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.analysis.Conservation;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.CommandI;
30 import jalview.commands.EditCommand;
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.ResidueProperties;
60 import jalview.schemes.StrandColourScheme;
61 import jalview.schemes.TCoffeeColourScheme;
62 import jalview.schemes.TaylorColourScheme;
63 import jalview.schemes.TurnColourScheme;
64 import jalview.schemes.ZappoColourScheme;
65 import jalview.structure.StructureSelectionManager;
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()))
327 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
329 switch (evt.getKeyCode())
331 case 27: // escape key
332 deselectAllSequenceMenuItem_actionPerformed();
334 alignPanel.alabels.cancelDrag();
337 if (evt.isControlDown() || evt.isMetaDown())
339 cut_actionPerformed();
343 if (viewport.cursorMode && !evt.isControlDown())
345 alignPanel.seqPanel.setCursorColumn();
347 if (evt.isControlDown() || evt.isMetaDown())
349 copy_actionPerformed();
353 if (evt.isControlDown())
355 paste(evt.isShiftDown());
359 if (evt.isControlDown() || evt.isMetaDown())
361 selectAllSequenceMenuItem_actionPerformed();
364 case KeyEvent.VK_DOWN:
365 if (viewport.cursorMode)
367 alignPanel.seqPanel.moveCursor(0, 1);
371 moveSelectedSequences(false);
376 if (viewport.cursorMode)
378 alignPanel.seqPanel.moveCursor(0, -1);
382 moveSelectedSequences(true);
386 case KeyEvent.VK_LEFT:
387 if (evt.isAltDown() || !viewport.cursorMode)
388 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
390 alignPanel.seqPanel.moveCursor(-1, 0);
393 case KeyEvent.VK_RIGHT:
394 if (evt.isAltDown() || !viewport.cursorMode)
395 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
397 alignPanel.seqPanel.moveCursor(1, 0);
400 case KeyEvent.VK_SPACE:
401 if (viewport.cursorMode)
403 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
404 || evt.isShiftDown() || evt.isAltDown());
408 case KeyEvent.VK_DELETE:
409 case KeyEvent.VK_BACK_SPACE:
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
413 || evt.isShiftDown() || evt.isAltDown());
417 cut_actionPerformed();
418 alignPanel.seqPanel.seqCanvas.repaint();
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.setCursorRow();
429 if (viewport.cursorMode)
431 alignPanel.seqPanel.setCursorPosition();
435 case KeyEvent.VK_ENTER:
436 case KeyEvent.VK_COMMA:
437 if (viewport.cursorMode)
439 alignPanel.seqPanel.setCursorRowAndColumn();
444 if (viewport.cursorMode)
446 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
450 if (viewport.cursorMode)
452 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
457 viewport.cursorMode = !viewport.cursorMode;
458 statusBar.setText(MessageManager.formatMessage(
459 "label.keyboard_editing_mode", new String[]
460 { (viewport.cursorMode ? "on" : "off") }));
461 if (viewport.cursorMode)
463 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
464 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
469 if (evt.isControlDown())
471 findMenuItem_actionPerformed();
477 boolean toggleSeqs = !evt.isControlDown();
478 boolean toggleCols = !evt.isShiftDown();
479 toggleHiddenRegions(toggleSeqs, toggleCols);
483 case KeyEvent.VK_PAGE_UP:
484 if (viewport.wrapAlignment)
486 alignPanel.scrollUp(true);
490 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
491 - viewport.endSeq + viewport.startSeq);
495 case KeyEvent.VK_PAGE_DOWN:
496 if (viewport.wrapAlignment)
498 alignPanel.scrollUp(false);
502 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
503 + viewport.endSeq - viewport.startSeq);
508 if (evt.isControlDown())
510 undoMenuItem_actionPerformed();
515 if (evt.isControlDown())
517 redoMenuItem_actionPerformed();
522 if (evt.isControlDown())
529 if (evt.isControlDown())
531 trimAlignment(false);
536 if (evt.isControlDown())
538 if (evt.isShiftDown())
540 this.removeAllGapsMenuItem_actionPerformed();
544 removeGappedColumnMenuItem_actionPerformed();
549 if (evt.isControlDown())
553 invertColSel_actionPerformed();
557 invertSequenceMenuItem_actionPerformed();
563 if (evt.isControlDown())
565 if (evt.isShiftDown())
567 this.unGroup_actionPerformed();
571 this.createGroup_actionPerformed();
577 if (evt.isControlDown())
579 this.deleteGroups_actionPerformed();
584 if (evt.isControlDown())
591 alignPanel.paintAlignment(true);
595 * called by key handler and the hide all/show all menu items
600 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
602 boolean hide = false;
603 SequenceGroup sg = viewport.getSelectionGroup();
604 if (!toggleSeqs && !toggleCols)
606 // Hide everything by the current selection - this is a hack - we do the
607 // invert and then hide
608 // first check that there will be visible columns after the invert.
609 if ((viewport.getColumnSelection() != null
610 && viewport.getColumnSelection().getSelected() != null && viewport
611 .getColumnSelection().getSelected().size() > 0)
612 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
615 // now invert the sequence set, if required - empty selection implies
616 // that no hiding is required.
619 invertSequenceMenuItem_actionPerformed();
620 sg = viewport.getSelectionGroup();
624 viewport.expandColSelection(sg, true);
625 // finally invert the column selection and get the new sequence
626 // selection and indicate it should be hidden.
627 invertColSel_actionPerformed();
634 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
637 viewport.hideAllSelectedSeqs();
639 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
642 viewport.showAllHiddenSeqs();
648 if (viewport.getColumnSelection().getSelected().size() > 0)
650 viewport.hideSelectedColumns();
653 viewport.setSelectionGroup(sg);
658 viewport.showAllHiddenColumns();
664 public void keyReleased(KeyEvent evt)
669 public void keyTyped(KeyEvent evt)
674 public void itemStateChanged(ItemEvent evt)
676 if (evt.getSource() == displayNonconservedMenuItem)
678 displayNonconservedMenuItem_actionPerformed();
680 else if (evt.getSource() == colourTextMenuItem)
682 colourTextMenuItem_actionPerformed();
684 else if (evt.getSource() == wrapMenuItem)
686 wrapMenuItem_actionPerformed();
688 else if (evt.getSource() == scaleAbove)
690 viewport.setScaleAboveWrapped(scaleAbove.getState());
692 else if (evt.getSource() == scaleLeft)
694 viewport.setScaleLeftWrapped(scaleLeft.getState());
696 else if (evt.getSource() == scaleRight)
698 viewport.setScaleRightWrapped(scaleRight.getState());
700 else if (evt.getSource() == seqLimits)
702 seqLimits_itemStateChanged();
704 else if (evt.getSource() == viewBoxesMenuItem)
706 viewport.setShowBoxes(viewBoxesMenuItem.getState());
708 else if (evt.getSource() == viewTextMenuItem)
710 viewport.setShowText(viewTextMenuItem.getState());
712 else if (evt.getSource() == renderGapsMenuItem)
714 viewport.setRenderGaps(renderGapsMenuItem.getState());
716 else if (evt.getSource() == annotationPanelMenuItem)
718 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
719 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
721 else if (evt.getSource() == sequenceFeatures)
723 viewport.showSequenceFeatures(sequenceFeatures.getState());
724 alignPanel.seqPanel.seqCanvas.repaint();
726 else if (evt.getSource() == conservationMenuItem)
728 conservationMenuItem_actionPerformed();
730 else if (evt.getSource() == abovePIDThreshold)
732 abovePIDThreshold_actionPerformed();
734 else if (evt.getSource() == applyToAllGroups)
736 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
738 else if (evt.getSource() == autoCalculate)
740 viewport.autoCalculateConsensus = autoCalculate.getState();
742 else if (evt.getSource() == sortByTree)
744 viewport.sortByTree = sortByTree.getState();
746 else if (evt.getSource() == this.centreColumnLabelFlag)
748 centreColumnLabelFlag_stateChanged();
750 else if (evt.getSource() == this.followMouseOverFlag)
752 mouseOverFlag_stateChanged();
754 else if (evt.getSource() == showGroupConsensus)
756 showGroupConsensus_actionPerformed();
758 else if (evt.getSource() == showGroupConservation)
760 showGroupConservation_actionPerformed();
762 else if (evt.getSource() == showSequenceLogo)
764 showSequenceLogo_actionPerformed();
766 else if (evt.getSource() == normSequenceLogo)
768 normSequenceLogo_actionPerformed();
770 else if (evt.getSource() == showConsensusHistogram)
772 showConsensusHistogram_actionPerformed();
774 else if (evt.getSource() == applyAutoAnnotationSettings)
776 applyAutoAnnotationSettings_actionPerformed();
778 alignPanel.paintAlignment(true);
781 private void mouseOverFlag_stateChanged()
783 viewport.followHighlight = followMouseOverFlag.getState();
784 // TODO: could kick the scrollTo mechanism to reset view for current
788 private void centreColumnLabelFlag_stateChanged()
790 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
791 this.alignPanel.annotationPanel.repaint();
795 public void actionPerformed(ActionEvent evt)
797 Object source = evt.getSource();
799 if (source == inputText)
801 inputText_actionPerformed();
803 else if (source == loadTree)
805 loadTree_actionPerformed();
807 else if (source == loadApplication)
809 launchFullApplication();
811 else if (source == loadAnnotations)
815 else if (source == outputAnnotations)
817 outputAnnotations(true);
819 else if (source == outputFeatures)
821 outputFeatures(true, "Jalview");
823 else if (source == closeMenuItem)
825 closeMenuItem_actionPerformed();
827 else if (source == copy)
829 copy_actionPerformed();
831 else if (source == undoMenuItem)
833 undoMenuItem_actionPerformed();
835 else if (source == redoMenuItem)
837 redoMenuItem_actionPerformed();
839 else if (source == inputText)
841 inputText_actionPerformed();
843 else if (source == closeMenuItem)
845 closeMenuItem_actionPerformed();
847 else if (source == undoMenuItem)
849 undoMenuItem_actionPerformed();
851 else if (source == redoMenuItem)
853 redoMenuItem_actionPerformed();
855 else if (source == copy)
857 copy_actionPerformed();
859 else if (source == pasteNew)
861 pasteNew_actionPerformed();
863 else if (source == pasteThis)
865 pasteThis_actionPerformed();
867 else if (source == cut)
869 cut_actionPerformed();
871 else if (source == delete)
873 delete_actionPerformed();
875 else if (source == grpsFromSelection)
877 makeGrpsFromSelection_actionPerformed();
879 else if (source == deleteGroups)
881 deleteGroups_actionPerformed();
883 else if (source == selectAllSequenceMenuItem)
885 selectAllSequenceMenuItem_actionPerformed();
887 else if (source == deselectAllSequenceMenuItem)
889 deselectAllSequenceMenuItem_actionPerformed();
891 else if (source == invertSequenceMenuItem)
893 invertSequenceMenuItem_actionPerformed();
895 else if (source == invertColSel)
897 viewport.invertColumnSelection();
898 alignPanel.paintAlignment(true);
900 else if (source == remove2LeftMenuItem)
904 else if (source == remove2RightMenuItem)
906 trimAlignment(false);
908 else if (source == removeGappedColumnMenuItem)
910 removeGappedColumnMenuItem_actionPerformed();
912 else if (source == removeAllGapsMenuItem)
914 removeAllGapsMenuItem_actionPerformed();
916 else if (source == findMenuItem)
918 findMenuItem_actionPerformed();
920 else if (source == font)
922 new FontChooser(alignPanel);
924 else if (source == newView)
928 else if (source == showColumns)
