2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
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
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.SequenceStructureBinding;
27 import jalview.bin.JalviewLite;
28 import jalview.commands.CommandI;
29 import jalview.commands.EditCommand;
30 import jalview.commands.EditCommand.Action;
31 import jalview.commands.OrderCommand;
32 import jalview.commands.RemoveGapColCommand;
33 import jalview.commands.RemoveGapsCommand;
34 import jalview.commands.SlideSequencesCommand;
35 import jalview.commands.TrimRegionCommand;
36 import jalview.datamodel.Alignment;
37 import jalview.datamodel.AlignmentI;
38 import jalview.datamodel.AlignmentOrder;
39 import jalview.datamodel.ColumnSelection;
40 import jalview.datamodel.PDBEntry;
41 import jalview.datamodel.Sequence;
42 import jalview.datamodel.SequenceGroup;
43 import jalview.datamodel.SequenceI;
44 import jalview.io.AnnotationFile;
45 import jalview.io.AppletFormatAdapter;
46 import jalview.io.FeaturesFile;
47 import jalview.io.TCoffeeScoreFile;
48 import jalview.schemes.Blosum62ColourScheme;
49 import jalview.schemes.BuriedColourScheme;
50 import jalview.schemes.ClustalxColourScheme;
51 import jalview.schemes.ColourSchemeI;
52 import jalview.schemes.HelixColourScheme;
53 import jalview.schemes.HydrophobicColourScheme;
54 import jalview.schemes.NucleotideColourScheme;
55 import jalview.schemes.PIDColourScheme;
56 import jalview.schemes.PurinePyrimidineColourScheme;
57 import jalview.schemes.RNAHelicesColourChooser;
58 import jalview.schemes.RNAInteractionColourScheme;
59 import jalview.schemes.StrandColourScheme;
60 import jalview.schemes.TCoffeeColourScheme;
61 import jalview.schemes.TaylorColourScheme;
62 import jalview.schemes.TurnColourScheme;
63 import jalview.schemes.ZappoColourScheme;
64 import jalview.structure.StructureSelectionManager;
65 import jalview.util.MessageManager;
67 import java.awt.BorderLayout;
68 import java.awt.Canvas;
69 import java.awt.CheckboxMenuItem;
70 import java.awt.Color;
72 import java.awt.FontMetrics;
73 import java.awt.Frame;
74 import java.awt.Graphics;
75 import java.awt.Label;
77 import java.awt.MenuBar;
78 import java.awt.MenuItem;
79 import java.awt.event.ActionEvent;
80 import java.awt.event.ActionListener;
81 import java.awt.event.FocusEvent;
82 import java.awt.event.FocusListener;
83 import java.awt.event.ItemEvent;
84 import java.awt.event.ItemListener;
85 import java.awt.event.KeyEvent;
86 import java.awt.event.KeyListener;
87 import java.awt.event.WindowAdapter;
88 import java.awt.event.WindowEvent;
89 import java.io.IOException;
91 import java.net.URLEncoder;
92 import java.util.Enumeration;
93 import java.util.Hashtable;
94 import java.util.List;
95 import java.util.StringTokenizer;
96 import java.util.Vector;
98 public class AlignFrame extends EmbmenuFrame implements ActionListener,
99 ItemListener, KeyListener, AlignViewControllerGuiI
101 public AlignViewControllerI avc;
103 public AlignmentPanel alignPanel;
105 public AlignViewport viewport;
107 int DEFAULT_WIDTH = 700;
109 int DEFAULT_HEIGHT = 500;
111 String jalviewServletURL;
113 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
114 String title, boolean embedded)
118 jalviewServletURL = applet.getParameter("APPLICATION_URL");
124 } catch (Exception ex)
126 ex.printStackTrace();
128 // need to get window geometry before we calculate alignment layout
134 param = applet.getParameter("windowWidth");
137 int width = Integer.parseInt(param);
138 DEFAULT_WIDTH = width;
140 param = applet.getParameter("windowHeight");
143 int height = Integer.parseInt(param);
144 DEFAULT_HEIGHT = height;
146 } catch (Exception ex)
150 viewport = new AlignViewport(al, applet);
151 alignPanel = new AlignmentPanel(this, viewport);
152 avc = new jalview.controller.AlignViewController(this, viewport,
154 viewport.updateConservation(alignPanel);
155 viewport.updateConsensus(alignPanel);
157 annotationPanelMenuItem.setState(viewport.showAnnotation);
158 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
159 followMouseOverFlag.setState(viewport.getFollowHighlight());
160 showGroupConsensus.setState(viewport.isShowGroupConsensus());
161 showGroupConservation.setState(viewport.isShowGroupConservation());
162 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
163 showSequenceLogo.setState(viewport.isShowSequenceLogo());
164 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
165 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
167 seqLimits.setState(viewport.showJVSuffix);
171 String param = applet.getParameter("sortBy");
174 if (param.equalsIgnoreCase("Id"))
176 sortIDMenuItem_actionPerformed();
178 else if (param.equalsIgnoreCase("Pairwise Identity"))
180 sortPairwiseMenuItem_actionPerformed();
182 else if (param.equalsIgnoreCase("Length"))
184 sortLengthMenuItem_actionPerformed();
188 param = applet.getParameter("wrap");
191 if (param.equalsIgnoreCase("true"))
193 wrapMenuItem.setState(true);
194 wrapMenuItem_actionPerformed();
197 param = applet.getParameter("centrecolumnlabels");
200 centreColumnLabelFlag.setState(true);
201 centreColumnLabelFlag_stateChanged();
205 if (viewport.getAlignment().isNucleotide())
207 viewport.updateStrucConsensus(alignPanel);
208 if (viewport.getAlignment().hasRNAStructure())
210 RNAHelixColour.setEnabled(true);
214 RNAHelixColour.setEnabled(false);
219 RNAHelixColour.setEnabled(false);
220 purinePyrimidineColour.setEnabled(false);
222 // Some JVMS send keyevents to Top frame or lowest panel,
223 // Havent worked out why yet. So add to both this frame and seqCanvas for
225 this.addKeyListener(this);
226 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
227 alignPanel.idPanel.idCanvas.addKeyListener(this);
228 alignPanel.scalePanel.addKeyListener(this);
229 alignPanel.annotationPanel.addKeyListener(this);
230 alignPanel.annotationPanelHolder.addKeyListener(this);
231 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
232 alignPanel.alabels.addKeyListener(this);
233 createAlignFrameWindow(embedded, title);
236 alignPanel.adjustAnnotationHeight();
237 alignPanel.paintAlignment(true);
240 public AlignViewport getAlignViewport()
245 public SeqCanvas getSeqcanvas()
247 return alignPanel.seqPanel.seqCanvas;
251 * Load a features file onto the alignment
254 * file URL, content, or other resolvable path
256 * is protocol for accessing data referred to by file
259 public boolean parseFeaturesFile(String file, String type)
261 return parseFeaturesFile(file, type, true);
265 * Load a features file onto the alignment
268 * file URL, content, or other resolvable path
270 * is protocol for accessing data referred to by file
271 * @param autoenabledisplay
272 * when true, display features flag will be automatically enabled if
273 * features are loaded
274 * @return true if data parsed as a features file
276 public boolean parseFeaturesFile(String file, String type,
277 boolean autoenabledisplay)
279 // TODO: test if importing a features file onto an alignment which already
280 // has features with links overwrites the original links.
282 Hashtable featureLinks = new Hashtable();
283 boolean featuresFile = false;
286 featuresFile = new jalview.io.FeaturesFile(file, type)
287 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
288 .getFeatureRenderer().featureColours, featureLinks,
289 true, viewport.applet.getDefaultParameter(
290 "relaxedidmatch", false));
291 } catch (Exception ex)
293 ex.printStackTrace();
298 if (featureLinks.size() > 0)
300 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
302 if (autoenabledisplay)
304 viewport.showSequenceFeatures = true;
305 sequenceFeatures.setState(true);
307 if (viewport.featureSettings != null)
309 viewport.featureSettings.refreshTable();
311 alignPanel.paintAlignment(true);
312 statusBar.setText(MessageManager
313 .getString("label.successfully_added_features_alignment"));
319 public void keyPressed(KeyEvent evt)
321 if (viewport.cursorMode
322 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
323 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
324 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
325 && Character.isDigit(evt.getKeyChar()))
327 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
330 switch (evt.getKeyCode())
332 case 27: // escape key
333 deselectAllSequenceMenuItem_actionPerformed();
335 alignPanel.alabels.cancelDrag();
338 if (evt.isControlDown() || evt.isMetaDown())
340 cut_actionPerformed();
344 if (viewport.cursorMode && !evt.isControlDown())
346 alignPanel.seqPanel.setCursorColumn();
348 if (evt.isControlDown() || evt.isMetaDown())
350 copy_actionPerformed();
354 if (evt.isControlDown())
356 paste(evt.isShiftDown());
360 if (evt.isControlDown() || evt.isMetaDown())
362 selectAllSequenceMenuItem_actionPerformed();
365 case KeyEvent.VK_DOWN:
366 if (viewport.cursorMode)
368 alignPanel.seqPanel.moveCursor(0, 1);
372 moveSelectedSequences(false);
377 if (viewport.cursorMode)
379 alignPanel.seqPanel.moveCursor(0, -1);
383 moveSelectedSequences(true);
387 case KeyEvent.VK_LEFT:
388 if (evt.isAltDown() || !viewport.cursorMode)
390 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
394 alignPanel.seqPanel.moveCursor(-1, 0);
398 case KeyEvent.VK_RIGHT:
399 if (evt.isAltDown() || !viewport.cursorMode)
401 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
405 alignPanel.seqPanel.moveCursor(1, 0);
409 case KeyEvent.VK_SPACE:
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
413 || evt.isShiftDown() || evt.isAltDown());
417 case KeyEvent.VK_DELETE:
418 case KeyEvent.VK_BACK_SPACE:
419 if (viewport.cursorMode)
421 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
422 || evt.isShiftDown() || evt.isAltDown());
426 cut_actionPerformed();
427 alignPanel.seqPanel.seqCanvas.repaint();
432 if (viewport.cursorMode)
434 alignPanel.seqPanel.setCursorRow();
438 if (viewport.cursorMode)
440 alignPanel.seqPanel.setCursorPosition();
444 case KeyEvent.VK_ENTER:
445 case KeyEvent.VK_COMMA:
446 if (viewport.cursorMode)
448 alignPanel.seqPanel.setCursorRowAndColumn();
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
459 if (viewport.cursorMode)
461 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
466 viewport.cursorMode = !viewport.cursorMode;
467 statusBar.setText(MessageManager.formatMessage(
468 "label.keyboard_editing_mode", new String[]
469 { (viewport.cursorMode ? "on" : "off") }));
470 if (viewport.cursorMode)
472 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
473 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
478 if (evt.isControlDown())
480 findMenuItem_actionPerformed();
486 boolean toggleSeqs = !evt.isControlDown();
487 boolean toggleCols = !evt.isShiftDown();
488 toggleHiddenRegions(toggleSeqs, toggleCols);
492 case KeyEvent.VK_PAGE_UP:
493 if (viewport.wrapAlignment)
495 alignPanel.scrollUp(true);
499 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
500 - viewport.endSeq + viewport.startSeq);
504 case KeyEvent.VK_PAGE_DOWN:
505 if (viewport.wrapAlignment)
507 alignPanel.scrollUp(false);
511 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
512 + viewport.endSeq - viewport.startSeq);
517 if (evt.isControlDown())
519 undoMenuItem_actionPerformed();
524 if (evt.isControlDown())
526 redoMenuItem_actionPerformed();
531 if (evt.isControlDown())
538 if (evt.isControlDown())
540 trimAlignment(false);
545 if (evt.isControlDown())
547 if (evt.isShiftDown())
549 this.removeAllGapsMenuItem_actionPerformed();
553 removeGappedColumnMenuItem_actionPerformed();
558 if (evt.isControlDown())
562 invertColSel_actionPerformed();
566 invertSequenceMenuItem_actionPerformed();
572 if (evt.isControlDown())
574 if (evt.isShiftDown())
576 this.unGroup_actionPerformed();
580 this.createGroup_actionPerformed();
586 if (evt.isControlDown())
588 this.deleteGroups_actionPerformed();
593 if (evt.isControlDown())
600 alignPanel.paintAlignment(true);
604 * called by key handler and the hide all/show all menu items
609 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
611 boolean hide = false;
612 SequenceGroup sg = viewport.getSelectionGroup();
613 if (!toggleSeqs && !toggleCols)
615 // Hide everything by the current selection - this is a hack - we do the
616 // invert and then hide
617 // first check that there will be visible columns after the invert.
