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.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
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.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.DataSourceType;
53 import jalview.io.FeaturesFile;
54 import jalview.io.FileFormat;
55 import jalview.io.FileFormatI;
56 import jalview.io.FileFormats;
57 import jalview.io.TCoffeeScoreFile;
58 import jalview.schemes.Blosum62ColourScheme;
59 import jalview.schemes.BuriedColourScheme;
60 import jalview.schemes.ClustalxColourScheme;
61 import jalview.schemes.ColourSchemeI;
62 import jalview.schemes.HelixColourScheme;
63 import jalview.schemes.HydrophobicColourScheme;
64 import jalview.schemes.NucleotideColourScheme;
65 import jalview.schemes.PIDColourScheme;
66 import jalview.schemes.PurinePyrimidineColourScheme;
67 import jalview.schemes.RNAHelicesColour;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TCoffeeColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.ZappoColourScheme;
73 import jalview.structure.StructureSelectionManager;
74 import jalview.structures.models.AAStructureBindingModel;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
78 import jalview.viewmodel.ViewportRanges;
80 import java.awt.BorderLayout;
81 import java.awt.Canvas;
82 import java.awt.CheckboxMenuItem;
83 import java.awt.Color;
84 import java.awt.FlowLayout;
86 import java.awt.FontMetrics;
87 import java.awt.Frame;
88 import java.awt.Graphics;
89 import java.awt.Label;
91 import java.awt.MenuBar;
92 import java.awt.MenuItem;
93 import java.awt.MenuShortcut;
94 import java.awt.Panel;
95 import java.awt.event.ActionEvent;
96 import java.awt.event.ActionListener;
97 import java.awt.event.FocusEvent;
98 import java.awt.event.FocusListener;
99 import java.awt.event.ItemEvent;
100 import java.awt.event.ItemListener;
101 import java.awt.event.KeyEvent;
102 import java.awt.event.KeyListener;
103 import java.awt.event.WindowAdapter;
104 import java.awt.event.WindowEvent;
105 import java.io.IOException;
107 import java.net.URLEncoder;
108 import java.util.Arrays;
109 import java.util.Deque;
110 import java.util.HashMap;
111 import java.util.List;
112 import java.util.Map;
113 import java.util.StringTokenizer;
114 import java.util.Vector;
116 import org.jmol.viewer.Viewer;
118 public class AlignFrame extends EmbmenuFrame implements ActionListener,
119 ItemListener, KeyListener, AlignViewControllerGuiI
121 public AlignViewControllerI avc;
123 public AlignmentPanel alignPanel;
125 public AlignViewport viewport;
127 // width and height may be overridden by applet parameters
128 int frameWidth = 700;
130 int frameHeight = 500;
132 String jalviewServletURL;
135 * Flag for showing autocalculated consensus above or below other consensus
138 private boolean showAutoCalculatedAbove;
140 private SequenceAnnotationOrder annotationSortOrder;
143 * Constructor that creates the frame and adds it to the display.
150 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
153 this(al, applet, title, embedded, true);
157 * Constructor that optionally allows the frame to be displayed or only
164 * @param addToDisplay
166 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
167 boolean embedded, boolean addToDisplay)
169 this(al, null, null, applet, title, embedded, addToDisplay);
172 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
173 ColumnSelection columnSelection, JalviewLite applet,
174 String title, boolean embedded)
176 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
179 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
180 ColumnSelection columnSelection, JalviewLite applet,
181 String title, boolean embedded, boolean addToDisplay)
185 jalviewServletURL = applet.getParameter("APPLICATION_URL");
191 } catch (Exception ex)
193 ex.printStackTrace();
195 // need to get window geometry before we calculate alignment layout
201 param = applet.getParameter("windowWidth");
204 int width = Integer.parseInt(param);
207 param = applet.getParameter("windowHeight");
210 int height = Integer.parseInt(param);
211 frameHeight = height;
213 } catch (Exception ex)
217 viewport = new AlignViewport(al, applet);
219 if (hiddenSeqs != null && hiddenSeqs.length > 0)
221 viewport.hideSequence(hiddenSeqs);
223 if (columnSelection != null)
225 viewport.setColumnSelection(columnSelection);
227 viewport.setScaleAboveWrapped(scaleAbove.getState());
229 alignPanel = new AlignmentPanel(this, viewport);
230 avc = new jalview.controller.AlignViewController(this, viewport,
232 viewport.updateConservation(alignPanel);
233 viewport.updateConsensus(alignPanel);
235 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
236 followMouseOverFlag.setState(viewport.isFollowHighlight());
237 showGroupConsensus.setState(viewport.isShowGroupConsensus());
238 showGroupConservation.setState(viewport.isShowGroupConservation());
239 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
240 showSequenceLogo.setState(viewport.isShowSequenceLogo());
241 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
242 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
243 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
244 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
245 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
246 showAlignmentAnnotations.setState(true);
247 showSequenceAnnotations.setState(false);
249 seqLimits.setState(viewport.getShowJVSuffix());
253 String param = applet.getParameter("sortBy");
256 if (param.equalsIgnoreCase("Id"))
258 sortIDMenuItem_actionPerformed();
260 else if (param.equalsIgnoreCase("Pairwise Identity"))
262 sortPairwiseMenuItem_actionPerformed();
264 else if (param.equalsIgnoreCase("Length"))
266 sortLengthMenuItem_actionPerformed();
270 param = applet.getParameter("wrap");
273 if (param.equalsIgnoreCase("true"))
275 wrapMenuItem.setState(true);
276 wrapMenuItem_actionPerformed();
279 param = applet.getParameter("centrecolumnlabels");
282 centreColumnLabelFlag.setState(true);
283 centreColumnLabelFlag_stateChanged();
287 if (viewport.getAlignment().isNucleotide())
289 conservationMenuItem.setEnabled(false);
290 clustalColour.setEnabled(false);
291 BLOSUM62Colour.setEnabled(false);
292 zappoColour.setEnabled(false);
293 taylorColour.setEnabled(false);
294 hydrophobicityColour.setEnabled(false);
295 helixColour.setEnabled(false);
296 strandColour.setEnabled(false);
297 turnColour.setEnabled(false);
298 buriedColour.setEnabled(false);
299 viewport.updateStrucConsensus(alignPanel);
300 if (viewport.getAlignment().hasRNAStructure())
302 RNAHelixColour.setEnabled(true);
306 RNAHelixColour.setEnabled(false);
311 RNAHelixColour.setEnabled(false);
312 purinePyrimidineColour.setEnabled(false);
313 nucleotideColour.setEnabled(false);
315 // Some JVMS send keyevents to Top frame or lowest panel,
316 // Havent worked out why yet. So add to both this frame and seqCanvas for
318 this.addKeyListener(this);
319 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
320 alignPanel.idPanel.idCanvas.addKeyListener(this);
321 alignPanel.scalePanel.addKeyListener(this);
322 alignPanel.annotationPanel.addKeyListener(this);
323 alignPanel.annotationPanelHolder.addKeyListener(this);
324 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
325 alignPanel.alabels.addKeyListener(this);
327 setAnnotationsVisibility();
331 addToDisplay(embedded);
338 public void addToDisplay(boolean embedded)
340 createAlignFrameWindow(embedded);
342 alignPanel.adjustAnnotationHeight();
343 alignPanel.paintAlignment(true);
346 public AlignViewport getAlignViewport()
351 public SeqCanvas getSeqcanvas()
353 return alignPanel.seqPanel.seqCanvas;
357 * Load a features file onto the alignment
360 * file URL, content, or other resolvable path
362 * is protocol for accessing data referred to by file
365 public boolean parseFeaturesFile(String file, DataSourceType type)
367 return parseFeaturesFile(file, type, true);
371 * Load a features file onto the alignment
374 * file URL, content, or other resolvable path
376 * is protocol for accessing data referred to by file
377 * @param autoenabledisplay
378 * when true, display features flag will be automatically enabled if
379 * features are loaded
380 * @return true if data parsed as a features file
382 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
383 boolean autoenabledisplay)
385 boolean featuresFile = false;
388 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
389 .getFeatureRenderer().getFeatureColours();
390 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
391 "relaxedidmatch", false);
392 featuresFile = new FeaturesFile(file, sourceType).parse(
393 viewport.getAlignment(), colours, true, relaxedIdMatching);
394 } catch (Exception ex)
396 ex.printStackTrace();
401 if (autoenabledisplay)
403 viewport.setShowSequenceFeatures(true);
404 sequenceFeatures.setState(true);
406 if (alignPanel.seqPanel.seqCanvas.fr != null)
408 // update the min/max ranges where necessary
409 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
411 if (viewport.featureSettings != null)
413 viewport.featureSettings.refreshTable();
415 alignPanel.paintAlignment(true);
416 statusBar.setText(MessageManager
417 .getString("label.successfully_added_features_alignment"));
423 public void keyPressed(KeyEvent evt)
425 ViewportRanges ranges = viewport.getRanges();
427 if (viewport.cursorMode
428 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
429 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
430 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
431 && Character.isDigit(evt.getKeyChar()))
433 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
436 switch (evt.getKeyCode())
438 case 27: // escape key
439 deselectAllSequenceMenuItem_actionPerformed();
441 alignPanel.alabels.cancelDrag();
444 if (evt.isControlDown() || evt.isMetaDown())
446 cut_actionPerformed();
450 if (viewport.cursorMode && !evt.isControlDown())
452 alignPanel.seqPanel.setCursorColumn();
454 if (evt.isControlDown() || evt.isMetaDown())
456 copy_actionPerformed();
460 if (evt.isControlDown())
462 paste(evt.isShiftDown());
466 if (evt.isControlDown() || evt.isMetaDown())
468 selectAllSequenceMenuItem_actionPerformed();
471 case KeyEvent.VK_DOWN:
472 if (viewport.cursorMode)
474 alignPanel.seqPanel.moveCursor(0, 1);
478 moveSelectedSequences(false);
483 if (viewport.cursorMode)
485 alignPanel.seqPanel.moveCursor(0, -1);
489 moveSelectedSequences(true);
493 case KeyEvent.VK_LEFT:
494 if (evt.isAltDown() || !viewport.cursorMode)
496 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
500 alignPanel.seqPanel.moveCursor(-1, 0);
504 case KeyEvent.VK_RIGHT:
505 if (evt.isAltDown() || !viewport.cursorMode)
507 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
511 alignPanel.seqPanel.moveCursor(1, 0);
515 case KeyEvent.VK_SPACE:
516 if (viewport.cursorMode)
518 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
519 || evt.isShiftDown() || evt.isAltDown());
523 case KeyEvent.VK_DELETE:
524 case KeyEvent.VK_BACK_SPACE:
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
528 || evt.isShiftDown() || evt.isAltDown());
532 cut_actionPerformed();
533 alignPanel.seqPanel.seqCanvas.repaint();
538 if (viewport.cursorMode)
540 alignPanel.seqPanel.setCursorRow();
544 if (viewport.cursorMode)
546 alignPanel.seqPanel.setCursorPosition();
550 case KeyEvent.VK_ENTER:
551 case KeyEvent.VK_COMMA:
552 if (viewport.cursorMode)
554 alignPanel.seqPanel.setCursorRowAndColumn();
559 if (viewport.cursorMode)
561 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
565 if (viewport.cursorMode)
567 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
572 viewport.cursorMode = !viewport.cursorMode;
573 statusBar.setText(MessageManager.formatMessage(
574 "label.keyboard_editing_mode",
575 new String[] { (viewport.cursorMode ? "on" : "off") }));
576 if (viewport.cursorMode)
578 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
579 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
584 if (evt.isControlDown())
586 findMenuItem_actionPerformed();
592 boolean toggleSeqs = !evt.isControlDown();
593 boolean toggleCols = !evt.isShiftDown();
594 toggleHiddenRegions(toggleSeqs, toggleCols);
598 case KeyEvent.VK_PAGE_UP:
599 if (viewport.getWrapAlignment())
601 alignPanel.scrollUp(true);
605 alignPanel.setScrollValues(ranges.getStartRes(),
606 2 * ranges.getStartSeq() - ranges.getEndSeq());
610 case KeyEvent.VK_PAGE_DOWN:
611 if (viewport.getWrapAlignment())
613 alignPanel.scrollUp(false);
618 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
623 if (evt.isControlDown())
625 undoMenuItem_actionPerformed();
630 if (evt.isControlDown())
632 redoMenuItem_actionPerformed();
637 if (evt.isControlDown())
644 if (evt.isControlDown())
646 trimAlignment(false);
651 if (evt.isControlDown())
653 if (evt.isShiftDown())
655 this.removeAllGapsMenuItem_actionPerformed();
659 removeGappedColumnMenuItem_actionPerformed();
664 if (evt.isControlDown())
668 invertColSel_actionPerformed();
672 invertSequenceMenuItem_actionPerformed();
678 if (evt.isControlDown())
680 if (evt.isShiftDown())
682 this.unGroup_actionPerformed();
686 this.createGroup_actionPerformed();
692 if (evt.isControlDown())
694 this.deleteGroups_actionPerformed();
699 if (evt.isControlDown())
706 alignPanel.paintAlignment(true);
710 * called by key handler and the hide all/show all menu items
715 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
717 boolean hide = false;
718 SequenceGroup sg = viewport.getSelectionGroup();
719 if (!toggleSeqs && !toggleCols)
721 // Hide everything by the current selection - this is a hack - we do the
722 // invert and then hide
723 // first check that there will be visible columns after the invert.