930 viewport.showAllHiddenColumns();
931 alignPanel.paintAlignment(true);
933 else if (source == showSeqs)
935 viewport.showAllHiddenSeqs();
936 alignPanel.paintAlignment(true);
938 else if (source == hideColumns)
940 viewport.hideSelectedColumns();
941 alignPanel.paintAlignment(true);
943 else if (source == hideSequences
944 && viewport.getSelectionGroup() != null)
946 viewport.hideAllSelectedSeqs();
947 alignPanel.paintAlignment(true);
949 else if (source == hideAllButSelection)
951 toggleHiddenRegions(false, false);
952 alignPanel.paintAlignment(true);
954 else if (source == hideAllSelection)
956 SequenceGroup sg = viewport.getSelectionGroup();
957 viewport.expandColSelection(sg, false);
958 viewport.hideAllSelectedSeqs();
959 viewport.hideSelectedColumns();
960 alignPanel.paintAlignment(true);
962 else if (source == showAllHidden)
964 viewport.showAllHiddenColumns();
965 viewport.showAllHiddenSeqs();
966 alignPanel.paintAlignment(true);
968 else if (source == showGroupConsensus)
970 showGroupConsensus_actionPerformed();
972 else if (source == showGroupConservation)
974 showGroupConservation_actionPerformed();
976 else if (source == showSequenceLogo)
978 showSequenceLogo_actionPerformed();
980 else if (source == normSequenceLogo)
982 normSequenceLogo_actionPerformed();
984 else if (source == showConsensusHistogram)
986 showConsensusHistogram_actionPerformed();
988 else if (source == applyAutoAnnotationSettings)
990 applyAutoAnnotationSettings_actionPerformed();
992 else if (source == featureSettings)
994 new FeatureSettings(alignPanel);
996 else if (source == alProperties)
998 StringBuffer contents = new jalview.io.AlignmentProperties(
999 viewport.getAlignment()).formatAsString();
1000 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1001 cap.setText(contents.toString());
1002 Frame frame = new Frame();
1004 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1005 "label.alignment_properties", new String[]
1006 { getTitle() }), 400, 250);
1008 else if (source == overviewMenuItem)
1010 overviewMenuItem_actionPerformed();
1012 else if (source == noColourmenuItem)
1016 else if (source == clustalColour)
1018 abovePIDThreshold.setState(false);
1019 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1021 else if (source == zappoColour)
1023 changeColour(new ZappoColourScheme());
1025 else if (source == taylorColour)
1027 changeColour(new TaylorColourScheme());
1029 else if (source == hydrophobicityColour)
1031 changeColour(new HydrophobicColourScheme());
1033 else if (source == helixColour)
1035 changeColour(new HelixColourScheme());
1037 else if (source == strandColour)
1039 changeColour(new StrandColourScheme());
1041 else if (source == turnColour)
1043 changeColour(new TurnColourScheme());
1045 else if (source == buriedColour)
1047 changeColour(new BuriedColourScheme());
1049 else if (source == nucleotideColour)
1051 changeColour(new NucleotideColourScheme());
1053 else if (source == purinePyrimidineColour)
1055 changeColour(new PurinePyrimidineColourScheme());
1057 else if (source == RNAInteractionColour)
1059 changeColour(new RNAInteractionColourScheme());
1061 else if (source == RNAHelixColour)
1063 new RNAHelicesColourChooser(viewport, alignPanel);
1065 else if (source == modifyPID)
1067 modifyPID_actionPerformed();
1069 else if (source == modifyConservation)
1071 modifyConservation_actionPerformed();
1073 else if (source == userDefinedColour)
1075 new UserDefinedColours(alignPanel, null);
1077 else if (source == PIDColour)
1079 changeColour(new PIDColourScheme());
1081 else if (source == BLOSUM62Colour)
1083 changeColour(new Blosum62ColourScheme());
1085 else if (source == tcoffeeColour)
1087 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1089 else if (source == annotationColour)
1091 new AnnotationColourChooser(viewport, alignPanel);
1093 else if (source == sortPairwiseMenuItem)
1095 sortPairwiseMenuItem_actionPerformed();
1097 else if (source == sortIDMenuItem)
1099 sortIDMenuItem_actionPerformed();
1101 else if (source == sortLengthMenuItem)
1103 sortLengthMenuItem_actionPerformed();
1105 else if (source == sortGroupMenuItem)
1107 sortGroupMenuItem_actionPerformed();
1109 else if (source == removeRedundancyMenuItem)
1111 removeRedundancyMenuItem_actionPerformed();
1113 else if (source == pairwiseAlignmentMenuItem)
1115 pairwiseAlignmentMenuItem_actionPerformed();
1117 else if (source == PCAMenuItem)
1119 PCAMenuItem_actionPerformed();
1121 else if (source == averageDistanceTreeMenuItem)
1123 averageDistanceTreeMenuItem_actionPerformed();
1125 else if (source == neighbourTreeMenuItem)
1127 neighbourTreeMenuItem_actionPerformed();
1129 else if (source == njTreeBlosumMenuItem)
1131 njTreeBlosumMenuItem_actionPerformed();
1133 else if (source == avDistanceTreeBlosumMenuItem)
1135 avTreeBlosumMenuItem_actionPerformed();
1137 else if (source == documentation)
1139 documentation_actionPerformed();
1141 else if (source == about)
1143 about_actionPerformed();
1148 public void inputText_actionPerformed()
1150 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1151 Frame frame = new Frame();
1153 jalview.bin.JalviewLite.addFrame(frame,
1154 MessageManager.getString("label.input_cut_paste"), 500, 500);
1157 protected void outputText_actionPerformed(ActionEvent e)
1159 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1160 Frame frame = new Frame();
1162 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1163 "label.alignment_output_command", new String[]
1164 { e.getActionCommand() }), 600, 500);
1165 cap.setText(new AppletFormatAdapter().formatSequences(
1166 e.getActionCommand(), viewport.getAlignment(),
1167 viewport.showJVSuffix));
1170 public void loadAnnotations()
1172 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1173 cap.setText(MessageManager
1174 .getString("label.paste_features_annotations_Tcoffee_here"));
1175 cap.setAnnotationImport();
1176 Frame frame = new Frame();
1178 jalview.bin.JalviewLite.addFrame(frame,
1179 MessageManager.getString("action.paste_annotations"), 400, 300);
1183 public String outputAnnotations(boolean displayTextbox)
1185 String annotation = new AnnotationFile().printAnnotations(
1186 viewport.showAnnotation ? viewport.getAlignment()
1187 .getAlignmentAnnotation() : null, viewport
1188 .getAlignment().getGroups(), ((Alignment) viewport
1189 .getAlignment()).alignmentProperties);
1193 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1194 Frame frame = new Frame();
1196 jalview.bin.JalviewLite.addFrame(frame,
1197 MessageManager.getString("label.annotations"), 600, 500);
1198 cap.setText(annotation);
1204 private Hashtable getDisplayedFeatureCols()
1206 if (alignPanel.getFeatureRenderer() != null
1207 && viewport.featuresDisplayed != null)
1209 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1210 Hashtable fcols = new Hashtable();
1211 Enumeration en = viewport.featuresDisplayed.keys();
1212 while (en.hasMoreElements())
1214 Object col = en.nextElement();
1215 fcols.put(col, fr.featureColours.get(col));
1222 public String outputFeatures(boolean displayTextbox, String format)
1225 if (format.equalsIgnoreCase("Jalview"))
1227 features = new FeaturesFile().printJalviewFormat(viewport
1228 .getAlignment().getSequencesArray(),
1229 getDisplayedFeatureCols());
1233 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1234 .getSequencesArray(), getDisplayedFeatureCols());
1239 boolean frimport = false;
1240 if (features == null || features.equals("No Features Visible"))
1242 features = "# No features visible - paste some and import them here.";
1246 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1249 cap.setAnnotationImport();
1251 Frame frame = new Frame();
1253 jalview.bin.JalviewLite.addFrame(frame,
1254 MessageManager.getString("label.features"), 600, 500);
1255 cap.setText(features);
1259 if (features == null)
1266 void launchFullApplication()
1268 StringBuffer url = new StringBuffer(jalviewServletURL);
1271 + appendProtocol(viewport.applet.getParameter("file")));
1273 if (viewport.applet.getParameter("features") != null)
1275 url.append("&features=");
1276 url.append(appendProtocol(viewport.applet.getParameter("features")));
1279 if (viewport.applet.getParameter("annotations") != null)
1281 url.append("&annotations=");
1282 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1285 if (viewport.applet.getParameter("jnetfile") != null)
1287 url.append("&annotations=");
1288 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1291 if (viewport.applet.getParameter("defaultColour") != null)
1293 url.append("&colour="
1294 + removeWhiteSpace(viewport.applet
1295 .getParameter("defaultColour")));
1298 if (viewport.applet.getParameter("userDefinedColour") != null)
1300 url.append("&colour="
1301 + removeWhiteSpace(viewport.applet
1302 .getParameter("userDefinedColour")));
1304 if (viewport.applet.getParameter("tree") != null)
1307 + appendProtocol(viewport.applet.getParameter("tree")));
1309 if (viewport.applet.getParameter("treeFile") != null)
1312 + appendProtocol(viewport.applet.getParameter("treeFile")));
1315 showURL(url.toString(), "FULL_APP");
1318 String removeWhiteSpace(String colour)
1320 StringBuffer sb = new StringBuffer();
1321 for (int i = 0; i < colour.length(); i++)
1323 if (Character.isWhitespace(colour.charAt(i)))
1329 sb.append(colour.charAt(i));
1333 return sb.toString();
1336 String appendProtocol(String url)
1341 url = URLEncoder.encode(url);
1344 * When we finally deprecate 1.1 compatibility, we can start to use
1345 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1346 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1347 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1348 * ex.printStackTrace(); }
1350 catch (java.net.MalformedURLException ex)
1352 url = viewport.applet.getCodeBase() + url;
1357 public void closeMenuItem_actionPerformed()
1359 PaintRefresher.RemoveComponent(alignPanel);
1360 if (alignPanel.seqPanel != null
1361 && alignPanel.seqPanel.seqCanvas != null)
1363 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1365 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1367 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1370 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1385 void updateEditMenuBar()
1388 if (viewport.historyList.size() > 0)
1390 undoMenuItem.setEnabled(true);
1391 CommandI command = (CommandI) viewport.historyList.peek();
1392 undoMenuItem.setLabel(MessageManager.formatMessage(
1393 "label.undo_command", new String[]
1394 { command.getDescription() }));
1398 undoMenuItem.setEnabled(false);
1399 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1402 if (viewport.redoList.size() > 0)
1404 redoMenuItem.setEnabled(true);
1406 CommandI command = (CommandI) viewport.redoList.peek();
1407 redoMenuItem.setLabel(MessageManager.formatMessage(
1408 "label.redo_command", new String[]
1409 { command.getDescription() }));
1413 redoMenuItem.setEnabled(false);
1414 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1421 public void addHistoryItem(CommandI command)
1423 if (command.getSize() > 0)
1425 viewport.historyList.push(command);
1426 viewport.redoList.removeAllElements();
1427 updateEditMenuBar();
1428 viewport.updateHiddenColumns();
1433 * TODO: JAL-1104 DOCUMENT ME!
