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.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.controller.AlignViewController;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AlignmentProperties;
51 import jalview.io.AnnotationFile;
52 import jalview.io.AppletFormatAdapter;
53 import jalview.io.FeaturesFile;
54 import jalview.io.NewickFile;
55 import jalview.io.TCoffeeScoreFile;
56 import jalview.schemes.Blosum62ColourScheme;
57 import jalview.schemes.BuriedColourScheme;
58 import jalview.schemes.ClustalxColourScheme;
59 import jalview.schemes.ColourSchemeI;
60 import jalview.schemes.HelixColourScheme;
61 import jalview.schemes.HydrophobicColourScheme;
62 import jalview.schemes.NucleotideColourScheme;
63 import jalview.schemes.PIDColourScheme;
64 import jalview.schemes.PurinePyrimidineColourScheme;
65 import jalview.schemes.RNAHelicesColourChooser;
66 import jalview.schemes.RNAInteractionColourScheme;
67 import jalview.schemes.StrandColourScheme;
68 import jalview.schemes.TCoffeeColourScheme;
69 import jalview.schemes.TaylorColourScheme;
70 import jalview.schemes.TurnColourScheme;
71 import jalview.schemes.ZappoColourScheme;
72 import jalview.structure.StructureSelectionManager;
73 import jalview.structures.models.AAStructureBindingModel;
74 import jalview.util.Comparison;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
79 import java.awt.BorderLayout;
80 import java.awt.Canvas;
81 import java.awt.CheckboxMenuItem;
82 import java.awt.Color;
84 import java.awt.FontMetrics;
85 import java.awt.Frame;
86 import java.awt.Graphics;
87 import java.awt.Label;
89 import java.awt.MenuBar;
90 import java.awt.MenuItem;
91 import java.awt.event.ActionEvent;
92 import java.awt.event.ActionListener;
93 import java.awt.event.FocusEvent;
94 import java.awt.event.FocusListener;
95 import java.awt.event.ItemEvent;
96 import java.awt.event.ItemListener;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.KeyListener;
99 import java.awt.event.WindowAdapter;
100 import java.awt.event.WindowEvent;
101 import java.io.IOException;
103 import java.net.URLEncoder;
104 import java.util.Arrays;
105 import java.util.Deque;
106 import java.util.HashMap;
107 import java.util.Hashtable;
108 import java.util.List;
109 import java.util.Map;
110 import java.util.StringTokenizer;
111 import java.util.Vector;
113 import org.jmol.viewer.Viewer;
115 public class AlignFrame extends EmbmenuFrame implements ActionListener,
116 ItemListener, KeyListener, AlignViewControllerGuiI
118 public AlignViewControllerI avc;
120 public AlignmentPanel alignPanel;
122 public AlignViewport viewport;
124 // width and height may be overridden by applet parameters
125 int frameWidth = 700;
127 int frameHeight = 500;
129 String jalviewServletURL;
132 * Flag for showing autocalculated consensus above or below other consensus
135 private boolean showAutoCalculatedAbove;
137 private SequenceAnnotationOrder annotationSortOrder;
140 * Constructor that creates the frame and adds it to the display.
147 public AlignFrame(AlignmentI al, JalviewLite applet,
148 String title, boolean embedded)
150 this(al, applet, title, embedded, true);
154 * Constructor that optionally allows the frame to be displayed or only
161 * @param addToDisplay
163 public AlignFrame(AlignmentI al, JalviewLite applet,
164 String title, boolean embedded, boolean addToDisplay)
166 this(al, null, null, applet, title, embedded, addToDisplay);
169 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
170 ColumnSelection columnSelection, JalviewLite applet,
171 String title, boolean embedded)
173 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
176 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
177 ColumnSelection columnSelection, JalviewLite applet,
178 String title, boolean embedded, boolean addToDisplay)
182 jalviewServletURL = applet.getParameter("APPLICATION_URL");
188 } catch (Exception ex)
190 ex.printStackTrace();
192 // need to get window geometry before we calculate alignment layout
198 param = applet.getParameter("windowWidth");
201 int width = Integer.parseInt(param);
204 param = applet.getParameter("windowHeight");
207 int height = Integer.parseInt(param);
208 frameHeight = height;
210 } catch (Exception ex)
214 viewport = new AlignViewport(al, applet);
216 if (hiddenSeqs != null && hiddenSeqs.length > 0)
218 viewport.hideSequence(hiddenSeqs);
220 if (columnSelection != null)
222 viewport.setColumnSelection(columnSelection);
225 alignPanel = new AlignmentPanel(this, viewport);
226 avc = new AlignViewController(this, viewport,
228 viewport.updateConservation(alignPanel);
229 viewport.updateConsensus(alignPanel);
231 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
232 followMouseOverFlag.setState(viewport.isFollowHighlight());
233 showGroupConsensus.setState(viewport.isShowGroupConsensus());
234 showGroupConservation.setState(viewport.isShowGroupConservation());
235 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
236 showSequenceLogo.setState(viewport.isShowSequenceLogo());
237 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
238 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
239 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
240 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
241 showSequenceAnnotations.setState(viewport.isShowAnnotation());
243 seqLimits.setState(viewport.getShowJVSuffix());
247 String param = applet.getParameter("sortBy");
250 if (param.equalsIgnoreCase("Id"))
252 sortIDMenuItem_actionPerformed();
254 else if (param.equalsIgnoreCase("Pairwise Identity"))
256 sortPairwiseMenuItem_actionPerformed();
258 else if (param.equalsIgnoreCase("Length"))
260 sortLengthMenuItem_actionPerformed();
264 param = applet.getParameter("wrap");
267 if (param.equalsIgnoreCase("true"))
269 wrapMenuItem.setState(true);
270 wrapMenuItem_actionPerformed();
273 param = applet.getParameter("centrecolumnlabels");
276 centreColumnLabelFlag.setState(true);
277 centreColumnLabelFlag_stateChanged();
281 if (viewport.getAlignment().isNucleotide())
283 viewport.updateStrucConsensus(alignPanel);
284 if (viewport.getAlignment().hasRNAStructure())
286 RNAHelixColour.setEnabled(true);
290 RNAHelixColour.setEnabled(false);
295 RNAHelixColour.setEnabled(false);
296 purinePyrimidineColour.setEnabled(false);
298 // Some JVMS send keyevents to Top frame or lowest panel,
299 // Havent worked out why yet. So add to both this frame and seqCanvas for
301 this.addKeyListener(this);
302 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
303 alignPanel.idPanel.idCanvas.addKeyListener(this);
304 alignPanel.scalePanel.addKeyListener(this);
305 alignPanel.annotationPanel.addKeyListener(this);
306 alignPanel.annotationPanelHolder.addKeyListener(this);
307 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
308 alignPanel.alabels.addKeyListener(this);
312 addToDisplay(embedded);
319 public void addToDisplay(boolean embedded)
321 createAlignFrameWindow(embedded);
323 alignPanel.adjustAnnotationHeight();
324 alignPanel.paintAlignment(true);
327 public AlignViewport getAlignViewport()
332 public SeqCanvas getSeqcanvas()
334 return alignPanel.seqPanel.seqCanvas;
338 * Load a features file onto the alignment
341 * file URL, content, or other resolvable path
343 * is protocol for accessing data referred to by file
346 public boolean parseFeaturesFile(String file, String type)
348 return parseFeaturesFile(file, type, true);
352 * Load a features file onto the alignment
355 * file URL, content, or other resolvable path
357 * is protocol for accessing data referred to by file
358 * @param autoenabledisplay
359 * when true, display features flag will be automatically enabled if
360 * features are loaded
361 * @return true if data parsed as a features file
363 public boolean parseFeaturesFile(String file, String type,
364 boolean autoenabledisplay)
366 // TODO: test if importing a features file onto an alignment which already
367 // has features with links overwrites the original links.
369 Hashtable featureLinks = new Hashtable();
370 boolean featuresFile = false;
373 featuresFile = new FeaturesFile(file, type)
374 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
375 .getFeatureRenderer().getFeatureColours(), featureLinks,
376 true, viewport.applet.getDefaultParameter(
377 "relaxedidmatch", false));
378 } catch (Exception ex)
380 ex.printStackTrace();
385 if (featureLinks.size() > 0)
387 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
389 if (autoenabledisplay)
391 viewport.setShowSequenceFeatures(true);
392 sequenceFeatures.setState(true);
394 if (alignPanel.seqPanel.seqCanvas.fr != null)
396 // update the min/max ranges where necessary
397 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
399 if (viewport.featureSettings != null)
401 viewport.featureSettings.refreshTable();
403 alignPanel.paintAlignment(true);
404 statusBar.setText(MessageManager
405 .getString("label.successfully_added_features_alignment"));
411 public void keyPressed(KeyEvent evt)
413 if (viewport.cursorMode
414 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
415 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
416 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
417 && Character.isDigit(evt.getKeyChar()))
419 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
422 switch (evt.getKeyCode())
424 case 27: // escape key
425 deselectAllSequenceMenuItem_actionPerformed();
427 alignPanel.alabels.cancelDrag();
430 if (evt.isControlDown() || evt.isMetaDown())
432 cut_actionPerformed();
436 if (viewport.cursorMode && !evt.isControlDown())
438 alignPanel.seqPanel.setCursorColumn();
440 if (evt.isControlDown() || evt.isMetaDown())
442 copy_actionPerformed();
446 if (evt.isControlDown())
448 paste(evt.isShiftDown());
452 if (evt.isControlDown() || evt.isMetaDown())
454 selectAllSequenceMenuItem_actionPerformed();
457 case KeyEvent.VK_DOWN:
458 if (viewport.cursorMode)
460 alignPanel.seqPanel.moveCursor(0, 1);
464 moveSelectedSequences(false);
469 if (viewport.cursorMode)
471 alignPanel.seqPanel.moveCursor(0, -1);
475 moveSelectedSequences(true);
479 case KeyEvent.VK_LEFT:
480 if (evt.isAltDown() || !viewport.cursorMode)
482 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
486 alignPanel.seqPanel.moveCursor(-1, 0);
490 case KeyEvent.VK_RIGHT:
491 if (evt.isAltDown() || !viewport.cursorMode)
493 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
497 alignPanel.seqPanel.moveCursor(1, 0);
501 case KeyEvent.VK_SPACE:
502 if (viewport.cursorMode)
504 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
505 || evt.isShiftDown() || evt.isAltDown());
509 case KeyEvent.VK_DELETE:
510 case KeyEvent.VK_BACK_SPACE:
511 if (viewport.cursorMode)
513 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
514 || evt.isShiftDown() || evt.isAltDown());
518 cut_actionPerformed();
519 alignPanel.seqPanel.seqCanvas.repaint();
524 if (viewport.cursorMode)
526 alignPanel.seqPanel.setCursorRow();
530 if (viewport.cursorMode)
532 alignPanel.seqPanel.setCursorPosition();
536 case KeyEvent.VK_ENTER:
537 case KeyEvent.VK_COMMA:
538 if (viewport.cursorMode)
540 alignPanel.seqPanel.setCursorRowAndColumn();
545 if (viewport.cursorMode)
547 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
551 if (viewport.cursorMode)
553 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
558 viewport.cursorMode = !viewport.cursorMode;
559 statusBar.setText(MessageManager.formatMessage(
560 "label.keyboard_editing_mode", new String[]
561 { (viewport.cursorMode ? "on" : "off") }));
562 if (viewport.cursorMode)
564 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
565 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
570 if (evt.isControlDown())
572 findMenuItem_actionPerformed();
578 boolean toggleSeqs = !evt.isControlDown();
579 boolean toggleCols = !evt.isShiftDown();
580 toggleHiddenRegions(toggleSeqs, toggleCols);
584 case KeyEvent.VK_PAGE_UP:
585 if (viewport.getWrapAlignment())
587 alignPanel.scrollUp(true);
591 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
592 - viewport.endSeq + viewport.startSeq);
596 case KeyEvent.VK_PAGE_DOWN:
597 if (viewport.getWrapAlignment())
599 alignPanel.scrollUp(false);
603 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
604 + viewport.endSeq - viewport.startSeq);
609 if (evt.isControlDown())
611 undoMenuItem_actionPerformed();
616 if (evt.isControlDown())
618 redoMenuItem_actionPerformed();
623 if (evt.isControlDown())
630 if (evt.isControlDown())
632 trimAlignment(false);
637 if (evt.isControlDown())
639 if (evt.isShiftDown())
641 this.removeAllGapsMenuItem_actionPerformed();
645 removeGappedColumnMenuItem_actionPerformed();
650 if (evt.isControlDown())
654 invertColSel_actionPerformed();
658 invertSequenceMenuItem_actionPerformed();
664 if (evt.isControlDown())
666 if (evt.isShiftDown())
668 this.unGroup_actionPerformed();
672 this.createGroup_actionPerformed();
678 if (evt.isControlDown())
680 this.deleteGroups_actionPerformed();
685 if (evt.isControlDown())
692 alignPanel.paintAlignment(true);
696 * called by key handler and the hide all/show all menu items
701 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
703 boolean hide = false;
704 SequenceGroup sg = viewport.getSelectionGroup();
705 if (!toggleSeqs && !toggleCols)
707 // Hide everything by the current selection - this is a hack - we do the
708 // invert and then hide
709 // first check that there will be visible columns after the invert.