724 if (viewport.hasSelectedColumns()
725 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
728 // now invert the sequence set, if required - empty selection implies
729 // that no hiding is required.
732 invertSequenceMenuItem_actionPerformed();
733 sg = viewport.getSelectionGroup();
737 viewport.expandColSelection(sg, true);
738 // finally invert the column selection and get the new sequence
739 // selection and indicate it should be hidden.
740 invertColSel_actionPerformed();
747 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
750 viewport.hideAllSelectedSeqs();
752 else if (!(toggleCols && viewport.hasSelectedColumns()))
754 viewport.showAllHiddenSeqs();
760 if (viewport.hasSelectedColumns())
762 viewport.hideSelectedColumns();
765 viewport.setSelectionGroup(sg);
770 viewport.showAllHiddenColumns();
772 viewport.sendSelection();
777 public void keyReleased(KeyEvent evt)
782 public void keyTyped(KeyEvent evt)
787 public void itemStateChanged(ItemEvent evt)
789 final Object source = evt.getSource();
790 if (source == displayNonconservedMenuItem)
792 displayNonconservedMenuItem_actionPerformed();
794 else if (source == colourTextMenuItem)
796 colourTextMenuItem_actionPerformed();
798 else if (source == wrapMenuItem)
800 wrapMenuItem_actionPerformed();
802 else if (source == scaleAbove)
804 viewport.setScaleAboveWrapped(scaleAbove.getState());
806 else if (source == scaleLeft)
808 viewport.setScaleLeftWrapped(scaleLeft.getState());
810 else if (source == scaleRight)
812 viewport.setScaleRightWrapped(scaleRight.getState());
814 else if (source == seqLimits)
816 seqLimits_itemStateChanged();
818 else if (source == viewBoxesMenuItem)
820 viewport.setShowBoxes(viewBoxesMenuItem.getState());
822 else if (source == viewTextMenuItem)
824 viewport.setShowText(viewTextMenuItem.getState());
826 else if (source == renderGapsMenuItem)
828 viewport.setRenderGaps(renderGapsMenuItem.getState());
830 else if (source == annotationPanelMenuItem)
832 boolean showAnnotations = annotationPanelMenuItem.getState();
833 showAlignmentAnnotations.setEnabled(showAnnotations);
834 showSequenceAnnotations.setEnabled(showAnnotations);
835 viewport.setShowAnnotation(showAnnotations);
836 alignPanel.setAnnotationVisible(showAnnotations);
838 else if (source == sequenceFeatures)
840 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
841 alignPanel.seqPanel.seqCanvas.repaint();
843 else if (source == showAlignmentAnnotations)
845 setAnnotationsVisibility();
847 else if (source == showSequenceAnnotations)
849 setAnnotationsVisibility();
851 else if (source == sortAnnBySequence)
853 boolean newState = sortAnnBySequence.getState();
854 sortAnnByLabel.setState(false);
855 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
856 : SequenceAnnotationOrder.NONE);
857 setViewportAnnotationOrder();
859 else if (source == sortAnnByLabel)
861 boolean newState = sortAnnByLabel.getState();
862 sortAnnBySequence.setState(false);
863 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
864 : SequenceAnnotationOrder.NONE);
865 setViewportAnnotationOrder();
867 else if (source == showAutoFirst)
869 showAutoLast.setState(!showAutoFirst.getState());
870 setShowAutoCalculatedAbove(showAutoFirst.getState());
871 setViewportAnnotationOrder();
873 else if (source == showAutoLast)
875 showAutoFirst.setState(!showAutoLast.getState());
876 setShowAutoCalculatedAbove(showAutoFirst.getState());
877 setViewportAnnotationOrder();
879 else if (source == conservationMenuItem)
881 conservationMenuItem_actionPerformed();
883 else if (source == abovePIDThreshold)
885 abovePIDThreshold_actionPerformed();
887 else if (source == applyToAllGroups)
889 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
891 else if (source == autoCalculate)
893 viewport.autoCalculateConsensus = autoCalculate.getState();
895 else if (source == sortByTree)
897 viewport.sortByTree = sortByTree.getState();
899 else if (source == this.centreColumnLabelFlag)
901 centreColumnLabelFlag_stateChanged();
903 else if (source == this.followMouseOverFlag)
905 mouseOverFlag_stateChanged();
907 else if (source == showGroupConsensus)
909 showGroupConsensus_actionPerformed();
911 else if (source == showGroupConservation)
913 showGroupConservation_actionPerformed();
915 else if (source == showSequenceLogo)
917 showSequenceLogo_actionPerformed();
919 else if (source == normSequenceLogo)
921 normSequenceLogo_actionPerformed();
923 else if (source == showConsensusHistogram)
925 showConsensusHistogram_actionPerformed();
927 else if (source == applyAutoAnnotationSettings)
929 applyAutoAnnotationSettings_actionPerformed();
931 alignPanel.paintAlignment(true);
935 * Set the visibility state of sequence-related and/or alignment-related
936 * annotations depending on checkbox selections, and repaint.
940 private void setAnnotationsVisibility()
942 boolean showForAlignment = showAlignmentAnnotations.getState();
943 boolean showForSequences = showSequenceAnnotations.getState();
944 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
946 for (AlignmentAnnotation aa : alignPanel.getAlignment()
947 .getAlignmentAnnotation())
949 boolean visible = (aa.sequenceRef == null ? showForAlignment
951 aa.visible = visible;
954 alignPanel.validateAnnotationDimensions(true);
959 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
961 this.annotationSortOrder = order;
965 * Set flags on the viewport that control annotation ordering
967 private void setViewportAnnotationOrder()
969 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
971 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
974 private void setShowAutoCalculatedAbove(boolean showAbove)
976 this.showAutoCalculatedAbove = showAbove;
979 private void mouseOverFlag_stateChanged()
981 viewport.setFollowHighlight(followMouseOverFlag.getState());
982 // TODO: could kick the scrollTo mechanism to reset view for current
986 private void centreColumnLabelFlag_stateChanged()
988 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
989 this.alignPanel.annotationPanel.repaint();
993 public void actionPerformed(ActionEvent evt)
995 viewport.applet.currentAlignFrame = this;
997 Object source = evt.getSource();
999 if (source == inputText)
1001 inputText_actionPerformed();
1003 else if (source == loadTree)
1005 loadTree_actionPerformed();
1007 else if (source == loadApplication)
1009 launchFullApplication();
1011 else if (source == loadAnnotations)
1015 else if (source == outputAnnotations)
1017 outputAnnotations(true);
1019 else if (source == outputFeatures)
1021 outputFeatures(true, "Jalview");
1023 else if (source == closeMenuItem)
1025 closeMenuItem_actionPerformed();
1027 else if (source == copy)
1029 copy_actionPerformed();
1031 else if (source == undoMenuItem)
1033 undoMenuItem_actionPerformed();
1035 else if (source == redoMenuItem)
1037 redoMenuItem_actionPerformed();
1039 else if (source == inputText)
1041 inputText_actionPerformed();
1043 else if (source == closeMenuItem)
1045 closeMenuItem_actionPerformed();
1047 else if (source == undoMenuItem)
1049 undoMenuItem_actionPerformed();
1051 else if (source == redoMenuItem)
1053 redoMenuItem_actionPerformed();
1055 else if (source == copy)
1057 copy_actionPerformed();
1059 else if (source == pasteNew)
1061 pasteNew_actionPerformed();
1063 else if (source == pasteThis)
1065 pasteThis_actionPerformed();
1067 else if (source == cut)
1069 cut_actionPerformed();
1071 else if (source == delete)
1073 delete_actionPerformed();
1075 else if (source == createGroup)
1077 createGroup_actionPerformed();
1079 else if (source == unGroup)
1081 unGroup_actionPerformed();
1083 else if (source == grpsFromSelection)
1085 makeGrpsFromSelection_actionPerformed();
1087 else if (source == deleteGroups)
1089 deleteGroups_actionPerformed();
1091 else if (source == selectAllSequenceMenuItem)
1093 selectAllSequenceMenuItem_actionPerformed();
1095 else if (source == deselectAllSequenceMenuItem)
1097 deselectAllSequenceMenuItem_actionPerformed();
1099 else if (source == invertSequenceMenuItem)
1101 invertSequenceMenuItem_actionPerformed();
1102 // uncomment to slave sequence selections in split frame
1103 // viewport.sendSelection();
1105 else if (source == invertColSel)
1107 viewport.invertColumnSelection();
1108 alignPanel.paintAlignment(true);
1109 viewport.sendSelection();
1111 else if (source == remove2LeftMenuItem)
1113 trimAlignment(true);
1115 else if (source == remove2RightMenuItem)
1117 trimAlignment(false);
1119 else if (source == removeGappedColumnMenuItem)
1121 removeGappedColumnMenuItem_actionPerformed();
1123 else if (source == removeAllGapsMenuItem)
1125 removeAllGapsMenuItem_actionPerformed();
1127 else if (source == findMenuItem)
1129 findMenuItem_actionPerformed();
1131 else if (source == font)
1133 new FontChooser(alignPanel);
1135 else if (source == newView)
1139 else if (source == showColumns)
1141 viewport.showAllHiddenColumns();
1142 alignPanel.paintAlignment(true);
1143 viewport.sendSelection();
1145 else if (source == showSeqs)
1147 viewport.showAllHiddenSeqs();
1148 alignPanel.paintAlignment(true);
1149 // uncomment if we want to slave sequence selections in split frame
1150 // viewport.sendSelection();
1152 else if (source == hideColumns)
1154 viewport.hideSelectedColumns();
1155 alignPanel.paintAlignment(true);
1156 viewport.sendSelection();
1158 else if (source == hideSequences
1159 && viewport.getSelectionGroup() != null)
1161 viewport.hideAllSelectedSeqs();
1162 alignPanel.paintAlignment(true);
1163 // uncomment if we want to slave sequence selections in split frame
1164 // viewport.sendSelection();
1166 else if (source == hideAllButSelection)
1168 toggleHiddenRegions(false, false);
1169 alignPanel.paintAlignment(true);
1170 viewport.sendSelection();
1172 else if (source == hideAllSelection)
1174 SequenceGroup sg = viewport.getSelectionGroup();
1175 viewport.expandColSelection(sg, false);
1176 viewport.hideAllSelectedSeqs();
1177 viewport.hideSelectedColumns();
1178 alignPanel.paintAlignment(true);
1179 viewport.sendSelection();
1181 else if (source == showAllHidden)
1183 viewport.showAllHiddenColumns();
1184 viewport.showAllHiddenSeqs();
1185 alignPanel.paintAlignment(true);
1186 viewport.sendSelection();
1188 else if (source == showGroupConsensus)
1190 showGroupConsensus_actionPerformed();
1192 else if (source == showGroupConservation)
1194 showGroupConservation_actionPerformed();
1196 else if (source == showSequenceLogo)
1198 showSequenceLogo_actionPerformed();
1200 else if (source == normSequenceLogo)
1202 normSequenceLogo_actionPerformed();
1204 else if (source == showConsensusHistogram)
1206 showConsensusHistogram_actionPerformed();
1208 else if (source == applyAutoAnnotationSettings)