1438 protected void undoMenuItem_actionPerformed()
1440 if (viewport.historyList.size() < 1)
1445 CommandI command = (CommandI) viewport.historyList.pop();
1446 viewport.redoList.push(command);
1447 command.undoCommand(null);
1449 AlignViewport originalSource = getOriginatingSource(command);
1451 if (originalSource != viewport)
1454 .println("Warning: Viewport object mismatch whilst undoing");
1456 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1457 // viewport.getColumnSelection().getHiddenColumns()
1459 updateEditMenuBar();
1460 originalSource.firePropertyChange("alignment", null, originalSource
1461 .getAlignment().getSequences());
1465 * TODO: JAL-1104 DOCUMENT ME!
1470 protected void redoMenuItem_actionPerformed()
1472 if (viewport.redoList.size() < 1)
1477 CommandI command = (CommandI) viewport.redoList.pop();
1478 viewport.historyList.push(command);
1479 command.doCommand(null);
1481 AlignViewport originalSource = getOriginatingSource(command);
1483 if (originalSource != viewport)
1486 .println("Warning: Viewport object mismatch whilst re-doing");
1488 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1489 // viewport.getColumnSelection().getHiddenColumns()
1492 updateEditMenuBar();
1493 originalSource.firePropertyChange("alignment", null, originalSource
1494 .getAlignment().getSequences());
1497 AlignViewport getOriginatingSource(CommandI command)
1499 AlignViewport originalSource = null;
1500 // For sequence removal and addition, we need to fire
1501 // the property change event FROM the viewport where the
1502 // original alignment was altered
1503 AlignmentI al = null;
1504 if (command instanceof EditCommand)
1506 EditCommand editCommand = (EditCommand) command;
1507 al = editCommand.getAlignment();
1508 Vector comps = (Vector) PaintRefresher.components.get(viewport
1509 .getSequenceSetId());
1510 for (int i = 0; i < comps.size(); i++)
1512 if (comps.elementAt(i) instanceof AlignmentPanel)
1514 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1516 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1523 if (originalSource == null)
1525 // The original view is closed, we must validate
1526 // the current view against the closed view first
1529 PaintRefresher.validateSequences(al, viewport.getAlignment());
1532 originalSource = viewport;
1535 return originalSource;
1538 public void moveSelectedSequences(boolean up)
1540 SequenceGroup sg = viewport.getSelectionGroup();
1545 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1546 up ? null : viewport.getHiddenRepSequences(), up);
1547 alignPanel.paintAlignment(true);
1550 synchronized void slideSequences(boolean right, int size)
1552 List<SequenceI> sg = new Vector<SequenceI>();
1553 if (viewport.cursorMode)
1555 sg.add(viewport.getAlignment().getSequenceAt(
1556 alignPanel.seqPanel.seqCanvas.cursorY));
1558 else if (viewport.getSelectionGroup() != null
1559 && viewport.getSelectionGroup().getSize() != viewport
1560 .getAlignment().getHeight())
1562 sg = viewport.getSelectionGroup().getSequences(
1563 viewport.getHiddenRepSequences());
1571 Vector<SequenceI> invertGroup = new Vector();
1573 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1575 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1576 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1579 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1581 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1583 for (int i = 0; i < invertGroup.size(); i++)
1584 seqs2[i] = invertGroup.elementAt(i);
1586 SlideSequencesCommand ssc;
1588 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1589 size, viewport.getGapCharacter());
1591 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1592 size, viewport.getGapCharacter());
1594 int groupAdjustment = 0;
1595 if (ssc.getGapsInsertedBegin() && right)
1597 if (viewport.cursorMode)
1598 alignPanel.seqPanel.moveCursor(size, 0);
1600 groupAdjustment = size;
1602 else if (!ssc.getGapsInsertedBegin() && !right)
1604 if (viewport.cursorMode)
1605 alignPanel.seqPanel.moveCursor(-size, 0);
1607 groupAdjustment = -size;
1610 if (groupAdjustment != 0)
1612 viewport.getSelectionGroup().setStartRes(
1613 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1614 viewport.getSelectionGroup().setEndRes(
1615 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1618 boolean appendHistoryItem = false;
1619 if (viewport.historyList != null && viewport.historyList.size() > 0
1620 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1622 appendHistoryItem = ssc
1623 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1627 if (!appendHistoryItem)
1628 addHistoryItem(ssc);
1633 static StringBuffer copiedSequences;
1635 static Vector copiedHiddenColumns;
1637 protected void copy_actionPerformed()
1639 if (viewport.getSelectionGroup() == null)
1644 SequenceGroup sg = viewport.getSelectionGroup();
1645 copiedSequences = new StringBuffer();
1646 Hashtable orderedSeqs = new Hashtable();
1647 for (int i = 0; i < sg.getSize(); i++)
1649 SequenceI seq = sg.getSequenceAt(i);
1650 int index = viewport.getAlignment().findIndex(seq);
1651 orderedSeqs.put(index + "", seq);
1654 int index = 0, startRes, endRes;
1657 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1659 copiedHiddenColumns = new Vector();
1660 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1661 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1664 int[] region = (int[]) viewport.getColumnSelection()
1665 .getHiddenColumns().elementAt(i);
1667 copiedHiddenColumns.addElement(new int[]
1668 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1673 copiedHiddenColumns = null;
1676 for (int i = 0; i < sg.getSize(); i++)
1678 SequenceI seq = null;
1682 if (orderedSeqs.containsKey(index + ""))
1684 seq = (SequenceI) orderedSeqs.get(index + "");
1696 // Returns residue following index if gap
1697 startRes = seq.findPosition(sg.getStartRes());
1700 // Need to find the residue preceeding index if gap
1703 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1705 ch = seq.getCharAt(j);
1706 if (!jalview.util.Comparison.isGap((ch)))
1714 endRes += seq.getStart() - 1;
1717 copiedSequences.append(seq.getName()
1723 + seq.getSequenceAsString(sg.getStartRes(),
1724 sg.getEndRes() + 1) + "\n");
1729 protected void pasteNew_actionPerformed()
1734 protected void pasteThis_actionPerformed()
1739 void paste(boolean newAlignment)
1744 if (copiedSequences == null)
1749 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1750 Vector seqs = new Vector();
1751 while (st.hasMoreElements())
1753 String name = st.nextToken();
1754 int start = Integer.parseInt(st.nextToken());
1755 int end = Integer.parseInt(st.nextToken());
1756 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1758 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1759 for (int i = 0; i < seqs.size(); i++)
1761 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1766 String newtitle = MessageManager.getString("label.copied_sequences");
1767 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1769 newtitle = getTitle();
1773 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1775 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1776 viewport.applet, newtitle, false);
1777 if (copiedHiddenColumns != null)
1779 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1781 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1782 af.viewport.hideColumns(region[0], region[1]);
1786 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1791 addSequences(newSeqs);
1794 } catch (Exception ex)
1796 } // could be anything being pasted in here
1800 void addSequences(SequenceI[] seqs)
1802 for (int i = 0; i < seqs.length; i++)
1804 viewport.getAlignment().addSequence(seqs[i]);
1808 addHistoryItem(new EditCommand(MessageManager.getString("label.add_sequences"), EditCommand.PASTE,
1809 seqs, 0, viewport.getAlignment().getWidth(),
1810 viewport.getAlignment()));
1812 viewport.setEndSeq(viewport.getAlignment().getHeight());
1813 viewport.getAlignment().getWidth();
1814 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1819 protected void cut_actionPerformed()
1821 copy_actionPerformed();
1822 delete_actionPerformed();
1825 protected void delete_actionPerformed()
1828 SequenceGroup sg = viewport.getSelectionGroup();
1834 Vector seqs = new Vector();
1836 for (int i = 0; i < sg.getSize(); i++)
1838 seq = sg.getSequenceAt(i);
1839 seqs.addElement(seq);
1842 // If the cut affects all sequences, remove highlighted columns
1843 if (sg.getSize() == viewport.getAlignment().getHeight())
1845 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1846 sg.getEndRes() + 1);
1849 SequenceI[] cut = new SequenceI[seqs.size()];
1850 for (int i = 0; i < seqs.size(); i++)
1852 cut[i] = (SequenceI) seqs.elementAt(i);
1856 * //ADD HISTORY ITEM
1858 addHistoryItem(new EditCommand(MessageManager.getString("label.cut_sequences"), EditCommand.CUT, cut,
1859 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1860 viewport.getAlignment()));
1862 viewport.setSelectionGroup(null);
1863 viewport.getAlignment().deleteGroup(sg);
1865 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1868 if (viewport.getAlignment().getHeight() < 1)
1870 this.setVisible(false);
1872 viewport.sendSelection();
1876 * group consensus toggled
1879 protected void showGroupConsensus_actionPerformed()
1881 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1882 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1887 * group conservation toggled.
