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.TreeBuilder;
26 import jalview.analysis.scoremodels.PIDModel;
27 import jalview.analysis.scoremodels.ScoreModels;
28 import jalview.api.AlignViewControllerGuiI;
29 import jalview.api.AlignViewControllerI;
30 import jalview.api.AlignViewportI;
31 import jalview.api.FeatureColourI;
32 import jalview.api.FeatureRenderer;
33 import jalview.api.FeatureSettingsControllerI;
34 import jalview.api.SequenceStructureBinding;
35 import jalview.bin.JalviewLite;
36 import jalview.commands.CommandI;
37 import jalview.commands.EditCommand;
38 import jalview.commands.EditCommand.Action;
39 import jalview.commands.OrderCommand;
40 import jalview.commands.RemoveGapColCommand;
41 import jalview.commands.RemoveGapsCommand;
42 import jalview.commands.SlideSequencesCommand;
43 import jalview.commands.TrimRegionCommand;
44 import jalview.datamodel.Alignment;
45 import jalview.datamodel.AlignmentAnnotation;
46 import jalview.datamodel.AlignmentI;
47 import jalview.datamodel.AlignmentOrder;
48 import jalview.datamodel.ColumnSelection;
49 import jalview.datamodel.HiddenColumns;
50 import jalview.datamodel.PDBEntry;
51 import jalview.datamodel.Sequence;
52 import jalview.datamodel.SequenceGroup;
53 import jalview.datamodel.SequenceI;
54 import jalview.io.AnnotationFile;
55 import jalview.io.AppletFormatAdapter;
56 import jalview.io.DataSourceType;
57 import jalview.io.FeaturesFile;
58 import jalview.io.FileFormat;
59 import jalview.io.FileFormatI;
60 import jalview.io.FileFormats;
61 import jalview.io.TCoffeeScoreFile;
62 import jalview.schemes.Blosum62ColourScheme;
63 import jalview.schemes.BuriedColourScheme;
64 import jalview.schemes.ClustalxColourScheme;
65 import jalview.schemes.ColourSchemeI;
66 import jalview.schemes.HelixColourScheme;
67 import jalview.schemes.HydrophobicColourScheme;
68 import jalview.schemes.NucleotideColourScheme;
69 import jalview.schemes.PIDColourScheme;
70 import jalview.schemes.PurinePyrimidineColourScheme;
71 import jalview.schemes.RNAHelicesColour;
72 import jalview.schemes.StrandColourScheme;
73 import jalview.schemes.TCoffeeColourScheme;
74 import jalview.schemes.TaylorColourScheme;
75 import jalview.schemes.TurnColourScheme;
76 import jalview.schemes.ZappoColourScheme;
77 import jalview.structure.StructureSelectionManager;
78 import jalview.structures.models.AAStructureBindingModel;
79 import jalview.util.MappingUtils;
80 import jalview.util.MessageManager;
81 import jalview.viewmodel.AlignmentViewport;
82 import jalview.viewmodel.ViewportRanges;
84 import java.awt.BorderLayout;
85 import java.awt.Canvas;
86 import java.awt.CheckboxMenuItem;
87 import java.awt.Color;
88 import java.awt.FlowLayout;
90 import java.awt.FontMetrics;
91 import java.awt.Frame;
92 import java.awt.Graphics;
93 import java.awt.Label;
95 import java.awt.MenuBar;
96 import java.awt.MenuItem;
97 import java.awt.Panel;
98 import java.awt.event.ActionEvent;
99 import java.awt.event.ActionListener;
100 import java.awt.event.FocusEvent;
101 import java.awt.event.FocusListener;
102 import java.awt.event.ItemEvent;
103 import java.awt.event.ItemListener;
104 import java.awt.event.KeyEvent;
105 import java.awt.event.KeyListener;
106 import java.awt.event.WindowAdapter;
107 import java.awt.event.WindowEvent;
108 import java.io.IOException;
110 import java.net.URLEncoder;
111 import java.util.Arrays;
112 import java.util.Deque;
113 import java.util.HashMap;
114 import java.util.List;
115 import java.util.Map;
116 import java.util.StringTokenizer;
117 import java.util.Vector;
119 import org.jmol.viewer.Viewer;
121 public class AlignFrame extends EmbmenuFrame implements ActionListener,
122 ItemListener, KeyListener, AlignViewControllerGuiI
124 public AlignViewControllerI avc;
126 public AlignmentPanel alignPanel;
128 public AlignViewport viewport;
130 // width and height may be overridden by applet parameters
131 int frameWidth = 700;
133 int frameHeight = 500;
135 String jalviewServletURL;
138 * Flag for showing autocalculated consensus above or below other consensus
141 private boolean showAutoCalculatedAbove;
143 private SequenceAnnotationOrder annotationSortOrder;
146 * Constructor that creates the frame and adds it to the display.
153 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
156 this(al, applet, title, embedded, true);
160 * Constructor that optionally allows the frame to be displayed or only
167 * @param addToDisplay
169 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
170 boolean embedded, boolean addToDisplay)
172 this(al, null, null, applet, title, embedded, addToDisplay);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 HiddenColumns hidden, JalviewLite applet,
177 String title, boolean embedded)
179 this(al, hiddenSeqs, hidden, applet, title, embedded, true);
182 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
183 HiddenColumns hidden, JalviewLite applet,
184 String title, boolean embedded, boolean addToDisplay)
188 jalviewServletURL = applet.getParameter("APPLICATION_URL");
194 } catch (Exception ex)
196 ex.printStackTrace();
198 // need to get window geometry before we calculate alignment layout
204 param = applet.getParameter("windowWidth");
207 int width = Integer.parseInt(param);
210 param = applet.getParameter("windowHeight");
213 int height = Integer.parseInt(param);
214 frameHeight = height;
216 } catch (Exception ex)
220 viewport = new AlignViewport(al, applet);
222 if (hiddenSeqs != null && hiddenSeqs.length > 0)
224 viewport.hideSequence(hiddenSeqs);
228 viewport.getAlignment().setHiddenColumns(hidden);
230 viewport.setScaleAboveWrapped(scaleAbove.getState());
232 alignPanel = new AlignmentPanel(this, viewport);
233 avc = new jalview.controller.AlignViewController(this, viewport,
235 viewport.updateConservation(alignPanel);
236 viewport.updateConsensus(alignPanel);
238 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
239 followMouseOverFlag.setState(viewport.isFollowHighlight());
240 showGroupConsensus.setState(viewport.isShowGroupConsensus());
241 showGroupConservation.setState(viewport.isShowGroupConservation());
242 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
243 showSequenceLogo.setState(viewport.isShowSequenceLogo());
244 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
245 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
246 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
247 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
248 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
249 showAlignmentAnnotations.setState(true);
250 showSequenceAnnotations.setState(false);
252 seqLimits.setState(viewport.getShowJVSuffix());
256 String param = applet.getParameter("sortBy");
259 if (param.equalsIgnoreCase("Id"))
261 sortIDMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Pairwise Identity"))
265 sortPairwiseMenuItem_actionPerformed();
267 else if (param.equalsIgnoreCase("Length"))
269 sortLengthMenuItem_actionPerformed();
273 param = applet.getParameter("wrap");
276 if (param.equalsIgnoreCase("true"))
278 wrapMenuItem.setState(true);
279 wrapMenuItem_actionPerformed();
282 param = applet.getParameter("centrecolumnlabels");
285 centreColumnLabelFlag.setState(true);
286 centreColumnLabelFlag_stateChanged();
290 if (viewport.getAlignment().isNucleotide())
292 conservationMenuItem.setEnabled(false);
293 clustalColour.setEnabled(false);
294 BLOSUM62Colour.setEnabled(false);
295 zappoColour.setEnabled(false);
296 taylorColour.setEnabled(false);
297 hydrophobicityColour.setEnabled(false);
298 helixColour.setEnabled(false);
299 strandColour.setEnabled(false);
300 turnColour.setEnabled(false);
301 buriedColour.setEnabled(false);
302 viewport.updateStrucConsensus(alignPanel);
303 if (viewport.getAlignment().hasRNAStructure())
305 RNAHelixColour.setEnabled(true);
309 RNAHelixColour.setEnabled(false);
314 RNAHelixColour.setEnabled(false);
315 purinePyrimidineColour.setEnabled(false);
316 nucleotideColour.setEnabled(false);
318 // Some JVMS send keyevents to Top frame or lowest panel,
319 // Havent worked out why yet. So add to both this frame and seqCanvas for
321 this.addKeyListener(this);
322 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
323 alignPanel.idPanel.idCanvas.addKeyListener(this);
324 alignPanel.scalePanel.addKeyListener(this);
325 alignPanel.annotationPanel.addKeyListener(this);
326 alignPanel.annotationPanelHolder.addKeyListener(this);
327 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
328 alignPanel.alabels.addKeyListener(this);
330 setAnnotationsVisibility();
334 addToDisplay(embedded);
341 public void addToDisplay(boolean embedded)
343 createAlignFrameWindow(embedded);
345 alignPanel.adjustAnnotationHeight();
346 alignPanel.paintAlignment(true);
349 public AlignViewport getAlignViewport()
354 public SeqCanvas getSeqcanvas()
356 return alignPanel.seqPanel.seqCanvas;
360 * Load a features file onto the alignment
363 * file URL, content, or other resolvable path
365 * is protocol for accessing data referred to by file
368 public boolean parseFeaturesFile(String file, DataSourceType type)
370 return parseFeaturesFile(file, type, true);
374 * Load a features file onto the alignment
377 * file URL, content, or other resolvable path
379 * is protocol for accessing data referred to by file
380 * @param autoenabledisplay
381 * when true, display features flag will be automatically enabled if
382 * features are loaded
383 * @return true if data parsed as a features file
385 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
386 boolean autoenabledisplay)
388 boolean featuresFile = false;
391 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
392 .getFeatureRenderer().getFeatureColours();
393 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
394 "relaxedidmatch", false);
395 featuresFile = new FeaturesFile(file, sourceType).parse(
396 viewport.getAlignment(), colours, true, relaxedIdMatching);
397 } catch (Exception ex)
399 ex.printStackTrace();
404 if (autoenabledisplay)
406 viewport.setShowSequenceFeatures(true);
407 sequenceFeatures.setState(true);
409 if (alignPanel.seqPanel.seqCanvas.fr != null)
411 // update the min/max ranges where necessary
412 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
414 if (viewport.featureSettings != null)
416 viewport.featureSettings.refreshTable();
418 alignPanel.paintAlignment(true);
419 statusBar.setText(MessageManager
420 .getString("label.successfully_added_features_alignment"));
426 public void keyPressed(KeyEvent evt)
428 ViewportRanges ranges = viewport.getRanges();
430 if (viewport.cursorMode
431 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
432 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
433 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
434 && Character.isDigit(evt.getKeyChar()))
436 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
439 switch (evt.getKeyCode())
441 case 27: // escape key
442 deselectAllSequenceMenuItem_actionPerformed();
444 alignPanel.alabels.cancelDrag();
447 if (evt.isControlDown() || evt.isMetaDown())
449 cut_actionPerformed();
453 if (viewport.cursorMode && !evt.isControlDown())
455 alignPanel.seqPanel.setCursorColumn();
457 if (evt.isControlDown() || evt.isMetaDown())
459 copy_actionPerformed();
463 if (evt.isControlDown())
465 paste(evt.isShiftDown());
469 if (evt.isControlDown() || evt.isMetaDown())
471 selectAllSequenceMenuItem_actionPerformed();
474 case KeyEvent.VK_DOWN:
475 if (viewport.cursorMode)
477 alignPanel.seqPanel.moveCursor(0, 1);
481 moveSelectedSequences(false);
486 if (viewport.cursorMode)
488 alignPanel.seqPanel.moveCursor(0, -1);
492 moveSelectedSequences(true);
496 case KeyEvent.VK_LEFT:
497 if (evt.isAltDown() || !viewport.cursorMode)
499 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
503 alignPanel.seqPanel.moveCursor(-1, 0);
507 case KeyEvent.VK_RIGHT:
508 if (evt.isAltDown() || !viewport.cursorMode)
510 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
514 alignPanel.seqPanel.moveCursor(1, 0);
518 case KeyEvent.VK_SPACE:
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
522 || evt.isShiftDown() || evt.isAltDown());
526 case KeyEvent.VK_DELETE:
527 case KeyEvent.VK_BACK_SPACE:
528 if (viewport.cursorMode)
530 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
531 || evt.isShiftDown() || evt.isAltDown());
535 cut_actionPerformed();
536 alignPanel.seqPanel.seqCanvas.repaint();
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setCursorRow();
547 if (viewport.cursorMode)
549 alignPanel.seqPanel.setCursorPosition();
553 case KeyEvent.VK_ENTER:
554 case KeyEvent.VK_COMMA:
555 if (viewport.cursorMode)
557 alignPanel.seqPanel.setCursorRowAndColumn();
562 if (viewport.cursorMode)
564 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
568 if (viewport.cursorMode)
570 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
575 viewport.cursorMode = !viewport.cursorMode;
576 statusBar.setText(MessageManager.formatMessage(
577 "label.keyboard_editing_mode",
578 new String[] { (viewport.cursorMode ? "on" : "off") }));
579 if (viewport.cursorMode)
581 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
582 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
587 if (evt.isControlDown())
589 findMenuItem_actionPerformed();
595 boolean toggleSeqs = !evt.isControlDown();
596 boolean toggleCols = !evt.isShiftDown();
597 toggleHiddenRegions(toggleSeqs, toggleCols);
601 case KeyEvent.VK_PAGE_UP:
602 if (viewport.getWrapAlignment())
604 alignPanel.scrollUp(true);
608 alignPanel.setScrollValues(ranges.getStartRes(),
609 2 * ranges.getStartSeq() - ranges.getEndSeq());
613 case KeyEvent.VK_PAGE_DOWN:
614 if (viewport.getWrapAlignment())
616 alignPanel.scrollUp(false);
621 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
626 if (evt.isControlDown())
628 undoMenuItem_actionPerformed();
633 if (evt.isControlDown())
635 redoMenuItem_actionPerformed();
640 if (evt.isControlDown())
647 if (evt.isControlDown())
649 trimAlignment(false);
654 if (evt.isControlDown())
656 if (evt.isShiftDown())
658 this.removeAllGapsMenuItem_actionPerformed();
662 removeGappedColumnMenuItem_actionPerformed();
667 if (evt.isControlDown())
671 invertColSel_actionPerformed();
675 invertSequenceMenuItem_actionPerformed();
681 if (evt.isControlDown())
683 if (evt.isShiftDown())
685 this.unGroup_actionPerformed();
689 this.createGroup_actionPerformed();
695 if (evt.isControlDown())
697 this.deleteGroups_actionPerformed();
702 if (evt.isControlDown())
709 alignPanel.paintAlignment(true);
713 * called by key handler and the hide all/show all menu items
718 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
720 boolean hide = false;
721 SequenceGroup sg = viewport.getSelectionGroup();
722 if (!toggleSeqs && !toggleCols)
724 // Hide everything by the current selection - this is a hack - we do the
725 // invert and then hide
726 // first check that there will be visible columns after the invert.
