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.analysis.NJTree;
26 import jalview.api.AlignViewControllerGuiI;
27 import jalview.api.AlignViewControllerI;
28 import jalview.api.AlignViewportI;
29 import jalview.api.FeatureColourI;
30 import jalview.api.FeatureRenderer;
31 import jalview.api.FeatureSettingsControllerI;
32 import jalview.api.SequenceStructureBinding;
33 import jalview.bin.JalviewLite;
34 import jalview.commands.CommandI;
35 import jalview.commands.EditCommand;
36 import jalview.commands.EditCommand.Action;
37 import jalview.commands.OrderCommand;
38 import jalview.commands.RemoveGapColCommand;
39 import jalview.commands.RemoveGapsCommand;
40 import jalview.commands.SlideSequencesCommand;
41 import jalview.commands.TrimRegionCommand;
42 import jalview.datamodel.Alignment;
43 import jalview.datamodel.AlignmentAnnotation;
44 import jalview.datamodel.AlignmentI;
45 import jalview.datamodel.AlignmentOrder;
46 import jalview.datamodel.ColumnSelection;
47 import jalview.datamodel.PDBEntry;
48 import jalview.datamodel.Sequence;
49 import jalview.datamodel.SequenceGroup;
50 import jalview.datamodel.SequenceI;
51 import jalview.io.AnnotationFile;
52 import jalview.io.AppletFormatAdapter;
53 import jalview.io.DataSourceType;
54 import jalview.io.FeaturesFile;
55 import jalview.io.FileFormat;
56 import jalview.io.FileFormatI;
57 import jalview.io.FileFormats;
58 import jalview.io.TCoffeeScoreFile;
59 import jalview.schemes.Blosum62ColourScheme;
60 import jalview.schemes.BuriedColourScheme;
61 import jalview.schemes.ClustalxColourScheme;
62 import jalview.schemes.ColourSchemeI;
63 import jalview.schemes.HelixColourScheme;
64 import jalview.schemes.HydrophobicColourScheme;
65 import jalview.schemes.NucleotideColourScheme;
66 import jalview.schemes.PIDColourScheme;
67 import jalview.schemes.PurinePyrimidineColourScheme;
68 import jalview.schemes.RNAHelicesColour;
69 import jalview.schemes.StrandColourScheme;
70 import jalview.schemes.TCoffeeColourScheme;
71 import jalview.schemes.TaylorColourScheme;
72 import jalview.schemes.TurnColourScheme;
73 import jalview.schemes.ZappoColourScheme;
74 import jalview.structure.StructureSelectionManager;
75 import jalview.structures.models.AAStructureBindingModel;
76 import jalview.util.MappingUtils;
77 import jalview.util.MessageManager;
78 import jalview.viewmodel.AlignmentViewport;
79 import jalview.viewmodel.ViewportRanges;
81 import java.awt.BorderLayout;
82 import java.awt.Canvas;
83 import java.awt.CheckboxMenuItem;
84 import java.awt.Color;
85 import java.awt.FlowLayout;
87 import java.awt.FontMetrics;
88 import java.awt.Frame;
89 import java.awt.Graphics;
90 import java.awt.Label;
92 import java.awt.MenuBar;
93 import java.awt.MenuItem;
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 == grpsFromSelection)
1077 makeGrpsFromSelection_actionPerformed();
1079 else if (source == deleteGroups)
1081 deleteGroups_actionPerformed();
1083 else if (source == selectAllSequenceMenuItem)
1085 selectAllSequenceMenuItem_actionPerformed();
1087 else if (source == deselectAllSequenceMenuItem)
1089 deselectAllSequenceMenuItem_actionPerformed();
1091 else if (source == invertSequenceMenuItem)
1093 invertSequenceMenuItem_actionPerformed();
1094 // uncomment to slave sequence selections in split frame
1095 // viewport.sendSelection();
1097 else if (source == invertColSel)
1099 viewport.invertColumnSelection();
1100 alignPanel.paintAlignment(true);
1101 viewport.sendSelection();
1103 else if (source == remove2LeftMenuItem)
1105 trimAlignment(true);
1107 else if (source == remove2RightMenuItem)
1109 trimAlignment(false);
1111 else if (source == removeGappedColumnMenuItem)
1113 removeGappedColumnMenuItem_actionPerformed();
1115 else if (source == removeAllGapsMenuItem)
1117 removeAllGapsMenuItem_actionPerformed();
1119 else if (source == findMenuItem)
1121 findMenuItem_actionPerformed();
1123 else if (source == font)
1125 new FontChooser(alignPanel);
1127 else if (source == newView)
1131 else if (source == showColumns)
1133 viewport.showAllHiddenColumns();
1134 alignPanel.paintAlignment(true);
1135 viewport.sendSelection();
1137 else if (source == showSeqs)
1139 viewport.showAllHiddenSeqs();
1140 alignPanel.paintAlignment(true);
1141 // uncomment if we want to slave sequence selections in split frame
1142 // viewport.sendSelection();
1144 else if (source == hideColumns)
1146 viewport.hideSelectedColumns();
1147 alignPanel.paintAlignment(true);
1148 viewport.sendSelection();
1150 else if (source == hideSequences
1151 && viewport.getSelectionGroup() != null)
1153 viewport.hideAllSelectedSeqs();
1154 alignPanel.paintAlignment(true);
1155 // uncomment if we want to slave sequence selections in split frame
1156 // viewport.sendSelection();
1158 else if (source == hideAllButSelection)
1160 toggleHiddenRegions(false, false);
1161 alignPanel.paintAlignment(true);
1162 viewport.sendSelection();
1164 else if (source == hideAllSelection)
1166 SequenceGroup sg = viewport.getSelectionGroup();
1167 viewport.expandColSelection(sg, false);
1168 viewport.hideAllSelectedSeqs();
1169 viewport.hideSelectedColumns();
1170 alignPanel.paintAlignment(true);
1171 viewport.sendSelection();
1173 else if (source == showAllHidden)
1175 viewport.showAllHiddenColumns();
1176 viewport.showAllHiddenSeqs();
1177 alignPanel.paintAlignment(true);
1178 viewport.sendSelection();
1180 else if (source == showGroupConsensus)
1182 showGroupConsensus_actionPerformed();
1184 else if (source == showGroupConservation)
1186 showGroupConservation_actionPerformed();
1188 else if (source == showSequenceLogo)
1190 showSequenceLogo_actionPerformed();
1192 else if (source == normSequenceLogo)
1194 normSequenceLogo_actionPerformed();
1196 else if (source == showConsensusHistogram)
1198 showConsensusHistogram_actionPerformed();
1200 else if (source == applyAutoAnnotationSettings)
1202 applyAutoAnnotationSettings_actionPerformed();
1204 else if (source == featureSettings)
1206 new FeatureSettings(alignPanel);
1208 else if (source == alProperties)
1210 StringBuffer contents = new jalview.io.AlignmentProperties(
1211 viewport.getAlignment()).formatAsString();
1212 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1213 cap.setText(contents.toString());
1214 Frame frame = new Frame();
1216 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1217 "label.alignment_properties", new String[] { getTitle() }),
1220 else if (source == overviewMenuItem)
1222 overviewMenuItem_actionPerformed();
1224 else if (source == noColourmenuItem)
1228 else if (source == clustalColour)
1230 abovePIDThreshold.setState(false);
1231 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1233 else if (source == zappoColour)
1235 changeColour(new ZappoColourScheme());
1237 else if (source == taylorColour)
1239 changeColour(new TaylorColourScheme());
1241 else if (source == hydrophobicityColour)
1243 changeColour(new HydrophobicColourScheme());
1245 else if (source == helixColour)
1247 changeColour(new HelixColourScheme());
1249 else if (source == strandColour)
1251 changeColour(new StrandColourScheme());
1253 else if (source == turnColour)
1255 changeColour(new TurnColourScheme());
1257 else if (source == buriedColour)
1259 changeColour(new BuriedColourScheme());
1261 else if (source == nucleotideColour)
1263 changeColour(new NucleotideColourScheme());
1265 else if (source == purinePyrimidineColour)
1267 changeColour(new PurinePyrimidineColourScheme());
1269 // else if (source == RNAInteractionColour)
1271 // changeColour(new RNAInteractionColourScheme());
1273 else if (source == RNAHelixColour)
1275 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1276 // new RNAHelicesColourChooser(viewport, alignPanel);
1278 else if (source == modifyPID)
1280 modifyPID_actionPerformed();
1282 else if (source == modifyConservation)
1284 modifyConservation_actionPerformed();
1286 else if (source == userDefinedColour)
1288 new UserDefinedColours(alignPanel, null);
1290 else if (source == PIDColour)
1292 changeColour(new PIDColourScheme());
1294 else if (source == BLOSUM62Colour)
1296 changeColour(new Blosum62ColourScheme());
1298 else if (source == tcoffeeColour)
1300 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1302 else if (source == annotationColour)
1304 new AnnotationColourChooser(viewport, alignPanel);
1306 else if (source == annotationColumnSelection)
1308 new AnnotationColumnChooser(viewport, alignPanel);
1310 else if (source == sortPairwiseMenuItem)
1312 sortPairwiseMenuItem_actionPerformed();
1314 else if (source == sortIDMenuItem)
1316 sortIDMenuItem_actionPerformed();
1318 else if (source == sortLengthMenuItem)
1320 sortLengthMenuItem_actionPerformed();
1322 else if (source == sortGroupMenuItem)
1324 sortGroupMenuItem_actionPerformed();
1326 else if (source == removeRedundancyMenuItem)
1328 removeRedundancyMenuItem_actionPerformed();
1330 else if (source == pairwiseAlignmentMenuItem)
1332 pairwiseAlignmentMenuItem_actionPerformed();
1334 else if (source == PCAMenuItem)
1336 PCAMenuItem_actionPerformed();
1338 else if (source == averageDistanceTreeMenuItem)
1340 averageDistanceTreeMenuItem_actionPerformed();
1342 else if (source == neighbourTreeMenuItem)
1344 neighbourTreeMenuItem_actionPerformed();
1346 else if (source == njTreeBlosumMenuItem)
1348 njTreeBlosumMenuItem_actionPerformed();
1350 else if (source == avDistanceTreeBlosumMenuItem)
1352 avTreeBlosumMenuItem_actionPerformed();
1354 else if (source == documentation)
1356 documentation_actionPerformed();
1358 else if (source == about)
1360 about_actionPerformed();
1365 public void inputText_actionPerformed()
1367 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1368 Frame frame = new Frame();
1370 jalview.bin.JalviewLite.addFrame(frame,
1371 MessageManager.getString("label.input_cut_paste"), 500, 500);
1374 protected void outputText_actionPerformed(ActionEvent e)
1376 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1377 Frame frame = new Frame();
1379 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1380 "label.alignment_output_command",
1381 new Object[] { e.getActionCommand() }), 600, 500);
1383 FileFormatI fileFormat = FileFormats.getInstance().forName(
1384 e.getActionCommand());
1385 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1386 fileFormat, viewport.getAlignment(),
1387 viewport.getShowJVSuffix()));
1390 public void loadAnnotations()
1392 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1393 cap.setText(MessageManager
1394 .getString("label.paste_features_annotations_Tcoffee_here"));