1889 protected void showGroupConservation_actionPerformed()
1891 viewport.setShowGroupConservation(showGroupConservation.getState());
1892 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1899 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1900 * .event.ActionEvent)
1902 protected void showConsensusHistogram_actionPerformed()
1904 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1905 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1912 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1913 * .event.ActionEvent)
1915 protected void showSequenceLogo_actionPerformed()
1917 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1918 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1921 protected void normSequenceLogo_actionPerformed()
1923 showSequenceLogo.setState(true);
1924 viewport.setShowSequenceLogo(true);
1925 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1926 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1929 protected void applyAutoAnnotationSettings_actionPerformed()
1931 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1934 protected void makeGrpsFromSelection_actionPerformed()
1936 if (avc.makeGroupsFromSelection())
1938 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1939 alignPanel.updateAnnotation();
1940 alignPanel.paintAlignment(true);
1944 protected void createGroup_actionPerformed()
1949 protected void unGroup_actionPerformed()
1953 alignPanel.alignmentChanged();
1957 protected void deleteGroups_actionPerformed()
1959 if (avc.deleteGroups())
1961 alignPanel.alignmentChanged();
1965 public void selectAllSequenceMenuItem_actionPerformed()
1967 SequenceGroup sg = new SequenceGroup();
1968 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1970 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1972 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1973 viewport.setSelectionGroup(sg);
1974 alignPanel.paintAlignment(true);
1975 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1976 viewport.sendSelection();
1979 public void deselectAllSequenceMenuItem_actionPerformed()
1981 if (viewport.cursorMode)
1983 alignPanel.seqPanel.keyboardNo1 = null;
1984 alignPanel.seqPanel.keyboardNo2 = null;
1986 viewport.setSelectionGroup(null);
1987 viewport.getColumnSelection().clear();
1988 viewport.setSelectionGroup(null);
1989 alignPanel.idPanel.idCanvas.searchResults = null;
1990 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1991 alignPanel.paintAlignment(true);
1992 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1993 viewport.sendSelection();
1996 public void invertSequenceMenuItem_actionPerformed()
1998 SequenceGroup sg = viewport.getSelectionGroup();
1999 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2001 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2004 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2005 viewport.sendSelection();
2008 public void invertColSel_actionPerformed()
2010 viewport.invertColumnSelection();
2011 alignPanel.paintAlignment(true);
2012 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2013 viewport.sendSelection();
2016 void trimAlignment(boolean trimLeft)
2018 ColumnSelection colSel = viewport.getColumnSelection();
2021 if (colSel.size() > 0)
2025 column = colSel.getMin();
2029 column = colSel.getMax();
2033 if (viewport.getSelectionGroup() != null)
2035 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2036 viewport.getHiddenRepSequences());
2040 seqs = viewport.getAlignment().getSequencesArray();
2043 TrimRegionCommand trimRegion;
2046 trimRegion = new TrimRegionCommand("Remove Left",
2047 TrimRegionCommand.TRIM_LEFT, seqs, column,
2048 viewport.getAlignment(), viewport.getColumnSelection(),
2049 viewport.getSelectionGroup());
2050 viewport.setStartRes(0);
2054 trimRegion = new TrimRegionCommand("Remove Right",
2055 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2056 viewport.getAlignment(), viewport.getColumnSelection(),
2057 viewport.getSelectionGroup());
2060 statusBar.setText(MessageManager.formatMessage(
2061 "label.removed_columns", new String[]
2062 { Integer.valueOf(trimRegion.getSize()).toString() }));
2063 addHistoryItem(trimRegion);
2065 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2067 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2068 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2070 viewport.getAlignment().deleteGroup(sg);
2074 viewport.firePropertyChange("alignment", null, viewport
2075 .getAlignment().getSequences());
2079 public void removeGappedColumnMenuItem_actionPerformed()
2081 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2084 if (viewport.getSelectionGroup() != null)
2086 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2087 viewport.getHiddenRepSequences());
2088 start = viewport.getSelectionGroup().getStartRes();
2089 end = viewport.getSelectionGroup().getEndRes();
2093 seqs = viewport.getAlignment().getSequencesArray();
2096 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2097 "Remove Gapped Columns", seqs, start, end,
2098 viewport.getAlignment());
2100 addHistoryItem(removeGapCols);
2102 statusBar.setText(MessageManager.formatMessage(
2103 "label.removed_empty_columns", new String[]
2104 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2106 // This is to maintain viewport position on first residue
2107 // of first sequence
2108 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2109 int startRes = seq.findPosition(viewport.startRes);
2110 // ShiftList shifts;
2111 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2112 // edit.alColumnChanges=shifts.getInverse();
2113 // if (viewport.hasHiddenColumns)
2114 // viewport.getColumnSelection().compensateForEdits(shifts);
2115 viewport.setStartRes(seq.findIndex(startRes) - 1);
2116 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2121 public void removeAllGapsMenuItem_actionPerformed()
2123 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2126 if (viewport.getSelectionGroup() != null)
2128 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2129 viewport.getHiddenRepSequences());
2130 start = viewport.getSelectionGroup().getStartRes();
2131 end = viewport.getSelectionGroup().getEndRes();
2135 seqs = viewport.getAlignment().getSequencesArray();
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);
2143 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2144 viewport.getAlignment()));
2146 viewport.setStartRes(seq.findIndex(startRes) - 1);
2148 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2153 public void findMenuItem_actionPerformed()
2155 new Finder(alignPanel);
2159 * create a new view derived from the current view
2162 * @return frame for the new view
2164 public AlignFrame newView(String viewtitle)
2167 if (viewport.hasHiddenRows())
2169 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2170 .getFullAlignment().getSequencesArray());
2174 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2177 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2179 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2181 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2183 newal.addAnnotation(viewport.getAlignment()
2184 .getAlignmentAnnotation()[i]);
2189 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2191 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2192 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2193 PaintRefresher.Register(newaf.alignPanel,
2194 newaf.alignPanel.av.getSequenceSetId());
2196 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2197 newaf.alignPanel.av.getSequenceSetId());
2198 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2199 newaf.alignPanel.av.getSequenceSetId());
2201 Vector comps = (Vector) PaintRefresher.components.get(viewport
2202 .getSequenceSetId());
2204 for (int i = 0; i < comps.size(); i++)
2206 if (comps.elementAt(i) instanceof AlignmentPanel)
2212 String title = new String(this.getTitle());
2213 if (viewtitle != null)
2215 title = viewtitle + " ( " + title + ")";
2219 if (title.indexOf("(View") > -1)
2221 title = title.substring(0, title.indexOf("(View"));
2223 title += "(View " + viewSize + ")";
2226 newaf.setTitle(title.toString());
2228 newaf.viewport.historyList = viewport.historyList;
2229 newaf.viewport.redoList = viewport.redoList;
2235 * @return list of feature groups on the view
2237 public String[] getFeatureGroups()
2239 FeatureRenderer fr = null;
2240 if (alignPanel != null
2241 && (fr = alignPanel.getFeatureRenderer()) != null)
2243 return fr.getGroups();
2249 * get sequence feature groups that are hidden or shown
2255 public String[] getFeatureGroupsOfState(boolean visible)
2257 FeatureRenderer fr = null;
2258 if (alignPanel != null
2259 && (fr = alignPanel.getFeatureRenderer()) != null)
2261 return fr.getGroups(visible);
2267 * Change the display state for the given feature groups
2270 * list of group strings
2272 * visible or invisible
2274 public void setFeatureGroupState(String[] groups, boolean state)
2276 FeatureRenderer fr = null;
2277 this.sequenceFeatures.setState(true);
2278 viewport.showSequenceFeatures(true);
2279 if (alignPanel != null
2280 && (fr = alignPanel.getFeatureRenderer()) != null)
2282 fr.setGroupState(groups, state);
2283 alignPanel.seqPanel.seqCanvas.repaint();
2284 if (alignPanel.overviewPanel != null)
2286 alignPanel.overviewPanel.updateOverviewImage();
2291 public void seqLimits_itemStateChanged()
2293 viewport.setShowJVSuffix(seqLimits.getState());
2294 alignPanel.fontChanged();
2295 alignPanel.paintAlignment(true);
2298 protected void colourTextMenuItem_actionPerformed()
2300 viewport.setColourText(colourTextMenuItem.getState());
2301 alignPanel.paintAlignment(true);
2304 protected void displayNonconservedMenuItem_actionPerformed()
2306 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2307 alignPanel.paintAlignment(true);
2310 protected void wrapMenuItem_actionPerformed()
2312 viewport.setWrapAlignment(wrapMenuItem.getState());
2313 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2314 scaleAbove.setEnabled(wrapMenuItem.getState());
2315 scaleLeft.setEnabled(wrapMenuItem.getState());
2316 scaleRight.setEnabled(wrapMenuItem.getState());
2317 alignPanel.paintAlignment(true);
2320 public void overviewMenuItem_actionPerformed()
2322 if (alignPanel.overviewPanel != null)
2327 Frame frame = new Frame();
2328 OverviewPanel overview = new OverviewPanel(alignPanel);
2329 frame.add(overview);
2330 // +50 must allow for applet frame window
2331 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2332 "label.overview_params", new String[]
2333 { this.getTitle() }), overview.getPreferredSize().width,
2334 overview.getPreferredSize().height + 50);
2337 final AlignmentPanel ap = alignPanel;
2338 frame.addWindowListener(new WindowAdapter()
2341 public void windowClosing(WindowEvent e)
2345 ap.setOverviewPanel(null);
2350 alignPanel.setOverviewPanel(overview);
2354 void changeColour(ColourSchemeI cs)
2360 if (viewport.getAbovePIDThreshold())
2362 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2366 if (viewport.getConservationSelected())
2368 cs.setConservationApplied(true);
2369 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2374 cs.setConservationApplied(false);
2377 viewport.setGlobalColourScheme(cs);
2379 if (alignPanel.getOverviewPanel() != null)
2381 alignPanel.getOverviewPanel().updateOverviewImage();
2384 jalview.structure.StructureSelectionManager
2385 .getStructureSelectionManager(viewport.applet)
2386 .sequenceColoursChanged(alignPanel);
2388 alignPanel.paintAlignment(true);
2391 protected void modifyPID_actionPerformed()
2393 if (viewport.getAbovePIDThreshold()
2394 && viewport.getGlobalColourScheme() != null)
2396 SliderPanel.setPIDSliderSource(alignPanel,
2397 viewport.getGlobalColourScheme(), "Background");
2398 SliderPanel.showPIDSlider();
2402 protected void modifyConservation_actionPerformed()
2404 if (viewport.getConservationSelected()
2405 && viewport.getGlobalColourScheme() != null)
2407 SliderPanel.setConservationSlider(alignPanel,
2408 viewport.getGlobalColourScheme(), "Background");
2409 SliderPanel.showConservationSlider();
2413 protected void conservationMenuItem_actionPerformed()
2415 viewport.setConservationSelected(conservationMenuItem.getState());
2417 viewport.setAbovePIDThreshold(false);
2418 abovePIDThreshold.setState(false);
2420 changeColour(viewport.getGlobalColourScheme());
2422 modifyConservation_actionPerformed();
2425 public void abovePIDThreshold_actionPerformed()
2427 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2429 conservationMenuItem.setState(false);
2430 viewport.setConservationSelected(false);
2432 changeColour(viewport.getGlobalColourScheme());
2434 modifyPID_actionPerformed();
2437 public void sortPairwiseMenuItem_actionPerformed()
2439 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2440 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2441 .getAlignment().getSequenceAt(0), null);
2443 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2444 viewport.getAlignment()));
2445 alignPanel.paintAlignment(true);
2448 public void sortIDMenuItem_actionPerformed()
2450 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2451 AlignmentSorter.sortByID(viewport.getAlignment());
2452 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2453 viewport.getAlignment()));
2454 alignPanel.paintAlignment(true);
2457 public void sortLengthMenuItem_actionPerformed()
2459 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2460 AlignmentSorter.sortByLength(viewport.getAlignment());
2461 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2462 viewport.getAlignment()));
2463 alignPanel.paintAlignment(true);
2466 public void sortGroupMenuItem_actionPerformed()
2468 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2469 AlignmentSorter.sortByGroup(viewport.getAlignment());
2470 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2471 viewport.getAlignment()));
2472 alignPanel.paintAlignment(true);
2476 public void removeRedundancyMenuItem_actionPerformed()
2478 new RedundancyPanel(alignPanel);
2481 public void pairwiseAlignmentMenuItem_actionPerformed()
2483 if (viewport.getSelectionGroup() != null
2484 && viewport.getSelectionGroup().getSize() > 1)
2486 Frame frame = new Frame();
2487 frame.add(new PairwiseAlignPanel(alignPanel));
2488 jalview.bin.JalviewLite.addFrame(frame,
2489 MessageManager.getString("action.pairwise_alignment"), 600,
2494 public void PCAMenuItem_actionPerformed()
2496 // are the sequences aligned?