727 if (viewport.hasSelectedColumns()
728 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
731 // now invert the sequence set, if required - empty selection implies
732 // that no hiding is required.
735 invertSequenceMenuItem_actionPerformed();
736 sg = viewport.getSelectionGroup();
740 viewport.expandColSelection(sg, true);
741 // finally invert the column selection and get the new sequence
742 // selection and indicate it should be hidden.
743 invertColSel_actionPerformed();
750 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
753 viewport.hideAllSelectedSeqs();
755 else if (!(toggleCols && viewport.hasSelectedColumns()))
757 viewport.showAllHiddenSeqs();
763 if (viewport.hasSelectedColumns())
765 viewport.hideSelectedColumns();
768 viewport.setSelectionGroup(sg);
773 viewport.showAllHiddenColumns();
775 viewport.sendSelection();
780 public void keyReleased(KeyEvent evt)
785 public void keyTyped(KeyEvent evt)
790 public void itemStateChanged(ItemEvent evt)
792 final Object source = evt.getSource();
793 if (source == displayNonconservedMenuItem)
795 displayNonconservedMenuItem_actionPerformed();
797 else if (source == colourTextMenuItem)
799 colourTextMenuItem_actionPerformed();
801 else if (source == wrapMenuItem)
803 wrapMenuItem_actionPerformed();
805 else if (source == scaleAbove)
807 viewport.setScaleAboveWrapped(scaleAbove.getState());
809 else if (source == scaleLeft)
811 viewport.setScaleLeftWrapped(scaleLeft.getState());
813 else if (source == scaleRight)
815 viewport.setScaleRightWrapped(scaleRight.getState());
817 else if (source == seqLimits)
819 seqLimits_itemStateChanged();
821 else if (source == viewBoxesMenuItem)
823 viewport.setShowBoxes(viewBoxesMenuItem.getState());
825 else if (source == viewTextMenuItem)
827 viewport.setShowText(viewTextMenuItem.getState());
829 else if (source == renderGapsMenuItem)
831 viewport.setRenderGaps(renderGapsMenuItem.getState());
833 else if (source == annotationPanelMenuItem)
835 boolean showAnnotations = annotationPanelMenuItem.getState();
836 showAlignmentAnnotations.setEnabled(showAnnotations);
837 showSequenceAnnotations.setEnabled(showAnnotations);
838 viewport.setShowAnnotation(showAnnotations);
839 alignPanel.setAnnotationVisible(showAnnotations);
841 else if (source == sequenceFeatures)
843 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
844 alignPanel.seqPanel.seqCanvas.repaint();
846 else if (source == showAlignmentAnnotations)
848 setAnnotationsVisibility();
850 else if (source == showSequenceAnnotations)
852 setAnnotationsVisibility();
854 else if (source == sortAnnBySequence)
856 boolean newState = sortAnnBySequence.getState();
857 sortAnnByLabel.setState(false);
858 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
859 : SequenceAnnotationOrder.NONE);
860 setViewportAnnotationOrder();
862 else if (source == sortAnnByLabel)
864 boolean newState = sortAnnByLabel.getState();
865 sortAnnBySequence.setState(false);
866 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
867 : SequenceAnnotationOrder.NONE);
868 setViewportAnnotationOrder();
870 else if (source == showAutoFirst)
872 showAutoLast.setState(!showAutoFirst.getState());
873 setShowAutoCalculatedAbove(showAutoFirst.getState());
874 setViewportAnnotationOrder();
876 else if (source == showAutoLast)
878 showAutoFirst.setState(!showAutoLast.getState());
879 setShowAutoCalculatedAbove(showAutoFirst.getState());
880 setViewportAnnotationOrder();
882 else if (source == conservationMenuItem)
884 conservationMenuItem_actionPerformed();
886 else if (source == abovePIDThreshold)
888 abovePIDThreshold_actionPerformed();
890 else if (source == applyToAllGroups)
892 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
894 else if (source == autoCalculate)
896 viewport.autoCalculateConsensus = autoCalculate.getState();
898 else if (source == sortByTree)
900 viewport.sortByTree = sortByTree.getState();
902 else if (source == this.centreColumnLabelFlag)
904 centreColumnLabelFlag_stateChanged();
906 else if (source == this.followMouseOverFlag)
908 mouseOverFlag_stateChanged();
910 else if (source == showGroupConsensus)
912 showGroupConsensus_actionPerformed();
914 else if (source == showGroupConservation)
916 showGroupConservation_actionPerformed();
918 else if (source == showSequenceLogo)
920 showSequenceLogo_actionPerformed();
922 else if (source == normSequenceLogo)
924 normSequenceLogo_actionPerformed();
926 else if (source == showConsensusHistogram)
928 showConsensusHistogram_actionPerformed();
930 else if (source == applyAutoAnnotationSettings)
932 applyAutoAnnotationSettings_actionPerformed();
934 alignPanel.paintAlignment(true);
938 * Set the visibility state of sequence-related and/or alignment-related
939 * annotations depending on checkbox selections, and repaint.
943 private void setAnnotationsVisibility()
945 boolean showForAlignment = showAlignmentAnnotations.getState();
946 boolean showForSequences = showSequenceAnnotations.getState();
947 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
949 for (AlignmentAnnotation aa : alignPanel.getAlignment()
950 .getAlignmentAnnotation())
952 boolean visible = (aa.sequenceRef == null ? showForAlignment
954 aa.visible = visible;
957 alignPanel.validateAnnotationDimensions(true);
962 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
964 this.annotationSortOrder = order;
968 * Set flags on the viewport that control annotation ordering
970 private void setViewportAnnotationOrder()
972 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
974 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
977 private void setShowAutoCalculatedAbove(boolean showAbove)
979 this.showAutoCalculatedAbove = showAbove;
982 private void mouseOverFlag_stateChanged()
984 viewport.setFollowHighlight(followMouseOverFlag.getState());
985 // TODO: could kick the scrollTo mechanism to reset view for current
989 private void centreColumnLabelFlag_stateChanged()
991 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
992 this.alignPanel.annotationPanel.repaint();
996 public void actionPerformed(ActionEvent evt)
998 viewport.applet.currentAlignFrame = this;
1000 Object source = evt.getSource();
1002 if (source == inputText)
1004 inputText_actionPerformed();
1006 else if (source == loadTree)
1008 loadTree_actionPerformed();
1010 else if (source == loadApplication)
1012 launchFullApplication();
1014 else if (source == loadAnnotations)
1018 else if (source == outputAnnotations)
1020 outputAnnotations(true);
1022 else if (source == outputFeatures)
1024 outputFeatures(true, "Jalview");
1026 else if (source == closeMenuItem)
1028 closeMenuItem_actionPerformed();
1030 else if (source == copy)
1032 copy_actionPerformed();
1034 else if (source == undoMenuItem)
1036 undoMenuItem_actionPerformed();
1038 else if (source == redoMenuItem)
1040 redoMenuItem_actionPerformed();
1042 else if (source == inputText)
1044 inputText_actionPerformed();
1046 else if (source == closeMenuItem)
1048 closeMenuItem_actionPerformed();
1050 else if (source == undoMenuItem)
1052 undoMenuItem_actionPerformed();
1054 else if (source == redoMenuItem)
1056 redoMenuItem_actionPerformed();
1058 else if (source == copy)
1060 copy_actionPerformed();
1062 else if (source == pasteNew)
1064 pasteNew_actionPerformed();
1066 else if (source == pasteThis)
1068 pasteThis_actionPerformed();
1070 else if (source == cut)
1072 cut_actionPerformed();
1074 else if (source == delete)
1076 delete_actionPerformed();
1078 else if (source == createGroup)
1080 createGroup_actionPerformed();
1082 else if (source == unGroup)
1084 unGroup_actionPerformed();
1086 else if (source == grpsFromSelection)
1088 makeGrpsFromSelection_actionPerformed();
1090 else if (source == deleteGroups)
1092 deleteGroups_actionPerformed();
1094 else if (source == selectAllSequenceMenuItem)
1096 selectAllSequenceMenuItem_actionPerformed();
1098 else if (source == deselectAllSequenceMenuItem)
1100 deselectAllSequenceMenuItem_actionPerformed();
1102 else if (source == invertSequenceMenuItem)
1104 invertSequenceMenuItem_actionPerformed();
1105 // uncomment to slave sequence selections in split frame
1106 // viewport.sendSelection();
1108 else if (source == invertColSel)
1110 viewport.invertColumnSelection();
1111 alignPanel.paintAlignment(true);
1112 viewport.sendSelection();
1114 else if (source == remove2LeftMenuItem)
1116 trimAlignment(true);
1118 else if (source == remove2RightMenuItem)
1120 trimAlignment(false);
1122 else if (source == removeGappedColumnMenuItem)
1124 removeGappedColumnMenuItem_actionPerformed();
1126 else if (source == removeAllGapsMenuItem)
1128 removeAllGapsMenuItem_actionPerformed();
1130 else if (source == findMenuItem)
1132 findMenuItem_actionPerformed();
1134 else if (source == font)
1136 new FontChooser(alignPanel);
1138 else if (source == newView)
1142 else if (source == showColumns)
1144 viewport.showAllHiddenColumns();
1145 alignPanel.paintAlignment(true);
1146 viewport.sendSelection();
1148 else if (source == showSeqs)
1150 viewport.showAllHiddenSeqs();
1151 alignPanel.paintAlignment(true);
1152 // uncomment if we want to slave sequence selections in split frame
1153 // viewport.sendSelection();
1155 else if (source == hideColumns)
1157 viewport.hideSelectedColumns();
1158 alignPanel.paintAlignment(true);
1159 viewport.sendSelection();
1161 else if (source == hideSequences
1162 && viewport.getSelectionGroup() != null)
1164 viewport.hideAllSelectedSeqs();
1165 alignPanel.paintAlignment(true);
1166 // uncomment if we want to slave sequence selections in split frame
1167 // viewport.sendSelection();
1169 else if (source == hideAllButSelection)
1171 toggleHiddenRegions(false, false);
1172 alignPanel.paintAlignment(true);
1173 viewport.sendSelection();
1175 else if (source == hideAllSelection)
1177 SequenceGroup sg = viewport.getSelectionGroup();
1178 viewport.expandColSelection(sg, false);
1179 viewport.hideAllSelectedSeqs();
1180 viewport.hideSelectedColumns();
1181 alignPanel.paintAlignment(true);
1182 viewport.sendSelection();
1184 else if (source == showAllHidden)
1186 viewport.showAllHiddenColumns();
1187 viewport.showAllHiddenSeqs();
1188 alignPanel.paintAlignment(true);
1189 viewport.sendSelection();
1191 else if (source == showGroupConsensus)
1193 showGroupConsensus_actionPerformed();
1195 else if (source == showGroupConservation)
1197 showGroupConservation_actionPerformed();
1199 else if (source == showSequenceLogo)
1201 showSequenceLogo_actionPerformed();
1203 else if (source == normSequenceLogo)
1205 normSequenceLogo_actionPerformed();
1207 else if (source == showConsensusHistogram)
1209 showConsensusHistogram_actionPerformed();
1211 else if (source == applyAutoAnnotationSettings)
