences)
677 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
679 StringBuffer contents = new StringBuffer();
680 for (SequenceI seq : sequences)
682 contents.append(MessageManager.formatMessage("label.annotation_for_displayid",new String[]{seq.getDisplayId(true)}));
683 new SequenceAnnotationReport(null)
684 .createSequenceAnnotationReport(
690 (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax
692 contents.append("</p>");
694 Frame frame = new Frame();
696 jalview.bin.JalviewLite.addFrame(frame, "Sequence Details for "
697 + (sequences.length == 1 ? sequences[0].getDisplayId(true)
698 : "Selection"), 600, 500);
699 cap.setText(MessageManager.formatMessage("label.html_content", new String[]{contents.toString()}));
704 EditNameDialog dialog = new EditNameDialog(seq.getName(),
705 seq.getDescription(), " Sequence Name",
706 "Sequence Description", ap.alignFrame,
707 "Edit Sequence Name / Description", 500, 100, true);
711 seq.setName(dialog.getName());
712 seq.setDescription(dialog.getDescription());
713 ap.paintAlignment(false);
719 if (seq.getPDBId() != null)
721 PDBEntry entry = (PDBEntry) seq.getPDBId().firstElement();
723 if (ap.av.applet.jmolAvailable)
724 new jalview.appletgui.AppletJmol(entry, new Sequence[]
725 { seq }, null, ap, AppletFormatAdapter.URL);
727 new MCview.AppletPDBViewer(entry, new Sequence[]
728 { seq }, null, ap, AppletFormatAdapter.URL);
733 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, ap.alignFrame);
734 cap.setText(MessageManager.getString("label.paste_pdb_file"));
735 cap.setPDBImport(seq);
736 Frame frame = new Frame();
738 jalview.bin.JalviewLite.addFrame(frame,
739 MessageManager.formatMessage("label.paste_pdb_file_for_sequence", new String[]{seq.getName()}), 400, 300);
743 private void jbInit() throws Exception
745 groupMenu.setLabel(MessageManager.getString("label.selection"));
746 sequenceFeature.addActionListener(this);
748 editGroupName.addActionListener(this);
749 unGroupMenuItem.setLabel(MessageManager.getString("action.remove_group"));
750 unGroupMenuItem.addActionListener(this);
752 createGroupMenuItem.setLabel(MessageManager.getString("action.create_group"));
753 createGroupMenuItem.addActionListener(this);
755 nucleotideMenuItem.setLabel(MessageManager.getString("label.nucleotide"));
756 nucleotideMenuItem.addActionListener(this);
757 conservationMenuItem.addItemListener(this);
758 abovePIDColour.addItemListener(this);
759 colourMenu.setLabel(MessageManager.getString("label.group_colour"));
760 showBoxes.setLabel(MessageManager.getString("action.boxes"));
761 showBoxes.setState(true);
762 showBoxes.addItemListener(this);
763 sequenceName.addActionListener(this);
764 sequenceDetails.addActionListener(this);
765 selSeqDetails.addActionListener(this);
766 displayNonconserved.setLabel(MessageManager.getString("label.show_non_conversed"));
767 displayNonconserved.setState(false);
768 displayNonconserved.addItemListener(this);
769 showText.setLabel(MessageManager.getString("action.text"));
770 showText.addItemListener(this);
771 showColourText.setLabel(MessageManager.getString("label.colour_text"));
772 showColourText.addItemListener(this);
773 outputmenu.setLabel(MessageManager.getString("label.out_to_textbox"));
774 seqMenu.setLabel(MessageManager.getString("label.sequence"));
775 pdb.setLabel(MessageManager.getString("label.view_pdb_structure"));
776 hideSeqs.setLabel(MessageManager.getString("action.hide_sequences"));
777 repGroup.setLabel(MessageManager.formatMessage("label.represent_group_with", new String[]{""}));