1210 applyAutoAnnotationSettings_actionPerformed();
1212 else if (source == featureSettings)
1214 new FeatureSettings(alignPanel);
1216 else if (source == alProperties)
1218 StringBuffer contents = new jalview.io.AlignmentProperties(
1219 viewport.getAlignment()).formatAsString();
1220 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1221 cap.setText(contents.toString());
1222 Frame frame = new Frame();
1224 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1225 "label.alignment_properties", new String[] { getTitle() }),
1228 else if (source == overviewMenuItem)
1230 overviewMenuItem_actionPerformed();
1232 else if (source == noColourmenuItem)
1236 else if (source == clustalColour)
1238 abovePIDThreshold.setState(false);
1239 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1241 else if (source == zappoColour)
1243 changeColour(new ZappoColourScheme());
1245 else if (source == taylorColour)
1247 changeColour(new TaylorColourScheme());
1249 else if (source == hydrophobicityColour)
1251 changeColour(new HydrophobicColourScheme());
1253 else if (source == helixColour)
1255 changeColour(new HelixColourScheme());
1257 else if (source == strandColour)
1259 changeColour(new StrandColourScheme());
1261 else if (source == turnColour)
1263 changeColour(new TurnColourScheme());
1265 else if (source == buriedColour)
1267 changeColour(new BuriedColourScheme());
1269 else if (source == nucleotideColour)
1271 changeColour(new NucleotideColourScheme());
1273 else if (source == purinePyrimidineColour)
1275 changeColour(new PurinePyrimidineColourScheme());
1277 // else if (source == RNAInteractionColour)
1279 // changeColour(new RNAInteractionColourScheme());
1281 else if (source == RNAHelixColour)
1283 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1284 // new RNAHelicesColourChooser(viewport, alignPanel);
1286 else if (source == modifyPID)
1288 modifyPID_actionPerformed();
1290 else if (source == modifyConservation)
1292 modifyConservation_actionPerformed();
1294 else if (source == userDefinedColour)
1296 new UserDefinedColours(alignPanel, null);
1298 else if (source == PIDColour)
1300 changeColour(new PIDColourScheme());
1302 else if (source == BLOSUM62Colour)
1304 changeColour(new Blosum62ColourScheme());
1306 else if (source == tcoffeeColour)
1308 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1310 else if (source == annotationColour)
1312 new AnnotationColourChooser(viewport, alignPanel);
1314 else if (source == annotationColumnSelection)
1316 new AnnotationColumnChooser(viewport, alignPanel);
1318 else if (source == sortPairwiseMenuItem)
1320 sortPairwiseMenuItem_actionPerformed();
1322 else if (source == sortIDMenuItem)
1324 sortIDMenuItem_actionPerformed();
1326 else if (source == sortLengthMenuItem)
1328 sortLengthMenuItem_actionPerformed();
1330 else if (source == sortGroupMenuItem)
1332 sortGroupMenuItem_actionPerformed();
1334 else if (source == removeRedundancyMenuItem)
1336 removeRedundancyMenuItem_actionPerformed();
1338 else if (source == pairwiseAlignmentMenuItem)
1340 pairwiseAlignmentMenuItem_actionPerformed();
1342 else if (source == PCAMenuItem)
1344 PCAMenuItem_actionPerformed();
1346 else if (source == averageDistanceTreeMenuItem)
1348 averageDistanceTreeMenuItem_actionPerformed();
1350 else if (source == neighbourTreeMenuItem)
1352 neighbourTreeMenuItem_actionPerformed();
1354 else if (source == njTreeBlosumMenuItem)
1356 njTreeBlosumMenuItem_actionPerformed();
1358 else if (source == avDistanceTreeBlosumMenuItem)
1360 avTreeBlosumMenuItem_actionPerformed();
1362 else if (source == documentation)
1364 documentation_actionPerformed();
1366 else if (source == about)
1368 about_actionPerformed();
1373 public void inputText_actionPerformed()
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376 Frame frame = new Frame();
1378 jalview.bin.JalviewLite.addFrame(frame,
1379 MessageManager.getString("label.input_cut_paste"), 500, 500);
1382 protected void outputText_actionPerformed(ActionEvent e)
1384 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1385 Frame frame = new Frame();
1387 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1388 "label.alignment_output_command",
1389 new Object[] { e.getActionCommand() }), 600, 500);
1391 FileFormatI fileFormat = FileFormats.getInstance().forName(
1392 e.getActionCommand());
1393 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1394 fileFormat, viewport.getAlignment(),
1395 viewport.getShowJVSuffix()));
1398 public void loadAnnotations()
1400 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1401 cap.setText(MessageManager
1402 .getString("label.paste_features_annotations_Tcoffee_here"));
1403 cap.setAnnotationImport();
1404 Frame frame = new Frame();
1406 jalview.bin.JalviewLite.addFrame(frame,
1407 MessageManager.getString("action.paste_annotations"), 400, 300);
1411 public String outputAnnotations(boolean displayTextbox)
1413 String annotation = new AnnotationFile()
1414 .printAnnotationsForView(viewport);
1418 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1419 Frame frame = new Frame();
1421 jalview.bin.JalviewLite.addFrame(frame,
1422 MessageManager.getString("label.annotations"), 600, 500);
1423 cap.setText(annotation);
1429 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1431 if (alignPanel.getFeatureRenderer() != null
1432 && viewport.getFeaturesDisplayed() != null)
1434 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1440 public String outputFeatures(boolean displayTextbox, String format)
1443 FeaturesFile formatter = new FeaturesFile();
1444 if (format.equalsIgnoreCase("Jalview"))
1446 features = formatter.printJalviewFormat(viewport.getAlignment()
1447 .getSequencesArray(), getDisplayedFeatureCols());
1451 features = formatter.printGffFormat(viewport.getAlignment()
1452 .getSequencesArray(), getDisplayedFeatureCols());
1457 boolean frimport = false;
1458 if (features == null || features.equals("No Features Visible"))
1460 features = "# No features visible - paste some and import them here.";
1464 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1467 cap.setAnnotationImport();
1469 Frame frame = new Frame();
1471 jalview.bin.JalviewLite.addFrame(frame,
1472 MessageManager.getString("label.features"), 600, 500);
1473 cap.setText(features);
1477 if (features == null)
1486 void launchFullApplication()
1488 StringBuffer url = new StringBuffer(jalviewServletURL);
1490 // allow servlet parameters to be passed in applet parameter
1491 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1493 url.append(firstSep);
1496 + appendProtocol(viewport.applet.getParameter("file")));
1498 if (viewport.applet.getParameter("features") != null)
1500 url.append("&features=");
1501 url.append(appendProtocol(viewport.applet.getParameter("features")));
1504 if (viewport.applet.getParameter("annotations") != null)
1506 url.append("&annotations=");
1507 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1510 if (viewport.applet.getParameter("jnetfile") != null
1511 || viewport.applet.getParameter("jpredfile") != null)
1513 url.append("&annotations=");
1514 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1515 .getParameter("jnetfile") : viewport.applet
1516 .getParameter("jpredfile")));
1519 if (viewport.applet.getParameter("defaultColour") != null)
1521 url.append("&colour="
1522 + removeWhiteSpace(viewport.applet
1523 .getParameter("defaultColour")));
1526 if (viewport.applet.getParameter("userDefinedColour") != null)
1528 url.append("&colour="
1529 + removeWhiteSpace(viewport.applet
1530 .getParameter("userDefinedColour")));
1532 if (viewport.applet.getParameter("tree") != null)
1535 + appendProtocol(viewport.applet.getParameter("tree")));
1537 if (viewport.applet.getParameter("treeFile") != null)
1540 + appendProtocol(viewport.applet.getParameter("treeFile")));
1543 showURL(url.toString(), "FULL_APP");
1546 String removeWhiteSpace(String colour)
1548 StringBuffer sb = new StringBuffer();
1549 for (int i = 0; i < colour.length(); i++)
1551 if (Character.isWhitespace(colour.charAt(i)))
1557 sb.append(colour.charAt(i));
1561 return sb.toString();
1564 String appendProtocol(String url)
1569 url = URLEncoder.encode(url);
1572 * When we finally deprecate 1.1 compatibility, we can start to use
1573 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1574 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1575 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1576 * ex.printStackTrace(); }
1578 catch (java.net.MalformedURLException ex)
1580 url = viewport.applet.getCodeBase() + url;
1585 public void closeMenuItem_actionPerformed()
1587 PaintRefresher.RemoveComponent(alignPanel);
1588 if (alignPanel.seqPanel != null
1589 && alignPanel.seqPanel.seqCanvas != null)
1591 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1593 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1595 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1598 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1613 void updateEditMenuBar()
1616 if (viewport.getHistoryList().size() > 0)
1618 undoMenuItem.setEnabled(true);
1619 CommandI command = viewport.getHistoryList().peek();
1620 undoMenuItem.setLabel(MessageManager.formatMessage(
1621 "label.undo_command",
1622 new Object[] { command.getDescription() }));
1626 undoMenuItem.setEnabled(false);
1627 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1630 if (viewport.getRedoList().size() > 0)
1632 redoMenuItem.setEnabled(true);
1634 CommandI command = viewport.getRedoList().peek();
1635 redoMenuItem.setLabel(MessageManager.formatMessage(
1636 "label.redo_command",
1637 new Object[] { command.getDescription() }));
1641 redoMenuItem.setEnabled(false);
1642 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1650 public void addHistoryItem(CommandI command)
1652 if (command.getSize() > 0)
1654 viewport.addToHistoryList(command);
1655 viewport.clearRedoList();
1656 updateEditMenuBar();
1657 viewport.updateHiddenColumns();
1662 * TODO: JAL-1104 DOCUMENT ME!
1667 protected void undoMenuItem_actionPerformed()
1669 if (viewport.getHistoryList().isEmpty())
1674 CommandI command = viewport.getHistoryList().pop();
1675 viewport.addToRedoList(command);
1676 command.undoCommand(null);
1678 AlignmentViewport originalSource = getOriginatingSource(command);
1680 if (originalSource != viewport)
1683 .println("Warning: Viewport object mismatch whilst undoing");
1685 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1686 // viewport.getColumnSelection().getHiddenColumns()
1688 updateEditMenuBar();
1689 originalSource.firePropertyChange("alignment", null, originalSource
1690 .getAlignment().getSequences());
1694 * TODO: JAL-1104 DOCUMENT ME!