2497 if (!viewport.getAlignment().isAligned(false))
2500 int Width = viewport.getAlignment().getWidth();
2502 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2504 current = viewport.getAlignment().getSequenceAt(i);
2506 if (current.getLength() < Width)
2508 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2511 alignPanel.paintAlignment(true);
2514 if ((viewport.getSelectionGroup() != null
2515 && viewport.getSelectionGroup().getSize() < 4 && viewport
2516 .getSelectionGroup().getSize() > 0)
2517 || viewport.getAlignment().getHeight() < 4)
2524 new PCAPanel(viewport);
2525 } catch (java.lang.OutOfMemoryError ex)
2531 public void averageDistanceTreeMenuItem_actionPerformed()
2533 NewTreePanel("AV", "PID", "Average distance tree using PID");
2536 public void neighbourTreeMenuItem_actionPerformed()
2538 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2541 protected void njTreeBlosumMenuItem_actionPerformed()
2543 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2546 protected void avTreeBlosumMenuItem_actionPerformed()
2548 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2551 void NewTreePanel(String type, String pwType, String title)
2553 // are the sequences aligned?
2554 if (!viewport.getAlignment().isAligned(false))
2557 int Width = viewport.getAlignment().getWidth();
2559 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2561 current = viewport.getAlignment().getSequenceAt(i);
2563 if (current.getLength() < Width)
2565 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2568 alignPanel.paintAlignment(true);
2572 if ((viewport.getSelectionGroup() != null && viewport
2573 .getSelectionGroup().getSize() > 1)
2574 || (viewport.getAlignment().getHeight() > 1))
2576 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2578 addTreeMenuItem(tp, title);
2580 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2584 void loadTree_actionPerformed()
2586 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2587 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2588 cap.setTreeImport();
2589 Frame frame = new Frame();
2591 jalview.bin.JalviewLite.addFrame(frame,
2592 MessageManager.getString("label.paste_newick_file"), 400, 300);
2595 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2597 TreePanel tp = new TreePanel(alignPanel, treeFile,
2598 MessageManager.getString("label.load_tree_from_file"), tree);
2599 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2600 addTreeMenuItem(tp, treeFile);
2604 * sort the alignment using the given treePanel
2607 * tree used to sort view
2609 * string used for undo event name
2611 public void sortByTree(TreePanel treePanel, String title)
2613 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2615 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2616 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2617 // HistoryItem.SORT));
2618 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2619 "label.order_by_params", new String[]
2620 { title }), oldOrder, viewport.getAlignment()));
2621 alignPanel.paintAlignment(true);
2625 * Do any automatic reordering of the alignment and add the necessary bits to
2626 * the menu structure for the new tree
2631 protected void addTreeMenuItem(final TreePanel treePanel,
2634 final MenuItem item = new MenuItem(title);
2635 sortByTreeMenu.add(item);
2636 item.addActionListener(new java.awt.event.ActionListener()
2639 public void actionPerformed(ActionEvent evt)
2641 sortByTree(treePanel, title); // treePanel.getTitle());
2645 treePanel.addWindowListener(new WindowAdapter()
2648 public void windowOpened(WindowEvent e)
2650 if (viewport.sortByTree)
2652 sortByTree(treePanel, title);
2654 super.windowOpened(e);
2658 public void windowClosing(WindowEvent e)
2660 sortByTreeMenu.remove(item);
2665 public boolean sortBy(AlignmentOrder alorder, String undoname)
2667 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2668 if (viewport.applet.debug)
2670 System.err.println("Sorting " + alorder.getOrder().size()
2671 + " in alignment '" + getTitle() + "'");
2673 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2674 if (undoname != null)
2676 addHistoryItem(new OrderCommand(undoname, oldOrder,
2677 viewport.getAlignment()));
2679 alignPanel.paintAlignment(true);
2683 protected void documentation_actionPerformed()
2685 alignPanel.av.applet.openJalviewHelpUrl();
2688 protected void about_actionPerformed()
2691 class AboutPanel extends Canvas
2697 public AboutPanel(String version, String builddate)
2699 this.version = version;
2700 this.builddate = builddate;
2704 public void paint(Graphics g)
2706 g.setColor(Color.white);
2707 g.fillRect(0, 0, getSize().width, getSize().height);
2708 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2709 FontMetrics fm = g.getFontMetrics();
2710 int fh = fm.getHeight();
2712 g.setColor(Color.black);
2713 // TODO: update this text for each release or centrally store it for
2714 // lite and application
2715 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2716 g.drawString(MessageManager.formatMessage(
2717 "label.jalviewLite_release", new String[]
2718 { version }), x, y += fh);
2719 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2720 g.drawString(MessageManager.formatMessage(
2721 "label.jaview_build_date", new String[]
2722 { builddate }), x, y += fh);
2723 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2724 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2726 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2727 x + 50, y += fh + 8);
2729 MessageManager.getString("label.jalview_dev_managers"), x,
2731 g.drawString(MessageManager
2732 .getString("label.jalview_distribution_lists"), x, y += fh);
2733 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2736 MessageManager.getString("label.jalview_cite_1_authors"),
2739 MessageManager.getString("label.jalview_cite_1_title"), x,
2741 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2746 Frame frame = new Frame();
2747 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2749 jalview.bin.JalviewLite.addFrame(frame,
2750 MessageManager.getString("label.jalview"), 580, 220);
2754 public void showURL(String url, String target)
2756 if (viewport.applet == null)
2758 System.out.println("Not running as applet - no browser available.");
2762 viewport.applet.showURL(url, target);
2766 // ////////////////////////////////////////////////////////////////////////////////
2767 // JBuilder Graphics here
2769 MenuBar alignFrameMenuBar = new MenuBar();
2771 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2773 MenuItem loadApplication = new MenuItem(
2774 MessageManager.getString("label.view_full_application"));
2776 MenuItem loadTree = new MenuItem(
2777 MessageManager.getString("label.load_associated_tree"));
2779 MenuItem loadAnnotations = new MenuItem(
2780 MessageManager.getString("label.load_features_annotations"));
2782 MenuItem outputFeatures = new MenuItem(
2783 MessageManager.getString("label.export_features").concat("..."));
2785 MenuItem outputAnnotations = new MenuItem(
2786 MessageManager.getString("label.export_annotations").concat("..."));
2788 MenuItem closeMenuItem = new MenuItem(
2789 MessageManager.getString("action.close"));
2791 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2793 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2795 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2797 Menu calculateMenu = new Menu(
2798 MessageManager.getString("action.calculate"));
2800 MenuItem selectAllSequenceMenuItem = new MenuItem(
2801 MessageManager.getString("action.select_all"));
2803 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2804 MessageManager.getString("action.deselect_all"));
2806 MenuItem invertSequenceMenuItem = new MenuItem(
2807 MessageManager.getString("action.invert_selection"));
2809 MenuItem remove2LeftMenuItem = new MenuItem();
2811 MenuItem remove2RightMenuItem = new MenuItem();
2813 MenuItem removeGappedColumnMenuItem = new MenuItem();
2815 MenuItem removeAllGapsMenuItem = new MenuItem();
2817 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2819 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2821 MenuItem sortPairwiseMenuItem = new MenuItem();
2823 MenuItem sortIDMenuItem = new MenuItem();
2825 MenuItem sortLengthMenuItem = new MenuItem();
2827 MenuItem sortGroupMenuItem = new MenuItem();
2829 MenuItem removeRedundancyMenuItem = new MenuItem();
2831 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2833 MenuItem PCAMenuItem = new MenuItem();
2835 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2837 MenuItem neighbourTreeMenuItem = new MenuItem();
2839 BorderLayout borderLayout1 = new BorderLayout();
2841 public Label statusBar = new Label();
2843 Menu outputTextboxMenu = new Menu();
2845 MenuItem clustalColour = new MenuItem();
2847 MenuItem zappoColour = new MenuItem();
2849 MenuItem taylorColour = new MenuItem();
2851 MenuItem hydrophobicityColour = new MenuItem();
2853 MenuItem helixColour = new MenuItem();
2855 MenuItem strandColour = new MenuItem();
2857 MenuItem turnColour = new MenuItem();
2859 MenuItem buriedColour = new MenuItem();
2861 MenuItem purinePyrimidineColour = new MenuItem();
2863 MenuItem RNAInteractionColour = new MenuItem();
2865 MenuItem RNAHelixColour = new MenuItem();
2867 MenuItem userDefinedColour = new MenuItem();
2869 MenuItem PIDColour = new MenuItem();
2871 MenuItem BLOSUM62Colour = new MenuItem();
2873 MenuItem tcoffeeColour = new MenuItem();
2875 MenuItem njTreeBlosumMenuItem = new MenuItem();
2877 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2879 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2881 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2883 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2885 MenuItem alProperties = new MenuItem(
2886 MessageManager.getString("label.alignment_props"));
2888 MenuItem overviewMenuItem = new MenuItem();
2890 MenuItem undoMenuItem = new MenuItem();
2892 MenuItem redoMenuItem = new MenuItem();
2894 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2896 MenuItem noColourmenuItem = new MenuItem();
2898 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2900 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2902 MenuItem findMenuItem = new MenuItem();
2904 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2906 MenuItem nucleotideColour = new MenuItem();
2908 MenuItem deleteGroups = new MenuItem();
2910 MenuItem grpsFromSelection = new MenuItem();
2912 MenuItem createGroup = new MenuItem();
2914 MenuItem unGroup = new MenuItem();
