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.structures.models.AAStructureBindingModel;
66 import jalview.util.MessageManager;
68 import java.awt.BorderLayout;
69 import java.awt.Canvas;
70 import java.awt.CheckboxMenuItem;
71 import java.awt.Color;
73 import java.awt.FontMetrics;
74 import java.awt.Frame;
75 import java.awt.Graphics;
76 import java.awt.Label;
78 import java.awt.MenuBar;
79 import java.awt.MenuItem;
80 import java.awt.event.ActionEvent;
81 import java.awt.event.ActionListener;
82 import java.awt.event.FocusEvent;
83 import java.awt.event.FocusListener;
84 import java.awt.event.ItemEvent;
85 import java.awt.event.ItemListener;
86 import java.awt.event.KeyEvent;
87 import java.awt.event.KeyListener;
88 import java.awt.event.WindowAdapter;
89 import java.awt.event.WindowEvent;
90 import java.io.IOException;
92 import java.net.URLEncoder;
93 import java.util.Enumeration;
94 import java.util.Hashtable;
95 import java.util.List;
96 import java.util.StringTokenizer;
97 import java.util.Vector;
99 public class AlignFrame extends EmbmenuFrame implements ActionListener,
100 ItemListener, KeyListener, AlignViewControllerGuiI
102 public AlignViewControllerI avc;
104 public AlignmentPanel alignPanel;
106 public AlignViewport viewport;
108 int DEFAULT_WIDTH = 700;
110 int DEFAULT_HEIGHT = 500;
112 String jalviewServletURL;
114 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
115 String title, boolean embedded)
119 jalviewServletURL = applet.getParameter("APPLICATION_URL");
125 } catch (Exception ex)
127 ex.printStackTrace();
129 // need to get window geometry before we calculate alignment layout
135 param = applet.getParameter("windowWidth");
138 int width = Integer.parseInt(param);
139 DEFAULT_WIDTH = width;
141 param = applet.getParameter("windowHeight");
144 int height = Integer.parseInt(param);
145 DEFAULT_HEIGHT = height;
147 } catch (Exception ex)
151 viewport = new AlignViewport(al, applet);
152 alignPanel = new AlignmentPanel(this, viewport);
153 avc = new jalview.controller.AlignViewController(this, viewport,
155 viewport.updateConservation(alignPanel);
156 viewport.updateConsensus(alignPanel);
158 annotationPanelMenuItem.setState(viewport.showAnnotation);
159 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
160 followMouseOverFlag.setState(viewport.getFollowHighlight());
161 showGroupConsensus.setState(viewport.isShowGroupConsensus());
162 showGroupConservation.setState(viewport.isShowGroupConservation());
163 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
164 showSequenceLogo.setState(viewport.isShowSequenceLogo());
165 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
166 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
168 seqLimits.setState(viewport.showJVSuffix);
172 String param = applet.getParameter("sortBy");
175 if (param.equalsIgnoreCase("Id"))
177 sortIDMenuItem_actionPerformed();
179 else if (param.equalsIgnoreCase("Pairwise Identity"))
181 sortPairwiseMenuItem_actionPerformed();
183 else if (param.equalsIgnoreCase("Length"))
185 sortLengthMenuItem_actionPerformed();
189 param = applet.getParameter("wrap");
192 if (param.equalsIgnoreCase("true"))
194 wrapMenuItem.setState(true);
195 wrapMenuItem_actionPerformed();
198 param = applet.getParameter("centrecolumnlabels");
201 centreColumnLabelFlag.setState(true);
202 centreColumnLabelFlag_stateChanged();
206 if (viewport.getAlignment().isNucleotide())
208 viewport.updateStrucConsensus(alignPanel);
209 if (viewport.getAlignment().hasRNAStructure())
211 RNAHelixColour.setEnabled(true);
215 RNAHelixColour.setEnabled(false);
220 RNAHelixColour.setEnabled(false);
221 purinePyrimidineColour.setEnabled(false);
223 // Some JVMS send keyevents to Top frame or lowest panel,
224 // Havent worked out why yet. So add to both this frame and seqCanvas for
226 this.addKeyListener(this);
227 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
228 alignPanel.idPanel.idCanvas.addKeyListener(this);
229 alignPanel.scalePanel.addKeyListener(this);
230 alignPanel.annotationPanel.addKeyListener(this);
231 alignPanel.annotationPanelHolder.addKeyListener(this);
232 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
233 alignPanel.alabels.addKeyListener(this);
234 createAlignFrameWindow(embedded, title);
237 alignPanel.adjustAnnotationHeight();
238 alignPanel.paintAlignment(true);
241 public AlignViewport getAlignViewport()
246 public SeqCanvas getSeqcanvas()
248 return alignPanel.seqPanel.seqCanvas;
252 * Load a features file onto the alignment
255 * file URL, content, or other resolvable path
257 * is protocol for accessing data referred to by file
260 public boolean parseFeaturesFile(String file, String type)
262 return parseFeaturesFile(file, type, true);
266 * Load a features file onto the alignment
269 * file URL, content, or other resolvable path
271 * is protocol for accessing data referred to by file
272 * @param autoenabledisplay
273 * when true, display features flag will be automatically enabled if
274 * features are loaded
275 * @return true if data parsed as a features file
277 public boolean parseFeaturesFile(String file, String type,
278 boolean autoenabledisplay)
280 // TODO: test if importing a features file onto an alignment which already
281 // has features with links overwrites the original links.
283 Hashtable featureLinks = new Hashtable();
284 boolean featuresFile = false;
287 featuresFile = new jalview.io.FeaturesFile(file, type)
288 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
289 .getFeatureRenderer().featureColours, featureLinks,
290 true, viewport.applet.getDefaultParameter(
291 "relaxedidmatch", false));
292 } catch (Exception ex)
294 ex.printStackTrace();
299 if (featureLinks.size() > 0)
301 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
303 if (autoenabledisplay)
305 viewport.showSequenceFeatures = true;
306 sequenceFeatures.setState(true);
308 if (viewport.featureSettings != null)
310 viewport.featureSettings.refreshTable();
312 alignPanel.paintAlignment(true);
313 statusBar.setText(MessageManager
314 .getString("label.successfully_added_features_alignment"));
320 public void keyPressed(KeyEvent evt)
322 if (viewport.cursorMode
323 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
324 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
325 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
326 && Character.isDigit(evt.getKeyChar()))
328 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
331 switch (evt.getKeyCode())
333 case 27: // escape key
334 deselectAllSequenceMenuItem_actionPerformed();
336 alignPanel.alabels.cancelDrag();
339 if (evt.isControlDown() || evt.isMetaDown())
341 cut_actionPerformed();
345 if (viewport.cursorMode && !evt.isControlDown())
347 alignPanel.seqPanel.setCursorColumn();
349 if (evt.isControlDown() || evt.isMetaDown())
351 copy_actionPerformed();
355 if (evt.isControlDown())
357 paste(evt.isShiftDown());
361 if (evt.isControlDown() || evt.isMetaDown())
363 selectAllSequenceMenuItem_actionPerformed();
366 case KeyEvent.VK_DOWN:
367 if (viewport.cursorMode)
369 alignPanel.seqPanel.moveCursor(0, 1);
373 moveSelectedSequences(false);
378 if (viewport.cursorMode)
380 alignPanel.seqPanel.moveCursor(0, -1);
384 moveSelectedSequences(true);
388 case KeyEvent.VK_LEFT:
389 if (evt.isAltDown() || !viewport.cursorMode)
391 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
395 alignPanel.seqPanel.moveCursor(-1, 0);
399 case KeyEvent.VK_RIGHT:
400 if (evt.isAltDown() || !viewport.cursorMode)
402 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
406 alignPanel.seqPanel.moveCursor(1, 0);
410 case KeyEvent.VK_SPACE:
411 if (viewport.cursorMode)
413 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
414 || evt.isShiftDown() || evt.isAltDown());
418 case KeyEvent.VK_DELETE:
419 case KeyEvent.VK_BACK_SPACE:
420 if (viewport.cursorMode)
422 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
423 || evt.isShiftDown() || evt.isAltDown());
427 cut_actionPerformed();
428 alignPanel.seqPanel.seqCanvas.repaint();
433 if (viewport.cursorMode)
435 alignPanel.seqPanel.setCursorRow();
439 if (viewport.cursorMode)
441 alignPanel.seqPanel.setCursorPosition();
445 case KeyEvent.VK_ENTER:
446 case KeyEvent.VK_COMMA:
447 if (viewport.cursorMode)
449 alignPanel.seqPanel.setCursorRowAndColumn();
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
460 if (viewport.cursorMode)
462 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
467 viewport.cursorMode = !viewport.cursorMode;
468 statusBar.setText(MessageManager.formatMessage(
469 "label.keyboard_editing_mode", new String[]
470 { (viewport.cursorMode ? "on" : "off") }));
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
474 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
479 if (evt.isControlDown())
481 findMenuItem_actionPerformed();
487 boolean toggleSeqs = !evt.isControlDown();
488 boolean toggleCols = !evt.isShiftDown();
489 toggleHiddenRegions(toggleSeqs, toggleCols);
493 case KeyEvent.VK_PAGE_UP:
494 if (viewport.wrapAlignment)
496 alignPanel.scrollUp(true);
500 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
501 - viewport.endSeq + viewport.startSeq);
505 case KeyEvent.VK_PAGE_DOWN:
506 if (viewport.wrapAlignment)
508 alignPanel.scrollUp(false);
512 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
513 + viewport.endSeq - viewport.startSeq);
518 if (evt.isControlDown())
520 undoMenuItem_actionPerformed();
525 if (evt.isControlDown())
527 redoMenuItem_actionPerformed();
532 if (evt.isControlDown())
539 if (evt.isControlDown())
541 trimAlignment(false);
546 if (evt.isControlDown())
548 if (evt.isShiftDown())
550 this.removeAllGapsMenuItem_actionPerformed();
554 removeGappedColumnMenuItem_actionPerformed();
559 if (evt.isControlDown())
563 invertColSel_actionPerformed();
567 invertSequenceMenuItem_actionPerformed();
573 if (evt.isControlDown())
575 if (evt.isShiftDown())
577 this.unGroup_actionPerformed();
581 this.createGroup_actionPerformed();
587 if (evt.isControlDown())
589 this.deleteGroups_actionPerformed();
594 if (evt.isControlDown())
601 alignPanel.paintAlignment(true);
605 * called by key handler and the hide all/show all menu items
610 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
612 boolean hide = false;
613 SequenceGroup sg = viewport.getSelectionGroup();
614 if (!toggleSeqs && !toggleCols)
616 // Hide everything by the current selection - this is a hack - we do the
617 // invert and then hide
618 // first check that there will be visible columns after the invert.
619 if ((viewport.getColumnSelection() != null
620 && viewport.getColumnSelection().getSelected() != null && viewport
621 .getColumnSelection().getSelected().size() > 0)
622 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
625 // now invert the sequence set, if required - empty selection implies
626 // that no hiding is required.
629 invertSequenceMenuItem_actionPerformed();
630 sg = viewport.getSelectionGroup();
634 viewport.expandColSelection(sg, true);
635 // finally invert the column selection and get the new sequence
636 // selection and indicate it should be hidden.