710 if ((viewport.getColumnSelection() != null
711 && viewport.getColumnSelection().getSelected() != null && viewport
712 .getColumnSelection().getSelected().size() > 0)
713 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
716 // now invert the sequence set, if required - empty selection implies
717 // that no hiding is required.
720 invertSequenceMenuItem_actionPerformed();
721 sg = viewport.getSelectionGroup();
725 viewport.expandColSelection(sg, true);
726 // finally invert the column selection and get the new sequence
727 // selection and indicate it should be hidden.
728 invertColSel_actionPerformed();
735 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
738 viewport.hideAllSelectedSeqs();
740 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
743 viewport.showAllHiddenSeqs();
749 if (viewport.getColumnSelection().getSelected().size() > 0)
751 viewport.hideSelectedColumns();
754 viewport.setSelectionGroup(sg);
759 viewport.showAllHiddenColumns();
765 public void keyReleased(KeyEvent evt)
770 public void keyTyped(KeyEvent evt)
775 public void itemStateChanged(ItemEvent evt)
777 final Object source = evt.getSource();
778 if (source == displayNonconservedMenuItem)
780 displayNonconservedMenuItem_actionPerformed();
782 else if (source == colourTextMenuItem)
784 colourTextMenuItem_actionPerformed();
786 else if (source == wrapMenuItem)
788 wrapMenuItem_actionPerformed();
790 else if (source == scaleAbove)
792 viewport.setScaleAboveWrapped(scaleAbove.getState());
794 else if (source == scaleLeft)
796 viewport.setScaleLeftWrapped(scaleLeft.getState());
798 else if (source == scaleRight)
800 viewport.setScaleRightWrapped(scaleRight.getState());
802 else if (source == seqLimits)
804 seqLimits_itemStateChanged();
806 else if (source == viewBoxesMenuItem)
808 viewport.setShowBoxes(viewBoxesMenuItem.getState());
810 else if (source == viewTextMenuItem)
812 viewport.setShowText(viewTextMenuItem.getState());
814 else if (source == renderGapsMenuItem)
816 viewport.setRenderGaps(renderGapsMenuItem.getState());
818 else if (source == annotationPanelMenuItem)
820 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
821 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
823 else if (source == sequenceFeatures)
825 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
826 alignPanel.seqPanel.seqCanvas.repaint();
828 else if (source == showAlignmentAnnotations)
830 setAnnotationsVisibility();
832 else if (source == showSequenceAnnotations)
834 setAnnotationsVisibility();
836 else if (source == sortAnnBySequence)
838 boolean newState = sortAnnBySequence.getState();
839 sortAnnByLabel.setState(false);
840 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
841 : SequenceAnnotationOrder.NONE);
842 setViewportAnnotationOrder();
844 else if (source == sortAnnByLabel)
846 boolean newState = sortAnnByLabel.getState();
847 sortAnnBySequence.setState(false);
848 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
849 : SequenceAnnotationOrder.NONE);
850 setViewportAnnotationOrder();
852 else if (source == showAutoFirst)
854 showAutoLast.setState(!showAutoFirst.getState());
855 setShowAutoCalculatedAbove(showAutoFirst.getState());
856 setViewportAnnotationOrder();
858 else if (source == showAutoLast)
860 showAutoFirst.setState(!showAutoLast.getState());
861 setShowAutoCalculatedAbove(showAutoFirst.getState());
862 setViewportAnnotationOrder();
864 else if (source == conservationMenuItem)
866 conservationMenuItem_actionPerformed();
868 else if (source == abovePIDThreshold)
870 abovePIDThreshold_actionPerformed();
872 else if (source == applyToAllGroups)
874 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
876 else if (source == autoCalculate)
878 viewport.autoCalculateConsensus = autoCalculate.getState();
880 else if (source == sortByTree)
882 viewport.sortByTree = sortByTree.getState();
884 else if (source == this.centreColumnLabelFlag)
886 centreColumnLabelFlag_stateChanged();
888 else if (source == this.followMouseOverFlag)
890 mouseOverFlag_stateChanged();
892 else if (source == showGroupConsensus)
894 showGroupConsensus_actionPerformed();
896 else if (source == showGroupConservation)
898 showGroupConservation_actionPerformed();
900 else if (source == showSequenceLogo)
902 showSequenceLogo_actionPerformed();
904 else if (source == normSequenceLogo)
906 normSequenceLogo_actionPerformed();
908 else if (source == showConsensusHistogram)
910 showConsensusHistogram_actionPerformed();
912 else if (source == applyAutoAnnotationSettings)
914 applyAutoAnnotationSettings_actionPerformed();
916 alignPanel.paintAlignment(true);
920 * Set the visibility state of sequence-related and/or alignment-related
921 * annotations depending on checkbox selections. Repaint after calling.
925 private void setAnnotationsVisibility()
927 boolean showForAlignment = showAlignmentAnnotations.getState();
928 boolean showForSequences = showSequenceAnnotations.getState();
929 for (AlignmentAnnotation aa : alignPanel.getAlignment()
930 .getAlignmentAnnotation())
932 boolean visible = (aa.sequenceRef == null ? showForAlignment
934 aa.visible = visible;
936 alignPanel.validateAnnotationDimensions(true);
941 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
943 this.annotationSortOrder = order;
947 * Set flags on the viewport that control annotation ordering
949 private void setViewportAnnotationOrder()
951 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
953 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
956 private void setShowAutoCalculatedAbove(boolean showAbove)
958 this.showAutoCalculatedAbove = showAbove;
961 private void mouseOverFlag_stateChanged()
963 viewport.setFollowHighlight(followMouseOverFlag.getState());
964 // TODO: could kick the scrollTo mechanism to reset view for current
968 private void centreColumnLabelFlag_stateChanged()
970 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
971 this.alignPanel.annotationPanel.repaint();
975 public void actionPerformed(ActionEvent evt)
977 Object source = evt.getSource();
979 if (source == inputText)
981 inputText_actionPerformed();
983 else if (source == loadTree)
985 loadTree_actionPerformed();
987 else if (source == loadApplication)
989 launchFullApplication();
991 else if (source == loadAnnotations)
995 else if (source == outputAnnotations)
997 outputAnnotations(true);
999 else if (source == outputFeatures)
1001 outputFeatures(true, "Jalview");
1003 else if (source == closeMenuItem)
1005 closeMenuItem_actionPerformed();
1007 else if (source == copy)
1009 copy_actionPerformed();
1011 else if (source == undoMenuItem)
1013 undoMenuItem_actionPerformed();
1015 else if (source == redoMenuItem)
1017 redoMenuItem_actionPerformed();
1019 else if (source == inputText)
1021 inputText_actionPerformed();
1023 else if (source == closeMenuItem)
1025 closeMenuItem_actionPerformed();
1027 else if (source == undoMenuItem)
1029 undoMenuItem_actionPerformed();
1031 else if (source == redoMenuItem)
1033 redoMenuItem_actionPerformed();
1035 else if (source == copy)
1037 copy_actionPerformed();
1039 else if (source == pasteNew)
1041 pasteNew_actionPerformed();
1043 else if (source == pasteThis)
1045 pasteThis_actionPerformed();
1047 else if (source == cut)
1049 cut_actionPerformed();
1051 else if (source == delete)
1053 delete_actionPerformed();
1055 else if (source == grpsFromSelection)
1057 makeGrpsFromSelection_actionPerformed();
1059 else if (source == deleteGroups)
1061 deleteGroups_actionPerformed();
1063 else if (source == selectAllSequenceMenuItem)
1065 selectAllSequenceMenuItem_actionPerformed();
1067 else if (source == deselectAllSequenceMenuItem)
1069 deselectAllSequenceMenuItem_actionPerformed();
1071 else if (source == invertSequenceMenuItem)
1073 invertSequenceMenuItem_actionPerformed();
1075 else if (source == invertColSel)
1077 viewport.invertColumnSelection();
1078 alignPanel.paintAlignment(true);
1080 else if (source == remove2LeftMenuItem)
1082 trimAlignment(true);
1084 else if (source == remove2RightMenuItem)
1086 trimAlignment(false);
1088 else if (source == removeGappedColumnMenuItem)
1090 removeGappedColumnMenuItem_actionPerformed();
1092 else if (source == removeAllGapsMenuItem)
1094 removeAllGapsMenuItem_actionPerformed();
1096 else if (source == findMenuItem)
1098 findMenuItem_actionPerformed();
1100 else if (source == font)
1102 new FontChooser(alignPanel);
1104 else if (source == newView)
1108 else if (source == showColumns)
1110 viewport.showAllHiddenColumns();
1111 alignPanel.paintAlignment(true);
1113 else if (source == showSeqs)
1115 viewport.showAllHiddenSeqs();
1116 alignPanel.paintAlignment(true);
1118 else if (source == hideColumns)
1120 viewport.hideSelectedColumns();
1121 alignPanel.paintAlignment(true);
1123 else if (source == hideSequences
1124 && viewport.getSelectionGroup() != null)
1126 viewport.hideAllSelectedSeqs();
1127 alignPanel.paintAlignment(true);
1129 else if (source == hideAllButSelection)
1131 toggleHiddenRegions(false, false);
1132 alignPanel.paintAlignment(true);
1134 else if (source == hideAllSelection)
1136 SequenceGroup sg = viewport.getSelectionGroup();
1137 viewport.expandColSelection(sg, false);
1138 viewport.hideAllSelectedSeqs();
1139 viewport.hideSelectedColumns();
1140 alignPanel.paintAlignment(true);
1142 else if (source == showAllHidden)
1144 viewport.showAllHiddenColumns();
1145 viewport.showAllHiddenSeqs();
1146 alignPanel.paintAlignment(true);
1148 else if (source == showGroupConsensus)
1150 showGroupConsensus_actionPerformed();
1152 else if (source == showGroupConservation)
1154 showGroupConservation_actionPerformed();
1156 else if (source == showSequenceLogo)
1158 showSequenceLogo_actionPerformed();
1160 else if (source == normSequenceLogo)
1162 normSequenceLogo_actionPerformed();
1164 else if (source == showConsensusHistogram)
1166 showConsensusHistogram_actionPerformed();
1168 else if (source == applyAutoAnnotationSettings)
1170 applyAutoAnnotationSettings_actionPerformed();
1172 else if (source == featureSettings)
1174 new FeatureSettings(alignPanel);
1176 else if (source == alProperties)
1178 StringBuffer contents = new AlignmentProperties(
1179 viewport.getAlignment()).formatAsString();
1180 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1181 cap.setText(contents.toString());
1182 Frame frame = new Frame();
1184 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1185 "label.alignment_properties", new String[]
1186 { getTitle() }), 400, 250);
1188 else if (source == overviewMenuItem)
1190 overviewMenuItem_actionPerformed();
1192 else if (source == noColourmenuItem)
1196 else if (source == clustalColour)
1198 abovePIDThreshold.setState(false);
1199 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1201 else if (source == zappoColour)
1203 changeColour(new ZappoColourScheme());
1205 else if (source == taylorColour)
1207 changeColour(new TaylorColourScheme());
1209 else if (source == hydrophobicityColour)
1211 changeColour(new HydrophobicColourScheme());
1213 else if (source == helixColour)
1215 changeColour(new HelixColourScheme());
1217 else if (source == strandColour)
1219 changeColour(new StrandColourScheme());
1221 else if (source == turnColour)
1223 changeColour(new TurnColourScheme());
1225 else if (source == buriedColour)
1227 changeColour(new BuriedColourScheme());
1229 else if (source == nucleotideColour)