1213 applyAutoAnnotationSettings_actionPerformed();
1215 else if (source == featureSettings)
1217 new FeatureSettings(alignPanel);
1219 else if (source == alProperties)
1221 StringBuffer contents = new jalview.io.AlignmentProperties(
1222 viewport.getAlignment()).formatAsString();
1223 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1224 cap.setText(contents.toString());
1225 Frame frame = new Frame();
1227 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1228 "label.alignment_properties", new String[] { getTitle() }),
1231 else if (source == overviewMenuItem)
1233 overviewMenuItem_actionPerformed();
1235 else if (source == noColourmenuItem)
1239 else if (source == clustalColour)
1241 abovePIDThreshold.setState(false);
1242 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1244 else if (source == zappoColour)
1246 changeColour(new ZappoColourScheme());
1248 else if (source == taylorColour)
1250 changeColour(new TaylorColourScheme());
1252 else if (source == hydrophobicityColour)
1254 changeColour(new HydrophobicColourScheme());
1256 else if (source == helixColour)
1258 changeColour(new HelixColourScheme());
1260 else if (source == strandColour)
1262 changeColour(new StrandColourScheme());
1264 else if (source == turnColour)
1266 changeColour(new TurnColourScheme());
1268 else if (source == buriedColour)
1270 changeColour(new BuriedColourScheme());
1272 else if (source == nucleotideColour)
1274 changeColour(new NucleotideColourScheme());
1276 else if (source == purinePyrimidineColour)
1278 changeColour(new PurinePyrimidineColourScheme());
1280 // else if (source == RNAInteractionColour)
1282 // changeColour(new RNAInteractionColourScheme());
1284 else if (source == RNAHelixColour)
1286 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1287 // new RNAHelicesColourChooser(viewport, alignPanel);
1289 else if (source == modifyPID)
1291 modifyPID_actionPerformed();
1293 else if (source == modifyConservation)
1295 modifyConservation_actionPerformed();
1297 else if (source == userDefinedColour)
1299 new UserDefinedColours(alignPanel, null);
1301 else if (source == PIDColour)
1303 changeColour(new PIDColourScheme());
1305 else if (source == BLOSUM62Colour)
1307 changeColour(new Blosum62ColourScheme());
1309 else if (source == tcoffeeColour)
1311 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1313 else if (source == annotationColour)
1315 new AnnotationColourChooser(viewport, alignPanel);
1317 else if (source == annotationColumnSelection)
1319 new AnnotationColumnChooser(viewport, alignPanel);
1321 else if (source == sortPairwiseMenuItem)
1323 sortPairwiseMenuItem_actionPerformed();
1325 else if (source == sortIDMenuItem)
1327 sortIDMenuItem_actionPerformed();
1329 else if (source == sortLengthMenuItem)
1331 sortLengthMenuItem_actionPerformed();
1333 else if (source == sortGroupMenuItem)
1335 sortGroupMenuItem_actionPerformed();
1337 else if (source == removeRedundancyMenuItem)
1339 removeRedundancyMenuItem_actionPerformed();
1341 else if (source == pairwiseAlignmentMenuItem)
1343 pairwiseAlignmentMenuItem_actionPerformed();
1345 else if (source == PCAMenuItem)
1347 PCAMenuItem_actionPerformed();
1349 else if (source == averageDistanceTreeMenuItem)
1351 averageDistanceTreeMenuItem_actionPerformed();
1353 else if (source == neighbourTreeMenuItem)
1355 neighbourTreeMenuItem_actionPerformed();
1357 else if (source == njTreeBlosumMenuItem)
1359 njTreeBlosumMenuItem_actionPerformed();
1361 else if (source == avDistanceTreeBlosumMenuItem)
1363 avTreeBlosumMenuItem_actionPerformed();
1365 else if (source == documentation)
1367 documentation_actionPerformed();
1369 else if (source == about)
1371 about_actionPerformed();
1376 public void inputText_actionPerformed()
1378 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1379 Frame frame = new Frame();
1381 jalview.bin.JalviewLite.addFrame(frame,
1382 MessageManager.getString("label.input_cut_paste"), 500, 500);
1385 protected void outputText_actionPerformed(ActionEvent e)
1387 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1388 Frame frame = new Frame();
1390 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1391 "label.alignment_output_command",
1392 new Object[] { e.getActionCommand() }), 600, 500);
1394 FileFormatI fileFormat = FileFormats.getInstance().forName(
1395 e.getActionCommand());
1396 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1397 fileFormat, viewport.getAlignment(),
1398 viewport.getShowJVSuffix()));
1401 public void loadAnnotations()
1403 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1404 cap.setText(MessageManager
1405 .getString("label.paste_features_annotations_Tcoffee_here"));
1406 cap.setAnnotationImport();
1407 Frame frame = new Frame();
1409 jalview.bin.JalviewLite.addFrame(frame,
1410 MessageManager.getString("action.paste_annotations"), 400, 300);
1414 public String outputAnnotations(boolean displayTextbox)
1416 String annotation = new AnnotationFile()
1417 .printAnnotationsForView(viewport);
1421 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1422 Frame frame = new Frame();
1424 jalview.bin.JalviewLite.addFrame(frame,
1425 MessageManager.getString("label.annotations"), 600, 500);
1426 cap.setText(annotation);
1432 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1434 if (alignPanel.getFeatureRenderer() != null
1435 && viewport.getFeaturesDisplayed() != null)
1437 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1443 public String outputFeatures(boolean displayTextbox, String format)
1446 FeaturesFile formatter = new FeaturesFile();
1447 if (format.equalsIgnoreCase("Jalview"))
1449 features = formatter.printJalviewFormat(viewport.getAlignment()
1450 .getSequencesArray(), getDisplayedFeatureCols());
1454 features = formatter.printGffFormat(viewport.getAlignment()
1455 .getSequencesArray(), getDisplayedFeatureCols());
1460 boolean frimport = false;
1461 if (features == null || features.equals("No Features Visible"))
1463 features = "# No features visible - paste some and import them here.";
1467 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1470 cap.setAnnotationImport();
1472 Frame frame = new Frame();
1474 jalview.bin.JalviewLite.addFrame(frame,
1475 MessageManager.getString("label.features"), 600, 500);
1476 cap.setText(features);
1480 if (features == null)
1489 void launchFullApplication()
1491 StringBuffer url = new StringBuffer(jalviewServletURL);
1493 // allow servlet parameters to be passed in applet parameter
1494 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1496 url.append(firstSep);
1499 + appendProtocol(viewport.applet.getParameter("file")));
1501 if (viewport.applet.getParameter("features") != null)
1503 url.append("&features=");
1504 url.append(appendProtocol(viewport.applet.getParameter("features")));
1507 if (viewport.applet.getParameter("annotations") != null)
1509 url.append("&annotations=");
1510 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1513 if (viewport.applet.getParameter("jnetfile") != null
1514 || viewport.applet.getParameter("jpredfile") != null)
1516 url.append("&annotations=");
1517 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1518 .getParameter("jnetfile") : viewport.applet
1519 .getParameter("jpredfile")));
1522 if (viewport.applet.getParameter("defaultColour") != null)
1524 url.append("&colour="
1525 + removeWhiteSpace(viewport.applet
1526 .getParameter("defaultColour")));
1529 if (viewport.applet.getParameter("userDefinedColour") != null)
1531 url.append("&colour="
1532 + removeWhiteSpace(viewport.applet
1533 .getParameter("userDefinedColour")));
1535 if (viewport.applet.getParameter("tree") != null)
1538 + appendProtocol(viewport.applet.getParameter("tree")));
1540 if (viewport.applet.getParameter("treeFile") != null)
1543 + appendProtocol(viewport.applet.getParameter("treeFile")));
1546 showURL(url.toString(), "FULL_APP");
1549 String removeWhiteSpace(String colour)
1551 StringBuffer sb = new StringBuffer();
1552 for (int i = 0; i < colour.length(); i++)
1554 if (Character.isWhitespace(colour.charAt(i)))
1560 sb.append(colour.charAt(i));
1564 return sb.toString();
1567 String appendProtocol(String url)
1572 url = URLEncoder.encode(url);
1575 * When we finally deprecate 1.1 compatibility, we can start to use
1576 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1577 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1578 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1579 * ex.printStackTrace(); }
1581 catch (java.net.MalformedURLException ex)
1583 url = viewport.applet.getCodeBase() + url;
1588 public void closeMenuItem_actionPerformed()
1590 PaintRefresher.RemoveComponent(alignPanel);
1591 if (alignPanel.seqPanel != null
1592 && alignPanel.seqPanel.seqCanvas != null)
1594 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1596 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1598 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1601 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1616 void updateEditMenuBar()
1619 if (viewport.getHistoryList().size() > 0)
1621 undoMenuItem.setEnabled(true);
1622 CommandI command = viewport.getHistoryList().peek();
1623 undoMenuItem.setLabel(MessageManager.formatMessage(
1624 "label.undo_command",
1625 new Object[] { command.getDescription() }));
1629 undoMenuItem.setEnabled(false);
1630 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1633 if (viewport.getRedoList().size() > 0)
1635 redoMenuItem.setEnabled(true);
1637 CommandI command = viewport.getRedoList().peek();
1638 redoMenuItem.setLabel(MessageManager.formatMessage(
1639 "label.redo_command",
1640 new Object[] { command.getDescription() }));
1644 redoMenuItem.setEnabled(false);
1645 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1653 public void addHistoryItem(CommandI command)
1655 if (command.getSize() > 0)
1657 viewport.addToHistoryList(command);
1658 viewport.clearRedoList();
1659 updateEditMenuBar();
1660 viewport.updateHiddenColumns();
1665 * TODO: JAL-1104 DOCUMENT ME!
1670 protected void undoMenuItem_actionPerformed()
1672 if (viewport.getHistoryList().isEmpty())
1677 CommandI command = viewport.getHistoryList().pop();
1678 viewport.addToRedoList(command);
1679 command.undoCommand(null);
1681 AlignmentViewport originalSource = getOriginatingSource(command);
1683 if (originalSource != viewport)
1686 .println("Warning: Viewport object mismatch whilst undoing");
1688 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1689 // viewport.getColumnSelection().getHiddenColumns()
1691 updateEditMenuBar();
1692 originalSource.firePropertyChange("alignment", null, originalSource
1693 .getAlignment().getSequences());
1697 * TODO: JAL-1104 DOCUMENT ME!