1395 cap.setAnnotationImport();
1396 Frame frame = new Frame();
1398 jalview.bin.JalviewLite.addFrame(frame,
1399 MessageManager.getString("action.paste_annotations"), 400, 300);
1403 public String outputAnnotations(boolean displayTextbox)
1405 String annotation = new AnnotationFile()
1406 .printAnnotationsForView(viewport);
1410 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1411 Frame frame = new Frame();
1413 jalview.bin.JalviewLite.addFrame(frame,
1414 MessageManager.getString("label.annotations"), 600, 500);
1415 cap.setText(annotation);
1421 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1423 if (alignPanel.getFeatureRenderer() != null
1424 && viewport.getFeaturesDisplayed() != null)
1426 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1432 public String outputFeatures(boolean displayTextbox, String format)
1435 FeaturesFile formatter = new FeaturesFile();
1436 if (format.equalsIgnoreCase("Jalview"))
1438 features = formatter.printJalviewFormat(viewport.getAlignment()
1439 .getSequencesArray(), getDisplayedFeatureCols());
1443 features = formatter.printGffFormat(viewport.getAlignment()
1444 .getSequencesArray(), getDisplayedFeatureCols());
1449 boolean frimport = false;
1450 if (features == null || features.equals("No Features Visible"))
1452 features = "# No features visible - paste some and import them here.";
1456 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1459 cap.setAnnotationImport();
1461 Frame frame = new Frame();
1463 jalview.bin.JalviewLite.addFrame(frame,
1464 MessageManager.getString("label.features"), 600, 500);
1465 cap.setText(features);
1469 if (features == null)
1478 void launchFullApplication()
1480 StringBuffer url = new StringBuffer(jalviewServletURL);
1482 // allow servlet parameters to be passed in applet parameter
1483 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1485 url.append(firstSep);
1488 + appendProtocol(viewport.applet.getParameter("file")));
1490 if (viewport.applet.getParameter("features") != null)
1492 url.append("&features=");
1493 url.append(appendProtocol(viewport.applet.getParameter("features")));
1496 if (viewport.applet.getParameter("annotations") != null)
1498 url.append("&annotations=");
1499 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1502 if (viewport.applet.getParameter("jnetfile") != null
1503 || viewport.applet.getParameter("jpredfile") != null)
1505 url.append("&annotations=");
1506 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1507 .getParameter("jnetfile") : viewport.applet
1508 .getParameter("jpredfile")));
1511 if (viewport.applet.getParameter("defaultColour") != null)
1513 url.append("&colour="
1514 + removeWhiteSpace(viewport.applet
1515 .getParameter("defaultColour")));
1518 if (viewport.applet.getParameter("userDefinedColour") != null)
1520 url.append("&colour="
1521 + removeWhiteSpace(viewport.applet
1522 .getParameter("userDefinedColour")));
1524 if (viewport.applet.getParameter("tree") != null)
1527 + appendProtocol(viewport.applet.getParameter("tree")));
1529 if (viewport.applet.getParameter("treeFile") != null)
1532 + appendProtocol(viewport.applet.getParameter("treeFile")));
1535 showURL(url.toString(), "FULL_APP");
1538 String removeWhiteSpace(String colour)
1540 StringBuffer sb = new StringBuffer();
1541 for (int i = 0; i < colour.length(); i++)
1543 if (Character.isWhitespace(colour.charAt(i)))
1549 sb.append(colour.charAt(i));
1553 return sb.toString();
1556 String appendProtocol(String url)
1561 url = URLEncoder.encode(url);
1564 * When we finally deprecate 1.1 compatibility, we can start to use
1565 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1566 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1567 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1568 * ex.printStackTrace(); }
1570 catch (java.net.MalformedURLException ex)
1572 url = viewport.applet.getCodeBase() + url;
1577 public void closeMenuItem_actionPerformed()
1579 PaintRefresher.RemoveComponent(alignPanel);
1580 if (alignPanel.seqPanel != null
1581 && alignPanel.seqPanel.seqCanvas != null)
1583 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1585 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1587 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1590 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1605 void updateEditMenuBar()
1608 if (viewport.getHistoryList().size() > 0)
1610 undoMenuItem.setEnabled(true);
1611 CommandI command = viewport.getHistoryList().peek();
1612 undoMenuItem.setLabel(MessageManager.formatMessage(
1613 "label.undo_command",
1614 new Object[] { command.getDescription() }));
1618 undoMenuItem.setEnabled(false);
1619 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1622 if (viewport.getRedoList().size() > 0)
1624 redoMenuItem.setEnabled(true);
1626 CommandI command = viewport.getRedoList().peek();
1627 redoMenuItem.setLabel(MessageManager.formatMessage(
1628 "label.redo_command",
1629 new Object[] { command.getDescription() }));
1633 redoMenuItem.setEnabled(false);
1634 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1642 public void addHistoryItem(CommandI command)
1644 if (command.getSize() > 0)
1646 viewport.addToHistoryList(command);
1647 viewport.clearRedoList();
1648 updateEditMenuBar();
1649 viewport.updateHiddenColumns();
1654 * TODO: JAL-1104 DOCUMENT ME!
1659 protected void undoMenuItem_actionPerformed()
1661 if (viewport.getHistoryList().isEmpty())
1666 CommandI command = viewport.getHistoryList().pop();
1667 viewport.addToRedoList(command);
1668 command.undoCommand(null);
1670 AlignmentViewport originalSource = getOriginatingSource(command);
1672 if (originalSource != viewport)
1675 .println("Warning: Viewport object mismatch whilst undoing");
1677 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1678 // viewport.getColumnSelection().getHiddenColumns()
1680 updateEditMenuBar();
1681 originalSource.firePropertyChange("alignment", null, originalSource
1682 .getAlignment().getSequences());
1686 * TODO: JAL-1104 DOCUMENT ME!
1691 protected void redoMenuItem_actionPerformed()
1693 if (viewport.getRedoList().isEmpty())
1698 CommandI command = viewport.getRedoList().pop();
1699 viewport.addToHistoryList(command);
1700 command.doCommand(null);
1702 AlignmentViewport originalSource = getOriginatingSource(command);
1704 if (originalSource != viewport)
1707 .println("Warning: Viewport object mismatch whilst re-doing");
1709 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1710 // viewport.getColumnSelection().getHiddenColumns()
1713 updateEditMenuBar();
1714 originalSource.firePropertyChange("alignment", null, originalSource
1715 .getAlignment().getSequences());
1718 AlignmentViewport getOriginatingSource(CommandI command)
1720 AlignmentViewport originalSource = null;
1721 // For sequence removal and addition, we need to fire
1722 // the property change event FROM the viewport where the
1723 // original alignment was altered
1724 AlignmentI al = null;
1725 if (command instanceof EditCommand)
1727 EditCommand editCommand = (EditCommand) command;
1728 al = editCommand.getAlignment();
1729 Vector comps = (Vector) PaintRefresher.components.get(viewport
1730 .getSequenceSetId());
1731 for (int i = 0; i < comps.size(); i++)
1733 if (comps.elementAt(i) instanceof AlignmentPanel)
1735 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1737 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1744 if (originalSource == null)
1746 // The original view is closed, we must validate
1747 // the current view against the closed view first
1750 PaintRefresher.validateSequences(al, viewport.getAlignment());
1753 originalSource = viewport;
1756 return originalSource;
1760 * Move the currently selected sequences up or down one position in the
1765 public void moveSelectedSequences(boolean up)
1767 SequenceGroup sg = viewport.getSelectionGroup();
1772 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1773 up ? null : viewport.getHiddenRepSequences(), up);
1774 alignPanel.paintAlignment(true);
1777 * Also move cDNA/protein complement sequences
1779 AlignViewportI complement = viewport.getCodingComplement();
1780 if (complement != null)
1782 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1783 viewport, complement);
1784 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1785 up ? null : complement.getHiddenRepSequences(), up);
1786 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1790 synchronized void slideSequences(boolean right, int size)
1792 List<SequenceI> sg = new Vector<SequenceI>();
1793 if (viewport.cursorMode)
1795 sg.add(viewport.getAlignment().getSequenceAt(
1796 alignPanel.seqPanel.seqCanvas.cursorY));
1798 else if (viewport.getSelectionGroup() != null
1799 && viewport.getSelectionGroup().getSize() != viewport
1800 .getAlignment().getHeight())
1802 sg = viewport.getSelectionGroup().getSequences(
1803 viewport.getHiddenRepSequences());
1811 Vector<SequenceI> invertGroup = new Vector();
1813 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1815 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1817 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1821 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1823 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1825 for (int i = 0; i < invertGroup.size(); i++)
1827 seqs2[i] = invertGroup.elementAt(i);
1830 SlideSequencesCommand ssc;
1833 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1834 size, viewport.getGapCharacter());
1838 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1839 size, viewport.getGapCharacter());
1842 int groupAdjustment = 0;
1843 if (ssc.getGapsInsertedBegin() && right)
1845 if (viewport.cursorMode)
1847 alignPanel.seqPanel.moveCursor(size, 0);
1851 groupAdjustment = size;
1854 else if (!ssc.getGapsInsertedBegin() && !right)
1856 if (viewport.cursorMode)
1858 alignPanel.seqPanel.moveCursor(-size, 0);
1862 groupAdjustment = -size;
1866 if (groupAdjustment != 0)
1868 viewport.getSelectionGroup().setStartRes(
1869 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1870 viewport.getSelectionGroup().setEndRes(
1871 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1874 boolean appendHistoryItem = false;
1875 Deque<CommandI> historyList = viewport.getHistoryList();
1876 if (historyList != null && historyList.size() > 0
1877 && historyList.peek() instanceof SlideSequencesCommand)
1879 appendHistoryItem = ssc
1880 .appendSlideCommand((SlideSequencesCommand) historyList
1884 if (!appendHistoryItem)
1886 addHistoryItem(ssc);
1892 static StringBuffer copiedSequences;