778 revealAll.setLabel(MessageManager.getString("action.reveal_all"));
779 revealSeq.setLabel(MessageManager.getString("action.reveal_sequences"));
780 menu1.setLabel(MessageManager.getString("label.group")+":");
786 // groupMenu.add(selSeqDetails);
787 groupMenu.add(editMenu);
788 groupMenu.add(outputmenu);
789 groupMenu.add(sequenceFeature);
790 groupMenu.add(createGroupMenuItem);
791 groupMenu.add(unGroupMenuItem);
792 groupMenu.add(menu1);
794 colourMenu.add(noColourmenuItem);
795 colourMenu.add(clustalColour);
796 colourMenu.add(BLOSUM62Colour);
797 colourMenu.add(PIDColour);
798 colourMenu.add(zappoColour);
799 colourMenu.add(taylorColour);
800 colourMenu.add(hydrophobicityColour);
801 colourMenu.add(helixColour);
802 colourMenu.add(strandColour);
803 colourMenu.add(turnColour);
804 colourMenu.add(buriedColour);
805 colourMenu.add(nucleotideMenuItem);
806 colourMenu.add(userDefinedColour);
807 colourMenu.addSeparator();
808 colourMenu.add(abovePIDColour);
809 colourMenu.add(conservationMenuItem);
811 noColourmenuItem.setLabel("None");
812 noColourmenuItem.addActionListener(this);
814 clustalColour.setLabel("Clustalx colours");
815 clustalColour.addActionListener(this);
816 zappoColour.setLabel("Zappo");
817 zappoColour.addActionListener(this);
818 taylorColour.setLabel("Taylor");
819 taylorColour.addActionListener(this);
820 hydrophobicityColour.setLabel("Hydrophobicity");
821 hydrophobicityColour.addActionListener(this);
822 helixColour.setLabel("Helix propensity");
823 helixColour.addActionListener(this);
824 strandColour.setLabel("Strand propensity");
825 strandColour.addActionListener(this);
826 turnColour.setLabel("Turn propensity");
827 turnColour.addActionListener(this);
828 buriedColour.setLabel("Buried Index");
829 buriedColour.addActionListener(this);
830 abovePIDColour.setLabel("Above % Identity");
832 userDefinedColour.setLabel("User Defined");
833 userDefinedColour.addActionListener(this);
834 PIDColour.setLabel("Percentage Identity");
835 PIDColour.addActionListener(this);
836 BLOSUM62Colour.setLabel("BLOSUM62");
837 BLOSUM62Colour.addActionListener(this);
838 conservationMenuItem.setLabel("Conservation");
841 copy.addActionListener(this);
843 cut.addActionListener(this);
845 editMenu.add(editSequence);
846 editSequence.addActionListener(this);
848 editMenu.add(toUpper);
849 toUpper.addActionListener(this);
850 editMenu.add(toLower);
851 toLower.addActionListener(this);
852 editMenu.add(toggleCase);
853 seqMenu.add(sequenceName);
854 // seqMenu.add(sequenceDetails);
856 if (!ap.av.applet.useXtrnalSviewer)
860 seqMenu.add(repGroup);
861 menu1.add(editGroupName);
862 menu1.add(colourMenu);
863 menu1.add(showBoxes);
865 menu1.add(showColourText);
866 menu1.add(displayNonconserved);
867 toggleCase.addActionListener(this);
868 pdb.addActionListener(this);
869 hideSeqs.addActionListener(this);
870 repGroup.addActionListener(this);
871 revealAll.addActionListener(this);
872 revealSeq.addActionListener(this);
877 ap.paintAlignment(true);
880 protected void clustalColour_actionPerformed()
882 SequenceGroup sg = getGroup();
883 sg.cs = new ClustalxColourScheme(sg, ap.av.getHiddenRepSequences());
887 protected void zappoColour_actionPerformed()
889 getGroup().cs = new ZappoColourScheme();
893 protected void taylorColour_actionPerformed()
895 getGroup().cs = new TaylorColourScheme();
899 protected void hydrophobicityColour_actionPerformed()
901 getGroup().cs = new HydrophobicColourScheme();
905 protected void helixColour_actionPerformed()
