2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.AlignViewportI;
27 import jalview.api.FeatureRenderer;
28 import jalview.api.SequenceStructureBinding;
29 import jalview.bin.JalviewLite;
30 import jalview.commands.CommandI;
31 import jalview.commands.EditCommand;
32 import jalview.commands.EditCommand.Action;
33 import jalview.commands.OrderCommand;
34 import jalview.commands.RemoveGapColCommand;
35 import jalview.commands.RemoveGapsCommand;
36 import jalview.commands.SlideSequencesCommand;
37 import jalview.commands.TrimRegionCommand;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentI;
40 import jalview.datamodel.AlignmentOrder;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.Sequence;
44 import jalview.datamodel.SequenceGroup;
45 import jalview.datamodel.SequenceI;
46 import jalview.io.AnnotationFile;
47 import jalview.io.AppletFormatAdapter;
48 import jalview.io.FeaturesFile;
49 import jalview.io.TCoffeeScoreFile;
50 import jalview.schemes.Blosum62ColourScheme;
51 import jalview.schemes.BuriedColourScheme;
52 import jalview.schemes.ClustalxColourScheme;
53 import jalview.schemes.ColourSchemeI;
54 import jalview.schemes.HelixColourScheme;
55 import jalview.schemes.HydrophobicColourScheme;
56 import jalview.schemes.NucleotideColourScheme;
57 import jalview.schemes.PIDColourScheme;
58 import jalview.schemes.PurinePyrimidineColourScheme;
59 import jalview.schemes.RNAHelicesColourChooser;
60 import jalview.schemes.RNAInteractionColourScheme;
61 import jalview.schemes.StrandColourScheme;
62 import jalview.schemes.TCoffeeColourScheme;
63 import jalview.schemes.TaylorColourScheme;
64 import jalview.schemes.TurnColourScheme;
65 import jalview.schemes.ZappoColourScheme;
66 import jalview.structure.StructureSelectionManager;
67 import jalview.structures.models.AAStructureBindingModel;
68 import jalview.util.MappingUtils;
69 import jalview.util.MessageManager;
71 import java.awt.BorderLayout;
72 import java.awt.Canvas;
73 import java.awt.CheckboxMenuItem;
74 import java.awt.Color;
76 import java.awt.FontMetrics;
77 import java.awt.Frame;
78 import java.awt.Graphics;
79 import java.awt.Label;
81 import java.awt.MenuBar;
82 import java.awt.MenuItem;
83 import java.awt.event.ActionEvent;
84 import java.awt.event.ActionListener;
85 import java.awt.event.FocusEvent;
86 import java.awt.event.FocusListener;
87 import java.awt.event.ItemEvent;
88 import java.awt.event.ItemListener;
89 import java.awt.event.KeyEvent;
90 import java.awt.event.KeyListener;
91 import java.awt.event.WindowAdapter;
92 import java.awt.event.WindowEvent;
93 import java.io.IOException;
95 import java.net.URLEncoder;
96 import java.util.Arrays;
97 import java.util.Deque;
98 import java.util.Hashtable;
99 import java.util.List;
100 import java.util.Map;
101 import java.util.StringTokenizer;
102 import java.util.Vector;
104 public class AlignFrame extends EmbmenuFrame implements ActionListener,
105 ItemListener, KeyListener, AlignViewControllerGuiI
107 public AlignViewControllerI avc;
109 public AlignmentPanel alignPanel;
111 public AlignViewport viewport;
113 int DEFAULT_WIDTH = 700;
115 int DEFAULT_HEIGHT = 500;
117 String jalviewServletURL;
120 * Constructor that creates the frame and adds it to the display.
127 public AlignFrame(AlignmentI al, JalviewLite applet,
128 String title, boolean embedded)
130 this(al, applet, title, embedded, true);
134 * Constructor that optionally allows the frame to be displayed or only
141 * @param addToDisplay
143 public AlignFrame(AlignmentI al, JalviewLite applet,
144 String title, boolean embedded, boolean addToDisplay)
148 jalviewServletURL = applet.getParameter("APPLICATION_URL");
154 } catch (Exception ex)
156 ex.printStackTrace();
158 // need to get window geometry before we calculate alignment layout
164 param = applet.getParameter("windowWidth");
167 int width = Integer.parseInt(param);
168 DEFAULT_WIDTH = width;
170 param = applet.getParameter("windowHeight");
173 int height = Integer.parseInt(param);
174 DEFAULT_HEIGHT = height;
176 } catch (Exception ex)
180 viewport = new AlignViewport(al, applet);
181 alignPanel = new AlignmentPanel(this, viewport);
182 avc = new jalview.controller.AlignViewController(this, viewport,
184 viewport.updateConservation(alignPanel);
185 viewport.updateConsensus(alignPanel);
187 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
188 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
189 followMouseOverFlag.setState(viewport.getFollowHighlight());
190 showGroupConsensus.setState(viewport.isShowGroupConsensus());
191 showGroupConservation.setState(viewport.isShowGroupConservation());
192 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
193 showSequenceLogo.setState(viewport.isShowSequenceLogo());
194 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
195 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
197 seqLimits.setState(viewport.getShowJVSuffix());
201 String param = applet.getParameter("sortBy");
204 if (param.equalsIgnoreCase("Id"))
206 sortIDMenuItem_actionPerformed();
208 else if (param.equalsIgnoreCase("Pairwise Identity"))
210 sortPairwiseMenuItem_actionPerformed();
212 else if (param.equalsIgnoreCase("Length"))
214 sortLengthMenuItem_actionPerformed();
218 param = applet.getParameter("wrap");
221 if (param.equalsIgnoreCase("true"))
223 wrapMenuItem.setState(true);
224 wrapMenuItem_actionPerformed();
227 param = applet.getParameter("centrecolumnlabels");
230 centreColumnLabelFlag.setState(true);
231 centreColumnLabelFlag_stateChanged();
235 if (viewport.getAlignment().isNucleotide())
237 viewport.updateStrucConsensus(alignPanel);
238 if (viewport.getAlignment().hasRNAStructure())
240 RNAHelixColour.setEnabled(true);
244 RNAHelixColour.setEnabled(false);
249 RNAHelixColour.setEnabled(false);
250 purinePyrimidineColour.setEnabled(false);
252 // Some JVMS send keyevents to Top frame or lowest panel,
253 // Havent worked out why yet. So add to both this frame and seqCanvas for
255 this.addKeyListener(this);
256 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
257 alignPanel.idPanel.idCanvas.addKeyListener(this);
258 alignPanel.scalePanel.addKeyListener(this);
259 alignPanel.annotationPanel.addKeyListener(this);
260 alignPanel.annotationPanelHolder.addKeyListener(this);
261 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
262 alignPanel.alabels.addKeyListener(this);
266 addToDisplay(embedded);
273 public void addToDisplay(boolean embedded)
275 createAlignFrameWindow(embedded);
277 alignPanel.adjustAnnotationHeight();
278 alignPanel.paintAlignment(true);
281 public AlignViewport getAlignViewport()
286 public SeqCanvas getSeqcanvas()
288 return alignPanel.seqPanel.seqCanvas;
292 * Load a features file onto the alignment
295 * file URL, content, or other resolvable path
297 * is protocol for accessing data referred to by file
300 public boolean parseFeaturesFile(String file, String type)
302 return parseFeaturesFile(file, type, true);
306 * Load a features file onto the alignment
309 * file URL, content, or other resolvable path
311 * is protocol for accessing data referred to by file
312 * @param autoenabledisplay
313 * when true, display features flag will be automatically enabled if
314 * features are loaded
315 * @return true if data parsed as a features file
317 public boolean parseFeaturesFile(String file, String type,
318 boolean autoenabledisplay)
320 // TODO: test if importing a features file onto an alignment which already
321 // has features with links overwrites the original links.
323 Hashtable featureLinks = new Hashtable();
324 boolean featuresFile = false;
327 featuresFile = new jalview.io.FeaturesFile(file, type)
328 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
329 .getFeatureRenderer().getFeatureColours(), featureLinks,
330 true, viewport.applet.getDefaultParameter(
331 "relaxedidmatch", false));
332 } catch (Exception ex)
334 ex.printStackTrace();
339 if (featureLinks.size() > 0)
341 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
343 if (autoenabledisplay)
345 viewport.setShowSequenceFeatures(true);
346 sequenceFeatures.setState(true);
348 if (alignPanel.seqPanel.seqCanvas.fr != null)
350 // update the min/max ranges where necessary
351 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
353 if (viewport.featureSettings != null)
355 viewport.featureSettings.refreshTable();
357 alignPanel.paintAlignment(true);
358 statusBar.setText(MessageManager
359 .getString("label.successfully_added_features_alignment"));
365 public void keyPressed(KeyEvent evt)
367 if (viewport.cursorMode
368 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
369 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
370 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
371 && Character.isDigit(evt.getKeyChar()))
373 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
376 switch (evt.getKeyCode())
378 case 27: // escape key
379 deselectAllSequenceMenuItem_actionPerformed();
381 alignPanel.alabels.cancelDrag();
384 if (evt.isControlDown() || evt.isMetaDown())
386 cut_actionPerformed();
390 if (viewport.cursorMode && !evt.isControlDown())
392 alignPanel.seqPanel.setCursorColumn();
394 if (evt.isControlDown() || evt.isMetaDown())
396 copy_actionPerformed();
400 if (evt.isControlDown())
402 paste(evt.isShiftDown());
406 if (evt.isControlDown() || evt.isMetaDown())
408 selectAllSequenceMenuItem_actionPerformed();
411 case KeyEvent.VK_DOWN:
412 if (viewport.cursorMode)
414 alignPanel.seqPanel.moveCursor(0, 1);
418 moveSelectedSequences(false);
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.moveCursor(0, -1);
429 moveSelectedSequences(true);
433 case KeyEvent.VK_LEFT:
434 if (evt.isAltDown() || !viewport.cursorMode)
436 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
440 alignPanel.seqPanel.moveCursor(-1, 0);
444 case KeyEvent.VK_RIGHT:
445 if (evt.isAltDown() || !viewport.cursorMode)
447 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
451 alignPanel.seqPanel.moveCursor(1, 0);
455 case KeyEvent.VK_SPACE:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
459 || evt.isShiftDown() || evt.isAltDown());
463 case KeyEvent.VK_DELETE:
464 case KeyEvent.VK_BACK_SPACE:
465 if (viewport.cursorMode)
467 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
468 || evt.isShiftDown() || evt.isAltDown());
472 cut_actionPerformed();
473 alignPanel.seqPanel.seqCanvas.repaint();
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.setCursorRow();
484 if (viewport.cursorMode)
486 alignPanel.seqPanel.setCursorPosition();
490 case KeyEvent.VK_ENTER:
491 case KeyEvent.VK_COMMA:
492 if (viewport.cursorMode)
494 alignPanel.seqPanel.setCursorRowAndColumn();
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
512 viewport.cursorMode = !viewport.cursorMode;
513 statusBar.setText(MessageManager.formatMessage(
514 "label.keyboard_editing_mode", new String[]
515 { (viewport.cursorMode ? "on" : "off") }));
516 if (viewport.cursorMode)
518 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
519 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
524 if (evt.isControlDown())
526 findMenuItem_actionPerformed();
532 boolean toggleSeqs = !evt.isControlDown();
533 boolean toggleCols = !evt.isShiftDown();
534 toggleHiddenRegions(toggleSeqs, toggleCols);
538 case KeyEvent.VK_PAGE_UP:
539 if (viewport.getWrapAlignment())
541 alignPanel.scrollUp(true);
545 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
546 - viewport.endSeq + viewport.startSeq);
550 case KeyEvent.VK_PAGE_DOWN:
551 if (viewport.getWrapAlignment())
553 alignPanel.scrollUp(false);
557 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
558 + viewport.endSeq - viewport.startSeq);
563 if (evt.isControlDown())
565 undoMenuItem_actionPerformed();
570 if (evt.isControlDown())
572 redoMenuItem_actionPerformed();
577 if (evt.isControlDown())
584 if (evt.isControlDown())
586 trimAlignment(false);
591 if (evt.isControlDown())
593 if (evt.isShiftDown())
595 this.removeAllGapsMenuItem_actionPerformed();
599 removeGappedColumnMenuItem_actionPerformed();
604 if (evt.isControlDown())
608 invertColSel_actionPerformed();
612 invertSequenceMenuItem_actionPerformed();
618 if (evt.isControlDown())
620 if (evt.isShiftDown())
622 this.unGroup_actionPerformed();
626 this.createGroup_actionPerformed();
632 if (evt.isControlDown())
634 this.deleteGroups_actionPerformed();
639 if (evt.isControlDown())
646 alignPanel.paintAlignment(true);
650 * called by key handler and the hide all/show all menu items
655 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
657 boolean hide = false;
658 SequenceGroup sg = viewport.getSelectionGroup();
659 if (!toggleSeqs && !toggleCols)
661 // Hide everything by the current selection - this is a hack - we do the
662 // invert and then hide
663 // first check that there will be visible columns after the invert.