1894 static Vector copiedHiddenColumns;
1896 protected void copy_actionPerformed()
1898 if (viewport.getSelectionGroup() == null)
1903 SequenceGroup sg = viewport.getSelectionGroup();
1904 copiedSequences = new StringBuffer();
1905 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1906 for (int i = 0; i < sg.getSize(); i++)
1908 SequenceI seq = sg.getSequenceAt(i);
1909 int index = viewport.getAlignment().findIndex(seq);
1910 orderedSeqs.put(index, seq);
1913 int index = 0, startRes, endRes;
1916 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1918 copiedHiddenColumns = new Vector();
1919 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1920 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1922 copiedHiddenColumns.addElement(new int[] {
1923 region[0] - hiddenOffset, region[1] - hiddenOffset });
1928 copiedHiddenColumns = null;
1931 for (int i = 0; i < sg.getSize(); i++)
1933 SequenceI seq = null;
1937 if (orderedSeqs.containsKey(index))
1939 seq = orderedSeqs.get(index);
1950 // Returns residue following index if gap
1951 startRes = seq.findPosition(sg.getStartRes());
1954 // Need to find the residue preceeding index if gap
1957 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1959 ch = seq.getCharAt(j);
1960 if (!jalview.util.Comparison.isGap((ch)))
1968 endRes += seq.getStart() - 1;
1971 copiedSequences.append(seq.getName()
1977 + seq.getSequenceAsString(sg.getStartRes(),
1978 sg.getEndRes() + 1) + "\n");
1983 protected void pasteNew_actionPerformed()
1988 protected void pasteThis_actionPerformed()
1993 void paste(boolean newAlignment)
1998 if (copiedSequences == null)
2003 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2004 Vector seqs = new Vector();
2005 while (st.hasMoreElements())
2007 String name = st.nextToken();
2008 int start = Integer.parseInt(st.nextToken());
2009 int end = Integer.parseInt(st.nextToken());
2010 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2012 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2013 for (int i = 0; i < seqs.size(); i++)
2015 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2020 String newtitle = MessageManager
2021 .getString("label.copied_sequences");
2022 if (getTitle().startsWith(
2023 MessageManager.getString("label.copied_sequences")))
2025 newtitle = getTitle();
2029 newtitle = newtitle.concat(MessageManager.formatMessage(
2030 "label.from_msname", new String[] { getTitle() }));
2032 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2033 viewport.applet, newtitle, false);
2034 if (copiedHiddenColumns != null)
2036 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2038 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2039 af.viewport.hideColumns(region[0], region[1]);
2043 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2048 addSequences(newSeqs);
2051 } catch (Exception ex)
2053 } // could be anything being pasted in here
2057 void addSequences(SequenceI[] seqs)
2059 for (int i = 0; i < seqs.length; i++)
2061 viewport.getAlignment().addSequence(seqs[i]);
2065 addHistoryItem(new EditCommand(
2066 MessageManager.getString("label.add_sequences"), Action.PASTE,
2067 seqs, 0, viewport.getAlignment().getWidth(),
2068 viewport.getAlignment()));
2070 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2071 viewport.getAlignment().getWidth();
2072 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2077 protected void cut_actionPerformed()
2079 copy_actionPerformed();
2080 delete_actionPerformed();
2083 protected void delete_actionPerformed()
2086 SequenceGroup sg = viewport.getSelectionGroup();
2092 Vector seqs = new Vector();
2094 for (int i = 0; i < sg.getSize(); i++)
2096 seq = sg.getSequenceAt(i);
2097 seqs.addElement(seq);
2101 * If the cut affects all sequences, warn, remove highlighted columns
2103 if (sg.getSize() == viewport.getAlignment().getHeight())
2105 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2106 .getAlignment().getWidth()) ? true : false;
2107 if (isEntireAlignWidth)
2109 String title = MessageManager.getString("label.delete_all");
2110 Panel infoPanel = new Panel();
2111 infoPanel.setLayout(new FlowLayout());
2113 .add(new Label(MessageManager.getString("warn.delete_all")));
2115 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2116 dialog.setMainPanel(infoPanel);
2117 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2118 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2119 dialog.setVisible(true);
2126 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2127 sg.getEndRes() + 1);
2130 SequenceI[] cut = new SequenceI[seqs.size()];
2131 for (int i = 0; i < seqs.size(); i++)
2133 cut[i] = (SequenceI) seqs.elementAt(i);
2137 * //ADD HISTORY ITEM
2139 addHistoryItem(new EditCommand(
2140 MessageManager.getString("label.cut_sequences"), Action.CUT,
2141 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2142 viewport.getAlignment()));
2144 viewport.setSelectionGroup(null);
2145 viewport.getAlignment().deleteGroup(sg);
2147 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2150 if (viewport.getAlignment().getHeight() < 1)
2152 this.setVisible(false);
2154 viewport.sendSelection();
2158 * group consensus toggled
2161 protected void showGroupConsensus_actionPerformed()
2163 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2164 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2169 * group conservation toggled.
2171 protected void showGroupConservation_actionPerformed()
2173 viewport.setShowGroupConservation(showGroupConservation.getState());
2174 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2182 * .event.ActionEvent)
2184 protected void showConsensusHistogram_actionPerformed()
2186 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2187 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2195 * .event.ActionEvent)
2197 protected void showSequenceLogo_actionPerformed()
2199 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2200 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2203 protected void normSequenceLogo_actionPerformed()
2205 showSequenceLogo.setState(true);
2206 viewport.setShowSequenceLogo(true);
2207 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2208 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2211 protected void applyAutoAnnotationSettings_actionPerformed()
2213 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2216 protected void makeGrpsFromSelection_actionPerformed()
2218 if (avc.makeGroupsFromSelection())
2220 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2221 alignPanel.updateAnnotation();
2222 alignPanel.paintAlignment(true);
2226 protected void createGroup_actionPerformed()
2231 protected void unGroup_actionPerformed()
2235 alignPanel.alignmentChanged();
2239 protected void deleteGroups_actionPerformed()
2241 if (avc.deleteGroups())
2243 alignPanel.alignmentChanged();
2247 public void selectAllSequenceMenuItem_actionPerformed()
2249 SequenceGroup sg = new SequenceGroup();
2250 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2252 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2254 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2255 viewport.setSelectionGroup(sg);
2256 // JAL-2034 - should delegate to
2257 // alignPanel to decide if overview needs
2259 alignPanel.paintAlignment(false);
2260 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2261 viewport.sendSelection();
2264 public void deselectAllSequenceMenuItem_actionPerformed()
2266 if (viewport.cursorMode)
2268 alignPanel.seqPanel.keyboardNo1 = null;
2269 alignPanel.seqPanel.keyboardNo2 = null;
2271 viewport.setSelectionGroup(null);
2272 viewport.getColumnSelection().clear();
2273 viewport.setSelectionGroup(null);
2274 alignPanel.idPanel.idCanvas.searchResults = null;
2275 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2276 // JAL-2034 - should delegate to
2277 // alignPanel to decide if overview needs
2279 alignPanel.paintAlignment(false);
2280 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2281 viewport.sendSelection();
2284 public void invertSequenceMenuItem_actionPerformed()
2286 SequenceGroup sg = viewport.getSelectionGroup();
2287 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2289 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2292 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293 viewport.sendSelection();
2296 public void invertColSel_actionPerformed()
2298 viewport.invertColumnSelection();
2299 alignPanel.paintAlignment(true);
2300 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2301 viewport.sendSelection();
2304 void trimAlignment(boolean trimLeft)
2306 AlignmentI al = viewport.getAlignment();
2307 ViewportRanges ranges = viewport.getRanges();
2308 ColumnSelection colSel = viewport.getColumnSelection();
2311 if (!colSel.isEmpty())
2315 column = colSel.getMin();
2319 column = colSel.getMax();
2323 if (viewport.getSelectionGroup() != null)
2325 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2326 viewport.getHiddenRepSequences());
2330 seqs = al.getSequencesArray();
2333 TrimRegionCommand trimRegion;
2336 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2338 ranges.setStartRes(0);
2342 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2346 statusBar.setText(MessageManager.formatMessage(
2347 "label.removed_columns",
2348 new String[] { Integer.valueOf(trimRegion.getSize())
2350 addHistoryItem(trimRegion);
2352 for (SequenceGroup sg : al.getGroups())
2354 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2355 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2361 viewport.firePropertyChange("alignment", null, al.getSequences());
2365 public void removeGappedColumnMenuItem_actionPerformed()
2367 AlignmentI al = viewport.getAlignment();
2368 ViewportRanges ranges = viewport.getRanges();
2370 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2373 if (viewport.getSelectionGroup() != null)
2375 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2376 viewport.getHiddenRepSequences());
2377 start = viewport.getSelectionGroup().getStartRes();
2378 end = viewport.getSelectionGroup().getEndRes();
2382 seqs = viewport.getAlignment().getSequencesArray();
2385 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2386 "Remove Gapped Columns", seqs, start, end,
2387 viewport.getAlignment());
2389 addHistoryItem(removeGapCols);
2391 statusBar.setText(MessageManager.formatMessage(
2392 "label.removed_empty_columns",
2393 new String[] { Integer.valueOf(removeGapCols.getSize())
2396 // This is to maintain viewport position on first residue
2397 // of first sequence
2398 SequenceI seq = al.getSequenceAt(0);