1702 protected void redoMenuItem_actionPerformed()
1704 if (viewport.getRedoList().isEmpty())
1709 CommandI command = viewport.getRedoList().pop();
1710 viewport.addToHistoryList(command);
1711 command.doCommand(null);
1713 AlignmentViewport originalSource = getOriginatingSource(command);
1715 if (originalSource != viewport)
1718 .println("Warning: Viewport object mismatch whilst re-doing");
1720 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1721 // viewport.getColumnSelection().getHiddenColumns()
1724 updateEditMenuBar();
1725 originalSource.firePropertyChange("alignment", null, originalSource
1726 .getAlignment().getSequences());
1729 AlignmentViewport getOriginatingSource(CommandI command)
1731 AlignmentViewport originalSource = null;
1732 // For sequence removal and addition, we need to fire
1733 // the property change event FROM the viewport where the
1734 // original alignment was altered
1735 AlignmentI al = null;
1736 if (command instanceof EditCommand)
1738 EditCommand editCommand = (EditCommand) command;
1739 al = editCommand.getAlignment();
1740 Vector comps = (Vector) PaintRefresher.components.get(viewport
1741 .getSequenceSetId());
1742 for (int i = 0; i < comps.size(); i++)
1744 if (comps.elementAt(i) instanceof AlignmentPanel)
1746 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1748 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1755 if (originalSource == null)
1757 // The original view is closed, we must validate
1758 // the current view against the closed view first
1761 PaintRefresher.validateSequences(al, viewport.getAlignment());
1764 originalSource = viewport;
1767 return originalSource;
1771 * Move the currently selected sequences up or down one position in the
1776 public void moveSelectedSequences(boolean up)
1778 SequenceGroup sg = viewport.getSelectionGroup();
1783 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1784 up ? null : viewport.getHiddenRepSequences(), up);
1785 alignPanel.paintAlignment(true);
1788 * Also move cDNA/protein complement sequences
1790 AlignViewportI complement = viewport.getCodingComplement();
1791 if (complement != null)
1793 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1794 viewport, complement);
1795 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1796 up ? null : complement.getHiddenRepSequences(), up);
1797 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1801 synchronized void slideSequences(boolean right, int size)
1803 List<SequenceI> sg = new Vector<SequenceI>();
1804 if (viewport.cursorMode)
1806 sg.add(viewport.getAlignment().getSequenceAt(
1807 alignPanel.seqPanel.seqCanvas.cursorY));
1809 else if (viewport.getSelectionGroup() != null
1810 && viewport.getSelectionGroup().getSize() != viewport
1811 .getAlignment().getHeight())
1813 sg = viewport.getSelectionGroup().getSequences(
1814 viewport.getHiddenRepSequences());
1822 Vector<SequenceI> invertGroup = new Vector();
1824 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1826 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1828 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1832 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1834 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1836 for (int i = 0; i < invertGroup.size(); i++)
1838 seqs2[i] = invertGroup.elementAt(i);
1841 SlideSequencesCommand ssc;
1844 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1845 size, viewport.getGapCharacter());
1849 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1850 size, viewport.getGapCharacter());
1853 int groupAdjustment = 0;
1854 if (ssc.getGapsInsertedBegin() && right)
1856 if (viewport.cursorMode)
1858 alignPanel.seqPanel.moveCursor(size, 0);
1862 groupAdjustment = size;
1865 else if (!ssc.getGapsInsertedBegin() && !right)
1867 if (viewport.cursorMode)
1869 alignPanel.seqPanel.moveCursor(-size, 0);
1873 groupAdjustment = -size;
1877 if (groupAdjustment != 0)
1879 viewport.getSelectionGroup().setStartRes(
1880 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1881 viewport.getSelectionGroup().setEndRes(
1882 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1885 boolean appendHistoryItem = false;
1886 Deque<CommandI> historyList = viewport.getHistoryList();
1887 if (historyList != null && historyList.size() > 0
1888 && historyList.peek() instanceof SlideSequencesCommand)
1890 appendHistoryItem = ssc
1891 .appendSlideCommand((SlideSequencesCommand) historyList
1895 if (!appendHistoryItem)
1897 addHistoryItem(ssc);
1903 static StringBuffer copiedSequences;
1905 static Vector copiedHiddenColumns;
1907 protected void copy_actionPerformed()
1909 if (viewport.getSelectionGroup() == null)
1914 SequenceGroup sg = viewport.getSelectionGroup();
1915 copiedSequences = new StringBuffer();
1916 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1917 for (int i = 0; i < sg.getSize(); i++)
1919 SequenceI seq = sg.getSequenceAt(i);
1920 int index = viewport.getAlignment().findIndex(seq);
1921 orderedSeqs.put(index, seq);
1924 int index = 0, startRes, endRes;
1927 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1929 copiedHiddenColumns = new Vector();
1930 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1931 for (int[] region : viewport.getAlignment().getHiddenColumns()
1932 .getHiddenRegions())
1934 copiedHiddenColumns.addElement(new int[] {
1935 region[0] - hiddenOffset, region[1] - hiddenOffset });
1940 copiedHiddenColumns = null;
1943 for (int i = 0; i < sg.getSize(); i++)
1945 SequenceI seq = null;
1949 if (orderedSeqs.containsKey(index))
1951 seq = orderedSeqs.get(index);
1962 // Returns residue following index if gap
1963 startRes = seq.findPosition(sg.getStartRes());
1966 // Need to find the residue preceeding index if gap
1969 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1971 ch = seq.getCharAt(j);
1972 if (!jalview.util.Comparison.isGap((ch)))
1980 endRes += seq.getStart() - 1;
1983 copiedSequences.append(seq.getName()
1989 + seq.getSequenceAsString(sg.getStartRes(),
1990 sg.getEndRes() + 1) + "\n");
1995 protected void pasteNew_actionPerformed()
2000 protected void pasteThis_actionPerformed()
2005 void paste(boolean newAlignment)
2010 if (copiedSequences == null)
2015 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2016 Vector seqs = new Vector();
2017 while (st.hasMoreElements())
2019 String name = st.nextToken();
2020 int start = Integer.parseInt(st.nextToken());
2021 int end = Integer.parseInt(st.nextToken());
2022 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2024 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2025 for (int i = 0; i < seqs.size(); i++)
2027 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2032 String newtitle = MessageManager
2033 .getString("label.copied_sequences");
2034 if (getTitle().startsWith(
2035 MessageManager.getString("label.copied_sequences")))
2037 newtitle = getTitle();
2041 newtitle = newtitle.concat(MessageManager.formatMessage(
2042 "label.from_msname", new String[] { getTitle() }));
2044 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2045 viewport.applet, newtitle, false);
2046 if (copiedHiddenColumns != null)
2048 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2050 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2051 af.viewport.hideColumns(region[0], region[1]);
2055 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2060 addSequences(newSeqs);
2063 } catch (Exception ex)
2065 } // could be anything being pasted in here
2069 void addSequences(SequenceI[] seqs)
2071 for (int i = 0; i < seqs.length; i++)
2073 viewport.getAlignment().addSequence(seqs[i]);
2077 addHistoryItem(new EditCommand(
2078 MessageManager.getString("label.add_sequences"), Action.PASTE,
2079 seqs, 0, viewport.getAlignment().getWidth(),
2080 viewport.getAlignment()));
2082 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2083 viewport.getAlignment().getWidth();
2084 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2089 protected void cut_actionPerformed()
2091 copy_actionPerformed();
2092 delete_actionPerformed();
2095 protected void delete_actionPerformed()
2098 SequenceGroup sg = viewport.getSelectionGroup();
2104 Vector seqs = new Vector();
2106 for (int i = 0; i < sg.getSize(); i++)
2108 seq = sg.getSequenceAt(i);
2109 seqs.addElement(seq);
2113 * If the cut affects all sequences, warn, remove highlighted columns
2115 if (sg.getSize() == viewport.getAlignment().getHeight())
2117 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2118 .getAlignment().getWidth()) ? true : false;
2119 if (isEntireAlignWidth)
2121 String title = MessageManager.getString("label.delete_all");
2122 Panel infoPanel = new Panel();
2123 infoPanel.setLayout(new FlowLayout());
2125 .add(new Label(MessageManager.getString("warn.delete_all")));
2127 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2128 dialog.setMainPanel(infoPanel);
2129 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2130 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2131 dialog.setVisible(true);
2138 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2139 sg.getEndRes() + 1);
2142 SequenceI[] cut = new SequenceI[seqs.size()];
2143 for (int i = 0; i < seqs.size(); i++)
2145 cut[i] = (SequenceI) seqs.elementAt(i);
2149 * //ADD HISTORY ITEM
2151 addHistoryItem(new EditCommand(
2152 MessageManager.getString("label.cut_sequences"), Action.CUT,
2153 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2154 viewport.getAlignment()));
2156 viewport.setSelectionGroup(null);
2157 viewport.getAlignment().deleteGroup(sg);
2159 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2162 if (viewport.getAlignment().getHeight() < 1)
2164 this.setVisible(false);
2166 viewport.sendSelection();
2170 * group consensus toggled
2173 protected void showGroupConsensus_actionPerformed()
2175 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2176 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 * group conservation toggled.
2183 protected void showGroupConservation_actionPerformed()
2185 viewport.setShowGroupConservation(showGroupConservation.getState());
2186 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2194 * .event.ActionEvent)
2196 protected void showConsensusHistogram_actionPerformed()
2198 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2199 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2206 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2207 * .event.ActionEvent)
2209 protected void showSequenceLogo_actionPerformed()
2211 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2212 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2215 protected void normSequenceLogo_actionPerformed()
2217 showSequenceLogo.setState(true);
2218 viewport.setShowSequenceLogo(true);
2219 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2220 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2223 protected void applyAutoAnnotationSettings_actionPerformed()
2225 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2228 protected void makeGrpsFromSelection_actionPerformed()
2230 if (avc.makeGroupsFromSelection())
2232 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2233 alignPanel.updateAnnotation();
2234 alignPanel.paintAlignment(true);
2238 protected void createGroup_actionPerformed()
2243 protected void unGroup_actionPerformed()
2247 alignPanel.alignmentChanged();
2251 protected void deleteGroups_actionPerformed()
2253 if (avc.deleteGroups())
2255 alignPanel.alignmentChanged();
2259 public void selectAllSequenceMenuItem_actionPerformed()
2261 SequenceGroup sg = new SequenceGroup();
2262 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2264 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2266 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2267 viewport.setSelectionGroup(sg);
2268 // JAL-2034 - should delegate to
2269 // alignPanel to decide if overview needs
2271 alignPanel.paintAlignment(false);
2272 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2273 viewport.sendSelection();
2276 public void deselectAllSequenceMenuItem_actionPerformed()
2278 if (viewport.cursorMode)
2280 alignPanel.seqPanel.keyboardNo1 = null;
2281 alignPanel.seqPanel.keyboardNo2 = null;
2283 viewport.setSelectionGroup(null);
2284 viewport.getColumnSelection().clear();
2285 viewport.setSelectionGroup(null);
2286 alignPanel.idPanel.idCanvas.searchResults = null;
2287 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2288 // JAL-2034 - should delegate to
2289 // alignPanel to decide if overview needs
2291 alignPanel.paintAlignment(false);
2292 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2293 viewport.sendSelection();
2296 public void invertSequenceMenuItem_actionPerformed()
2298 SequenceGroup sg = viewport.getSelectionGroup();
2299 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2301 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2304 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2305 viewport.sendSelection();
2308 public void invertColSel_actionPerformed()
2310 viewport.invertColumnSelection();
2311 alignPanel.paintAlignment(true);
2312 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2313 viewport.sendSelection();
2316 void trimAlignment(boolean trimLeft)
2318 AlignmentI al = viewport.getAlignment();
2319 ViewportRanges ranges = viewport.getRanges();
2320 ColumnSelection colSel = viewport.getColumnSelection();
2323 if (!colSel.isEmpty())
2327 column = colSel.getMin();
2331 column = colSel.getMax();
2335 if (viewport.getSelectionGroup() != null)
2337 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2338 viewport.getHiddenRepSequences());
2342 seqs = al.getSequencesArray();
2345 TrimRegionCommand trimRegion;
2348 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2350 ranges.setStartRes(0);
2354 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2358 statusBar.setText(MessageManager.formatMessage(
2359 "label.removed_columns",
2360 new String[] { Integer.valueOf(trimRegion.getSize())
2362 addHistoryItem(trimRegion);
2364 for (SequenceGroup sg : al.getGroups())
2366 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2367 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2373 viewport.firePropertyChange("alignment", null, al.getSequences());
2377 public void removeGappedColumnMenuItem_actionPerformed()
2379 AlignmentI al = viewport.getAlignment();
2380 ViewportRanges ranges = viewport.getRanges();
2382 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2385 if (viewport.getSelectionGroup() != null)
2387 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2388 viewport.getHiddenRepSequences());
2389 start = viewport.getSelectionGroup().getStartRes();
2390 end = viewport.getSelectionGroup().getEndRes();
2394 seqs = viewport.getAlignment().getSequencesArray();