1231 changeColour(new NucleotideColourScheme());
1233 else if (source == purinePyrimidineColour)
1235 changeColour(new PurinePyrimidineColourScheme());
1237 else if (source == RNAInteractionColour)
1239 changeColour(new RNAInteractionColourScheme());
1241 else if (source == RNAHelixColour)
1243 new RNAHelicesColourChooser(viewport, alignPanel);
1245 else if (source == modifyPID)
1247 modifyPID_actionPerformed();
1249 else if (source == modifyConservation)
1251 modifyConservation_actionPerformed();
1253 else if (source == userDefinedColour)
1255 new UserDefinedColours(alignPanel, null);
1257 else if (source == PIDColour)
1259 changeColour(new PIDColourScheme());
1261 else if (source == BLOSUM62Colour)
1263 changeColour(new Blosum62ColourScheme());
1265 else if (source == tcoffeeColour)
1267 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1269 else if (source == annotationColour)
1271 new AnnotationColourChooser(viewport, alignPanel);
1273 else if (source == annotationColumnSelection)
1275 new AnnotationColumnChooser(viewport, alignPanel);
1277 else if (source == sortPairwiseMenuItem)
1279 sortPairwiseMenuItem_actionPerformed();
1281 else if (source == sortIDMenuItem)
1283 sortIDMenuItem_actionPerformed();
1285 else if (source == sortLengthMenuItem)
1287 sortLengthMenuItem_actionPerformed();
1289 else if (source == sortGroupMenuItem)
1291 sortGroupMenuItem_actionPerformed();
1293 else if (source == removeRedundancyMenuItem)
1295 removeRedundancyMenuItem_actionPerformed();
1297 else if (source == pairwiseAlignmentMenuItem)
1299 pairwiseAlignmentMenuItem_actionPerformed();
1301 else if (source == PCAMenuItem)
1303 PCAMenuItem_actionPerformed();
1305 else if (source == averageDistanceTreeMenuItem)
1307 averageDistanceTreeMenuItem_actionPerformed();
1309 else if (source == neighbourTreeMenuItem)
1311 neighbourTreeMenuItem_actionPerformed();
1313 else if (source == njTreeBlosumMenuItem)
1315 njTreeBlosumMenuItem_actionPerformed();
1317 else if (source == avDistanceTreeBlosumMenuItem)
1319 avTreeBlosumMenuItem_actionPerformed();
1321 else if (source == documentation)
1323 documentation_actionPerformed();
1325 else if (source == about)
1327 about_actionPerformed();
1332 public void inputText_actionPerformed()
1334 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1335 Frame frame = new Frame();
1337 JalviewLite.addFrame(frame,
1338 MessageManager.getString("label.input_cut_paste"), 500, 500);
1341 protected void outputText_actionPerformed(ActionEvent e)
1343 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1344 Frame frame = new Frame();
1346 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1347 "label.alignment_output_command", new Object[]
1348 { e.getActionCommand() }), 600, 500);
1350 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1351 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1352 e.getActionCommand(), viewport.getAlignment(),
1353 viewport.getShowJVSuffix()));
1356 public void loadAnnotations()
1358 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1359 cap.setText(MessageManager
1360 .getString("label.paste_features_annotations_Tcoffee_here"));
1361 cap.setAnnotationImport();
1362 Frame frame = new Frame();
1364 JalviewLite.addFrame(frame,
1365 MessageManager.getString("action.paste_annotations"), 400, 300);
1369 public String outputAnnotations(boolean displayTextbox)
1371 String annotation = new AnnotationFile()
1372 .printAnnotationsForView(viewport);
1376 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1377 Frame frame = new Frame();
1379 JalviewLite.addFrame(frame,
1380 MessageManager.getString("label.annotations"), 600, 500);
1381 cap.setText(annotation);
1387 private Map<String,Object> getDisplayedFeatureCols()
1389 if (alignPanel.getFeatureRenderer() != null
1390 && viewport.getFeaturesDisplayed()!= null)
1392 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1398 public String outputFeatures(boolean displayTextbox, String format)
1401 if (format.equalsIgnoreCase("Jalview"))
1403 features = new FeaturesFile().printJalviewFormat(viewport
1404 .getAlignment().getSequencesArray(),
1405 getDisplayedFeatureCols());
1409 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1410 .getSequencesArray(), getDisplayedFeatureCols());
1415 boolean frimport = false;
1416 if (features == null || features.equals("No Features Visible"))
1418 features = "# No features visible - paste some and import them here.";
1422 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1425 cap.setAnnotationImport();
1427 Frame frame = new Frame();
1429 JalviewLite.addFrame(frame,
1430 MessageManager.getString("label.features"), 600, 500);
1431 cap.setText(features);
1435 if (features == null)
1444 void launchFullApplication()
1446 StringBuffer url = new StringBuffer(jalviewServletURL);
1448 // allow servlet parameters to be passed in applet parameter
1449 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1451 url.append(firstSep);
1454 + appendProtocol(viewport.applet.getParameter("file")));
1456 if (viewport.applet.getParameter("features") != null)
1458 url.append("&features=");
1459 url.append(appendProtocol(viewport.applet.getParameter("features")));
1462 if (viewport.applet.getParameter("annotations") != null)
1464 url.append("&annotations=");
1465 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1468 if (viewport.applet.getParameter("jnetfile") != null)
1470 url.append("&annotations=");
1471 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1474 if (viewport.applet.getParameter("defaultColour") != null)
1476 url.append("&colour="
1477 + removeWhiteSpace(viewport.applet
1478 .getParameter("defaultColour")));
1481 if (viewport.applet.getParameter("userDefinedColour") != null)
1483 url.append("&colour="
1484 + removeWhiteSpace(viewport.applet
1485 .getParameter("userDefinedColour")));
1487 if (viewport.applet.getParameter("tree") != null)
1490 + appendProtocol(viewport.applet.getParameter("tree")));
1492 if (viewport.applet.getParameter("treeFile") != null)
1495 + appendProtocol(viewport.applet.getParameter("treeFile")));
1498 showURL(url.toString(), "FULL_APP");
1501 String removeWhiteSpace(String colour)
1503 StringBuffer sb = new StringBuffer();
1504 for (int i = 0; i < colour.length(); i++)
1506 if (Character.isWhitespace(colour.charAt(i)))
1512 sb.append(colour.charAt(i));
1516 return sb.toString();
1519 String appendProtocol(String url)
1524 url = URLEncoder.encode(url);
1527 * When we finally deprecate 1.1 compatibility, we can start to use
1528 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1529 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1530 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1531 * ex.printStackTrace(); }
1533 catch (java.net.MalformedURLException ex)
1535 url = viewport.applet.getCodeBase() + url;
1540 public void closeMenuItem_actionPerformed()
1542 PaintRefresher.RemoveComponent(alignPanel);
1543 if (alignPanel.seqPanel != null
1544 && alignPanel.seqPanel.seqCanvas != null)
1546 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1548 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1550 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1553 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1568 void updateEditMenuBar()
1571 if (viewport.getHistoryList().size() > 0)
1573 undoMenuItem.setEnabled(true);
1574 CommandI command = viewport.getHistoryList().peek();
1575 undoMenuItem.setLabel(MessageManager.formatMessage(
1576 "label.undo_command", new Object[]
1577 { command.getDescription() }));
1581 undoMenuItem.setEnabled(false);
1582 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1585 if (viewport.getRedoList().size() > 0)
1587 redoMenuItem.setEnabled(true);
1589 CommandI command = viewport.getRedoList().peek();
1590 redoMenuItem.setLabel(MessageManager.formatMessage(
1591 "label.redo_command", new Object[]
1592 { command.getDescription() }));
1596 redoMenuItem.setEnabled(false);
1597 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1605 public void addHistoryItem(CommandI command)
1607 if (command.getSize() > 0)
1609 viewport.addToHistoryList(command);
1610 viewport.clearRedoList();
1611 updateEditMenuBar();
1612 viewport.updateHiddenColumns();
1617 * TODO: JAL-1104 DOCUMENT ME!
1622 protected void undoMenuItem_actionPerformed()
1624 if (viewport.getHistoryList().isEmpty())
1629 CommandI command = viewport.getHistoryList().pop();
1630 viewport.addToRedoList(command);
1631 command.undoCommand(null);
1633 AlignmentViewport originalSource = getOriginatingSource(command);
1635 if (originalSource != viewport)
1638 .println("Warning: Viewport object mismatch whilst undoing");
1640 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1641 // viewport.getColumnSelection().getHiddenColumns()
1643 updateEditMenuBar();
1644 originalSource.firePropertyChange("alignment", null, originalSource
1645 .getAlignment().getSequences());
1649 * TODO: JAL-1104 DOCUMENT ME!
1654 protected void redoMenuItem_actionPerformed()
1656 if (viewport.getRedoList().isEmpty())
1661 CommandI command = viewport.getRedoList().pop();
1662 viewport.addToHistoryList(command);
1663 command.doCommand(null);
1665 AlignmentViewport originalSource = getOriginatingSource(command);
1667 if (originalSource != viewport)
1670 .println("Warning: Viewport object mismatch whilst re-doing");
1672 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1673 // viewport.getColumnSelection().getHiddenColumns()
1676 updateEditMenuBar();
1677 originalSource.firePropertyChange("alignment", null, originalSource
1678 .getAlignment().getSequences());
1681 AlignmentViewport getOriginatingSource(CommandI command)
1683 AlignmentViewport originalSource = null;
1684 // For sequence removal and addition, we need to fire
1685 // the property change event FROM the viewport where the
1686 // original alignment was altered
1687 AlignmentI al = null;
1688 if (command instanceof EditCommand)
1690 EditCommand editCommand = (EditCommand) command;
1691 al = editCommand.getAlignment();
1692 Vector comps = (Vector) PaintRefresher.components.get(viewport
1693 .getSequenceSetId());
1694 for (int i = 0; i < comps.size(); i++)
1696 if (comps.elementAt(i) instanceof AlignmentPanel)
1698 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1700 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1707 if (originalSource == null)
1709 // The original view is closed, we must validate
1710 // the current view against the closed view first
1713 PaintRefresher.validateSequences(al, viewport.getAlignment());
1716 originalSource = viewport;
1719 return originalSource;
1723 * Move the currently selected sequences up or down one position in the
1728 public void moveSelectedSequences(boolean up)
1730 SequenceGroup sg = viewport.getSelectionGroup();
1735 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1736 up ? null : viewport.getHiddenRepSequences(), up);
1737 alignPanel.paintAlignment(true);
1740 * Also move cDNA/protein complement sequences
1742 AlignViewportI complement = viewport.getCodingComplement();
1743 if (complement != null)
1745 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1746 viewport, complement);
1747 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1748 up ? null : complement.getHiddenRepSequences(), up);
1749 // TODO need to trigger a repaint of the complementary panel - how?