2399 int startRes = seq.findPosition(ranges.getStartRes());
2400 // ShiftList shifts;
2401 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2402 // edit.alColumnChanges=shifts.getInverse();
2403 // if (viewport.hasHiddenColumns)
2404 // viewport.getColumnSelection().compensateForEdits(shifts);
2405 ranges.setStartRes(seq.findIndex(startRes) - 1);
2406 viewport.firePropertyChange("alignment", null, al.getSequences());
2410 public void removeAllGapsMenuItem_actionPerformed()
2412 AlignmentI al = viewport.getAlignment();
2413 ViewportRanges ranges = viewport.getRanges();
2415 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2418 if (viewport.getSelectionGroup() != null)
2420 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2421 viewport.getHiddenRepSequences());
2422 start = viewport.getSelectionGroup().getStartRes();
2423 end = viewport.getSelectionGroup().getEndRes();
2427 seqs = viewport.getAlignment().getSequencesArray();
2430 // This is to maintain viewport position on first residue
2431 // of first sequence
2432 SequenceI seq = al.getSequenceAt(0);
2433 int startRes = seq.findPosition(ranges.getStartRes());
2435 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2438 ranges.setStartRes(seq.findIndex(startRes) - 1);
2440 viewport.firePropertyChange("alignment", null, al.getSequences());
2444 public void findMenuItem_actionPerformed()
2446 new Finder(alignPanel);
2450 * create a new view derived from the current view
2453 * @return frame for the new view
2455 public AlignFrame newView(String viewtitle)
2458 if (viewport.hasHiddenRows())
2460 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2461 .getFullAlignment().getSequencesArray());
2465 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2468 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2470 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2472 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2474 newal.addAnnotation(viewport.getAlignment()
2475 .getAlignmentAnnotation()[i]);
2480 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2482 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2483 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2484 PaintRefresher.Register(newaf.alignPanel,
2485 newaf.alignPanel.av.getSequenceSetId());
2487 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2488 newaf.alignPanel.av.getSequenceSetId());
2489 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2490 newaf.alignPanel.av.getSequenceSetId());
2492 Vector comps = (Vector) PaintRefresher.components.get(viewport
2493 .getSequenceSetId());
2495 for (int i = 0; i < comps.size(); i++)
2497 if (comps.elementAt(i) instanceof AlignmentPanel)
2503 String title = new String(this.getTitle());
2504 if (viewtitle != null)
2506 title = viewtitle + " ( " + title + ")";
2510 if (title.indexOf("(View") > -1)
2512 title = title.substring(0, title.indexOf("(View"));
2514 title += "(View " + viewSize + ")";
2517 newaf.setTitle(title.toString());
2519 newaf.viewport.setHistoryList(viewport.getHistoryList());
2520 newaf.viewport.setRedoList(viewport.getRedoList());
2526 * @return list of feature groups on the view
2528 public String[] getFeatureGroups()
2530 FeatureRenderer fr = null;
2531 if (alignPanel != null
2532 && (fr = alignPanel.getFeatureRenderer()) != null)
2534 List<String> gps = fr.getFeatureGroups();
2535 String[] _gps = gps.toArray(new String[gps.size()]);
2542 * get sequence feature groups that are hidden or shown
2548 public String[] getFeatureGroupsOfState(boolean visible)
2550 FeatureRenderer fr = null;
2551 if (alignPanel != null
2552 && (fr = alignPanel.getFeatureRenderer()) != null)
2554 List<String> gps = fr.getGroups(visible);
2555 String[] _gps = gps.toArray(new String[gps.size()]);
2562 * Change the display state for the given feature groups
2565 * list of group strings
2567 * visible or invisible
2569 public void setFeatureGroupState(String[] groups, boolean state)
2571 FeatureRenderer fr = null;
2572 this.sequenceFeatures.setState(true);
2573 viewport.setShowSequenceFeatures(true);
2574 if (alignPanel != null
2575 && (fr = alignPanel.getFeatureRenderer()) != null)
2578 fr.setGroupVisibility(Arrays.asList(groups), state);
2579 alignPanel.seqPanel.seqCanvas.repaint();
2580 if (alignPanel.overviewPanel != null)
2582 alignPanel.overviewPanel.updateOverviewImage();
2587 public void seqLimits_itemStateChanged()
2589 viewport.setShowJVSuffix(seqLimits.getState());
2590 alignPanel.fontChanged();
2591 alignPanel.paintAlignment(true);
2594 protected void colourTextMenuItem_actionPerformed()
2596 viewport.setColourText(colourTextMenuItem.getState());
2597 alignPanel.paintAlignment(true);
2600 protected void displayNonconservedMenuItem_actionPerformed()
2602 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2603 alignPanel.paintAlignment(true);
2606 protected void wrapMenuItem_actionPerformed()
2608 viewport.setWrapAlignment(wrapMenuItem.getState());
2609 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2610 scaleAbove.setEnabled(wrapMenuItem.getState());
2611 scaleLeft.setEnabled(wrapMenuItem.getState());
2612 scaleRight.setEnabled(wrapMenuItem.getState());
2613 alignPanel.paintAlignment(true);
2616 public void overviewMenuItem_actionPerformed()
2618 if (alignPanel.overviewPanel != null)
2623 Frame frame = new Frame();
2624 OverviewPanel overview = new OverviewPanel(alignPanel);
2625 frame.add(overview);
2626 // +50 must allow for applet frame window
2627 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2628 "label.overview_params", new String[] { this.getTitle() }),
2629 overview.getPreferredSize().width,
2630 overview.getPreferredSize().height + 50);
2633 final AlignmentPanel ap = alignPanel;
2634 frame.addWindowListener(new WindowAdapter()
2637 public void windowClosing(WindowEvent e)
2641 ap.setOverviewPanel(null);
2646 alignPanel.setOverviewPanel(overview);
2651 public void changeColour(ColourSchemeI cs)
2653 viewport.setGlobalColourScheme(cs);
2655 alignPanel.paintAlignment(true);
2658 protected void modifyPID_actionPerformed()
2660 if (viewport.getAbovePIDThreshold()
2661 && viewport.getGlobalColourScheme() != null)
2663 SliderPanel.setPIDSliderSource(alignPanel,
2664 viewport.getResidueShading(), alignPanel.getViewName());
2665 SliderPanel.showPIDSlider();
2669 protected void modifyConservation_actionPerformed()
2671 if (viewport.getConservationSelected()
2672 && viewport.getGlobalColourScheme() != null)
2674 SliderPanel.setConservationSlider(alignPanel,
2675 viewport.getResidueShading(), alignPanel.getViewName());
2676 SliderPanel.showConservationSlider();
2680 protected void conservationMenuItem_actionPerformed()
2682 boolean selected = conservationMenuItem.getState();
2683 modifyConservation.setEnabled(selected);
2684 viewport.setConservationSelected(selected);
2686 // viewport.setAbovePIDThreshold(false);
2687 // abovePIDThreshold.setState(false);
2689 changeColour(viewport.getGlobalColourScheme());
2693 modifyConservation_actionPerformed();
2697 SliderPanel.hideConservationSlider();
2701 public void abovePIDThreshold_actionPerformed()
2703 boolean selected = abovePIDThreshold.getState();
2704 modifyPID.setEnabled(selected);
2705 viewport.setAbovePIDThreshold(selected);
2706 // conservationMenuItem.setState(false);
2707 // viewport.setConservationSelected(false);
2709 changeColour(viewport.getGlobalColourScheme());
2713 modifyPID_actionPerformed();
2717 SliderPanel.hidePIDSlider();
2721 public void sortPairwiseMenuItem_actionPerformed()
2723 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2724 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2725 .getAlignment().getSequenceAt(0), null);
2727 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2728 viewport.getAlignment()));
2729 alignPanel.paintAlignment(true);
2732 public void sortIDMenuItem_actionPerformed()
2734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735 AlignmentSorter.sortByID(viewport.getAlignment());
2736 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2737 viewport.getAlignment()));
2738 alignPanel.paintAlignment(true);
2741 public void sortLengthMenuItem_actionPerformed()
2743 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2744 AlignmentSorter.sortByLength(viewport.getAlignment());
2745 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2746 viewport.getAlignment()));
2747 alignPanel.paintAlignment(true);
2750 public void sortGroupMenuItem_actionPerformed()
2752 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2753 AlignmentSorter.sortByGroup(viewport.getAlignment());
2754 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2755 viewport.getAlignment()));
2756 alignPanel.paintAlignment(true);
2760 public void removeRedundancyMenuItem_actionPerformed()
2762 new RedundancyPanel(alignPanel);
2765 public void pairwiseAlignmentMenuItem_actionPerformed()
2767 if (viewport.getSelectionGroup() != null
2768 && viewport.getSelectionGroup().getSize() > 1)
2770 Frame frame = new Frame();
2771 frame.add(new PairwiseAlignPanel(alignPanel));
2772 jalview.bin.JalviewLite.addFrame(frame,
2773 MessageManager.getString("action.pairwise_alignment"), 600,
2778 public void PCAMenuItem_actionPerformed()
2780 // are the sequences aligned?
2781 if (!viewport.getAlignment().isAligned(false))
2784 int Width = viewport.getAlignment().getWidth();
2786 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2788 current = viewport.getAlignment().getSequenceAt(i);
2790 if (current.getLength() < Width)
2792 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2795 alignPanel.paintAlignment(true);
2798 if ((viewport.getSelectionGroup() != null
2799 && viewport.getSelectionGroup().getSize() < 4 && viewport
2800 .getSelectionGroup().getSize() > 0)
2801 || viewport.getAlignment().getHeight() < 4)
2808 new PCAPanel(viewport);
2809 } catch (java.lang.OutOfMemoryError ex)
2815 public void averageDistanceTreeMenuItem_actionPerformed()
2817 NewTreePanel(NJTree.AVERAGE_DISTANCE, "PID",
2818 "Average distance tree using PID");
2821 public void neighbourTreeMenuItem_actionPerformed()
2823 NewTreePanel(NJTree.NEIGHBOUR_JOINING, "PID",
2824 "Neighbour joining tree using PID");
2827 protected void njTreeBlosumMenuItem_actionPerformed()
2829 NewTreePanel(NJTree.NEIGHBOUR_JOINING, "BL",
2830 "Neighbour joining tree using BLOSUM62");
2833 protected void avTreeBlosumMenuItem_actionPerformed()
2835 NewTreePanel(NJTree.AVERAGE_DISTANCE, "BL",
2836 "Average distance tree using BLOSUM62");
2839 void NewTreePanel(String type, String pwType, String title)
2841 // are the sequences aligned?