2916 MenuItem delete = new MenuItem();
2918 MenuItem copy = new MenuItem();
2920 MenuItem cut = new MenuItem();
2922 Menu pasteMenu = new Menu();
2924 MenuItem pasteNew = new MenuItem();
2926 MenuItem pasteThis = new MenuItem();
2928 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2930 MenuItem font = new MenuItem();
2932 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2934 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2936 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2938 MenuItem modifyPID = new MenuItem();
2940 MenuItem modifyConservation = new MenuItem();
2942 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2943 "Autocalculate Consensus", true);
2945 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2946 "Sort Alignment With New Tree", true);
2948 Menu sortByTreeMenu = new Menu();
2950 Menu sort = new Menu();
2952 Menu calculate = new Menu();
2954 MenuItem inputText = new MenuItem();
2956 Menu helpMenu = new Menu();
2958 MenuItem documentation = new MenuItem();
2960 MenuItem about = new MenuItem();
2962 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2964 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2966 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2968 Menu autoAnnMenu = new Menu();
2970 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2972 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2974 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2976 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2978 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2980 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2982 private void jbInit() throws Exception
2985 setMenuBar(alignFrameMenuBar);
2989 // dynamically fill save as menu with available formats
2990 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2993 item = new MenuItem(
2994 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2996 item.addActionListener(new java.awt.event.ActionListener()
2999 public void actionPerformed(ActionEvent e)
3001 outputText_actionPerformed(e);
3005 outputTextboxMenu.add(item);
3007 closeMenuItem.addActionListener(this);
3008 loadApplication.addActionListener(this);
3010 loadTree.addActionListener(this);
3011 loadAnnotations.addActionListener(this);
3012 outputFeatures.addActionListener(this);
3013 outputAnnotations.addActionListener(this);
3014 selectAllSequenceMenuItem.addActionListener(this);
3015 deselectAllSequenceMenuItem.addActionListener(this);
3016 invertSequenceMenuItem.addActionListener(this);
3017 remove2LeftMenuItem.setLabel(MessageManager
3018 .getString("action.remove_left"));
3019 remove2LeftMenuItem.addActionListener(this);
3020 remove2RightMenuItem.setLabel(MessageManager
3021 .getString("action.remove_right"));
3022 remove2RightMenuItem.addActionListener(this);
3023 removeGappedColumnMenuItem.setLabel(MessageManager
3024 .getString("action.remove_empty_columns"));
3025 removeGappedColumnMenuItem.addActionListener(this);
3026 removeAllGapsMenuItem.setLabel(MessageManager
3027 .getString("action.remove_all_gaps"));
3028 removeAllGapsMenuItem.addActionListener(this);
3029 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3030 viewBoxesMenuItem.setState(true);
3031 viewBoxesMenuItem.addItemListener(this);
3032 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3033 viewTextMenuItem.setState(true);
3034 viewTextMenuItem.addItemListener(this);
3035 sortPairwiseMenuItem.setLabel(MessageManager
3036 .getString("action.by_pairwise_id"));
3037 sortPairwiseMenuItem.addActionListener(this);
3038 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3039 sortIDMenuItem.addActionListener(this);
3040 sortLengthMenuItem.setLabel(MessageManager
3041 .getString("action.by_length"));
3042 sortLengthMenuItem.addActionListener(this);
3043 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3044 sortGroupMenuItem.addActionListener(this);
3045 removeRedundancyMenuItem.setLabel(MessageManager
3046 .getString("action.remove_redundancy").concat("..."));
3047 removeRedundancyMenuItem.addActionListener(this);
3048 pairwiseAlignmentMenuItem.setLabel(MessageManager
3049 .getString("action.pairwise_alignment"));
3050 pairwiseAlignmentMenuItem.addActionListener(this);
3051 PCAMenuItem.setLabel(MessageManager
3052 .getString("label.principal_component_analysis"));
3053 PCAMenuItem.addActionListener(this);
3054 averageDistanceTreeMenuItem.setLabel(MessageManager
3055 .getString("label.average_distance_identity"));
3056 averageDistanceTreeMenuItem.addActionListener(this);
3057 neighbourTreeMenuItem.setLabel(MessageManager
3058 .getString("label.neighbour_joining_identity"));
3059 neighbourTreeMenuItem.addActionListener(this);
3060 statusBar.setBackground(Color.white);
3061 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3062 statusBar.setText(MessageManager.getString("label.status_bar"));
3063 outputTextboxMenu.setLabel(MessageManager
3064 .getString("label.out_to_textbox"));
3065 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3067 clustalColour.addActionListener(this);
3068 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3069 zappoColour.addActionListener(this);
3070 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3071 taylorColour.addActionListener(this);
3072 hydrophobicityColour.setLabel(MessageManager
3073 .getString("label.hydrophobicity"));
3074 hydrophobicityColour.addActionListener(this);
3076 .setLabel(MessageManager.getString("label.helix_propensity"));
3077 helixColour.addActionListener(this);
3078 strandColour.setLabel(MessageManager
3079 .getString("label.strand_propensity"));
3080 strandColour.addActionListener(this);
3081 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3082 turnColour.addActionListener(this);
3083 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3084 buriedColour.addActionListener(this);
3085 purinePyrimidineColour.setLabel(MessageManager
3086 .getString("label.purine_pyrimidine"));
3087 purinePyrimidineColour.addActionListener(this);
3088 RNAInteractionColour.setLabel(MessageManager
3089 .getString("label.rna_interaction"));
3090 RNAInteractionColour.addActionListener(this);
3091 RNAHelixColour.setLabel(MessageManager
3092 .getString("action.by_rna_helixes"));
3093 RNAHelixColour.addActionListener(this);
3094 userDefinedColour.setLabel(MessageManager
3095 .getString("action.user_defined"));
3096 userDefinedColour.addActionListener(this);
3097 PIDColour.setLabel(MessageManager
3098 .getString("label.percentage_identity"));
3099 PIDColour.addActionListener(this);
3100 BLOSUM62Colour.setLabel(MessageManager
3101 .getString("label.blosum62_score"));
3102 BLOSUM62Colour.addActionListener(this);
3104 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3105 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3107 tcoffeeColour.addActionListener(this);
3108 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3109 .getString("label.average_distance_bloslum62"));
3110 avDistanceTreeBlosumMenuItem.addActionListener(this);
3111 njTreeBlosumMenuItem.setLabel(MessageManager
3112 .getString("label.neighbour_blosum62"));
3113 njTreeBlosumMenuItem.addActionListener(this);
3114 annotationPanelMenuItem.setLabel(MessageManager
3115 .getString("label.show_annotations"));
3116 annotationPanelMenuItem.addItemListener(this);
3117 colourTextMenuItem.setLabel(MessageManager
3118 .getString("label.colour_text"));
3119 colourTextMenuItem.addItemListener(this);
3120 displayNonconservedMenuItem.setLabel(MessageManager
3121 .getString("label.show_non_conversed"));
3122 displayNonconservedMenuItem.addItemListener(this);
3123 alProperties.addActionListener(this);
3124 overviewMenuItem.setLabel(MessageManager
3125 .getString("label.overview_window"));
3126 overviewMenuItem.addActionListener(this);
3127 undoMenuItem.setEnabled(false);
3128 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3129 undoMenuItem.addActionListener(this);
3130 redoMenuItem.setEnabled(false);
3131 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3132 redoMenuItem.addActionListener(this);
3133 conservationMenuItem.setLabel(MessageManager
3134 .getString("action.by_conservation"));
3135 conservationMenuItem.addItemListener(this);
3136 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3137 noColourmenuItem.addActionListener(this);
3138 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3139 wrapMenuItem.addItemListener(this);
3140 renderGapsMenuItem.setLabel(MessageManager
3141 .getString("action.show_gaps"));
3142 renderGapsMenuItem.setState(true);
3143 renderGapsMenuItem.addItemListener(this);
3144 findMenuItem.setLabel(MessageManager.getString("action.find"));
3145 findMenuItem.addActionListener(this);
3146 abovePIDThreshold.setLabel(MessageManager
3147 .getString("label.above_identity_threshold"));
3148 abovePIDThreshold.addItemListener(this);
3149 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3150 nucleotideColour.addActionListener(this);
3151 deleteGroups.setLabel(MessageManager
3152 .getString("action.undefine_groups"));
3153 deleteGroups.addActionListener(this);
3154 grpsFromSelection.setLabel(MessageManager
3155 .getString("action.make_groups_selection"));
3156 grpsFromSelection.addActionListener(this);
3157 createGroup.setLabel(MessageManager.getString("action.create_group"));
3158 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3159 copy.setLabel(MessageManager.getString("action.copy"));
3160 copy.addActionListener(this);
3161 cut.setLabel(MessageManager.getString("action.cut"));
3162 cut.addActionListener(this);
3163 delete.setLabel(MessageManager.getString("action.delete"));
3164 delete.addActionListener(this);
3165 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3166 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3167 pasteNew.addActionListener(this);
3168 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3169 pasteThis.addActionListener(this);
3170 applyToAllGroups.setLabel(MessageManager
3171 .getString("label.apply_colour_to_all_groups"));
3172 applyToAllGroups.setState(true);
3173 applyToAllGroups.addItemListener(this);
3174 font.setLabel(MessageManager.getString("action.font"));
3175 font.addActionListener(this);
3176 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3177 scaleAbove.setState(true);
3178 scaleAbove.setEnabled(false);
3179 scaleAbove.addItemListener(this);
3180 scaleLeft.setEnabled(false);
3181 scaleLeft.setState(true);
3182 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3183 scaleLeft.addItemListener(this);
3184 scaleRight.setEnabled(false);
3185 scaleRight.setState(true);