637 invertColSel_actionPerformed();
644 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
647 viewport.hideAllSelectedSeqs();
649 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
652 viewport.showAllHiddenSeqs();
658 if (viewport.getColumnSelection().getSelected().size() > 0)
660 viewport.hideSelectedColumns();
663 viewport.setSelectionGroup(sg);
668 viewport.showAllHiddenColumns();
674 public void keyReleased(KeyEvent evt)
679 public void keyTyped(KeyEvent evt)
684 public void itemStateChanged(ItemEvent evt)
686 if (evt.getSource() == displayNonconservedMenuItem)
688 displayNonconservedMenuItem_actionPerformed();
690 else if (evt.getSource() == colourTextMenuItem)
692 colourTextMenuItem_actionPerformed();
694 else if (evt.getSource() == wrapMenuItem)
696 wrapMenuItem_actionPerformed();
698 else if (evt.getSource() == scaleAbove)
700 viewport.setScaleAboveWrapped(scaleAbove.getState());
702 else if (evt.getSource() == scaleLeft)
704 viewport.setScaleLeftWrapped(scaleLeft.getState());
706 else if (evt.getSource() == scaleRight)
708 viewport.setScaleRightWrapped(scaleRight.getState());
710 else if (evt.getSource() == seqLimits)
712 seqLimits_itemStateChanged();
714 else if (evt.getSource() == viewBoxesMenuItem)
716 viewport.setShowBoxes(viewBoxesMenuItem.getState());
718 else if (evt.getSource() == viewTextMenuItem)
720 viewport.setShowText(viewTextMenuItem.getState());
722 else if (evt.getSource() == renderGapsMenuItem)
724 viewport.setRenderGaps(renderGapsMenuItem.getState());
726 else if (evt.getSource() == annotationPanelMenuItem)
728 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
729 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
731 else if (evt.getSource() == sequenceFeatures)
733 viewport.showSequenceFeatures(sequenceFeatures.getState());
734 alignPanel.seqPanel.seqCanvas.repaint();
736 else if (evt.getSource() == conservationMenuItem)
738 conservationMenuItem_actionPerformed();
740 else if (evt.getSource() == abovePIDThreshold)
742 abovePIDThreshold_actionPerformed();
744 else if (evt.getSource() == applyToAllGroups)
746 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
748 else if (evt.getSource() == autoCalculate)
750 viewport.autoCalculateConsensus = autoCalculate.getState();
752 else if (evt.getSource() == sortByTree)
754 viewport.sortByTree = sortByTree.getState();
756 else if (evt.getSource() == this.centreColumnLabelFlag)
758 centreColumnLabelFlag_stateChanged();
760 else if (evt.getSource() == this.followMouseOverFlag)
762 mouseOverFlag_stateChanged();
764 else if (evt.getSource() == showGroupConsensus)
766 showGroupConsensus_actionPerformed();
768 else if (evt.getSource() == showGroupConservation)
770 showGroupConservation_actionPerformed();
772 else if (evt.getSource() == showSequenceLogo)
774 showSequenceLogo_actionPerformed();
776 else if (evt.getSource() == normSequenceLogo)
778 normSequenceLogo_actionPerformed();
780 else if (evt.getSource() == showConsensusHistogram)
782 showConsensusHistogram_actionPerformed();
784 else if (evt.getSource() == applyAutoAnnotationSettings)
786 applyAutoAnnotationSettings_actionPerformed();
788 alignPanel.paintAlignment(true);
791 private void mouseOverFlag_stateChanged()
793 viewport.followHighlight = followMouseOverFlag.getState();
794 // TODO: could kick the scrollTo mechanism to reset view for current
798 private void centreColumnLabelFlag_stateChanged()
800 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
801 this.alignPanel.annotationPanel.repaint();
805 public void actionPerformed(ActionEvent evt)
807 Object source = evt.getSource();
809 if (source == inputText)
811 inputText_actionPerformed();
813 else if (source == loadTree)
815 loadTree_actionPerformed();
817 else if (source == loadApplication)
819 launchFullApplication();
821 else if (source == loadAnnotations)
825 else if (source == outputAnnotations)
827 outputAnnotations(true);
829 else if (source == outputFeatures)
831 outputFeatures(true, "Jalview");
833 else if (source == closeMenuItem)
835 closeMenuItem_actionPerformed();
837 else if (source == copy)
839 copy_actionPerformed();
841 else if (source == undoMenuItem)
843 undoMenuItem_actionPerformed();
845 else if (source == redoMenuItem)
847 redoMenuItem_actionPerformed();
849 else if (source == inputText)
851 inputText_actionPerformed();
853 else if (source == closeMenuItem)
855 closeMenuItem_actionPerformed();
857 else if (source == undoMenuItem)
859 undoMenuItem_actionPerformed();
861 else if (source == redoMenuItem)
863 redoMenuItem_actionPerformed();
865 else if (source == copy)
867 copy_actionPerformed();
869 else if (source == pasteNew)
871 pasteNew_actionPerformed();
873 else if (source == pasteThis)
875 pasteThis_actionPerformed();
877 else if (source == cut)
879 cut_actionPerformed();
881 else if (source == delete)
883 delete_actionPerformed();
885 else if (source == grpsFromSelection)
887 makeGrpsFromSelection_actionPerformed();
889 else if (source == deleteGroups)
891 deleteGroups_actionPerformed();
893 else if (source == selectAllSequenceMenuItem)
895 selectAllSequenceMenuItem_actionPerformed();
897 else if (source == deselectAllSequenceMenuItem)
899 deselectAllSequenceMenuItem_actionPerformed();
901 else if (source == invertSequenceMenuItem)
903 invertSequenceMenuItem_actionPerformed();
905 else if (source == invertColSel)
907 viewport.invertColumnSelection();
908 alignPanel.paintAlignment(true);
910 else if (source == remove2LeftMenuItem)
914 else if (source == remove2RightMenuItem)
916 trimAlignment(false);
918 else if (source == removeGappedColumnMenuItem)
920 removeGappedColumnMenuItem_actionPerformed();
922 else if (source == removeAllGapsMenuItem)
924 removeAllGapsMenuItem_actionPerformed();
926 else if (source == findMenuItem)
928 findMenuItem_actionPerformed();
930 else if (source == font)
932 new FontChooser(alignPanel);
934 else if (source == newView)
938 else if (source == showColumns)
940 viewport.showAllHiddenColumns();
941 alignPanel.paintAlignment(true);
943 else if (source == showSeqs)
945 viewport.showAllHiddenSeqs();
946 alignPanel.paintAlignment(true);
948 else if (source == hideColumns)
950 viewport.hideSelectedColumns();
951 alignPanel.paintAlignment(true);
953 else if (source == hideSequences
954 && viewport.getSelectionGroup() != null)
956 viewport.hideAllSelectedSeqs();
957 alignPanel.paintAlignment(true);
959 else if (source == hideAllButSelection)
961 toggleHiddenRegions(false, false);
962 alignPanel.paintAlignment(true);
964 else if (source == hideAllSelection)
966 SequenceGroup sg = viewport.getSelectionGroup();
967 viewport.expandColSelection(sg, false);
968 viewport.hideAllSelectedSeqs();
969 viewport.hideSelectedColumns();
970 alignPanel.paintAlignment(true);
972 else if (source == showAllHidden)
974 viewport.showAllHiddenColumns();
975 viewport.showAllHiddenSeqs();
976 alignPanel.paintAlignment(true);
978 else if (source == showGroupConsensus)
980 showGroupConsensus_actionPerformed();
982 else if (source == showGroupConservation)
984 showGroupConservation_actionPerformed();
986 else if (source == showSequenceLogo)
988 showSequenceLogo_actionPerformed();
990 else if (source == normSequenceLogo)
992 normSequenceLogo_actionPerformed();
994 else if (source == showConsensusHistogram)
996 showConsensusHistogram_actionPerformed();
998 else if (source == applyAutoAnnotationSettings)
1000 applyAutoAnnotationSettings_actionPerformed();
1002 else if (source == featureSettings)
1004 new FeatureSettings(alignPanel);
1006 else if (source == alProperties)
1008 StringBuffer contents = new jalview.io.AlignmentProperties(
1009 viewport.getAlignment()).formatAsString();
1010 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1011 cap.setText(contents.toString());
1012 Frame frame = new Frame();
1014 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1015 "label.alignment_properties", new String[]
1016 { getTitle() }), 400, 250);
1018 else if (source == overviewMenuItem)
1020 overviewMenuItem_actionPerformed();
1022 else if (source == noColourmenuItem)
1026 else if (source == clustalColour)
1028 abovePIDThreshold.setState(false);
1029 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1031 else if (source == zappoColour)
1033 changeColour(new ZappoColourScheme());
1035 else if (source == taylorColour)
1037 changeColour(new TaylorColourScheme());
1039 else if (source == hydrophobicityColour)
1041 changeColour(new HydrophobicColourScheme());
1043 else if (source == helixColour)
1045 changeColour(new HelixColourScheme());
1047 else if (source == strandColour)
1049 changeColour(new StrandColourScheme());
1051 else if (source == turnColour)
1053 changeColour(new TurnColourScheme());
1055 else if (source == buriedColour)
1057 changeColour(new BuriedColourScheme());
1059 else if (source == nucleotideColour)
1061 changeColour(new NucleotideColourScheme());
1063 else if (source == purinePyrimidineColour)
1065 changeColour(new PurinePyrimidineColourScheme());
1067 else if (source == RNAInteractionColour)
1069 changeColour(new RNAInteractionColourScheme());
1071 else if (source == RNAHelixColour)
1073 new RNAHelicesColourChooser(viewport, alignPanel);
1075 else if (source == modifyPID)
1077 modifyPID_actionPerformed();
1079 else if (source == modifyConservation)
1081 modifyConservation_actionPerformed();
1083 else if (source == userDefinedColour)
1085 new UserDefinedColours(alignPanel, null);
1087 else if (source == PIDColour)
1089 changeColour(new PIDColourScheme());
1091 else if (source == BLOSUM62Colour)
1093 changeColour(new Blosum62ColourScheme());
1095 else if (source == tcoffeeColour)
1097 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1099 else if (source == annotationColour)
1101 new AnnotationColourChooser(viewport, alignPanel);
1103 else if (source == sortPairwiseMenuItem)
1105 sortPairwiseMenuItem_actionPerformed();
1107 else if (source == sortIDMenuItem)
1109 sortIDMenuItem_actionPerformed();
1111 else if (source == sortLengthMenuItem)
1113 sortLengthMenuItem_actionPerformed();
1115 else if (source == sortGroupMenuItem)
1117 sortGroupMenuItem_actionPerformed();
1119 else if (source == removeRedundancyMenuItem)
1121 removeRedundancyMenuItem_actionPerformed();
1123 else if (source == pairwiseAlignmentMenuItem)
1125 pairwiseAlignmentMenuItem_actionPerformed();
1127 else if (source == PCAMenuItem)
1129 PCAMenuItem_actionPerformed();
1131 else if (source == averageDistanceTreeMenuItem)
1133 averageDistanceTreeMenuItem_actionPerformed();
1135 else if (source == neighbourTreeMenuItem)
1137 neighbourTreeMenuItem_actionPerformed();
1139 else if (source == njTreeBlosumMenuItem)
1141 njTreeBlosumMenuItem_actionPerformed();
1143 else if (source == avDistanceTreeBlosumMenuItem)
1145 avTreeBlosumMenuItem_actionPerformed();
1147 else if (source == documentation)
1149 documentation_actionPerformed();
1151 else if (source == about)
1153 about_actionPerformed();
1158 public void inputText_actionPerformed()
1160 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1161 Frame frame = new Frame();
1163 jalview.bin.JalviewLite.addFrame(frame,
1164 MessageManager.getString("label.input_cut_paste"), 500, 500);
1167 protected void outputText_actionPerformed(ActionEvent e)
1169 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1170 Frame frame = new Frame();
1172 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1173 "label.alignment_output_command", new String[]
1174 { e.getActionCommand() }), 600, 500);
1175 cap.setText(new AppletFormatAdapter().formatSequences(
1176 e.getActionCommand(), viewport.getAlignment(),
1177 viewport.showJVSuffix));
1180 public void loadAnnotations()
1182 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1183 cap.setText(MessageManager
1184 .getString("label.paste_features_annotations_Tcoffee_here"));
1185 cap.setAnnotationImport();
1186 Frame frame = new Frame();
1188 jalview.bin.JalviewLite.addFrame(frame,
1189 MessageManager.getString("action.paste_annotations"), 400, 300);
1193 public String outputAnnotations(boolean displayTextbox)
1195 String annotation = new AnnotationFile().printAnnotations(
1196 viewport.showAnnotation ? viewport.getAlignment()