664 if ((viewport.getColumnSelection() != null
665 && viewport.getColumnSelection().getSelected() != null && viewport
666 .getColumnSelection().getSelected().size() > 0)
667 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
670 // now invert the sequence set, if required - empty selection implies
671 // that no hiding is required.
674 invertSequenceMenuItem_actionPerformed();
675 sg = viewport.getSelectionGroup();
679 viewport.expandColSelection(sg, true);
680 // finally invert the column selection and get the new sequence
681 // selection and indicate it should be hidden.
682 invertColSel_actionPerformed();
689 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
692 viewport.hideAllSelectedSeqs();
694 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
697 viewport.showAllHiddenSeqs();
703 if (viewport.getColumnSelection().getSelected().size() > 0)
705 viewport.hideSelectedColumns();
708 viewport.setSelectionGroup(sg);
713 viewport.showAllHiddenColumns();
719 public void keyReleased(KeyEvent evt)
724 public void keyTyped(KeyEvent evt)
729 public void itemStateChanged(ItemEvent evt)
731 if (evt.getSource() == displayNonconservedMenuItem)
733 displayNonconservedMenuItem_actionPerformed();
735 else if (evt.getSource() == colourTextMenuItem)
737 colourTextMenuItem_actionPerformed();
739 else if (evt.getSource() == wrapMenuItem)
741 wrapMenuItem_actionPerformed();
743 else if (evt.getSource() == scaleAbove)
745 viewport.setScaleAboveWrapped(scaleAbove.getState());
747 else if (evt.getSource() == scaleLeft)
749 viewport.setScaleLeftWrapped(scaleLeft.getState());
751 else if (evt.getSource() == scaleRight)
753 viewport.setScaleRightWrapped(scaleRight.getState());
755 else if (evt.getSource() == seqLimits)
757 seqLimits_itemStateChanged();
759 else if (evt.getSource() == viewBoxesMenuItem)
761 viewport.setShowBoxes(viewBoxesMenuItem.getState());
763 else if (evt.getSource() == viewTextMenuItem)
765 viewport.setShowText(viewTextMenuItem.getState());
767 else if (evt.getSource() == renderGapsMenuItem)
769 viewport.setRenderGaps(renderGapsMenuItem.getState());
771 else if (evt.getSource() == annotationPanelMenuItem)
773 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
774 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
776 else if (evt.getSource() == sequenceFeatures)
778 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
779 alignPanel.seqPanel.seqCanvas.repaint();
781 else if (evt.getSource() == conservationMenuItem)
783 conservationMenuItem_actionPerformed();
785 else if (evt.getSource() == abovePIDThreshold)
787 abovePIDThreshold_actionPerformed();
789 else if (evt.getSource() == applyToAllGroups)
791 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
793 else if (evt.getSource() == autoCalculate)
795 viewport.autoCalculateConsensus = autoCalculate.getState();
797 else if (evt.getSource() == sortByTree)
799 viewport.sortByTree = sortByTree.getState();
801 else if (evt.getSource() == this.centreColumnLabelFlag)
803 centreColumnLabelFlag_stateChanged();
805 else if (evt.getSource() == this.followMouseOverFlag)
807 mouseOverFlag_stateChanged();
809 else if (evt.getSource() == showGroupConsensus)
811 showGroupConsensus_actionPerformed();
813 else if (evt.getSource() == showGroupConservation)
815 showGroupConservation_actionPerformed();
817 else if (evt.getSource() == showSequenceLogo)
819 showSequenceLogo_actionPerformed();
821 else if (evt.getSource() == normSequenceLogo)
823 normSequenceLogo_actionPerformed();
825 else if (evt.getSource() == showConsensusHistogram)
827 showConsensusHistogram_actionPerformed();
829 else if (evt.getSource() == applyAutoAnnotationSettings)
831 applyAutoAnnotationSettings_actionPerformed();
833 alignPanel.paintAlignment(true);
836 private void mouseOverFlag_stateChanged()
838 viewport.followHighlight = followMouseOverFlag.getState();
839 // TODO: could kick the scrollTo mechanism to reset view for current
843 private void centreColumnLabelFlag_stateChanged()
845 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
846 this.alignPanel.annotationPanel.repaint();
850 public void actionPerformed(ActionEvent evt)
852 Object source = evt.getSource();
854 if (source == inputText)
856 inputText_actionPerformed();
858 else if (source == loadTree)
860 loadTree_actionPerformed();
862 else if (source == loadApplication)
864 launchFullApplication();
866 else if (source == loadAnnotations)
870 else if (source == outputAnnotations)
872 outputAnnotations(true);
874 else if (source == outputFeatures)
876 outputFeatures(true, "Jalview");
878 else if (source == closeMenuItem)
880 closeMenuItem_actionPerformed();
882 else if (source == copy)
884 copy_actionPerformed();
886 else if (source == undoMenuItem)
888 undoMenuItem_actionPerformed();
890 else if (source == redoMenuItem)
892 redoMenuItem_actionPerformed();
894 else if (source == inputText)
896 inputText_actionPerformed();
898 else if (source == closeMenuItem)
900 closeMenuItem_actionPerformed();
902 else if (source == undoMenuItem)
904 undoMenuItem_actionPerformed();
906 else if (source == redoMenuItem)
908 redoMenuItem_actionPerformed();
910 else if (source == copy)
912 copy_actionPerformed();
914 else if (source == pasteNew)
916 pasteNew_actionPerformed();
918 else if (source == pasteThis)
920 pasteThis_actionPerformed();
922 else if (source == cut)
924 cut_actionPerformed();
926 else if (source == delete)
928 delete_actionPerformed();
930 else if (source == grpsFromSelection)
932 makeGrpsFromSelection_actionPerformed();
934 else if (source == deleteGroups)
936 deleteGroups_actionPerformed();
938 else if (source == selectAllSequenceMenuItem)
940 selectAllSequenceMenuItem_actionPerformed();
942 else if (source == deselectAllSequenceMenuItem)
944 deselectAllSequenceMenuItem_actionPerformed();
946 else if (source == invertSequenceMenuItem)
948 invertSequenceMenuItem_actionPerformed();
950 else if (source == invertColSel)
952 viewport.invertColumnSelection();
953 alignPanel.paintAlignment(true);
955 else if (source == remove2LeftMenuItem)
959 else if (source == remove2RightMenuItem)
961 trimAlignment(false);
963 else if (source == removeGappedColumnMenuItem)
965 removeGappedColumnMenuItem_actionPerformed();
967 else if (source == removeAllGapsMenuItem)
969 removeAllGapsMenuItem_actionPerformed();
971 else if (source == findMenuItem)
973 findMenuItem_actionPerformed();
975 else if (source == font)
977 new FontChooser(alignPanel);
979 else if (source == newView)
983 else if (source == showColumns)
985 viewport.showAllHiddenColumns();
986 alignPanel.paintAlignment(true);
988 else if (source == showSeqs)
990 viewport.showAllHiddenSeqs();
991 alignPanel.paintAlignment(true);
993 else if (source == hideColumns)
995 viewport.hideSelectedColumns();
996 alignPanel.paintAlignment(true);
998 else if (source == hideSequences
999 && viewport.getSelectionGroup() != null)
1001 viewport.hideAllSelectedSeqs();
1002 alignPanel.paintAlignment(true);
1004 else if (source == hideAllButSelection)
1006 toggleHiddenRegions(false, false);
1007 alignPanel.paintAlignment(true);
1009 else if (source == hideAllSelection)
1011 SequenceGroup sg = viewport.getSelectionGroup();
1012 viewport.expandColSelection(sg, false);
1013 viewport.hideAllSelectedSeqs();
1014 viewport.hideSelectedColumns();
1015 alignPanel.paintAlignment(true);
1017 else if (source == showAllHidden)
1019 viewport.showAllHiddenColumns();
1020 viewport.showAllHiddenSeqs();
1021 alignPanel.paintAlignment(true);
1023 else if (source == showGroupConsensus)
1025 showGroupConsensus_actionPerformed();
1027 else if (source == showGroupConservation)
1029 showGroupConservation_actionPerformed();
1031 else if (source == showSequenceLogo)
1033 showSequenceLogo_actionPerformed();
1035 else if (source == normSequenceLogo)
1037 normSequenceLogo_actionPerformed();
1039 else if (source == showConsensusHistogram)
1041 showConsensusHistogram_actionPerformed();
1043 else if (source == applyAutoAnnotationSettings)
1045 applyAutoAnnotationSettings_actionPerformed();
1047 else if (source == featureSettings)
1049 new FeatureSettings(alignPanel);
1051 else if (source == alProperties)
1053 StringBuffer contents = new jalview.io.AlignmentProperties(
1054 viewport.getAlignment()).formatAsString();
1055 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1056 cap.setText(contents.toString());
1057 Frame frame = new Frame();
1059 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1060 "label.alignment_properties", new String[]
1061 { getTitle() }), 400, 250);
1063 else if (source == overviewMenuItem)
1065 overviewMenuItem_actionPerformed();
1067 else if (source == noColourmenuItem)
1071 else if (source == clustalColour)
1073 abovePIDThreshold.setState(false);
1074 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1076 else if (source == zappoColour)
1078 changeColour(new ZappoColourScheme());
1080 else if (source == taylorColour)
1082 changeColour(new TaylorColourScheme());
1084 else if (source == hydrophobicityColour)
1086 changeColour(new HydrophobicColourScheme());
1088 else if (source == helixColour)
1090 changeColour(new HelixColourScheme());
1092 else if (source == strandColour)
1094 changeColour(new StrandColourScheme());
1096 else if (source == turnColour)
1098 changeColour(new TurnColourScheme());
1100 else if (source == buriedColour)
1102 changeColour(new BuriedColourScheme());
1104 else if (source == nucleotideColour)
1106 changeColour(new NucleotideColourScheme());
1108 else if (source == purinePyrimidineColour)
1110 changeColour(new PurinePyrimidineColourScheme());
1112 else if (source == RNAInteractionColour)
1114 changeColour(new RNAInteractionColourScheme());
1116 else if (source == RNAHelixColour)
1118 new RNAHelicesColourChooser(viewport, alignPanel);
1120 else if (source == modifyPID)
1122 modifyPID_actionPerformed();
1124 else if (source == modifyConservation)
1126 modifyConservation_actionPerformed();
1128 else if (source == userDefinedColour)
1130 new UserDefinedColours(alignPanel, null);
1132 else if (source == PIDColour)
1134 changeColour(new PIDColourScheme());
1136 else if (source == BLOSUM62Colour)
1138 changeColour(new Blosum62ColourScheme());
1140 else if (source == tcoffeeColour)
1142 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1144 else if (source == annotationColour)
1146 new AnnotationColourChooser(viewport, alignPanel);