2397 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2398 "Remove Gapped Columns", seqs, start, end,
2399 viewport.getAlignment());
2401 addHistoryItem(removeGapCols);
2403 statusBar.setText(MessageManager.formatMessage(
2404 "label.removed_empty_columns",
2405 new String[] { Integer.valueOf(removeGapCols.getSize())
2408 // This is to maintain viewport position on first residue
2409 // of first sequence
2410 SequenceI seq = al.getSequenceAt(0);
2411 int startRes = seq.findPosition(ranges.getStartRes());
2412 // ShiftList shifts;
2413 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2414 // edit.alColumnChanges=shifts.getInverse();
2415 // if (viewport.hasHiddenColumns)
2416 // viewport.getColumnSelection().compensateForEdits(shifts);
2417 ranges.setStartRes(seq.findIndex(startRes) - 1);
2418 viewport.firePropertyChange("alignment", null, al.getSequences());
2422 public void removeAllGapsMenuItem_actionPerformed()
2424 AlignmentI al = viewport.getAlignment();
2425 ViewportRanges ranges = viewport.getRanges();
2427 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2430 if (viewport.getSelectionGroup() != null)
2432 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2433 viewport.getHiddenRepSequences());
2434 start = viewport.getSelectionGroup().getStartRes();
2435 end = viewport.getSelectionGroup().getEndRes();
2439 seqs = viewport.getAlignment().getSequencesArray();
2442 // This is to maintain viewport position on first residue
2443 // of first sequence
2444 SequenceI seq = al.getSequenceAt(0);
2445 int startRes = seq.findPosition(ranges.getStartRes());
2447 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2450 ranges.setStartRes(seq.findIndex(startRes) - 1);
2452 viewport.firePropertyChange("alignment", null, al.getSequences());
2456 public void findMenuItem_actionPerformed()
2458 new Finder(alignPanel);
2462 * create a new view derived from the current view
2465 * @return frame for the new view
2467 public AlignFrame newView(String viewtitle)
2470 if (viewport.hasHiddenRows())
2472 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2473 .getFullAlignment().getSequencesArray());
2477 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2480 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2482 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2484 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2486 newal.addAnnotation(viewport.getAlignment()
2487 .getAlignmentAnnotation()[i]);
2492 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2494 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2495 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2496 PaintRefresher.Register(newaf.alignPanel,
2497 newaf.alignPanel.av.getSequenceSetId());
2499 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2500 newaf.alignPanel.av.getSequenceSetId());
2501 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2502 newaf.alignPanel.av.getSequenceSetId());
2504 Vector comps = (Vector) PaintRefresher.components.get(viewport
2505 .getSequenceSetId());
2507 for (int i = 0; i < comps.size(); i++)
2509 if (comps.elementAt(i) instanceof AlignmentPanel)
2515 String title = new String(this.getTitle());
2516 if (viewtitle != null)
2518 title = viewtitle + " ( " + title + ")";
2522 if (title.indexOf("(View") > -1)
2524 title = title.substring(0, title.indexOf("(View"));
2526 title += "(View " + viewSize + ")";
2529 newaf.setTitle(title.toString());
2531 newaf.viewport.setHistoryList(viewport.getHistoryList());
2532 newaf.viewport.setRedoList(viewport.getRedoList());
2538 * @return list of feature groups on the view
2540 public String[] getFeatureGroups()
2542 FeatureRenderer fr = null;
2543 if (alignPanel != null
2544 && (fr = alignPanel.getFeatureRenderer()) != null)
2546 List<String> gps = fr.getFeatureGroups();
2547 String[] _gps = gps.toArray(new String[gps.size()]);
2554 * get sequence feature groups that are hidden or shown
2560 public String[] getFeatureGroupsOfState(boolean visible)
2562 FeatureRenderer fr = null;
2563 if (alignPanel != null
2564 && (fr = alignPanel.getFeatureRenderer()) != null)
2566 List<String> gps = fr.getGroups(visible);
2567 String[] _gps = gps.toArray(new String[gps.size()]);
2574 * Change the display state for the given feature groups
2577 * list of group strings
2579 * visible or invisible
2581 public void setFeatureGroupState(String[] groups, boolean state)
2583 FeatureRenderer fr = null;
2584 this.sequenceFeatures.setState(true);
2585 viewport.setShowSequenceFeatures(true);
2586 if (alignPanel != null
2587 && (fr = alignPanel.getFeatureRenderer()) != null)
2590 fr.setGroupVisibility(Arrays.asList(groups), state);
2591 alignPanel.seqPanel.seqCanvas.repaint();
2592 if (alignPanel.overviewPanel != null)
2594 alignPanel.overviewPanel.updateOverviewImage();
2599 public void seqLimits_itemStateChanged()
2601 viewport.setShowJVSuffix(seqLimits.getState());
2602 alignPanel.fontChanged();
2603 alignPanel.paintAlignment(true);
2606 protected void colourTextMenuItem_actionPerformed()
2608 viewport.setColourText(colourTextMenuItem.getState());
2609 alignPanel.paintAlignment(true);
2612 protected void displayNonconservedMenuItem_actionPerformed()
2614 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2615 alignPanel.paintAlignment(true);
2618 protected void wrapMenuItem_actionPerformed()
2620 viewport.setWrapAlignment(wrapMenuItem.getState());
2621 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2622 scaleAbove.setEnabled(wrapMenuItem.getState());
2623 scaleLeft.setEnabled(wrapMenuItem.getState());
2624 scaleRight.setEnabled(wrapMenuItem.getState());
2625 alignPanel.paintAlignment(true);
2628 public void overviewMenuItem_actionPerformed()
2630 if (alignPanel.overviewPanel != null)
2635 Frame frame = new Frame();
2636 OverviewPanel overview = new OverviewPanel(alignPanel);
2637 frame.add(overview);
2638 // +50 must allow for applet frame window
2639 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2640 "label.overview_params", new String[] { this.getTitle() }),
2641 overview.getPreferredSize().width,
2642 overview.getPreferredSize().height + 50);
2645 final AlignmentPanel ap = alignPanel;
2646 frame.addWindowListener(new WindowAdapter()
2649 public void windowClosing(WindowEvent e)
2653 ap.setOverviewPanel(null);
2658 alignPanel.setOverviewPanel(overview);
2663 public void changeColour(ColourSchemeI cs)
2665 viewport.setGlobalColourScheme(cs);
2667 alignPanel.paintAlignment(true);
2670 protected void modifyPID_actionPerformed()
2672 if (viewport.getAbovePIDThreshold()
2673 && viewport.getGlobalColourScheme() != null)
2675 SliderPanel.setPIDSliderSource(alignPanel,
2676 viewport.getResidueShading(), alignPanel.getViewName());
2677 SliderPanel.showPIDSlider();
2681 protected void modifyConservation_actionPerformed()
2683 if (viewport.getConservationSelected()
2684 && viewport.getGlobalColourScheme() != null)
2686 SliderPanel.setConservationSlider(alignPanel,
2687 viewport.getResidueShading(), alignPanel.getViewName());
2688 SliderPanel.showConservationSlider();
2692 protected void conservationMenuItem_actionPerformed()
2694 boolean selected = conservationMenuItem.getState();
2695 modifyConservation.setEnabled(selected);
2696 viewport.setConservationSelected(selected);
2697 viewport.getResidueShading().setConservationApplied(selected);
2699 changeColour(viewport.getGlobalColourScheme());
2703 modifyConservation_actionPerformed();
2707 SliderPanel.hideConservationSlider();
2711 public void abovePIDThreshold_actionPerformed()
2713 boolean selected = abovePIDThreshold.getState();
2714 modifyPID.setEnabled(selected);
2715 viewport.setAbovePIDThreshold(selected);
2718 viewport.getResidueShading().setThreshold(0,
2719 viewport.isIgnoreGapsConsensus());
2722 changeColour(viewport.getGlobalColourScheme());
2726 modifyPID_actionPerformed();
2730 SliderPanel.hidePIDSlider();
2734 public void sortPairwiseMenuItem_actionPerformed()
2736 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2737 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2738 .getAlignment().getSequenceAt(0));
2740 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2741 viewport.getAlignment()));
2742 alignPanel.paintAlignment(true);
2745 public void sortIDMenuItem_actionPerformed()
2747 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2748 AlignmentSorter.sortByID(viewport.getAlignment());
2749 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2750 viewport.getAlignment()));
2751 alignPanel.paintAlignment(true);
2754 public void sortLengthMenuItem_actionPerformed()
2756 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2757 AlignmentSorter.sortByLength(viewport.getAlignment());
2758 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2759 viewport.getAlignment()));
2760 alignPanel.paintAlignment(true);
2763 public void sortGroupMenuItem_actionPerformed()
2765 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2766 AlignmentSorter.sortByGroup(viewport.getAlignment());
2767 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2768 viewport.getAlignment()));
2769 alignPanel.paintAlignment(true);
2773 public void removeRedundancyMenuItem_actionPerformed()
2775 new RedundancyPanel(alignPanel);
2778 public void pairwiseAlignmentMenuItem_actionPerformed()
2780 if (viewport.getSelectionGroup() != null
2781 && viewport.getSelectionGroup().getSize() > 1)
2783 Frame frame = new Frame();
2784 frame.add(new PairwiseAlignPanel(alignPanel));
2785 jalview.bin.JalviewLite.addFrame(frame,
2786 MessageManager.getString("action.pairwise_alignment"), 600,
2791 public void PCAMenuItem_actionPerformed()
2793 // are the sequences aligned?
2794 if (!viewport.getAlignment().isAligned(false))
2797 int Width = viewport.getAlignment().getWidth();
2799 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2801 current = viewport.getAlignment().getSequenceAt(i);
2803 if (current.getLength() < Width)
2805 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2808 alignPanel.paintAlignment(true);
2811 if ((viewport.getSelectionGroup() != null
2812 && viewport.getSelectionGroup().getSize() < 4 && viewport
2813 .getSelectionGroup().getSize() > 0)
2814 || viewport.getAlignment().getHeight() < 4)
2821 new PCAPanel(viewport);
2822 } catch (java.lang.OutOfMemoryError ex)
2828 public void averageDistanceTreeMenuItem_actionPerformed()
2830 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, new PIDModel().getName(),
2831 "Average distance tree using PID");
2834 public void neighbourTreeMenuItem_actionPerformed()
2836 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, new PIDModel().getName(),
2837 "Neighbour joining tree using PID");
2840 protected void njTreeBlosumMenuItem_actionPerformed()
2842 newTreePanel(TreeBuilder.NEIGHBOUR_JOINING, ScoreModels.getInstance()
2843 .getBlosum62().getName(),
2844 "Neighbour joining tree using BLOSUM62");
2847 protected void avTreeBlosumMenuItem_actionPerformed()
2849 newTreePanel(TreeBuilder.AVERAGE_DISTANCE, ScoreModels.getInstance()
2850 .getBlosum62().getName(),
2851 "Average distance tree using BLOSUM62");
2854 void newTreePanel(String type, String pwType, String title)
2856 // are the sequences aligned?
2857 if (!viewport.getAlignment().isAligned(false))
2860 int Width = viewport.getAlignment().getWidth();
2862 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2864 current = viewport.getAlignment().getSequenceAt(i);
2866 if (current.getLength() < Width)
2868 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2871 alignPanel.paintAlignment(true);
2875 if ((viewport.getSelectionGroup() != null && viewport
2876 .getSelectionGroup().getSize() > 1)
2877 || (viewport.getAlignment().getHeight() > 1))
2879 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2881 addTreeMenuItem(tp, title);
2883 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2887 void loadTree_actionPerformed()
2889 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2890 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2891 cap.setTreeImport();
2892 Frame frame = new Frame();
2894 jalview.bin.JalviewLite.addFrame(frame,
2895 MessageManager.getString("label.paste_newick_file"), 400, 300);
2898 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2900 TreePanel tp = new TreePanel(alignPanel, treeFile,
2901 MessageManager.getString("label.load_tree_from_file"), tree);
2902 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2903 addTreeMenuItem(tp, treeFile);
2907 * sort the alignment using the given treePanel
2910 * tree used to sort view
2912 * string used for undo event name
2914 public void sortByTree(TreePanel treePanel, String title)
2916 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2918 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2919 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2920 // HistoryItem.SORT));
2921 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2922 "label.order_by_params", new String[] { title }), oldOrder,
2923 viewport.getAlignment()));
2924 alignPanel.paintAlignment(true);
2928 * Do any automatic reordering of the alignment and add the necessary bits to
2929 * the menu structure for the new tree
2934 protected void addTreeMenuItem(final TreePanel treePanel,
2937 final MenuItem item = new MenuItem(title);
2938 sortByTreeMenu.add(item);
2939 item.addActionListener(new java.awt.event.ActionListener()
2942 public void actionPerformed(ActionEvent evt)
2944 sortByTree(treePanel, title); // treePanel.getTitle());
2948 treePanel.addWindowListener(new WindowAdapter()
2951 public void windowOpened(WindowEvent e)
2953 if (viewport.sortByTree)
2955 sortByTree(treePanel, title);
2957 super.windowOpened(e);
2961 public void windowClosing(WindowEvent e)
2963 sortByTreeMenu.remove(item);
2968 public boolean sortBy(AlignmentOrder alorder, String undoname)
2970 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2971 if (viewport.applet.debug)
2973 System.err.println("Sorting " + alorder.getOrder().size()
2974 + " in alignment '" + getTitle() + "'");
2976 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2977 if (undoname != null)
2979 addHistoryItem(new OrderCommand(undoname, oldOrder,
2980 viewport.getAlignment()));
2982 alignPanel.paintAlignment(true);
2986 protected void documentation_actionPerformed()
2988 alignPanel.av.applet.openJalviewHelpUrl();
2991 protected void about_actionPerformed()
2994 class AboutPanel extends Canvas
3000 public AboutPanel(String version, String builddate)
3002 this.version = version;
3003 this.builddate = builddate;
3007 public void paint(Graphics g)
3009 g.setColor(Color.white);
3010 g.fillRect(0, 0, getSize().width, getSize().height);
3011 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3012 FontMetrics fm = g.getFontMetrics();
3013 int fh = fm.getHeight();
3015 g.setColor(Color.black);