3186 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3187 scaleRight.addItemListener(this);
3188 modifyPID.setLabel(MessageManager
3189 .getString("label.modify_identity_thereshold"));
3190 modifyPID.addActionListener(this);
3191 modifyConservation.setLabel(MessageManager
3192 .getString("label.modify_conservation_thereshold"));
3193 modifyConservation.addActionListener(this);
3194 sortByTreeMenu.setLabel(MessageManager
3195 .getString("action.by_tree_order"));
3196 sort.setLabel(MessageManager.getString("action.sort"));
3197 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3198 autoCalculate.addItemListener(this);
3199 sortByTree.addItemListener(this);
3201 .setLabel(MessageManager.getString("label.input_from_textbox"));
3202 inputText.addActionListener(this);
3203 centreColumnLabelFlag.setLabel(MessageManager
3204 .getString("label.centre_column_labels"));
3205 centreColumnLabelFlag.addItemListener(this);
3206 followMouseOverFlag.setLabel(MessageManager
3207 .getString("label.automatic_scrolling"));
3208 followMouseOverFlag.addItemListener(this);
3209 helpMenu.setLabel(MessageManager.getString("action.help"));
3210 documentation.setLabel(MessageManager.getString("label.documentation"));
3211 documentation.addActionListener(this);
3213 about.setLabel(MessageManager.getString("label.about"));
3214 about.addActionListener(this);
3215 seqLimits.setState(true);
3216 seqLimits.setLabel(MessageManager
3217 .getString("label.show_sequence_limits"));
3218 seqLimits.addItemListener(this);
3219 featureSettings.setLabel(MessageManager
3220 .getString("label.feature_settings"));
3221 featureSettings.addActionListener(this);
3222 sequenceFeatures.setLabel(MessageManager
3223 .getString("label.sequence_features"));
3224 sequenceFeatures.addItemListener(this);
3225 sequenceFeatures.setState(false);
3226 annotationColour.setLabel(MessageManager
3227 .getString("action.by_annotation"));
3228 annotationColour.addActionListener(this);
3229 invertSequenceMenuItem.setLabel(MessageManager
3230 .getString("action.invert_sequence_selection"));
3231 invertColSel.setLabel(MessageManager
3232 .getString("action.invert_column_selection"));
3233 menu1.setLabel(MessageManager.getString("action.show"));
3234 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3235 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3236 menu2.setLabel(MessageManager.getString("action.hide"));
3238 .setLabel(MessageManager.getString("label.selected_columns"));
3239 hideSequences.setLabel(MessageManager
3240 .getString("label.selected_sequences"));
3241 hideAllButSelection.setLabel(MessageManager
3242 .getString("label.all_but_selected_region"));
3243 hideAllSelection.setLabel(MessageManager
3244 .getString("label.selected_region"));
3245 showAllHidden.setLabel(MessageManager
3246 .getString("label.all_sequences_columns"));
3247 showGroupConsensus.setLabel(MessageManager
3248 .getString("label.group_consensus"));
3249 showGroupConservation.setLabel(MessageManager
3250 .getString("label.group_conservation"));
3251 showConsensusHistogram.setLabel(MessageManager
3252 .getString("label.show_consensus_histogram"));
3253 showSequenceLogo.setLabel(MessageManager
3254 .getString("label.show_consensus_logo"));
3255 normSequenceLogo.setLabel(MessageManager
3256 .getString("label.norm_consensus_logo"));
3257 applyAutoAnnotationSettings.setLabel(MessageManager
3258 .getString("label.apply_all_groups"));
3259 applyAutoAnnotationSettings.setState(true);
3260 autoAnnMenu.setLabel(MessageManager
3261 .getString("label.autocalculated_annotation"));
3263 invertColSel.addActionListener(this);
3264 showColumns.addActionListener(this);
3265 showSeqs.addActionListener(this);
3266 hideColumns.addActionListener(this);
3267 hideSequences.addActionListener(this);
3268 hideAllButSelection.addActionListener(this);
3269 hideAllSelection.addActionListener(this);
3270 showAllHidden.addActionListener(this);
3271 showGroupConsensus.addItemListener(this);
3272 showGroupConservation.addItemListener(this);
3273 showConsensusHistogram.addItemListener(this);
3274 showSequenceLogo.addItemListener(this);
3275 normSequenceLogo.addItemListener(this);
3277 applyAutoAnnotationSettings.addItemListener(this);
3278 formatMenu.setLabel(MessageManager.getString("action.format"));
3279 selectMenu.setLabel(MessageManager.getString("action.select"));
3280 newView.setLabel(MessageManager.getString("action.new_view"));
3281 newView.addActionListener(this);
3282 alignFrameMenuBar.add(fileMenu);
3283 alignFrameMenuBar.add(editMenu);
3284 alignFrameMenuBar.add(selectMenu);
3285 alignFrameMenuBar.add(viewMenu);
3286 alignFrameMenuBar.add(formatMenu);
3287 alignFrameMenuBar.add(colourMenu);
3288 alignFrameMenuBar.add(calculateMenu);
3289 alignFrameMenuBar.add(helpMenu);
3291 fileMenu.add(inputText);
3292 fileMenu.add(loadTree);
3293 fileMenu.add(loadAnnotations);
3295 fileMenu.addSeparator();
3296 fileMenu.add(outputTextboxMenu);
3297 fileMenu.add(outputFeatures);
3298 fileMenu.add(outputAnnotations);
3300 if (jalviewServletURL != null)
3302 fileMenu.add(loadApplication);
3305 fileMenu.addSeparator();
3306 fileMenu.add(closeMenuItem);
3308 editMenu.add(undoMenuItem);
3309 editMenu.add(redoMenuItem);
3312 editMenu.add(pasteMenu);
3313 editMenu.add(delete);
3314 editMenu.addSeparator();
3315 editMenu.add(remove2LeftMenuItem);
3316 editMenu.add(remove2RightMenuItem);
3317 editMenu.add(removeGappedColumnMenuItem);
3318 editMenu.add(removeAllGapsMenuItem);
3319 editMenu.add(removeRedundancyMenuItem);
3320 viewMenu.add(newView);
3321 viewMenu.addSeparator();
3322 viewMenu.add(menu1);
3323 viewMenu.add(menu2);
3324 viewMenu.addSeparator();
3325 viewMenu.add(followMouseOverFlag);
3326 viewMenu.add(annotationPanelMenuItem);
3327 autoAnnMenu.add(applyAutoAnnotationSettings);
3328 autoAnnMenu.add(showConsensusHistogram);
3329 autoAnnMenu.add(showSequenceLogo);
3330 autoAnnMenu.add(normSequenceLogo);
3331 autoAnnMenu.addSeparator();
3332 autoAnnMenu.add(showGroupConservation);
3333 autoAnnMenu.add(showGroupConsensus);
3334 viewMenu.add(autoAnnMenu);
3335 viewMenu.addSeparator();
3336 viewMenu.add(sequenceFeatures);
3337 viewMenu.add(featureSettings);
3338 viewMenu.addSeparator();
3339 viewMenu.add(alProperties);
3340 viewMenu.addSeparator();
3341 viewMenu.add(overviewMenuItem);
3342 colourMenu.add(applyToAllGroups);
3343 colourMenu.addSeparator();
3344 colourMenu.add(noColourmenuItem);
3345 colourMenu.add(clustalColour);
3346 colourMenu.add(BLOSUM62Colour);
3347 colourMenu.add(PIDColour);
3348 colourMenu.add(zappoColour);
3349 colourMenu.add(taylorColour);
3350 colourMenu.add(hydrophobicityColour);
3351 colourMenu.add(helixColour);
3352 colourMenu.add(strandColour);
3353 colourMenu.add(turnColour);
3354 colourMenu.add(buriedColour);
3355 colourMenu.add(nucleotideColour);
3356 colourMenu.add(purinePyrimidineColour);
3357 // colourMenu.add(RNAInteractionColour);
3358 colourMenu.add(tcoffeeColour);
3359 colourMenu.add(userDefinedColour);
3360 colourMenu.addSeparator();
3361 colourMenu.add(conservationMenuItem);
3362 colourMenu.add(modifyConservation);
3363 colourMenu.add(abovePIDThreshold);
3364 colourMenu.add(modifyPID);
3365 colourMenu.add(annotationColour);
3366 colourMenu.add(RNAHelixColour);
3367 calculateMenu.add(sort);
3368 calculateMenu.add(calculate);
3369 calculateMenu.addSeparator();
3370 calculateMenu.add(pairwiseAlignmentMenuItem);
3371 calculateMenu.add(PCAMenuItem);
3372 calculateMenu.add(autoCalculate);
3373 calculateMenu.add(sortByTree);
3374 this.add(statusBar, BorderLayout.SOUTH);
3375 pasteMenu.add(pasteNew);
3376 pasteMenu.add(pasteThis);
3377 sort.add(sortIDMenuItem);
3378 sort.add(sortLengthMenuItem);
3379 sort.add(sortByTreeMenu);
3380 sort.add(sortGroupMenuItem);
3381 sort.add(sortPairwiseMenuItem);
3382 calculate.add(averageDistanceTreeMenuItem);
3383 calculate.add(neighbourTreeMenuItem);
3384 calculate.add(avDistanceTreeBlosumMenuItem);
3385 calculate.add(njTreeBlosumMenuItem);
3386 helpMenu.add(documentation);
3387 helpMenu.add(about);
3388 menu1.add(showColumns);
3389 menu1.add(showSeqs);
3390 menu1.add(showAllHidden);
3391 menu2.add(hideColumns);
3392 menu2.add(hideSequences);
3393 menu2.add(hideAllSelection);
3394 menu2.add(hideAllButSelection);
3395 formatMenu.add(font);
3396 formatMenu.add(seqLimits);
3397 formatMenu.add(wrapMenuItem);
3398 formatMenu.add(scaleAbove);
3399 formatMenu.add(scaleLeft);
3400 formatMenu.add(scaleRight);
3401 formatMenu.add(viewBoxesMenuItem);
3402 formatMenu.add(viewTextMenuItem);
3403 formatMenu.add(colourTextMenuItem);
3404 formatMenu.add(displayNonconservedMenuItem);
3405 formatMenu.add(renderGapsMenuItem);
3406 formatMenu.add(centreColumnLabelFlag);
3407 selectMenu.add(findMenuItem);
3408 selectMenu.addSeparator();
3409 selectMenu.add(selectAllSequenceMenuItem);
3410 selectMenu.add(deselectAllSequenceMenuItem);
3411 selectMenu.add(invertSequenceMenuItem);
3412 selectMenu.add(invertColSel);
3413 selectMenu.add(createGroup);
3414 selectMenu.add(unGroup);
3415 selectMenu.add(grpsFromSelection);
3416 selectMenu.add(deleteGroups);
3420 public void setStatus(String string)
3422 statusBar.setText(string);
3425 MenuItem featureSettings = new MenuItem();
3427 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3429 MenuItem annotationColour = new MenuItem();
3431 MenuItem invertColSel = new MenuItem();
3433 Menu menu1 = new Menu();
3435 MenuItem showColumns = new MenuItem();
3437 MenuItem showSeqs = new MenuItem();
3439 Menu menu2 = new Menu();
3441 MenuItem hideColumns = new MenuItem();
3443 MenuItem hideSequences = new MenuItem();
3445 MenuItem hideAllButSelection = new MenuItem();
3447 MenuItem hideAllSelection = new MenuItem();
3449 MenuItem showAllHidden = new MenuItem();
3451 Menu formatMenu = new Menu();
3453 Menu selectMenu = new Menu();
3455 MenuItem newView = new MenuItem();
3458 * Attach the alignFrame panels after embedding menus, if necessary. This used
3459 * to be called setEmbedded, but is now creates the dropdown menus in a
3460 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3462 * @param reallyEmbedded
3463 * true to attach the view to the applet area on the page rather than
3466 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3471 // Explicly build the embedded menu panel for the on-page applet
3473 // view cannot be closed if its actually on the page
3474 fileMenu.remove(closeMenuItem);
3475 fileMenu.remove(3); // Remove Seperator
3476 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3477 Font.PLAIN, 11, false); // use our own fonts.