1148 else if (source == annotationColumnSelection)
1150 new AnnotationColumnChooser(viewport, alignPanel);
1152 else if (source == sortPairwiseMenuItem)
1154 sortPairwiseMenuItem_actionPerformed();
1156 else if (source == sortIDMenuItem)
1158 sortIDMenuItem_actionPerformed();
1160 else if (source == sortLengthMenuItem)
1162 sortLengthMenuItem_actionPerformed();
1164 else if (source == sortGroupMenuItem)
1166 sortGroupMenuItem_actionPerformed();
1168 else if (source == removeRedundancyMenuItem)
1170 removeRedundancyMenuItem_actionPerformed();
1172 else if (source == pairwiseAlignmentMenuItem)
1174 pairwiseAlignmentMenuItem_actionPerformed();
1176 else if (source == PCAMenuItem)
1178 PCAMenuItem_actionPerformed();
1180 else if (source == averageDistanceTreeMenuItem)
1182 averageDistanceTreeMenuItem_actionPerformed();
1184 else if (source == neighbourTreeMenuItem)
1186 neighbourTreeMenuItem_actionPerformed();
1188 else if (source == njTreeBlosumMenuItem)
1190 njTreeBlosumMenuItem_actionPerformed();
1192 else if (source == avDistanceTreeBlosumMenuItem)
1194 avTreeBlosumMenuItem_actionPerformed();
1196 else if (source == documentation)
1198 documentation_actionPerformed();
1200 else if (source == about)
1202 about_actionPerformed();
1207 public void inputText_actionPerformed()
1209 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1210 Frame frame = new Frame();
1212 jalview.bin.JalviewLite.addFrame(frame,
1213 MessageManager.getString("label.input_cut_paste"), 500, 500);
1216 protected void outputText_actionPerformed(ActionEvent e)
1218 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1219 Frame frame = new Frame();
1221 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1222 "label.alignment_output_command", new Object[]
1223 { e.getActionCommand() }), 600, 500);
1224 cap.setText(new AppletFormatAdapter().formatSequences(
1225 e.getActionCommand(), viewport.getAlignment(),
1226 viewport.getShowJVSuffix()));
1229 public void loadAnnotations()
1231 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1232 cap.setText(MessageManager
1233 .getString("label.paste_features_annotations_Tcoffee_here"));
1234 cap.setAnnotationImport();
1235 Frame frame = new Frame();
1237 jalview.bin.JalviewLite.addFrame(frame,
1238 MessageManager.getString("action.paste_annotations"), 400, 300);
1242 public String outputAnnotations(boolean displayTextbox)
1244 String annotation = new AnnotationFile()
1245 .printAnnotationsForView(viewport);
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1250 Frame frame = new Frame();
1252 jalview.bin.JalviewLite.addFrame(frame,
1253 MessageManager.getString("label.annotations"), 600, 500);
1254 cap.setText(annotation);
1260 private Map<String,Object> getDisplayedFeatureCols()
1262 if (alignPanel.getFeatureRenderer() != null
1263 && viewport.getFeaturesDisplayed()!= null)
1265 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1271 public String outputFeatures(boolean displayTextbox, String format)
1274 if (format.equalsIgnoreCase("Jalview"))
1276 features = new FeaturesFile().printJalviewFormat(viewport
1277 .getAlignment().getSequencesArray(),
1278 getDisplayedFeatureCols());
1282 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1283 .getSequencesArray(), getDisplayedFeatureCols());
1288 boolean frimport = false;
1289 if (features == null || features.equals("No Features Visible"))
1291 features = "# No features visible - paste some and import them here.";
1295 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1298 cap.setAnnotationImport();
1300 Frame frame = new Frame();
1302 jalview.bin.JalviewLite.addFrame(frame,
1303 MessageManager.getString("label.features"), 600, 500);
1304 cap.setText(features);
1308 if (features == null)
1317 void launchFullApplication()
1319 StringBuffer url = new StringBuffer(jalviewServletURL);
1321 // allow servlet parameters to be passed in applet parameter
1322 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1324 url.append(firstSep);
1327 + appendProtocol(viewport.applet.getParameter("file")));
1329 if (viewport.applet.getParameter("features") != null)
1331 url.append("&features=");
1332 url.append(appendProtocol(viewport.applet.getParameter("features")));
1335 if (viewport.applet.getParameter("annotations") != null)
1337 url.append("&annotations=");
1338 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1341 if (viewport.applet.getParameter("jnetfile") != null)
1343 url.append("&annotations=");
1344 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1347 if (viewport.applet.getParameter("defaultColour") != null)
1349 url.append("&colour="
1350 + removeWhiteSpace(viewport.applet
1351 .getParameter("defaultColour")));
1354 if (viewport.applet.getParameter("userDefinedColour") != null)
1356 url.append("&colour="
1357 + removeWhiteSpace(viewport.applet
1358 .getParameter("userDefinedColour")));
1360 if (viewport.applet.getParameter("tree") != null)
1363 + appendProtocol(viewport.applet.getParameter("tree")));
1365 if (viewport.applet.getParameter("treeFile") != null)
1368 + appendProtocol(viewport.applet.getParameter("treeFile")));
1371 showURL(url.toString(), "FULL_APP");
1374 String removeWhiteSpace(String colour)
1376 StringBuffer sb = new StringBuffer();
1377 for (int i = 0; i < colour.length(); i++)
1379 if (Character.isWhitespace(colour.charAt(i)))
1385 sb.append(colour.charAt(i));
1389 return sb.toString();
1392 String appendProtocol(String url)
1397 url = URLEncoder.encode(url);
1400 * When we finally deprecate 1.1 compatibility, we can start to use
1401 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1402 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1403 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1404 * ex.printStackTrace(); }
1406 catch (java.net.MalformedURLException ex)
1408 url = viewport.applet.getCodeBase() + url;
1413 public void closeMenuItem_actionPerformed()
1415 PaintRefresher.RemoveComponent(alignPanel);
1416 if (alignPanel.seqPanel != null
1417 && alignPanel.seqPanel.seqCanvas != null)
1419 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1421 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1423 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1426 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1441 void updateEditMenuBar()
1444 if (viewport.getHistoryList().size() > 0)
1446 undoMenuItem.setEnabled(true);
1447 CommandI command = viewport.getHistoryList().peek();
1448 undoMenuItem.setLabel(MessageManager.formatMessage(
1449 "label.undo_command", new Object[]
1450 { command.getDescription() }));
1454 undoMenuItem.setEnabled(false);
1455 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1458 if (viewport.getRedoList().size() > 0)
1460 redoMenuItem.setEnabled(true);
1462 CommandI command = viewport.getRedoList().peek();
1463 redoMenuItem.setLabel(MessageManager.formatMessage(
1464 "label.redo_command", new Object[]
1465 { command.getDescription() }));
1469 redoMenuItem.setEnabled(false);
1470 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1478 public void addHistoryItem(CommandI command)
1480 if (command.getSize() > 0)
1482 viewport.addToHistoryList(command);
1483 viewport.clearRedoList();
1484 updateEditMenuBar();
1485 viewport.updateHiddenColumns();
1490 * TODO: JAL-1104 DOCUMENT ME!
1495 protected void undoMenuItem_actionPerformed()
1497 if (viewport.getHistoryList().isEmpty())
1502 CommandI command = viewport.getHistoryList().pop();
1503 viewport.addToRedoList(command);
1504 command.undoCommand(null);
1506 AlignViewport originalSource = getOriginatingSource(command);
1508 if (originalSource != viewport)
1511 .println("Warning: Viewport object mismatch whilst undoing");
1513 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1514 // viewport.getColumnSelection().getHiddenColumns()
1516 updateEditMenuBar();
1517 originalSource.firePropertyChange("alignment", null, originalSource
1518 .getAlignment().getSequences());
1522 * TODO: JAL-1104 DOCUMENT ME!
1527 protected void redoMenuItem_actionPerformed()
1529 if (viewport.getRedoList().isEmpty())
1534 CommandI command = viewport.getRedoList().pop();
1535 viewport.addToHistoryList(command);
1536 command.doCommand(null);
1538 AlignViewport originalSource = getOriginatingSource(command);
1540 if (originalSource != viewport)
1543 .println("Warning: Viewport object mismatch whilst re-doing");
1545 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1546 // viewport.getColumnSelection().getHiddenColumns()
1549 updateEditMenuBar();
1550 originalSource.firePropertyChange("alignment", null, originalSource
1551 .getAlignment().getSequences());
1554 AlignViewport getOriginatingSource(CommandI command)
1556 AlignViewport originalSource = null;
1557 // For sequence removal and addition, we need to fire
1558 // the property change event FROM the viewport where the
1559 // original alignment was altered
1560 AlignmentI al = null;
1561 if (command instanceof EditCommand)
1563 EditCommand editCommand = (EditCommand) command;
1564 al = editCommand.getAlignment();
1565 Vector comps = (Vector) PaintRefresher.components.get(viewport
1566 .getSequenceSetId());
1567 for (int i = 0; i < comps.size(); i++)
1569 if (comps.elementAt(i) instanceof AlignmentPanel)
1571 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1573 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1580 if (originalSource == null)
1582 // The original view is closed, we must validate
1583 // the current view against the closed view first
1586 PaintRefresher.validateSequences(al, viewport.getAlignment());
1589 originalSource = viewport;
1592 return originalSource;
1596 * Move the currently selected sequences up or down one position in the
1601 public void moveSelectedSequences(boolean up)
1603 SequenceGroup sg = viewport.getSelectionGroup();
1608 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1609 up ? null : viewport.getHiddenRepSequences(), up);
1610 alignPanel.paintAlignment(true);
1613 * Also move cDNA/protein complement sequences
1615 AlignViewportI complement = viewport.getCodingComplement();
1616 if (complement != null)
1618 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1619 viewport, complement);
1620 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1621 up ? null : complement.getHiddenRepSequences(), up);
1622 // TODO need to trigger a repaint of the complementary panel - how?