2842 if (!viewport.getAlignment().isAligned(false))
2845 int Width = viewport.getAlignment().getWidth();
2847 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2849 current = viewport.getAlignment().getSequenceAt(i);
2851 if (current.getLength() < Width)
2853 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2856 alignPanel.paintAlignment(true);
2860 if ((viewport.getSelectionGroup() != null && viewport
2861 .getSelectionGroup().getSize() > 1)
2862 || (viewport.getAlignment().getHeight() > 1))
2864 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2866 addTreeMenuItem(tp, title);
2868 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2872 void loadTree_actionPerformed()
2874 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2875 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2876 cap.setTreeImport();
2877 Frame frame = new Frame();
2879 jalview.bin.JalviewLite.addFrame(frame,
2880 MessageManager.getString("label.paste_newick_file"), 400, 300);
2883 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2885 TreePanel tp = new TreePanel(alignPanel, treeFile,
2886 MessageManager.getString("label.load_tree_from_file"), tree);
2887 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2888 addTreeMenuItem(tp, treeFile);
2892 * sort the alignment using the given treePanel
2895 * tree used to sort view
2897 * string used for undo event name
2899 public void sortByTree(TreePanel treePanel, String title)
2901 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2903 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2904 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2905 // HistoryItem.SORT));
2906 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2907 "label.order_by_params", new String[] { title }), oldOrder,
2908 viewport.getAlignment()));
2909 alignPanel.paintAlignment(true);
2913 * Do any automatic reordering of the alignment and add the necessary bits to
2914 * the menu structure for the new tree
2919 protected void addTreeMenuItem(final TreePanel treePanel,
2922 final MenuItem item = new MenuItem(title);
2923 sortByTreeMenu.add(item);
2924 item.addActionListener(new java.awt.event.ActionListener()
2927 public void actionPerformed(ActionEvent evt)
2929 sortByTree(treePanel, title); // treePanel.getTitle());
2933 treePanel.addWindowListener(new WindowAdapter()
2936 public void windowOpened(WindowEvent e)
2938 if (viewport.sortByTree)
2940 sortByTree(treePanel, title);
2942 super.windowOpened(e);
2946 public void windowClosing(WindowEvent e)
2948 sortByTreeMenu.remove(item);
2953 public boolean sortBy(AlignmentOrder alorder, String undoname)
2955 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2956 if (viewport.applet.debug)
2958 System.err.println("Sorting " + alorder.getOrder().size()
2959 + " in alignment '" + getTitle() + "'");
2961 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2962 if (undoname != null)
2964 addHistoryItem(new OrderCommand(undoname, oldOrder,
2965 viewport.getAlignment()));
2967 alignPanel.paintAlignment(true);
2971 protected void documentation_actionPerformed()
2973 alignPanel.av.applet.openJalviewHelpUrl();
2976 protected void about_actionPerformed()
2979 class AboutPanel extends Canvas
2985 public AboutPanel(String version, String builddate)
2987 this.version = version;
2988 this.builddate = builddate;
2992 public void paint(Graphics g)
2994 g.setColor(Color.white);
2995 g.fillRect(0, 0, getSize().width, getSize().height);
2996 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2997 FontMetrics fm = g.getFontMetrics();
2998 int fh = fm.getHeight();
3000 g.setColor(Color.black);
3001 // TODO: update this text for each release or centrally store it for
3002 // lite and application
3003 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3004 g.drawString(MessageManager.formatMessage(
3005 "label.jalviewLite_release", new String[] { version }), x,
3007 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3008 g.drawString(MessageManager.formatMessage(
3009 "label.jaview_build_date", new String[] { builddate }), x,
3011 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3012 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3014 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3015 x + 50, y += fh + 8);
3017 MessageManager.getString("label.jalview_dev_managers"), x,
3019 g.drawString(MessageManager
3020 .getString("label.jalview_distribution_lists"), x, y += fh);
3021 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3024 MessageManager.getString("label.jalview_cite_1_authors"),
3027 MessageManager.getString("label.jalview_cite_1_title"), x,
3029 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3034 Frame frame = new Frame();
3035 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3037 jalview.bin.JalviewLite.addFrame(frame,
3038 MessageManager.getString("label.jalview"), 580, 220);
3042 public void showURL(String url, String target)
3044 if (viewport.applet == null)
3046 System.out.println("Not running as applet - no browser available.");
3050 viewport.applet.showURL(url, target);
3054 // ////////////////////////////////////////////////////////////////////////////////
3055 // JBuilder Graphics here
3057 MenuBar alignFrameMenuBar = new MenuBar();
3059 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3061 MenuItem loadApplication = new MenuItem(
3062 MessageManager.getString("label.view_full_application"));
3064 MenuItem loadTree = new MenuItem(
3065 MessageManager.getString("label.load_associated_tree"));
3067 MenuItem loadAnnotations = new MenuItem(
3068 MessageManager.getString("label.load_features_annotations"));
3070 MenuItem outputFeatures = new MenuItem(
3071 MessageManager.getString("label.export_features"));
3073 MenuItem outputAnnotations = new MenuItem(
3074 MessageManager.getString("label.export_annotations"));
3076 MenuItem closeMenuItem = new MenuItem(
3077 MessageManager.getString("action.close"));
3079 MenuItem selectAllSequenceMenuItem = new MenuItem(
3080 MessageManager.getString("action.select_all"));
3082 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3083 MessageManager.getString("action.deselect_all"));
3085 MenuItem invertSequenceMenuItem = new MenuItem(
3086 MessageManager.getString("action.invert_selection"));
3088 MenuItem remove2LeftMenuItem = new MenuItem();
3090 MenuItem remove2RightMenuItem = new MenuItem();
3092 MenuItem removeGappedColumnMenuItem = new MenuItem();
3094 MenuItem removeAllGapsMenuItem = new MenuItem();
3096 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3098 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3100 MenuItem sortPairwiseMenuItem = new MenuItem();
3102 MenuItem sortIDMenuItem = new MenuItem();
3104 MenuItem sortLengthMenuItem = new MenuItem();
3106 MenuItem sortGroupMenuItem = new MenuItem();
3108 MenuItem removeRedundancyMenuItem = new MenuItem();
3110 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3112 MenuItem PCAMenuItem = new MenuItem();
3114 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3116 MenuItem neighbourTreeMenuItem = new MenuItem();
3118 BorderLayout borderLayout1 = new BorderLayout();
3120 public Label statusBar = new Label();
3122 MenuItem clustalColour = new MenuItem();
3124 MenuItem zappoColour = new MenuItem();
3126 MenuItem taylorColour = new MenuItem();
3128 MenuItem hydrophobicityColour = new MenuItem();
3130 MenuItem helixColour = new MenuItem();
3132 MenuItem strandColour = new MenuItem();
3134 MenuItem turnColour = new MenuItem();
3136 MenuItem buriedColour = new MenuItem();
3138 MenuItem purinePyrimidineColour = new MenuItem();
3140 // MenuItem RNAInteractionColour = new MenuItem();
3142 MenuItem RNAHelixColour = new MenuItem();
3144 MenuItem userDefinedColour = new MenuItem();
3146 MenuItem PIDColour = new MenuItem();
3148 MenuItem BLOSUM62Colour = new MenuItem();
3150 MenuItem tcoffeeColour = new MenuItem();
3152 MenuItem njTreeBlosumMenuItem = new MenuItem();
3154 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3156 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3158 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3160 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3162 MenuItem alProperties = new MenuItem(
3163 MessageManager.getString("label.alignment_props"));
3165 MenuItem overviewMenuItem = new MenuItem();
3167 MenuItem undoMenuItem = new MenuItem();
3169 MenuItem redoMenuItem = new MenuItem();
3171 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3173 MenuItem noColourmenuItem = new MenuItem();
3175 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3177 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3179 MenuItem findMenuItem = new MenuItem();
3181 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3183 MenuItem nucleotideColour = new MenuItem();
3185 MenuItem deleteGroups = new MenuItem();
3187 MenuItem grpsFromSelection = new MenuItem();
3189 MenuItem createGroup = new MenuItem();
3191 MenuItem unGroup = new MenuItem();
3193 MenuItem delete = new MenuItem();
3195 MenuItem copy = new MenuItem();
3197 MenuItem cut = new MenuItem();
3199 Menu pasteMenu = new Menu();
3201 MenuItem pasteNew = new MenuItem();
3203 MenuItem pasteThis = new MenuItem();
3205 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3207 MenuItem font = new MenuItem();
3209 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3211 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3213 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3215 MenuItem modifyPID = new MenuItem();
3217 MenuItem modifyConservation = new MenuItem();
3219 CheckboxMenuItem autoCalculate = null;
3221 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3222 "Sort Alignment With New Tree", true);
3224 Menu sortByTreeMenu = new Menu();
3226 MenuItem inputText = new MenuItem();
3228 MenuItem documentation = new MenuItem();
3230 MenuItem about = new MenuItem();
3232 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3234 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3236 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3238 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3240 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3242 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3244 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3246 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3248 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3251 * Initialise menus and other items
3255 private void jbInit() throws Exception
3257 setMenuBar(alignFrameMenuBar);
3260 * Configure File menu items and actions
3263 .setLabel(MessageManager.getString("label.input_from_textbox"));
3264 inputText.addActionListener(this);
3265 Menu outputTextboxMenu = new Menu(
3266 MessageManager.getString("label.out_to_textbox"));
3267 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3269 MenuItem item = new MenuItem(ff);
3271 item.addActionListener(new java.awt.event.ActionListener()
3274 public void actionPerformed(ActionEvent e)
3276 outputText_actionPerformed(e);
3280 outputTextboxMenu.add(item);