3016 // TODO: update this text for each release or centrally store it for
3017 // lite and application
3018 g.setFont(new Font("Helvetica", Font.BOLD, 14));
3019 g.drawString(MessageManager.formatMessage(
3020 "label.jalviewLite_release", new String[] { version }), x,
3022 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3023 g.drawString(MessageManager.formatMessage(
3024 "label.jaview_build_date", new String[] { builddate }), x,
3026 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3027 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3029 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3030 x + 50, y += fh + 8);
3032 MessageManager.getString("label.jalview_dev_managers"), x,
3034 g.drawString(MessageManager
3035 .getString("label.jalview_distribution_lists"), x, y += fh);
3036 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3039 MessageManager.getString("label.jalview_cite_1_authors"),
3042 MessageManager.getString("label.jalview_cite_1_title"), x,
3044 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3049 Frame frame = new Frame();
3050 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3052 jalview.bin.JalviewLite.addFrame(frame,
3053 MessageManager.getString("label.jalview"), 580, 220);
3057 public void showURL(String url, String target)
3059 if (viewport.applet == null)
3061 System.out.println("Not running as applet - no browser available.");
3065 viewport.applet.showURL(url, target);
3069 // ////////////////////////////////////////////////////////////////////////////////
3070 // JBuilder Graphics here
3072 MenuBar alignFrameMenuBar = new MenuBar();
3074 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3076 MenuItem loadApplication = new MenuItem(
3077 MessageManager.getString("label.view_full_application"));
3079 MenuItem loadTree = new MenuItem(
3080 MessageManager.getString("label.load_associated_tree"));
3082 MenuItem loadAnnotations = new MenuItem(
3083 MessageManager.getString("label.load_features_annotations"));
3085 MenuItem outputFeatures = new MenuItem(
3086 MessageManager.getString("label.export_features"));
3088 MenuItem outputAnnotations = new MenuItem(
3089 MessageManager.getString("label.export_annotations"));
3091 MenuItem closeMenuItem = new MenuItem(
3092 MessageManager.getString("action.close"));
3094 MenuItem selectAllSequenceMenuItem = new MenuItem(
3095 MessageManager.getString("action.select_all"));
3097 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3098 MessageManager.getString("action.deselect_all"));
3100 MenuItem invertSequenceMenuItem = new MenuItem(
3101 MessageManager.getString("action.invert_selection"));
3103 MenuItem remove2LeftMenuItem = new MenuItem();
3105 MenuItem remove2RightMenuItem = new MenuItem();
3107 MenuItem removeGappedColumnMenuItem = new MenuItem();
3109 MenuItem removeAllGapsMenuItem = new MenuItem();
3111 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3113 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3115 MenuItem sortPairwiseMenuItem = new MenuItem();
3117 MenuItem sortIDMenuItem = new MenuItem();
3119 MenuItem sortLengthMenuItem = new MenuItem();
3121 MenuItem sortGroupMenuItem = new MenuItem();
3123 MenuItem removeRedundancyMenuItem = new MenuItem();
3125 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3127 MenuItem PCAMenuItem = new MenuItem();
3129 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3131 MenuItem neighbourTreeMenuItem = new MenuItem();
3133 BorderLayout borderLayout1 = new BorderLayout();
3135 public Label statusBar = new Label();
3137 MenuItem clustalColour = new MenuItem();
3139 MenuItem zappoColour = new MenuItem();
3141 MenuItem taylorColour = new MenuItem();
3143 MenuItem hydrophobicityColour = new MenuItem();
3145 MenuItem helixColour = new MenuItem();
3147 MenuItem strandColour = new MenuItem();
3149 MenuItem turnColour = new MenuItem();
3151 MenuItem buriedColour = new MenuItem();
3153 MenuItem purinePyrimidineColour = new MenuItem();
3155 // MenuItem RNAInteractionColour = new MenuItem();
3157 MenuItem RNAHelixColour = new MenuItem();
3159 MenuItem userDefinedColour = new MenuItem();
3161 MenuItem PIDColour = new MenuItem();
3163 MenuItem BLOSUM62Colour = new MenuItem();
3165 MenuItem tcoffeeColour = new MenuItem();
3167 MenuItem njTreeBlosumMenuItem = new MenuItem();
3169 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3171 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3173 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3175 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3177 MenuItem alProperties = new MenuItem(
3178 MessageManager.getString("label.alignment_props"));
3180 MenuItem overviewMenuItem = new MenuItem();
3182 MenuItem undoMenuItem = new MenuItem();
3184 MenuItem redoMenuItem = new MenuItem();
3186 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3188 MenuItem noColourmenuItem = new MenuItem();
3190 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3192 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3194 MenuItem findMenuItem = new MenuItem();
3196 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3198 MenuItem nucleotideColour = new MenuItem();
3200 MenuItem deleteGroups = new MenuItem();
3202 MenuItem grpsFromSelection = new MenuItem();
3204 MenuItem createGroup = new MenuItem();
3206 MenuItem unGroup = new MenuItem();
3208 MenuItem delete = new MenuItem();
3210 MenuItem copy = new MenuItem();
3212 MenuItem cut = new MenuItem();
3214 Menu pasteMenu = new Menu();
3216 MenuItem pasteNew = new MenuItem();
3218 MenuItem pasteThis = new MenuItem();
3220 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3222 MenuItem font = new MenuItem();
3224 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3226 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3228 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3230 MenuItem modifyPID = new MenuItem();
3232 MenuItem modifyConservation = new MenuItem();
3234 CheckboxMenuItem autoCalculate = null;
3236 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3237 "Sort Alignment With New Tree", true);
3239 Menu sortByTreeMenu = new Menu();
3241 MenuItem inputText = new MenuItem();
3243 MenuItem documentation = new MenuItem();
3245 MenuItem about = new MenuItem();
3247 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3249 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3251 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3253 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3255 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3257 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3259 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3261 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3263 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3266 * Initialise menus and other items
3270 private void jbInit() throws Exception
3272 setMenuBar(alignFrameMenuBar);
3275 * Configure File menu items and actions
3278 .setLabel(MessageManager.getString("label.input_from_textbox"));
3279 inputText.addActionListener(this);
3280 Menu outputTextboxMenu = new Menu(
3281 MessageManager.getString("label.out_to_textbox"));
3282 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3284 MenuItem item = new MenuItem(ff);
3286 item.addActionListener(new java.awt.event.ActionListener()
3289 public void actionPerformed(ActionEvent e)
3291 outputText_actionPerformed(e);
3295 outputTextboxMenu.add(item);
3297 closeMenuItem.addActionListener(this);
3298 loadApplication.addActionListener(this);
3299 loadTree.addActionListener(this);
3300 loadAnnotations.addActionListener(this);
3301 outputFeatures.addActionListener(this);
3302 outputAnnotations.addActionListener(this);
3305 * Configure Edit menu items and actions
3307 undoMenuItem.setEnabled(false);
3308 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3309 undoMenuItem.addActionListener(this);
3310 redoMenuItem.setEnabled(false);
3311 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3312 redoMenuItem.addActionListener(this);
3313 copy.setLabel(MessageManager.getString("action.copy"));
3314 copy.addActionListener(this);
3315 cut.setLabel(MessageManager.getString("action.cut"));
3316 cut.addActionListener(this);
3317 delete.setLabel(MessageManager.getString("action.delete"));
3318 delete.addActionListener(this);
3319 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3320 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3321 pasteNew.addActionListener(this);
3322 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3323 pasteThis.addActionListener(this);
3324 remove2LeftMenuItem.setLabel(MessageManager
3325 .getString("action.remove_left"));
3326 remove2LeftMenuItem.addActionListener(this);
3327 remove2RightMenuItem.setLabel(MessageManager
3328 .getString("action.remove_right"));
3329 remove2RightMenuItem.addActionListener(this);
3330 removeGappedColumnMenuItem.setLabel(MessageManager
3331 .getString("action.remove_empty_columns"));
3332 removeGappedColumnMenuItem.addActionListener(this);
3333 removeAllGapsMenuItem.setLabel(MessageManager
3334 .getString("action.remove_all_gaps"));
3335 removeAllGapsMenuItem.addActionListener(this);
3336 removeRedundancyMenuItem.setLabel(MessageManager
3337 .getString("action.remove_redundancy"));
3338 removeRedundancyMenuItem.addActionListener(this);
3341 * Configure Select menu items and actions
3343 findMenuItem.setLabel(MessageManager.getString("action.find"));
3344 findMenuItem.addActionListener(this);
3345 selectAllSequenceMenuItem.addActionListener(this);
3346 deselectAllSequenceMenuItem.addActionListener(this);
3347 invertSequenceMenuItem.setLabel(MessageManager
3348 .getString("action.invert_sequence_selection"));
3349 invertSequenceMenuItem.addActionListener(this);
3350 invertColSel.setLabel(MessageManager
3351 .getString("action.invert_column_selection"));
3352 invertColSel.addActionListener(this);
3353 deleteGroups.setLabel(MessageManager
3354 .getString("action.undefine_groups"));
3355 deleteGroups.addActionListener(this);
3356 grpsFromSelection.setLabel(MessageManager
3357 .getString("action.make_groups_selection"));
3358 grpsFromSelection.addActionListener(this);
3359 createGroup.setLabel(MessageManager.getString("action.create_group"));
3360 createGroup.addActionListener(this);
3361 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3362 unGroup.addActionListener(this);
3364 annotationColumnSelection.setLabel(MessageManager
3365 .getString("action.select_by_annotation"));
3366 annotationColumnSelection.addActionListener(this);
3369 * Configure View menu items and actions
3371 newView.setLabel(MessageManager.getString("action.new_view"));
3372 newView.addActionListener(this);
3373 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3374 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3375 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3376 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3378 .setLabel(MessageManager.getString("label.selected_columns"));
3379 hideSequences.setLabel(MessageManager
3380 .getString("label.selected_sequences"));
3381 hideAllButSelection.setLabel(MessageManager
3382 .getString("label.all_but_selected_region"));
3383 hideAllSelection.setLabel(MessageManager
3384 .getString("label.selected_region"));
3385 showAllHidden.setLabel(MessageManager
3386 .getString("label.all_sequences_columns"));
3387 showColumns.addActionListener(this);
3388 showSeqs.addActionListener(this);
3389 hideColumns.addActionListener(this);
3390 hideSequences.addActionListener(this);
3391 hideAllButSelection.addActionListener(this);
3392 hideAllSelection.addActionListener(this);
3393 showAllHidden.addActionListener(this);
3394 featureSettings.setLabel(MessageManager
3395 .getString("action.feature_settings"));
3396 featureSettings.addActionListener(this);
3397 sequenceFeatures.setLabel(MessageManager
3398 .getString("label.show_sequence_features"));
3399 sequenceFeatures.addItemListener(this);
3400 sequenceFeatures.setState(false);
3401 followMouseOverFlag.setLabel(MessageManager
3402 .getString("label.automatic_scrolling"));
3403 followMouseOverFlag.addItemListener(this);
3404 alProperties.addActionListener(this);
3405 overviewMenuItem.setLabel(MessageManager
3406 .getString("label.overview_window"));
3407 overviewMenuItem.addActionListener(this);
3410 * Configure Annotations menu items and actions
3412 annotationPanelMenuItem.setLabel(MessageManager
3413 .getString("label.show_annotations"));
3414 annotationPanelMenuItem.addItemListener(this);
3415 showGroupConsensus.setLabel(MessageManager
3416 .getString("label.group_consensus"));
3417 showGroupConservation.setLabel(MessageManager
3418 .getString("label.group_conservation"));
3419 showConsensusHistogram.setLabel(MessageManager
3420 .getString("label.show_consensus_histogram"));
3421 showSequenceLogo.setLabel(MessageManager
3422 .getString("label.show_consensus_logo"));
3423 normSequenceLogo.setLabel(MessageManager
3424 .getString("label.norm_consensus_logo"));
3425 applyAutoAnnotationSettings.setLabel(MessageManager
3426 .getString("label.apply_all_groups"));
3427 applyAutoAnnotationSettings.setState(true);
3428 Menu autoAnnMenu = new Menu(
3429 MessageManager.getString("label.autocalculated_annotation"));
3430 showGroupConsensus.addItemListener(this);
3431 showGroupConservation.addItemListener(this);
3432 showConsensusHistogram.addItemListener(this);
3433 showSequenceLogo.addItemListener(this);
3434 normSequenceLogo.addItemListener(this);
3435 applyAutoAnnotationSettings.addItemListener(this);
3436 showAlignmentAnnotations = new CheckboxMenuItem(
3437 MessageManager.getString("label.show_all_al_annotations"));
3438 showSequenceAnnotations = new CheckboxMenuItem(
3439 MessageManager.getString("label.show_all_seq_annotations"));
3440 sortAnnBySequence = new CheckboxMenuItem(
3441 MessageManager.getString("label.sort_annotations_by_sequence"));
3442 sortAnnByLabel = new CheckboxMenuItem(
3443 MessageManager.getString("label.sort_annotations_by_label"));
3444 showAutoFirst = new CheckboxMenuItem(
3445 MessageManager.getString("label.show_first"));
3446 showAutoFirst.setState(false); // pending applet parameter
3447 setShowAutoCalculatedAbove(showAutoFirst.getState());
3448 showAutoLast = new CheckboxMenuItem(
3449 MessageManager.getString("label.show_last"));
3450 showAutoLast.setState(!showAutoFirst.getState());
3451 showAlignmentAnnotations.addItemListener(this);
3452 showSequenceAnnotations.addItemListener(this);
3453 sortAnnBySequence.addItemListener(this);
3454 sortAnnByLabel.addItemListener(this);
3455 showAutoFirst.addItemListener(this);
3456 showAutoLast.addItemListener(this);
3459 * Configure Format menu items and actions
3461 font.setLabel(MessageManager.getString("action.font"));
3462 font.addActionListener(this);