1623 // would prefer to handle in SplitFrame but it is not overriding key
1628 synchronized void slideSequences(boolean right, int size)
1630 List<SequenceI> sg = new Vector<SequenceI>();
1631 if (viewport.cursorMode)
1633 sg.add(viewport.getAlignment().getSequenceAt(
1634 alignPanel.seqPanel.seqCanvas.cursorY));
1636 else if (viewport.getSelectionGroup() != null
1637 && viewport.getSelectionGroup().getSize() != viewport
1638 .getAlignment().getHeight())
1640 sg = viewport.getSelectionGroup().getSequences(
1641 viewport.getHiddenRepSequences());
1649 Vector<SequenceI> invertGroup = new Vector();
1651 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1653 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1655 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1659 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1661 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1663 for (int i = 0; i < invertGroup.size(); i++)
1665 seqs2[i] = invertGroup.elementAt(i);
1668 SlideSequencesCommand ssc;
1671 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1672 size, viewport.getGapCharacter());
1676 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1677 size, viewport.getGapCharacter());
1680 int groupAdjustment = 0;
1681 if (ssc.getGapsInsertedBegin() && right)
1683 if (viewport.cursorMode)
1685 alignPanel.seqPanel.moveCursor(size, 0);
1689 groupAdjustment = size;
1692 else if (!ssc.getGapsInsertedBegin() && !right)
1694 if (viewport.cursorMode)
1696 alignPanel.seqPanel.moveCursor(-size, 0);
1700 groupAdjustment = -size;
1704 if (groupAdjustment != 0)
1706 viewport.getSelectionGroup().setStartRes(
1707 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1708 viewport.getSelectionGroup().setEndRes(
1709 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1712 boolean appendHistoryItem = false;
1713 Deque<CommandI> historyList = viewport.getHistoryList();
1714 if (historyList != null && historyList.size() > 0
1715 && historyList.peek() instanceof SlideSequencesCommand)
1717 appendHistoryItem = ssc
1718 .appendSlideCommand((SlideSequencesCommand) historyList
1722 if (!appendHistoryItem)
1724 addHistoryItem(ssc);
1730 static StringBuffer copiedSequences;
1732 static Vector copiedHiddenColumns;
1734 protected void copy_actionPerformed()
1736 if (viewport.getSelectionGroup() == null)
1741 SequenceGroup sg = viewport.getSelectionGroup();
1742 copiedSequences = new StringBuffer();
1743 Hashtable orderedSeqs = new Hashtable();
1744 for (int i = 0; i < sg.getSize(); i++)
1746 SequenceI seq = sg.getSequenceAt(i);
1747 int index = viewport.getAlignment().findIndex(seq);
1748 orderedSeqs.put(index + "", seq);
1751 int index = 0, startRes, endRes;
1754 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1756 copiedHiddenColumns = new Vector();
1757 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1758 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1760 copiedHiddenColumns.addElement(new int[]
1761 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1766 copiedHiddenColumns = null;
1769 for (int i = 0; i < sg.getSize(); i++)
1771 SequenceI seq = null;
1775 if (orderedSeqs.containsKey(index + ""))
1777 seq = (SequenceI) orderedSeqs.get(index + "");
1789 // Returns residue following index if gap
1790 startRes = seq.findPosition(sg.getStartRes());
1793 // Need to find the residue preceeding index if gap
1796 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1798 ch = seq.getCharAt(j);
1799 if (!jalview.util.Comparison.isGap((ch)))
1807 endRes += seq.getStart() - 1;
1810 copiedSequences.append(seq.getName()
1816 + seq.getSequenceAsString(sg.getStartRes(),
1817 sg.getEndRes() + 1) + "\n");
1822 protected void pasteNew_actionPerformed()
1827 protected void pasteThis_actionPerformed()
1832 void paste(boolean newAlignment)
1837 if (copiedSequences == null)
1842 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1843 Vector seqs = new Vector();
1844 while (st.hasMoreElements())
1846 String name = st.nextToken();
1847 int start = Integer.parseInt(st.nextToken());
1848 int end = Integer.parseInt(st.nextToken());
1849 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1851 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1852 for (int i = 0; i < seqs.size(); i++)
1854 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1859 String newtitle = MessageManager.getString("label.copied_sequences");
1860 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1862 newtitle = getTitle();
1866 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1868 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1869 viewport.applet, newtitle, false);
1870 if (copiedHiddenColumns != null)
1872 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1874 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1875 af.viewport.hideColumns(region[0], region[1]);
1879 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1884 addSequences(newSeqs);
1887 } catch (Exception ex)
1889 } // could be anything being pasted in here
1893 void addSequences(SequenceI[] seqs)
1895 for (int i = 0; i < seqs.length; i++)
1897 viewport.getAlignment().addSequence(seqs[i]);
1901 addHistoryItem(new EditCommand(
1902 MessageManager.getString("label.add_sequences"), Action.PASTE,
1903 seqs, 0, viewport.getAlignment().getWidth(),
1904 viewport.getAlignment()));
1906 viewport.setEndSeq(viewport.getAlignment().getHeight());
1907 viewport.getAlignment().getWidth();
1908 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1913 protected void cut_actionPerformed()
1915 copy_actionPerformed();
1916 delete_actionPerformed();
1919 protected void delete_actionPerformed()
1922 SequenceGroup sg = viewport.getSelectionGroup();
1928 Vector seqs = new Vector();
1930 for (int i = 0; i < sg.getSize(); i++)
1932 seq = sg.getSequenceAt(i);
1933 seqs.addElement(seq);
1936 // If the cut affects all sequences, remove highlighted columns
1937 if (sg.getSize() == viewport.getAlignment().getHeight())
1939 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1940 sg.getEndRes() + 1);
1943 SequenceI[] cut = new SequenceI[seqs.size()];
1944 for (int i = 0; i < seqs.size(); i++)
1946 cut[i] = (SequenceI) seqs.elementAt(i);
1950 * //ADD HISTORY ITEM
1952 addHistoryItem(new EditCommand(
1953 MessageManager.getString("label.cut_sequences"), Action.CUT,
1954 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1955 viewport.getAlignment()));
1957 viewport.setSelectionGroup(null);
1958 viewport.getAlignment().deleteGroup(sg);
1960 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1963 if (viewport.getAlignment().getHeight() < 1)
1965 this.setVisible(false);
1967 viewport.sendSelection();
1971 * group consensus toggled
1974 protected void showGroupConsensus_actionPerformed()
1976 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1977 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1982 * group conservation toggled.
1984 protected void showGroupConservation_actionPerformed()
1986 viewport.setShowGroupConservation(showGroupConservation.getState());
1987 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1994 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1995 * .event.ActionEvent)
1997 protected void showConsensusHistogram_actionPerformed()
1999 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2000 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2007 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2008 * .event.ActionEvent)
2010 protected void showSequenceLogo_actionPerformed()
2012 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2013 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2016 protected void normSequenceLogo_actionPerformed()
2018 showSequenceLogo.setState(true);
2019 viewport.setShowSequenceLogo(true);
2020 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2021 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2024 protected void applyAutoAnnotationSettings_actionPerformed()
2026 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2029 protected void makeGrpsFromSelection_actionPerformed()
2031 if (avc.makeGroupsFromSelection())
2033 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2034 alignPanel.updateAnnotation();
2035 alignPanel.paintAlignment(true);
2039 protected void createGroup_actionPerformed()
2044 protected void unGroup_actionPerformed()
2048 alignPanel.alignmentChanged();
2052 protected void deleteGroups_actionPerformed()
2054 if (avc.deleteGroups())
2056 alignPanel.alignmentChanged();
2060 public void selectAllSequenceMenuItem_actionPerformed()
2062 SequenceGroup sg = new SequenceGroup();
2063 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2065 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2067 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2068 viewport.setSelectionGroup(sg);
2069 alignPanel.paintAlignment(true);
2070 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2071 viewport.sendSelection();
2074 public void deselectAllSequenceMenuItem_actionPerformed()
2076 if (viewport.cursorMode)
2078 alignPanel.seqPanel.keyboardNo1 = null;
2079 alignPanel.seqPanel.keyboardNo2 = null;
2081 viewport.setSelectionGroup(null);
2082 viewport.getColumnSelection().clear();
2083 viewport.setSelectionGroup(null);
2084 alignPanel.idPanel.idCanvas.searchResults = null;
2085 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2086 alignPanel.paintAlignment(true);
2087 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2088 viewport.sendSelection();
2091 public void invertSequenceMenuItem_actionPerformed()
2093 SequenceGroup sg = viewport.getSelectionGroup();
2094 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2096 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2099 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2100 viewport.sendSelection();
2103 public void invertColSel_actionPerformed()
2105 viewport.invertColumnSelection();
2106 alignPanel.paintAlignment(true);
2107 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2108 viewport.sendSelection();
2111 void trimAlignment(boolean trimLeft)
2113 ColumnSelection colSel = viewport.getColumnSelection();
2116 if (colSel.size() > 0)
2120 column = colSel.getMin();
2124 column = colSel.getMax();
2128 if (viewport.getSelectionGroup() != null)
2130 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2131 viewport.getHiddenRepSequences());
2135 seqs = viewport.getAlignment().getSequencesArray();
2138 TrimRegionCommand trimRegion;
2141 trimRegion = new TrimRegionCommand("Remove Left",
2142 TrimRegionCommand.TRIM_LEFT, seqs, column,
2143 viewport.getAlignment(), viewport.getColumnSelection(),
2144 viewport.getSelectionGroup());
2145 viewport.setStartRes(0);
2149 trimRegion = new TrimRegionCommand("Remove Right",
2150 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2151 viewport.getAlignment(), viewport.getColumnSelection(),
2152 viewport.getSelectionGroup());
2155 statusBar.setText(MessageManager.formatMessage(
2156 "label.removed_columns", new String[]
2157 { Integer.valueOf(trimRegion.getSize()).toString() }));
2158 addHistoryItem(trimRegion);
2160 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2162 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2163 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2165 viewport.getAlignment().deleteGroup(sg);
2169 viewport.firePropertyChange("alignment", null, viewport
2170 .getAlignment().getSequences());
2174 public void removeGappedColumnMenuItem_actionPerformed()
2176 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2179 if (viewport.getSelectionGroup() != null)
2181 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2182 viewport.getHiddenRepSequences());
2183 start = viewport.getSelectionGroup().getStartRes();
2184 end = viewport.getSelectionGroup().getEndRes();
2188 seqs = viewport.getAlignment().getSequencesArray();
2191 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2192 "Remove Gapped Columns", seqs, start, end,
2193 viewport.getAlignment());
2195 addHistoryItem(removeGapCols);
2197 statusBar.setText(MessageManager.formatMessage(
2198 "label.removed_empty_columns", new String[]
2199 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2201 // This is to maintain viewport position on first residue
2202 // of first sequence
2203 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2204 int startRes = seq.findPosition(viewport.startRes);
2205 // ShiftList shifts;
2206 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2207 // edit.alColumnChanges=shifts.getInverse();
2208 // if (viewport.hasHiddenColumns)
2209 // viewport.getColumnSelection().compensateForEdits(shifts);
2210 viewport.setStartRes(seq.findIndex(startRes) - 1);
2211 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2216 public void removeAllGapsMenuItem_actionPerformed()
2218 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2221 if (viewport.getSelectionGroup() != null)
2223 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2224 viewport.getHiddenRepSequences());
2225 start = viewport.getSelectionGroup().getStartRes();
2226 end = viewport.getSelectionGroup().getEndRes();
2230 seqs = viewport.getAlignment().getSequencesArray();
2233 // This is to maintain viewport position on first residue
2234 // of first sequence
2235 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2236 int startRes = seq.findPosition(viewport.startRes);