1750 // would prefer to handle in SplitFrame but it is not overriding key
1755 synchronized void slideSequences(boolean right, int size)
1757 List<SequenceI> sg = new Vector<SequenceI>();
1758 if (viewport.cursorMode)
1760 sg.add(viewport.getAlignment().getSequenceAt(
1761 alignPanel.seqPanel.seqCanvas.cursorY));
1763 else if (viewport.getSelectionGroup() != null
1764 && viewport.getSelectionGroup().getSize() != viewport
1765 .getAlignment().getHeight())
1767 sg = viewport.getSelectionGroup().getSequences(
1768 viewport.getHiddenRepSequences());
1776 Vector<SequenceI> invertGroup = new Vector();
1778 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1780 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1782 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1786 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1788 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1790 for (int i = 0; i < invertGroup.size(); i++)
1792 seqs2[i] = invertGroup.elementAt(i);
1795 SlideSequencesCommand ssc;
1798 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1799 size, viewport.getGapCharacter());
1803 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1804 size, viewport.getGapCharacter());
1807 int groupAdjustment = 0;
1808 if (ssc.getGapsInsertedBegin() && right)
1810 if (viewport.cursorMode)
1812 alignPanel.seqPanel.moveCursor(size, 0);
1816 groupAdjustment = size;
1819 else if (!ssc.getGapsInsertedBegin() && !right)
1821 if (viewport.cursorMode)
1823 alignPanel.seqPanel.moveCursor(-size, 0);
1827 groupAdjustment = -size;
1831 if (groupAdjustment != 0)
1833 viewport.getSelectionGroup().setStartRes(
1834 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1835 viewport.getSelectionGroup().setEndRes(
1836 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1839 boolean appendHistoryItem = false;
1840 Deque<CommandI> historyList = viewport.getHistoryList();
1841 if (historyList != null && historyList.size() > 0
1842 && historyList.peek() instanceof SlideSequencesCommand)
1844 appendHistoryItem = ssc
1845 .appendSlideCommand((SlideSequencesCommand) historyList
1849 if (!appendHistoryItem)
1851 addHistoryItem(ssc);
1857 static StringBuffer copiedSequences;
1859 static Vector copiedHiddenColumns;
1861 protected void copy_actionPerformed()
1863 if (viewport.getSelectionGroup() == null)
1868 SequenceGroup sg = viewport.getSelectionGroup();
1869 copiedSequences = new StringBuffer();
1870 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1871 for (int i = 0; i < sg.getSize(); i++)
1873 SequenceI seq = sg.getSequenceAt(i);
1874 int index = viewport.getAlignment().findIndex(seq);
1875 orderedSeqs.put(index, seq);
1878 int index = 0, startRes, endRes;
1881 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1883 copiedHiddenColumns = new Vector();
1884 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1885 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1887 copiedHiddenColumns.addElement(new int[]
1888 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1893 copiedHiddenColumns = null;
1896 for (int i = 0; i < sg.getSize(); i++)
1898 SequenceI seq = null;
1902 if (orderedSeqs.containsKey(index))
1904 seq = orderedSeqs.get(index);
1915 // Returns residue following index if gap
1916 startRes = seq.findPosition(sg.getStartRes());
1919 // Need to find the residue preceeding index if gap
1922 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1924 ch = seq.getCharAt(j);
1925 if (!Comparison.isGap((ch)))
1933 endRes += seq.getStart() - 1;
1936 copiedSequences.append(seq.getName()
1942 + seq.getSequenceAsString(sg.getStartRes(),
1943 sg.getEndRes() + 1) + "\n");
1948 protected void pasteNew_actionPerformed()
1953 protected void pasteThis_actionPerformed()
1958 void paste(boolean newAlignment)
1963 if (copiedSequences == null)
1968 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1969 Vector seqs = new Vector();
1970 while (st.hasMoreElements())
1972 String name = st.nextToken();
1973 int start = Integer.parseInt(st.nextToken());
1974 int end = Integer.parseInt(st.nextToken());
1975 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1977 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1978 for (int i = 0; i < seqs.size(); i++)
1980 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1985 String newtitle = MessageManager.getString("label.copied_sequences");
1986 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1988 newtitle = getTitle();
1992 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1994 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1995 viewport.applet, newtitle, false);
1996 if (copiedHiddenColumns != null)
1998 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2000 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2001 af.viewport.hideColumns(region[0], region[1]);
2005 JalviewLite.addFrame(af, newtitle, frameWidth,
2010 addSequences(newSeqs);
2013 } catch (Exception ex)
2015 } // could be anything being pasted in here
2019 void addSequences(SequenceI[] seqs)
2021 for (int i = 0; i < seqs.length; i++)
2023 viewport.getAlignment().addSequence(seqs[i]);
2027 addHistoryItem(new EditCommand(
2028 MessageManager.getString("label.add_sequences"), Action.PASTE,
2029 seqs, 0, viewport.getAlignment().getWidth(),
2030 viewport.getAlignment()));
2032 viewport.setEndSeq(viewport.getAlignment().getHeight());
2033 viewport.getAlignment().getWidth();
2034 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2039 protected void cut_actionPerformed()
2041 copy_actionPerformed();
2042 delete_actionPerformed();
2045 protected void delete_actionPerformed()
2048 SequenceGroup sg = viewport.getSelectionGroup();
2054 Vector seqs = new Vector();
2056 for (int i = 0; i < sg.getSize(); i++)
2058 seq = sg.getSequenceAt(i);
2059 seqs.addElement(seq);
2062 // If the cut affects all sequences, remove highlighted columns
2063 if (sg.getSize() == viewport.getAlignment().getHeight())
2065 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2066 sg.getEndRes() + 1);
2069 SequenceI[] cut = new SequenceI[seqs.size()];
2070 for (int i = 0; i < seqs.size(); i++)
2072 cut[i] = (SequenceI) seqs.elementAt(i);
2076 * //ADD HISTORY ITEM
2078 addHistoryItem(new EditCommand(
2079 MessageManager.getString("label.cut_sequences"), Action.CUT,
2080 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2081 viewport.getAlignment()));
2083 viewport.setSelectionGroup(null);
2084 viewport.getAlignment().deleteGroup(sg);
2086 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2089 if (viewport.getAlignment().getHeight() < 1)
2091 this.setVisible(false);
2093 viewport.sendSelection();
2097 * group consensus toggled
2100 protected void showGroupConsensus_actionPerformed()
2102 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2103 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2108 * group conservation toggled.
2110 protected void showGroupConservation_actionPerformed()
2112 viewport.setShowGroupConservation(showGroupConservation.getState());
2113 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2120 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2121 * .event.ActionEvent)
2123 protected void showConsensusHistogram_actionPerformed()
2125 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2126 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2133 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2134 * .event.ActionEvent)
2136 protected void showSequenceLogo_actionPerformed()
2138 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2139 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2142 protected void normSequenceLogo_actionPerformed()
2144 showSequenceLogo.setState(true);
2145 viewport.setShowSequenceLogo(true);
2146 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2147 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2150 protected void applyAutoAnnotationSettings_actionPerformed()
2152 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2155 protected void makeGrpsFromSelection_actionPerformed()
2157 if (avc.makeGroupsFromSelection())
2159 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2160 alignPanel.updateAnnotation();
2161 alignPanel.paintAlignment(true);
2165 protected void createGroup_actionPerformed()
2170 protected void unGroup_actionPerformed()
2174 alignPanel.alignmentChanged();
2178 protected void deleteGroups_actionPerformed()
2180 if (avc.deleteGroups())
2182 alignPanel.alignmentChanged();
2186 public void selectAllSequenceMenuItem_actionPerformed()
2188 SequenceGroup sg = new SequenceGroup();
2189 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2191 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2193 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2194 viewport.setSelectionGroup(sg);
2195 alignPanel.paintAlignment(true);
2196 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2197 viewport.sendSelection();
2200 public void deselectAllSequenceMenuItem_actionPerformed()
2202 if (viewport.cursorMode)
2204 alignPanel.seqPanel.keyboardNo1 = null;
2205 alignPanel.seqPanel.keyboardNo2 = null;
2207 viewport.setSelectionGroup(null);
2208 viewport.getColumnSelection().clear();
2209 viewport.setSelectionGroup(null);
2210 alignPanel.idPanel.idCanvas.searchResults = null;
2211 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2212 alignPanel.paintAlignment(true);
2213 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2214 viewport.sendSelection();
2217 public void invertSequenceMenuItem_actionPerformed()
2219 SequenceGroup sg = viewport.getSelectionGroup();
2220 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2222 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2225 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226 viewport.sendSelection();
2229 public void invertColSel_actionPerformed()
2231 viewport.invertColumnSelection();
2232 alignPanel.paintAlignment(true);
2233 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2234 viewport.sendSelection();
2237 void trimAlignment(boolean trimLeft)
2239 ColumnSelection colSel = viewport.getColumnSelection();
2242 if (colSel.size() > 0)
2246 column = colSel.getMin();
2250 column = colSel.getMax();
2254 if (viewport.getSelectionGroup() != null)
2256 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2257 viewport.getHiddenRepSequences());
2261 seqs = viewport.getAlignment().getSequencesArray();
2264 TrimRegionCommand trimRegion;
2267 trimRegion = new TrimRegionCommand("Remove Left",
2268 TrimRegionCommand.TRIM_LEFT, seqs, column,
2269 viewport.getAlignment(), viewport.getColumnSelection(),
2270 viewport.getSelectionGroup());
2271 viewport.setStartRes(0);
2275 trimRegion = new TrimRegionCommand("Remove Right",
2276 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2277 viewport.getAlignment(), viewport.getColumnSelection(),
2278 viewport.getSelectionGroup());
2281 statusBar.setText(MessageManager.formatMessage(
2282 "label.removed_columns", new String[]
2283 { Integer.valueOf(trimRegion.getSize()).toString() }));
2284 addHistoryItem(trimRegion);
2286 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2288 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2289 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2291 viewport.getAlignment().deleteGroup(sg);
2295 viewport.firePropertyChange("alignment", null, viewport
2296 .getAlignment().getSequences());
2300 public void removeGappedColumnMenuItem_actionPerformed()
2302 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2305 if (viewport.getSelectionGroup() != null)
2307 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2308 viewport.getHiddenRepSequences());
2309 start = viewport.getSelectionGroup().getStartRes();
2310 end = viewport.getSelectionGroup().getEndRes();
2314 seqs = viewport.getAlignment().getSequencesArray();
2317 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2318 "Remove Gapped Columns", seqs, start, end,
2319 viewport.getAlignment());
2321 addHistoryItem(removeGapCols);
2323 statusBar.setText(MessageManager.formatMessage(
2324 "label.removed_empty_columns", new String[]
2325 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2327 // This is to maintain viewport position on first residue
2328 // of first sequence
2329 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2330 int startRes = seq.findPosition(viewport.startRes);
2331 // ShiftList shifts;
2332 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2333 // edit.alColumnChanges=shifts.getInverse();
2334 // if (viewport.hasHiddenColumns)
2335 // viewport.getColumnSelection().compensateForEdits(shifts);
2336 viewport.setStartRes(seq.findIndex(startRes) - 1);
2337 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2342 public void removeAllGapsMenuItem_actionPerformed()
2344 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347 if (viewport.getSelectionGroup() != null)
2349 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2350 viewport.getHiddenRepSequences());
2351 start = viewport.getSelectionGroup().getStartRes();
2352 end = viewport.getSelectionGroup().getEndRes();
2356 seqs = viewport.getAlignment().getSequencesArray();
2359 // This is to maintain viewport position on first residue
2360 // of first sequence
2361 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2362 int startRes = seq.findPosition(viewport.startRes);
2364 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2365 viewport.getAlignment()));
2367 viewport.setStartRes(seq.findIndex(startRes) - 1);
2369 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2374 public void findMenuItem_actionPerformed()
2376 new Finder(alignPanel);
2380 * create a new view derived from the current view
2383 * @return frame for the new view
2385 public AlignFrame newView(String viewtitle)
2388 if (viewport.hasHiddenRows())
2390 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2391 .getFullAlignment().getSequencesArray());