1699 protected void redoMenuItem_actionPerformed()
1701 if (viewport.getRedoList().isEmpty())
1706 CommandI command = viewport.getRedoList().pop();
1707 viewport.addToHistoryList(command);
1708 command.doCommand(null);
1710 AlignmentViewport originalSource = getOriginatingSource(command);
1712 if (originalSource != viewport)
1715 .println("Warning: Viewport object mismatch whilst re-doing");
1717 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1718 // viewport.getColumnSelection().getHiddenColumns()
1721 updateEditMenuBar();
1722 originalSource.firePropertyChange("alignment", null, originalSource
1723 .getAlignment().getSequences());
1726 AlignmentViewport getOriginatingSource(CommandI command)
1728 AlignmentViewport originalSource = null;
1729 // For sequence removal and addition, we need to fire
1730 // the property change event FROM the viewport where the
1731 // original alignment was altered
1732 AlignmentI al = null;
1733 if (command instanceof EditCommand)
1735 EditCommand editCommand = (EditCommand) command;
1736 al = editCommand.getAlignment();
1737 Vector comps = (Vector) PaintRefresher.components.get(viewport
1738 .getSequenceSetId());
1739 for (int i = 0; i < comps.size(); i++)
1741 if (comps.elementAt(i) instanceof AlignmentPanel)
1743 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1745 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1752 if (originalSource == null)
1754 // The original view is closed, we must validate
1755 // the current view against the closed view first
1758 PaintRefresher.validateSequences(al, viewport.getAlignment());
1761 originalSource = viewport;
1764 return originalSource;
1768 * Move the currently selected sequences up or down one position in the
1773 public void moveSelectedSequences(boolean up)
1775 SequenceGroup sg = viewport.getSelectionGroup();
1780 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1781 up ? null : viewport.getHiddenRepSequences(), up);
1782 alignPanel.paintAlignment(true);
1785 * Also move cDNA/protein complement sequences
1787 AlignViewportI complement = viewport.getCodingComplement();
1788 if (complement != null)
1790 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1791 viewport, complement);
1792 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1793 up ? null : complement.getHiddenRepSequences(), up);
1794 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1798 synchronized void slideSequences(boolean right, int size)
1800 List<SequenceI> sg = new Vector<SequenceI>();
1801 if (viewport.cursorMode)
1803 sg.add(viewport.getAlignment().getSequenceAt(
1804 alignPanel.seqPanel.seqCanvas.cursorY));
1806 else if (viewport.getSelectionGroup() != null
1807 && viewport.getSelectionGroup().getSize() != viewport
1808 .getAlignment().getHeight())
1810 sg = viewport.getSelectionGroup().getSequences(
1811 viewport.getHiddenRepSequences());
1819 Vector<SequenceI> invertGroup = new Vector();
1821 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1823 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1825 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1829 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1831 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1833 for (int i = 0; i < invertGroup.size(); i++)
1835 seqs2[i] = invertGroup.elementAt(i);
1838 SlideSequencesCommand ssc;
1841 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1842 size, viewport.getGapCharacter());
1846 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1847 size, viewport.getGapCharacter());
1850 int groupAdjustment = 0;
1851 if (ssc.getGapsInsertedBegin() && right)
1853 if (viewport.cursorMode)
1855 alignPanel.seqPanel.moveCursor(size, 0);
1859 groupAdjustment = size;
1862 else if (!ssc.getGapsInsertedBegin() && !right)
1864 if (viewport.cursorMode)
1866 alignPanel.seqPanel.moveCursor(-size, 0);
1870 groupAdjustment = -size;
1874 if (groupAdjustment != 0)
1876 viewport.getSelectionGroup().setStartRes(
1877 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1878 viewport.getSelectionGroup().setEndRes(
1879 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1882 boolean appendHistoryItem = false;
1883 Deque<CommandI> historyList = viewport.getHistoryList();
1884 if (historyList != null && historyList.size() > 0
1885 && historyList.peek() instanceof SlideSequencesCommand)
1887 appendHistoryItem = ssc
1888 .appendSlideCommand((SlideSequencesCommand) historyList
1892 if (!appendHistoryItem)
1894 addHistoryItem(ssc);
1900 static StringBuffer copiedSequences;
1902 static Vector copiedHiddenColumns;
1904 protected void copy_actionPerformed()
1906 if (viewport.getSelectionGroup() == null)
1911 SequenceGroup sg = viewport.getSelectionGroup();
1912 copiedSequences = new StringBuffer();
1913 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1914 for (int i = 0; i < sg.getSize(); i++)
1916 SequenceI seq = sg.getSequenceAt(i);
1917 int index = viewport.getAlignment().findIndex(seq);
1918 orderedSeqs.put(index, seq);
1921 int index = 0, startRes, endRes;
1924 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1926 copiedHiddenColumns = new Vector();
1927 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1928 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1930 copiedHiddenColumns.addElement(new int[] {
1931 region[0] - hiddenOffset, region[1] - hiddenOffset });
1936 copiedHiddenColumns = null;
1939 for (int i = 0; i < sg.getSize(); i++)
1941 SequenceI seq = null;
1945 if (orderedSeqs.containsKey(index))
1947 seq = orderedSeqs.get(index);
1958 // Returns residue following index if gap
1959 startRes = seq.findPosition(sg.getStartRes());
1962 // Need to find the residue preceeding index if gap
1965 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1967 ch = seq.getCharAt(j);
1968 if (!jalview.util.Comparison.isGap((ch)))
1976 endRes += seq.getStart() - 1;
1979 copiedSequences.append(seq.getName()
1985 + seq.getSequenceAsString(sg.getStartRes(),
1986 sg.getEndRes() + 1) + "\n");
1991 protected void pasteNew_actionPerformed()
1996 protected void pasteThis_actionPerformed()
2001 void paste(boolean newAlignment)
2006 if (copiedSequences == null)
2011 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2012 Vector seqs = new Vector();
2013 while (st.hasMoreElements())
2015 String name = st.nextToken();
2016 int start = Integer.parseInt(st.nextToken());
2017 int end = Integer.parseInt(st.nextToken());
2018 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2020 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2021 for (int i = 0; i < seqs.size(); i++)
2023 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2028 String newtitle = MessageManager
2029 .getString("label.copied_sequences");
2030 if (getTitle().startsWith(
2031 MessageManager.getString("label.copied_sequences")))
2033 newtitle = getTitle();
2037 newtitle = newtitle.concat(MessageManager.formatMessage(
2038 "label.from_msname", new String[] { getTitle() }));
2040 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2041 viewport.applet, newtitle, false);
2042 if (copiedHiddenColumns != null)
2044 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2046 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2047 af.viewport.hideColumns(region[0], region[1]);
2051 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2056 addSequences(newSeqs);
2059 } catch (Exception ex)
2061 } // could be anything being pasted in here
2065 void addSequences(SequenceI[] seqs)
2067 for (int i = 0; i < seqs.length; i++)
2069 viewport.getAlignment().addSequence(seqs[i]);
2073 addHistoryItem(new EditCommand(
2074 MessageManager.getString("label.add_sequences"), Action.PASTE,
2075 seqs, 0, viewport.getAlignment().getWidth(),
2076 viewport.getAlignment()));
2078 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2079 viewport.getAlignment().getWidth();
2080 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2085 protected void cut_actionPerformed()
2087 copy_actionPerformed();
2088 delete_actionPerformed();
2091 protected void delete_actionPerformed()
2094 SequenceGroup sg = viewport.getSelectionGroup();
2100 Vector seqs = new Vector();
2102 for (int i = 0; i < sg.getSize(); i++)
2104 seq = sg.getSequenceAt(i);
2105 seqs.addElement(seq);
2109 * If the cut affects all sequences, warn, remove highlighted columns
2111 if (sg.getSize() == viewport.getAlignment().getHeight())
2113 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2114 .getAlignment().getWidth()) ? true : false;
2115 if (isEntireAlignWidth)
2117 String title = MessageManager.getString("label.delete_all");
2118 Panel infoPanel = new Panel();
2119 infoPanel.setLayout(new FlowLayout());
2121 .add(new Label(MessageManager.getString("warn.delete_all")));
2123 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2124 dialog.setMainPanel(infoPanel);
2125 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2126 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2127 dialog.setVisible(true);
2134 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2135 sg.getEndRes() + 1);
2138 SequenceI[] cut = new SequenceI[seqs.size()];
2139 for (int i = 0; i < seqs.size(); i++)
2141 cut[i] = (SequenceI) seqs.elementAt(i);
2145 * //ADD HISTORY ITEM
2147 addHistoryItem(new EditCommand(
2148 MessageManager.getString("label.cut_sequences"), Action.CUT,
2149 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2150 viewport.getAlignment()));
2152 viewport.setSelectionGroup(null);
2153 viewport.getAlignment().deleteGroup(sg);
2155 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2158 if (viewport.getAlignment().getHeight() < 1)
2160 this.setVisible(false);
2162 viewport.sendSelection();
2166 * group consensus toggled
2169 protected void showGroupConsensus_actionPerformed()
2171 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2172 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177 * group conservation toggled.
2179 protected void showGroupConservation_actionPerformed()
2181 viewport.setShowGroupConservation(showGroupConservation.getState());
2182 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2190 * .event.ActionEvent)
2192 protected void showConsensusHistogram_actionPerformed()
2194 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2195 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2202 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2203 * .event.ActionEvent)
2205 protected void showSequenceLogo_actionPerformed()
2207 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2208 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2211 protected void normSequenceLogo_actionPerformed()
2213 showSequenceLogo.setState(true);
2214 viewport.setShowSequenceLogo(true);
2215 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2216 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2219 protected void applyAutoAnnotationSettings_actionPerformed()
2221 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2224 protected void makeGrpsFromSelection_actionPerformed()
2226 if (avc.makeGroupsFromSelection())
2228 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2229 alignPanel.updateAnnotation();
2230 alignPanel.paintAlignment(true);
2234 protected void createGroup_actionPerformed()
2239 protected void unGroup_actionPerformed()
2243 alignPanel.alignmentChanged();
2247 protected void deleteGroups_actionPerformed()
2249 if (avc.deleteGroups())
2251 alignPanel.alignmentChanged();
2255 public void selectAllSequenceMenuItem_actionPerformed()
2257 SequenceGroup sg = new SequenceGroup();
2258 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2260 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2262 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2263 viewport.setSelectionGroup(sg);
2264 // JAL-2034 - should delegate to
2265 // alignPanel to decide if overview needs
2267 alignPanel.paintAlignment(false);
2268 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2269 viewport.sendSelection();
2272 public void deselectAllSequenceMenuItem_actionPerformed()
2274 if (viewport.cursorMode)
2276 alignPanel.seqPanel.keyboardNo1 = null;
2277 alignPanel.seqPanel.keyboardNo2 = null;
2279 viewport.setSelectionGroup(null);
2280 viewport.getColumnSelection().clear();
2281 viewport.setSelectionGroup(null);
2282 alignPanel.idPanel.idCanvas.searchResults = null;
2283 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2284 // JAL-2034 - should delegate to
2285 // alignPanel to decide if overview needs
2287 alignPanel.paintAlignment(false);
2288 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289 viewport.sendSelection();
2292 public void invertSequenceMenuItem_actionPerformed()
2294 SequenceGroup sg = viewport.getSelectionGroup();
2295 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2297 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2300 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301 viewport.sendSelection();
2304 public void invertColSel_actionPerformed()
2306 viewport.invertColumnSelection();
2307 alignPanel.paintAlignment(true);
2308 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2309 viewport.sendSelection();
2312 void trimAlignment(boolean trimLeft)
2314 AlignmentI al = viewport.getAlignment();
2315 ViewportRanges ranges = viewport.getRanges();
2316 ColumnSelection colSel = viewport.getColumnSelection();
2319 if (!colSel.isEmpty())
2323 column = colSel.getMin();
2327 column = colSel.getMax();
2331 if (viewport.getSelectionGroup() != null)
2333 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2334 viewport.getHiddenRepSequences());
2338 seqs = al.getSequencesArray();
2341 TrimRegionCommand trimRegion;
2344 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2346 ranges.setStartRes(0);
2350 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2354 statusBar.setText(MessageManager.formatMessage(
2355 "label.removed_columns",
2356 new String[] { Integer.valueOf(trimRegion.getSize())
2358 addHistoryItem(trimRegion);
2360 for (SequenceGroup sg : al.getGroups())
2362 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2363 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2369 viewport.firePropertyChange("alignment", null, al.getSequences());
2373 public void removeGappedColumnMenuItem_actionPerformed()
2375 AlignmentI al = viewport.getAlignment();
2376 ViewportRanges ranges = viewport.getRanges();
2378 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2381 if (viewport.getSelectionGroup() != null)
2383 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2384 viewport.getHiddenRepSequences());
2385 start = viewport.getSelectionGroup().getStartRes();
2386 end = viewport.getSelectionGroup().getEndRes();
2390 seqs = viewport.getAlignment().getSequencesArray();