618 if ((viewport.getColumnSelection() != null
619 && viewport.getColumnSelection().getSelected() != null && viewport
620 .getColumnSelection().getSelected().size() > 0)
621 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
624 // now invert the sequence set, if required - empty selection implies
625 // that no hiding is required.
628 invertSequenceMenuItem_actionPerformed();
629 sg = viewport.getSelectionGroup();
633 viewport.expandColSelection(sg, true);
634 // finally invert the column selection and get the new sequence
635 // selection and indicate it should be hidden.
636 invertColSel_actionPerformed();
643 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
646 viewport.hideAllSelectedSeqs();
648 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
651 viewport.showAllHiddenSeqs();
657 if (viewport.getColumnSelection().getSelected().size() > 0)
659 viewport.hideSelectedColumns();
662 viewport.setSelectionGroup(sg);
667 viewport.showAllHiddenColumns();
673 public void keyReleased(KeyEvent evt)
678 public void keyTyped(KeyEvent evt)
683 public void itemStateChanged(ItemEvent evt)
685 if (evt.getSource() == displayNonconservedMenuItem)
687 displayNonconservedMenuItem_actionPerformed();
689 else if (evt.getSource() == colourTextMenuItem)
691 colourTextMenuItem_actionPerformed();
693 else if (evt.getSource() == wrapMenuItem)
695 wrapMenuItem_actionPerformed();
697 else if (evt.getSource() == scaleAbove)
699 viewport.setScaleAboveWrapped(scaleAbove.getState());
701 else if (evt.getSource() == scaleLeft)
703 viewport.setScaleLeftWrapped(scaleLeft.getState());
705 else if (evt.getSource() == scaleRight)
707 viewport.setScaleRightWrapped(scaleRight.getState());
709 else if (evt.getSource() == seqLimits)
711 seqLimits_itemStateChanged();
713 else if (evt.getSource() == viewBoxesMenuItem)
715 viewport.setShowBoxes(viewBoxesMenuItem.getState());
717 else if (evt.getSource() == viewTextMenuItem)
719 viewport.setShowText(viewTextMenuItem.getState());
721 else if (evt.getSource() == renderGapsMenuItem)
723 viewport.setRenderGaps(renderGapsMenuItem.getState());
725 else if (evt.getSource() == annotationPanelMenuItem)
727 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
728 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
730 else if (evt.getSource() == sequenceFeatures)
732 viewport.showSequenceFeatures(sequenceFeatures.getState());
733 alignPanel.seqPanel.seqCanvas.repaint();
735 else if (evt.getSource() == conservationMenuItem)
737 conservationMenuItem_actionPerformed();
739 else if (evt.getSource() == abovePIDThreshold)
741 abovePIDThreshold_actionPerformed();
743 else if (evt.getSource() == applyToAllGroups)
745 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
747 else if (evt.getSource() == autoCalculate)
749 viewport.autoCalculateConsensus = autoCalculate.getState();
751 else if (evt.getSource() == sortByTree)
753 viewport.sortByTree = sortByTree.getState();
755 else if (evt.getSource() == this.centreColumnLabelFlag)
757 centreColumnLabelFlag_stateChanged();
759 else if (evt.getSource() == this.followMouseOverFlag)
761 mouseOverFlag_stateChanged();
763 else if (evt.getSource() == showGroupConsensus)
765 showGroupConsensus_actionPerformed();
767 else if (evt.getSource() == showGroupConservation)
769 showGroupConservation_actionPerformed();
771 else if (evt.getSource() == showSequenceLogo)
773 showSequenceLogo_actionPerformed();
775 else if (evt.getSource() == normSequenceLogo)
777 normSequenceLogo_actionPerformed();
779 else if (evt.getSource() == showConsensusHistogram)
781 showConsensusHistogram_actionPerformed();
783 else if (evt.getSource() == applyAutoAnnotationSettings)
785 applyAutoAnnotationSettings_actionPerformed();
787 alignPanel.paintAlignment(true);
790 private void mouseOverFlag_stateChanged()
792 viewport.followHighlight = followMouseOverFlag.getState();
793 // TODO: could kick the scrollTo mechanism to reset view for current
797 private void centreColumnLabelFlag_stateChanged()
799 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
800 this.alignPanel.annotationPanel.repaint();
804 public void actionPerformed(ActionEvent evt)
806 Object source = evt.getSource();
808 if (source == inputText)
810 inputText_actionPerformed();
812 else if (source == loadTree)
814 loadTree_actionPerformed();
816 else if (source == loadApplication)
818 launchFullApplication();
820 else if (source == loadAnnotations)
824 else if (source == outputAnnotations)
826 outputAnnotations(true);
828 else if (source == outputFeatures)
830 outputFeatures(true, "Jalview");
832 else if (source == closeMenuItem)
834 closeMenuItem_actionPerformed();
836 else if (source == copy)
838 copy_actionPerformed();
840 else if (source == undoMenuItem)
842 undoMenuItem_actionPerformed();
844 else if (source == redoMenuItem)
846 redoMenuItem_actionPerformed();
848 else if (source == inputText)
850 inputText_actionPerformed();
852 else if (source == closeMenuItem)
854 closeMenuItem_actionPerformed();
856 else if (source == undoMenuItem)
858 undoMenuItem_actionPerformed();
860 else if (source == redoMenuItem)
862 redoMenuItem_actionPerformed();
864 else if (source == copy)
866 copy_actionPerformed();
868 else if (source == pasteNew)
870 pasteNew_actionPerformed();
872 else if (source == pasteThis)
874 pasteThis_actionPerformed();
876 else if (source == cut)
878 cut_actionPerformed();
880 else if (source == delete)
882 delete_actionPerformed();
884 else if (source == grpsFromSelection)
886 makeGrpsFromSelection_actionPerformed();
888 else if (source == deleteGroups)
890 deleteGroups_actionPerformed();
892 else if (source == selectAllSequenceMenuItem)
894 selectAllSequenceMenuItem_actionPerformed();
896 else if (source == deselectAllSequenceMenuItem)
898 deselectAllSequenceMenuItem_actionPerformed();
900 else if (source == invertSequenceMenuItem)
902 invertSequenceMenuItem_actionPerformed();
904 else if (source == invertColSel)
906 viewport.invertColumnSelection();
907 alignPanel.paintAlignment(true);
909 else if (source == remove2LeftMenuItem)
913 else if (source == remove2RightMenuItem)
915 trimAlignment(false);
917 else if (source == removeGappedColumnMenuItem)
919 removeGappedColumnMenuItem_actionPerformed();
921 else if (source == removeAllGapsMenuItem)
923 removeAllGapsMenuItem_actionPerformed();
925 else if (source == findMenuItem)
927 findMenuItem_actionPerformed();
929 else if (source == font)
931 new FontChooser(alignPanel);
933 else if (source == newView)
937 else if (source == showColumns)
939 viewport.showAllHiddenColumns();
940 alignPanel.paintAlignment(true);
942 else if (source == showSeqs)
944 viewport.showAllHiddenSeqs();
945 alignPanel.paintAlignment(true);
947 else if (source == hideColumns)
949 viewport.hideSelectedColumns();
950 alignPanel.paintAlignment(true);
952 else if (source == hideSequences
953 && viewport.getSelectionGroup() != null)
955 viewport.hideAllSelectedSeqs();
956 alignPanel.paintAlignment(true);
958 else if (source == hideAllButSelection)
960 toggleHiddenRegions(false, false);
961 alignPanel.paintAlignment(true);
963 else if (source == hideAllSelection)
965 SequenceGroup sg = viewport.getSelectionGroup();
966 viewport.expandColSelection(sg, false);
967 viewport.hideAllSelectedSeqs();
968 viewport.hideSelectedColumns();
969 alignPanel.paintAlignment(true);
971 else if (source == showAllHidden)
973 viewport.showAllHiddenColumns();
974 viewport.showAllHiddenSeqs();
975 alignPanel.paintAlignment(true);
977 else if (source == showGroupConsensus)
979 showGroupConsensus_actionPerformed();
981 else if (source == showGroupConservation)
983 showGroupConservation_actionPerformed();
985 else if (source == showSequenceLogo)
987 showSequenceLogo_actionPerformed();
989 else if (source == normSequenceLogo)
991 normSequenceLogo_actionPerformed();
993 else if (source == showConsensusHistogram)
995 showConsensusHistogram_actionPerformed();
997 else if (source == applyAutoAnnotationSettings)
999 applyAutoAnnotationSettings_actionPerformed();
1001 else if (source == featureSettings)
1003 new FeatureSettings(alignPanel);
1005 else if (source == alProperties)
1007 StringBuffer contents = new jalview.io.AlignmentProperties(
1008 viewport.getAlignment()).formatAsString();
1009 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1010 cap.setText(contents.toString());
1011 Frame frame = new Frame();
1013 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1014 "label.alignment_properties", new String[]
1015 { getTitle() }), 400, 250);
1017 else if (source == overviewMenuItem)
1019 overviewMenuItem_actionPerformed();
1021 else if (source == noColourmenuItem)
1025 else if (source == clustalColour)
1027 abovePIDThreshold.setState(false);
1028 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1030 else if (source == zappoColour)
1032 changeColour(new ZappoColourScheme());
1034 else if (source == taylorColour)
1036 changeColour(new TaylorColourScheme());
1038 else if (source == hydrophobicityColour)
1040 changeColour(new HydrophobicColourScheme());
1042 else if (source == helixColour)
1044 changeColour(new HelixColourScheme());
1046 else if (source == strandColour)
1048 changeColour(new StrandColourScheme());
1050 else if (source == turnColour)