2395 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2398 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2400 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2402 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2404 newal.addAnnotation(viewport.getAlignment()
2405 .getAlignmentAnnotation()[i]);
2410 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2412 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2413 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2414 PaintRefresher.Register(newaf.alignPanel,
2415 newaf.alignPanel.av.getSequenceSetId());
2417 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2418 newaf.alignPanel.av.getSequenceSetId());
2419 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2420 newaf.alignPanel.av.getSequenceSetId());
2422 Vector comps = (Vector) PaintRefresher.components.get(viewport
2423 .getSequenceSetId());
2425 for (int i = 0; i < comps.size(); i++)
2427 if (comps.elementAt(i) instanceof AlignmentPanel)
2433 String title = new String(this.getTitle());
2434 if (viewtitle != null)
2436 title = viewtitle + " ( " + title + ")";
2440 if (title.indexOf("(View") > -1)
2442 title = title.substring(0, title.indexOf("(View"));
2444 title += "(View " + viewSize + ")";
2447 newaf.setTitle(title.toString());
2449 newaf.viewport.setHistoryList(viewport.getHistoryList());
2450 newaf.viewport.setRedoList(viewport.getRedoList());
2456 * @return list of feature groups on the view
2458 public String[] getFeatureGroups()
2460 FeatureRenderer fr = null;
2461 if (alignPanel != null
2462 && (fr = alignPanel.getFeatureRenderer()) != null)
2464 List<String> gps = fr.getFeatureGroups();
2465 String[] _gps = gps.toArray(new String[gps.size()]);
2472 * get sequence feature groups that are hidden or shown
2478 public String[] getFeatureGroupsOfState(boolean visible)
2480 FeatureRenderer fr = null;
2481 if (alignPanel != null
2482 && (fr = alignPanel.getFeatureRenderer()) != null)
2484 List<String> gps = fr.getGroups(visible);
2485 String[] _gps = gps.toArray(new String[gps.size()]);
2492 * Change the display state for the given feature groups
2495 * list of group strings
2497 * visible or invisible
2499 public void setFeatureGroupState(String[] groups, boolean state)
2501 FeatureRenderer fr = null;
2502 this.sequenceFeatures.setState(true);
2503 viewport.setShowSequenceFeatures(true);
2504 if (alignPanel != null
2505 && (fr = alignPanel.getFeatureRenderer()) != null)
2508 fr.setGroupVisibility(Arrays.asList(groups), state);
2509 alignPanel.seqPanel.seqCanvas.repaint();
2510 if (alignPanel.overviewPanel != null)
2512 alignPanel.overviewPanel.updateOverviewImage();
2517 public void seqLimits_itemStateChanged()
2519 viewport.setShowJVSuffix(seqLimits.getState());
2520 alignPanel.fontChanged();
2521 alignPanel.paintAlignment(true);
2524 protected void colourTextMenuItem_actionPerformed()
2526 viewport.setColourText(colourTextMenuItem.getState());
2527 alignPanel.paintAlignment(true);
2530 protected void displayNonconservedMenuItem_actionPerformed()
2532 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2533 alignPanel.paintAlignment(true);
2536 protected void wrapMenuItem_actionPerformed()
2538 viewport.setWrapAlignment(wrapMenuItem.getState());
2539 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2540 scaleAbove.setEnabled(wrapMenuItem.getState());
2541 scaleLeft.setEnabled(wrapMenuItem.getState());
2542 scaleRight.setEnabled(wrapMenuItem.getState());
2543 alignPanel.paintAlignment(true);
2546 public void overviewMenuItem_actionPerformed()
2548 if (alignPanel.overviewPanel != null)
2553 Frame frame = new Frame();
2554 OverviewPanel overview = new OverviewPanel(alignPanel);
2555 frame.add(overview);
2556 // +50 must allow for applet frame window
2557 JalviewLite.addFrame(frame, MessageManager.formatMessage(
2558 "label.overview_params", new String[]
2559 { this.getTitle() }), overview.getPreferredSize().width,
2560 overview.getPreferredSize().height + 50);
2563 final AlignmentPanel ap = alignPanel;
2564 frame.addWindowListener(new WindowAdapter()
2567 public void windowClosing(WindowEvent e)
2571 ap.setOverviewPanel(null);
2576 alignPanel.setOverviewPanel(overview);
2580 public void changeColour(ColourSchemeI cs)
2586 if (viewport.getAbovePIDThreshold())
2588 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2592 if (viewport.getConservationSelected())
2594 cs.setConservationApplied(true);
2595 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2600 cs.setConservationApplied(false);
2603 viewport.setGlobalColourScheme(cs);
2605 if (alignPanel.getOverviewPanel() != null)
2607 alignPanel.getOverviewPanel().updateOverviewImage();
2610 StructureSelectionManager.getStructureSelectionManager(viewport.applet)
2611 .sequenceColoursChanged(alignPanel);
2613 alignPanel.paintAlignment(true);
2616 protected void modifyPID_actionPerformed()
2618 if (viewport.getAbovePIDThreshold()
2619 && viewport.getGlobalColourScheme() != null)
2621 SliderPanel.setPIDSliderSource(alignPanel,
2622 viewport.getGlobalColourScheme(), "Background");
2623 SliderPanel.showPIDSlider();
2627 protected void modifyConservation_actionPerformed()
2629 if (viewport.getConservationSelected()
2630 && viewport.getGlobalColourScheme() != null)
2632 SliderPanel.setConservationSlider(alignPanel,
2633 viewport.getGlobalColourScheme(), "Background");
2634 SliderPanel.showConservationSlider();
2638 protected void conservationMenuItem_actionPerformed()
2640 viewport.setConservationSelected(conservationMenuItem.getState());
2642 viewport.setAbovePIDThreshold(false);
2643 abovePIDThreshold.setState(false);
2645 changeColour(viewport.getGlobalColourScheme());
2647 modifyConservation_actionPerformed();
2650 public void abovePIDThreshold_actionPerformed()
2652 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2654 conservationMenuItem.setState(false);
2655 viewport.setConservationSelected(false);
2657 changeColour(viewport.getGlobalColourScheme());
2659 modifyPID_actionPerformed();
2662 public void sortPairwiseMenuItem_actionPerformed()
2664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2665 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2666 .getAlignment().getSequenceAt(0), null);
2668 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2669 viewport.getAlignment()));
2670 alignPanel.paintAlignment(true);
2673 public void sortIDMenuItem_actionPerformed()
2675 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2676 AlignmentSorter.sortByID(viewport.getAlignment());
2677 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2678 viewport.getAlignment()));
2679 alignPanel.paintAlignment(true);
2682 public void sortLengthMenuItem_actionPerformed()
2684 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2685 AlignmentSorter.sortByLength(viewport.getAlignment());
2686 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2687 viewport.getAlignment()));
2688 alignPanel.paintAlignment(true);
2691 public void sortGroupMenuItem_actionPerformed()
2693 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2694 AlignmentSorter.sortByGroup(viewport.getAlignment());
2695 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2696 viewport.getAlignment()));
2697 alignPanel.paintAlignment(true);
2701 public void removeRedundancyMenuItem_actionPerformed()
2703 new RedundancyPanel(alignPanel);
2706 public void pairwiseAlignmentMenuItem_actionPerformed()
2708 if (viewport.getSelectionGroup() != null
2709 && viewport.getSelectionGroup().getSize() > 1)
2711 Frame frame = new Frame();
2712 frame.add(new PairwiseAlignPanel(alignPanel));
2713 JalviewLite.addFrame(frame,
2714 MessageManager.getString("action.pairwise_alignment"), 600,
2719 public void PCAMenuItem_actionPerformed()
2721 // are the sequences aligned?
2722 if (!viewport.getAlignment().isAligned(false))
2725 int Width = viewport.getAlignment().getWidth();
2727 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2729 current = viewport.getAlignment().getSequenceAt(i);
2731 if (current.getLength() < Width)
2733 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2736 alignPanel.paintAlignment(true);
2739 if ((viewport.getSelectionGroup() != null
2740 && viewport.getSelectionGroup().getSize() < 4 && viewport
2741 .getSelectionGroup().getSize() > 0)
2742 || viewport.getAlignment().getHeight() < 4)
2749 new PCAPanel(viewport);
2750 } catch (java.lang.OutOfMemoryError ex)
2756 public void averageDistanceTreeMenuItem_actionPerformed()
2758 NewTreePanel("AV", "PID", "Average distance tree using PID");
2761 public void neighbourTreeMenuItem_actionPerformed()
2763 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2766 protected void njTreeBlosumMenuItem_actionPerformed()
2768 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2771 protected void avTreeBlosumMenuItem_actionPerformed()
2773 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2776 void NewTreePanel(String type, String pwType, String title)
2778 // are the sequences aligned?
2779 if (!viewport.getAlignment().isAligned(false))
2782 int Width = viewport.getAlignment().getWidth();
2784 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2786 current = viewport.getAlignment().getSequenceAt(i);
2788 if (current.getLength() < Width)
2790 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2793 alignPanel.paintAlignment(true);
2797 if ((viewport.getSelectionGroup() != null && viewport
2798 .getSelectionGroup().getSize() > 1)
2799 || (viewport.getAlignment().getHeight() > 1))
2801 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2803 addTreeMenuItem(tp, title);
2805 JalviewLite.addFrame(tp, title, 600, 500);
2809 void loadTree_actionPerformed()
2811 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2812 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2813 cap.setTreeImport();
2814 Frame frame = new Frame();
2816 JalviewLite.addFrame(frame,
2817 MessageManager.getString("label.paste_newick_file"), 400, 300);
2820 public void loadTree(NewickFile tree, String treeFile)
2822 TreePanel tp = new TreePanel(alignPanel, treeFile,
2823 MessageManager.getString("label.load_tree_from_file"), tree);
2824 JalviewLite.addFrame(tp, treeFile, 600, 500);
2825 addTreeMenuItem(tp, treeFile);
2829 * sort the alignment using the given treePanel
2832 * tree used to sort view
2834 * string used for undo event name
2836 public void sortByTree(TreePanel treePanel, String title)
2838 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2840 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2841 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2842 // HistoryItem.SORT));
2843 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2844 "label.order_by_params", new String[]
2845 { title }), oldOrder, viewport.getAlignment()));
2846 alignPanel.paintAlignment(true);
2850 * Do any automatic reordering of the alignment and add the necessary bits to
2851 * the menu structure for the new tree
2856 protected void addTreeMenuItem(final TreePanel treePanel,
2859 final MenuItem item = new MenuItem(title);
2860 sortByTreeMenu.add(item);
2861 item.addActionListener(new java.awt.event.ActionListener()
2864 public void actionPerformed(ActionEvent evt)
2866 sortByTree(treePanel, title); // treePanel.getTitle());
2870 treePanel.addWindowListener(new WindowAdapter()
2873 public void windowOpened(WindowEvent e)
2875 if (viewport.sortByTree)
2877 sortByTree(treePanel, title);
2879 super.windowOpened(e);
2883 public void windowClosing(WindowEvent e)
2885 sortByTreeMenu.remove(item);
2890 public boolean sortBy(AlignmentOrder alorder, String undoname)
2892 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2893 if (viewport.applet.debug)
2895 System.err.println("Sorting " + alorder.getOrder().size()
2896 + " in alignment '" + getTitle() + "'");
2898 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2899 if (undoname != null)
2901 addHistoryItem(new OrderCommand(undoname, oldOrder,
2902 viewport.getAlignment()));
2904 alignPanel.paintAlignment(true);
2908 protected void documentation_actionPerformed()
2910 alignPanel.av.applet.openJalviewHelpUrl();
2913 protected void about_actionPerformed()
2916 class AboutPanel extends Canvas
2922 public AboutPanel(String version, String builddate)
2924 this.version = version;
2925 this.builddate = builddate;
2929 public void paint(Graphics g)
2931 g.setColor(Color.white);
2932 g.fillRect(0, 0, getSize().width, getSize().height);
2933 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2934 FontMetrics fm = g.getFontMetrics();
2935 int fh = fm.getHeight();
2937 g.setColor(Color.black);
2938 // TODO: update this text for each release or centrally store it for
2939 // lite and application
2940 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2941 g.drawString(MessageManager.formatMessage(
2942 "label.jalviewLite_release", new String[]
2943 { version }), x, y += fh);
2944 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2945 g.drawString(MessageManager.formatMessage(
2946 "label.jaview_build_date", new String[]
2947 { builddate }), x, y += fh);
2948 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2949 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2951 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2952 x + 50, y += fh + 8);
2954 MessageManager.getString("label.jalview_dev_managers"), x,
2956 g.drawString(MessageManager
2957 .getString("label.jalview_distribution_lists"), x, y += fh);
2958 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2961 MessageManager.getString("label.jalview_cite_1_authors"),
2964 MessageManager.getString("label.jalview_cite_1_title"), x,
2966 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2971 Frame frame = new Frame();
2972 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2974 JalviewLite.addFrame(frame,
2975 MessageManager.getString("label.jalview"), 580, 220);