2393 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2394 "Remove Gapped Columns", seqs, start, end,
2395 viewport.getAlignment());
2397 addHistoryItem(removeGapCols);
2399 statusBar.setText(MessageManager.formatMessage(
2400 "label.removed_empty_columns",
2401 new String[] { Integer.valueOf(removeGapCols.getSize())
2404 // This is to maintain viewport position on first residue
2405 // of first sequence
2406 SequenceI seq = al.getSequenceAt(0);
2407 int startRes = seq.findPosition(ranges.getStartRes());
2408 // ShiftList shifts;
2409 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2410 // edit.alColumnChanges=shifts.getInverse();
2411 // if (viewport.hasHiddenColumns)
2412 // viewport.getColumnSelection().compensateForEdits(shifts);
2413 ranges.setStartRes(seq.findIndex(startRes) - 1);
2414 viewport.firePropertyChange("alignment", null, al.getSequences());
2418 public void removeAllGapsMenuItem_actionPerformed()
2420 AlignmentI al = viewport.getAlignment();
2421 ViewportRanges ranges = viewport.getRanges();
2423 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2426 if (viewport.getSelectionGroup() != null)
2428 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2429 viewport.getHiddenRepSequences());
2430 start = viewport.getSelectionGroup().getStartRes();
2431 end = viewport.getSelectionGroup().getEndRes();
2435 seqs = viewport.getAlignment().getSequencesArray();
2438 // This is to maintain viewport position on first residue
2439 // of first sequence
2440 SequenceI seq = al.getSequenceAt(0);
2441 int startRes = seq.findPosition(ranges.getStartRes());
2443 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2446 ranges.setStartRes(seq.findIndex(startRes) - 1);
2448 viewport.firePropertyChange("alignment", null, al.getSequences());
2452 public void findMenuItem_actionPerformed()
2454 new Finder(alignPanel);
2458 * create a new view derived from the current view
2461 * @return frame for the new view
2463 public AlignFrame newView(String viewtitle)
2466 if (viewport.hasHiddenRows())
2468 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2469 .getFullAlignment().getSequencesArray());
2473 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2476 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2478 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2480 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2482 newal.addAnnotation(viewport.getAlignment()
2483 .getAlignmentAnnotation()[i]);
2488 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2490 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2491 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2492 PaintRefresher.Register(newaf.alignPanel,
2493 newaf.alignPanel.av.getSequenceSetId());
2495 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2496 newaf.alignPanel.av.getSequenceSetId());
2497 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2498 newaf.alignPanel.av.getSequenceSetId());
2500 Vector comps = (Vector) PaintRefresher.components.get(viewport
2501 .getSequenceSetId());
2503 for (int i = 0; i < comps.size(); i++)
2505 if (comps.elementAt(i) instanceof AlignmentPanel)
2511 String title = new String(this.getTitle());
2512 if (viewtitle != null)
2514 title = viewtitle + " ( " + title + ")";
2518 if (title.indexOf("(View") > -1)
2520 title = title.substring(0, title.indexOf("(View"));
2522 title += "(View " + viewSize + ")";
2525 newaf.setTitle(title.toString());
2527 newaf.viewport.setHistoryList(viewport.getHistoryList());
2528 newaf.viewport.setRedoList(viewport.getRedoList());
2534 * @return list of feature groups on the view
2536 public String[] getFeatureGroups()
2538 FeatureRenderer fr = null;
2539 if (alignPanel != null
2540 && (fr = alignPanel.getFeatureRenderer()) != null)
2542 List<String> gps = fr.getFeatureGroups();
2543 String[] _gps = gps.toArray(new String[gps.size()]);
2550 * get sequence feature groups that are hidden or shown
2556 public String[] getFeatureGroupsOfState(boolean visible)
2558 FeatureRenderer fr = null;
2559 if (alignPanel != null
2560 && (fr = alignPanel.getFeatureRenderer()) != null)
2562 List<String> gps = fr.getGroups(visible);
2563 String[] _gps = gps.toArray(new String[gps.size()]);
2570 * Change the display state for the given feature groups
2573 * list of group strings
2575 * visible or invisible
2577 public void setFeatureGroupState(String[] groups, boolean state)
2579 FeatureRenderer fr = null;
2580 this.sequenceFeatures.setState(true);
2581 viewport.setShowSequenceFeatures(true);
2582 if (alignPanel != null
2583 && (fr = alignPanel.getFeatureRenderer()) != null)
2586 fr.setGroupVisibility(Arrays.asList(groups), state);
2587 alignPanel.seqPanel.seqCanvas.repaint();
2588 if (alignPanel.overviewPanel != null)
2590 alignPanel.overviewPanel.updateOverviewImage();
2595 public void seqLimits_itemStateChanged()
2597 viewport.setShowJVSuffix(seqLimits.getState());
2598 alignPanel.fontChanged();
2599 alignPanel.paintAlignment(true);
2602 protected void colourTextMenuItem_actionPerformed()
2604 viewport.setColourText(colourTextMenuItem.getState());
2605 alignPanel.paintAlignment(true);
2608 protected void displayNonconservedMenuItem_actionPerformed()
2610 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2611 alignPanel.paintAlignment(true);
2614 protected void wrapMenuItem_actionPerformed()
2616 viewport.setWrapAlignment(wrapMenuItem.getState());
2617 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2618 scaleAbove.setEnabled(wrapMenuItem.getState());
2619 scaleLeft.setEnabled(wrapMenuItem.getState());
2620 scaleRight.setEnabled(wrapMenuItem.getState());
2621 alignPanel.paintAlignment(true);
2624 public void overviewMenuItem_actionPerformed()
2626 if (alignPanel.overviewPanel != null)
2631 Frame frame = new Frame();
2632 OverviewPanel overview = new OverviewPanel(alignPanel);
2633 frame.add(overview);
2634 // +50 must allow for applet frame window
2635 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2636 "label.overview_params", new String[] { this.getTitle() }),
2637 overview.getPreferredSize().width,
2638 overview.getPreferredSize().height + 50);
2641 final AlignmentPanel ap = alignPanel;
2642 frame.addWindowListener(new WindowAdapter()
2645 public void windowClosing(WindowEvent e)
2649 ap.setOverviewPanel(null);
2654 alignPanel.setOverviewPanel(overview);
2659 public void changeColour(ColourSchemeI cs)
2661 viewport.setGlobalColourScheme(cs);
2663 alignPanel.paintAlignment(true);
2666 protected void modifyPID_actionPerformed()
2668 if (viewport.getAbovePIDThreshold()
2669 && viewport.getGlobalColourScheme() != null)
2671 SliderPanel.setPIDSliderSource(alignPanel,
2672 viewport.getResidueShading(), alignPanel.getViewName());
2673 SliderPanel.showPIDSlider();
2677 protected void modifyConservation_actionPerformed()
2679 if (viewport.getConservationSelected()
2680 && viewport.getGlobalColourScheme() != null)
2682 SliderPanel.setConservationSlider(alignPanel,
2683 viewport.getResidueShading(), alignPanel.getViewName());
2684 SliderPanel.showConservationSlider();
2688 protected void conservationMenuItem_actionPerformed()
2690 boolean selected = conservationMenuItem.getState();
2691 modifyConservation.setEnabled(selected);
2692 viewport.setConservationSelected(selected);
2694 // viewport.setAbovePIDThreshold(false);
2695 // abovePIDThreshold.setState(false);
2697 changeColour(viewport.getGlobalColourScheme());
2701 modifyConservation_actionPerformed();
2705 SliderPanel.hideConservationSlider();
2709 public void abovePIDThreshold_actionPerformed()
2711 boolean selected = abovePIDThreshold.getState();
2712 modifyPID.setEnabled(selected);
2713 viewport.setAbovePIDThreshold(selected);
2714 // conservationMenuItem.setState(false);
2715 // viewport.setConservationSelected(false);
2717 changeColour(viewport.getGlobalColourScheme());
2721 modifyPID_actionPerformed();
2725 SliderPanel.hidePIDSlider();
2729 public void sortPairwiseMenuItem_actionPerformed()
2731 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2732 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2733 .getAlignment().getSequenceAt(0), null);
2735 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2736 viewport.getAlignment()));
2737 alignPanel.paintAlignment(true);
2740 public void sortIDMenuItem_actionPerformed()
2742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743 AlignmentSorter.sortByID(viewport.getAlignment());
2744 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2745 viewport.getAlignment()));
2746 alignPanel.paintAlignment(true);
2749 public void sortLengthMenuItem_actionPerformed()
2751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752 AlignmentSorter.sortByLength(viewport.getAlignment());
2753 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2754 viewport.getAlignment()));
2755 alignPanel.paintAlignment(true);
2758 public void sortGroupMenuItem_actionPerformed()
2760 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2761 AlignmentSorter.sortByGroup(viewport.getAlignment());
2762 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2763 viewport.getAlignment()));
2764 alignPanel.paintAlignment(true);
2768 public void removeRedundancyMenuItem_actionPerformed()
2770 new RedundancyPanel(alignPanel);
2773 public void pairwiseAlignmentMenuItem_actionPerformed()
2775 if (viewport.getSelectionGroup() != null
2776 && viewport.getSelectionGroup().getSize() > 1)
2778 Frame frame = new Frame();
2779 frame.add(new PairwiseAlignPanel(alignPanel));
2780 jalview.bin.JalviewLite.addFrame(frame,
2781 MessageManager.getString("action.pairwise_alignment"), 600,
2786 public void PCAMenuItem_actionPerformed()
2788 // are the sequences aligned?
2789 if (!viewport.getAlignment().isAligned(false))
2792 int Width = viewport.getAlignment().getWidth();
2794 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2796 current = viewport.getAlignment().getSequenceAt(i);
2798 if (current.getLength() < Width)
2800 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2803 alignPanel.paintAlignment(true);
2806 if ((viewport.getSelectionGroup() != null
2807 && viewport.getSelectionGroup().getSize() < 4 && viewport
2808 .getSelectionGroup().getSize() > 0)
2809 || viewport.getAlignment().getHeight() < 4)
2816 new PCAPanel(viewport);
2817 } catch (java.lang.OutOfMemoryError ex)
2823 public void averageDistanceTreeMenuItem_actionPerformed()
2825 NewTreePanel("AV", "PID", "Average distance tree using PID");
2828 public void neighbourTreeMenuItem_actionPerformed()
2830 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2833 protected void njTreeBlosumMenuItem_actionPerformed()
2835 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2838 protected void avTreeBlosumMenuItem_actionPerformed()
2840 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2843 void NewTreePanel(String type, String pwType, String title)
2845 // are the sequences aligned?
2846 if (!viewport.getAlignment().isAligned(false))
2849 int Width = viewport.getAlignment().getWidth();
2851 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2853 current = viewport.getAlignment().getSequenceAt(i);
2855 if (current.getLength() < Width)
2857 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2860 alignPanel.paintAlignment(true);
2864 if ((viewport.getSelectionGroup() != null && viewport
2865 .getSelectionGroup().getSize() > 1)
2866 || (viewport.getAlignment().getHeight() > 1))
2868 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2870 addTreeMenuItem(tp, title);
2872 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2876 void loadTree_actionPerformed()
2878 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2879 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2880 cap.setTreeImport();
2881 Frame frame = new Frame();
2883 jalview.bin.JalviewLite.addFrame(frame,
2884 MessageManager.getString("label.paste_newick_file"), 400, 300);
2887 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2889 TreePanel tp = new TreePanel(alignPanel, treeFile,
2890 MessageManager.getString("label.load_tree_from_file"), tree);
2891 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2892 addTreeMenuItem(tp, treeFile);
2896 * sort the alignment using the given treePanel
2899 * tree used to sort view
2901 * string used for undo event name
2903 public void sortByTree(TreePanel treePanel, String title)
2905 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2907 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2908 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2909 // HistoryItem.SORT));
2910 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2911 "label.order_by_params", new String[] { title }), oldOrder,
2912 viewport.getAlignment()));
2913 alignPanel.paintAlignment(true);
2917 * Do any automatic reordering of the alignment and add the necessary bits to
2918 * the menu structure for the new tree
2923 protected void addTreeMenuItem(final TreePanel treePanel,
2926 final MenuItem item = new MenuItem(title);
2927 sortByTreeMenu.add(item);
2928 item.addActionListener(new java.awt.event.ActionListener()
2931 public void actionPerformed(ActionEvent evt)
2933 sortByTree(treePanel, title); // treePanel.getTitle());
2937 treePanel.addWindowListener(new WindowAdapter()
2940 public void windowOpened(WindowEvent e)
2942 if (viewport.sortByTree)
2944 sortByTree(treePanel, title);
2946 super.windowOpened(e);
2950 public void windowClosing(WindowEvent e)
2952 sortByTreeMenu.remove(item);
2957 public boolean sortBy(AlignmentOrder alorder, String undoname)
2959 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2960 if (viewport.applet.debug)
2962 System.err.println("Sorting " + alorder.getOrder().size()
2963 + " in alignment '" + getTitle() + "'");
2965 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2966 if (undoname != null)
2968 addHistoryItem(new OrderCommand(undoname, oldOrder,
2969 viewport.getAlignment()));
2971 alignPanel.paintAlignment(true);
2975 protected void documentation_actionPerformed()
2977 alignPanel.av.applet.openJalviewHelpUrl();
2980 protected void about_actionPerformed()
2983 class AboutPanel extends Canvas
2989 public AboutPanel(String version, String builddate)
2991 this.version = version;
2992 this.builddate = builddate;
2996 public void paint(Graphics g)
2998 g.setColor(Color.white);
2999 g.fillRect(0, 0, getSize().width, getSize().height);
3000 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3001 FontMetrics fm = g.getFontMetrics();
3002 int fh = fm.getHeight();
3004 g.setColor(Color.black);
3005 // TODO: update this text for each release or centrally store it for
3006 // lite and application
3007 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3008 g.drawString(MessageManager.formatMessage(