1052 changeColour(new TurnColourScheme());
1054 else if (source == buriedColour)
1056 changeColour(new BuriedColourScheme());
1058 else if (source == nucleotideColour)
1060 changeColour(new NucleotideColourScheme());
1062 else if (source == purinePyrimidineColour)
1064 changeColour(new PurinePyrimidineColourScheme());
1066 else if (source == RNAInteractionColour)
1068 changeColour(new RNAInteractionColourScheme());
1070 else if (source == RNAHelixColour)
1072 new RNAHelicesColourChooser(viewport, alignPanel);
1074 else if (source == modifyPID)
1076 modifyPID_actionPerformed();
1078 else if (source == modifyConservation)
1080 modifyConservation_actionPerformed();
1082 else if (source == userDefinedColour)
1084 new UserDefinedColours(alignPanel, null);
1086 else if (source == PIDColour)
1088 changeColour(new PIDColourScheme());
1090 else if (source == BLOSUM62Colour)
1092 changeColour(new Blosum62ColourScheme());
1094 else if (source == tcoffeeColour)
1096 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1098 else if (source == annotationColour)
1100 new AnnotationColourChooser(viewport, alignPanel);
1102 else if (source == sortPairwiseMenuItem)
1104 sortPairwiseMenuItem_actionPerformed();
1106 else if (source == sortIDMenuItem)
1108 sortIDMenuItem_actionPerformed();
1110 else if (source == sortLengthMenuItem)
1112 sortLengthMenuItem_actionPerformed();
1114 else if (source == sortGroupMenuItem)
1116 sortGroupMenuItem_actionPerformed();
1118 else if (source == removeRedundancyMenuItem)
1120 removeRedundancyMenuItem_actionPerformed();
1122 else if (source == pairwiseAlignmentMenuItem)
1124 pairwiseAlignmentMenuItem_actionPerformed();
1126 else if (source == PCAMenuItem)
1128 PCAMenuItem_actionPerformed();
1130 else if (source == averageDistanceTreeMenuItem)
1132 averageDistanceTreeMenuItem_actionPerformed();
1134 else if (source == neighbourTreeMenuItem)
1136 neighbourTreeMenuItem_actionPerformed();
1138 else if (source == njTreeBlosumMenuItem)
1140 njTreeBlosumMenuItem_actionPerformed();
1142 else if (source == avDistanceTreeBlosumMenuItem)
1144 avTreeBlosumMenuItem_actionPerformed();
1146 else if (source == documentation)
1148 documentation_actionPerformed();
1150 else if (source == about)
1152 about_actionPerformed();
1157 public void inputText_actionPerformed()
1159 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1160 Frame frame = new Frame();
1162 jalview.bin.JalviewLite.addFrame(frame,
1163 MessageManager.getString("label.input_cut_paste"), 500, 500);
1166 protected void outputText_actionPerformed(ActionEvent e)
1168 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1169 Frame frame = new Frame();
1171 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1172 "label.alignment_output_command", new String[]
1173 { e.getActionCommand() }), 600, 500);
1174 cap.setText(new AppletFormatAdapter().formatSequences(
1175 e.getActionCommand(), viewport.getAlignment(),
1176 viewport.showJVSuffix));
1179 public void loadAnnotations()
1181 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1182 cap.setText(MessageManager
1183 .getString("label.paste_features_annotations_Tcoffee_here"));
1184 cap.setAnnotationImport();
1185 Frame frame = new Frame();
1187 jalview.bin.JalviewLite.addFrame(frame,
1188 MessageManager.getString("action.paste_annotations"), 400, 300);
1192 public String outputAnnotations(boolean displayTextbox)
1194 String annotation = new AnnotationFile().printAnnotations(
1195 viewport.showAnnotation ? viewport.getAlignment()
1196 .getAlignmentAnnotation() : null, viewport
1197 .getAlignment().getGroups(), ((Alignment) viewport
1198 .getAlignment()).alignmentProperties);
1202 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1203 Frame frame = new Frame();
1205 jalview.bin.JalviewLite.addFrame(frame,
1206 MessageManager.getString("label.annotations"), 600, 500);
1207 cap.setText(annotation);
1213 private Hashtable getDisplayedFeatureCols()
1215 if (alignPanel.getFeatureRenderer() != null
1216 && viewport.featuresDisplayed != null)
1218 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1219 Hashtable fcols = new Hashtable();
1220 Enumeration en = viewport.featuresDisplayed.keys();
1221 while (en.hasMoreElements())
1223 Object col = en.nextElement();
1224 fcols.put(col, fr.featureColours.get(col));
1231 public String outputFeatures(boolean displayTextbox, String format)
1234 if (format.equalsIgnoreCase("Jalview"))
1236 features = new FeaturesFile().printJalviewFormat(viewport
1237 .getAlignment().getSequencesArray(),
1238 getDisplayedFeatureCols());
1242 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1243 .getSequencesArray(), getDisplayedFeatureCols());
1248 boolean frimport = false;
1249 if (features == null || features.equals("No Features Visible"))
1251 features = "# No features visible - paste some and import them here.";
1255 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1258 cap.setAnnotationImport();
1260 Frame frame = new Frame();
1262 jalview.bin.JalviewLite.addFrame(frame,
1263 MessageManager.getString("label.features"), 600, 500);
1264 cap.setText(features);
1268 if (features == null)
1277 void launchFullApplication()
1279 StringBuffer url = new StringBuffer(jalviewServletURL);
1282 + appendProtocol(viewport.applet.getParameter("file")));
1284 if (viewport.applet.getParameter("features") != null)
1286 url.append("&features=");
1287 url.append(appendProtocol(viewport.applet.getParameter("features")));
1290 if (viewport.applet.getParameter("annotations") != null)
1292 url.append("&annotations=");
1293 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1296 if (viewport.applet.getParameter("jnetfile") != null)
1298 url.append("&annotations=");
1299 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1302 if (viewport.applet.getParameter("defaultColour") != null)
1304 url.append("&colour="
1305 + removeWhiteSpace(viewport.applet
1306 .getParameter("defaultColour")));
1309 if (viewport.applet.getParameter("userDefinedColour") != null)
1311 url.append("&colour="
1312 + removeWhiteSpace(viewport.applet
1313 .getParameter("userDefinedColour")));
1315 if (viewport.applet.getParameter("tree") != null)
1318 + appendProtocol(viewport.applet.getParameter("tree")));
1320 if (viewport.applet.getParameter("treeFile") != null)
1323 + appendProtocol(viewport.applet.getParameter("treeFile")));
1326 showURL(url.toString(), "FULL_APP");
1329 String removeWhiteSpace(String colour)
1331 StringBuffer sb = new StringBuffer();
1332 for (int i = 0; i < colour.length(); i++)
1334 if (Character.isWhitespace(colour.charAt(i)))
1340 sb.append(colour.charAt(i));
1344 return sb.toString();
1347 String appendProtocol(String url)
1352 url = URLEncoder.encode(url);
1355 * When we finally deprecate 1.1 compatibility, we can start to use
1356 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1357 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1358 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1359 * ex.printStackTrace(); }
1361 catch (java.net.MalformedURLException ex)
1363 url = viewport.applet.getCodeBase() + url;
1368 public void closeMenuItem_actionPerformed()
1370 PaintRefresher.RemoveComponent(alignPanel);
1371 if (alignPanel.seqPanel != null
1372 && alignPanel.seqPanel.seqCanvas != null)
1374 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1376 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1378 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1381 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1396 void updateEditMenuBar()
1399 if (viewport.historyList.size() > 0)
1401 undoMenuItem.setEnabled(true);
1402 CommandI command = (CommandI) viewport.historyList.peek();
1403 undoMenuItem.setLabel(MessageManager.formatMessage(
1404 "label.undo_command", new String[]
1405 { command.getDescription() }));
1409 undoMenuItem.setEnabled(false);
1410 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1413 if (viewport.redoList.size() > 0)
1415 redoMenuItem.setEnabled(true);
1417 CommandI command = (CommandI) viewport.redoList.peek();
1418 redoMenuItem.setLabel(MessageManager.formatMessage(
1419 "label.redo_command", new String[]
1420 { command.getDescription() }));
1424 redoMenuItem.setEnabled(false);
1425 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1432 public void addHistoryItem(CommandI command)
1434 if (command.getSize() > 0)
1436 viewport.historyList.push(command);
1437 viewport.redoList.removeAllElements();
1438 updateEditMenuBar();
1439 viewport.updateHiddenColumns();
1444 * TODO: JAL-1104 DOCUMENT ME!
1449 protected void undoMenuItem_actionPerformed()
1451 if (viewport.historyList.size() < 1)
1456 CommandI command = (CommandI) viewport.historyList.pop();
1457 viewport.redoList.push(command);
1458 command.undoCommand(null);
1460 AlignViewport originalSource = getOriginatingSource(command);
1462 if (originalSource != viewport)
1465 .println("Warning: Viewport object mismatch whilst undoing");
1467 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1468 // viewport.getColumnSelection().getHiddenColumns()
1470 updateEditMenuBar();
1471 originalSource.firePropertyChange("alignment", null, originalSource
1472 .getAlignment().getSequences());
1476 * TODO: JAL-1104 DOCUMENT ME!