2979 public void showURL(String url, String target)
2981 if (viewport.applet == null)
2983 System.out.println("Not running as applet - no browser available.");
2987 viewport.applet.showURL(url, target);
2991 // ////////////////////////////////////////////////////////////////////////////////
2992 // JBuilder Graphics here
2994 MenuBar alignFrameMenuBar = new MenuBar();
2996 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2998 MenuItem loadApplication = new MenuItem(
2999 MessageManager.getString("label.view_full_application"));
3001 MenuItem loadTree = new MenuItem(
3002 MessageManager.getString("label.load_associated_tree"));
3004 MenuItem loadAnnotations = new MenuItem(
3005 MessageManager.getString("label.load_features_annotations"));
3007 MenuItem outputFeatures = new MenuItem(
3008 MessageManager.getString("label.export_features").concat("..."));
3010 MenuItem outputAnnotations = new MenuItem(
3011 MessageManager.getString("label.export_annotations").concat("..."));
3013 MenuItem closeMenuItem = new MenuItem(
3014 MessageManager.getString("action.close"));
3016 MenuItem selectAllSequenceMenuItem = new MenuItem(
3017 MessageManager.getString("action.select_all"));
3019 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3020 MessageManager.getString("action.deselect_all"));
3022 MenuItem invertSequenceMenuItem = new MenuItem(
3023 MessageManager.getString("action.invert_selection"));
3025 MenuItem remove2LeftMenuItem = new MenuItem();
3027 MenuItem remove2RightMenuItem = new MenuItem();
3029 MenuItem removeGappedColumnMenuItem = new MenuItem();
3031 MenuItem removeAllGapsMenuItem = new MenuItem();
3033 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3035 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3037 MenuItem sortPairwiseMenuItem = new MenuItem();
3039 MenuItem sortIDMenuItem = new MenuItem();
3041 MenuItem sortLengthMenuItem = new MenuItem();
3043 MenuItem sortGroupMenuItem = new MenuItem();
3045 MenuItem removeRedundancyMenuItem = new MenuItem();
3047 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3049 MenuItem PCAMenuItem = new MenuItem();
3051 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3053 MenuItem neighbourTreeMenuItem = new MenuItem();
3055 BorderLayout borderLayout1 = new BorderLayout();
3057 public Label statusBar = new Label();
3059 MenuItem clustalColour = new MenuItem();
3061 MenuItem zappoColour = new MenuItem();
3063 MenuItem taylorColour = new MenuItem();
3065 MenuItem hydrophobicityColour = new MenuItem();
3067 MenuItem helixColour = new MenuItem();
3069 MenuItem strandColour = new MenuItem();
3071 MenuItem turnColour = new MenuItem();
3073 MenuItem buriedColour = new MenuItem();
3075 MenuItem purinePyrimidineColour = new MenuItem();
3077 MenuItem RNAInteractionColour = new MenuItem();
3079 MenuItem RNAHelixColour = new MenuItem();
3081 MenuItem userDefinedColour = new MenuItem();
3083 MenuItem PIDColour = new MenuItem();
3085 MenuItem BLOSUM62Colour = new MenuItem();
3087 MenuItem tcoffeeColour = new MenuItem();
3089 MenuItem njTreeBlosumMenuItem = new MenuItem();
3091 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3093 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3095 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3097 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3099 MenuItem alProperties = new MenuItem(
3100 MessageManager.getString("label.alignment_props"));
3102 MenuItem overviewMenuItem = new MenuItem();
3104 MenuItem undoMenuItem = new MenuItem();
3106 MenuItem redoMenuItem = new MenuItem();
3108 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3110 MenuItem noColourmenuItem = new MenuItem();
3112 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3114 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3116 MenuItem findMenuItem = new MenuItem();
3118 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3120 MenuItem nucleotideColour = new MenuItem();
3122 MenuItem deleteGroups = new MenuItem();
3124 MenuItem grpsFromSelection = new MenuItem();
3126 MenuItem createGroup = new MenuItem();
3128 MenuItem unGroup = new MenuItem();
3130 MenuItem delete = new MenuItem();
3132 MenuItem copy = new MenuItem();
3134 MenuItem cut = new MenuItem();
3136 Menu pasteMenu = new Menu();
3138 MenuItem pasteNew = new MenuItem();
3140 MenuItem pasteThis = new MenuItem();
3142 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3144 MenuItem font = new MenuItem();
3146 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3148 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3150 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3152 MenuItem modifyPID = new MenuItem();
3154 MenuItem modifyConservation = new MenuItem();
3156 CheckboxMenuItem autoCalculate = null;
3158 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3159 "Sort Alignment With New Tree", true);
3161 Menu sortByTreeMenu = new Menu();
3163 MenuItem inputText = new MenuItem();
3165 MenuItem documentation = new MenuItem();
3167 MenuItem about = new MenuItem();
3169 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3171 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3173 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3175 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3177 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3179 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3181 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3183 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3185 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3188 * Initialise menus and other items
3192 private void jbInit() throws Exception
3194 setMenuBar(alignFrameMenuBar);
3197 * Configure File menu items and actions
3200 .setLabel(MessageManager.getString("label.input_from_textbox"));
3201 inputText.addActionListener(this);
3202 Menu outputTextboxMenu = new Menu(
3203 MessageManager.getString("label.out_to_textbox"));
3204 for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3207 MenuItem item = new MenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3209 item.addActionListener(new java.awt.event.ActionListener()
3212 public void actionPerformed(ActionEvent e)
3214 outputText_actionPerformed(e);
3218 outputTextboxMenu.add(item);
3220 closeMenuItem.addActionListener(this);
3221 loadApplication.addActionListener(this);
3222 loadTree.addActionListener(this);
3223 loadAnnotations.addActionListener(this);
3224 outputFeatures.addActionListener(this);
3225 outputAnnotations.addActionListener(this);
3228 * Configure Edit menu items and actions
3230 undoMenuItem.setEnabled(false);
3231 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3232 undoMenuItem.addActionListener(this);
3233 redoMenuItem.setEnabled(false);
3234 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3235 redoMenuItem.addActionListener(this);
3236 copy.setLabel(MessageManager.getString("action.copy"));
3237 copy.addActionListener(this);
3238 cut.setLabel(MessageManager.getString("action.cut"));
3239 cut.addActionListener(this);
3240 delete.setLabel(MessageManager.getString("action.delete"));
3241 delete.addActionListener(this);
3242 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3243 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3244 pasteNew.addActionListener(this);
3245 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3246 pasteThis.addActionListener(this);
3247 remove2LeftMenuItem.setLabel(MessageManager
3248 .getString("action.remove_left"));
3249 remove2LeftMenuItem.addActionListener(this);
3250 remove2RightMenuItem.setLabel(MessageManager
3251 .getString("action.remove_right"));
3252 remove2RightMenuItem.addActionListener(this);
3253 removeGappedColumnMenuItem.setLabel(MessageManager
3254 .getString("action.remove_empty_columns"));
3255 removeGappedColumnMenuItem.addActionListener(this);
3256 removeAllGapsMenuItem.setLabel(MessageManager
3257 .getString("action.remove_all_gaps"));
3258 removeAllGapsMenuItem.addActionListener(this);
3259 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3260 "action.remove_redundancy").concat("..."));
3261 removeRedundancyMenuItem.addActionListener(this);
3264 * Configure Select menu items and actions
3266 findMenuItem.setLabel(MessageManager.getString("action.find"));
3267 findMenuItem.addActionListener(this);
3268 selectAllSequenceMenuItem.addActionListener(this);
3269 deselectAllSequenceMenuItem.addActionListener(this);
3270 invertSequenceMenuItem.setLabel(MessageManager
3271 .getString("action.invert_sequence_selection"));
3272 invertSequenceMenuItem.addActionListener(this);
3273 invertColSel.setLabel(MessageManager
3274 .getString("action.invert_column_selection"));
3275 invertColSel.addActionListener(this);
3276 deleteGroups.setLabel(MessageManager
3277 .getString("action.undefine_groups"));
3278 deleteGroups.addActionListener(this);
3279 grpsFromSelection.setLabel(MessageManager
3280 .getString("action.make_groups_selection"));
3281 grpsFromSelection.addActionListener(this);
3282 createGroup.setLabel(MessageManager.getString("action.create_group"));
3283 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3284 annotationColumnSelection.setLabel("Select by Annotation");
3285 annotationColumnSelection.addActionListener(this);
3288 * Configure View menu items and actions
3290 newView.setLabel(MessageManager.getString("action.new_view"));
3291 newView.addActionListener(this);
3292 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3293 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3294 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3295 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3297 .setLabel(MessageManager.getString("label.selected_columns"));
3298 hideSequences.setLabel(MessageManager
3299 .getString("label.selected_sequences"));
3300 hideAllButSelection.setLabel(MessageManager
3301 .getString("label.all_but_selected_region"));
3302 hideAllSelection.setLabel(MessageManager
3303 .getString("label.selected_region"));
3304 showAllHidden.setLabel(MessageManager
3305 .getString("label.all_sequences_columns"));
3306 showColumns.addActionListener(this);
3307 showSeqs.addActionListener(this);
3308 hideColumns.addActionListener(this);
3309 hideSequences.addActionListener(this);
3310 hideAllButSelection.addActionListener(this);
3311 hideAllSelection.addActionListener(this);
3312 showAllHidden.addActionListener(this);
3313 featureSettings.setLabel(MessageManager
3314 .getString("label.feature_settings"));
3315 featureSettings.addActionListener(this);
3316 sequenceFeatures.setLabel(MessageManager
3317 .getString("label.show_sequence_features"));
3318 sequenceFeatures.addItemListener(this);
3319 sequenceFeatures.setState(false);
3320 followMouseOverFlag.setLabel(MessageManager
3321 .getString("label.automatic_scrolling"));
3322 followMouseOverFlag.addItemListener(this);
3323 alProperties.addActionListener(this);
3324 overviewMenuItem.setLabel(MessageManager
3325 .getString("label.overview_window"));
3326 overviewMenuItem.addActionListener(this);
3329 * Configure Annotations menu items and actions
3331 annotationPanelMenuItem.setLabel(MessageManager
3332 .getString("label.show_annotations"));
3333 annotationPanelMenuItem.addItemListener(this);
3334 showGroupConsensus.setLabel(MessageManager
3335 .getString("label.group_consensus"));
3336 showGroupConservation.setLabel(MessageManager
3337 .getString("label.group_conservation"));
3338 showConsensusHistogram.setLabel(MessageManager
3339 .getString("label.show_consensus_histogram"));
3340 showSequenceLogo.setLabel(MessageManager
3341 .getString("label.show_consensus_logo"));
3342 normSequenceLogo.setLabel(MessageManager
3343 .getString("label.norm_consensus_logo"));
3344 applyAutoAnnotationSettings.setLabel(MessageManager
3345 .getString("label.apply_all_groups"));
3346 applyAutoAnnotationSettings.setState(true);
3347 Menu autoAnnMenu = new Menu(
3348 MessageManager.getString("label.autocalculated_annotation"));
3349 showGroupConsensus.addItemListener(this);
3350 showGroupConservation.addItemListener(this);
3351 showConsensusHistogram.addItemListener(this);
3352 showSequenceLogo.addItemListener(this);
3353 normSequenceLogo.addItemListener(this);
3354 applyAutoAnnotationSettings.addItemListener(this);
3355 showAlignmentAnnotations = new CheckboxMenuItem(
3356 MessageManager.getString("label.show_all_al_annotations"));
3357 showSequenceAnnotations = new CheckboxMenuItem(
3358 MessageManager.getString("label.show_all_seq_annotations"));
3359 sortAnnBySequence = new CheckboxMenuItem(
3360 MessageManager.getString("label.sort_annotations_by_sequence"));
3361 sortAnnByLabel = new CheckboxMenuItem(
3362 MessageManager.getString("label.sort_annotations_by_label"));
3363 showAutoFirst = new CheckboxMenuItem(
3364 MessageManager.getString("label.show_first"));
3365 showAutoLast = new CheckboxMenuItem(
3366 MessageManager.getString("label.show_last"));
3367 showAlignmentAnnotations.addItemListener(this);
3368 showSequenceAnnotations.addItemListener(this);
3369 sortAnnBySequence.addItemListener(this);
3370 sortAnnByLabel.addItemListener(this);
3371 showAutoFirst.addItemListener(this);
3372 showAutoLast.addItemListener(this);
3375 * Configure Format menu items and actions
3377 font.setLabel(MessageManager.getString("action.font"));
3378 font.addActionListener(this);
3379 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3380 scaleAbove.setState(true);
3381 scaleAbove.setEnabled(false);
3382 scaleAbove.addItemListener(this);
3383 scaleLeft.setEnabled(false);
3384 scaleLeft.setState(true);
3385 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3386 scaleLeft.addItemListener(this);
3387 scaleRight.setEnabled(false);
3388 scaleRight.setState(true);
3389 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3390 scaleRight.addItemListener(this);