1197 .getAlignmentAnnotation() : null, viewport
1198 .getAlignment().getGroups(), ((Alignment) viewport
1199 .getAlignment()).alignmentProperties);
1203 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1204 Frame frame = new Frame();
1206 jalview.bin.JalviewLite.addFrame(frame,
1207 MessageManager.getString("label.annotations"), 600, 500);
1208 cap.setText(annotation);
1214 private Hashtable getDisplayedFeatureCols()
1216 if (alignPanel.getFeatureRenderer() != null
1217 && viewport.featuresDisplayed != null)
1219 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1220 Hashtable fcols = new Hashtable();
1221 Enumeration en = viewport.featuresDisplayed.keys();
1222 while (en.hasMoreElements())
1224 Object col = en.nextElement();
1225 fcols.put(col, fr.featureColours.get(col));
1232 public String outputFeatures(boolean displayTextbox, String format)
1235 if (format.equalsIgnoreCase("Jalview"))
1237 features = new FeaturesFile().printJalviewFormat(viewport
1238 .getAlignment().getSequencesArray(),
1239 getDisplayedFeatureCols());
1243 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1244 .getSequencesArray(), getDisplayedFeatureCols());
1249 boolean frimport = false;
1250 if (features == null || features.equals("No Features Visible"))
1252 features = "# No features visible - paste some and import them here.";
1256 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1259 cap.setAnnotationImport();
1261 Frame frame = new Frame();
1263 jalview.bin.JalviewLite.addFrame(frame,
1264 MessageManager.getString("label.features"), 600, 500);
1265 cap.setText(features);
1269 if (features == null)
1278 void launchFullApplication()
1280 StringBuffer url = new StringBuffer(jalviewServletURL);
1283 + appendProtocol(viewport.applet.getParameter("file")));
1285 if (viewport.applet.getParameter("features") != null)
1287 url.append("&features=");
1288 url.append(appendProtocol(viewport.applet.getParameter("features")));
1291 if (viewport.applet.getParameter("annotations") != null)
1293 url.append("&annotations=");
1294 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1297 if (viewport.applet.getParameter("jnetfile") != null)
1299 url.append("&annotations=");
1300 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1303 if (viewport.applet.getParameter("defaultColour") != null)
1305 url.append("&colour="
1306 + removeWhiteSpace(viewport.applet
1307 .getParameter("defaultColour")));
1310 if (viewport.applet.getParameter("userDefinedColour") != null)
1312 url.append("&colour="
1313 + removeWhiteSpace(viewport.applet
1314 .getParameter("userDefinedColour")));
1316 if (viewport.applet.getParameter("tree") != null)
1319 + appendProtocol(viewport.applet.getParameter("tree")));
1321 if (viewport.applet.getParameter("treeFile") != null)
1324 + appendProtocol(viewport.applet.getParameter("treeFile")));
1327 showURL(url.toString(), "FULL_APP");
1330 String removeWhiteSpace(String colour)
1332 StringBuffer sb = new StringBuffer();
1333 for (int i = 0; i < colour.length(); i++)
1335 if (Character.isWhitespace(colour.charAt(i)))
1341 sb.append(colour.charAt(i));
1345 return sb.toString();
1348 String appendProtocol(String url)
1353 url = URLEncoder.encode(url);
1356 * When we finally deprecate 1.1 compatibility, we can start to use
1357 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1358 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1359 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1360 * ex.printStackTrace(); }
1362 catch (java.net.MalformedURLException ex)
1364 url = viewport.applet.getCodeBase() + url;
1369 public void closeMenuItem_actionPerformed()
1371 PaintRefresher.RemoveComponent(alignPanel);
1372 if (alignPanel.seqPanel != null
1373 && alignPanel.seqPanel.seqCanvas != null)
1375 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1377 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1379 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1382 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1397 void updateEditMenuBar()
1400 if (viewport.historyList.size() > 0)
1402 undoMenuItem.setEnabled(true);
1403 CommandI command = (CommandI) viewport.historyList.peek();
1404 undoMenuItem.setLabel(MessageManager.formatMessage(
1405 "label.undo_command", new String[]
1406 { command.getDescription() }));
1410 undoMenuItem.setEnabled(false);
1411 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1414 if (viewport.redoList.size() > 0)
1416 redoMenuItem.setEnabled(true);
1418 CommandI command = (CommandI) viewport.redoList.peek();
1419 redoMenuItem.setLabel(MessageManager.formatMessage(
1420 "label.redo_command", new String[]
1421 { command.getDescription() }));
1425 redoMenuItem.setEnabled(false);
1426 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1433 public void addHistoryItem(CommandI command)
1435 if (command.getSize() > 0)
1437 viewport.historyList.push(command);
1438 viewport.redoList.removeAllElements();
1439 updateEditMenuBar();
1440 viewport.updateHiddenColumns();
1445 * TODO: JAL-1104 DOCUMENT ME!
1450 protected void undoMenuItem_actionPerformed()
1452 if (viewport.historyList.size() < 1)
1457 CommandI command = (CommandI) viewport.historyList.pop();
1458 viewport.redoList.push(command);
1459 command.undoCommand(null);
1461 AlignViewport originalSource = getOriginatingSource(command);
1463 if (originalSource != viewport)
1466 .println("Warning: Viewport object mismatch whilst undoing");
1468 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1469 // viewport.getColumnSelection().getHiddenColumns()
1471 updateEditMenuBar();
1472 originalSource.firePropertyChange("alignment", null, originalSource
1473 .getAlignment().getSequences());
1477 * TODO: JAL-1104 DOCUMENT ME!
1482 protected void redoMenuItem_actionPerformed()
1484 if (viewport.redoList.size() < 1)
1489 CommandI command = (CommandI) viewport.redoList.pop();
1490 viewport.historyList.push(command);
1491 command.doCommand(null);
1493 AlignViewport originalSource = getOriginatingSource(command);
1495 if (originalSource != viewport)
1498 .println("Warning: Viewport object mismatch whilst re-doing");
1500 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1501 // viewport.getColumnSelection().getHiddenColumns()
1504 updateEditMenuBar();
1505 originalSource.firePropertyChange("alignment", null, originalSource
1506 .getAlignment().getSequences());
1509 AlignViewport getOriginatingSource(CommandI command)
1511 AlignViewport originalSource = null;
1512 // For sequence removal and addition, we need to fire
1513 // the property change event FROM the viewport where the
1514 // original alignment was altered
1515 AlignmentI al = null;
1516 if (command instanceof EditCommand)
1518 EditCommand editCommand = (EditCommand) command;
1519 al = editCommand.getAlignment();
1520 Vector comps = (Vector) PaintRefresher.components.get(viewport
1521 .getSequenceSetId());
1522 for (int i = 0; i < comps.size(); i++)
1524 if (comps.elementAt(i) instanceof AlignmentPanel)
1526 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1528 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1535 if (originalSource == null)
1537 // The original view is closed, we must validate
1538 // the current view against the closed view first
1541 PaintRefresher.validateSequences(al, viewport.getAlignment());
1544 originalSource = viewport;
1547 return originalSource;
1550 public void moveSelectedSequences(boolean up)
1552 SequenceGroup sg = viewport.getSelectionGroup();
1557 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1558 up ? null : viewport.getHiddenRepSequences(), up);
1559 alignPanel.paintAlignment(true);
1562 synchronized void slideSequences(boolean right, int size)
1564 List<SequenceI> sg = new Vector<SequenceI>();
1565 if (viewport.cursorMode)
1567 sg.add(viewport.getAlignment().getSequenceAt(
1568 alignPanel.seqPanel.seqCanvas.cursorY));
1570 else if (viewport.getSelectionGroup() != null
1571 && viewport.getSelectionGroup().getSize() != viewport
1572 .getAlignment().getHeight())
1574 sg = viewport.getSelectionGroup().getSequences(
1575 viewport.getHiddenRepSequences());
1583 Vector<SequenceI> invertGroup = new Vector();
1585 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1587 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1589 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1593 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1595 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1597 for (int i = 0; i < invertGroup.size(); i++)
1599 seqs2[i] = invertGroup.elementAt(i);
1602 SlideSequencesCommand ssc;
1605 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1606 size, viewport.getGapCharacter());
1610 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1611 size, viewport.getGapCharacter());
1614 int groupAdjustment = 0;
1615 if (ssc.getGapsInsertedBegin() && right)
1617 if (viewport.cursorMode)
1619 alignPanel.seqPanel.moveCursor(size, 0);
1623 groupAdjustment = size;
1626 else if (!ssc.getGapsInsertedBegin() && !right)
1628 if (viewport.cursorMode)
1630 alignPanel.seqPanel.moveCursor(-size, 0);
1634 groupAdjustment = -size;
1638 if (groupAdjustment != 0)
1640 viewport.getSelectionGroup().setStartRes(
1641 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1642 viewport.getSelectionGroup().setEndRes(
1643 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1646 boolean appendHistoryItem = false;
1647 if (viewport.historyList != null && viewport.historyList.size() > 0
1648 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1650 appendHistoryItem = ssc
1651 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1655 if (!appendHistoryItem)
1657 addHistoryItem(ssc);
1663 static StringBuffer copiedSequences;
1665 static Vector copiedHiddenColumns;
1667 protected void copy_actionPerformed()
1669 if (viewport.getSelectionGroup() == null)
1674 SequenceGroup sg = viewport.getSelectionGroup();
1675 copiedSequences = new StringBuffer();
1676 Hashtable orderedSeqs = new Hashtable();
1677 for (int i = 0; i < sg.getSize(); i++)
1679 SequenceI seq = sg.getSequenceAt(i);
1680 int index = viewport.getAlignment().findIndex(seq);
1681 orderedSeqs.put(index + "", seq);
1684 int index = 0, startRes, endRes;
1687 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1689 copiedHiddenColumns = new Vector();
1690 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1691 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1694 int[] region = (int[]) viewport.getColumnSelection()
1695 .getHiddenColumns().elementAt(i);
1697 copiedHiddenColumns.addElement(new int[]
1698 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1703 copiedHiddenColumns = null;
1706 for (int i = 0; i < sg.getSize(); i++)
1708 SequenceI seq = null;
1712 if (orderedSeqs.containsKey(index + ""))
1714 seq = (SequenceI) orderedSeqs.get(index + "");
1726 // Returns residue following index if gap
1727 startRes = seq.findPosition(sg.getStartRes());
1730 // Need to find the residue preceeding index if gap
1733 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1735 ch = seq.getCharAt(j);
1736 if (!jalview.util.Comparison.isGap((ch)))
1744 endRes += seq.getStart() - 1;
1747 copiedSequences.append(seq.getName()
1753 + seq.getSequenceAsString(sg.getStartRes(),
1754 sg.getEndRes() + 1) + "\n");
1759 protected void pasteNew_actionPerformed()
1764 protected void pasteThis_actionPerformed()
1769 void paste(boolean newAlignment)
1774 if (copiedSequences == null)
1779 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1780 Vector seqs = new Vector();
1781 while (st.hasMoreElements())
1783 String name = st.nextToken();
1784 int start = Integer.parseInt(st.nextToken());
1785 int end = Integer.parseInt(st.nextToken());
1786 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1788 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1789 for (int i = 0; i < seqs.size(); i++)
1791 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1796 String newtitle = MessageManager.getString("label.copied_sequences");
1797 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1799 newtitle = getTitle();