3282 closeMenuItem.addActionListener(this);
3283 loadApplication.addActionListener(this);
3284 loadTree.addActionListener(this);
3285 loadAnnotations.addActionListener(this);
3286 outputFeatures.addActionListener(this);
3287 outputAnnotations.addActionListener(this);
3290 * Configure Edit menu items and actions
3292 undoMenuItem.setEnabled(false);
3293 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3294 undoMenuItem.addActionListener(this);
3295 redoMenuItem.setEnabled(false);
3296 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3297 redoMenuItem.addActionListener(this);
3298 copy.setLabel(MessageManager.getString("action.copy"));
3299 copy.addActionListener(this);
3300 cut.setLabel(MessageManager.getString("action.cut"));
3301 cut.addActionListener(this);
3302 delete.setLabel(MessageManager.getString("action.delete"));
3303 delete.addActionListener(this);
3304 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3305 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3306 pasteNew.addActionListener(this);
3307 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3308 pasteThis.addActionListener(this);
3309 remove2LeftMenuItem.setLabel(MessageManager
3310 .getString("action.remove_left"));
3311 remove2LeftMenuItem.addActionListener(this);
3312 remove2RightMenuItem.setLabel(MessageManager
3313 .getString("action.remove_right"));
3314 remove2RightMenuItem.addActionListener(this);
3315 removeGappedColumnMenuItem.setLabel(MessageManager
3316 .getString("action.remove_empty_columns"));
3317 removeGappedColumnMenuItem.addActionListener(this);
3318 removeAllGapsMenuItem.setLabel(MessageManager
3319 .getString("action.remove_all_gaps"));
3320 removeAllGapsMenuItem.addActionListener(this);
3321 removeRedundancyMenuItem.setLabel(MessageManager
3322 .getString("action.remove_redundancy"));
3323 removeRedundancyMenuItem.addActionListener(this);
3326 * Configure Select menu items and actions
3328 findMenuItem.setLabel(MessageManager.getString("action.find"));
3329 findMenuItem.addActionListener(this);
3330 selectAllSequenceMenuItem.addActionListener(this);
3331 deselectAllSequenceMenuItem.addActionListener(this);
3332 invertSequenceMenuItem.setLabel(MessageManager
3333 .getString("action.invert_sequence_selection"));
3334 invertSequenceMenuItem.addActionListener(this);
3335 invertColSel.setLabel(MessageManager
3336 .getString("action.invert_column_selection"));
3337 invertColSel.addActionListener(this);
3338 deleteGroups.setLabel(MessageManager
3339 .getString("action.undefine_groups"));
3340 deleteGroups.addActionListener(this);
3341 grpsFromSelection.setLabel(MessageManager
3342 .getString("action.make_groups_selection"));
3343 grpsFromSelection.addActionListener(this);
3344 createGroup.setLabel(MessageManager.getString("action.create_group"));
3345 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3346 annotationColumnSelection.setLabel(MessageManager
3347 .getString("action.select_by_annotation"));
3348 annotationColumnSelection.addActionListener(this);
3351 * Configure View menu items and actions
3353 newView.setLabel(MessageManager.getString("action.new_view"));
3354 newView.addActionListener(this);
3355 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3356 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3357 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3358 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3360 .setLabel(MessageManager.getString("label.selected_columns"));
3361 hideSequences.setLabel(MessageManager
3362 .getString("label.selected_sequences"));
3363 hideAllButSelection.setLabel(MessageManager
3364 .getString("label.all_but_selected_region"));
3365 hideAllSelection.setLabel(MessageManager
3366 .getString("label.selected_region"));
3367 showAllHidden.setLabel(MessageManager
3368 .getString("label.all_sequences_columns"));
3369 showColumns.addActionListener(this);
3370 showSeqs.addActionListener(this);
3371 hideColumns.addActionListener(this);
3372 hideSequences.addActionListener(this);
3373 hideAllButSelection.addActionListener(this);
3374 hideAllSelection.addActionListener(this);
3375 showAllHidden.addActionListener(this);
3376 featureSettings.setLabel(MessageManager
3377 .getString("action.feature_settings"));
3378 featureSettings.addActionListener(this);
3379 sequenceFeatures.setLabel(MessageManager
3380 .getString("label.show_sequence_features"));
3381 sequenceFeatures.addItemListener(this);
3382 sequenceFeatures.setState(false);
3383 followMouseOverFlag.setLabel(MessageManager
3384 .getString("label.automatic_scrolling"));
3385 followMouseOverFlag.addItemListener(this);
3386 alProperties.addActionListener(this);
3387 overviewMenuItem.setLabel(MessageManager
3388 .getString("label.overview_window"));
3389 overviewMenuItem.addActionListener(this);
3392 * Configure Annotations menu items and actions
3394 annotationPanelMenuItem.setLabel(MessageManager
3395 .getString("label.show_annotations"));
3396 annotationPanelMenuItem.addItemListener(this);
3397 showGroupConsensus.setLabel(MessageManager
3398 .getString("label.group_consensus"));
3399 showGroupConservation.setLabel(MessageManager
3400 .getString("label.group_conservation"));
3401 showConsensusHistogram.setLabel(MessageManager
3402 .getString("label.show_consensus_histogram"));
3403 showSequenceLogo.setLabel(MessageManager
3404 .getString("label.show_consensus_logo"));
3405 normSequenceLogo.setLabel(MessageManager
3406 .getString("label.norm_consensus_logo"));
3407 applyAutoAnnotationSettings.setLabel(MessageManager
3408 .getString("label.apply_all_groups"));
3409 applyAutoAnnotationSettings.setState(true);
3410 Menu autoAnnMenu = new Menu(
3411 MessageManager.getString("label.autocalculated_annotation"));
3412 showGroupConsensus.addItemListener(this);
3413 showGroupConservation.addItemListener(this);
3414 showConsensusHistogram.addItemListener(this);
3415 showSequenceLogo.addItemListener(this);
3416 normSequenceLogo.addItemListener(this);
3417 applyAutoAnnotationSettings.addItemListener(this);
3418 showAlignmentAnnotations = new CheckboxMenuItem(
3419 MessageManager.getString("label.show_all_al_annotations"));
3420 showSequenceAnnotations = new CheckboxMenuItem(
3421 MessageManager.getString("label.show_all_seq_annotations"));
3422 sortAnnBySequence = new CheckboxMenuItem(
3423 MessageManager.getString("label.sort_annotations_by_sequence"));
3424 sortAnnByLabel = new CheckboxMenuItem(
3425 MessageManager.getString("label.sort_annotations_by_label"));
3426 showAutoFirst = new CheckboxMenuItem(
3427 MessageManager.getString("label.show_first"));
3428 showAutoFirst.setState(false); // pending applet parameter
3429 setShowAutoCalculatedAbove(showAutoFirst.getState());
3430 showAutoLast = new CheckboxMenuItem(
3431 MessageManager.getString("label.show_last"));
3432 showAutoLast.setState(!showAutoFirst.getState());
3433 showAlignmentAnnotations.addItemListener(this);
3434 showSequenceAnnotations.addItemListener(this);
3435 sortAnnBySequence.addItemListener(this);
3436 sortAnnByLabel.addItemListener(this);
3437 showAutoFirst.addItemListener(this);
3438 showAutoLast.addItemListener(this);
3441 * Configure Format menu items and actions
3443 font.setLabel(MessageManager.getString("action.font"));
3444 font.addActionListener(this);
3445 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3446 scaleAbove.setState(true);
3447 scaleAbove.setEnabled(false);
3448 scaleAbove.addItemListener(this);
3449 scaleLeft.setEnabled(false);
3450 scaleLeft.setState(true);
3451 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3452 scaleLeft.addItemListener(this);
3453 scaleRight.setEnabled(false);
3454 scaleRight.setState(true);
3455 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3456 scaleRight.addItemListener(this);
3457 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3458 viewBoxesMenuItem.setState(true);
3459 viewBoxesMenuItem.addItemListener(this);
3460 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3461 viewTextMenuItem.setState(true);
3462 viewTextMenuItem.addItemListener(this);
3463 colourTextMenuItem.setLabel(MessageManager
3464 .getString("label.colour_text"));
3465 colourTextMenuItem.addItemListener(this);
3466 displayNonconservedMenuItem.setLabel(MessageManager
3467 .getString("label.show_non_conserved"));
3468 displayNonconservedMenuItem.addItemListener(this);
3469 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3470 wrapMenuItem.addItemListener(this);
3471 renderGapsMenuItem.setLabel(MessageManager
3472 .getString("action.show_gaps"));
3473 renderGapsMenuItem.setState(true);
3474 renderGapsMenuItem.addItemListener(this);
3475 centreColumnLabelFlag.setLabel(MessageManager
3476 .getString("label.centre_column_labels"));
3477 centreColumnLabelFlag.addItemListener(this);
3478 seqLimits.setState(true);
3479 seqLimits.setLabel(MessageManager
3480 .getString("label.show_sequence_limits"));
3481 seqLimits.addItemListener(this);
3484 * Configure Colour menu items and actions
3486 applyToAllGroups.setLabel(MessageManager
3487 .getString("label.apply_colour_to_all_groups"));
3488 applyToAllGroups.setState(true);
3489 applyToAllGroups.addItemListener(this);
3490 clustalColour.setLabel(MessageManager
3491 .getString("label.colourScheme_clustal"));
3492 clustalColour.addActionListener(this);
3493 zappoColour.setLabel(MessageManager
3494 .getString("label.colourScheme_zappo"));
3495 zappoColour.addActionListener(this);
3496 taylorColour.setLabel(MessageManager
3497 .getString("label.colourScheme_taylor"));
3498 taylorColour.addActionListener(this);
3499 hydrophobicityColour.setLabel(MessageManager
3500 .getString("label.colourScheme_hydrophobic"));
3501 hydrophobicityColour.addActionListener(this);
3502 helixColour.setLabel(MessageManager
3503 .getString("label.colourScheme_helix_propensity"));
3504 helixColour.addActionListener(this);
3505 strandColour.setLabel(MessageManager
3506 .getString("label.colourScheme_strand_propensity"));
3507 strandColour.addActionListener(this);
3508 turnColour.setLabel(MessageManager
3509 .getString("label.colourScheme_turn_propensity"));
3510 turnColour.addActionListener(this);
3511 buriedColour.setLabel(MessageManager
3512 .getString("label.colourScheme_buried_index"));
3513 buriedColour.addActionListener(this);
3514 purinePyrimidineColour.setLabel(MessageManager
3515 .getString("label.colourScheme_purine/pyrimidine"));
3516 purinePyrimidineColour.addActionListener(this);
3517 // RNAInteractionColour.setLabel(MessageManager
3518 // .getString("label.rna_interaction"));
3519 // RNAInteractionColour.addActionListener(this);
3520 RNAHelixColour.setLabel(MessageManager
3521 .getString("label.colourScheme_rna_helices"));
3522 RNAHelixColour.addActionListener(this);
3523 userDefinedColour.setLabel(MessageManager
3524 .getString("action.user_defined"));
3525 userDefinedColour.addActionListener(this);
3526 PIDColour.setLabel(MessageManager
3527 .getString("label.colourScheme_%_identity"));
3528 PIDColour.addActionListener(this);
3529 BLOSUM62Colour.setLabel(MessageManager