2238 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2239 viewport.getAlignment()));
2241 viewport.setStartRes(seq.findIndex(startRes) - 1);
2243 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2248 public void findMenuItem_actionPerformed()
2250 new Finder(alignPanel);
2254 * create a new view derived from the current view
2257 * @return frame for the new view
2259 public AlignFrame newView(String viewtitle)
2262 if (viewport.hasHiddenRows())
2264 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2265 .getFullAlignment().getSequencesArray());
2269 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2272 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2274 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2276 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2278 newal.addAnnotation(viewport.getAlignment()
2279 .getAlignmentAnnotation()[i]);
2284 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2286 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2287 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2288 PaintRefresher.Register(newaf.alignPanel,
2289 newaf.alignPanel.av.getSequenceSetId());
2291 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2292 newaf.alignPanel.av.getSequenceSetId());
2293 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2294 newaf.alignPanel.av.getSequenceSetId());
2296 Vector comps = (Vector) PaintRefresher.components.get(viewport
2297 .getSequenceSetId());
2299 for (int i = 0; i < comps.size(); i++)
2301 if (comps.elementAt(i) instanceof AlignmentPanel)
2307 String title = new String(this.getTitle());
2308 if (viewtitle != null)
2310 title = viewtitle + " ( " + title + ")";
2314 if (title.indexOf("(View") > -1)
2316 title = title.substring(0, title.indexOf("(View"));
2318 title += "(View " + viewSize + ")";
2321 newaf.setTitle(title.toString());
2323 newaf.viewport.setHistoryList(viewport.getHistoryList());
2324 newaf.viewport.setRedoList(viewport.getRedoList());
2330 * @return list of feature groups on the view
2332 public String[] getFeatureGroups()
2334 FeatureRenderer fr = null;
2335 if (alignPanel != null
2336 && (fr = alignPanel.getFeatureRenderer()) != null)
2338 List gps = fr.getFeatureGroups();
2340 String[] _gps = new String[gps.size()];
2343 _gps[p++] = gp.toString();
2351 * get sequence feature groups that are hidden or shown
2357 public String[] getFeatureGroupsOfState(boolean visible)
2359 FeatureRenderer fr = null;
2360 if (alignPanel != null
2361 && (fr = alignPanel.getFeatureRenderer()) != null)
2363 List gps = fr.getGroups(visible);
2365 String[] _gps = new String[gps.size()];
2368 _gps[p++] = gp.toString();
2376 * Change the display state for the given feature groups
2379 * list of group strings
2381 * visible or invisible
2383 public void setFeatureGroupState(String[] groups, boolean state)
2385 FeatureRenderer fr = null;
2386 this.sequenceFeatures.setState(true);
2387 viewport.setShowSequenceFeatures(true);
2388 if (alignPanel != null
2389 && (fr = alignPanel.getFeatureRenderer()) != null)
2392 fr.setGroupVisibility(Arrays.asList(groups), state);
2393 alignPanel.seqPanel.seqCanvas.repaint();
2394 if (alignPanel.overviewPanel != null)
2396 alignPanel.overviewPanel.updateOverviewImage();
2401 public void seqLimits_itemStateChanged()
2403 viewport.setShowJVSuffix(seqLimits.getState());
2404 alignPanel.fontChanged();
2405 alignPanel.paintAlignment(true);
2408 protected void colourTextMenuItem_actionPerformed()
2410 viewport.setColourText(colourTextMenuItem.getState());
2411 alignPanel.paintAlignment(true);
2414 protected void displayNonconservedMenuItem_actionPerformed()
2416 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2417 alignPanel.paintAlignment(true);
2420 protected void wrapMenuItem_actionPerformed()
2422 viewport.setWrapAlignment(wrapMenuItem.getState());
2423 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2424 scaleAbove.setEnabled(wrapMenuItem.getState());
2425 scaleLeft.setEnabled(wrapMenuItem.getState());
2426 scaleRight.setEnabled(wrapMenuItem.getState());
2427 alignPanel.paintAlignment(true);
2430 public void overviewMenuItem_actionPerformed()
2432 if (alignPanel.overviewPanel != null)
2437 Frame frame = new Frame();
2438 OverviewPanel overview = new OverviewPanel(alignPanel);
2439 frame.add(overview);
2440 // +50 must allow for applet frame window
2441 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2442 "label.overview_params", new String[]
2443 { this.getTitle() }), overview.getPreferredSize().width,
2444 overview.getPreferredSize().height + 50);
2447 final AlignmentPanel ap = alignPanel;
2448 frame.addWindowListener(new WindowAdapter()
2451 public void windowClosing(WindowEvent e)
2455 ap.setOverviewPanel(null);
2460 alignPanel.setOverviewPanel(overview);
2464 void changeColour(ColourSchemeI cs)
2470 if (viewport.getAbovePIDThreshold())
2472 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2476 if (viewport.getConservationSelected())
2478 cs.setConservationApplied(true);
2479 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2484 cs.setConservationApplied(false);
2487 viewport.setGlobalColourScheme(cs);
2489 if (alignPanel.getOverviewPanel() != null)
2491 alignPanel.getOverviewPanel().updateOverviewImage();
2494 jalview.structure.StructureSelectionManager
2495 .getStructureSelectionManager(viewport.applet)
2496 .sequenceColoursChanged(alignPanel);
2498 alignPanel.paintAlignment(true);
2501 protected void modifyPID_actionPerformed()
2503 if (viewport.getAbovePIDThreshold()
2504 && viewport.getGlobalColourScheme() != null)
2506 SliderPanel.setPIDSliderSource(alignPanel,
2507 viewport.getGlobalColourScheme(), "Background");
2508 SliderPanel.showPIDSlider();
2512 protected void modifyConservation_actionPerformed()
2514 if (viewport.getConservationSelected()
2515 && viewport.getGlobalColourScheme() != null)
2517 SliderPanel.setConservationSlider(alignPanel,
2518 viewport.getGlobalColourScheme(), "Background");
2519 SliderPanel.showConservationSlider();
2523 protected void conservationMenuItem_actionPerformed()
2525 viewport.setConservationSelected(conservationMenuItem.getState());
2527 viewport.setAbovePIDThreshold(false);
2528 abovePIDThreshold.setState(false);
2530 changeColour(viewport.getGlobalColourScheme());
2532 modifyConservation_actionPerformed();
2535 public void abovePIDThreshold_actionPerformed()
2537 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2539 conservationMenuItem.setState(false);
2540 viewport.setConservationSelected(false);
2542 changeColour(viewport.getGlobalColourScheme());
2544 modifyPID_actionPerformed();
2547 public void sortPairwiseMenuItem_actionPerformed()
2549 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2550 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2551 .getAlignment().getSequenceAt(0), null);
2553 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2554 viewport.getAlignment()));
2555 alignPanel.paintAlignment(true);
2558 public void sortIDMenuItem_actionPerformed()
2560 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2561 AlignmentSorter.sortByID(viewport.getAlignment());
2562 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2563 viewport.getAlignment()));
2564 alignPanel.paintAlignment(true);
2567 public void sortLengthMenuItem_actionPerformed()
2569 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2570 AlignmentSorter.sortByLength(viewport.getAlignment());
2571 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2572 viewport.getAlignment()));
2573 alignPanel.paintAlignment(true);
2576 public void sortGroupMenuItem_actionPerformed()
2578 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2579 AlignmentSorter.sortByGroup(viewport.getAlignment());
2580 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2581 viewport.getAlignment()));
2582 alignPanel.paintAlignment(true);
2586 public void removeRedundancyMenuItem_actionPerformed()
2588 new RedundancyPanel(alignPanel);
2591 public void pairwiseAlignmentMenuItem_actionPerformed()
2593 if (viewport.getSelectionGroup() != null
2594 && viewport.getSelectionGroup().getSize() > 1)
2596 Frame frame = new Frame();
2597 frame.add(new PairwiseAlignPanel(alignPanel));
2598 jalview.bin.JalviewLite.addFrame(frame,
2599 MessageManager.getString("action.pairwise_alignment"), 600,
2604 public void PCAMenuItem_actionPerformed()
2606 // are the sequences aligned?
2607 if (!viewport.getAlignment().isAligned(false))
2610 int Width = viewport.getAlignment().getWidth();
2612 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2614 current = viewport.getAlignment().getSequenceAt(i);
2616 if (current.getLength() < Width)
2618 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2621 alignPanel.paintAlignment(true);
2624 if ((viewport.getSelectionGroup() != null
2625 && viewport.getSelectionGroup().getSize() < 4 && viewport
2626 .getSelectionGroup().getSize() > 0)
2627 || viewport.getAlignment().getHeight() < 4)
2634 new PCAPanel(viewport);
2635 } catch (java.lang.OutOfMemoryError ex)
2641 public void averageDistanceTreeMenuItem_actionPerformed()
2643 NewTreePanel("AV", "PID", "Average distance tree using PID");
2646 public void neighbourTreeMenuItem_actionPerformed()
2648 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2651 protected void njTreeBlosumMenuItem_actionPerformed()
2653 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2656 protected void avTreeBlosumMenuItem_actionPerformed()
2658 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2661 void NewTreePanel(String type, String pwType, String title)
2663 // are the sequences aligned?
2664 if (!viewport.getAlignment().isAligned(false))
2667 int Width = viewport.getAlignment().getWidth();
2669 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2671 current = viewport.getAlignment().getSequenceAt(i);
2673 if (current.getLength() < Width)
2675 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2678 alignPanel.paintAlignment(true);
2682 if ((viewport.getSelectionGroup() != null && viewport
2683 .getSelectionGroup().getSize() > 1)
2684 || (viewport.getAlignment().getHeight() > 1))
2686 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2688 addTreeMenuItem(tp, title);
2690 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2694 void loadTree_actionPerformed()
2696 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2697 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2698 cap.setTreeImport();
2699 Frame frame = new Frame();
2701 jalview.bin.JalviewLite.addFrame(frame,
2702 MessageManager.getString("label.paste_newick_file"), 400, 300);
2705 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2707 TreePanel tp = new TreePanel(alignPanel, treeFile,
2708 MessageManager.getString("label.load_tree_from_file"), tree);
2709 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2710 addTreeMenuItem(tp, treeFile);
2714 * sort the alignment using the given treePanel
2717 * tree used to sort view
2719 * string used for undo event name
2721 public void sortByTree(TreePanel treePanel, String title)
2723 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2726 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2727 // HistoryItem.SORT));
2728 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2729 "label.order_by_params", new String[]
2730 { title }), oldOrder, viewport.getAlignment()));
2731 alignPanel.paintAlignment(true);
2735 * Do any automatic reordering of the alignment and add the necessary bits to
2736 * the menu structure for the new tree
2741 protected void addTreeMenuItem(final TreePanel treePanel,
2744 final MenuItem item = new MenuItem(title);
2745 sortByTreeMenu.add(item);
2746 item.addActionListener(new java.awt.event.ActionListener()
2749 public void actionPerformed(ActionEvent evt)
2751 sortByTree(treePanel, title); // treePanel.getTitle());
2755 treePanel.addWindowListener(new WindowAdapter()
2758 public void windowOpened(WindowEvent e)
2760 if (viewport.sortByTree)
2762 sortByTree(treePanel, title);
2764 super.windowOpened(e);
2768 public void windowClosing(WindowEvent e)
2770 sortByTreeMenu.remove(item);
2775 public boolean sortBy(AlignmentOrder alorder, String undoname)
2777 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2778 if (viewport.applet.debug)
2780 System.err.println("Sorting " + alorder.getOrder().size()
2781 + " in alignment '" + getTitle() + "'");
2783 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2784 if (undoname != null)
2786 addHistoryItem(new OrderCommand(undoname, oldOrder,
2787 viewport.getAlignment()));
2789 alignPanel.paintAlignment(true);
2793 protected void documentation_actionPerformed()
2795 alignPanel.av.applet.openJalviewHelpUrl();
2798 protected void about_actionPerformed()
2801 class AboutPanel extends Canvas
2807 public AboutPanel(String version, String builddate)
2809 this.version = version;
2810 this.builddate = builddate;
2814 public void paint(Graphics g)
2816 g.setColor(Color.white);
2817 g.fillRect(0, 0, getSize().width, getSize().height);
2818 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2819 FontMetrics fm = g.getFontMetrics();
2820 int fh = fm.getHeight();
2822 g.setColor(Color.black);
2823 // TODO: update this text for each release or centrally store it for
2824 // lite and application