1803 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1805 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1806 viewport.applet, newtitle, false);
1807 if (copiedHiddenColumns != null)
1809 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1811 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1812 af.viewport.hideColumns(region[0], region[1]);
1816 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1821 addSequences(newSeqs);
1824 } catch (Exception ex)
1826 } // could be anything being pasted in here
1830 void addSequences(SequenceI[] seqs)
1832 for (int i = 0; i < seqs.length; i++)
1834 viewport.getAlignment().addSequence(seqs[i]);
1838 addHistoryItem(new EditCommand(
1839 MessageManager.getString("label.add_sequences"), Action.PASTE,
1840 seqs, 0, viewport.getAlignment().getWidth(),
1841 viewport.getAlignment()));
1843 viewport.setEndSeq(viewport.getAlignment().getHeight());
1844 viewport.getAlignment().getWidth();
1845 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1850 protected void cut_actionPerformed()
1852 copy_actionPerformed();
1853 delete_actionPerformed();
1856 protected void delete_actionPerformed()
1859 SequenceGroup sg = viewport.getSelectionGroup();
1865 Vector seqs = new Vector();
1867 for (int i = 0; i < sg.getSize(); i++)
1869 seq = sg.getSequenceAt(i);
1870 seqs.addElement(seq);
1873 // If the cut affects all sequences, remove highlighted columns
1874 if (sg.getSize() == viewport.getAlignment().getHeight())
1876 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1877 sg.getEndRes() + 1);
1880 SequenceI[] cut = new SequenceI[seqs.size()];
1881 for (int i = 0; i < seqs.size(); i++)
1883 cut[i] = (SequenceI) seqs.elementAt(i);
1887 * //ADD HISTORY ITEM
1889 addHistoryItem(new EditCommand(
1890 MessageManager.getString("label.cut_sequences"), Action.CUT,
1891 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1892 viewport.getAlignment()));
1894 viewport.setSelectionGroup(null);
1895 viewport.getAlignment().deleteGroup(sg);
1897 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1900 if (viewport.getAlignment().getHeight() < 1)
1902 this.setVisible(false);
1904 viewport.sendSelection();
1908 * group consensus toggled
1911 protected void showGroupConsensus_actionPerformed()
1913 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1914 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1919 * group conservation toggled.
1921 protected void showGroupConservation_actionPerformed()
1923 viewport.setShowGroupConservation(showGroupConservation.getState());
1924 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1931 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1932 * .event.ActionEvent)
1934 protected void showConsensusHistogram_actionPerformed()
1936 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1937 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1944 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1945 * .event.ActionEvent)
1947 protected void showSequenceLogo_actionPerformed()
1949 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1950 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1953 protected void normSequenceLogo_actionPerformed()
1955 showSequenceLogo.setState(true);
1956 viewport.setShowSequenceLogo(true);
1957 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1958 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1961 protected void applyAutoAnnotationSettings_actionPerformed()
1963 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1966 protected void makeGrpsFromSelection_actionPerformed()
1968 if (avc.makeGroupsFromSelection())
1970 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1971 alignPanel.updateAnnotation();
1972 alignPanel.paintAlignment(true);
1976 protected void createGroup_actionPerformed()
1981 protected void unGroup_actionPerformed()
1985 alignPanel.alignmentChanged();
1989 protected void deleteGroups_actionPerformed()
1991 if (avc.deleteGroups())
1993 alignPanel.alignmentChanged();
1997 public void selectAllSequenceMenuItem_actionPerformed()
1999 SequenceGroup sg = new SequenceGroup();
2000 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2002 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2004 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2005 viewport.setSelectionGroup(sg);
2006 alignPanel.paintAlignment(true);
2007 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2008 viewport.sendSelection();
2011 public void deselectAllSequenceMenuItem_actionPerformed()
2013 if (viewport.cursorMode)
2015 alignPanel.seqPanel.keyboardNo1 = null;
2016 alignPanel.seqPanel.keyboardNo2 = null;
2018 viewport.setSelectionGroup(null);
2019 viewport.getColumnSelection().clear();
2020 viewport.setSelectionGroup(null);
2021 alignPanel.idPanel.idCanvas.searchResults = null;
2022 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2023 alignPanel.paintAlignment(true);
2024 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2025 viewport.sendSelection();
2028 public void invertSequenceMenuItem_actionPerformed()
2030 SequenceGroup sg = viewport.getSelectionGroup();
2031 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2033 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2036 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2037 viewport.sendSelection();
2040 public void invertColSel_actionPerformed()
2042 viewport.invertColumnSelection();
2043 alignPanel.paintAlignment(true);
2044 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2045 viewport.sendSelection();
2048 void trimAlignment(boolean trimLeft)
2050 ColumnSelection colSel = viewport.getColumnSelection();
2053 if (colSel.size() > 0)
2057 column = colSel.getMin();
2061 column = colSel.getMax();
2065 if (viewport.getSelectionGroup() != null)
2067 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2068 viewport.getHiddenRepSequences());
2072 seqs = viewport.getAlignment().getSequencesArray();
2075 TrimRegionCommand trimRegion;
2078 trimRegion = new TrimRegionCommand("Remove Left",
2079 TrimRegionCommand.TRIM_LEFT, seqs, column,
2080 viewport.getAlignment(), viewport.getColumnSelection(),
2081 viewport.getSelectionGroup());
2082 viewport.setStartRes(0);
2086 trimRegion = new TrimRegionCommand("Remove Right",
2087 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2088 viewport.getAlignment(), viewport.getColumnSelection(),
2089 viewport.getSelectionGroup());
2092 statusBar.setText(MessageManager.formatMessage(
2093 "label.removed_columns", new String[]
2094 { Integer.valueOf(trimRegion.getSize()).toString() }));
2095 addHistoryItem(trimRegion);
2097 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2099 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2100 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2102 viewport.getAlignment().deleteGroup(sg);
2106 viewport.firePropertyChange("alignment", null, viewport
2107 .getAlignment().getSequences());
2111 public void removeGappedColumnMenuItem_actionPerformed()
2113 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2116 if (viewport.getSelectionGroup() != null)
2118 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2119 viewport.getHiddenRepSequences());
2120 start = viewport.getSelectionGroup().getStartRes();
2121 end = viewport.getSelectionGroup().getEndRes();
2125 seqs = viewport.getAlignment().getSequencesArray();
2128 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2129 "Remove Gapped Columns", seqs, start, end,
2130 viewport.getAlignment());
2132 addHistoryItem(removeGapCols);
2134 statusBar.setText(MessageManager.formatMessage(
2135 "label.removed_empty_columns", new String[]
2136 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2138 // This is to maintain viewport position on first residue
2139 // of first sequence
2140 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2141 int startRes = seq.findPosition(viewport.startRes);
2142 // ShiftList shifts;
2143 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2144 // edit.alColumnChanges=shifts.getInverse();
2145 // if (viewport.hasHiddenColumns)
2146 // viewport.getColumnSelection().compensateForEdits(shifts);
2147 viewport.setStartRes(seq.findIndex(startRes) - 1);
2148 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153 public void removeAllGapsMenuItem_actionPerformed()
2155 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2158 if (viewport.getSelectionGroup() != null)
2160 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2161 viewport.getHiddenRepSequences());
2162 start = viewport.getSelectionGroup().getStartRes();
2163 end = viewport.getSelectionGroup().getEndRes();
2167 seqs = viewport.getAlignment().getSequencesArray();
2170 // This is to maintain viewport position on first residue
2171 // of first sequence
2172 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2173 int startRes = seq.findPosition(viewport.startRes);
2175 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2176 viewport.getAlignment()));
2178 viewport.setStartRes(seq.findIndex(startRes) - 1);
2180 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2185 public void findMenuItem_actionPerformed()
2187 new Finder(alignPanel);
2191 * create a new view derived from the current view
2194 * @return frame for the new view
2196 public AlignFrame newView(String viewtitle)
2199 if (viewport.hasHiddenRows())
2201 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2202 .getFullAlignment().getSequencesArray());
2206 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2209 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2211 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2213 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2215 newal.addAnnotation(viewport.getAlignment()
2216 .getAlignmentAnnotation()[i]);
2221 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2223 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2224 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2225 PaintRefresher.Register(newaf.alignPanel,
2226 newaf.alignPanel.av.getSequenceSetId());
2228 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2229 newaf.alignPanel.av.getSequenceSetId());
2230 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2231 newaf.alignPanel.av.getSequenceSetId());
2233 Vector comps = (Vector) PaintRefresher.components.get(viewport
2234 .getSequenceSetId());
2236 for (int i = 0; i < comps.size(); i++)
2238 if (comps.elementAt(i) instanceof AlignmentPanel)
2244 String title = new String(this.getTitle());
2245 if (viewtitle != null)
2247 title = viewtitle + " ( " + title + ")";
2251 if (title.indexOf("(View") > -1)
2253 title = title.substring(0, title.indexOf("(View"));
2255 title += "(View " + viewSize + ")";
2258 newaf.setTitle(title.toString());
2260 newaf.viewport.historyList = viewport.historyList;
2261 newaf.viewport.redoList = viewport.redoList;
2267 * @return list of feature groups on the view
2269 public String[] getFeatureGroups()
2271 FeatureRenderer fr = null;
2272 if (alignPanel != null
2273 && (fr = alignPanel.getFeatureRenderer()) != null)
2275 return fr.getGroups();
2281 * get sequence feature groups that are hidden or shown
2287 public String[] getFeatureGroupsOfState(boolean visible)
2289 FeatureRenderer fr = null;
2290 if (alignPanel != null
2291 && (fr = alignPanel.getFeatureRenderer()) != null)
2293 return fr.getGroups(visible);
2299 * Change the display state for the given feature groups
2302 * list of group strings
2304 * visible or invisible
2306 public void setFeatureGroupState(String[] groups, boolean state)
2308 FeatureRenderer fr = null;
2309 this.sequenceFeatures.setState(true);
2310 viewport.showSequenceFeatures(true);
2311 if (alignPanel != null
2312 && (fr = alignPanel.getFeatureRenderer()) != null)
2314 fr.setGroupState(groups, state);
2315 alignPanel.seqPanel.seqCanvas.repaint();
2316 if (alignPanel.overviewPanel != null)
2318 alignPanel.overviewPanel.updateOverviewImage();
2323 public void seqLimits_itemStateChanged()
2325 viewport.setShowJVSuffix(seqLimits.getState());
2326 alignPanel.fontChanged();
2327 alignPanel.paintAlignment(true);
2330 protected void colourTextMenuItem_actionPerformed()
2332 viewport.setColourText(colourTextMenuItem.getState());