1481 protected void redoMenuItem_actionPerformed()
1483 if (viewport.redoList.size() < 1)
1488 CommandI command = (CommandI) viewport.redoList.pop();
1489 viewport.historyList.push(command);
1490 command.doCommand(null);
1492 AlignViewport originalSource = getOriginatingSource(command);
1494 if (originalSource != viewport)
1497 .println("Warning: Viewport object mismatch whilst re-doing");
1499 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1500 // viewport.getColumnSelection().getHiddenColumns()
1503 updateEditMenuBar();
1504 originalSource.firePropertyChange("alignment", null, originalSource
1505 .getAlignment().getSequences());
1508 AlignViewport getOriginatingSource(CommandI command)
1510 AlignViewport originalSource = null;
1511 // For sequence removal and addition, we need to fire
1512 // the property change event FROM the viewport where the
1513 // original alignment was altered
1514 AlignmentI al = null;
1515 if (command instanceof EditCommand)
1517 EditCommand editCommand = (EditCommand) command;
1518 al = editCommand.getAlignment();
1519 Vector comps = (Vector) PaintRefresher.components.get(viewport
1520 .getSequenceSetId());
1521 for (int i = 0; i < comps.size(); i++)
1523 if (comps.elementAt(i) instanceof AlignmentPanel)
1525 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1527 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1534 if (originalSource == null)
1536 // The original view is closed, we must validate
1537 // the current view against the closed view first
1540 PaintRefresher.validateSequences(al, viewport.getAlignment());
1543 originalSource = viewport;
1546 return originalSource;
1549 public void moveSelectedSequences(boolean up)
1551 SequenceGroup sg = viewport.getSelectionGroup();
1556 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1557 up ? null : viewport.getHiddenRepSequences(), up);
1558 alignPanel.paintAlignment(true);
1561 synchronized void slideSequences(boolean right, int size)
1563 List<SequenceI> sg = new Vector<SequenceI>();
1564 if (viewport.cursorMode)
1566 sg.add(viewport.getAlignment().getSequenceAt(
1567 alignPanel.seqPanel.seqCanvas.cursorY));
1569 else if (viewport.getSelectionGroup() != null
1570 && viewport.getSelectionGroup().getSize() != viewport
1571 .getAlignment().getHeight())
1573 sg = viewport.getSelectionGroup().getSequences(
1574 viewport.getHiddenRepSequences());
1582 Vector<SequenceI> invertGroup = new Vector();
1584 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1586 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1588 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1592 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1594 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1596 for (int i = 0; i < invertGroup.size(); i++)
1598 seqs2[i] = invertGroup.elementAt(i);
1601 SlideSequencesCommand ssc;
1604 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1605 size, viewport.getGapCharacter());
1609 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1610 size, viewport.getGapCharacter());
1613 int groupAdjustment = 0;
1614 if (ssc.getGapsInsertedBegin() && right)
1616 if (viewport.cursorMode)
1618 alignPanel.seqPanel.moveCursor(size, 0);
1622 groupAdjustment = size;
1625 else if (!ssc.getGapsInsertedBegin() && !right)
1627 if (viewport.cursorMode)
1629 alignPanel.seqPanel.moveCursor(-size, 0);
1633 groupAdjustment = -size;
1637 if (groupAdjustment != 0)
1639 viewport.getSelectionGroup().setStartRes(
1640 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1641 viewport.getSelectionGroup().setEndRes(
1642 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1645 boolean appendHistoryItem = false;
1646 if (viewport.historyList != null && viewport.historyList.size() > 0
1647 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1649 appendHistoryItem = ssc
1650 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1654 if (!appendHistoryItem)
1656 addHistoryItem(ssc);
1662 static StringBuffer copiedSequences;
1664 static Vector copiedHiddenColumns;
1666 protected void copy_actionPerformed()
1668 if (viewport.getSelectionGroup() == null)
1673 SequenceGroup sg = viewport.getSelectionGroup();
1674 copiedSequences = new StringBuffer();
1675 Hashtable orderedSeqs = new Hashtable();
1676 for (int i = 0; i < sg.getSize(); i++)
1678 SequenceI seq = sg.getSequenceAt(i);
1679 int index = viewport.getAlignment().findIndex(seq);
1680 orderedSeqs.put(index + "", seq);
1683 int index = 0, startRes, endRes;
1686 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1688 copiedHiddenColumns = new Vector();
1689 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1690 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1693 int[] region = (int[]) viewport.getColumnSelection()
1694 .getHiddenColumns().elementAt(i);
1696 copiedHiddenColumns.addElement(new int[]
1697 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1702 copiedHiddenColumns = null;
1705 for (int i = 0; i < sg.getSize(); i++)
1707 SequenceI seq = null;
1711 if (orderedSeqs.containsKey(index + ""))
1713 seq = (SequenceI) orderedSeqs.get(index + "");
1725 // Returns residue following index if gap
1726 startRes = seq.findPosition(sg.getStartRes());
1729 // Need to find the residue preceeding index if gap
1732 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1734 ch = seq.getCharAt(j);
1735 if (!jalview.util.Comparison.isGap((ch)))
1743 endRes += seq.getStart() - 1;
1746 copiedSequences.append(seq.getName()
1752 + seq.getSequenceAsString(sg.getStartRes(),
1753 sg.getEndRes() + 1) + "\n");
1758 protected void pasteNew_actionPerformed()
1763 protected void pasteThis_actionPerformed()
1768 void paste(boolean newAlignment)
1773 if (copiedSequences == null)
1778 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1779 Vector seqs = new Vector();
1780 while (st.hasMoreElements())
1782 String name = st.nextToken();
1783 int start = Integer.parseInt(st.nextToken());
1784 int end = Integer.parseInt(st.nextToken());
1785 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1787 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1788 for (int i = 0; i < seqs.size(); i++)
1790 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1795 String newtitle = MessageManager.getString("label.copied_sequences");
1796 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1798 newtitle = getTitle();
1802 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1804 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1805 viewport.applet, newtitle, false);
1806 if (copiedHiddenColumns != null)
1808 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1810 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1811 af.viewport.hideColumns(region[0], region[1]);
1815 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1820 addSequences(newSeqs);
1823 } catch (Exception ex)
1825 } // could be anything being pasted in here
1829 void addSequences(SequenceI[] seqs)
1831 for (int i = 0; i < seqs.length; i++)
1833 viewport.getAlignment().addSequence(seqs[i]);
1837 addHistoryItem(new EditCommand(
1838 MessageManager.getString("label.add_sequences"), Action.PASTE,
1839 seqs, 0, viewport.getAlignment().getWidth(),
1840 viewport.getAlignment()));
1842 viewport.setEndSeq(viewport.getAlignment().getHeight());
1843 viewport.getAlignment().getWidth();
1844 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1849 protected void cut_actionPerformed()
1851 copy_actionPerformed();
1852 delete_actionPerformed();
1855 protected void delete_actionPerformed()
1858 SequenceGroup sg = viewport.getSelectionGroup();
1864 Vector seqs = new Vector();
1866 for (int i = 0; i < sg.getSize(); i++)
1868 seq = sg.getSequenceAt(i);
1869 seqs.addElement(seq);
1872 // If the cut affects all sequences, remove highlighted columns
1873 if (sg.getSize() == viewport.getAlignment().getHeight())
1875 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1876 sg.getEndRes() + 1);
1879 SequenceI[] cut = new SequenceI[seqs.size()];
1880 for (int i = 0; i < seqs.size(); i++)
1882 cut[i] = (SequenceI) seqs.elementAt(i);
1886 * //ADD HISTORY ITEM
1888 addHistoryItem(new EditCommand(
1889 MessageManager.getString("label.cut_sequences"), Action.CUT,
1890 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1891 viewport.getAlignment()));
1893 viewport.setSelectionGroup(null);
1894 viewport.getAlignment().deleteGroup(sg);
1896 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1899 if (viewport.getAlignment().getHeight() < 1)
1901 this.setVisible(false);
1903 viewport.sendSelection();
1907 * group consensus toggled
1910 protected void showGroupConsensus_actionPerformed()
1912 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1913 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1918 * group conservation toggled.
1920 protected void showGroupConservation_actionPerformed()
1922 viewport.setShowGroupConservation(showGroupConservation.getState());
1923 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1930 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1931 * .event.ActionEvent)
1933 protected void showConsensusHistogram_actionPerformed()
1935 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1936 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1943 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1944 * .event.ActionEvent)
1946 protected void showSequenceLogo_actionPerformed()
1948 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1949 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1952 protected void normSequenceLogo_actionPerformed()
1954 showSequenceLogo.setState(true);
1955 viewport.setShowSequenceLogo(true);
1956 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1957 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1960 protected void applyAutoAnnotationSettings_actionPerformed()
1962 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1965 protected void makeGrpsFromSelection_actionPerformed()
1967 if (avc.makeGroupsFromSelection())
1969 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1970 alignPanel.updateAnnotation();
1971 alignPanel.paintAlignment(true);
1975 protected void createGroup_actionPerformed()
1980 protected void unGroup_actionPerformed()
1984 alignPanel.alignmentChanged();
1988 protected void deleteGroups_actionPerformed()
1990 if (avc.deleteGroups())
1992 alignPanel.alignmentChanged();
1996 public void selectAllSequenceMenuItem_actionPerformed()
1998 SequenceGroup sg = new SequenceGroup();
1999 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2001 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2003 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2004 viewport.setSelectionGroup(sg);
2005 alignPanel.paintAlignment(true);
2006 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2007 viewport.sendSelection();
2010 public void deselectAllSequenceMenuItem_actionPerformed()
2012 if (viewport.cursorMode)
2014 alignPanel.seqPanel.keyboardNo1 = null;
2015 alignPanel.seqPanel.keyboardNo2 = null;
2017 viewport.setSelectionGroup(null);
2018 viewport.getColumnSelection().clear();
2019 viewport.setSelectionGroup(null);
2020 alignPanel.idPanel.idCanvas.searchResults = null;
2021 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2022 alignPanel.paintAlignment(true);
2023 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2024 viewport.sendSelection();
2027 public void invertSequenceMenuItem_actionPerformed()
2029 SequenceGroup sg = viewport.getSelectionGroup();
2030 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2032 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2035 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2036 viewport.sendSelection();
2039 public void invertColSel_actionPerformed()
2041 viewport.invertColumnSelection();
2042 alignPanel.paintAlignment(true);
2043 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2044 viewport.sendSelection();
2047 void trimAlignment(boolean trimLeft)
2049 ColumnSelection colSel = viewport.getColumnSelection();
2052 if (colSel.size() > 0)
2056 column = colSel.getMin();
2060 column = colSel.getMax();
2064 if (viewport.getSelectionGroup() != null)
2066 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2067 viewport.getHiddenRepSequences());
2071 seqs = viewport.getAlignment().getSequencesArray();
2074 TrimRegionCommand trimRegion;
2077 trimRegion = new TrimRegionCommand("Remove Left",
2078 TrimRegionCommand.TRIM_LEFT, seqs, column,
2079 viewport.getAlignment(), viewport.getColumnSelection(),
2080 viewport.getSelectionGroup());
2081 viewport.setStartRes(0);
2085 trimRegion = new TrimRegionCommand("Remove Right",
2086 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2087 viewport.getAlignment(), viewport.getColumnSelection(),
2088 viewport.getSelectionGroup());
2091 statusBar.setText(MessageManager.formatMessage(