2825 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2826 g.drawString(MessageManager.formatMessage(
2827 "label.jalviewLite_release", new String[]
2828 { version }), x, y += fh);
2829 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2830 g.drawString(MessageManager.formatMessage(
2831 "label.jaview_build_date", new String[]
2832 { builddate }), x, y += fh);
2833 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2834 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2836 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2837 x + 50, y += fh + 8);
2839 MessageManager.getString("label.jalview_dev_managers"), x,
2841 g.drawString(MessageManager
2842 .getString("label.jalview_distribution_lists"), x, y += fh);
2843 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2846 MessageManager.getString("label.jalview_cite_1_authors"),
2849 MessageManager.getString("label.jalview_cite_1_title"), x,
2851 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2856 Frame frame = new Frame();
2857 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2859 jalview.bin.JalviewLite.addFrame(frame,
2860 MessageManager.getString("label.jalview"), 580, 220);
2864 public void showURL(String url, String target)
2866 if (viewport.applet == null)
2868 System.out.println("Not running as applet - no browser available.");
2872 viewport.applet.showURL(url, target);
2876 // ////////////////////////////////////////////////////////////////////////////////
2877 // JBuilder Graphics here
2879 MenuBar alignFrameMenuBar = new MenuBar();
2881 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2883 MenuItem loadApplication = new MenuItem(
2884 MessageManager.getString("label.view_full_application"));
2886 MenuItem loadTree = new MenuItem(
2887 MessageManager.getString("label.load_associated_tree"));
2889 MenuItem loadAnnotations = new MenuItem(
2890 MessageManager.getString("label.load_features_annotations"));
2892 MenuItem outputFeatures = new MenuItem(
2893 MessageManager.getString("label.export_features").concat("..."));
2895 MenuItem outputAnnotations = new MenuItem(
2896 MessageManager.getString("label.export_annotations").concat("..."));
2898 MenuItem closeMenuItem = new MenuItem(
2899 MessageManager.getString("action.close"));
2901 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2903 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2905 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2907 Menu calculateMenu = new Menu(
2908 MessageManager.getString("action.calculate"));
2910 MenuItem selectAllSequenceMenuItem = new MenuItem(
2911 MessageManager.getString("action.select_all"));
2913 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2914 MessageManager.getString("action.deselect_all"));
2916 MenuItem invertSequenceMenuItem = new MenuItem(
2917 MessageManager.getString("action.invert_selection"));
2919 MenuItem remove2LeftMenuItem = new MenuItem();
2921 MenuItem remove2RightMenuItem = new MenuItem();
2923 MenuItem removeGappedColumnMenuItem = new MenuItem();
2925 MenuItem removeAllGapsMenuItem = new MenuItem();
2927 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2929 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2931 MenuItem sortPairwiseMenuItem = new MenuItem();
2933 MenuItem sortIDMenuItem = new MenuItem();
2935 MenuItem sortLengthMenuItem = new MenuItem();
2937 MenuItem sortGroupMenuItem = new MenuItem();
2939 MenuItem removeRedundancyMenuItem = new MenuItem();
2941 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2943 MenuItem PCAMenuItem = new MenuItem();
2945 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2947 MenuItem neighbourTreeMenuItem = new MenuItem();
2949 BorderLayout borderLayout1 = new BorderLayout();
2951 public Label statusBar = new Label();
2953 Menu outputTextboxMenu = new Menu();
2955 MenuItem clustalColour = new MenuItem();
2957 MenuItem zappoColour = new MenuItem();
2959 MenuItem taylorColour = new MenuItem();
2961 MenuItem hydrophobicityColour = new MenuItem();
2963 MenuItem helixColour = new MenuItem();
2965 MenuItem strandColour = new MenuItem();
2967 MenuItem turnColour = new MenuItem();
2969 MenuItem buriedColour = new MenuItem();
2971 MenuItem purinePyrimidineColour = new MenuItem();
2973 MenuItem RNAInteractionColour = new MenuItem();
2975 MenuItem RNAHelixColour = new MenuItem();
2977 MenuItem userDefinedColour = new MenuItem();
2979 MenuItem PIDColour = new MenuItem();
2981 MenuItem BLOSUM62Colour = new MenuItem();
2983 MenuItem tcoffeeColour = new MenuItem();
2985 MenuItem njTreeBlosumMenuItem = new MenuItem();
2987 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2989 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2991 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2993 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2995 MenuItem alProperties = new MenuItem(
2996 MessageManager.getString("label.alignment_props"));
2998 MenuItem overviewMenuItem = new MenuItem();
3000 MenuItem undoMenuItem = new MenuItem();
3002 MenuItem redoMenuItem = new MenuItem();
3004 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3006 MenuItem noColourmenuItem = new MenuItem();
3008 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3010 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3012 MenuItem findMenuItem = new MenuItem();
3014 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3016 MenuItem nucleotideColour = new MenuItem();
3018 MenuItem deleteGroups = new MenuItem();
3020 MenuItem grpsFromSelection = new MenuItem();
3022 MenuItem createGroup = new MenuItem();
3024 MenuItem unGroup = new MenuItem();
3026 MenuItem delete = new MenuItem();
3028 MenuItem copy = new MenuItem();
3030 MenuItem cut = new MenuItem();
3032 Menu pasteMenu = new Menu();
3034 MenuItem pasteNew = new MenuItem();
3036 MenuItem pasteThis = new MenuItem();
3038 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3040 MenuItem font = new MenuItem();
3042 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3044 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3046 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3048 MenuItem modifyPID = new MenuItem();
3050 MenuItem modifyConservation = new MenuItem();
3052 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
3053 "Autocalculate Consensus", true);
3055 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3056 "Sort Alignment With New Tree", true);
3058 Menu sortByTreeMenu = new Menu();
3060 Menu sort = new Menu();
3062 Menu calculate = new Menu();
3064 MenuItem inputText = new MenuItem();
3066 Menu helpMenu = new Menu();
3068 MenuItem documentation = new MenuItem();
3070 MenuItem about = new MenuItem();
3072 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3074 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3076 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3078 Menu autoAnnMenu = new Menu();
3080 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3082 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3084 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3086 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3088 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3090 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3092 private void jbInit() throws Exception
3095 setMenuBar(alignFrameMenuBar);
3099 // dynamically fill save as menu with available formats
3100 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3103 item = new MenuItem(
3104 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3106 item.addActionListener(new java.awt.event.ActionListener()
3109 public void actionPerformed(ActionEvent e)
3111 outputText_actionPerformed(e);
3115 outputTextboxMenu.add(item);
3117 closeMenuItem.addActionListener(this);
3118 loadApplication.addActionListener(this);
3120 loadTree.addActionListener(this);
3121 loadAnnotations.addActionListener(this);
3122 outputFeatures.addActionListener(this);
3123 outputAnnotations.addActionListener(this);
3124 selectAllSequenceMenuItem.addActionListener(this);
3125 deselectAllSequenceMenuItem.addActionListener(this);
3126 invertSequenceMenuItem.addActionListener(this);
3127 remove2LeftMenuItem.setLabel(MessageManager
3128 .getString("action.remove_left"));
3129 remove2LeftMenuItem.addActionListener(this);
3130 remove2RightMenuItem.setLabel(MessageManager
3131 .getString("action.remove_right"));
3132 remove2RightMenuItem.addActionListener(this);
3133 removeGappedColumnMenuItem.setLabel(MessageManager
3134 .getString("action.remove_empty_columns"));
3135 removeGappedColumnMenuItem.addActionListener(this);
3136 removeAllGapsMenuItem.setLabel(MessageManager
3137 .getString("action.remove_all_gaps"));
3138 removeAllGapsMenuItem.addActionListener(this);
3139 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3140 viewBoxesMenuItem.setState(true);
3141 viewBoxesMenuItem.addItemListener(this);
3142 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3143 viewTextMenuItem.setState(true);
3144 viewTextMenuItem.addItemListener(this);
3145 sortPairwiseMenuItem.setLabel(MessageManager
3146 .getString("action.by_pairwise_id"));
3147 sortPairwiseMenuItem.addActionListener(this);
3148 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3149 sortIDMenuItem.addActionListener(this);
3150 sortLengthMenuItem.setLabel(MessageManager
3151 .getString("action.by_length"));
3152 sortLengthMenuItem.addActionListener(this);
3153 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3154 sortGroupMenuItem.addActionListener(this);
3155 removeRedundancyMenuItem.setLabel(MessageManager
3156 .getString("action.remove_redundancy").concat("..."));
3157 removeRedundancyMenuItem.addActionListener(this);
3158 pairwiseAlignmentMenuItem.setLabel(MessageManager
3159 .getString("action.pairwise_alignment"));
3160 pairwiseAlignmentMenuItem.addActionListener(this);
3161 PCAMenuItem.setLabel(MessageManager
3162 .getString("label.principal_component_analysis"));
3163 PCAMenuItem.addActionListener(this);
3164 averageDistanceTreeMenuItem.setLabel(MessageManager
3165 .getString("label.average_distance_identity"));
3166 averageDistanceTreeMenuItem.addActionListener(this);
3167 neighbourTreeMenuItem.setLabel(MessageManager
3168 .getString("label.neighbour_joining_identity"));
3169 neighbourTreeMenuItem.addActionListener(this);
3170 statusBar.setBackground(Color.white);
3171 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3172 statusBar.setText(MessageManager.getString("label.status_bar"));
3173 outputTextboxMenu.setLabel(MessageManager
3174 .getString("label.out_to_textbox"));
3175 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3177 clustalColour.addActionListener(this);
3178 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3179 zappoColour.addActionListener(this);
3180 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3181 taylorColour.addActionListener(this);
3182 hydrophobicityColour.setLabel(MessageManager
3183 .getString("label.hydrophobicity"));
3184 hydrophobicityColour.addActionListener(this);
3186 .setLabel(MessageManager.getString("label.helix_propensity"));
3187 helixColour.addActionListener(this);
3188 strandColour.setLabel(MessageManager
3189 .getString("label.strand_propensity"));
3190 strandColour.addActionListener(this);
3191 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3192 turnColour.addActionListener(this);
3193 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3194 buriedColour.addActionListener(this);
3195 purinePyrimidineColour.setLabel(MessageManager
3196 .getString("label.purine_pyrimidine"));
3197 purinePyrimidineColour.addActionListener(this);
3198 RNAInteractionColour.setLabel(MessageManager
3199 .getString("label.rna_interaction"));
3200 RNAInteractionColour.addActionListener(this);
3201 RNAHelixColour.setLabel(MessageManager
3202 .getString("action.by_rna_helixes"));
3203 RNAHelixColour.addActionListener(this);
3204 userDefinedColour.setLabel(MessageManager
3205 .getString("action.user_defined"));
3206 userDefinedColour.addActionListener(this);
3207 PIDColour.setLabel(MessageManager
3208 .getString("label.percentage_identity"));
3209 PIDColour.addActionListener(this);
3210 BLOSUM62Colour.setLabel(MessageManager
3211 .getString("label.blosum62_score"));
3212 BLOSUM62Colour.addActionListener(this);
3214 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3215 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3217 tcoffeeColour.addActionListener(this);
3218 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3219 .getString("label.average_distance_bloslum62"));
3220 avDistanceTreeBlosumMenuItem.addActionListener(this);
3221 njTreeBlosumMenuItem.setLabel(MessageManager
3222 .getString("label.neighbour_blosum62"));
3223 njTreeBlosumMenuItem.addActionListener(this);
3224 annotationPanelMenuItem.setLabel(MessageManager
3225 .getString("label.show_annotations"));
3226 annotationPanelMenuItem.addItemListener(this);
3227 colourTextMenuItem.setLabel(MessageManager
3228 .getString("label.colour_text"));
3229 colourTextMenuItem.addItemListener(this);
3230 displayNonconservedMenuItem.setLabel(MessageManager
3231 .getString("label.show_non_conversed"));
3232 displayNonconservedMenuItem.addItemListener(this);
3233 alProperties.addActionListener(this);
3234 overviewMenuItem.setLabel(MessageManager
3235 .getString("label.overview_window"));
3236 overviewMenuItem.addActionListener(this);
3237 undoMenuItem.setEnabled(false);