2333 alignPanel.paintAlignment(true);
2336 protected void displayNonconservedMenuItem_actionPerformed()
2338 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2339 alignPanel.paintAlignment(true);
2342 protected void wrapMenuItem_actionPerformed()
2344 viewport.setWrapAlignment(wrapMenuItem.getState());
2345 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2346 scaleAbove.setEnabled(wrapMenuItem.getState());
2347 scaleLeft.setEnabled(wrapMenuItem.getState());
2348 scaleRight.setEnabled(wrapMenuItem.getState());
2349 alignPanel.paintAlignment(true);
2352 public void overviewMenuItem_actionPerformed()
2354 if (alignPanel.overviewPanel != null)
2359 Frame frame = new Frame();
2360 OverviewPanel overview = new OverviewPanel(alignPanel);
2361 frame.add(overview);
2362 // +50 must allow for applet frame window
2363 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2364 "label.overview_params", new String[]
2365 { this.getTitle() }), overview.getPreferredSize().width,
2366 overview.getPreferredSize().height + 50);
2369 final AlignmentPanel ap = alignPanel;
2370 frame.addWindowListener(new WindowAdapter()
2373 public void windowClosing(WindowEvent e)
2377 ap.setOverviewPanel(null);
2382 alignPanel.setOverviewPanel(overview);
2386 void changeColour(ColourSchemeI cs)
2392 if (viewport.getAbovePIDThreshold())
2394 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2398 if (viewport.getConservationSelected())
2400 cs.setConservationApplied(true);
2401 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2406 cs.setConservationApplied(false);
2409 viewport.setGlobalColourScheme(cs);
2411 if (alignPanel.getOverviewPanel() != null)
2413 alignPanel.getOverviewPanel().updateOverviewImage();
2416 jalview.structure.StructureSelectionManager
2417 .getStructureSelectionManager(viewport.applet)
2418 .sequenceColoursChanged(alignPanel);
2420 alignPanel.paintAlignment(true);
2423 protected void modifyPID_actionPerformed()
2425 if (viewport.getAbovePIDThreshold()
2426 && viewport.getGlobalColourScheme() != null)
2428 SliderPanel.setPIDSliderSource(alignPanel,
2429 viewport.getGlobalColourScheme(), "Background");
2430 SliderPanel.showPIDSlider();
2434 protected void modifyConservation_actionPerformed()
2436 if (viewport.getConservationSelected()
2437 && viewport.getGlobalColourScheme() != null)
2439 SliderPanel.setConservationSlider(alignPanel,
2440 viewport.getGlobalColourScheme(), "Background");
2441 SliderPanel.showConservationSlider();
2445 protected void conservationMenuItem_actionPerformed()
2447 viewport.setConservationSelected(conservationMenuItem.getState());
2449 viewport.setAbovePIDThreshold(false);
2450 abovePIDThreshold.setState(false);
2452 changeColour(viewport.getGlobalColourScheme());
2454 modifyConservation_actionPerformed();
2457 public void abovePIDThreshold_actionPerformed()
2459 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2461 conservationMenuItem.setState(false);
2462 viewport.setConservationSelected(false);
2464 changeColour(viewport.getGlobalColourScheme());
2466 modifyPID_actionPerformed();
2469 public void sortPairwiseMenuItem_actionPerformed()
2471 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2472 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2473 .getAlignment().getSequenceAt(0), null);
2475 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2476 viewport.getAlignment()));
2477 alignPanel.paintAlignment(true);
2480 public void sortIDMenuItem_actionPerformed()
2482 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2483 AlignmentSorter.sortByID(viewport.getAlignment());
2484 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2485 viewport.getAlignment()));
2486 alignPanel.paintAlignment(true);
2489 public void sortLengthMenuItem_actionPerformed()
2491 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2492 AlignmentSorter.sortByLength(viewport.getAlignment());
2493 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2494 viewport.getAlignment()));
2495 alignPanel.paintAlignment(true);
2498 public void sortGroupMenuItem_actionPerformed()
2500 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2501 AlignmentSorter.sortByGroup(viewport.getAlignment());
2502 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2503 viewport.getAlignment()));
2504 alignPanel.paintAlignment(true);
2508 public void removeRedundancyMenuItem_actionPerformed()
2510 new RedundancyPanel(alignPanel);
2513 public void pairwiseAlignmentMenuItem_actionPerformed()
2515 if (viewport.getSelectionGroup() != null
2516 && viewport.getSelectionGroup().getSize() > 1)
2518 Frame frame = new Frame();
2519 frame.add(new PairwiseAlignPanel(alignPanel));
2520 jalview.bin.JalviewLite.addFrame(frame,
2521 MessageManager.getString("action.pairwise_alignment"), 600,
2526 public void PCAMenuItem_actionPerformed()
2528 // are the sequences aligned?
2529 if (!viewport.getAlignment().isAligned(false))
2532 int Width = viewport.getAlignment().getWidth();
2534 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2536 current = viewport.getAlignment().getSequenceAt(i);
2538 if (current.getLength() < Width)
2540 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2543 alignPanel.paintAlignment(true);
2546 if ((viewport.getSelectionGroup() != null
2547 && viewport.getSelectionGroup().getSize() < 4 && viewport
2548 .getSelectionGroup().getSize() > 0)
2549 || viewport.getAlignment().getHeight() < 4)
2556 new PCAPanel(viewport);
2557 } catch (java.lang.OutOfMemoryError ex)
2563 public void averageDistanceTreeMenuItem_actionPerformed()
2565 NewTreePanel("AV", "PID", "Average distance tree using PID");
2568 public void neighbourTreeMenuItem_actionPerformed()
2570 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2573 protected void njTreeBlosumMenuItem_actionPerformed()
2575 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2578 protected void avTreeBlosumMenuItem_actionPerformed()
2580 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2583 void NewTreePanel(String type, String pwType, String title)
2585 // are the sequences aligned?
2586 if (!viewport.getAlignment().isAligned(false))
2589 int Width = viewport.getAlignment().getWidth();
2591 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2593 current = viewport.getAlignment().getSequenceAt(i);
2595 if (current.getLength() < Width)
2597 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2600 alignPanel.paintAlignment(true);
2604 if ((viewport.getSelectionGroup() != null && viewport
2605 .getSelectionGroup().getSize() > 1)
2606 || (viewport.getAlignment().getHeight() > 1))
2608 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2610 addTreeMenuItem(tp, title);
2612 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2616 void loadTree_actionPerformed()
2618 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2619 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2620 cap.setTreeImport();
2621 Frame frame = new Frame();
2623 jalview.bin.JalviewLite.addFrame(frame,
2624 MessageManager.getString("label.paste_newick_file"), 400, 300);
2627 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2629 TreePanel tp = new TreePanel(alignPanel, treeFile,
2630 MessageManager.getString("label.load_tree_from_file"), tree);
2631 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2632 addTreeMenuItem(tp, treeFile);
2636 * sort the alignment using the given treePanel
2639 * tree used to sort view
2641 * string used for undo event name
2643 public void sortByTree(TreePanel treePanel, String title)
2645 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2647 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2648 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2649 // HistoryItem.SORT));
2650 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2651 "label.order_by_params", new String[]
2652 { title }), oldOrder, viewport.getAlignment()));
2653 alignPanel.paintAlignment(true);
2657 * Do any automatic reordering of the alignment and add the necessary bits to
2658 * the menu structure for the new tree
2663 protected void addTreeMenuItem(final TreePanel treePanel,
2666 final MenuItem item = new MenuItem(title);
2667 sortByTreeMenu.add(item);
2668 item.addActionListener(new java.awt.event.ActionListener()
2671 public void actionPerformed(ActionEvent evt)
2673 sortByTree(treePanel, title); // treePanel.getTitle());
2677 treePanel.addWindowListener(new WindowAdapter()
2680 public void windowOpened(WindowEvent e)
2682 if (viewport.sortByTree)
2684 sortByTree(treePanel, title);
2686 super.windowOpened(e);
2690 public void windowClosing(WindowEvent e)
2692 sortByTreeMenu.remove(item);
2697 public boolean sortBy(AlignmentOrder alorder, String undoname)
2699 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2700 if (viewport.applet.debug)
2702 System.err.println("Sorting " + alorder.getOrder().size()
2703 + " in alignment '" + getTitle() + "'");
2705 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2706 if (undoname != null)
2708 addHistoryItem(new OrderCommand(undoname, oldOrder,
2709 viewport.getAlignment()));
2711 alignPanel.paintAlignment(true);
2715 protected void documentation_actionPerformed()
2717 alignPanel.av.applet.openJalviewHelpUrl();
2720 protected void about_actionPerformed()
2723 class AboutPanel extends Canvas
2729 public AboutPanel(String version, String builddate)
2731 this.version = version;
2732 this.builddate = builddate;
2736 public void paint(Graphics g)
2738 g.setColor(Color.white);
2739 g.fillRect(0, 0, getSize().width, getSize().height);
2740 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2741 FontMetrics fm = g.getFontMetrics();
2742 int fh = fm.getHeight();
2744 g.setColor(Color.black);
2745 // TODO: update this text for each release or centrally store it for
2746 // lite and application
2747 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2748 g.drawString(MessageManager.formatMessage(
2749 "label.jalviewLite_release", new String[]
2750 { version }), x, y += fh);
2751 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2752 g.drawString(MessageManager.formatMessage(
2753 "label.jaview_build_date", new String[]
2754 { builddate }), x, y += fh);
2755 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2756 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2758 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2759 x + 50, y += fh + 8);
2761 MessageManager.getString("label.jalview_dev_managers"), x,
2763 g.drawString(MessageManager
2764 .getString("label.jalview_distribution_lists"), x, y += fh);
2765 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2768 MessageManager.getString("label.jalview_cite_1_authors"),
2771 MessageManager.getString("label.jalview_cite_1_title"), x,
2773 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2778 Frame frame = new Frame();
2779 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2781 jalview.bin.JalviewLite.addFrame(frame,
2782 MessageManager.getString("label.jalview"), 580, 220);
2786 public void showURL(String url, String target)
2788 if (viewport.applet == null)
2790 System.out.println("Not running as applet - no browser available.");
2794 viewport.applet.showURL(url, target);
2798 // ////////////////////////////////////////////////////////////////////////////////
2799 // JBuilder Graphics here
2801 MenuBar alignFrameMenuBar = new MenuBar();
2803 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2805 MenuItem loadApplication = new MenuItem(
2806 MessageManager.getString("label.view_full_application"));
2808 MenuItem loadTree = new MenuItem(
2809 MessageManager.getString("label.load_associated_tree"));
2811 MenuItem loadAnnotations = new MenuItem(
2812 MessageManager.getString("label.load_features_annotations"));
2814 MenuItem outputFeatures = new MenuItem(
2815 MessageManager.getString("label.export_features").concat("..."));
2817 MenuItem outputAnnotations = new MenuItem(
2818 MessageManager.getString("label.export_annotations").concat("..."));
2820 MenuItem closeMenuItem = new MenuItem(
2821 MessageManager.getString("action.close"));
2823 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2825 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2827 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2829 Menu calculateMenu = new Menu(