2092 "label.removed_columns", new String[]
2093 { Integer.valueOf(trimRegion.getSize()).toString() }));
2094 addHistoryItem(trimRegion);
2096 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2098 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2099 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2101 viewport.getAlignment().deleteGroup(sg);
2105 viewport.firePropertyChange("alignment", null, viewport
2106 .getAlignment().getSequences());
2110 public void removeGappedColumnMenuItem_actionPerformed()
2112 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2115 if (viewport.getSelectionGroup() != null)
2117 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2118 viewport.getHiddenRepSequences());
2119 start = viewport.getSelectionGroup().getStartRes();
2120 end = viewport.getSelectionGroup().getEndRes();
2124 seqs = viewport.getAlignment().getSequencesArray();
2127 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2128 "Remove Gapped Columns", seqs, start, end,
2129 viewport.getAlignment());
2131 addHistoryItem(removeGapCols);
2133 statusBar.setText(MessageManager.formatMessage(
2134 "label.removed_empty_columns", new String[]
2135 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2137 // This is to maintain viewport position on first residue
2138 // of first sequence
2139 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2140 int startRes = seq.findPosition(viewport.startRes);
2141 // ShiftList shifts;
2142 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2143 // edit.alColumnChanges=shifts.getInverse();
2144 // if (viewport.hasHiddenColumns)
2145 // viewport.getColumnSelection().compensateForEdits(shifts);
2146 viewport.setStartRes(seq.findIndex(startRes) - 1);
2147 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2152 public void removeAllGapsMenuItem_actionPerformed()
2154 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2157 if (viewport.getSelectionGroup() != null)
2159 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2160 viewport.getHiddenRepSequences());
2161 start = viewport.getSelectionGroup().getStartRes();
2162 end = viewport.getSelectionGroup().getEndRes();
2166 seqs = viewport.getAlignment().getSequencesArray();
2169 // This is to maintain viewport position on first residue
2170 // of first sequence
2171 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2172 int startRes = seq.findPosition(viewport.startRes);
2174 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2175 viewport.getAlignment()));
2177 viewport.setStartRes(seq.findIndex(startRes) - 1);
2179 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2184 public void findMenuItem_actionPerformed()
2186 new Finder(alignPanel);
2190 * create a new view derived from the current view
2193 * @return frame for the new view
2195 public AlignFrame newView(String viewtitle)
2198 if (viewport.hasHiddenRows())
2200 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2201 .getFullAlignment().getSequencesArray());
2205 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2208 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2210 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2212 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2214 newal.addAnnotation(viewport.getAlignment()
2215 .getAlignmentAnnotation()[i]);
2220 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2222 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2223 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2224 PaintRefresher.Register(newaf.alignPanel,
2225 newaf.alignPanel.av.getSequenceSetId());
2227 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2228 newaf.alignPanel.av.getSequenceSetId());
2229 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2230 newaf.alignPanel.av.getSequenceSetId());
2232 Vector comps = (Vector) PaintRefresher.components.get(viewport
2233 .getSequenceSetId());
2235 for (int i = 0; i < comps.size(); i++)
2237 if (comps.elementAt(i) instanceof AlignmentPanel)
2243 String title = new String(this.getTitle());
2244 if (viewtitle != null)
2246 title = viewtitle + " ( " + title + ")";
2250 if (title.indexOf("(View") > -1)
2252 title = title.substring(0, title.indexOf("(View"));
2254 title += "(View " + viewSize + ")";
2257 newaf.setTitle(title.toString());
2259 newaf.viewport.historyList = viewport.historyList;
2260 newaf.viewport.redoList = viewport.redoList;
2266 * @return list of feature groups on the view
2268 public String[] getFeatureGroups()
2270 FeatureRenderer fr = null;
2271 if (alignPanel != null
2272 && (fr = alignPanel.getFeatureRenderer()) != null)
2274 return fr.getGroups();
2280 * get sequence feature groups that are hidden or shown
2286 public String[] getFeatureGroupsOfState(boolean visible)
2288 FeatureRenderer fr = null;
2289 if (alignPanel != null
2290 && (fr = alignPanel.getFeatureRenderer()) != null)
2292 return fr.getGroups(visible);
2298 * Change the display state for the given feature groups
2301 * list of group strings
2303 * visible or invisible
2305 public void setFeatureGroupState(String[] groups, boolean state)
2307 FeatureRenderer fr = null;
2308 this.sequenceFeatures.setState(true);
2309 viewport.showSequenceFeatures(true);
2310 if (alignPanel != null
2311 && (fr = alignPanel.getFeatureRenderer()) != null)
2313 fr.setGroupState(groups, state);
2314 alignPanel.seqPanel.seqCanvas.repaint();
2315 if (alignPanel.overviewPanel != null)
2317 alignPanel.overviewPanel.updateOverviewImage();
2322 public void seqLimits_itemStateChanged()
2324 viewport.setShowJVSuffix(seqLimits.getState());
2325 alignPanel.fontChanged();
2326 alignPanel.paintAlignment(true);
2329 protected void colourTextMenuItem_actionPerformed()
2331 viewport.setColourText(colourTextMenuItem.getState());
2332 alignPanel.paintAlignment(true);
2335 protected void displayNonconservedMenuItem_actionPerformed()
2337 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2338 alignPanel.paintAlignment(true);
2341 protected void wrapMenuItem_actionPerformed()
2343 viewport.setWrapAlignment(wrapMenuItem.getState());
2344 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2345 scaleAbove.setEnabled(wrapMenuItem.getState());
2346 scaleLeft.setEnabled(wrapMenuItem.getState());
2347 scaleRight.setEnabled(wrapMenuItem.getState());
2348 alignPanel.paintAlignment(true);
2351 public void overviewMenuItem_actionPerformed()
2353 if (alignPanel.overviewPanel != null)
2358 Frame frame = new Frame();
2359 OverviewPanel overview = new OverviewPanel(alignPanel);
2360 frame.add(overview);
2361 // +50 must allow for applet frame window
2362 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2363 "label.overview_params", new String[]
2364 { this.getTitle() }), overview.getPreferredSize().width,
2365 overview.getPreferredSize().height + 50);
2368 final AlignmentPanel ap = alignPanel;
2369 frame.addWindowListener(new WindowAdapter()
2372 public void windowClosing(WindowEvent e)
2376 ap.setOverviewPanel(null);
2381 alignPanel.setOverviewPanel(overview);
2385 void changeColour(ColourSchemeI cs)
2391 if (viewport.getAbovePIDThreshold())
2393 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2397 if (viewport.getConservationSelected())
2399 cs.setConservationApplied(true);
2400 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2405 cs.setConservationApplied(false);
2408 viewport.setGlobalColourScheme(cs);
2410 if (alignPanel.getOverviewPanel() != null)
2412 alignPanel.getOverviewPanel().updateOverviewImage();
2415 jalview.structure.StructureSelectionManager
2416 .getStructureSelectionManager(viewport.applet)
2417 .sequenceColoursChanged(alignPanel);
2419 alignPanel.paintAlignment(true);
2422 protected void modifyPID_actionPerformed()
2424 if (viewport.getAbovePIDThreshold()
2425 && viewport.getGlobalColourScheme() != null)
2427 SliderPanel.setPIDSliderSource(alignPanel,
2428 viewport.getGlobalColourScheme(), "Background");
2429 SliderPanel.showPIDSlider();
2433 protected void modifyConservation_actionPerformed()
2435 if (viewport.getConservationSelected()
2436 && viewport.getGlobalColourScheme() != null)
2438 SliderPanel.setConservationSlider(alignPanel,
2439 viewport.getGlobalColourScheme(), "Background");
2440 SliderPanel.showConservationSlider();
2444 protected void conservationMenuItem_actionPerformed()
2446 viewport.setConservationSelected(conservationMenuItem.getState());
2448 viewport.setAbovePIDThreshold(false);
2449 abovePIDThreshold.setState(false);
2451 changeColour(viewport.getGlobalColourScheme());
2453 modifyConservation_actionPerformed();
2456 public void abovePIDThreshold_actionPerformed()
2458 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2460 conservationMenuItem.setState(false);
2461 viewport.setConservationSelected(false);
2463 changeColour(viewport.getGlobalColourScheme());
2465 modifyPID_actionPerformed();
2468 public void sortPairwiseMenuItem_actionPerformed()
2470 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2471 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2472 .getAlignment().getSequenceAt(0), null);
2474 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2475 viewport.getAlignment()));
2476 alignPanel.paintAlignment(true);
2479 public void sortIDMenuItem_actionPerformed()
2481 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2482 AlignmentSorter.sortByID(viewport.getAlignment());
2483 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2484 viewport.getAlignment()));
2485 alignPanel.paintAlignment(true);
2488 public void sortLengthMenuItem_actionPerformed()
2490 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2491 AlignmentSorter.sortByLength(viewport.getAlignment());
2492 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2493 viewport.getAlignment()));
2494 alignPanel.paintAlignment(true);
2497 public void sortGroupMenuItem_actionPerformed()
2499 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2500 AlignmentSorter.sortByGroup(viewport.getAlignment());
2501 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2502 viewport.getAlignment()));
2503 alignPanel.paintAlignment(true);
2507 public void removeRedundancyMenuItem_actionPerformed()
2509 new RedundancyPanel(alignPanel);
2512 public void pairwiseAlignmentMenuItem_actionPerformed()
2514 if (viewport.getSelectionGroup() != null
2515 && viewport.getSelectionGroup().getSize() > 1)
2517 Frame frame = new Frame();
2518 frame.add(new PairwiseAlignPanel(alignPanel));
2519 jalview.bin.JalviewLite.addFrame(frame,
2520 MessageManager.getString("action.pairwise_alignment"), 600,
2525 public void PCAMenuItem_actionPerformed()
2527 // are the sequences aligned?
2528 if (!viewport.getAlignment().isAligned(false))
2531 int Width = viewport.getAlignment().getWidth();
2533 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2535 current = viewport.getAlignment().getSequenceAt(i);
2537 if (current.getLength() < Width)
2539 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2542 alignPanel.paintAlignment(true);
2545 if ((viewport.getSelectionGroup() != null
2546 && viewport.getSelectionGroup().getSize() < 4 && viewport
2547 .getSelectionGroup().getSize() > 0)
2548 || viewport.getAlignment().getHeight() < 4)
2555 new PCAPanel(viewport);
2556 } catch (java.lang.OutOfMemoryError ex)
2562 public void averageDistanceTreeMenuItem_actionPerformed()
2564 NewTreePanel("AV", "PID", "Average distance tree using PID");
2567 public void neighbourTreeMenuItem_actionPerformed()
2569 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2572 protected void njTreeBlosumMenuItem_actionPerformed()
2574 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2577 protected void avTreeBlosumMenuItem_actionPerformed()
2579 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2582 void NewTreePanel(String type, String pwType, String title)
2584 // are the sequences aligned?
2585 if (!viewport.getAlignment().isAligned(false))
2588 int Width = viewport.getAlignment().getWidth();
2590 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2592 current = viewport.getAlignment().getSequenceAt(i);
2594 if (current.getLength() < Width)
2596 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2599 alignPanel.paintAlignment(true);
2603 if ((viewport.getSelectionGroup() != null && viewport
2604 .getSelectionGroup().getSize() > 1)
2605 || (viewport.getAlignment().getHeight() > 1))
2607 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2609 addTreeMenuItem(tp, title);
2611 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2615 void loadTree_actionPerformed()
2617 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2618 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2619 cap.setTreeImport();
2620 Frame frame = new Frame();
2622 jalview.bin.JalviewLite.addFrame(frame,
2623 MessageManager.getString("label.paste_newick_file"), 400, 300);