3530 .getString("label.colourScheme_blosum62"));
3531 BLOSUM62Colour.addActionListener(this);
3532 tcoffeeColour.setLabel(MessageManager
3533 .getString("label.colourScheme_t-coffee_scores"));
3534 // it will be enabled only if a score file is provided
3535 tcoffeeColour.setEnabled(false);
3536 tcoffeeColour.addActionListener(this);
3537 conservationMenuItem.setLabel(MessageManager
3538 .getString("action.by_conservation"));
3539 conservationMenuItem.addItemListener(this);
3540 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3541 noColourmenuItem.addActionListener(this);
3542 abovePIDThreshold.setLabel(MessageManager
3543 .getString("label.above_identity_threshold"));
3544 abovePIDThreshold.addItemListener(this);
3545 nucleotideColour.setLabel(MessageManager
3546 .getString("label.colourScheme_nucleotide"));
3547 nucleotideColour.addActionListener(this);
3548 modifyPID.setLabel(MessageManager
3549 .getString("label.modify_identity_threshold"));
3550 modifyPID.setEnabled(abovePIDThreshold.getState());
3551 modifyPID.addActionListener(this);
3552 modifyConservation.setLabel(MessageManager
3553 .getString("label.modify_conservation_threshold"));
3554 modifyConservation.setEnabled(conservationMenuItem.getState());
3555 modifyConservation.addActionListener(this);
3556 annotationColour.setLabel(MessageManager
3557 .getString("action.by_annotation"));
3558 annotationColour.addActionListener(this);
3561 * Configure Calculate menu items and actions
3563 sortPairwiseMenuItem.setLabel(MessageManager
3564 .getString("action.by_pairwise_id"));
3565 sortPairwiseMenuItem.addActionListener(this);
3566 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3567 sortIDMenuItem.addActionListener(this);
3568 sortLengthMenuItem.setLabel(MessageManager
3569 .getString("action.by_length"));
3570 sortLengthMenuItem.addActionListener(this);
3571 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3572 sortGroupMenuItem.addActionListener(this);
3573 pairwiseAlignmentMenuItem.setLabel(MessageManager
3574 .getString("action.pairwise_alignment"));
3575 pairwiseAlignmentMenuItem.addActionListener(this);
3576 PCAMenuItem.setLabel(MessageManager
3577 .getString("label.principal_component_analysis"));
3578 PCAMenuItem.addActionListener(this);
3579 autoCalculate = new CheckboxMenuItem(
3580 MessageManager.getString("label.autocalculate_consensus"), true);
3581 averageDistanceTreeMenuItem.setLabel(MessageManager
3582 .getString("label.average_distance_identity"));
3583 averageDistanceTreeMenuItem.addActionListener(this);
3584 neighbourTreeMenuItem.setLabel(MessageManager
3585 .getString("label.neighbour_joining_identity"));
3586 neighbourTreeMenuItem.addActionListener(this);
3587 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3588 .getString("label.average_distance_blosum62"));
3589 avDistanceTreeBlosumMenuItem.addActionListener(this);
3590 njTreeBlosumMenuItem.setLabel(MessageManager
3591 .getString("label.neighbour_blosum62"));
3592 njTreeBlosumMenuItem.addActionListener(this);
3593 sortByTreeMenu.setLabel(MessageManager
3594 .getString("action.by_tree_order"));
3595 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3596 Menu calculateTreeMenu = new Menu(
3597 MessageManager.getString("action.calculate_tree"));
3598 autoCalculate.addItemListener(this);
3599 sortByTree.addItemListener(this);
3602 * Configure Help menu items and actions
3604 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3605 documentation.setLabel(MessageManager.getString("label.documentation"));
3606 documentation.addActionListener(this);
3607 about.setLabel(MessageManager.getString("label.about"));
3608 about.addActionListener(this);
3611 * Add top level menus to frame
3613 alignFrameMenuBar.add(fileMenu);
3614 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3615 alignFrameMenuBar.add(editMenu);
3616 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3617 alignFrameMenuBar.add(selectMenu);
3618 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3619 alignFrameMenuBar.add(viewMenu);
3620 Menu annotationsMenu = new Menu(
3621 MessageManager.getString("action.annotations"));
3622 alignFrameMenuBar.add(annotationsMenu);
3623 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3624 alignFrameMenuBar.add(formatMenu);
3625 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3626 alignFrameMenuBar.add(colourMenu);
3627 Menu calculateMenu = new Menu(
3628 MessageManager.getString("action.calculate"));
3629 alignFrameMenuBar.add(calculateMenu);
3630 alignFrameMenuBar.add(helpMenu);
3635 fileMenu.add(inputText);
3636 fileMenu.add(loadTree);
3637 fileMenu.add(loadAnnotations);
3638 fileMenu.addSeparator();
3639 fileMenu.add(outputTextboxMenu);
3640 fileMenu.add(outputFeatures);
3641 fileMenu.add(outputAnnotations);
3642 if (jalviewServletURL != null)
3644 fileMenu.add(loadApplication);
3646 fileMenu.addSeparator();
3647 fileMenu.add(closeMenuItem);
3652 editMenu.add(undoMenuItem);
3653 editMenu.add(redoMenuItem);
3656 pasteMenu.add(pasteNew);
3657 pasteMenu.add(pasteThis);
3658 editMenu.add(pasteMenu);
3659 editMenu.add(delete);
3660 editMenu.addSeparator();
3661 editMenu.add(remove2LeftMenuItem);
3662 editMenu.add(remove2RightMenuItem);
3663 editMenu.add(removeGappedColumnMenuItem);
3664 editMenu.add(removeAllGapsMenuItem);
3665 editMenu.add(removeRedundancyMenuItem);
3670 selectMenu.add(findMenuItem);
3671 selectMenu.addSeparator();
3672 selectMenu.add(selectAllSequenceMenuItem);
3673 selectMenu.add(deselectAllSequenceMenuItem);
3674 selectMenu.add(invertSequenceMenuItem);
3675 selectMenu.add(invertColSel);
3676 selectMenu.add(createGroup);
3677 selectMenu.add(unGroup);
3678 selectMenu.add(grpsFromSelection);
3679 selectMenu.add(deleteGroups);
3680 selectMenu.add(annotationColumnSelection);
3685 viewMenu.add(newView);
3686 viewMenu.addSeparator();
3687 showMenu.add(showColumns);
3688 showMenu.add(showSeqs);
3689 showMenu.add(showAllHidden);
3690 viewMenu.add(showMenu);
3691 hideMenu.add(hideColumns);
3692 hideMenu.add(hideSequences);
3693 hideMenu.add(hideAllSelection);
3694 hideMenu.add(hideAllButSelection);
3695 viewMenu.add(hideMenu);
3696 viewMenu.addSeparator();
3697 viewMenu.add(followMouseOverFlag);
3698 viewMenu.addSeparator();
3699 viewMenu.add(sequenceFeatures);
3700 viewMenu.add(featureSettings);
3701 viewMenu.addSeparator();
3702 viewMenu.add(alProperties);
3703 viewMenu.addSeparator();
3704 viewMenu.add(overviewMenuItem);
3709 annotationsMenu.add(annotationPanelMenuItem);
3710 annotationsMenu.addSeparator();
3711 annotationsMenu.add(showAlignmentAnnotations);
3712 annotationsMenu.add(showSequenceAnnotations);
3713 annotationsMenu.add(sortAnnBySequence);
3714 annotationsMenu.add(sortAnnByLabel);
3715 annotationsMenu.addSeparator();
3716 autoAnnMenu.add(showAutoFirst);
3717 autoAnnMenu.add(showAutoLast);
3718 autoAnnMenu.addSeparator();
3719 autoAnnMenu.add(applyAutoAnnotationSettings);
3720 autoAnnMenu.add(showConsensusHistogram);
3721 autoAnnMenu.add(showSequenceLogo);
3722 autoAnnMenu.add(normSequenceLogo);
3723 autoAnnMenu.addSeparator();
3724 autoAnnMenu.add(showGroupConservation);
3725 autoAnnMenu.add(showGroupConsensus);
3726 annotationsMenu.add(autoAnnMenu);
3731 formatMenu.add(font);
3732 formatMenu.add(seqLimits);
3733 formatMenu.add(wrapMenuItem);
3734 formatMenu.add(scaleAbove);
3735 formatMenu.add(scaleLeft);
3736 formatMenu.add(scaleRight);
3737 formatMenu.add(viewBoxesMenuItem);
3738 formatMenu.add(viewTextMenuItem);
3739 formatMenu.add(colourTextMenuItem);
3740 formatMenu.add(displayNonconservedMenuItem);
3741 formatMenu.add(renderGapsMenuItem);
3742 formatMenu.add(centreColumnLabelFlag);
3747 colourMenu.add(applyToAllGroups);
3748 colourMenu.addSeparator();
3749 colourMenu.add(noColourmenuItem);
3750 colourMenu.add(clustalColour);
3751 colourMenu.add(BLOSUM62Colour);
3752 colourMenu.add(PIDColour);
3753 colourMenu.add(zappoColour);
3754 colourMenu.add(taylorColour);
3755 colourMenu.add(hydrophobicityColour);
3756 colourMenu.add(helixColour);
3757 colourMenu.add(strandColour);
3758 colourMenu.add(turnColour);
3759 colourMenu.add(buriedColour);
3760 colourMenu.add(nucleotideColour);
3761 colourMenu.add(purinePyrimidineColour);
3762 // colourMenu.add(RNAInteractionColour);
3763 colourMenu.add(tcoffeeColour);
3764 colourMenu.add(userDefinedColour);
3765 colourMenu.addSeparator();
3766 colourMenu.add(conservationMenuItem);
3767 colourMenu.add(modifyConservation);
3768 colourMenu.add(abovePIDThreshold);
3769 colourMenu.add(modifyPID);
3770 colourMenu.add(annotationColour);
3771 colourMenu.add(RNAHelixColour);
3776 sortMenu.add(sortIDMenuItem);
3777 sortMenu.add(sortLengthMenuItem);
3778 sortMenu.add(sortByTreeMenu);
3779 sortMenu.add(sortGroupMenuItem);
3780 sortMenu.add(sortPairwiseMenuItem);
3781 calculateMenu.add(sortMenu);
3782 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3783 calculateTreeMenu.add(neighbourTreeMenuItem);
3784 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3785 calculateTreeMenu.add(njTreeBlosumMenuItem);
3786 calculateMenu.add(calculateTreeMenu);
3787 calculateMenu.addSeparator();
3788 calculateMenu.add(pairwiseAlignmentMenuItem);
3789 calculateMenu.add(PCAMenuItem);
3790 calculateMenu.add(autoCalculate);
3791 calculateMenu.add(sortByTree);
3796 helpMenu.add(documentation);
3797 helpMenu.add(about);
3802 statusBar.setBackground(Color.white);
3803 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3804 statusBar.setText(MessageManager.getString("label.status_bar"));
3805 this.add(statusBar, BorderLayout.SOUTH);
3809 public void setStatus(String string)
3811 statusBar.setText(string);
3814 MenuItem featureSettings = new MenuItem();
3816 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3818 MenuItem annotationColour = new MenuItem();
3820 MenuItem annotationColumnSelection = new MenuItem();
3822 MenuItem invertColSel = new MenuItem();
3824 MenuItem showColumns = new MenuItem();
3826 MenuItem showSeqs = new MenuItem();
3828 MenuItem hideColumns = new MenuItem();
3830 MenuItem hideSequences = new MenuItem();
3832 MenuItem hideAllButSelection = new MenuItem();
3834 MenuItem hideAllSelection = new MenuItem();
3836 MenuItem showAllHidden = new MenuItem();
3838 MenuItem newView = new MenuItem();
3840 private CheckboxMenuItem showAlignmentAnnotations;
3842 private CheckboxMenuItem showSequenceAnnotations;
3844 private CheckboxMenuItem sortAnnBySequence;
3846 private CheckboxMenuItem sortAnnByLabel;
3848 private CheckboxMenuItem showAutoFirst;
3850 private CheckboxMenuItem showAutoLast;
3852 private SplitFrame splitFrame;
3855 * Attach the alignFrame panels after embedding menus, if necessary. This used
3856 * to be called setEmbedded, but is now creates the dropdown menus in a
3857 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3859 * @param reallyEmbedded
3860 * true to attach the view to the applet area on the page rather than
3863 public void createAlignFrameWindow(boolean reallyEmbedded)
3867 embedAlignFrameInApplet(viewport.applet);
3872 // test and embed menu bar if necessary.