3009 "label.jalviewLite_release", new String[] { version }), x,
3011 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3012 g.drawString(MessageManager.formatMessage(
3013 "label.jaview_build_date", new String[] { builddate }), x,
3015 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3016 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3018 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3019 x + 50, y += fh + 8);
3021 MessageManager.getString("label.jalview_dev_managers"), x,
3023 g.drawString(MessageManager
3024 .getString("label.jalview_distribution_lists"), x, y += fh);
3025 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3028 MessageManager.getString("label.jalview_cite_1_authors"),
3031 MessageManager.getString("label.jalview_cite_1_title"), x,
3033 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3038 Frame frame = new Frame();
3039 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3041 jalview.bin.JalviewLite.addFrame(frame,
3042 MessageManager.getString("label.jalview"), 580, 220);
3046 public void showURL(String url, String target)
3048 if (viewport.applet == null)
3050 System.out.println("Not running as applet - no browser available.");
3054 viewport.applet.showURL(url, target);
3058 // ////////////////////////////////////////////////////////////////////////////////
3059 // JBuilder Graphics here
3061 MenuBar alignFrameMenuBar = new MenuBar();
3063 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3065 MenuItem loadApplication = new MenuItem(
3066 MessageManager.getString("label.view_full_application"));
3068 MenuItem loadTree = new MenuItem(
3069 MessageManager.getString("label.load_associated_tree"));
3071 MenuItem loadAnnotations = new MenuItem(
3072 MessageManager.getString("label.load_features_annotations"));
3074 MenuItem outputFeatures = new MenuItem(
3075 MessageManager.getString("label.export_features"));
3077 MenuItem outputAnnotations = new MenuItem(
3078 MessageManager.getString("label.export_annotations"));
3080 MenuItem closeMenuItem = new MenuItem(
3081 MessageManager.getString("action.close"));
3083 MenuItem selectAllSequenceMenuItem = new MenuItem(
3084 MessageManager.getString("action.select_all"));
3086 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3087 MessageManager.getString("action.deselect_all"));
3089 MenuItem invertSequenceMenuItem = new MenuItem(
3090 MessageManager.getString("action.invert_selection"));
3092 MenuItem remove2LeftMenuItem = new MenuItem();
3094 MenuItem remove2RightMenuItem = new MenuItem();
3096 MenuItem removeGappedColumnMenuItem = new MenuItem();
3098 MenuItem removeAllGapsMenuItem = new MenuItem();
3100 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3102 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3104 MenuItem sortPairwiseMenuItem = new MenuItem();
3106 MenuItem sortIDMenuItem = new MenuItem();
3108 MenuItem sortLengthMenuItem = new MenuItem();
3110 MenuItem sortGroupMenuItem = new MenuItem();
3112 MenuItem removeRedundancyMenuItem = new MenuItem();
3114 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3116 MenuItem PCAMenuItem = new MenuItem();
3118 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3120 MenuItem neighbourTreeMenuItem = new MenuItem();
3122 BorderLayout borderLayout1 = new BorderLayout();
3124 public Label statusBar = new Label();
3126 MenuItem clustalColour = new MenuItem();
3128 MenuItem zappoColour = new MenuItem();
3130 MenuItem taylorColour = new MenuItem();
3132 MenuItem hydrophobicityColour = new MenuItem();
3134 MenuItem helixColour = new MenuItem();
3136 MenuItem strandColour = new MenuItem();
3138 MenuItem turnColour = new MenuItem();
3140 MenuItem buriedColour = new MenuItem();
3142 MenuItem purinePyrimidineColour = new MenuItem();
3144 // MenuItem RNAInteractionColour = new MenuItem();
3146 MenuItem RNAHelixColour = new MenuItem();
3148 MenuItem userDefinedColour = new MenuItem();
3150 MenuItem PIDColour = new MenuItem();
3152 MenuItem BLOSUM62Colour = new MenuItem();
3154 MenuItem tcoffeeColour = new MenuItem();
3156 MenuItem njTreeBlosumMenuItem = new MenuItem();
3158 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3160 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3162 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3164 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3166 MenuItem alProperties = new MenuItem(
3167 MessageManager.getString("label.alignment_props"));
3169 MenuItem overviewMenuItem = new MenuItem();
3171 MenuItem undoMenuItem = new MenuItem();
3173 MenuItem redoMenuItem = new MenuItem();
3175 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3177 MenuItem noColourmenuItem = new MenuItem();
3179 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3181 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3183 MenuItem findMenuItem = new MenuItem();
3185 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3187 MenuItem nucleotideColour = new MenuItem();
3189 MenuItem deleteGroups = new MenuItem();
3191 MenuItem grpsFromSelection = new MenuItem();
3193 MenuItem createGroup = new MenuItem();
3195 MenuItem unGroup = new MenuItem();
3197 MenuItem delete = new MenuItem();
3199 MenuItem copy = new MenuItem();
3201 MenuItem cut = new MenuItem();
3203 Menu pasteMenu = new Menu();
3205 MenuItem pasteNew = new MenuItem();
3207 MenuItem pasteThis = new MenuItem();
3209 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3211 MenuItem font = new MenuItem();
3213 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3215 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3217 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3219 MenuItem modifyPID = new MenuItem();
3221 MenuItem modifyConservation = new MenuItem();
3223 CheckboxMenuItem autoCalculate = null;
3225 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3226 "Sort Alignment With New Tree", true);
3228 Menu sortByTreeMenu = new Menu();
3230 MenuItem inputText = new MenuItem();
3232 MenuItem documentation = new MenuItem();
3234 MenuItem about = new MenuItem();
3236 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3238 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3240 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3242 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3244 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3246 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3248 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3250 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3252 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3255 * Initialise menus and other items
3259 private void jbInit() throws Exception
3261 setMenuBar(alignFrameMenuBar);
3264 * Configure File menu items and actions
3267 .setLabel(MessageManager.getString("label.input_from_textbox"));
3268 inputText.addActionListener(this);
3269 Menu outputTextboxMenu = new Menu(
3270 MessageManager.getString("label.out_to_textbox"));
3271 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3273 MenuItem item = new MenuItem(ff);
3275 item.addActionListener(new java.awt.event.ActionListener()
3278 public void actionPerformed(ActionEvent e)
3280 outputText_actionPerformed(e);
3284 outputTextboxMenu.add(item);
3286 closeMenuItem.addActionListener(this);
3287 loadApplication.addActionListener(this);
3288 loadTree.addActionListener(this);
3289 loadAnnotations.addActionListener(this);
3290 outputFeatures.addActionListener(this);
3291 outputAnnotations.addActionListener(this);
3294 * Configure Edit menu items and actions
3296 undoMenuItem.setEnabled(false);
3297 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3298 undoMenuItem.addActionListener(this);
3299 redoMenuItem.setEnabled(false);
3300 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3301 redoMenuItem.addActionListener(this);
3302 copy.setLabel(MessageManager.getString("action.copy"));
3303 copy.addActionListener(this);
3304 cut.setLabel(MessageManager.getString("action.cut"));
3305 cut.addActionListener(this);
3306 delete.setLabel(MessageManager.getString("action.delete"));
3307 delete.addActionListener(this);
3308 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3309 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3310 pasteNew.addActionListener(this);
3311 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3312 pasteThis.addActionListener(this);
3313 remove2LeftMenuItem.setLabel(MessageManager
3314 .getString("action.remove_left"));
3315 remove2LeftMenuItem.addActionListener(this);
3316 remove2RightMenuItem.setLabel(MessageManager
3317 .getString("action.remove_right"));
3318 remove2RightMenuItem.addActionListener(this);
3319 removeGappedColumnMenuItem.setLabel(MessageManager
3320 .getString("action.remove_empty_columns"));
3321 removeGappedColumnMenuItem.addActionListener(this);
3322 removeAllGapsMenuItem.setLabel(MessageManager
3323 .getString("action.remove_all_gaps"));
3324 removeAllGapsMenuItem.addActionListener(this);
3325 removeRedundancyMenuItem.setLabel(MessageManager
3326 .getString("action.remove_redundancy"));
3327 removeRedundancyMenuItem.addActionListener(this);
3330 * Configure Select menu items and actions
3332 findMenuItem.setLabel(MessageManager.getString("action.find"));
3333 findMenuItem.addActionListener(this);
3334 selectAllSequenceMenuItem.addActionListener(this);
3335 deselectAllSequenceMenuItem.addActionListener(this);
3336 invertSequenceMenuItem.setLabel(MessageManager
3337 .getString("action.invert_sequence_selection"));
3338 invertSequenceMenuItem.addActionListener(this);
3339 invertColSel.setLabel(MessageManager
3340 .getString("action.invert_column_selection"));
3341 invertColSel.addActionListener(this);
3342 deleteGroups.setLabel(MessageManager
3343 .getString("action.undefine_groups"));
3344 deleteGroups.addActionListener(this);
3345 grpsFromSelection.setLabel(MessageManager
3346 .getString("action.make_groups_selection"));
3347 grpsFromSelection.addActionListener(this);
3348 createGroup.setLabel(MessageManager.getString("action.create_group"));
3349 createGroup.addActionListener(this);
3350 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3351 unGroup.addActionListener(this);
3353 annotationColumnSelection.setLabel(MessageManager
3354 .getString("action.select_by_annotation"));
3355 annotationColumnSelection.addActionListener(this);
3358 * Configure View menu items and actions
3360 newView.setLabel(MessageManager.getString("action.new_view"));
3361 newView.addActionListener(this);
3362 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3363 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3364 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3365 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3367 .setLabel(MessageManager.getString("label.selected_columns"));
3368 hideSequences.setLabel(MessageManager
3369 .getString("label.selected_sequences"));
3370 hideAllButSelection.setLabel(MessageManager
3371 .getString("label.all_but_selected_region"));
3372 hideAllSelection.setLabel(MessageManager
3373 .getString("label.selected_region"));
3374 showAllHidden.setLabel(MessageManager
3375 .getString("label.all_sequences_columns"));
3376 showColumns.addActionListener(this);
3377 showSeqs.addActionListener(this);
3378 hideColumns.addActionListener(this);
3379 hideSequences.addActionListener(this);
3380 hideAllButSelection.addActionListener(this);
3381 hideAllSelection.addActionListener(this);
3382 showAllHidden.addActionListener(this);
3383 featureSettings.setLabel(MessageManager
3384 .getString("action.feature_settings"));
3385 featureSettings.addActionListener(this);
3386 sequenceFeatures.setLabel(MessageManager
3387 .getString("label.show_sequence_features"));
3388 sequenceFeatures.addItemListener(this);
3389 sequenceFeatures.setState(false);
3390 followMouseOverFlag.setLabel(MessageManager
3391 .getString("label.automatic_scrolling"));
3392 followMouseOverFlag.addItemListener(this);
3393 alProperties.addActionListener(this);
3394 overviewMenuItem.setLabel(MessageManager
3395 .getString("label.overview_window"));
3396 overviewMenuItem.addActionListener(this);
3399 * Configure Annotations menu items and actions
3401 annotationPanelMenuItem.setLabel(MessageManager
3402 .getString("label.show_annotations"));
3403 annotationPanelMenuItem.addItemListener(this);
3404 showGroupConsensus.setLabel(MessageManager
3405 .getString("label.group_consensus"));
3406 showGroupConservation.setLabel(MessageManager
3407 .getString("label.group_conservation"));
3408 showConsensusHistogram.setLabel(MessageManager
3409 .getString("label.show_consensus_histogram"));
3410 showSequenceLogo.setLabel(MessageManager
3411 .getString("label.show_consensus_logo"));
3412 normSequenceLogo.setLabel(MessageManager
3413 .getString("label.norm_consensus_logo"));
3414 applyAutoAnnotationSettings.setLabel(MessageManager
3415 .getString("label.apply_all_groups"));
3416 applyAutoAnnotationSettings.setState(true);
3417 Menu autoAnnMenu = new Menu(
3418 MessageManager.getString("label.autocalculated_annotation"));
3419 showGroupConsensus.addItemListener(this);
3420 showGroupConservation.addItemListener(this);
3421 showConsensusHistogram.addItemListener(this);
3422 showSequenceLogo.addItemListener(this);
3423 normSequenceLogo.addItemListener(this);
3424 applyAutoAnnotationSettings.addItemListener(this);
3425 showAlignmentAnnotations = new CheckboxMenuItem(
3426 MessageManager.getString("label.show_all_al_annotations"));
3427 showSequenceAnnotations = new CheckboxMenuItem(
3428 MessageManager.getString("label.show_all_seq_annotations"));
3429 sortAnnBySequence = new CheckboxMenuItem(
3430 MessageManager.getString("label.sort_annotations_by_sequence"));
3431 sortAnnByLabel = new CheckboxMenuItem(
3432 MessageManager.getString("label.sort_annotations_by_label"));
3433 showAutoFirst = new CheckboxMenuItem(
3434 MessageManager.getString("label.show_first"));
3435 showAutoFirst.setState(false); // pending applet parameter
3436 setShowAutoCalculatedAbove(showAutoFirst.getState());
3437 showAutoLast = new CheckboxMenuItem(
3438 MessageManager.getString("label.show_last"));
3439 showAutoLast.setState(!showAutoFirst.getState());
3440 showAlignmentAnnotations.addItemListener(this);
3441 showSequenceAnnotations.addItemListener(this);
3442 sortAnnBySequence.addItemListener(this);
3443 sortAnnByLabel.addItemListener(this);
3444 showAutoFirst.addItemListener(this);
3445 showAutoLast.addItemListener(this);
3448 * Configure Format menu items and actions
3450 font.setLabel(MessageManager.getString("action.font"));
3451 font.addActionListener(this);
3452 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3453 scaleAbove.setState(true);