3478 // and actually add the components to the applet area
3479 viewport.applet.setLayout(new BorderLayout());
3480 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3481 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3482 alignPanel.setSize(viewport.applet.getSize().width,
3483 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3484 - statusBar.HEIGHT);
3485 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3486 final AlignFrame me = this;
3487 viewport.applet.addFocusListener(new FocusListener()
3491 public void focusLost(FocusEvent e)
3493 if (me.viewport.applet.currentAlignFrame == me)
3495 me.viewport.applet.currentAlignFrame = null;
3500 public void focusGained(FocusEvent e)
3502 me.viewport.applet.currentAlignFrame = me;
3505 viewport.applet.validate();
3510 // test and embed menu bar if necessary.
3512 if (embedMenuIfNeeded(alignPanel))
3514 // adjust for status bar height too
3515 alignPanel.setSize(getSize().width, getSize().height
3516 - statusBar.HEIGHT);
3518 add(statusBar, BorderLayout.SOUTH);
3519 add(alignPanel, BorderLayout.CENTER);
3520 // and register with the applet so it can pass external API calls to us
3521 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3527 * create a new binding between structures in an existing jmol viewer instance
3528 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3529 * this does not open a new Jmol window, or modify the display of the
3530 * structures in the original jmol window. Note This method doesn't work
3531 * without an additional javascript library to exchange messages between the
3532 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3535 * JmolViewer instance
3536 * @param sequenceIds
3537 * - sequence Ids to search for associations
3539 public SequenceStructureBinding addStructureViewInstance(
3540 Object jmolviewer, String[] sequenceIds)
3542 org.jmol.api.JmolViewer viewer = null;
3545 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3546 } catch (ClassCastException ex)
3548 System.err.println("Unsupported viewer object :"
3549 + jmolviewer.getClass());
3553 System.err.println("Can't use this object as a structure viewer:"
3554 + jmolviewer.getClass());
3557 SequenceI[] seqs = null;
3558 if (sequenceIds == null || sequenceIds.length == 0)
3560 seqs = viewport.getAlignment().getSequencesArray();
3564 Vector sqi = new Vector();
3565 AlignmentI al = viewport.getAlignment();
3566 for (int sid = 0; sid < sequenceIds.length; sid++)
3568 SequenceI sq = al.findName(sequenceIds[sid]);
3576 seqs = new SequenceI[sqi.size()];
3577 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3579 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3588 // TODO: search for a jmv that involves viewer
3590 { // create a new viewer/jalview binding.
3591 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3599 * bind a pdb file to a sequence in the current view
3602 * - sequenceId within the dataset.
3603 * @param pdbEntryString
3604 * - the short name for the PDB file
3606 * - pdb file - either a URL or a valid PDB file.
3607 * @return true if binding was as success TODO: consider making an exception
3608 * structure for indicating when PDB parsing or sequenceId location
3611 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3614 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3615 boolean needtoadd = false;
3616 if (toaddpdb != null)
3618 Vector pdbe = toaddpdb.getPDBId();
3619 PDBEntry pdbentry = null;
3620 if (pdbe != null && pdbe.size() > 0)
3622 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3624 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3625 if (!pdbentry.getId().equals(pdbEntryString)
3626 && !pdbentry.getFile().equals(pdbFile))
3636 if (pdbentry == null)
3638 pdbentry = new PDBEntry();
3639 pdbentry.setId(pdbEntryString);
3640 pdbentry.setFile(pdbFile);
3641 needtoadd = true; // add this new entry to sequence.
3643 // resolve data source
3644 // TODO: this code should be a refactored to an io package
3645 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3646 if (protocol == null)
3652 // make a note of the access mode and add
3653 if (pdbentry.getProperty() == null)
3655 pdbentry.setProperty(new Hashtable());
3657 pdbentry.getProperty().put("protocol", protocol);
3658 toaddpdb.addPDBId(pdbentry);
3664 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3668 Vector sequences = new Vector();
3669 for (int i = 0; i < seqs.length; i++)
3671 if (seqs[i] != null)
3673 sequences.addElement(new Object[]
3674 { seqs[i], (chains != null) ? chains[i] : null });
3677 seqs = new SequenceI[sequences.size()];
3678 chains = new String[sequences.size()];
3679 for (int i = 0, isize = sequences.size(); i < isize; i++)
3681 Object[] oj = (Object[]) sequences.elementAt(i);
3683 seqs[i] = (SequenceI) oj[0];
3684 chains[i] = (String) oj[1];
3692 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3693 SequenceI[] seqs, String[] chains, String protocol)
3695 // Scrub any null sequences from the array
3696 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3697 seqs = (SequenceI[]) sqch[0];
3698 chains = (String[]) sqch[1];
3699 if (seqs == null || seqs.length == 0)
3702 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3704 if (protocol == null || protocol.trim().length() == 0
3705 || protocol.equals("null"))
3707 protocol = (String) pdb.getProperty().get("protocol");
3708 if (protocol == null)
3710 System.err.println("Couldn't work out protocol to open structure: "
3715 if (applet.useXtrnalSviewer)
3717 // register the association(s) and quit, don't create any windows.
3718 if (StructureSelectionManager.getStructureSelectionManager(applet)
3719 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3721 System.err.println("Failed to map " + pdb.getFile() + " ("
3722 + protocol + ") to any sequences");
3726 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3728 // can only do alignments with Jmol
3729 // find the last jmol window assigned to this alignment
3730 jalview.appletgui.AppletJmol ajm = null, tajm;
3731 Vector jmols = applet
3732 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3733 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3735 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3736 if (tajm.ap.alignFrame == this)
3745 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3746 // try and add the pdb structure
3751 // otherwise, create a new window
3752 if (applet.jmolAvailable)
3754 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3756 applet.lastFrameX += 40;
3757 applet.lastFrameY += 40;
3761 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3766 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3767 SequenceI[][] seqs, String[][] chains, String[] protocols)
3769 // TODO Auto-generated method stub
3770 System.err.println("Aligned Structure View: Not yet implemented.");
3774 * modify the current selection, providing the user has not made a selection
3778 * - sequences from this alignment
3780 * - columns to be selected on the alignment
3782 public void select(SequenceGroup sel, ColumnSelection csel)
3784 alignPanel.seqPanel.selection(sel, csel, null);
3787 public void scrollTo(int row, int column)
3789 alignPanel.seqPanel.scrollTo(row, column);
3792 public void scrollToRow(int row)
3794 alignPanel.seqPanel.scrollToRow(row);
3797 public void scrollToColumn(int column)
3799 alignPanel.seqPanel.scrollToColumn(column);
3803 * @return the alignments unique ID.
3805 public String getSequenceSetId()
3807 return viewport.getSequenceSetId();
3811 * Load the (T-Coffee) score file from the specified url
3814 * File/URL/T-COFFEE score file contents
3815 * @throws IOException
3816 * @return true if alignment was annotated with data from source
3818 public boolean loadScoreFile(String source) throws IOException
3821 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3822 AppletFormatAdapter.checkProtocol(source));
3823 if (!file.isValid())
3825 // TODO: raise dialog for gui
3826 System.err.println("Problems parsing T-Coffee scores: "
3827 + file.getWarningMessage());
3828 System.err.println("Origin was:\n" + source);
3833 * check that the score matrix matches the alignment dimensions
3836 if ((aln = viewport.getAlignment()) != null
3837 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3840 // TODO: raise a dialog box here rather than bomb out.
3842 .println("The scores matrix does not match the alignment dimensions");
3846 // TODO add parameter to indicate if matching should be done
3847 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3849 alignPanel.fontChanged();
3850 tcoffeeColour.setEnabled(true);
3851 // switch to this color
3852 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3857 System.err.println("Problems resolving T-Coffee scores:");
3858 if (file.getWarningMessage() != null)
3860 System.err.println(file.getWarningMessage());