2626 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2628 TreePanel tp = new TreePanel(alignPanel, treeFile,
2629 MessageManager.getString("label.load_tree_from_file"), tree);
2630 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2631 addTreeMenuItem(tp, treeFile);
2635 * sort the alignment using the given treePanel
2638 * tree used to sort view
2640 * string used for undo event name
2642 public void sortByTree(TreePanel treePanel, String title)
2644 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2646 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2647 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2648 // HistoryItem.SORT));
2649 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2650 "label.order_by_params", new String[]
2651 { title }), oldOrder, viewport.getAlignment()));
2652 alignPanel.paintAlignment(true);
2656 * Do any automatic reordering of the alignment and add the necessary bits to
2657 * the menu structure for the new tree
2662 protected void addTreeMenuItem(final TreePanel treePanel,
2665 final MenuItem item = new MenuItem(title);
2666 sortByTreeMenu.add(item);
2667 item.addActionListener(new java.awt.event.ActionListener()
2670 public void actionPerformed(ActionEvent evt)
2672 sortByTree(treePanel, title); // treePanel.getTitle());
2676 treePanel.addWindowListener(new WindowAdapter()
2679 public void windowOpened(WindowEvent e)
2681 if (viewport.sortByTree)
2683 sortByTree(treePanel, title);
2685 super.windowOpened(e);
2689 public void windowClosing(WindowEvent e)
2691 sortByTreeMenu.remove(item);
2696 public boolean sortBy(AlignmentOrder alorder, String undoname)
2698 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2699 if (viewport.applet.debug)
2701 System.err.println("Sorting " + alorder.getOrder().size()
2702 + " in alignment '" + getTitle() + "'");
2704 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2705 if (undoname != null)
2707 addHistoryItem(new OrderCommand(undoname, oldOrder,
2708 viewport.getAlignment()));
2710 alignPanel.paintAlignment(true);
2714 protected void documentation_actionPerformed()
2716 alignPanel.av.applet.openJalviewHelpUrl();
2719 protected void about_actionPerformed()
2722 class AboutPanel extends Canvas
2728 public AboutPanel(String version, String builddate)
2730 this.version = version;
2731 this.builddate = builddate;
2735 public void paint(Graphics g)
2737 g.setColor(Color.white);
2738 g.fillRect(0, 0, getSize().width, getSize().height);
2739 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2740 FontMetrics fm = g.getFontMetrics();
2741 int fh = fm.getHeight();
2743 g.setColor(Color.black);
2744 // TODO: update this text for each release or centrally store it for
2745 // lite and application
2746 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2747 g.drawString(MessageManager.formatMessage(
2748 "label.jalviewLite_release", new String[]
2749 { version }), x, y += fh);
2750 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2751 g.drawString(MessageManager.formatMessage(
2752 "label.jaview_build_date", new String[]
2753 { builddate }), x, y += fh);
2754 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2755 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2757 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2758 x + 50, y += fh + 8);
2760 MessageManager.getString("label.jalview_dev_managers"), x,
2762 g.drawString(MessageManager
2763 .getString("label.jalview_distribution_lists"), x, y += fh);
2764 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2767 MessageManager.getString("label.jalview_cite_1_authors"),
2770 MessageManager.getString("label.jalview_cite_1_title"), x,
2772 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2777 Frame frame = new Frame();
2778 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2780 jalview.bin.JalviewLite.addFrame(frame,
2781 MessageManager.getString("label.jalview"), 580, 220);
2785 public void showURL(String url, String target)
2787 if (viewport.applet == null)
2789 System.out.println("Not running as applet - no browser available.");
2793 viewport.applet.showURL(url, target);
2797 // ////////////////////////////////////////////////////////////////////////////////
2798 // JBuilder Graphics here
2800 MenuBar alignFrameMenuBar = new MenuBar();
2802 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2804 MenuItem loadApplication = new MenuItem(
2805 MessageManager.getString("label.view_full_application"));
2807 MenuItem loadTree = new MenuItem(
2808 MessageManager.getString("label.load_associated_tree"));
2810 MenuItem loadAnnotations = new MenuItem(
2811 MessageManager.getString("label.load_features_annotations"));
2813 MenuItem outputFeatures = new MenuItem(
2814 MessageManager.getString("label.export_features").concat("..."));
2816 MenuItem outputAnnotations = new MenuItem(
2817 MessageManager.getString("label.export_annotations").concat("..."));
2819 MenuItem closeMenuItem = new MenuItem(
2820 MessageManager.getString("action.close"));
2822 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2824 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2826 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2828 Menu calculateMenu = new Menu(
2829 MessageManager.getString("action.calculate"));
2831 MenuItem selectAllSequenceMenuItem = new MenuItem(
2832 MessageManager.getString("action.select_all"));
2834 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2835 MessageManager.getString("action.deselect_all"));
2837 MenuItem invertSequenceMenuItem = new MenuItem(
2838 MessageManager.getString("action.invert_selection"));
2840 MenuItem remove2LeftMenuItem = new MenuItem();
2842 MenuItem remove2RightMenuItem = new MenuItem();
2844 MenuItem removeGappedColumnMenuItem = new MenuItem();
2846 MenuItem removeAllGapsMenuItem = new MenuItem();
2848 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2850 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2852 MenuItem sortPairwiseMenuItem = new MenuItem();
2854 MenuItem sortIDMenuItem = new MenuItem();
2856 MenuItem sortLengthMenuItem = new MenuItem();
2858 MenuItem sortGroupMenuItem = new MenuItem();
2860 MenuItem removeRedundancyMenuItem = new MenuItem();
2862 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2864 MenuItem PCAMenuItem = new MenuItem();
2866 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2868 MenuItem neighbourTreeMenuItem = new MenuItem();
2870 BorderLayout borderLayout1 = new BorderLayout();
2872 public Label statusBar = new Label();
2874 Menu outputTextboxMenu = new Menu();
2876 MenuItem clustalColour = new MenuItem();
2878 MenuItem zappoColour = new MenuItem();
2880 MenuItem taylorColour = new MenuItem();
2882 MenuItem hydrophobicityColour = new MenuItem();
2884 MenuItem helixColour = new MenuItem();
2886 MenuItem strandColour = new MenuItem();
2888 MenuItem turnColour = new MenuItem();
2890 MenuItem buriedColour = new MenuItem();
2892 MenuItem purinePyrimidineColour = new MenuItem();
2894 MenuItem RNAInteractionColour = new MenuItem();
2896 MenuItem RNAHelixColour = new MenuItem();
2898 MenuItem userDefinedColour = new MenuItem();
2900 MenuItem PIDColour = new MenuItem();
2902 MenuItem BLOSUM62Colour = new MenuItem();
2904 MenuItem tcoffeeColour = new MenuItem();
2906 MenuItem njTreeBlosumMenuItem = new MenuItem();
2908 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2910 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2912 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2914 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2916 MenuItem alProperties = new MenuItem(
2917 MessageManager.getString("label.alignment_props"));
2919 MenuItem overviewMenuItem = new MenuItem();
2921 MenuItem undoMenuItem = new MenuItem();
2923 MenuItem redoMenuItem = new MenuItem();
2925 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2927 MenuItem noColourmenuItem = new MenuItem();
2929 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2931 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2933 MenuItem findMenuItem = new MenuItem();
2935 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2937 MenuItem nucleotideColour = new MenuItem();
2939 MenuItem deleteGroups = new MenuItem();
2941 MenuItem grpsFromSelection = new MenuItem();
2943 MenuItem createGroup = new MenuItem();
2945 MenuItem unGroup = new MenuItem();
2947 MenuItem delete = new MenuItem();
2949 MenuItem copy = new MenuItem();
2951 MenuItem cut = new MenuItem();
2953 Menu pasteMenu = new Menu();
2955 MenuItem pasteNew = new MenuItem();
2957 MenuItem pasteThis = new MenuItem();
2959 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2961 MenuItem font = new MenuItem();
2963 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2965 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2967 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2969 MenuItem modifyPID = new MenuItem();
2971 MenuItem modifyConservation = new MenuItem();
2973 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2974 "Autocalculate Consensus", true);
2976 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2977 "Sort Alignment With New Tree", true);
2979 Menu sortByTreeMenu = new Menu();
2981 Menu sort = new Menu();
2983 Menu calculate = new Menu();
2985 MenuItem inputText = new MenuItem();
2987 Menu helpMenu = new Menu();
2989 MenuItem documentation = new MenuItem();
2991 MenuItem about = new MenuItem();
2993 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2995 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2997 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2999 Menu autoAnnMenu = new Menu();
3001 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3003 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3005 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3007 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3009 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3011 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3013 private void jbInit() throws Exception
3016 setMenuBar(alignFrameMenuBar);
3020 // dynamically fill save as menu with available formats
3021 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3024 item = new MenuItem(
3025 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3027 item.addActionListener(new java.awt.event.ActionListener()
3030 public void actionPerformed(ActionEvent e)
3032 outputText_actionPerformed(e);
3036 outputTextboxMenu.add(item);
3038 closeMenuItem.addActionListener(this);
3039 loadApplication.addActionListener(this);
3041 loadTree.addActionListener(this);
3042 loadAnnotations.addActionListener(this);
3043 outputFeatures.addActionListener(this);
3044 outputAnnotations.addActionListener(this);
3045 selectAllSequenceMenuItem.addActionListener(this);
3046 deselectAllSequenceMenuItem.addActionListener(this);
3047 invertSequenceMenuItem.addActionListener(this);
3048 remove2LeftMenuItem.setLabel(MessageManager
3049 .getString("action.remove_left"));
3050 remove2LeftMenuItem.addActionListener(this);
3051 remove2RightMenuItem.setLabel(MessageManager
3052 .getString("action.remove_right"));
3053 remove2RightMenuItem.addActionListener(this);
3054 removeGappedColumnMenuItem.setLabel(MessageManager
3055 .getString("action.remove_empty_columns"));
3056 removeGappedColumnMenuItem.addActionListener(this);
3057 removeAllGapsMenuItem.setLabel(MessageManager
3058 .getString("action.remove_all_gaps"));
3059 removeAllGapsMenuItem.addActionListener(this);
3060 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3061 viewBoxesMenuItem.setState(true);
3062 viewBoxesMenuItem.addItemListener(this);
3063 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3064 viewTextMenuItem.setState(true);
3065 viewTextMenuItem.addItemListener(this);
3066 sortPairwiseMenuItem.setLabel(MessageManager
3067 .getString("action.by_pairwise_id"));
3068 sortPairwiseMenuItem.addActionListener(this);
3069 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3070 sortIDMenuItem.addActionListener(this);
3071 sortLengthMenuItem.setLabel(MessageManager
3072 .getString("action.by_length"));
3073 sortLengthMenuItem.addActionListener(this);
3074 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3075 sortGroupMenuItem.addActionListener(this);
3076 removeRedundancyMenuItem.setLabel(MessageManager
3077 .getString("action.remove_redundancy").concat("..."));
3078 removeRedundancyMenuItem.addActionListener(this);
3079 pairwiseAlignmentMenuItem.setLabel(MessageManager
3080 .getString("action.pairwise_alignment"));
3081 pairwiseAlignmentMenuItem.addActionListener(this);
3082 PCAMenuItem.setLabel(MessageManager
3083 .getString("label.principal_component_analysis"));
3084 PCAMenuItem.addActionListener(this);
3085 averageDistanceTreeMenuItem.setLabel(MessageManager
3086 .getString("label.average_distance_identity"));