3463 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3464 scaleAbove.setState(true);
3465 scaleAbove.setEnabled(false);
3466 scaleAbove.addItemListener(this);
3467 scaleLeft.setEnabled(false);
3468 scaleLeft.setState(true);
3469 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3470 scaleLeft.addItemListener(this);
3471 scaleRight.setEnabled(false);
3472 scaleRight.setState(true);
3473 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3474 scaleRight.addItemListener(this);
3475 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3476 viewBoxesMenuItem.setState(true);
3477 viewBoxesMenuItem.addItemListener(this);
3478 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3479 viewTextMenuItem.setState(true);
3480 viewTextMenuItem.addItemListener(this);
3481 colourTextMenuItem.setLabel(MessageManager
3482 .getString("label.colour_text"));
3483 colourTextMenuItem.addItemListener(this);
3484 displayNonconservedMenuItem.setLabel(MessageManager
3485 .getString("label.show_non_conserved"));
3486 displayNonconservedMenuItem.addItemListener(this);
3487 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3488 wrapMenuItem.addItemListener(this);
3489 renderGapsMenuItem.setLabel(MessageManager
3490 .getString("action.show_gaps"));
3491 renderGapsMenuItem.setState(true);
3492 renderGapsMenuItem.addItemListener(this);
3493 centreColumnLabelFlag.setLabel(MessageManager
3494 .getString("label.centre_column_labels"));
3495 centreColumnLabelFlag.addItemListener(this);
3496 seqLimits.setState(true);
3497 seqLimits.setLabel(MessageManager
3498 .getString("label.show_sequence_limits"));
3499 seqLimits.addItemListener(this);
3502 * Configure Colour menu items and actions
3504 applyToAllGroups.setLabel(MessageManager
3505 .getString("label.apply_colour_to_all_groups"));
3506 applyToAllGroups.setState(true);
3507 applyToAllGroups.addItemListener(this);
3508 clustalColour.setLabel(MessageManager
3509 .getString("label.colourScheme_clustal"));
3510 clustalColour.addActionListener(this);
3511 zappoColour.setLabel(MessageManager
3512 .getString("label.colourScheme_zappo"));
3513 zappoColour.addActionListener(this);
3514 taylorColour.setLabel(MessageManager
3515 .getString("label.colourScheme_taylor"));
3516 taylorColour.addActionListener(this);
3517 hydrophobicityColour.setLabel(MessageManager
3518 .getString("label.colourScheme_hydrophobic"));
3519 hydrophobicityColour.addActionListener(this);
3520 helixColour.setLabel(MessageManager
3521 .getString("label.colourScheme_helix_propensity"));
3522 helixColour.addActionListener(this);
3523 strandColour.setLabel(MessageManager
3524 .getString("label.colourScheme_strand_propensity"));
3525 strandColour.addActionListener(this);
3526 turnColour.setLabel(MessageManager
3527 .getString("label.colourScheme_turn_propensity"));
3528 turnColour.addActionListener(this);
3529 buriedColour.setLabel(MessageManager
3530 .getString("label.colourScheme_buried_index"));
3531 buriedColour.addActionListener(this);
3532 purinePyrimidineColour.setLabel(MessageManager
3533 .getString("label.colourScheme_purine/pyrimidine"));
3534 purinePyrimidineColour.addActionListener(this);
3535 // RNAInteractionColour.setLabel(MessageManager
3536 // .getString("label.rna_interaction"));
3537 // RNAInteractionColour.addActionListener(this);
3538 RNAHelixColour.setLabel(MessageManager
3539 .getString("label.colourScheme_rna_helices"));
3540 RNAHelixColour.addActionListener(this);
3541 userDefinedColour.setLabel(MessageManager
3542 .getString("action.user_defined"));
3543 userDefinedColour.addActionListener(this);
3544 PIDColour.setLabel(MessageManager
3545 .getString("label.colourScheme_%_identity"));
3546 PIDColour.addActionListener(this);
3547 BLOSUM62Colour.setLabel(MessageManager
3548 .getString("label.colourScheme_blosum62"));
3549 BLOSUM62Colour.addActionListener(this);
3550 tcoffeeColour.setLabel(MessageManager
3551 .getString("label.colourScheme_t-coffee_scores"));
3552 // it will be enabled only if a score file is provided
3553 tcoffeeColour.setEnabled(false);
3554 tcoffeeColour.addActionListener(this);
3555 conservationMenuItem.setLabel(MessageManager
3556 .getString("action.by_conservation"));
3557 conservationMenuItem.addItemListener(this);
3558 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3559 noColourmenuItem.addActionListener(this);
3560 abovePIDThreshold.setLabel(MessageManager
3561 .getString("label.above_identity_threshold"));
3562 abovePIDThreshold.addItemListener(this);
3563 nucleotideColour.setLabel(MessageManager
3564 .getString("label.colourScheme_nucleotide"));
3565 nucleotideColour.addActionListener(this);
3566 modifyPID.setLabel(MessageManager
3567 .getString("label.modify_identity_threshold"));
3568 modifyPID.setEnabled(abovePIDThreshold.getState());
3569 modifyPID.addActionListener(this);
3570 modifyConservation.setLabel(MessageManager
3571 .getString("label.modify_conservation_threshold"));
3572 modifyConservation.setEnabled(conservationMenuItem.getState());
3573 modifyConservation.addActionListener(this);
3574 annotationColour.setLabel(MessageManager
3575 .getString("action.by_annotation"));
3576 annotationColour.addActionListener(this);
3579 * Configure Calculate menu items and actions
3581 sortPairwiseMenuItem.setLabel(MessageManager
3582 .getString("action.by_pairwise_id"));
3583 sortPairwiseMenuItem.addActionListener(this);
3584 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3585 sortIDMenuItem.addActionListener(this);
3586 sortLengthMenuItem.setLabel(MessageManager
3587 .getString("action.by_length"));
3588 sortLengthMenuItem.addActionListener(this);
3589 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3590 sortGroupMenuItem.addActionListener(this);
3591 pairwiseAlignmentMenuItem.setLabel(MessageManager
3592 .getString("action.pairwise_alignment"));
3593 pairwiseAlignmentMenuItem.addActionListener(this);
3594 PCAMenuItem.setLabel(MessageManager
3595 .getString("label.principal_component_analysis"));
3596 PCAMenuItem.addActionListener(this);
3597 autoCalculate = new CheckboxMenuItem(
3598 MessageManager.getString("label.autocalculate_consensus"), true);
3599 averageDistanceTreeMenuItem.setLabel(MessageManager
3600 .getString("label.average_distance_identity"));
3601 averageDistanceTreeMenuItem.addActionListener(this);
3602 neighbourTreeMenuItem.setLabel(MessageManager
3603 .getString("label.neighbour_joining_identity"));
3604 neighbourTreeMenuItem.addActionListener(this);
3605 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3606 .getString("label.average_distance_blosum62"));
3607 avDistanceTreeBlosumMenuItem.addActionListener(this);
3608 njTreeBlosumMenuItem.setLabel(MessageManager
3609 .getString("label.neighbour_blosum62"));
3610 njTreeBlosumMenuItem.addActionListener(this);
3611 sortByTreeMenu.setLabel(MessageManager
3612 .getString("action.by_tree_order"));
3613 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3614 Menu calculateTreeMenu = new Menu(
3615 MessageManager.getString("action.calculate_tree"));
3616 autoCalculate.addItemListener(this);
3617 sortByTree.addItemListener(this);
3620 * Configure Help menu items and actions
3622 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3623 documentation.setLabel(MessageManager.getString("label.documentation"));
3624 documentation.addActionListener(this);
3625 about.setLabel(MessageManager.getString("label.about"));
3626 about.addActionListener(this);
3629 * Add top level menus to frame
3631 alignFrameMenuBar.add(fileMenu);
3632 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3633 alignFrameMenuBar.add(editMenu);
3634 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3635 alignFrameMenuBar.add(selectMenu);
3636 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3637 alignFrameMenuBar.add(viewMenu);
3638 Menu annotationsMenu = new Menu(
3639 MessageManager.getString("action.annotations"));
3640 alignFrameMenuBar.add(annotationsMenu);
3641 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3642 alignFrameMenuBar.add(formatMenu);
3643 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3644 alignFrameMenuBar.add(colourMenu);
3645 Menu calculateMenu = new Menu(
3646 MessageManager.getString("action.calculate"));
3647 alignFrameMenuBar.add(calculateMenu);
3648 alignFrameMenuBar.add(helpMenu);
3653 fileMenu.add(inputText);
3654 fileMenu.add(loadTree);
3655 fileMenu.add(loadAnnotations);
3656 fileMenu.addSeparator();
3657 fileMenu.add(outputTextboxMenu);
3658 fileMenu.add(outputFeatures);
3659 fileMenu.add(outputAnnotations);
3660 if (jalviewServletURL != null)
3662 fileMenu.add(loadApplication);
3664 fileMenu.addSeparator();
3665 fileMenu.add(closeMenuItem);
3670 editMenu.add(undoMenuItem);
3671 editMenu.add(redoMenuItem);
3674 pasteMenu.add(pasteNew);
3675 pasteMenu.add(pasteThis);
3676 editMenu.add(pasteMenu);
3677 editMenu.add(delete);
3678 editMenu.addSeparator();
3679 editMenu.add(remove2LeftMenuItem);
3680 editMenu.add(remove2RightMenuItem);
3681 editMenu.add(removeGappedColumnMenuItem);
3682 editMenu.add(removeAllGapsMenuItem);
3683 editMenu.add(removeRedundancyMenuItem);
3688 selectMenu.add(findMenuItem);
3689 selectMenu.addSeparator();
3690 selectMenu.add(selectAllSequenceMenuItem);
3691 selectMenu.add(deselectAllSequenceMenuItem);
3692 selectMenu.add(invertSequenceMenuItem);
3693 selectMenu.add(invertColSel);
3694 selectMenu.add(createGroup);
3695 selectMenu.add(unGroup);
3696 selectMenu.add(grpsFromSelection);
3697 selectMenu.add(deleteGroups);
3698 selectMenu.add(annotationColumnSelection);
3703 viewMenu.add(newView);
3704 viewMenu.addSeparator();
3705 showMenu.add(showColumns);
3706 showMenu.add(showSeqs);
3707 showMenu.add(showAllHidden);
3708 viewMenu.add(showMenu);
3709 hideMenu.add(hideColumns);
3710 hideMenu.add(hideSequences);
3711 hideMenu.add(hideAllSelection);
3712 hideMenu.add(hideAllButSelection);
3713 viewMenu.add(hideMenu);
3714 viewMenu.addSeparator();
3715 viewMenu.add(followMouseOverFlag);
3716 viewMenu.addSeparator();
3717 viewMenu.add(sequenceFeatures);
3718 viewMenu.add(featureSettings);
3719 viewMenu.addSeparator();
3720 viewMenu.add(alProperties);
3721 viewMenu.addSeparator();
3722 viewMenu.add(overviewMenuItem);
3727 annotationsMenu.add(annotationPanelMenuItem);
3728 annotationsMenu.addSeparator();
3729 annotationsMenu.add(showAlignmentAnnotations);
3730 annotationsMenu.add(showSequenceAnnotations);
3731 annotationsMenu.add(sortAnnBySequence);
3732 annotationsMenu.add(sortAnnByLabel);
3733 annotationsMenu.addSeparator();
3734 autoAnnMenu.add(showAutoFirst);
3735 autoAnnMenu.add(showAutoLast);
3736 autoAnnMenu.addSeparator();
3737 autoAnnMenu.add(applyAutoAnnotationSettings);
3738 autoAnnMenu.add(showConsensusHistogram);
3739 autoAnnMenu.add(showSequenceLogo);
3740 autoAnnMenu.add(normSequenceLogo);
3741 autoAnnMenu.addSeparator();
3742 autoAnnMenu.add(showGroupConservation);
3743 autoAnnMenu.add(showGroupConsensus);
3744 annotationsMenu.add(autoAnnMenu);
3749 formatMenu.add(font);
3750 formatMenu.add(seqLimits);
3751 formatMenu.add(wrapMenuItem);
3752 formatMenu.add(scaleAbove);
3753 formatMenu.add(scaleLeft);
3754 formatMenu.add(scaleRight);
3755 formatMenu.add(viewBoxesMenuItem);
3756 formatMenu.add(viewTextMenuItem);
3757 formatMenu.add(colourTextMenuItem);
3758 formatMenu.add(displayNonconservedMenuItem);
3759 formatMenu.add(renderGapsMenuItem);
3760 formatMenu.add(centreColumnLabelFlag);
3765 colourMenu.add(applyToAllGroups);
3766 colourMenu.addSeparator();
3767 colourMenu.add(noColourmenuItem);
3768 colourMenu.add(clustalColour);
3769 colourMenu.add(BLOSUM62Colour);
3770 colourMenu.add(PIDColour);
3771 colourMenu.add(zappoColour);
3772 colourMenu.add(taylorColour);
3773 colourMenu.add(hydrophobicityColour);
3774 colourMenu.add(helixColour);
3775 colourMenu.add(strandColour);
3776 colourMenu.add(turnColour);
3777 colourMenu.add(buriedColour);
3778 colourMenu.add(nucleotideColour);
3779 colourMenu.add(purinePyrimidineColour);
3780 // colourMenu.add(RNAInteractionColour);
3781 colourMenu.add(tcoffeeColour);
3782 colourMenu.add(userDefinedColour);
3783 colourMenu.addSeparator();
3784 colourMenu.add(conservationMenuItem);
3785 colourMenu.add(modifyConservation);
3786 colourMenu.add(abovePIDThreshold);
3787 colourMenu.add(modifyPID);
3788 colourMenu.add(annotationColour);
3789 colourMenu.add(RNAHelixColour);
3794 sortMenu.add(sortIDMenuItem);
3795 sortMenu.add(sortLengthMenuItem);
3796 sortMenu.add(sortByTreeMenu);
3797 sortMenu.add(sortGroupMenuItem);
3798 sortMenu.add(sortPairwiseMenuItem);
3799 calculateMenu.add(sortMenu);
3800 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3801 calculateTreeMenu.add(neighbourTreeMenuItem);
3802 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3803 calculateTreeMenu.add(njTreeBlosumMenuItem);
3804 calculateMenu.add(calculateTreeMenu);
3805 calculateMenu.addSeparator();
3806 calculateMenu.add(pairwiseAlignmentMenuItem);
3807 calculateMenu.add(PCAMenuItem);
3808 calculateMenu.add(autoCalculate);
3809 calculateMenu.add(sortByTree);
3814 helpMenu.add(documentation);
3815 helpMenu.add(about);
3820 statusBar.setBackground(Color.white);
3821 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3822 statusBar.setText(MessageManager.getString("label.status_bar"));
3823 this.add(statusBar, BorderLayout.SOUTH);
3827 public void setStatus(String string)
3829 statusBar.setText(string);
3832 MenuItem featureSettings = new MenuItem();
3834 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3836 MenuItem annotationColour = new MenuItem();
3838 MenuItem annotationColumnSelection = new MenuItem();
3840 MenuItem invertColSel = new MenuItem();
3842 MenuItem showColumns = new MenuItem();
3844 MenuItem showSeqs = new MenuItem();
3846 MenuItem hideColumns = new MenuItem();
3848 MenuItem hideSequences = new MenuItem();
3850 MenuItem hideAllButSelection = new MenuItem();
3852 MenuItem hideAllSelection = new MenuItem();
3854 MenuItem showAllHidden = new MenuItem();
3856 MenuItem newView = new MenuItem();
3858 private CheckboxMenuItem showAlignmentAnnotations;
3860 private CheckboxMenuItem showSequenceAnnotations;
3862 private CheckboxMenuItem sortAnnBySequence;
3864 private CheckboxMenuItem sortAnnByLabel;
3866 private CheckboxMenuItem showAutoFirst;
3868 private CheckboxMenuItem showAutoLast;
3870 private SplitFrame splitFrame;
3873 * Attach the alignFrame panels after embedding menus, if necessary. This used
3874 * to be called setEmbedded, but is now creates the dropdown menus in a
3875 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3877 * @param reallyEmbedded
3878 * true to attach the view to the applet area on the page rather than
3881 public void createAlignFrameWindow(boolean reallyEmbedded)
3885 embedAlignFrameInApplet(viewport.applet);
3890 // test and embed menu bar if necessary.