2830 MessageManager.getString("action.calculate"));
2832 MenuItem selectAllSequenceMenuItem = new MenuItem(
2833 MessageManager.getString("action.select_all"));
2835 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2836 MessageManager.getString("action.deselect_all"));
2838 MenuItem invertSequenceMenuItem = new MenuItem(
2839 MessageManager.getString("action.invert_selection"));
2841 MenuItem remove2LeftMenuItem = new MenuItem();
2843 MenuItem remove2RightMenuItem = new MenuItem();
2845 MenuItem removeGappedColumnMenuItem = new MenuItem();
2847 MenuItem removeAllGapsMenuItem = new MenuItem();
2849 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2851 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2853 MenuItem sortPairwiseMenuItem = new MenuItem();
2855 MenuItem sortIDMenuItem = new MenuItem();
2857 MenuItem sortLengthMenuItem = new MenuItem();
2859 MenuItem sortGroupMenuItem = new MenuItem();
2861 MenuItem removeRedundancyMenuItem = new MenuItem();
2863 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2865 MenuItem PCAMenuItem = new MenuItem();
2867 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2869 MenuItem neighbourTreeMenuItem = new MenuItem();
2871 BorderLayout borderLayout1 = new BorderLayout();
2873 public Label statusBar = new Label();
2875 Menu outputTextboxMenu = new Menu();
2877 MenuItem clustalColour = new MenuItem();
2879 MenuItem zappoColour = new MenuItem();
2881 MenuItem taylorColour = new MenuItem();
2883 MenuItem hydrophobicityColour = new MenuItem();
2885 MenuItem helixColour = new MenuItem();
2887 MenuItem strandColour = new MenuItem();
2889 MenuItem turnColour = new MenuItem();
2891 MenuItem buriedColour = new MenuItem();
2893 MenuItem purinePyrimidineColour = new MenuItem();
2895 MenuItem RNAInteractionColour = new MenuItem();
2897 MenuItem RNAHelixColour = new MenuItem();
2899 MenuItem userDefinedColour = new MenuItem();
2901 MenuItem PIDColour = new MenuItem();
2903 MenuItem BLOSUM62Colour = new MenuItem();
2905 MenuItem tcoffeeColour = new MenuItem();
2907 MenuItem njTreeBlosumMenuItem = new MenuItem();
2909 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2911 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2913 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2915 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2917 MenuItem alProperties = new MenuItem(
2918 MessageManager.getString("label.alignment_props"));
2920 MenuItem overviewMenuItem = new MenuItem();
2922 MenuItem undoMenuItem = new MenuItem();
2924 MenuItem redoMenuItem = new MenuItem();
2926 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2928 MenuItem noColourmenuItem = new MenuItem();
2930 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2932 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2934 MenuItem findMenuItem = new MenuItem();
2936 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2938 MenuItem nucleotideColour = new MenuItem();
2940 MenuItem deleteGroups = new MenuItem();
2942 MenuItem grpsFromSelection = new MenuItem();
2944 MenuItem createGroup = new MenuItem();
2946 MenuItem unGroup = new MenuItem();
2948 MenuItem delete = new MenuItem();
2950 MenuItem copy = new MenuItem();
2952 MenuItem cut = new MenuItem();
2954 Menu pasteMenu = new Menu();
2956 MenuItem pasteNew = new MenuItem();
2958 MenuItem pasteThis = new MenuItem();
2960 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2962 MenuItem font = new MenuItem();
2964 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2966 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2968 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2970 MenuItem modifyPID = new MenuItem();
2972 MenuItem modifyConservation = new MenuItem();
2974 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2975 "Autocalculate Consensus", true);
2977 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2978 "Sort Alignment With New Tree", true);
2980 Menu sortByTreeMenu = new Menu();
2982 Menu sort = new Menu();
2984 Menu calculate = new Menu();
2986 MenuItem inputText = new MenuItem();
2988 Menu helpMenu = new Menu();
2990 MenuItem documentation = new MenuItem();
2992 MenuItem about = new MenuItem();
2994 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2996 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2998 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3000 Menu autoAnnMenu = new Menu();
3002 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3004 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3006 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3008 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3010 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3012 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3014 private void jbInit() throws Exception
3017 setMenuBar(alignFrameMenuBar);
3021 // dynamically fill save as menu with available formats
3022 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3025 item = new MenuItem(
3026 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3028 item.addActionListener(new java.awt.event.ActionListener()
3031 public void actionPerformed(ActionEvent e)
3033 outputText_actionPerformed(e);
3037 outputTextboxMenu.add(item);
3039 closeMenuItem.addActionListener(this);
3040 loadApplication.addActionListener(this);
3042 loadTree.addActionListener(this);
3043 loadAnnotations.addActionListener(this);
3044 outputFeatures.addActionListener(this);
3045 outputAnnotations.addActionListener(this);
3046 selectAllSequenceMenuItem.addActionListener(this);
3047 deselectAllSequenceMenuItem.addActionListener(this);
3048 invertSequenceMenuItem.addActionListener(this);
3049 remove2LeftMenuItem.setLabel(MessageManager
3050 .getString("action.remove_left"));
3051 remove2LeftMenuItem.addActionListener(this);
3052 remove2RightMenuItem.setLabel(MessageManager
3053 .getString("action.remove_right"));
3054 remove2RightMenuItem.addActionListener(this);
3055 removeGappedColumnMenuItem.setLabel(MessageManager
3056 .getString("action.remove_empty_columns"));
3057 removeGappedColumnMenuItem.addActionListener(this);
3058 removeAllGapsMenuItem.setLabel(MessageManager
3059 .getString("action.remove_all_gaps"));
3060 removeAllGapsMenuItem.addActionListener(this);
3061 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3062 viewBoxesMenuItem.setState(true);
3063 viewBoxesMenuItem.addItemListener(this);
3064 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3065 viewTextMenuItem.setState(true);
3066 viewTextMenuItem.addItemListener(this);
3067 sortPairwiseMenuItem.setLabel(MessageManager
3068 .getString("action.by_pairwise_id"));
3069 sortPairwiseMenuItem.addActionListener(this);
3070 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3071 sortIDMenuItem.addActionListener(this);
3072 sortLengthMenuItem.setLabel(MessageManager
3073 .getString("action.by_length"));
3074 sortLengthMenuItem.addActionListener(this);
3075 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3076 sortGroupMenuItem.addActionListener(this);
3077 removeRedundancyMenuItem.setLabel(MessageManager
3078 .getString("action.remove_redundancy").concat("..."));
3079 removeRedundancyMenuItem.addActionListener(this);
3080 pairwiseAlignmentMenuItem.setLabel(MessageManager
3081 .getString("action.pairwise_alignment"));
3082 pairwiseAlignmentMenuItem.addActionListener(this);
3083 PCAMenuItem.setLabel(MessageManager
3084 .getString("label.principal_component_analysis"));
3085 PCAMenuItem.addActionListener(this);
3086 averageDistanceTreeMenuItem.setLabel(MessageManager
3087 .getString("label.average_distance_identity"));
3088 averageDistanceTreeMenuItem.addActionListener(this);
3089 neighbourTreeMenuItem.setLabel(MessageManager
3090 .getString("label.neighbour_joining_identity"));
3091 neighbourTreeMenuItem.addActionListener(this);
3092 statusBar.setBackground(Color.white);
3093 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3094 statusBar.setText(MessageManager.getString("label.status_bar"));
3095 outputTextboxMenu.setLabel(MessageManager
3096 .getString("label.out_to_textbox"));
3097 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3099 clustalColour.addActionListener(this);
3100 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3101 zappoColour.addActionListener(this);
3102 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3103 taylorColour.addActionListener(this);
3104 hydrophobicityColour.setLabel(MessageManager
3105 .getString("label.hydrophobicity"));
3106 hydrophobicityColour.addActionListener(this);
3108 .setLabel(MessageManager.getString("label.helix_propensity"));
3109 helixColour.addActionListener(this);
3110 strandColour.setLabel(MessageManager
3111 .getString("label.strand_propensity"));
3112 strandColour.addActionListener(this);
3113 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3114 turnColour.addActionListener(this);
3115 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3116 buriedColour.addActionListener(this);
3117 purinePyrimidineColour.setLabel(MessageManager
3118 .getString("label.purine_pyrimidine"));
3119 purinePyrimidineColour.addActionListener(this);
3120 RNAInteractionColour.setLabel(MessageManager
3121 .getString("label.rna_interaction"));
3122 RNAInteractionColour.addActionListener(this);
3123 RNAHelixColour.setLabel(MessageManager
3124 .getString("action.by_rna_helixes"));
3125 RNAHelixColour.addActionListener(this);
3126 userDefinedColour.setLabel(MessageManager
3127 .getString("action.user_defined"));
3128 userDefinedColour.addActionListener(this);
3129 PIDColour.setLabel(MessageManager
3130 .getString("label.percentage_identity"));
3131 PIDColour.addActionListener(this);
3132 BLOSUM62Colour.setLabel(MessageManager
3133 .getString("label.blosum62_score"));
3134 BLOSUM62Colour.addActionListener(this);
3136 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3137 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3139 tcoffeeColour.addActionListener(this);
3140 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3141 .getString("label.average_distance_bloslum62"));
3142 avDistanceTreeBlosumMenuItem.addActionListener(this);
3143 njTreeBlosumMenuItem.setLabel(MessageManager
3144 .getString("label.neighbour_blosum62"));
3145 njTreeBlosumMenuItem.addActionListener(this);
3146 annotationPanelMenuItem.setLabel(MessageManager
3147 .getString("label.show_annotations"));
3148 annotationPanelMenuItem.addItemListener(this);
3149 colourTextMenuItem.setLabel(MessageManager
3150 .getString("label.colour_text"));
3151 colourTextMenuItem.addItemListener(this);
3152 displayNonconservedMenuItem.setLabel(MessageManager
3153 .getString("label.show_non_conversed"));
3154 displayNonconservedMenuItem.addItemListener(this);
3155 alProperties.addActionListener(this);
3156 overviewMenuItem.setLabel(MessageManager
3157 .getString("label.overview_window"));
3158 overviewMenuItem.addActionListener(this);
3159 undoMenuItem.setEnabled(false);
3160 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3161 undoMenuItem.addActionListener(this);
3162 redoMenuItem.setEnabled(false);
3163 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3164 redoMenuItem.addActionListener(this);
3165 conservationMenuItem.setLabel(MessageManager
3166 .getString("action.by_conservation"));
3167 conservationMenuItem.addItemListener(this);
3168 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3169 noColourmenuItem.addActionListener(this);
3170 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3171 wrapMenuItem.addItemListener(this);
3172 renderGapsMenuItem.setLabel(MessageManager
3173 .getString("action.show_gaps"));
3174 renderGapsMenuItem.setState(true);
3175 renderGapsMenuItem.addItemListener(this);
3176 findMenuItem.setLabel(MessageManager.getString("action.find"));
3177 findMenuItem.addActionListener(this);
3178 abovePIDThreshold.setLabel(MessageManager
3179 .getString("label.above_identity_threshold"));
3180 abovePIDThreshold.addItemListener(this);
3181 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3182 nucleotideColour.addActionListener(this);
3183 deleteGroups.setLabel(MessageManager