3087 averageDistanceTreeMenuItem.addActionListener(this);
3088 neighbourTreeMenuItem.setLabel(MessageManager
3089 .getString("label.neighbour_joining_identity"));
3090 neighbourTreeMenuItem.addActionListener(this);
3091 statusBar.setBackground(Color.white);
3092 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3093 statusBar.setText(MessageManager.getString("label.status_bar"));
3094 outputTextboxMenu.setLabel(MessageManager
3095 .getString("label.out_to_textbox"));
3096 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3098 clustalColour.addActionListener(this);
3099 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3100 zappoColour.addActionListener(this);
3101 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3102 taylorColour.addActionListener(this);
3103 hydrophobicityColour.setLabel(MessageManager
3104 .getString("label.hydrophobicity"));
3105 hydrophobicityColour.addActionListener(this);
3107 .setLabel(MessageManager.getString("label.helix_propensity"));
3108 helixColour.addActionListener(this);
3109 strandColour.setLabel(MessageManager
3110 .getString("label.strand_propensity"));
3111 strandColour.addActionListener(this);
3112 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3113 turnColour.addActionListener(this);
3114 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3115 buriedColour.addActionListener(this);
3116 purinePyrimidineColour.setLabel(MessageManager
3117 .getString("label.purine_pyrimidine"));
3118 purinePyrimidineColour.addActionListener(this);
3119 RNAInteractionColour.setLabel(MessageManager
3120 .getString("label.rna_interaction"));
3121 RNAInteractionColour.addActionListener(this);
3122 RNAHelixColour.setLabel(MessageManager
3123 .getString("action.by_rna_helixes"));
3124 RNAHelixColour.addActionListener(this);
3125 userDefinedColour.setLabel(MessageManager
3126 .getString("action.user_defined"));
3127 userDefinedColour.addActionListener(this);
3128 PIDColour.setLabel(MessageManager
3129 .getString("label.percentage_identity"));
3130 PIDColour.addActionListener(this);
3131 BLOSUM62Colour.setLabel(MessageManager
3132 .getString("label.blosum62_score"));
3133 BLOSUM62Colour.addActionListener(this);
3135 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3136 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3138 tcoffeeColour.addActionListener(this);
3139 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3140 .getString("label.average_distance_bloslum62"));
3141 avDistanceTreeBlosumMenuItem.addActionListener(this);
3142 njTreeBlosumMenuItem.setLabel(MessageManager
3143 .getString("label.neighbour_blosum62"));
3144 njTreeBlosumMenuItem.addActionListener(this);
3145 annotationPanelMenuItem.setLabel(MessageManager
3146 .getString("label.show_annotations"));
3147 annotationPanelMenuItem.addItemListener(this);
3148 colourTextMenuItem.setLabel(MessageManager
3149 .getString("label.colour_text"));
3150 colourTextMenuItem.addItemListener(this);
3151 displayNonconservedMenuItem.setLabel(MessageManager
3152 .getString("label.show_non_conversed"));
3153 displayNonconservedMenuItem.addItemListener(this);
3154 alProperties.addActionListener(this);
3155 overviewMenuItem.setLabel(MessageManager
3156 .getString("label.overview_window"));
3157 overviewMenuItem.addActionListener(this);
3158 undoMenuItem.setEnabled(false);
3159 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3160 undoMenuItem.addActionListener(this);
3161 redoMenuItem.setEnabled(false);
3162 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3163 redoMenuItem.addActionListener(this);
3164 conservationMenuItem.setLabel(MessageManager
3165 .getString("action.by_conservation"));
3166 conservationMenuItem.addItemListener(this);
3167 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3168 noColourmenuItem.addActionListener(this);
3169 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3170 wrapMenuItem.addItemListener(this);
3171 renderGapsMenuItem.setLabel(MessageManager
3172 .getString("action.show_gaps"));
3173 renderGapsMenuItem.setState(true);
3174 renderGapsMenuItem.addItemListener(this);
3175 findMenuItem.setLabel(MessageManager.getString("action.find"));
3176 findMenuItem.addActionListener(this);
3177 abovePIDThreshold.setLabel(MessageManager
3178 .getString("label.above_identity_threshold"));
3179 abovePIDThreshold.addItemListener(this);
3180 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3181 nucleotideColour.addActionListener(this);
3182 deleteGroups.setLabel(MessageManager
3183 .getString("action.undefine_groups"));
3184 deleteGroups.addActionListener(this);
3185 grpsFromSelection.setLabel(MessageManager
3186 .getString("action.make_groups_selection"));
3187 grpsFromSelection.addActionListener(this);
3188 createGroup.setLabel(MessageManager.getString("action.create_group"));
3189 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3190 copy.setLabel(MessageManager.getString("action.copy"));
3191 copy.addActionListener(this);
3192 cut.setLabel(MessageManager.getString("action.cut"));
3193 cut.addActionListener(this);
3194 delete.setLabel(MessageManager.getString("action.delete"));
3195 delete.addActionListener(this);
3196 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3197 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3198 pasteNew.addActionListener(this);
3199 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3200 pasteThis.addActionListener(this);
3201 applyToAllGroups.setLabel(MessageManager
3202 .getString("label.apply_colour_to_all_groups"));
3203 applyToAllGroups.setState(true);
3204 applyToAllGroups.addItemListener(this);
3205 font.setLabel(MessageManager.getString("action.font"));
3206 font.addActionListener(this);
3207 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3208 scaleAbove.setState(true);
3209 scaleAbove.setEnabled(false);
3210 scaleAbove.addItemListener(this);
3211 scaleLeft.setEnabled(false);
3212 scaleLeft.setState(true);
3213 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3214 scaleLeft.addItemListener(this);
3215 scaleRight.setEnabled(false);
3216 scaleRight.setState(true);
3217 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3218 scaleRight.addItemListener(this);
3219 modifyPID.setLabel(MessageManager
3220 .getString("label.modify_identity_thereshold"));
3221 modifyPID.addActionListener(this);
3222 modifyConservation.setLabel(MessageManager
3223 .getString("label.modify_conservation_thereshold"));
3224 modifyConservation.addActionListener(this);
3225 sortByTreeMenu.setLabel(MessageManager
3226 .getString("action.by_tree_order"));
3227 sort.setLabel(MessageManager.getString("action.sort"));
3228 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3229 autoCalculate.addItemListener(this);
3230 sortByTree.addItemListener(this);
3232 .setLabel(MessageManager.getString("label.input_from_textbox"));
3233 inputText.addActionListener(this);
3234 centreColumnLabelFlag.setLabel(MessageManager
3235 .getString("label.centre_column_labels"));
3236 centreColumnLabelFlag.addItemListener(this);
3237 followMouseOverFlag.setLabel(MessageManager
3238 .getString("label.automatic_scrolling"));
3239 followMouseOverFlag.addItemListener(this);
3240 helpMenu.setLabel(MessageManager.getString("action.help"));
3241 documentation.setLabel(MessageManager.getString("label.documentation"));
3242 documentation.addActionListener(this);
3244 about.setLabel(MessageManager.getString("label.about"));
3245 about.addActionListener(this);
3246 seqLimits.setState(true);
3247 seqLimits.setLabel(MessageManager
3248 .getString("label.show_sequence_limits"));
3249 seqLimits.addItemListener(this);
3250 featureSettings.setLabel(MessageManager
3251 .getString("label.feature_settings"));
3252 featureSettings.addActionListener(this);
3253 sequenceFeatures.setLabel(MessageManager
3254 .getString("label.sequence_features"));
3255 sequenceFeatures.addItemListener(this);
3256 sequenceFeatures.setState(false);
3257 annotationColour.setLabel(MessageManager
3258 .getString("action.by_annotation"));
3259 annotationColour.addActionListener(this);
3260 invertSequenceMenuItem.setLabel(MessageManager
3261 .getString("action.invert_sequence_selection"));
3262 invertColSel.setLabel(MessageManager
3263 .getString("action.invert_column_selection"));
3264 menu1.setLabel(MessageManager.getString("action.show"));
3265 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3266 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3267 menu2.setLabel(MessageManager.getString("action.hide"));
3269 .setLabel(MessageManager.getString("label.selected_columns"));
3270 hideSequences.setLabel(MessageManager
3271 .getString("label.selected_sequences"));
3272 hideAllButSelection.setLabel(MessageManager
3273 .getString("label.all_but_selected_region"));
3274 hideAllSelection.setLabel(MessageManager
3275 .getString("label.selected_region"));
3276 showAllHidden.setLabel(MessageManager
3277 .getString("label.all_sequences_columns"));
3278 showGroupConsensus.setLabel(MessageManager
3279 .getString("label.group_consensus"));
3280 showGroupConservation.setLabel(MessageManager
3281 .getString("label.group_conservation"));
3282 showConsensusHistogram.setLabel(MessageManager
3283 .getString("label.show_consensus_histogram"));
3284 showSequenceLogo.setLabel(MessageManager
3285 .getString("label.show_consensus_logo"));
3286 normSequenceLogo.setLabel(MessageManager
3287 .getString("label.norm_consensus_logo"));
3288 applyAutoAnnotationSettings.setLabel(MessageManager
3289 .getString("label.apply_all_groups"));
3290 applyAutoAnnotationSettings.setState(true);
3291 autoAnnMenu.setLabel(MessageManager
3292 .getString("label.autocalculated_annotation"));
3294 invertColSel.addActionListener(this);
3295 showColumns.addActionListener(this);
3296 showSeqs.addActionListener(this);
3297 hideColumns.addActionListener(this);
3298 hideSequences.addActionListener(this);
3299 hideAllButSelection.addActionListener(this);
3300 hideAllSelection.addActionListener(this);
3301 showAllHidden.addActionListener(this);
3302 showGroupConsensus.addItemListener(this);
3303 showGroupConservation.addItemListener(this);
3304 showConsensusHistogram.addItemListener(this);
3305 showSequenceLogo.addItemListener(this);
3306 normSequenceLogo.addItemListener(this);
3308 applyAutoAnnotationSettings.addItemListener(this);
3309 formatMenu.setLabel(MessageManager.getString("action.format"));
3310 selectMenu.setLabel(MessageManager.getString("action.select"));
3311 newView.setLabel(MessageManager.getString("action.new_view"));
3312 newView.addActionListener(this);
3313 alignFrameMenuBar.add(fileMenu);
3314 alignFrameMenuBar.add(editMenu);
3315 alignFrameMenuBar.add(selectMenu);
3316 alignFrameMenuBar.add(viewMenu);
3317 alignFrameMenuBar.add(formatMenu);
3318 alignFrameMenuBar.add(colourMenu);
3319 alignFrameMenuBar.add(calculateMenu);
3320 alignFrameMenuBar.add(helpMenu);
3322 fileMenu.add(inputText);
3323 fileMenu.add(loadTree);
3324 fileMenu.add(loadAnnotations);
3326 fileMenu.addSeparator();
3327 fileMenu.add(outputTextboxMenu);
3328 fileMenu.add(outputFeatures);
3329 fileMenu.add(outputAnnotations);
3331 if (jalviewServletURL != null)
3333 fileMenu.add(loadApplication);
3336 fileMenu.addSeparator();
3337 fileMenu.add(closeMenuItem);
3339 editMenu.add(undoMenuItem);
3340 editMenu.add(redoMenuItem);
3343 editMenu.add(pasteMenu);
3344 editMenu.add(delete);
3345 editMenu.addSeparator();
3346 editMenu.add(remove2LeftMenuItem);
3347 editMenu.add(remove2RightMenuItem);
3348 editMenu.add(removeGappedColumnMenuItem);
3349 editMenu.add(removeAllGapsMenuItem);
3350 editMenu.add(removeRedundancyMenuItem);
3351 viewMenu.add(newView);
3352 viewMenu.addSeparator();
3353 viewMenu.add(menu1);
3354 viewMenu.add(menu2);
3355 viewMenu.addSeparator();
3356 viewMenu.add(followMouseOverFlag);
3357 viewMenu.add(annotationPanelMenuItem);
3358 autoAnnMenu.add(applyAutoAnnotationSettings);
3359 autoAnnMenu.add(showConsensusHistogram);
3360 autoAnnMenu.add(showSequenceLogo);
3361 autoAnnMenu.add(normSequenceLogo);
3362 autoAnnMenu.addSeparator();
3363 autoAnnMenu.add(showGroupConservation);
3364 autoAnnMenu.add(showGroupConsensus);
3365 viewMenu.add(autoAnnMenu);
3366 viewMenu.addSeparator();
3367 viewMenu.add(sequenceFeatures);
3368 viewMenu.add(featureSettings);
3369 viewMenu.addSeparator();
3370 viewMenu.add(alProperties);
3371 viewMenu.addSeparator();
3372 viewMenu.add(overviewMenuItem);
3373 colourMenu.add(applyToAllGroups);
3374 colourMenu.addSeparator();
3375 colourMenu.add(noColourmenuItem);
3376 colourMenu.add(clustalColour);
3377 colourMenu.add(BLOSUM62Colour);
3378 colourMenu.add(PIDColour);
3379 colourMenu.add(zappoColour);
3380 colourMenu.add(taylorColour);
3381 colourMenu.add(hydrophobicityColour);
3382 colourMenu.add(helixColour);
3383 colourMenu.add(strandColour);