3892 if (embedMenuIfNeeded(alignPanel))
3895 * adjust for status bar height too. ? pointless as overridden by layout
3898 alignPanel.setSize(getSize().width,
3899 getSize().height - statusBar.getHeight());
3901 add(statusBar, BorderLayout.SOUTH);
3902 add(alignPanel, BorderLayout.CENTER);
3903 // and register with the applet so it can pass external API calls to us
3904 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3910 * Add the components of this AlignFrame to the applet container.
3914 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3917 // Explicitly build the embedded menu panel for the on-page applet
3919 // view cannot be closed if its actually on the page
3920 fileMenu.remove(closeMenuItem);
3921 fileMenu.remove(3); // Remove Separator
3922 // construct embedded menu, using default font
3923 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3924 // and actually add the components to the applet area
3925 theApplet.setLayout(new BorderLayout());
3926 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3927 theApplet.add(statusBar, BorderLayout.SOUTH);
3928 // TODO should size be left to the layout manager?
3929 alignPanel.setSize(theApplet.getSize().width,
3930 theApplet.getSize().height - embeddedMenu.getHeight()
3931 - statusBar.getHeight());
3932 theApplet.add(alignPanel, BorderLayout.CENTER);
3933 final AlignFrame me = this;
3934 theApplet.addFocusListener(new FocusListener()
3938 public void focusLost(FocusEvent e)
3940 if (theApplet.currentAlignFrame == me)
3942 theApplet.currentAlignFrame = null;
3947 public void focusGained(FocusEvent e)
3949 theApplet.currentAlignFrame = me;
3952 theApplet.validate();
3956 * create a new binding between structures in an existing jmol viewer instance
3957 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3958 * this does not open a new Jmol window, or modify the display of the
3959 * structures in the original jmol window. Note This method doesn't work
3960 * without an additional javascript library to exchange messages between the
3961 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3964 * JmolViewer instance
3965 * @param sequenceIds
3966 * - sequence Ids to search for associations
3968 public SequenceStructureBinding addStructureViewInstance(
3969 Object jmolviewer, String[] sequenceIds)
3971 Viewer viewer = null;
3974 viewer = (Viewer) jmolviewer;
3975 } catch (ClassCastException ex)
3977 System.err.println("Unsupported viewer object :"
3978 + jmolviewer.getClass());
3982 System.err.println("Can't use this object as a structure viewer:"
3983 + jmolviewer.getClass());
3986 SequenceI[] seqs = null;
3987 if (sequenceIds == null || sequenceIds.length == 0)
3989 seqs = viewport.getAlignment().getSequencesArray();
3993 Vector sqi = new Vector();
3994 AlignmentI al = viewport.getAlignment();
3995 for (int sid = 0; sid < sequenceIds.length; sid++)
3997 SequenceI sq = al.findName(sequenceIds[sid]);
4005 seqs = new SequenceI[sqi.size()];
4006 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
4008 seqs[sid] = (SequenceI) sqi.elementAt(sid);
4016 AAStructureBindingModel jmv = null;
4017 // TODO: search for a jmv that involves viewer
4019 { // create a new viewer/jalview binding.
4020 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4027 * bind a pdb file to a sequence in the current view
4030 * - sequenceId within the dataset.
4031 * @param pdbEntryString
4032 * - the short name for the PDB file
4034 * - pdb file - either a URL or a valid PDB file.
4035 * @return true if binding was as success TODO: consider making an exception
4036 * structure for indicating when PDB parsing or sequenceId location
4039 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4042 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4043 boolean needtoadd = false;
4044 if (toaddpdb != null)
4046 Vector pdbe = toaddpdb.getAllPDBEntries();
4047 PDBEntry pdbentry = null;
4048 if (pdbe != null && pdbe.size() > 0)
4050 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4052 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4053 if (!pdbentry.getId().equals(pdbEntryString)
4054 && !pdbentry.getFile().equals(pdbFile))
4064 if (pdbentry == null)
4066 pdbentry = new PDBEntry();
4067 pdbentry.setId(pdbEntryString);
4068 pdbentry.setFile(pdbFile);
4069 needtoadd = true; // add this new entry to sequence.
4071 // resolve data source
4072 // TODO: this code should be a refactored to an io package
4073 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4074 pdbFile, FileFormat.PDB);
4075 if (protocol == null)
4081 pdbentry.setProperty("protocol", protocol);
4082 toaddpdb.addPDBId(pdbentry);
4083 alignPanel.getStructureSelectionManager()
4084 .registerPDBEntry(pdbentry);
4090 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4094 Vector sequences = new Vector();
4095 for (int i = 0; i < seqs.length; i++)
4097 if (seqs[i] != null)
4099 sequences.addElement(new Object[] { seqs[i],
4100 (chains != null) ? chains[i] : null });
4103 seqs = new SequenceI[sequences.size()];
4104 chains = new String[sequences.size()];
4105 for (int i = 0, isize = sequences.size(); i < isize; i++)
4107 Object[] oj = (Object[]) sequences.elementAt(i);
4109 seqs[i] = (SequenceI) oj[0];
4110 chains[i] = (String) oj[1];
4113 return new Object[] { seqs, chains };
4117 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4118 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4120 // Scrub any null sequences from the array
4121 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4122 seqs = (SequenceI[]) sqch[0];
4123 chains = (String[]) sqch[1];
4124 if (seqs == null || seqs.length == 0)
4127 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4129 if (protocol == null)
4131 String sourceType = (String) pdb.getProperty("protocol");
4134 protocol = DataSourceType.valueOf(sourceType);
4135 } catch (IllegalArgumentException e)
4139 if (protocol == null)
4141 System.err.println("Couldn't work out protocol to open structure: "
4146 if (applet.useXtrnalSviewer)
4148 // register the association(s) and quit, don't create any windows.
4149 if (StructureSelectionManager.getStructureSelectionManager(applet)
4150 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4152 System.err.println("Failed to map " + pdb.getFile() + " ("
4153 + protocol + ") to any sequences");
4157 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4159 // can only do alignments with Jmol
4160 // find the last jmol window assigned to this alignment
4161 AppletJmol ajm = null, tajm;
4162 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4163 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4165 tajm = (AppletJmol) jmols.elementAt(i);
4166 if (tajm.ap.alignFrame == this)
4175 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4176 // try and add the pdb structure
4181 // otherwise, create a new window
4182 if (applet.jmolAvailable)
4184 new AppletJmol(pdb, seqs, chains, alignPanel,
4186 applet.lastFrameX += 40;
4187 applet.lastFrameY += 40;
4191 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4196 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4197 SequenceI[][] seqs, String[][] chains, String[] protocols)
4199 // TODO Auto-generated method stub
4200 System.err.println("Aligned Structure View: Not yet implemented.");
4204 * modify the current selection, providing the user has not made a selection
4208 * - sequences from this alignment
4210 * - columns to be selected on the alignment
4212 public void select(SequenceGroup sel, ColumnSelection csel,
4213 HiddenColumns hidden)
4215 alignPanel.seqPanel.selection(sel, csel, hidden, null);
4218 public void scrollTo(int row, int column)
4220 alignPanel.seqPanel.scrollTo(row, column);
4223 public void scrollToRow(int row)
4225 alignPanel.seqPanel.scrollToRow(row);
4228 public void scrollToColumn(int column)
4230 alignPanel.seqPanel.scrollToColumn(column);
4234 * @return the alignments unique ID.
4236 public String getSequenceSetId()
4238 return viewport.getSequenceSetId();
4242 * Load the (T-Coffee) score file from the specified url
4245 * File/URL/T-COFFEE score file contents
4246 * @throws IOException
4247 * @return true if alignment was annotated with data from source
4249 public boolean loadScoreFile(String source) throws IOException
4252 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4253 AppletFormatAdapter.checkProtocol(source));
4254 if (!file.isValid())
4256 // TODO: raise dialog for gui
4257 System.err.println("Problems parsing T-Coffee scores: "
4258 + file.getWarningMessage());
4259 System.err.println("Origin was:\n" + source);
4264 * check that the score matrix matches the alignment dimensions
4267 if ((aln = viewport.getAlignment()) != null
4268 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4271 // TODO: raise a dialog box here rather than bomb out.
4273 .println("The scores matrix does not match the alignment dimensions");
4277 // TODO add parameter to indicate if matching should be done
4278 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4280 alignPanel.fontChanged();
4281 tcoffeeColour.setEnabled(true);
4282 // switch to this color
4283 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4288 System.err.println("Problems resolving T-Coffee scores:");
4289 if (file.getWarningMessage() != null)
4291 System.err.println(file.getWarningMessage());
4297 public SplitFrame getSplitFrame()
4299 return this.splitFrame;
4302 public void setSplitFrame(SplitFrame sf)
4304 this.splitFrame = sf;
4307 // may not need this
4309 public void setShowSeqFeatures(boolean b)
4311 // showSeqFeatures.setSelected(b);
4312 viewport.setShowSequenceFeatures(b);
4317 public void setMenusForViewport()
4319 // setMenusFromViewport(viewport);
4324 public void refreshFeatureUI(boolean enableIfNecessary)
4326 if (enableIfNecessary)
4328 sequenceFeatures.setState(true);
4329 alignPanel.av.setShowSequenceFeatures(true);
4334 public FeatureSettingsControllerI getFeatureSettingsUI()
4336 return alignPanel.av.featureSettings;