3391 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3392 viewBoxesMenuItem.setState(true);
3393 viewBoxesMenuItem.addItemListener(this);
3394 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3395 viewTextMenuItem.setState(true);
3396 viewTextMenuItem.addItemListener(this);
3397 colourTextMenuItem.setLabel(MessageManager
3398 .getString("label.colour_text"));
3399 colourTextMenuItem.addItemListener(this);
3400 displayNonconservedMenuItem.setLabel(MessageManager
3401 .getString("label.show_non_conversed"));
3402 displayNonconservedMenuItem.addItemListener(this);
3403 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3404 wrapMenuItem.addItemListener(this);
3405 renderGapsMenuItem.setLabel(MessageManager
3406 .getString("action.show_gaps"));
3407 renderGapsMenuItem.setState(true);
3408 renderGapsMenuItem.addItemListener(this);
3409 centreColumnLabelFlag.setLabel(MessageManager
3410 .getString("label.centre_column_labels"));
3411 centreColumnLabelFlag.addItemListener(this);
3412 seqLimits.setState(true);
3413 seqLimits.setLabel(MessageManager
3414 .getString("label.show_sequence_limits"));
3415 seqLimits.addItemListener(this);
3418 * Configure Colour menu items and actions
3420 applyToAllGroups.setLabel(MessageManager
3421 .getString("label.apply_colour_to_all_groups"));
3422 applyToAllGroups.setState(true);
3423 applyToAllGroups.addItemListener(this);
3424 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3425 clustalColour.addActionListener(this);
3426 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3427 zappoColour.addActionListener(this);
3428 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3429 taylorColour.addActionListener(this);
3430 hydrophobicityColour.setLabel(MessageManager
3431 .getString("label.hydrophobicity"));
3432 hydrophobicityColour.addActionListener(this);
3434 .setLabel(MessageManager.getString("label.helix_propensity"));
3435 helixColour.addActionListener(this);
3436 strandColour.setLabel(MessageManager
3437 .getString("label.strand_propensity"));
3438 strandColour.addActionListener(this);
3439 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3440 turnColour.addActionListener(this);
3441 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3442 buriedColour.addActionListener(this);
3443 purinePyrimidineColour.setLabel(MessageManager
3444 .getString("label.purine_pyrimidine"));
3445 purinePyrimidineColour.addActionListener(this);
3446 RNAInteractionColour.setLabel(MessageManager
3447 .getString("label.rna_interaction"));
3448 RNAInteractionColour.addActionListener(this);
3449 RNAHelixColour.setLabel(MessageManager
3450 .getString("action.by_rna_helixes"));
3451 RNAHelixColour.addActionListener(this);
3452 userDefinedColour.setLabel(MessageManager
3453 .getString("action.user_defined"));
3454 userDefinedColour.addActionListener(this);
3455 PIDColour.setLabel(MessageManager
3456 .getString("label.percentage_identity"));
3457 PIDColour.addActionListener(this);
3458 BLOSUM62Colour.setLabel(MessageManager
3459 .getString("label.blosum62_score"));
3460 BLOSUM62Colour.addActionListener(this);
3462 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3463 // it will be enabled only if a score file is provided
3464 tcoffeeColour.setEnabled(false);
3465 tcoffeeColour.addActionListener(this);
3466 conservationMenuItem.setLabel(MessageManager
3467 .getString("action.by_conservation"));
3468 conservationMenuItem.addItemListener(this);
3469 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3470 noColourmenuItem.addActionListener(this);
3471 abovePIDThreshold.setLabel(MessageManager
3472 .getString("label.above_identity_threshold"));
3473 abovePIDThreshold.addItemListener(this);
3474 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3475 nucleotideColour.addActionListener(this);
3476 modifyPID.setLabel(MessageManager
3477 .getString("label.modify_identity_thereshold"));
3478 modifyPID.addActionListener(this);
3479 modifyConservation.setLabel(MessageManager
3480 .getString("label.modify_conservation_thereshold"));
3481 modifyConservation.addActionListener(this);
3482 annotationColour.setLabel(MessageManager
3483 .getString("action.by_annotation"));
3484 annotationColour.addActionListener(this);
3487 * Configure Calculate menu items and actions
3489 sortPairwiseMenuItem.setLabel(MessageManager
3490 .getString("action.by_pairwise_id"));
3491 sortPairwiseMenuItem.addActionListener(this);
3492 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3493 sortIDMenuItem.addActionListener(this);
3494 sortLengthMenuItem.setLabel(MessageManager
3495 .getString("action.by_length"));
3496 sortLengthMenuItem.addActionListener(this);
3497 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3498 sortGroupMenuItem.addActionListener(this);
3499 pairwiseAlignmentMenuItem.setLabel(MessageManager
3500 .getString("action.pairwise_alignment"));
3501 pairwiseAlignmentMenuItem.addActionListener(this);
3502 PCAMenuItem.setLabel(MessageManager
3503 .getString("label.principal_component_analysis"));
3504 PCAMenuItem.addActionListener(this);
3505 autoCalculate = new CheckboxMenuItem(
3506 MessageManager.getString("label.autocalculate_consensus"), true);
3507 averageDistanceTreeMenuItem.setLabel(MessageManager
3508 .getString("label.average_distance_identity"));
3509 averageDistanceTreeMenuItem.addActionListener(this);
3510 neighbourTreeMenuItem.setLabel(MessageManager
3511 .getString("label.neighbour_joining_identity"));
3512 neighbourTreeMenuItem.addActionListener(this);
3513 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3514 .getString("label.average_distance_bloslum62"));
3515 avDistanceTreeBlosumMenuItem.addActionListener(this);
3516 njTreeBlosumMenuItem.setLabel(MessageManager
3517 .getString("label.neighbour_blosum62"));
3518 njTreeBlosumMenuItem.addActionListener(this);
3519 sortByTreeMenu.setLabel(MessageManager
3520 .getString("action.by_tree_order"));
3521 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3522 Menu calculateTreeMenu = new Menu(
3523 MessageManager.getString("action.calculate_tree"));
3524 autoCalculate.addItemListener(this);
3525 sortByTree.addItemListener(this);
3528 * Configure Help menu items and actions
3530 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3531 documentation.setLabel(MessageManager.getString("label.documentation"));
3532 documentation.addActionListener(this);
3533 about.setLabel(MessageManager.getString("label.about"));
3534 about.addActionListener(this);
3537 * Add top level menus to frame
3539 alignFrameMenuBar.add(fileMenu);
3540 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3541 alignFrameMenuBar.add(editMenu);
3542 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3543 alignFrameMenuBar.add(selectMenu);
3544 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3545 alignFrameMenuBar.add(viewMenu);
3546 Menu annotationsMenu = new Menu(
3547 MessageManager.getString("action.annotations"));
3548 alignFrameMenuBar.add(annotationsMenu);
3549 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3550 alignFrameMenuBar.add(formatMenu);
3551 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3552 alignFrameMenuBar.add(colourMenu);
3553 Menu calculateMenu = new Menu(
3554 MessageManager.getString("action.calculate"));
3555 alignFrameMenuBar.add(calculateMenu);
3556 alignFrameMenuBar.add(helpMenu);
3561 fileMenu.add(inputText);
3562 fileMenu.add(loadTree);
3563 fileMenu.add(loadAnnotations);
3564 fileMenu.addSeparator();
3565 fileMenu.add(outputTextboxMenu);
3566 fileMenu.add(outputFeatures);
3567 fileMenu.add(outputAnnotations);
3568 if (jalviewServletURL != null)
3570 fileMenu.add(loadApplication);
3572 fileMenu.addSeparator();
3573 fileMenu.add(closeMenuItem);
3578 editMenu.add(undoMenuItem);
3579 editMenu.add(redoMenuItem);
3582 pasteMenu.add(pasteNew);
3583 pasteMenu.add(pasteThis);
3584 editMenu.add(pasteMenu);
3585 editMenu.add(delete);
3586 editMenu.addSeparator();
3587 editMenu.add(remove2LeftMenuItem);
3588 editMenu.add(remove2RightMenuItem);
3589 editMenu.add(removeGappedColumnMenuItem);
3590 editMenu.add(removeAllGapsMenuItem);
3591 editMenu.add(removeRedundancyMenuItem);
3596 selectMenu.add(findMenuItem);
3597 selectMenu.addSeparator();
3598 selectMenu.add(selectAllSequenceMenuItem);
3599 selectMenu.add(deselectAllSequenceMenuItem);
3600 selectMenu.add(invertSequenceMenuItem);
3601 selectMenu.add(invertColSel);
3602 selectMenu.add(createGroup);
3603 selectMenu.add(unGroup);
3604 selectMenu.add(grpsFromSelection);
3605 selectMenu.add(deleteGroups);
3606 selectMenu.add(annotationColumnSelection);
3611 viewMenu.add(newView);
3612 viewMenu.addSeparator();
3613 showMenu.add(showColumns);
3614 showMenu.add(showSeqs);
3615 showMenu.add(showAllHidden);
3616 viewMenu.add(showMenu);
3617 hideMenu.add(hideColumns);
3618 hideMenu.add(hideSequences);
3619 hideMenu.add(hideAllSelection);
3620 hideMenu.add(hideAllButSelection);
3621 viewMenu.add(hideMenu);
3622 viewMenu.addSeparator();
3623 viewMenu.add(followMouseOverFlag);
3624 viewMenu.addSeparator();
3625 viewMenu.add(sequenceFeatures);
3626 viewMenu.add(featureSettings);
3627 viewMenu.addSeparator();
3628 viewMenu.add(alProperties);
3629 viewMenu.addSeparator();
3630 viewMenu.add(overviewMenuItem);
3635 annotationsMenu.add(annotationPanelMenuItem);
3636 annotationsMenu.addSeparator();
3637 annotationsMenu.add(showAlignmentAnnotations);
3638 annotationsMenu.add(showSequenceAnnotations);
3639 annotationsMenu.add(sortAnnBySequence);
3640 annotationsMenu.add(sortAnnByLabel);
3641 annotationsMenu.addSeparator();
3642 autoAnnMenu.add(showAutoFirst);
3643 autoAnnMenu.add(showAutoLast);
3644 autoAnnMenu.addSeparator();
3645 autoAnnMenu.add(applyAutoAnnotationSettings);
3646 autoAnnMenu.add(showConsensusHistogram);
3647 autoAnnMenu.add(showSequenceLogo);
3648 autoAnnMenu.add(normSequenceLogo);
3649 autoAnnMenu.addSeparator();
3650 autoAnnMenu.add(showGroupConservation);
3651 autoAnnMenu.add(showGroupConsensus);
3652 annotationsMenu.add(autoAnnMenu);
3657 formatMenu.add(font);
3658 formatMenu.add(seqLimits);
3659 formatMenu.add(wrapMenuItem);
3660 formatMenu.add(scaleAbove);
3661 formatMenu.add(scaleLeft);
3662 formatMenu.add(scaleRight);
3663 formatMenu.add(viewBoxesMenuItem);
3664 formatMenu.add(viewTextMenuItem);
3665 formatMenu.add(colourTextMenuItem);
3666 formatMenu.add(displayNonconservedMenuItem);
3667 formatMenu.add(renderGapsMenuItem);
3668 formatMenu.add(centreColumnLabelFlag);
3673 colourMenu.add(applyToAllGroups);
3674 colourMenu.addSeparator();
3675 colourMenu.add(noColourmenuItem);
3676 colourMenu.add(clustalColour);
3677 colourMenu.add(BLOSUM62Colour);
3678 colourMenu.add(PIDColour);
3679 colourMenu.add(zappoColour);
3680 colourMenu.add(taylorColour);
3681 colourMenu.add(hydrophobicityColour);
3682 colourMenu.add(helixColour);
3683 colourMenu.add(strandColour);
3684 colourMenu.add(turnColour);
3685 colourMenu.add(buriedColour);
3686 colourMenu.add(nucleotideColour);
3687 colourMenu.add(purinePyrimidineColour);
3688 // colourMenu.add(RNAInteractionColour);
3689 colourMenu.add(tcoffeeColour);
3690 colourMenu.add(userDefinedColour);
3691 colourMenu.addSeparator();
3692 colourMenu.add(conservationMenuItem);
3693 colourMenu.add(modifyConservation);
3694 colourMenu.add(abovePIDThreshold);
3695 colourMenu.add(modifyPID);
3696 colourMenu.add(annotationColour);
3697 colourMenu.add(RNAHelixColour);
3702 sortMenu.add(sortIDMenuItem);
3703 sortMenu.add(sortLengthMenuItem);
3704 sortMenu.add(sortByTreeMenu);
3705 sortMenu.add(sortGroupMenuItem);
3706 sortMenu.add(sortPairwiseMenuItem);
3707 calculateMenu.add(sortMenu);
3708 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3709 calculateTreeMenu.add(neighbourTreeMenuItem);
3710 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3711 calculateTreeMenu.add(njTreeBlosumMenuItem);
3712 calculateMenu.add(calculateTreeMenu);
3713 calculateMenu.addSeparator();
3714 calculateMenu.add(pairwiseAlignmentMenuItem);
3715 calculateMenu.add(PCAMenuItem);
3716 calculateMenu.add(autoCalculate);
3717 calculateMenu.add(sortByTree);
3722 helpMenu.add(documentation);
3723 helpMenu.add(about);
3728 statusBar.setBackground(Color.white);
3729 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3730 statusBar.setText(MessageManager.getString("label.status_bar"));
3731 this.add(statusBar, BorderLayout.SOUTH);
3734 public void setStatus(String string)
3736 statusBar.setText(string);
3739 MenuItem featureSettings = new MenuItem();
3741 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3743 MenuItem annotationColour = new MenuItem();
3745 MenuItem annotationColumnSelection = new MenuItem();
3747 MenuItem invertColSel = new MenuItem();
3749 MenuItem showColumns = new MenuItem();
3751 MenuItem showSeqs = new MenuItem();
3753 MenuItem hideColumns = new MenuItem();
3755 MenuItem hideSequences = new MenuItem();
3757 MenuItem hideAllButSelection = new MenuItem();
3759 MenuItem hideAllSelection = new MenuItem();
3761 MenuItem showAllHidden = new MenuItem();
3763 MenuItem newView = new MenuItem();
3765 private CheckboxMenuItem showAlignmentAnnotations;
3767 private CheckboxMenuItem showSequenceAnnotations;
3769 private CheckboxMenuItem sortAnnBySequence;
3771 private CheckboxMenuItem sortAnnByLabel;
3773 private CheckboxMenuItem showAutoFirst;
3775 private CheckboxMenuItem showAutoLast;
3777 private SplitFrame splitFrame;
3780 * Attach the alignFrame panels after embedding menus, if necessary. This used
3781 * to be called setEmbedded, but is now creates the dropdown menus in a
3782 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3784 * @param reallyEmbedded
3785 * true to attach the view to the applet area on the page rather than
3788 public void createAlignFrameWindow(boolean reallyEmbedded)
3792 embedAlignFrameInApplet(viewport.applet);
3797 // test and embed menu bar if necessary.