3238 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3239 undoMenuItem.addActionListener(this);
3240 redoMenuItem.setEnabled(false);
3241 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3242 redoMenuItem.addActionListener(this);
3243 conservationMenuItem.setLabel(MessageManager
3244 .getString("action.by_conservation"));
3245 conservationMenuItem.addItemListener(this);
3246 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3247 noColourmenuItem.addActionListener(this);
3248 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3249 wrapMenuItem.addItemListener(this);
3250 renderGapsMenuItem.setLabel(MessageManager
3251 .getString("action.show_gaps"));
3252 renderGapsMenuItem.setState(true);
3253 renderGapsMenuItem.addItemListener(this);
3254 findMenuItem.setLabel(MessageManager.getString("action.find"));
3255 findMenuItem.addActionListener(this);
3256 abovePIDThreshold.setLabel(MessageManager
3257 .getString("label.above_identity_threshold"));
3258 abovePIDThreshold.addItemListener(this);
3259 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3260 nucleotideColour.addActionListener(this);
3261 deleteGroups.setLabel(MessageManager
3262 .getString("action.undefine_groups"));
3263 deleteGroups.addActionListener(this);
3264 grpsFromSelection.setLabel(MessageManager
3265 .getString("action.make_groups_selection"));
3266 grpsFromSelection.addActionListener(this);
3267 createGroup.setLabel(MessageManager.getString("action.create_group"));
3268 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3269 copy.setLabel(MessageManager.getString("action.copy"));
3270 copy.addActionListener(this);
3271 cut.setLabel(MessageManager.getString("action.cut"));
3272 cut.addActionListener(this);
3273 delete.setLabel(MessageManager.getString("action.delete"));
3274 delete.addActionListener(this);
3275 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3276 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3277 pasteNew.addActionListener(this);
3278 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3279 pasteThis.addActionListener(this);
3280 applyToAllGroups.setLabel(MessageManager
3281 .getString("label.apply_colour_to_all_groups"));
3282 applyToAllGroups.setState(true);
3283 applyToAllGroups.addItemListener(this);
3284 font.setLabel(MessageManager.getString("action.font"));
3285 font.addActionListener(this);
3286 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3287 scaleAbove.setState(true);
3288 scaleAbove.setEnabled(false);
3289 scaleAbove.addItemListener(this);
3290 scaleLeft.setEnabled(false);
3291 scaleLeft.setState(true);
3292 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3293 scaleLeft.addItemListener(this);
3294 scaleRight.setEnabled(false);
3295 scaleRight.setState(true);
3296 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3297 scaleRight.addItemListener(this);
3298 modifyPID.setLabel(MessageManager
3299 .getString("label.modify_identity_thereshold"));
3300 modifyPID.addActionListener(this);
3301 modifyConservation.setLabel(MessageManager
3302 .getString("label.modify_conservation_thereshold"));
3303 modifyConservation.addActionListener(this);
3304 sortByTreeMenu.setLabel(MessageManager
3305 .getString("action.by_tree_order"));
3306 sort.setLabel(MessageManager.getString("action.sort"));
3307 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3308 autoCalculate.addItemListener(this);
3309 sortByTree.addItemListener(this);
3311 .setLabel(MessageManager.getString("label.input_from_textbox"));
3312 inputText.addActionListener(this);
3313 centreColumnLabelFlag.setLabel(MessageManager
3314 .getString("label.centre_column_labels"));
3315 centreColumnLabelFlag.addItemListener(this);
3316 followMouseOverFlag.setLabel(MessageManager
3317 .getString("label.automatic_scrolling"));
3318 followMouseOverFlag.addItemListener(this);
3319 helpMenu.setLabel(MessageManager.getString("action.help"));
3320 documentation.setLabel(MessageManager.getString("label.documentation"));
3321 documentation.addActionListener(this);
3323 about.setLabel(MessageManager.getString("label.about"));
3324 about.addActionListener(this);
3325 seqLimits.setState(true);
3326 seqLimits.setLabel(MessageManager
3327 .getString("label.show_sequence_limits"));
3328 seqLimits.addItemListener(this);
3329 featureSettings.setLabel(MessageManager
3330 .getString("label.feature_settings"));
3331 featureSettings.addActionListener(this);
3332 sequenceFeatures.setLabel(MessageManager
3333 .getString("label.sequence_features"));
3334 sequenceFeatures.addItemListener(this);
3335 sequenceFeatures.setState(false);
3336 annotationColour.setLabel(MessageManager
3337 .getString("action.by_annotation"));
3338 annotationColour.addActionListener(this);
3340 annotationColumnSelection.setLabel("Select by Annotation");
3341 annotationColumnSelection.addActionListener(this);
3343 invertSequenceMenuItem.setLabel(MessageManager
3344 .getString("action.invert_sequence_selection"));
3345 invertColSel.setLabel(MessageManager
3346 .getString("action.invert_column_selection"));
3347 menu1.setLabel(MessageManager.getString("action.show"));
3348 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3349 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3350 menu2.setLabel(MessageManager.getString("action.hide"));
3352 .setLabel(MessageManager.getString("label.selected_columns"));
3353 hideSequences.setLabel(MessageManager
3354 .getString("label.selected_sequences"));
3355 hideAllButSelection.setLabel(MessageManager
3356 .getString("label.all_but_selected_region"));
3357 hideAllSelection.setLabel(MessageManager
3358 .getString("label.selected_region"));
3359 showAllHidden.setLabel(MessageManager
3360 .getString("label.all_sequences_columns"));
3361 showGroupConsensus.setLabel(MessageManager
3362 .getString("label.group_consensus"));
3363 showGroupConservation.setLabel(MessageManager
3364 .getString("label.group_conservation"));
3365 showConsensusHistogram.setLabel(MessageManager
3366 .getString("label.show_consensus_histogram"));
3367 showSequenceLogo.setLabel(MessageManager
3368 .getString("label.show_consensus_logo"));
3369 normSequenceLogo.setLabel(MessageManager
3370 .getString("label.norm_consensus_logo"));
3371 applyAutoAnnotationSettings.setLabel(MessageManager
3372 .getString("label.apply_all_groups"));
3373 applyAutoAnnotationSettings.setState(true);
3374 autoAnnMenu.setLabel(MessageManager
3375 .getString("label.autocalculated_annotation"));
3377 invertColSel.addActionListener(this);
3378 showColumns.addActionListener(this);
3379 showSeqs.addActionListener(this);
3380 hideColumns.addActionListener(this);
3381 hideSequences.addActionListener(this);
3382 hideAllButSelection.addActionListener(this);
3383 hideAllSelection.addActionListener(this);
3384 showAllHidden.addActionListener(this);
3385 showGroupConsensus.addItemListener(this);
3386 showGroupConservation.addItemListener(this);
3387 showConsensusHistogram.addItemListener(this);
3388 showSequenceLogo.addItemListener(this);
3389 normSequenceLogo.addItemListener(this);
3391 applyAutoAnnotationSettings.addItemListener(this);
3392 formatMenu.setLabel(MessageManager.getString("action.format"));
3393 selectMenu.setLabel(MessageManager.getString("action.select"));
3394 newView.setLabel(MessageManager.getString("action.new_view"));
3395 newView.addActionListener(this);
3396 alignFrameMenuBar.add(fileMenu);
3397 alignFrameMenuBar.add(editMenu);
3398 alignFrameMenuBar.add(selectMenu);
3399 alignFrameMenuBar.add(viewMenu);
3400 alignFrameMenuBar.add(formatMenu);
3401 alignFrameMenuBar.add(colourMenu);
3402 alignFrameMenuBar.add(calculateMenu);
3403 alignFrameMenuBar.add(helpMenu);
3405 fileMenu.add(inputText);
3406 fileMenu.add(loadTree);
3407 fileMenu.add(loadAnnotations);
3409 fileMenu.addSeparator();
3410 fileMenu.add(outputTextboxMenu);
3411 fileMenu.add(outputFeatures);
3412 fileMenu.add(outputAnnotations);
3414 if (jalviewServletURL != null)
3416 fileMenu.add(loadApplication);
3419 fileMenu.addSeparator();
3420 fileMenu.add(closeMenuItem);
3422 editMenu.add(undoMenuItem);
3423 editMenu.add(redoMenuItem);
3426 editMenu.add(pasteMenu);
3427 editMenu.add(delete);
3428 editMenu.addSeparator();
3429 editMenu.add(remove2LeftMenuItem);
3430 editMenu.add(remove2RightMenuItem);
3431 editMenu.add(removeGappedColumnMenuItem);
3432 editMenu.add(removeAllGapsMenuItem);
3433 editMenu.add(removeRedundancyMenuItem);
3434 viewMenu.add(newView);
3435 viewMenu.addSeparator();
3436 viewMenu.add(menu1);
3437 viewMenu.add(menu2);
3438 viewMenu.addSeparator();
3439 viewMenu.add(followMouseOverFlag);
3440 viewMenu.add(annotationPanelMenuItem);
3441 autoAnnMenu.add(applyAutoAnnotationSettings);
3442 autoAnnMenu.add(showConsensusHistogram);
3443 autoAnnMenu.add(showSequenceLogo);
3444 autoAnnMenu.add(normSequenceLogo);
3445 autoAnnMenu.addSeparator();
3446 autoAnnMenu.add(showGroupConservation);
3447 autoAnnMenu.add(showGroupConsensus);
3448 viewMenu.add(autoAnnMenu);
3449 viewMenu.addSeparator();
3450 viewMenu.add(sequenceFeatures);
3451 viewMenu.add(featureSettings);
3452 viewMenu.addSeparator();
3453 viewMenu.add(alProperties);
3454 viewMenu.addSeparator();
3455 viewMenu.add(overviewMenuItem);
3456 colourMenu.add(applyToAllGroups);
3457 colourMenu.addSeparator();
3458 colourMenu.add(noColourmenuItem);
3459 colourMenu.add(clustalColour);
3460 colourMenu.add(BLOSUM62Colour);
3461 colourMenu.add(PIDColour);
3462 colourMenu.add(zappoColour);
3463 colourMenu.add(taylorColour);
3464 colourMenu.add(hydrophobicityColour);
3465 colourMenu.add(helixColour);
3466 colourMenu.add(strandColour);
3467 colourMenu.add(turnColour);
3468 colourMenu.add(buriedColour);
3469 colourMenu.add(nucleotideColour);
3470 colourMenu.add(purinePyrimidineColour);
3471 // colourMenu.add(RNAInteractionColour);
3472 colourMenu.add(tcoffeeColour);
3473 colourMenu.add(userDefinedColour);
3474 colourMenu.addSeparator();
3475 colourMenu.add(conservationMenuItem);
3476 colourMenu.add(modifyConservation);
3477 colourMenu.add(abovePIDThreshold);
3478 colourMenu.add(modifyPID);
3479 colourMenu.add(annotationColour);
3480 colourMenu.add(RNAHelixColour);
3481 calculateMenu.add(sort);
3482 calculateMenu.add(calculate);
3483 calculateMenu.addSeparator();
3484 calculateMenu.add(pairwiseAlignmentMenuItem);
3485 calculateMenu.add(PCAMenuItem);
3486 calculateMenu.add(autoCalculate);
3487 calculateMenu.add(sortByTree);
3488 this.add(statusBar, BorderLayout.SOUTH);
3489 pasteMenu.add(pasteNew);
3490 pasteMenu.add(pasteThis);
3491 sort.add(sortIDMenuItem);
3492 sort.add(sortLengthMenuItem);
3493 sort.add(sortByTreeMenu);
3494 sort.add(sortGroupMenuItem);
3495 sort.add(sortPairwiseMenuItem);
3496 calculate.add(averageDistanceTreeMenuItem);
3497 calculate.add(neighbourTreeMenuItem);
3498 calculate.add(avDistanceTreeBlosumMenuItem);
3499 calculate.add(njTreeBlosumMenuItem);
3500 helpMenu.add(documentation);
3501 helpMenu.add(about);
3502 menu1.add(showColumns);
3503 menu1.add(showSeqs);
3504 menu1.add(showAllHidden);
3505 menu2.add(hideColumns);
3506 menu2.add(hideSequences);
3507 menu2.add(hideAllSelection);
3508 menu2.add(hideAllButSelection);
3509 formatMenu.add(font);
3510 formatMenu.add(seqLimits);
3511 formatMenu.add(wrapMenuItem);
3512 formatMenu.add(scaleAbove);
3513 formatMenu.add(scaleLeft);
3514 formatMenu.add(scaleRight);
3515 formatMenu.add(viewBoxesMenuItem);
3516 formatMenu.add(viewTextMenuItem);
3517 formatMenu.add(colourTextMenuItem);
3518 formatMenu.add(displayNonconservedMenuItem);
3519 formatMenu.add(renderGapsMenuItem);
3520 formatMenu.add(centreColumnLabelFlag);
3521 selectMenu.add(findMenuItem);
3522 selectMenu.addSeparator();
3523 selectMenu.add(selectAllSequenceMenuItem);
3524 selectMenu.add(deselectAllSequenceMenuItem);
3525 selectMenu.add(invertSequenceMenuItem);
3526 selectMenu.add(invertColSel);
3527 selectMenu.add(createGroup);
3528 selectMenu.add(unGroup);
3529 selectMenu.add(grpsFromSelection);
3530 selectMenu.add(deleteGroups);
3531 selectMenu.add(annotationColumnSelection);
3535 public void setStatus(String string)
3537 statusBar.setText(string);
3540 MenuItem featureSettings = new MenuItem();
3542 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3544 MenuItem annotationColour = new MenuItem();
3546 MenuItem annotationColumnSelection = new MenuItem();
3548 MenuItem invertColSel = new MenuItem();
3550 Menu menu1 = new Menu();
3552 MenuItem showColumns = new MenuItem();
3554 MenuItem showSeqs = new MenuItem();
3556 Menu menu2 = new Menu();
3558 MenuItem hideColumns = new MenuItem();
3560 MenuItem hideSequences = new MenuItem();
3562 MenuItem hideAllButSelection = new MenuItem();
3564 MenuItem hideAllSelection = new MenuItem();
3566 MenuItem showAllHidden = new MenuItem();
3568 Menu formatMenu = new Menu();
3570 Menu selectMenu = new Menu();
3572 MenuItem newView = new MenuItem();
3575 * Attach the alignFrame panels after embedding menus, if necessary. This used
3576 * to be called setEmbedded, but is now creates the dropdown menus in a
3577 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3579 * @param reallyEmbedded
3580 * true to attach the view to the applet area on the page rather than
3583 public void createAlignFrameWindow(boolean reallyEmbedded)
3587 embedAlignFrameInApplet(viewport.applet);
3592 // test and embed menu bar if necessary.