3184 .getString("action.undefine_groups"));
3185 deleteGroups.addActionListener(this);
3186 grpsFromSelection.setLabel(MessageManager
3187 .getString("action.make_groups_selection"));
3188 grpsFromSelection.addActionListener(this);
3189 createGroup.setLabel(MessageManager.getString("action.create_group"));
3190 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3191 copy.setLabel(MessageManager.getString("action.copy"));
3192 copy.addActionListener(this);
3193 cut.setLabel(MessageManager.getString("action.cut"));
3194 cut.addActionListener(this);
3195 delete.setLabel(MessageManager.getString("action.delete"));
3196 delete.addActionListener(this);
3197 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3198 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3199 pasteNew.addActionListener(this);
3200 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3201 pasteThis.addActionListener(this);
3202 applyToAllGroups.setLabel(MessageManager
3203 .getString("label.apply_colour_to_all_groups"));
3204 applyToAllGroups.setState(true);
3205 applyToAllGroups.addItemListener(this);
3206 font.setLabel(MessageManager.getString("action.font"));
3207 font.addActionListener(this);
3208 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3209 scaleAbove.setState(true);
3210 scaleAbove.setEnabled(false);
3211 scaleAbove.addItemListener(this);
3212 scaleLeft.setEnabled(false);
3213 scaleLeft.setState(true);
3214 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3215 scaleLeft.addItemListener(this);
3216 scaleRight.setEnabled(false);
3217 scaleRight.setState(true);
3218 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3219 scaleRight.addItemListener(this);
3220 modifyPID.setLabel(MessageManager
3221 .getString("label.modify_identity_thereshold"));
3222 modifyPID.addActionListener(this);
3223 modifyConservation.setLabel(MessageManager
3224 .getString("label.modify_conservation_thereshold"));
3225 modifyConservation.addActionListener(this);
3226 sortByTreeMenu.setLabel(MessageManager
3227 .getString("action.by_tree_order"));
3228 sort.setLabel(MessageManager.getString("action.sort"));
3229 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3230 autoCalculate.addItemListener(this);
3231 sortByTree.addItemListener(this);
3233 .setLabel(MessageManager.getString("label.input_from_textbox"));
3234 inputText.addActionListener(this);
3235 centreColumnLabelFlag.setLabel(MessageManager
3236 .getString("label.centre_column_labels"));
3237 centreColumnLabelFlag.addItemListener(this);
3238 followMouseOverFlag.setLabel(MessageManager
3239 .getString("label.automatic_scrolling"));
3240 followMouseOverFlag.addItemListener(this);
3241 helpMenu.setLabel(MessageManager.getString("action.help"));
3242 documentation.setLabel(MessageManager.getString("label.documentation"));
3243 documentation.addActionListener(this);
3245 about.setLabel(MessageManager.getString("label.about"));
3246 about.addActionListener(this);
3247 seqLimits.setState(true);
3248 seqLimits.setLabel(MessageManager
3249 .getString("label.show_sequence_limits"));
3250 seqLimits.addItemListener(this);
3251 featureSettings.setLabel(MessageManager
3252 .getString("label.feature_settings"));
3253 featureSettings.addActionListener(this);
3254 sequenceFeatures.setLabel(MessageManager
3255 .getString("label.sequence_features"));
3256 sequenceFeatures.addItemListener(this);
3257 sequenceFeatures.setState(false);
3258 annotationColour.setLabel(MessageManager
3259 .getString("action.by_annotation"));
3260 annotationColour.addActionListener(this);
3261 invertSequenceMenuItem.setLabel(MessageManager
3262 .getString("action.invert_sequence_selection"));
3263 invertColSel.setLabel(MessageManager
3264 .getString("action.invert_column_selection"));
3265 menu1.setLabel(MessageManager.getString("action.show"));
3266 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3267 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3268 menu2.setLabel(MessageManager.getString("action.hide"));
3270 .setLabel(MessageManager.getString("label.selected_columns"));
3271 hideSequences.setLabel(MessageManager
3272 .getString("label.selected_sequences"));
3273 hideAllButSelection.setLabel(MessageManager
3274 .getString("label.all_but_selected_region"));
3275 hideAllSelection.setLabel(MessageManager
3276 .getString("label.selected_region"));
3277 showAllHidden.setLabel(MessageManager
3278 .getString("label.all_sequences_columns"));
3279 showGroupConsensus.setLabel(MessageManager
3280 .getString("label.group_consensus"));
3281 showGroupConservation.setLabel(MessageManager
3282 .getString("label.group_conservation"));
3283 showConsensusHistogram.setLabel(MessageManager
3284 .getString("label.show_consensus_histogram"));
3285 showSequenceLogo.setLabel(MessageManager
3286 .getString("label.show_consensus_logo"));
3287 normSequenceLogo.setLabel(MessageManager
3288 .getString("label.norm_consensus_logo"));
3289 applyAutoAnnotationSettings.setLabel(MessageManager
3290 .getString("label.apply_all_groups"));
3291 applyAutoAnnotationSettings.setState(true);
3292 autoAnnMenu.setLabel(MessageManager
3293 .getString("label.autocalculated_annotation"));
3295 invertColSel.addActionListener(this);
3296 showColumns.addActionListener(this);
3297 showSeqs.addActionListener(this);
3298 hideColumns.addActionListener(this);
3299 hideSequences.addActionListener(this);
3300 hideAllButSelection.addActionListener(this);
3301 hideAllSelection.addActionListener(this);
3302 showAllHidden.addActionListener(this);
3303 showGroupConsensus.addItemListener(this);
3304 showGroupConservation.addItemListener(this);
3305 showConsensusHistogram.addItemListener(this);
3306 showSequenceLogo.addItemListener(this);
3307 normSequenceLogo.addItemListener(this);
3309 applyAutoAnnotationSettings.addItemListener(this);
3310 formatMenu.setLabel(MessageManager.getString("action.format"));
3311 selectMenu.setLabel(MessageManager.getString("action.select"));
3312 newView.setLabel(MessageManager.getString("action.new_view"));
3313 newView.addActionListener(this);
3314 alignFrameMenuBar.add(fileMenu);
3315 alignFrameMenuBar.add(editMenu);
3316 alignFrameMenuBar.add(selectMenu);
3317 alignFrameMenuBar.add(viewMenu);
3318 alignFrameMenuBar.add(formatMenu);
3319 alignFrameMenuBar.add(colourMenu);
3320 alignFrameMenuBar.add(calculateMenu);
3321 alignFrameMenuBar.add(helpMenu);
3323 fileMenu.add(inputText);
3324 fileMenu.add(loadTree);
3325 fileMenu.add(loadAnnotations);
3327 fileMenu.addSeparator();
3328 fileMenu.add(outputTextboxMenu);
3329 fileMenu.add(outputFeatures);
3330 fileMenu.add(outputAnnotations);
3332 if (jalviewServletURL != null)
3334 fileMenu.add(loadApplication);
3337 fileMenu.addSeparator();
3338 fileMenu.add(closeMenuItem);
3340 editMenu.add(undoMenuItem);
3341 editMenu.add(redoMenuItem);
3344 editMenu.add(pasteMenu);
3345 editMenu.add(delete);
3346 editMenu.addSeparator();
3347 editMenu.add(remove2LeftMenuItem);
3348 editMenu.add(remove2RightMenuItem);
3349 editMenu.add(removeGappedColumnMenuItem);
3350 editMenu.add(removeAllGapsMenuItem);
3351 editMenu.add(removeRedundancyMenuItem);
3352 viewMenu.add(newView);
3353 viewMenu.addSeparator();
3354 viewMenu.add(menu1);
3355 viewMenu.add(menu2);
3356 viewMenu.addSeparator();
3357 viewMenu.add(followMouseOverFlag);
3358 viewMenu.add(annotationPanelMenuItem);
3359 autoAnnMenu.add(applyAutoAnnotationSettings);
3360 autoAnnMenu.add(showConsensusHistogram);
3361 autoAnnMenu.add(showSequenceLogo);
3362 autoAnnMenu.add(normSequenceLogo);
3363 autoAnnMenu.addSeparator();
3364 autoAnnMenu.add(showGroupConservation);
3365 autoAnnMenu.add(showGroupConsensus);
3366 viewMenu.add(autoAnnMenu);
3367 viewMenu.addSeparator();
3368 viewMenu.add(sequenceFeatures);
3369 viewMenu.add(featureSettings);
3370 viewMenu.addSeparator();
3371 viewMenu.add(alProperties);
3372 viewMenu.addSeparator();
3373 viewMenu.add(overviewMenuItem);
3374 colourMenu.add(applyToAllGroups);
3375 colourMenu.addSeparator();
3376 colourMenu.add(noColourmenuItem);
3377 colourMenu.add(clustalColour);
3378 colourMenu.add(BLOSUM62Colour);
3379 colourMenu.add(PIDColour);
3380 colourMenu.add(zappoColour);
3381 colourMenu.add(taylorColour);
3382 colourMenu.add(hydrophobicityColour);
3383 colourMenu.add(helixColour);
3384 colourMenu.add(strandColour);
3385 colourMenu.add(turnColour);
3386 colourMenu.add(buriedColour);
3387 colourMenu.add(nucleotideColour);
3388 colourMenu.add(purinePyrimidineColour);
3389 // colourMenu.add(RNAInteractionColour);
3390 colourMenu.add(tcoffeeColour);
3391 colourMenu.add(userDefinedColour);
3392 colourMenu.addSeparator();
3393 colourMenu.add(conservationMenuItem);
3394 colourMenu.add(modifyConservation);
3395 colourMenu.add(abovePIDThreshold);
3396 colourMenu.add(modifyPID);
3397 colourMenu.add(annotationColour);
3398 colourMenu.add(RNAHelixColour);
3399 calculateMenu.add(sort);
3400 calculateMenu.add(calculate);
3401 calculateMenu.addSeparator();
3402 calculateMenu.add(pairwiseAlignmentMenuItem);
3403 calculateMenu.add(PCAMenuItem);
3404 calculateMenu.add(autoCalculate);
3405 calculateMenu.add(sortByTree);
3406 this.add(statusBar, BorderLayout.SOUTH);
3407 pasteMenu.add(pasteNew);
3408 pasteMenu.add(pasteThis);
3409 sort.add(sortIDMenuItem);
3410 sort.add(sortLengthMenuItem);
3411 sort.add(sortByTreeMenu);
3412 sort.add(sortGroupMenuItem);
3413 sort.add(sortPairwiseMenuItem);
3414 calculate.add(averageDistanceTreeMenuItem);
3415 calculate.add(neighbourTreeMenuItem);
3416 calculate.add(avDistanceTreeBlosumMenuItem);
3417 calculate.add(njTreeBlosumMenuItem);
3418 helpMenu.add(documentation);
3419 helpMenu.add(about);
3420 menu1.add(showColumns);
3421 menu1.add(showSeqs);
3422 menu1.add(showAllHidden);
3423 menu2.add(hideColumns);
3424 menu2.add(hideSequences);
3425 menu2.add(hideAllSelection);
3426 menu2.add(hideAllButSelection);
3427 formatMenu.add(font);
3428 formatMenu.add(seqLimits);
3429 formatMenu.add(wrapMenuItem);
3430 formatMenu.add(scaleAbove);
3431 formatMenu.add(scaleLeft);
3432 formatMenu.add(scaleRight);
3433 formatMenu.add(viewBoxesMenuItem);
3434 formatMenu.add(viewTextMenuItem);
3435 formatMenu.add(colourTextMenuItem);
3436 formatMenu.add(displayNonconservedMenuItem);
3437 formatMenu.add(renderGapsMenuItem);
3438 formatMenu.add(centreColumnLabelFlag);
3439 selectMenu.add(findMenuItem);
3440 selectMenu.addSeparator();
3441 selectMenu.add(selectAllSequenceMenuItem);
3442 selectMenu.add(deselectAllSequenceMenuItem);
3443 selectMenu.add(invertSequenceMenuItem);
3444 selectMenu.add(invertColSel);
3445 selectMenu.add(createGroup);
3446 selectMenu.add(unGroup);
3447 selectMenu.add(grpsFromSelection);
3448 selectMenu.add(deleteGroups);
3452 public void setStatus(String string)
3454 statusBar.setText(string);
3457 MenuItem featureSettings = new MenuItem();
3459 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3461 MenuItem annotationColour = new MenuItem();
3463 MenuItem invertColSel = new MenuItem();
3465 Menu menu1 = new Menu();
3467 MenuItem showColumns = new MenuItem();
3469 MenuItem showSeqs = new MenuItem();
3471 Menu menu2 = new Menu();
3473 MenuItem hideColumns = new MenuItem();
3475 MenuItem hideSequences = new MenuItem();
3477 MenuItem hideAllButSelection = new MenuItem();
3479 MenuItem hideAllSelection = new MenuItem();
3481 MenuItem showAllHidden = new MenuItem();
3483 Menu formatMenu = new Menu();
3485 Menu selectMenu = new Menu();
3487 MenuItem newView = new MenuItem();
3490 * Attach the alignFrame panels after embedding menus, if necessary. This used
3491 * to be called setEmbedded, but is now creates the dropdown menus in a
3492 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3494 * @param reallyEmbedded
3495 * true to attach the view to the applet area on the page rather than
3498 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3503 // Explicly build the embedded menu panel for the on-page applet
3505 // view cannot be closed if its actually on the page
3506 fileMenu.remove(closeMenuItem);
3507 fileMenu.remove(3); // Remove Seperator
3508 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3509 Font.PLAIN, 11, false); // use our own fonts.