3874 if (embedMenuIfNeeded(alignPanel))
3877 * adjust for status bar height too. ? pointless as overridden by layout
3880 alignPanel.setSize(getSize().width,
3881 getSize().height - statusBar.getHeight());
3883 add(statusBar, BorderLayout.SOUTH);
3884 add(alignPanel, BorderLayout.CENTER);
3885 // and register with the applet so it can pass external API calls to us
3886 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3892 * Add the components of this AlignFrame to the applet container.
3896 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3899 // Explicitly build the embedded menu panel for the on-page applet
3901 // view cannot be closed if its actually on the page
3902 fileMenu.remove(closeMenuItem);
3903 fileMenu.remove(3); // Remove Separator
3904 // construct embedded menu, using default font
3905 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3906 // and actually add the components to the applet area
3907 theApplet.setLayout(new BorderLayout());
3908 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3909 theApplet.add(statusBar, BorderLayout.SOUTH);
3910 // TODO should size be left to the layout manager?
3911 alignPanel.setSize(theApplet.getSize().width,
3912 theApplet.getSize().height - embeddedMenu.getHeight()
3913 - statusBar.getHeight());
3914 theApplet.add(alignPanel, BorderLayout.CENTER);
3915 final AlignFrame me = this;
3916 theApplet.addFocusListener(new FocusListener()
3920 public void focusLost(FocusEvent e)
3922 if (theApplet.currentAlignFrame == me)
3924 theApplet.currentAlignFrame = null;
3929 public void focusGained(FocusEvent e)
3931 theApplet.currentAlignFrame = me;
3934 theApplet.validate();
3938 * create a new binding between structures in an existing jmol viewer instance
3939 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3940 * this does not open a new Jmol window, or modify the display of the
3941 * structures in the original jmol window. Note This method doesn't work
3942 * without an additional javascript library to exchange messages between the
3943 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3946 * JmolViewer instance
3947 * @param sequenceIds
3948 * - sequence Ids to search for associations
3950 public SequenceStructureBinding addStructureViewInstance(
3951 Object jmolviewer, String[] sequenceIds)
3953 Viewer viewer = null;
3956 viewer = (Viewer) jmolviewer;
3957 } catch (ClassCastException ex)
3959 System.err.println("Unsupported viewer object :"
3960 + jmolviewer.getClass());
3964 System.err.println("Can't use this object as a structure viewer:"
3965 + jmolviewer.getClass());
3968 SequenceI[] seqs = null;
3969 if (sequenceIds == null || sequenceIds.length == 0)
3971 seqs = viewport.getAlignment().getSequencesArray();
3975 Vector sqi = new Vector();
3976 AlignmentI al = viewport.getAlignment();
3977 for (int sid = 0; sid < sequenceIds.length; sid++)
3979 SequenceI sq = al.findName(sequenceIds[sid]);
3987 seqs = new SequenceI[sqi.size()];
3988 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3990 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3998 AAStructureBindingModel jmv = null;
3999 // TODO: search for a jmv that involves viewer
4001 { // create a new viewer/jalview binding.
4002 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4009 * bind a pdb file to a sequence in the current view
4012 * - sequenceId within the dataset.
4013 * @param pdbEntryString
4014 * - the short name for the PDB file
4016 * - pdb file - either a URL or a valid PDB file.
4017 * @return true if binding was as success TODO: consider making an exception
4018 * structure for indicating when PDB parsing or sequenceId location
4021 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4024 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4025 boolean needtoadd = false;
4026 if (toaddpdb != null)
4028 Vector pdbe = toaddpdb.getAllPDBEntries();
4029 PDBEntry pdbentry = null;
4030 if (pdbe != null && pdbe.size() > 0)
4032 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4034 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4035 if (!pdbentry.getId().equals(pdbEntryString)
4036 && !pdbentry.getFile().equals(pdbFile))
4046 if (pdbentry == null)
4048 pdbentry = new PDBEntry();
4049 pdbentry.setId(pdbEntryString);
4050 pdbentry.setFile(pdbFile);
4051 needtoadd = true; // add this new entry to sequence.
4053 // resolve data source
4054 // TODO: this code should be a refactored to an io package
4055 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4056 pdbFile, FileFormat.PDB);
4057 if (protocol == null)
4063 pdbentry.setProperty("protocol", protocol);
4064 toaddpdb.addPDBId(pdbentry);
4065 alignPanel.getStructureSelectionManager()
4066 .registerPDBEntry(pdbentry);
4072 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4076 Vector sequences = new Vector();
4077 for (int i = 0; i < seqs.length; i++)
4079 if (seqs[i] != null)
4081 sequences.addElement(new Object[] { seqs[i],
4082 (chains != null) ? chains[i] : null });
4085 seqs = new SequenceI[sequences.size()];
4086 chains = new String[sequences.size()];
4087 for (int i = 0, isize = sequences.size(); i < isize; i++)
4089 Object[] oj = (Object[]) sequences.elementAt(i);
4091 seqs[i] = (SequenceI) oj[0];
4092 chains[i] = (String) oj[1];
4095 return new Object[] { seqs, chains };
4099 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4100 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4102 // Scrub any null sequences from the array
4103 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4104 seqs = (SequenceI[]) sqch[0];
4105 chains = (String[]) sqch[1];
4106 if (seqs == null || seqs.length == 0)
4109 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4111 if (protocol == null)
4113 String sourceType = (String) pdb.getProperty("protocol");
4116 protocol = DataSourceType.valueOf(sourceType);
4117 } catch (IllegalArgumentException e)
4121 if (protocol == null)
4123 System.err.println("Couldn't work out protocol to open structure: "
4128 if (applet.useXtrnalSviewer)
4130 // register the association(s) and quit, don't create any windows.
4131 if (StructureSelectionManager.getStructureSelectionManager(applet)
4132 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4134 System.err.println("Failed to map " + pdb.getFile() + " ("
4135 + protocol + ") to any sequences");
4139 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4141 // can only do alignments with Jmol
4142 // find the last jmol window assigned to this alignment
4143 AppletJmol ajm = null, tajm;
4144 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4145 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4147 tajm = (AppletJmol) jmols.elementAt(i);
4148 if (tajm.ap.alignFrame == this)
4157 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4158 // try and add the pdb structure
4163 // otherwise, create a new window
4164 if (applet.jmolAvailable)
4166 new AppletJmol(pdb, seqs, chains, alignPanel,
4168 applet.lastFrameX += 40;
4169 applet.lastFrameY += 40;
4173 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4178 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4179 SequenceI[][] seqs, String[][] chains, String[] protocols)
4181 // TODO Auto-generated method stub
4182 System.err.println("Aligned Structure View: Not yet implemented.");
4186 * modify the current selection, providing the user has not made a selection
4190 * - sequences from this alignment
4192 * - columns to be selected on the alignment
4194 public void select(SequenceGroup sel, ColumnSelection csel)
4196 alignPanel.seqPanel.selection(sel, csel, null);
4199 public void scrollTo(int row, int column)
4201 alignPanel.seqPanel.scrollTo(row, column);
4204 public void scrollToRow(int row)
4206 alignPanel.seqPanel.scrollToRow(row);
4209 public void scrollToColumn(int column)
4211 alignPanel.seqPanel.scrollToColumn(column);
4215 * @return the alignments unique ID.
4217 public String getSequenceSetId()
4219 return viewport.getSequenceSetId();
4223 * Load the (T-Coffee) score file from the specified url
4226 * File/URL/T-COFFEE score file contents
4227 * @throws IOException
4228 * @return true if alignment was annotated with data from source
4230 public boolean loadScoreFile(String source) throws IOException
4233 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4234 AppletFormatAdapter.checkProtocol(source));
4235 if (!file.isValid())
4237 // TODO: raise dialog for gui
4238 System.err.println("Problems parsing T-Coffee scores: "
4239 + file.getWarningMessage());
4240 System.err.println("Origin was:\n" + source);
4245 * check that the score matrix matches the alignment dimensions
4248 if ((aln = viewport.getAlignment()) != null
4249 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4252 // TODO: raise a dialog box here rather than bomb out.
4254 .println("The scores matrix does not match the alignment dimensions");
4258 // TODO add parameter to indicate if matching should be done
4259 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4261 alignPanel.fontChanged();
4262 tcoffeeColour.setEnabled(true);
4263 // switch to this color
4264 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4269 System.err.println("Problems resolving T-Coffee scores:");
4270 if (file.getWarningMessage() != null)
4272 System.err.println(file.getWarningMessage());
4278 public SplitFrame getSplitFrame()
4280 return this.splitFrame;
4283 public void setSplitFrame(SplitFrame sf)
4285 this.splitFrame = sf;
4288 // may not need this
4290 public void setShowSeqFeatures(boolean b)
4292 // showSeqFeatures.setSelected(b);
4293 viewport.setShowSequenceFeatures(b);
4298 public void setMenusForViewport()
4300 // setMenusFromViewport(viewport);
4305 public void refreshFeatureUI(boolean enableIfNecessary)
4307 if (enableIfNecessary)
4309 sequenceFeatures.setState(true);
4310 alignPanel.av.setShowSequenceFeatures(true);
4315 public FeatureSettingsControllerI getFeatureSettingsUI()
4317 return alignPanel.av.featureSettings;