3799 if (embedMenuIfNeeded(alignPanel))
3802 * adjust for status bar height too. ? pointless as overridden by layout
3805 alignPanel.setSize(getSize().width,
3806 getSize().height - statusBar.getHeight());
3808 add(statusBar, BorderLayout.SOUTH);
3809 add(alignPanel, BorderLayout.CENTER);
3810 // and register with the applet so it can pass external API calls to us
3811 JalviewLite.addFrame(this, this.getTitle(),
3818 * Add the components of this AlignFrame to the applet container.
3822 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3825 // Explicitly build the embedded menu panel for the on-page applet
3827 // view cannot be closed if its actually on the page
3828 fileMenu.remove(closeMenuItem);
3829 fileMenu.remove(3); // Remove Separator
3830 // construct embedded menu, using default font
3831 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3832 // and actually add the components to the applet area
3833 theApplet.setLayout(new BorderLayout());
3834 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3835 theApplet.add(statusBar, BorderLayout.SOUTH);
3836 // TODO should size be left to the layout manager?
3837 alignPanel.setSize(theApplet.getSize().width,
3838 theApplet.getSize().height - embeddedMenu.getHeight()
3839 - statusBar.getHeight());
3840 theApplet.add(alignPanel, BorderLayout.CENTER);
3841 final AlignFrame me = this;
3842 theApplet.addFocusListener(new FocusListener()
3846 public void focusLost(FocusEvent e)
3848 if (theApplet.currentAlignFrame == me)
3850 theApplet.currentAlignFrame = null;
3855 public void focusGained(FocusEvent e)
3857 theApplet.currentAlignFrame = me;
3860 theApplet.validate();
3864 * create a new binding between structures in an existing jmol viewer instance
3865 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3866 * this does not open a new Jmol window, or modify the display of the
3867 * structures in the original jmol window. Note This method doesn't work
3868 * without an additional javascript library to exchange messages between the
3869 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3872 * JmolViewer instance
3873 * @param sequenceIds
3874 * - sequence Ids to search for associations
3876 public SequenceStructureBinding addStructureViewInstance(
3877 Object jmolviewer, String[] sequenceIds)
3879 Viewer viewer = null;
3882 viewer = (Viewer) jmolviewer;
3883 } catch (ClassCastException ex)
3885 System.err.println("Unsupported viewer object :"
3886 + jmolviewer.getClass());
3890 System.err.println("Can't use this object as a structure viewer:"
3891 + jmolviewer.getClass());
3894 SequenceI[] seqs = null;
3895 if (sequenceIds == null || sequenceIds.length == 0)
3897 seqs = viewport.getAlignment().getSequencesArray();
3901 Vector sqi = new Vector();
3902 AlignmentI al = viewport.getAlignment();
3903 for (int sid = 0; sid < sequenceIds.length; sid++)
3905 SequenceI sq = al.findName(sequenceIds[sid]);
3913 seqs = new SequenceI[sqi.size()];
3914 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3916 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3924 AAStructureBindingModel jmv = null;
3925 // TODO: search for a jmv that involves viewer
3927 { // create a new viewer/jalview binding.
3928 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3936 * bind a pdb file to a sequence in the current view
3939 * - sequenceId within the dataset.
3940 * @param pdbEntryString
3941 * - the short name for the PDB file
3943 * - pdb file - either a URL or a valid PDB file.
3944 * @return true if binding was as success TODO: consider making an exception
3945 * structure for indicating when PDB parsing or sequenceId location
3948 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3951 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3952 boolean needtoadd = false;
3953 if (toaddpdb != null)
3955 Vector pdbe = toaddpdb.getPDBId();
3956 PDBEntry pdbentry = null;
3957 if (pdbe != null && pdbe.size() > 0)
3959 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3961 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3962 if (!pdbentry.getId().equals(pdbEntryString)
3963 && !pdbentry.getFile().equals(pdbFile))
3973 if (pdbentry == null)
3975 pdbentry = new PDBEntry();
3976 pdbentry.setId(pdbEntryString);
3977 pdbentry.setFile(pdbFile);
3978 needtoadd = true; // add this new entry to sequence.
3980 // resolve data source
3981 // TODO: this code should be a refactored to an io package
3982 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3983 if (protocol == null)
3989 // make a note of the access mode and add
3990 if (pdbentry.getProperty() == null)
3992 pdbentry.setProperty(new Hashtable());
3994 pdbentry.getProperty().put("protocol", protocol);
3995 toaddpdb.addPDBId(pdbentry);
3996 alignPanel.getStructureSelectionManager()
3997 .registerPDBEntry(pdbentry);
4003 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4007 Vector sequences = new Vector();
4008 for (int i = 0; i < seqs.length; i++)
4010 if (seqs[i] != null)
4012 sequences.addElement(new Object[]
4013 { seqs[i], (chains != null) ? chains[i] : null });
4016 seqs = new SequenceI[sequences.size()];
4017 chains = new String[sequences.size()];
4018 for (int i = 0, isize = sequences.size(); i < isize; i++)
4020 Object[] oj = (Object[]) sequences.elementAt(i);
4022 seqs[i] = (SequenceI) oj[0];
4023 chains[i] = (String) oj[1];
4031 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4032 SequenceI[] seqs, String[] chains, String protocol)
4034 // Scrub any null sequences from the array
4035 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4036 seqs = (SequenceI[]) sqch[0];
4037 chains = (String[]) sqch[1];
4038 if (seqs == null || seqs.length == 0)
4041 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4043 if (protocol == null || protocol.trim().length() == 0
4044 || protocol.equals("null"))
4046 protocol = (String) pdb.getProperty().get("protocol");
4047 if (protocol == null)
4049 System.err.println("Couldn't work out protocol to open structure: "
4054 if (applet.useXtrnalSviewer)
4056 // register the association(s) and quit, don't create any windows.
4057 if (StructureSelectionManager.getStructureSelectionManager(applet)
4058 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4060 System.err.println("Failed to map " + pdb.getFile() + " ("
4061 + protocol + ") to any sequences");
4065 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4067 // can only do alignments with Jmol
4068 // find the last jmol window assigned to this alignment
4069 AppletJmol ajm = null, tajm;
4070 Vector jmols = applet
4071 .getAppletWindow(AppletJmol.class);
4072 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4074 tajm = (AppletJmol) jmols.elementAt(i);
4075 if (tajm.ap.alignFrame == this)
4084 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4085 // try and add the pdb structure
4090 // otherwise, create a new window
4091 if (applet.jmolAvailable)
4093 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4094 applet.lastFrameX += 40;
4095 applet.lastFrameY += 40;
4099 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4104 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4105 SequenceI[][] seqs, String[][] chains, String[] protocols)
4107 // TODO Auto-generated method stub
4108 System.err.println("Aligned Structure View: Not yet implemented.");
4112 * modify the current selection, providing the user has not made a selection
4116 * - sequences from this alignment
4118 * - columns to be selected on the alignment
4120 public void select(SequenceGroup sel, ColumnSelection csel)
4122 alignPanel.seqPanel.selection(sel, csel, null);
4125 public void scrollTo(int row, int column)
4127 alignPanel.seqPanel.scrollTo(row, column);
4130 public void scrollToRow(int row)
4132 alignPanel.seqPanel.scrollToRow(row);
4135 public void scrollToColumn(int column)
4137 alignPanel.seqPanel.scrollToColumn(column);
4141 * @return the alignments unique ID.
4143 public String getSequenceSetId()
4145 return viewport.getSequenceSetId();
4149 * Load the (T-Coffee) score file from the specified url
4152 * File/URL/T-COFFEE score file contents
4153 * @throws IOException
4154 * @return true if alignment was annotated with data from source
4156 public boolean loadScoreFile(String source) throws IOException
4159 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4160 AppletFormatAdapter.checkProtocol(source));
4161 if (!file.isValid())
4163 // TODO: raise dialog for gui
4164 System.err.println("Problems parsing T-Coffee scores: "
4165 + file.getWarningMessage());
4166 System.err.println("Origin was:\n" + source);
4171 * check that the score matrix matches the alignment dimensions
4174 if ((aln = viewport.getAlignment()) != null
4175 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4178 // TODO: raise a dialog box here rather than bomb out.
4180 .println("The scores matrix does not match the alignment dimensions");
4184 // TODO add parameter to indicate if matching should be done
4185 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4187 alignPanel.fontChanged();
4188 tcoffeeColour.setEnabled(true);
4189 // switch to this color
4190 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4195 System.err.println("Problems resolving T-Coffee scores:");
4196 if (file.getWarningMessage() != null)
4198 System.err.println(file.getWarningMessage());
4204 public SplitFrame getSplitFrame()
4206 return this.splitFrame;
4209 public void setSplitFrame(SplitFrame sf)
4211 this.splitFrame = sf;
4214 // may not need this
4216 public void setShowSeqFeatures(boolean b)
4218 // showSeqFeatures.setSelected(b);
4219 viewport.setShowSequenceFeatures(b);
4224 public void setMenusForViewport()
4226 // setMenusFromViewport(viewport);
4230 public void refreshFeatureUI(boolean enableIfNecessary)
4232 if (enableIfNecessary)
4234 sequenceFeatures.setState(true);
4235 alignPanel.av.setShowSequenceFeatures(true);
4240 public FeatureSettingsControllerI getFeatureSettingsUI()
4242 return alignPanel.av.featureSettings;