3454 scaleAbove.setEnabled(false);
3455 scaleAbove.addItemListener(this);
3456 scaleLeft.setEnabled(false);
3457 scaleLeft.setState(true);
3458 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3459 scaleLeft.addItemListener(this);
3460 scaleRight.setEnabled(false);
3461 scaleRight.setState(true);
3462 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3463 scaleRight.addItemListener(this);
3464 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3465 viewBoxesMenuItem.setState(true);
3466 viewBoxesMenuItem.addItemListener(this);
3467 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3468 viewTextMenuItem.setState(true);
3469 viewTextMenuItem.addItemListener(this);
3470 colourTextMenuItem.setLabel(MessageManager
3471 .getString("label.colour_text"));
3472 colourTextMenuItem.addItemListener(this);
3473 displayNonconservedMenuItem.setLabel(MessageManager
3474 .getString("label.show_non_conserved"));
3475 displayNonconservedMenuItem.addItemListener(this);
3476 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3477 wrapMenuItem.addItemListener(this);
3478 renderGapsMenuItem.setLabel(MessageManager
3479 .getString("action.show_gaps"));
3480 renderGapsMenuItem.setState(true);
3481 renderGapsMenuItem.addItemListener(this);
3482 centreColumnLabelFlag.setLabel(MessageManager
3483 .getString("label.centre_column_labels"));
3484 centreColumnLabelFlag.addItemListener(this);
3485 seqLimits.setState(true);
3486 seqLimits.setLabel(MessageManager
3487 .getString("label.show_sequence_limits"));
3488 seqLimits.addItemListener(this);
3491 * Configure Colour menu items and actions
3493 applyToAllGroups.setLabel(MessageManager
3494 .getString("label.apply_colour_to_all_groups"));
3495 applyToAllGroups.setState(true);
3496 applyToAllGroups.addItemListener(this);
3497 clustalColour.setLabel(MessageManager
3498 .getString("label.colourScheme_clustal"));
3499 clustalColour.addActionListener(this);
3500 zappoColour.setLabel(MessageManager
3501 .getString("label.colourScheme_zappo"));
3502 zappoColour.addActionListener(this);
3503 taylorColour.setLabel(MessageManager
3504 .getString("label.colourScheme_taylor"));
3505 taylorColour.addActionListener(this);
3506 hydrophobicityColour.setLabel(MessageManager
3507 .getString("label.colourScheme_hydrophobic"));
3508 hydrophobicityColour.addActionListener(this);
3509 helixColour.setLabel(MessageManager
3510 .getString("label.colourScheme_helix_propensity"));
3511 helixColour.addActionListener(this);
3512 strandColour.setLabel(MessageManager
3513 .getString("label.colourScheme_strand_propensity"));
3514 strandColour.addActionListener(this);
3515 turnColour.setLabel(MessageManager
3516 .getString("label.colourScheme_turn_propensity"));
3517 turnColour.addActionListener(this);
3518 buriedColour.setLabel(MessageManager
3519 .getString("label.colourScheme_buried_index"));
3520 buriedColour.addActionListener(this);
3521 purinePyrimidineColour.setLabel(MessageManager
3522 .getString("label.colourScheme_purine/pyrimidine"));
3523 purinePyrimidineColour.addActionListener(this);
3524 // RNAInteractionColour.setLabel(MessageManager
3525 // .getString("label.rna_interaction"));
3526 // RNAInteractionColour.addActionListener(this);
3527 RNAHelixColour.setLabel(MessageManager
3528 .getString("label.colourScheme_rna_helices"));
3529 RNAHelixColour.addActionListener(this);
3530 userDefinedColour.setLabel(MessageManager
3531 .getString("action.user_defined"));
3532 userDefinedColour.addActionListener(this);
3533 PIDColour.setLabel(MessageManager
3534 .getString("label.colourScheme_%_identity"));
3535 PIDColour.addActionListener(this);
3536 BLOSUM62Colour.setLabel(MessageManager
3537 .getString("label.colourScheme_blosum62"));
3538 BLOSUM62Colour.addActionListener(this);
3539 tcoffeeColour.setLabel(MessageManager
3540 .getString("label.colourScheme_t-coffee_scores"));
3541 // it will be enabled only if a score file is provided
3542 tcoffeeColour.setEnabled(false);
3543 tcoffeeColour.addActionListener(this);
3544 conservationMenuItem.setLabel(MessageManager
3545 .getString("action.by_conservation"));
3546 conservationMenuItem.addItemListener(this);
3547 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3548 noColourmenuItem.addActionListener(this);
3549 abovePIDThreshold.setLabel(MessageManager
3550 .getString("label.above_identity_threshold"));
3551 abovePIDThreshold.addItemListener(this);
3552 nucleotideColour.setLabel(MessageManager
3553 .getString("label.colourScheme_nucleotide"));
3554 nucleotideColour.addActionListener(this);
3555 modifyPID.setLabel(MessageManager
3556 .getString("label.modify_identity_threshold"));
3557 modifyPID.setEnabled(abovePIDThreshold.getState());
3558 modifyPID.addActionListener(this);
3559 modifyConservation.setLabel(MessageManager
3560 .getString("label.modify_conservation_threshold"));
3561 modifyConservation.setEnabled(conservationMenuItem.getState());
3562 modifyConservation.addActionListener(this);
3563 annotationColour.setLabel(MessageManager
3564 .getString("action.by_annotation"));
3565 annotationColour.addActionListener(this);
3568 * Configure Calculate menu items and actions
3570 sortPairwiseMenuItem.setLabel(MessageManager
3571 .getString("action.by_pairwise_id"));
3572 sortPairwiseMenuItem.addActionListener(this);
3573 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3574 sortIDMenuItem.addActionListener(this);
3575 sortLengthMenuItem.setLabel(MessageManager
3576 .getString("action.by_length"));
3577 sortLengthMenuItem.addActionListener(this);
3578 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3579 sortGroupMenuItem.addActionListener(this);
3580 pairwiseAlignmentMenuItem.setLabel(MessageManager
3581 .getString("action.pairwise_alignment"));
3582 pairwiseAlignmentMenuItem.addActionListener(this);
3583 PCAMenuItem.setLabel(MessageManager
3584 .getString("label.principal_component_analysis"));
3585 PCAMenuItem.addActionListener(this);
3586 autoCalculate = new CheckboxMenuItem(
3587 MessageManager.getString("label.autocalculate_consensus"), true);
3588 averageDistanceTreeMenuItem.setLabel(MessageManager
3589 .getString("label.average_distance_identity"));
3590 averageDistanceTreeMenuItem.addActionListener(this);
3591 neighbourTreeMenuItem.setLabel(MessageManager
3592 .getString("label.neighbour_joining_identity"));
3593 neighbourTreeMenuItem.addActionListener(this);
3594 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3595 .getString("label.average_distance_blosum62"));
3596 avDistanceTreeBlosumMenuItem.addActionListener(this);
3597 njTreeBlosumMenuItem.setLabel(MessageManager
3598 .getString("label.neighbour_blosum62"));
3599 njTreeBlosumMenuItem.addActionListener(this);
3600 sortByTreeMenu.setLabel(MessageManager
3601 .getString("action.by_tree_order"));
3602 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3603 Menu calculateTreeMenu = new Menu(
3604 MessageManager.getString("action.calculate_tree"));
3605 autoCalculate.addItemListener(this);
3606 sortByTree.addItemListener(this);
3609 * Configure Help menu items and actions
3611 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3612 documentation.setLabel(MessageManager.getString("label.documentation"));
3613 documentation.addActionListener(this);
3614 about.setLabel(MessageManager.getString("label.about"));
3615 about.addActionListener(this);
3618 * Add top level menus to frame
3620 alignFrameMenuBar.add(fileMenu);
3621 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3622 alignFrameMenuBar.add(editMenu);
3623 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3624 alignFrameMenuBar.add(selectMenu);
3625 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3626 alignFrameMenuBar.add(viewMenu);
3627 Menu annotationsMenu = new Menu(
3628 MessageManager.getString("action.annotations"));
3629 alignFrameMenuBar.add(annotationsMenu);
3630 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3631 alignFrameMenuBar.add(formatMenu);
3632 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3633 alignFrameMenuBar.add(colourMenu);
3634 Menu calculateMenu = new Menu(
3635 MessageManager.getString("action.calculate"));
3636 alignFrameMenuBar.add(calculateMenu);
3637 alignFrameMenuBar.add(helpMenu);
3642 fileMenu.add(inputText);
3643 fileMenu.add(loadTree);
3644 fileMenu.add(loadAnnotations);
3645 fileMenu.addSeparator();
3646 fileMenu.add(outputTextboxMenu);
3647 fileMenu.add(outputFeatures);
3648 fileMenu.add(outputAnnotations);
3649 if (jalviewServletURL != null)
3651 fileMenu.add(loadApplication);
3653 fileMenu.addSeparator();
3654 fileMenu.add(closeMenuItem);
3659 editMenu.add(undoMenuItem);
3660 editMenu.add(redoMenuItem);
3663 pasteMenu.add(pasteNew);
3664 pasteMenu.add(pasteThis);
3665 editMenu.add(pasteMenu);
3666 editMenu.add(delete);
3667 editMenu.addSeparator();
3668 editMenu.add(remove2LeftMenuItem);
3669 editMenu.add(remove2RightMenuItem);
3670 editMenu.add(removeGappedColumnMenuItem);
3671 editMenu.add(removeAllGapsMenuItem);
3672 editMenu.add(removeRedundancyMenuItem);
3677 selectMenu.add(findMenuItem);
3678 selectMenu.addSeparator();
3679 selectMenu.add(selectAllSequenceMenuItem);
3680 selectMenu.add(deselectAllSequenceMenuItem);
3681 selectMenu.add(invertSequenceMenuItem);
3682 selectMenu.add(invertColSel);
3683 selectMenu.add(createGroup);
3684 selectMenu.add(unGroup);
3685 selectMenu.add(grpsFromSelection);
3686 selectMenu.add(deleteGroups);
3687 selectMenu.add(annotationColumnSelection);
3692 viewMenu.add(newView);
3693 viewMenu.addSeparator();
3694 showMenu.add(showColumns);
3695 showMenu.add(showSeqs);
3696 showMenu.add(showAllHidden);
3697 viewMenu.add(showMenu);
3698 hideMenu.add(hideColumns);
3699 hideMenu.add(hideSequences);
3700 hideMenu.add(hideAllSelection);
3701 hideMenu.add(hideAllButSelection);
3702 viewMenu.add(hideMenu);
3703 viewMenu.addSeparator();
3704 viewMenu.add(followMouseOverFlag);
3705 viewMenu.addSeparator();
3706 viewMenu.add(sequenceFeatures);
3707 viewMenu.add(featureSettings);
3708 viewMenu.addSeparator();
3709 viewMenu.add(alProperties);
3710 viewMenu.addSeparator();
3711 viewMenu.add(overviewMenuItem);
3716 annotationsMenu.add(annotationPanelMenuItem);
3717 annotationsMenu.addSeparator();
3718 annotationsMenu.add(showAlignmentAnnotations);
3719 annotationsMenu.add(showSequenceAnnotations);
3720 annotationsMenu.add(sortAnnBySequence);
3721 annotationsMenu.add(sortAnnByLabel);
3722 annotationsMenu.addSeparator();
3723 autoAnnMenu.add(showAutoFirst);
3724 autoAnnMenu.add(showAutoLast);
3725 autoAnnMenu.addSeparator();
3726 autoAnnMenu.add(applyAutoAnnotationSettings);
3727 autoAnnMenu.add(showConsensusHistogram);
3728 autoAnnMenu.add(showSequenceLogo);
3729 autoAnnMenu.add(normSequenceLogo);
3730 autoAnnMenu.addSeparator();
3731 autoAnnMenu.add(showGroupConservation);
3732 autoAnnMenu.add(showGroupConsensus);
3733 annotationsMenu.add(autoAnnMenu);
3738 formatMenu.add(font);
3739 formatMenu.add(seqLimits);
3740 formatMenu.add(wrapMenuItem);
3741 formatMenu.add(scaleAbove);
3742 formatMenu.add(scaleLeft);
3743 formatMenu.add(scaleRight);
3744 formatMenu.add(viewBoxesMenuItem);
3745 formatMenu.add(viewTextMenuItem);
3746 formatMenu.add(colourTextMenuItem);
3747 formatMenu.add(displayNonconservedMenuItem);
3748 formatMenu.add(renderGapsMenuItem);
3749 formatMenu.add(centreColumnLabelFlag);
3754 colourMenu.add(applyToAllGroups);
3755 colourMenu.addSeparator();
3756 colourMenu.add(noColourmenuItem);
3757 colourMenu.add(clustalColour);
3758 colourMenu.add(BLOSUM62Colour);
3759 colourMenu.add(PIDColour);
3760 colourMenu.add(zappoColour);
3761 colourMenu.add(taylorColour);
3762 colourMenu.add(hydrophobicityColour);
3763 colourMenu.add(helixColour);
3764 colourMenu.add(strandColour);
3765 colourMenu.add(turnColour);
3766 colourMenu.add(buriedColour);
3767 colourMenu.add(nucleotideColour);
3768 colourMenu.add(purinePyrimidineColour);
3769 // colourMenu.add(RNAInteractionColour);
3770 colourMenu.add(tcoffeeColour);
3771 colourMenu.add(userDefinedColour);
3772 colourMenu.addSeparator();
3773 colourMenu.add(conservationMenuItem);
3774 colourMenu.add(modifyConservation);
3775 colourMenu.add(abovePIDThreshold);
3776 colourMenu.add(modifyPID);
3777 colourMenu.add(annotationColour);
3778 colourMenu.add(RNAHelixColour);
3783 sortMenu.add(sortIDMenuItem);
3784 sortMenu.add(sortLengthMenuItem);
3785 sortMenu.add(sortByTreeMenu);
3786 sortMenu.add(sortGroupMenuItem);
3787 sortMenu.add(sortPairwiseMenuItem);
3788 calculateMenu.add(sortMenu);
3789 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3790 calculateTreeMenu.add(neighbourTreeMenuItem);
3791 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3792 calculateTreeMenu.add(njTreeBlosumMenuItem);
3793 calculateMenu.add(calculateTreeMenu);
3794 calculateMenu.addSeparator();
3795 calculateMenu.add(pairwiseAlignmentMenuItem);
3796 calculateMenu.add(PCAMenuItem);
3797 calculateMenu.add(autoCalculate);
3798 calculateMenu.add(sortByTree);
3803 helpMenu.add(documentation);
3804 helpMenu.add(about);
3809 statusBar.setBackground(Color.white);
3810 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3811 statusBar.setText(MessageManager.getString("label.status_bar"));
3812 this.add(statusBar, BorderLayout.SOUTH);
3816 public void setStatus(String string)
3818 statusBar.setText(string);
3821 MenuItem featureSettings = new MenuItem();
3823 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3825 MenuItem annotationColour = new MenuItem();
3827 MenuItem annotationColumnSelection = new MenuItem();
3829 MenuItem invertColSel = new MenuItem();
3831 MenuItem showColumns = new MenuItem();
3833 MenuItem showSeqs = new MenuItem();
3835 MenuItem hideColumns = new MenuItem();
3837 MenuItem hideSequences = new MenuItem();
3839 MenuItem hideAllButSelection = new MenuItem();
3841 MenuItem hideAllSelection = new MenuItem();
3843 MenuItem showAllHidden = new MenuItem();
3845 MenuItem newView = new MenuItem();
3847 private CheckboxMenuItem showAlignmentAnnotations;
3849 private CheckboxMenuItem showSequenceAnnotations;
3851 private CheckboxMenuItem sortAnnBySequence;
3853 private CheckboxMenuItem sortAnnByLabel;
3855 private CheckboxMenuItem showAutoFirst;
3857 private CheckboxMenuItem showAutoLast;
3859 private SplitFrame splitFrame;
3862 * Attach the alignFrame panels after embedding menus, if necessary. This used
3863 * to be called setEmbedded, but is now creates the dropdown menus in a
3864 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3866 * @param reallyEmbedded
3867 * true to attach the view to the applet area on the page rather than
3870 public void createAlignFrameWindow(boolean reallyEmbedded)
3874 embedAlignFrameInApplet(viewport.applet);
3879 // test and embed menu bar if necessary.