3510 // and actually add the components to the applet area
3511 viewport.applet.setLayout(new BorderLayout());
3512 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3513 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3514 alignPanel.setSize(viewport.applet.getSize().width,
3515 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3516 - statusBar.HEIGHT);
3517 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3518 final AlignFrame me = this;
3519 viewport.applet.addFocusListener(new FocusListener()
3523 public void focusLost(FocusEvent e)
3525 if (me.viewport.applet.currentAlignFrame == me)
3527 me.viewport.applet.currentAlignFrame = null;
3532 public void focusGained(FocusEvent e)
3534 me.viewport.applet.currentAlignFrame = me;
3537 viewport.applet.validate();
3542 // test and embed menu bar if necessary.
3544 if (embedMenuIfNeeded(alignPanel))
3546 // adjust for status bar height too
3547 alignPanel.setSize(getSize().width, getSize().height
3548 - statusBar.HEIGHT);
3550 add(statusBar, BorderLayout.SOUTH);
3551 add(alignPanel, BorderLayout.CENTER);
3552 // and register with the applet so it can pass external API calls to us
3553 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3559 * create a new binding between structures in an existing jmol viewer instance
3560 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3561 * this does not open a new Jmol window, or modify the display of the
3562 * structures in the original jmol window. Note This method doesn't work
3563 * without an additional javascript library to exchange messages between the
3564 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3567 * JmolViewer instance
3568 * @param sequenceIds
3569 * - sequence Ids to search for associations
3571 public SequenceStructureBinding addStructureViewInstance(
3572 Object jmolviewer, String[] sequenceIds)
3574 org.jmol.api.JmolViewer viewer = null;
3577 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3578 } catch (ClassCastException ex)
3580 System.err.println("Unsupported viewer object :"
3581 + jmolviewer.getClass());
3585 System.err.println("Can't use this object as a structure viewer:"
3586 + jmolviewer.getClass());
3589 SequenceI[] seqs = null;
3590 if (sequenceIds == null || sequenceIds.length == 0)
3592 seqs = viewport.getAlignment().getSequencesArray();
3596 Vector sqi = new Vector();
3597 AlignmentI al = viewport.getAlignment();
3598 for (int sid = 0; sid < sequenceIds.length; sid++)
3600 SequenceI sq = al.findName(sequenceIds[sid]);
3608 seqs = new SequenceI[sqi.size()];
3609 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3611 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3619 AAStructureBindingModel jmv = null;
3620 // TODO: search for a jmv that involves viewer
3622 { // create a new viewer/jalview binding.
3623 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3631 * bind a pdb file to a sequence in the current view
3634 * - sequenceId within the dataset.
3635 * @param pdbEntryString
3636 * - the short name for the PDB file
3638 * - pdb file - either a URL or a valid PDB file.
3639 * @return true if binding was as success TODO: consider making an exception
3640 * structure for indicating when PDB parsing or sequenceId location
3643 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3646 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3647 boolean needtoadd = false;
3648 if (toaddpdb != null)
3650 Vector pdbe = toaddpdb.getPDBId();
3651 PDBEntry pdbentry = null;
3652 if (pdbe != null && pdbe.size() > 0)
3654 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3656 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3657 if (!pdbentry.getId().equals(pdbEntryString)
3658 && !pdbentry.getFile().equals(pdbFile))
3668 if (pdbentry == null)
3670 pdbentry = new PDBEntry();
3671 pdbentry.setId(pdbEntryString);
3672 pdbentry.setFile(pdbFile);
3673 needtoadd = true; // add this new entry to sequence.
3675 // resolve data source
3676 // TODO: this code should be a refactored to an io package
3677 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3678 if (protocol == null)
3684 // make a note of the access mode and add
3685 if (pdbentry.getProperty() == null)
3687 pdbentry.setProperty(new Hashtable());
3689 pdbentry.getProperty().put("protocol", protocol);
3690 toaddpdb.addPDBId(pdbentry);
3691 alignPanel.getStructureSelectionManager()
3692 .registerPDBEntry(pdbentry);
3698 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3702 Vector sequences = new Vector();
3703 for (int i = 0; i < seqs.length; i++)
3705 if (seqs[i] != null)
3707 sequences.addElement(new Object[]
3708 { seqs[i], (chains != null) ? chains[i] : null });
3711 seqs = new SequenceI[sequences.size()];
3712 chains = new String[sequences.size()];
3713 for (int i = 0, isize = sequences.size(); i < isize; i++)
3715 Object[] oj = (Object[]) sequences.elementAt(i);
3717 seqs[i] = (SequenceI) oj[0];
3718 chains[i] = (String) oj[1];
3726 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3727 SequenceI[] seqs, String[] chains, String protocol)
3729 // Scrub any null sequences from the array
3730 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3731 seqs = (SequenceI[]) sqch[0];
3732 chains = (String[]) sqch[1];
3733 if (seqs == null || seqs.length == 0)
3736 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3738 if (protocol == null || protocol.trim().length() == 0
3739 || protocol.equals("null"))
3741 protocol = (String) pdb.getProperty().get("protocol");
3742 if (protocol == null)
3744 System.err.println("Couldn't work out protocol to open structure: "
3749 if (applet.useXtrnalSviewer)
3751 // register the association(s) and quit, don't create any windows.
3752 if (StructureSelectionManager.getStructureSelectionManager(applet)
3753 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3755 System.err.println("Failed to map " + pdb.getFile() + " ("
3756 + protocol + ") to any sequences");
3760 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3762 // can only do alignments with Jmol
3763 // find the last jmol window assigned to this alignment
3764 jalview.appletgui.AppletJmol ajm = null, tajm;
3765 Vector jmols = applet
3766 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3767 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3769 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3770 if (tajm.ap.alignFrame == this)
3779 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3780 // try and add the pdb structure
3785 // otherwise, create a new window
3786 if (applet.jmolAvailable)
3788 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3790 applet.lastFrameX += 40;
3791 applet.lastFrameY += 40;
3795 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3800 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3801 SequenceI[][] seqs, String[][] chains, String[] protocols)
3803 // TODO Auto-generated method stub
3804 System.err.println("Aligned Structure View: Not yet implemented.");
3808 * modify the current selection, providing the user has not made a selection
3812 * - sequences from this alignment
3814 * - columns to be selected on the alignment
3816 public void select(SequenceGroup sel, ColumnSelection csel)
3818 alignPanel.seqPanel.selection(sel, csel, null);
3821 public void scrollTo(int row, int column)
3823 alignPanel.seqPanel.scrollTo(row, column);
3826 public void scrollToRow(int row)
3828 alignPanel.seqPanel.scrollToRow(row);
3831 public void scrollToColumn(int column)
3833 alignPanel.seqPanel.scrollToColumn(column);
3837 * @return the alignments unique ID.
3839 public String getSequenceSetId()
3841 return viewport.getSequenceSetId();
3845 * Load the (T-Coffee) score file from the specified url
3848 * File/URL/T-COFFEE score file contents
3849 * @throws IOException
3850 * @return true if alignment was annotated with data from source
3852 public boolean loadScoreFile(String source) throws IOException
3855 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3856 AppletFormatAdapter.checkProtocol(source));
3857 if (!file.isValid())
3859 // TODO: raise dialog for gui
3860 System.err.println("Problems parsing T-Coffee scores: "
3861 + file.getWarningMessage());
3862 System.err.println("Origin was:\n" + source);
3867 * check that the score matrix matches the alignment dimensions
3870 if ((aln = viewport.getAlignment()) != null
3871 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3874 // TODO: raise a dialog box here rather than bomb out.
3876 .println("The scores matrix does not match the alignment dimensions");
3880 // TODO add parameter to indicate if matching should be done
3881 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3883 alignPanel.fontChanged();
3884 tcoffeeColour.setEnabled(true);
3885 // switch to this color
3886 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3891 System.err.println("Problems resolving T-Coffee scores:");
3892 if (file.getWarningMessage() != null)
3894 System.err.println(file.getWarningMessage());