907 getGroup().cs = new HelixColourScheme();
911 protected void strandColour_actionPerformed()
913 getGroup().cs = new StrandColourScheme();
917 protected void turnColour_actionPerformed()
919 getGroup().cs = new TurnColourScheme();
923 protected void buriedColour_actionPerformed()
925 getGroup().cs = new BuriedColourScheme();
929 public void nucleotideMenuItem_actionPerformed()
931 getGroup().cs = new NucleotideColourScheme();
935 protected void abovePIDColour_itemStateChanged()
937 SequenceGroup sg = getGroup();
943 if (abovePIDColour.getState())
945 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
946 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
947 int threshold = SliderPanel.setPIDSliderSource(ap, sg.cs, getGroup()
950 sg.cs.setThreshold(threshold, ap.av.getIgnoreGapsConsensus());
952 SliderPanel.showPIDSlider();
956 // remove PIDColouring
958 sg.cs.setThreshold(0, ap.av.getIgnoreGapsConsensus());
965 protected void userDefinedColour_actionPerformed()
967 new UserDefinedColours(ap, getGroup());
970 protected void PIDColour_actionPerformed()
972 SequenceGroup sg = getGroup();
973 sg.cs = new PIDColourScheme();
974 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
975 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
979 protected void BLOSUM62Colour_actionPerformed()
981 SequenceGroup sg = getGroup();
983 sg.cs = new Blosum62ColourScheme();
985 sg.cs.setConsensus(AAFrequency.calculate(sg.getSequences(ap.av
986 .getHiddenRepSequences()), 0, ap.av.getAlignment().getWidth()));
991 protected void noColourmenuItem_actionPerformed()
993 getGroup().cs = null;
997 protected void conservationMenuItem_itemStateChanged()
999 SequenceGroup sg = getGroup();
1005 if (conservationMenuItem.getState())
1008 sg.cs.setConservation(Conservation.calculateConservation("Group",
1009 ResidueProperties.propHash, 3, sg.getSequences(ap.av
1010 .getHiddenRepSequences()), 0, ap.av.getAlignment()
1011 .getWidth(), false, ap.av.getConsPercGaps(), false));
1012 SliderPanel.setConservationSlider(ap, sg.cs, sg.getName());
1013 SliderPanel.showConservationSlider();
1016 // remove ConservationColouring
1018 sg.cs.setConservation(null);
1024 SequenceGroup getGroup()
1026 SequenceGroup sg = ap.av.getSelectionGroup();
1028 // this method won't add a new group if it already exists
1031 ap.av.getAlignment().addGroup(sg);
1037 void unGroupMenuItem_actionPerformed()
1039 SequenceGroup sg = ap.av.getSelectionGroup();
1040 ap.av.getAlignment().deleteGroup(sg);
1041 ap.av.setSelectionGroup(null);
1042 ap.paintAlignment(true);
1045 void createGroupMenuItem_actionPerformed()
1047 getGroup(); // implicitly create group
1051 public void showColourText_itemStateChanged()
1053 getGroup().setColourText(showColourText.getState());
1057 public void showText_itemStateChanged()
1059 getGroup().setDisplayText(showText.getState());
1063 public void showNonconserved_itemStateChanged()
1065 getGroup().setShowNonconserved(this.displayNonconserved.getState());
1069 public void showBoxes_itemStateChanged()
1071 getGroup().setDisplayBoxes(showBoxes.getState());
1075 void hideSequences(boolean representGroup)
1077 SequenceGroup sg = ap.av.getSelectionGroup();
1078 if (sg == null || sg.getSize() < 1)
1080 ap.av.hideSequence(new SequenceI[]
1085 ap.av.setSelectionGroup(null);
1089 ap.av.hideRepSequences(seq, sg);
1094 int gsize = sg.getSize();
1097 hseqs = new SequenceI[gsize];
1100 for (int i = 0; i < gsize; i++)
1102 hseqs[index++] = sg.getSequenceAt(i);
1105 ap.av.hideSequence(hseqs);
1106 ap.av.sendSelection();