3881 if (embedMenuIfNeeded(alignPanel))
3884 * adjust for status bar height too. ? pointless as overridden by layout
3887 alignPanel.setSize(getSize().width,
3888 getSize().height - statusBar.getHeight());
3890 add(statusBar, BorderLayout.SOUTH);
3891 add(alignPanel, BorderLayout.CENTER);
3892 // and register with the applet so it can pass external API calls to us
3893 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3899 * Add the components of this AlignFrame to the applet container.
3903 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3906 // Explicitly build the embedded menu panel for the on-page applet
3908 // view cannot be closed if its actually on the page
3909 fileMenu.remove(closeMenuItem);
3910 fileMenu.remove(3); // Remove Separator
3911 // construct embedded menu, using default font
3912 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3913 // and actually add the components to the applet area
3914 theApplet.setLayout(new BorderLayout());
3915 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3916 theApplet.add(statusBar, BorderLayout.SOUTH);
3917 // TODO should size be left to the layout manager?
3918 alignPanel.setSize(theApplet.getSize().width,
3919 theApplet.getSize().height - embeddedMenu.getHeight()
3920 - statusBar.getHeight());
3921 theApplet.add(alignPanel, BorderLayout.CENTER);
3922 final AlignFrame me = this;
3923 theApplet.addFocusListener(new FocusListener()
3927 public void focusLost(FocusEvent e)
3929 if (theApplet.currentAlignFrame == me)
3931 theApplet.currentAlignFrame = null;
3936 public void focusGained(FocusEvent e)
3938 theApplet.currentAlignFrame = me;
3941 theApplet.validate();
3945 * create a new binding between structures in an existing jmol viewer instance
3946 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3947 * this does not open a new Jmol window, or modify the display of the
3948 * structures in the original jmol window. Note This method doesn't work
3949 * without an additional javascript library to exchange messages between the
3950 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3953 * JmolViewer instance
3954 * @param sequenceIds
3955 * - sequence Ids to search for associations
3957 public SequenceStructureBinding addStructureViewInstance(
3958 Object jmolviewer, String[] sequenceIds)
3960 Viewer viewer = null;
3963 viewer = (Viewer) jmolviewer;
3964 } catch (ClassCastException ex)
3966 System.err.println("Unsupported viewer object :"
3967 + jmolviewer.getClass());
3971 System.err.println("Can't use this object as a structure viewer:"
3972 + jmolviewer.getClass());
3975 SequenceI[] seqs = null;
3976 if (sequenceIds == null || sequenceIds.length == 0)
3978 seqs = viewport.getAlignment().getSequencesArray();
3982 Vector sqi = new Vector();
3983 AlignmentI al = viewport.getAlignment();
3984 for (int sid = 0; sid < sequenceIds.length; sid++)
3986 SequenceI sq = al.findName(sequenceIds[sid]);
3994 seqs = new SequenceI[sqi.size()];
3995 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3997 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4005 AAStructureBindingModel jmv = null;
4006 // TODO: search for a jmv that involves viewer
4008 { // create a new viewer/jalview binding.
4009 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4016 * bind a pdb file to a sequence in the current view
4019 * - sequenceId within the dataset.
4020 * @param pdbEntryString
4021 * - the short name for the PDB file
4023 * - pdb file - either a URL or a valid PDB file.
4024 * @return true if binding was as success TODO: consider making an exception
4025 * structure for indicating when PDB parsing or sequenceId location
4028 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4031 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4032 boolean needtoadd = false;
4033 if (toaddpdb != null)
4035 Vector pdbe = toaddpdb.getAllPDBEntries();
4036 PDBEntry pdbentry = null;
4037 if (pdbe != null && pdbe.size() > 0)
4039 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4041 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4042 if (!pdbentry.getId().equals(pdbEntryString)
4043 && !pdbentry.getFile().equals(pdbFile))
4053 if (pdbentry == null)
4055 pdbentry = new PDBEntry();
4056 pdbentry.setId(pdbEntryString);
4057 pdbentry.setFile(pdbFile);
4058 needtoadd = true; // add this new entry to sequence.
4060 // resolve data source
4061 // TODO: this code should be a refactored to an io package
4062 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4063 pdbFile, FileFormat.PDB);
4064 if (protocol == null)
4070 pdbentry.setProperty("protocol", protocol);
4071 toaddpdb.addPDBId(pdbentry);
4072 alignPanel.getStructureSelectionManager()
4073 .registerPDBEntry(pdbentry);
4079 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4083 Vector sequences = new Vector();
4084 for (int i = 0; i < seqs.length; i++)
4086 if (seqs[i] != null)
4088 sequences.addElement(new Object[] { seqs[i],
4089 (chains != null) ? chains[i] : null });
4092 seqs = new SequenceI[sequences.size()];
4093 chains = new String[sequences.size()];
4094 for (int i = 0, isize = sequences.size(); i < isize; i++)
4096 Object[] oj = (Object[]) sequences.elementAt(i);
4098 seqs[i] = (SequenceI) oj[0];
4099 chains[i] = (String) oj[1];
4102 return new Object[] { seqs, chains };
4106 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4107 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4109 // Scrub any null sequences from the array
4110 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4111 seqs = (SequenceI[]) sqch[0];
4112 chains = (String[]) sqch[1];
4113 if (seqs == null || seqs.length == 0)
4116 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4118 if (protocol == null)
4120 String sourceType = (String) pdb.getProperty("protocol");
4123 protocol = DataSourceType.valueOf(sourceType);
4124 } catch (IllegalArgumentException e)
4128 if (protocol == null)
4130 System.err.println("Couldn't work out protocol to open structure: "
4135 if (applet.useXtrnalSviewer)
4137 // register the association(s) and quit, don't create any windows.
4138 if (StructureSelectionManager.getStructureSelectionManager(applet)
4139 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4141 System.err.println("Failed to map " + pdb.getFile() + " ("
4142 + protocol + ") to any sequences");
4146 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4148 // can only do alignments with Jmol
4149 // find the last jmol window assigned to this alignment
4150 AppletJmol ajm = null, tajm;
4151 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4152 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4154 tajm = (AppletJmol) jmols.elementAt(i);
4155 if (tajm.ap.alignFrame == this)
4164 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4165 // try and add the pdb structure
4170 // otherwise, create a new window
4171 if (applet.jmolAvailable)
4173 new AppletJmol(pdb, seqs, chains, alignPanel,
4175 applet.lastFrameX += 40;
4176 applet.lastFrameY += 40;
4180 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4185 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4186 SequenceI[][] seqs, String[][] chains, String[] protocols)
4188 // TODO Auto-generated method stub
4189 System.err.println("Aligned Structure View: Not yet implemented.");
4193 * modify the current selection, providing the user has not made a selection
4197 * - sequences from this alignment
4199 * - columns to be selected on the alignment
4201 public void select(SequenceGroup sel, ColumnSelection csel)
4203 alignPanel.seqPanel.selection(sel, csel, null);
4206 public void scrollTo(int row, int column)
4208 alignPanel.seqPanel.scrollTo(row, column);
4211 public void scrollToRow(int row)
4213 alignPanel.seqPanel.scrollToRow(row);
4216 public void scrollToColumn(int column)
4218 alignPanel.seqPanel.scrollToColumn(column);
4222 * @return the alignments unique ID.
4224 public String getSequenceSetId()
4226 return viewport.getSequenceSetId();
4230 * Load the (T-Coffee) score file from the specified url
4233 * File/URL/T-COFFEE score file contents
4234 * @throws IOException
4235 * @return true if alignment was annotated with data from source
4237 public boolean loadScoreFile(String source) throws IOException
4240 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4241 AppletFormatAdapter.checkProtocol(source));
4242 if (!file.isValid())
4244 // TODO: raise dialog for gui
4245 System.err.println("Problems parsing T-Coffee scores: "
4246 + file.getWarningMessage());
4247 System.err.println("Origin was:\n" + source);
4252 * check that the score matrix matches the alignment dimensions
4255 if ((aln = viewport.getAlignment()) != null
4256 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4259 // TODO: raise a dialog box here rather than bomb out.
4261 .println("The scores matrix does not match the alignment dimensions");
4265 // TODO add parameter to indicate if matching should be done
4266 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4268 alignPanel.fontChanged();
4269 tcoffeeColour.setEnabled(true);
4270 // switch to this color
4271 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4276 System.err.println("Problems resolving T-Coffee scores:");
4277 if (file.getWarningMessage() != null)
4279 System.err.println(file.getWarningMessage());
4285 public SplitFrame getSplitFrame()
4287 return this.splitFrame;
4290 public void setSplitFrame(SplitFrame sf)
4292 this.splitFrame = sf;
4295 // may not need this
4297 public void setShowSeqFeatures(boolean b)
4299 // showSeqFeatures.setSelected(b);
4300 viewport.setShowSequenceFeatures(b);
4305 public void setMenusForViewport()
4307 // setMenusFromViewport(viewport);
4312 public void refreshFeatureUI(boolean enableIfNecessary)
4314 if (enableIfNecessary)
4316 sequenceFeatures.setState(true);
4317 alignPanel.av.setShowSequenceFeatures(true);
4322 public FeatureSettingsControllerI getFeatureSettingsUI()
4324 return alignPanel.av.featureSettings;