3594 if (embedMenuIfNeeded(alignPanel))
3597 * adjust for status bar height too. ? pointless as overridden by layout
3600 alignPanel.setSize(getSize().width,
3601 getSize().height - statusBar.getHeight());
3603 add(statusBar, BorderLayout.SOUTH);
3604 add(alignPanel, BorderLayout.CENTER);
3605 // and register with the applet so it can pass external API calls to us
3606 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3613 * Add the components of this AlignFrame to the applet container.
3617 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3620 // Explicitly build the embedded menu panel for the on-page applet
3622 // view cannot be closed if its actually on the page
3623 fileMenu.remove(closeMenuItem);
3624 fileMenu.remove(3); // Remove Separator
3625 // construct embedded menu, using default font
3626 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3627 // and actually add the components to the applet area
3628 theApplet.setLayout(new BorderLayout());
3629 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3630 theApplet.add(statusBar, BorderLayout.SOUTH);
3631 // TODO should size be left to the layout manager?
3632 alignPanel.setSize(theApplet.getSize().width,
3633 theApplet.getSize().height - embeddedMenu.getHeight()
3634 - statusBar.getHeight());
3635 theApplet.add(alignPanel, BorderLayout.CENTER);
3636 final AlignFrame me = this;
3637 theApplet.addFocusListener(new FocusListener()
3641 public void focusLost(FocusEvent e)
3643 if (theApplet.currentAlignFrame == me)
3645 theApplet.currentAlignFrame = null;
3650 public void focusGained(FocusEvent e)
3652 theApplet.currentAlignFrame = me;
3655 theApplet.validate();
3659 * create a new binding between structures in an existing jmol viewer instance
3660 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3661 * this does not open a new Jmol window, or modify the display of the
3662 * structures in the original jmol window. Note This method doesn't work
3663 * without an additional javascript library to exchange messages between the
3664 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3667 * JmolViewer instance
3668 * @param sequenceIds
3669 * - sequence Ids to search for associations
3671 public SequenceStructureBinding addStructureViewInstance(
3672 Object jmolviewer, String[] sequenceIds)
3674 org.jmol.api.JmolViewer viewer = null;
3677 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3678 } catch (ClassCastException ex)
3680 System.err.println("Unsupported viewer object :"
3681 + jmolviewer.getClass());
3685 System.err.println("Can't use this object as a structure viewer:"
3686 + jmolviewer.getClass());
3689 SequenceI[] seqs = null;
3690 if (sequenceIds == null || sequenceIds.length == 0)
3692 seqs = viewport.getAlignment().getSequencesArray();
3696 Vector sqi = new Vector();
3697 AlignmentI al = viewport.getAlignment();
3698 for (int sid = 0; sid < sequenceIds.length; sid++)
3700 SequenceI sq = al.findName(sequenceIds[sid]);
3708 seqs = new SequenceI[sqi.size()];
3709 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3711 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3719 AAStructureBindingModel jmv = null;
3720 // TODO: search for a jmv that involves viewer
3722 { // create a new viewer/jalview binding.
3723 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3731 * bind a pdb file to a sequence in the current view
3734 * - sequenceId within the dataset.
3735 * @param pdbEntryString
3736 * - the short name for the PDB file
3738 * - pdb file - either a URL or a valid PDB file.
3739 * @return true if binding was as success TODO: consider making an exception
3740 * structure for indicating when PDB parsing or sequenceId location
3743 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3746 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3747 boolean needtoadd = false;
3748 if (toaddpdb != null)
3750 Vector pdbe = toaddpdb.getPDBId();
3751 PDBEntry pdbentry = null;
3752 if (pdbe != null && pdbe.size() > 0)
3754 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3756 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3757 if (!pdbentry.getId().equals(pdbEntryString)
3758 && !pdbentry.getFile().equals(pdbFile))
3768 if (pdbentry == null)
3770 pdbentry = new PDBEntry();
3771 pdbentry.setId(pdbEntryString);
3772 pdbentry.setFile(pdbFile);
3773 needtoadd = true; // add this new entry to sequence.
3775 // resolve data source
3776 // TODO: this code should be a refactored to an io package
3777 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3778 if (protocol == null)
3784 // make a note of the access mode and add
3785 if (pdbentry.getProperty() == null)
3787 pdbentry.setProperty(new Hashtable());
3789 pdbentry.getProperty().put("protocol", protocol);
3790 toaddpdb.addPDBId(pdbentry);
3791 alignPanel.getStructureSelectionManager()
3792 .registerPDBEntry(pdbentry);
3798 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3802 Vector sequences = new Vector();
3803 for (int i = 0; i < seqs.length; i++)
3805 if (seqs[i] != null)
3807 sequences.addElement(new Object[]
3808 { seqs[i], (chains != null) ? chains[i] : null });
3811 seqs = new SequenceI[sequences.size()];
3812 chains = new String[sequences.size()];
3813 for (int i = 0, isize = sequences.size(); i < isize; i++)
3815 Object[] oj = (Object[]) sequences.elementAt(i);
3817 seqs[i] = (SequenceI) oj[0];
3818 chains[i] = (String) oj[1];
3826 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3827 SequenceI[] seqs, String[] chains, String protocol)
3829 // Scrub any null sequences from the array
3830 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3831 seqs = (SequenceI[]) sqch[0];
3832 chains = (String[]) sqch[1];
3833 if (seqs == null || seqs.length == 0)
3836 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3838 if (protocol == null || protocol.trim().length() == 0
3839 || protocol.equals("null"))
3841 protocol = (String) pdb.getProperty().get("protocol");
3842 if (protocol == null)
3844 System.err.println("Couldn't work out protocol to open structure: "
3849 if (applet.useXtrnalSviewer)
3851 // register the association(s) and quit, don't create any windows.
3852 if (StructureSelectionManager.getStructureSelectionManager(applet)
3853 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3855 System.err.println("Failed to map " + pdb.getFile() + " ("
3856 + protocol + ") to any sequences");
3860 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3862 // can only do alignments with Jmol
3863 // find the last jmol window assigned to this alignment
3864 jalview.appletgui.AppletJmol ajm = null, tajm;
3865 Vector jmols = applet
3866 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3867 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3869 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3870 if (tajm.ap.alignFrame == this)
3879 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3880 // try and add the pdb structure
3885 // otherwise, create a new window
3886 if (applet.jmolAvailable)
3888 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3890 applet.lastFrameX += 40;
3891 applet.lastFrameY += 40;
3895 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3900 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3901 SequenceI[][] seqs, String[][] chains, String[] protocols)
3903 // TODO Auto-generated method stub
3904 System.err.println("Aligned Structure View: Not yet implemented.");
3908 * modify the current selection, providing the user has not made a selection
3912 * - sequences from this alignment
3914 * - columns to be selected on the alignment
3916 public void select(SequenceGroup sel, ColumnSelection csel)
3918 alignPanel.seqPanel.selection(sel, csel, null);
3921 public void scrollTo(int row, int column)
3923 alignPanel.seqPanel.scrollTo(row, column);
3926 public void scrollToRow(int row)
3928 alignPanel.seqPanel.scrollToRow(row);
3931 public void scrollToColumn(int column)
3933 alignPanel.seqPanel.scrollToColumn(column);
3937 * @return the alignments unique ID.
3939 public String getSequenceSetId()
3941 return viewport.getSequenceSetId();
3945 * Load the (T-Coffee) score file from the specified url
3948 * File/URL/T-COFFEE score file contents
3949 * @throws IOException
3950 * @return true if alignment was annotated with data from source
3952 public boolean loadScoreFile(String source) throws IOException
3955 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3956 AppletFormatAdapter.checkProtocol(source));
3957 if (!file.isValid())
3959 // TODO: raise dialog for gui
3960 System.err.println("Problems parsing T-Coffee scores: "
3961 + file.getWarningMessage());
3962 System.err.println("Origin was:\n" + source);
3967 * check that the score matrix matches the alignment dimensions
3970 if ((aln = viewport.getAlignment()) != null
3971 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3974 // TODO: raise a dialog box here rather than bomb out.
3976 .println("The scores matrix does not match the alignment dimensions");
3980 // TODO add parameter to indicate if matching should be done
3981 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3983 alignPanel.fontChanged();
3984 tcoffeeColour.setEnabled(true);
3985 // switch to this color
3986 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3991 System.err.println("Problems resolving T-Coffee scores:");
3992 if (file.getWarningMessage() != null)
3994 System.err.println(file.getWarningMessage());