3384 colourMenu.add(turnColour);
3385 colourMenu.add(buriedColour);
3386 colourMenu.add(nucleotideColour);
3387 colourMenu.add(purinePyrimidineColour);
3388 // colourMenu.add(RNAInteractionColour);
3389 colourMenu.add(tcoffeeColour);
3390 colourMenu.add(userDefinedColour);
3391 colourMenu.addSeparator();
3392 colourMenu.add(conservationMenuItem);
3393 colourMenu.add(modifyConservation);
3394 colourMenu.add(abovePIDThreshold);
3395 colourMenu.add(modifyPID);
3396 colourMenu.add(annotationColour);
3397 colourMenu.add(RNAHelixColour);
3398 calculateMenu.add(sort);
3399 calculateMenu.add(calculate);
3400 calculateMenu.addSeparator();
3401 calculateMenu.add(pairwiseAlignmentMenuItem);
3402 calculateMenu.add(PCAMenuItem);
3403 calculateMenu.add(autoCalculate);
3404 calculateMenu.add(sortByTree);
3405 this.add(statusBar, BorderLayout.SOUTH);
3406 pasteMenu.add(pasteNew);
3407 pasteMenu.add(pasteThis);
3408 sort.add(sortIDMenuItem);
3409 sort.add(sortLengthMenuItem);
3410 sort.add(sortByTreeMenu);
3411 sort.add(sortGroupMenuItem);
3412 sort.add(sortPairwiseMenuItem);
3413 calculate.add(averageDistanceTreeMenuItem);
3414 calculate.add(neighbourTreeMenuItem);
3415 calculate.add(avDistanceTreeBlosumMenuItem);
3416 calculate.add(njTreeBlosumMenuItem);
3417 helpMenu.add(documentation);
3418 helpMenu.add(about);
3419 menu1.add(showColumns);
3420 menu1.add(showSeqs);
3421 menu1.add(showAllHidden);
3422 menu2.add(hideColumns);
3423 menu2.add(hideSequences);
3424 menu2.add(hideAllSelection);
3425 menu2.add(hideAllButSelection);
3426 formatMenu.add(font);
3427 formatMenu.add(seqLimits);
3428 formatMenu.add(wrapMenuItem);
3429 formatMenu.add(scaleAbove);
3430 formatMenu.add(scaleLeft);
3431 formatMenu.add(scaleRight);
3432 formatMenu.add(viewBoxesMenuItem);
3433 formatMenu.add(viewTextMenuItem);
3434 formatMenu.add(colourTextMenuItem);
3435 formatMenu.add(displayNonconservedMenuItem);
3436 formatMenu.add(renderGapsMenuItem);
3437 formatMenu.add(centreColumnLabelFlag);
3438 selectMenu.add(findMenuItem);
3439 selectMenu.addSeparator();
3440 selectMenu.add(selectAllSequenceMenuItem);
3441 selectMenu.add(deselectAllSequenceMenuItem);
3442 selectMenu.add(invertSequenceMenuItem);
3443 selectMenu.add(invertColSel);
3444 selectMenu.add(createGroup);
3445 selectMenu.add(unGroup);
3446 selectMenu.add(grpsFromSelection);
3447 selectMenu.add(deleteGroups);
3451 public void setStatus(String string)
3453 statusBar.setText(string);
3456 MenuItem featureSettings = new MenuItem();
3458 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3460 MenuItem annotationColour = new MenuItem();
3462 MenuItem invertColSel = new MenuItem();
3464 Menu menu1 = new Menu();
3466 MenuItem showColumns = new MenuItem();
3468 MenuItem showSeqs = new MenuItem();
3470 Menu menu2 = new Menu();
3472 MenuItem hideColumns = new MenuItem();
3474 MenuItem hideSequences = new MenuItem();
3476 MenuItem hideAllButSelection = new MenuItem();
3478 MenuItem hideAllSelection = new MenuItem();
3480 MenuItem showAllHidden = new MenuItem();
3482 Menu formatMenu = new Menu();
3484 Menu selectMenu = new Menu();
3486 MenuItem newView = new MenuItem();
3489 * Attach the alignFrame panels after embedding menus, if necessary. This used
3490 * to be called setEmbedded, but is now creates the dropdown menus in a
3491 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3493 * @param reallyEmbedded
3494 * true to attach the view to the applet area on the page rather than
3497 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3502 // Explicly build the embedded menu panel for the on-page applet
3504 // view cannot be closed if its actually on the page
3505 fileMenu.remove(closeMenuItem);
3506 fileMenu.remove(3); // Remove Seperator
3507 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3508 Font.PLAIN, 11, false); // use our own fonts.
3509 // and actually add the components to the applet area
3510 viewport.applet.setLayout(new BorderLayout());
3511 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3512 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3513 alignPanel.setSize(viewport.applet.getSize().width,
3514 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3515 - statusBar.HEIGHT);
3516 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3517 final AlignFrame me = this;
3518 viewport.applet.addFocusListener(new FocusListener()
3522 public void focusLost(FocusEvent e)
3524 if (me.viewport.applet.currentAlignFrame == me)
3526 me.viewport.applet.currentAlignFrame = null;
3531 public void focusGained(FocusEvent e)
3533 me.viewport.applet.currentAlignFrame = me;
3536 viewport.applet.validate();
3541 // test and embed menu bar if necessary.
3543 if (embedMenuIfNeeded(alignPanel))
3545 // adjust for status bar height too
3546 alignPanel.setSize(getSize().width, getSize().height
3547 - statusBar.HEIGHT);
3549 add(statusBar, BorderLayout.SOUTH);
3550 add(alignPanel, BorderLayout.CENTER);
3551 // and register with the applet so it can pass external API calls to us
3552 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3558 * create a new binding between structures in an existing jmol viewer instance
3559 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3560 * this does not open a new Jmol window, or modify the display of the
3561 * structures in the original jmol window. Note This method doesn't work
3562 * without an additional javascript library to exchange messages between the
3563 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3566 * JmolViewer instance
3567 * @param sequenceIds
3568 * - sequence Ids to search for associations
3570 public SequenceStructureBinding addStructureViewInstance(
3571 Object jmolviewer, String[] sequenceIds)
3573 org.jmol.api.JmolViewer viewer = null;
3576 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3577 } catch (ClassCastException ex)
3579 System.err.println("Unsupported viewer object :"
3580 + jmolviewer.getClass());
3584 System.err.println("Can't use this object as a structure viewer:"
3585 + jmolviewer.getClass());
3588 SequenceI[] seqs = null;
3589 if (sequenceIds == null || sequenceIds.length == 0)
3591 seqs = viewport.getAlignment().getSequencesArray();
3595 Vector sqi = new Vector();
3596 AlignmentI al = viewport.getAlignment();
3597 for (int sid = 0; sid < sequenceIds.length; sid++)
3599 SequenceI sq = al.findName(sequenceIds[sid]);
3607 seqs = new SequenceI[sqi.size()];
3608 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3610 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3619 // TODO: search for a jmv that involves viewer
3621 { // create a new viewer/jalview binding.
3622 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3630 * bind a pdb file to a sequence in the current view
3633 * - sequenceId within the dataset.
3634 * @param pdbEntryString
3635 * - the short name for the PDB file
3637 * - pdb file - either a URL or a valid PDB file.
3638 * @return true if binding was as success TODO: consider making an exception
3639 * structure for indicating when PDB parsing or sequenceId location
3642 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3645 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3646 boolean needtoadd = false;
3647 if (toaddpdb != null)
3649 Vector pdbe = toaddpdb.getPDBId();
3650 PDBEntry pdbentry = null;
3651 if (pdbe != null && pdbe.size() > 0)
3653 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3655 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3656 if (!pdbentry.getId().equals(pdbEntryString)
3657 && !pdbentry.getFile().equals(pdbFile))
3667 if (pdbentry == null)
3669 pdbentry = new PDBEntry();
3670 pdbentry.setId(pdbEntryString);
3671 pdbentry.setFile(pdbFile);
3672 needtoadd = true; // add this new entry to sequence.
3674 // resolve data source
3675 // TODO: this code should be a refactored to an io package
3676 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3677 if (protocol == null)
3683 // make a note of the access mode and add
3684 if (pdbentry.getProperty() == null)
3686 pdbentry.setProperty(new Hashtable());
3688 pdbentry.getProperty().put("protocol", protocol);
3689 toaddpdb.addPDBId(pdbentry);
3690 alignPanel.getStructureSelectionManager()
3691 .registerPDBEntry(pdbentry);
3697 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3701 Vector sequences = new Vector();
3702 for (int i = 0; i < seqs.length; i++)
3704 if (seqs[i] != null)
3706 sequences.addElement(new Object[]
3707 { seqs[i], (chains != null) ? chains[i] : null });
3710 seqs = new SequenceI[sequences.size()];
3711 chains = new String[sequences.size()];
3712 for (int i = 0, isize = sequences.size(); i < isize; i++)
3714 Object[] oj = (Object[]) sequences.elementAt(i);
3716 seqs[i] = (SequenceI) oj[0];
3717 chains[i] = (String) oj[1];
3725 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3726 SequenceI[] seqs, String[] chains, String protocol)
3728 // Scrub any null sequences from the array
3729 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3730 seqs = (SequenceI[]) sqch[0];
3731 chains = (String[]) sqch[1];
3732 if (seqs == null || seqs.length == 0)
3735 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3737 if (protocol == null || protocol.trim().length() == 0
3738 || protocol.equals("null"))
3740 protocol = (String) pdb.getProperty().get("protocol");
3741 if (protocol == null)
3743 System.err.println("Couldn't work out protocol to open structure: "
3748 if (applet.useXtrnalSviewer)
3750 // register the association(s) and quit, don't create any windows.
3751 if (StructureSelectionManager.getStructureSelectionManager(applet)
3752 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3754 System.err.println("Failed to map " + pdb.getFile() + " ("
3755 + protocol + ") to any sequences");
3759 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3761 // can only do alignments with Jmol
3762 // find the last jmol window assigned to this alignment
3763 jalview.appletgui.AppletJmol ajm = null, tajm;
3764 Vector jmols = applet
3765 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3766 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3768 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3769 if (tajm.ap.alignFrame == this)
3778 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3779 // try and add the pdb structure
3784 // otherwise, create a new window
3785 if (applet.jmolAvailable)
3787 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3789 applet.lastFrameX += 40;
3790 applet.lastFrameY += 40;
3794 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3799 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3800 SequenceI[][] seqs, String[][] chains, String[] protocols)
3802 // TODO Auto-generated method stub
3803 System.err.println("Aligned Structure View: Not yet implemented.");
3807 * modify the current selection, providing the user has not made a selection
3811 * - sequences from this alignment
3813 * - columns to be selected on the alignment
3815 public void select(SequenceGroup sel, ColumnSelection csel)
3817 alignPanel.seqPanel.selection(sel, csel, null);
3820 public void scrollTo(int row, int column)
3822 alignPanel.seqPanel.scrollTo(row, column);
3825 public void scrollToRow(int row)
3827 alignPanel.seqPanel.scrollToRow(row);
3830 public void scrollToColumn(int column)
3832 alignPanel.seqPanel.scrollToColumn(column);
3836 * @return the alignments unique ID.
3838 public String getSequenceSetId()
3840 return viewport.getSequenceSetId();
3844 * Load the (T-Coffee) score file from the specified url
3847 * File/URL/T-COFFEE score file contents
3848 * @throws IOException
3849 * @return true if alignment was annotated with data from source
3851 public boolean loadScoreFile(String source) throws IOException
3854 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3855 AppletFormatAdapter.checkProtocol(source));
3856 if (!file.isValid())
3858 // TODO: raise dialog for gui
3859 System.err.println("Problems parsing T-Coffee scores: "
3860 + file.getWarningMessage());
3861 System.err.println("Origin was:\n" + source);
3866 * check that the score matrix matches the alignment dimensions
3869 if ((aln = viewport.getAlignment()) != null
3870 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3873 // TODO: raise a dialog box here rather than bomb out.
3875 .println("The scores matrix does not match the alignment dimensions");
3879 // TODO add parameter to indicate if matching should be done
3880 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3882 alignPanel.fontChanged();
3883 tcoffeeColour.setEnabled(true);
3884 // switch to this color
3885 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3890 System.err.println("Problems resolving T-Coffee scores:");
3891 if (file.getWarningMessage() != null)
3893 System.err.println(file.getWarningMessage());