2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.DataSourceType;
53 import jalview.io.FeaturesFile;
54 import jalview.io.FileFormat;
55 import jalview.io.FileFormatI;
56 import jalview.io.FileFormats;
57 import jalview.io.TCoffeeScoreFile;
58 import jalview.schemes.Blosum62ColourScheme;
59 import jalview.schemes.BuriedColourScheme;
60 import jalview.schemes.ClustalxColourScheme;
61 import jalview.schemes.ColourSchemeI;
62 import jalview.schemes.HelixColourScheme;
63 import jalview.schemes.HydrophobicColourScheme;
64 import jalview.schemes.NucleotideColourScheme;
65 import jalview.schemes.PIDColourScheme;
66 import jalview.schemes.PurinePyrimidineColourScheme;
67 import jalview.schemes.RNAHelicesColour;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TCoffeeColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.ZappoColourScheme;
73 import jalview.structure.StructureSelectionManager;
74 import jalview.structures.models.AAStructureBindingModel;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
78 import jalview.viewmodel.ViewportRanges;
80 import java.awt.BorderLayout;
81 import java.awt.Canvas;
82 import java.awt.CheckboxMenuItem;
83 import java.awt.Color;
84 import java.awt.FlowLayout;
86 import java.awt.FontMetrics;
87 import java.awt.Frame;
88 import java.awt.Graphics;
89 import java.awt.Label;
91 import java.awt.MenuBar;
92 import java.awt.MenuItem;
93 import java.awt.Panel;
94 import java.awt.event.ActionEvent;
95 import java.awt.event.ActionListener;
96 import java.awt.event.FocusEvent;
97 import java.awt.event.FocusListener;
98 import java.awt.event.ItemEvent;
99 import java.awt.event.ItemListener;
100 import java.awt.event.KeyEvent;
101 import java.awt.event.KeyListener;
102 import java.awt.event.WindowAdapter;
103 import java.awt.event.WindowEvent;
104 import java.io.IOException;
106 import java.net.URLEncoder;
107 import java.util.Arrays;
108 import java.util.Deque;
109 import java.util.HashMap;
110 import java.util.List;
111 import java.util.Map;
112 import java.util.StringTokenizer;
113 import java.util.Vector;
115 import org.jmol.viewer.Viewer;
117 public class AlignFrame extends EmbmenuFrame implements ActionListener,
118 ItemListener, KeyListener, AlignViewControllerGuiI
120 public AlignViewControllerI avc;
122 public AlignmentPanel alignPanel;
124 public AlignViewport viewport;
126 // width and height may be overridden by applet parameters
127 int frameWidth = 700;
129 int frameHeight = 500;
131 String jalviewServletURL;
134 * Flag for showing autocalculated consensus above or below other consensus
137 private boolean showAutoCalculatedAbove;
139 private SequenceAnnotationOrder annotationSortOrder;
142 * Constructor that creates the frame and adds it to the display.
149 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
152 this(al, applet, title, embedded, true);
156 * Constructor that optionally allows the frame to be displayed or only
163 * @param addToDisplay
165 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
166 boolean embedded, boolean addToDisplay)
168 this(al, null, null, applet, title, embedded, addToDisplay);
171 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
172 ColumnSelection columnSelection, JalviewLite applet,
173 String title, boolean embedded)
175 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
178 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
179 ColumnSelection columnSelection, JalviewLite applet,
180 String title, boolean embedded, boolean addToDisplay)
184 jalviewServletURL = applet.getParameter("APPLICATION_URL");
190 } catch (Exception ex)
192 ex.printStackTrace();
194 // need to get window geometry before we calculate alignment layout
200 param = applet.getParameter("windowWidth");
203 int width = Integer.parseInt(param);
206 param = applet.getParameter("windowHeight");
209 int height = Integer.parseInt(param);
210 frameHeight = height;
212 } catch (Exception ex)
216 viewport = new AlignViewport(al, applet);
218 if (hiddenSeqs != null && hiddenSeqs.length > 0)
220 viewport.hideSequence(hiddenSeqs);
222 if (columnSelection != null)
224 viewport.setColumnSelection(columnSelection);
226 viewport.setScaleAboveWrapped(scaleAbove.getState());
228 alignPanel = new AlignmentPanel(this, viewport);
229 avc = new jalview.controller.AlignViewController(this, viewport,
231 viewport.updateConservation(alignPanel);
232 viewport.updateConsensus(alignPanel);
234 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
235 followMouseOverFlag.setState(viewport.isFollowHighlight());
236 showGroupConsensus.setState(viewport.isShowGroupConsensus());
237 showGroupConservation.setState(viewport.isShowGroupConservation());
238 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
239 showSequenceLogo.setState(viewport.isShowSequenceLogo());
240 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
241 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
242 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
243 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
244 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
245 showAlignmentAnnotations.setState(true);
246 showSequenceAnnotations.setState(false);
248 seqLimits.setState(viewport.getShowJVSuffix());
252 String param = applet.getParameter("sortBy");
255 if (param.equalsIgnoreCase("Id"))
257 sortIDMenuItem_actionPerformed();
259 else if (param.equalsIgnoreCase("Pairwise Identity"))
261 sortPairwiseMenuItem_actionPerformed();
263 else if (param.equalsIgnoreCase("Length"))
265 sortLengthMenuItem_actionPerformed();
269 param = applet.getParameter("wrap");
272 if (param.equalsIgnoreCase("true"))
274 wrapMenuItem.setState(true);
275 wrapMenuItem_actionPerformed();
278 param = applet.getParameter("centrecolumnlabels");
281 centreColumnLabelFlag.setState(true);
282 centreColumnLabelFlag_stateChanged();
286 if (viewport.getAlignment().isNucleotide())
288 conservationMenuItem.setEnabled(false);
289 clustalColour.setEnabled(false);
290 BLOSUM62Colour.setEnabled(false);
291 zappoColour.setEnabled(false);
292 taylorColour.setEnabled(false);
293 hydrophobicityColour.setEnabled(false);
294 helixColour.setEnabled(false);
295 strandColour.setEnabled(false);
296 turnColour.setEnabled(false);
297 buriedColour.setEnabled(false);
298 viewport.updateStrucConsensus(alignPanel);
299 if (viewport.getAlignment().hasRNAStructure())
301 RNAHelixColour.setEnabled(true);
305 RNAHelixColour.setEnabled(false);
310 RNAHelixColour.setEnabled(false);
311 purinePyrimidineColour.setEnabled(false);
312 nucleotideColour.setEnabled(false);
314 // Some JVMS send keyevents to Top frame or lowest panel,
315 // Havent worked out why yet. So add to both this frame and seqCanvas for
317 this.addKeyListener(this);
318 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
319 alignPanel.idPanel.idCanvas.addKeyListener(this);
320 alignPanel.scalePanel.addKeyListener(this);
321 alignPanel.annotationPanel.addKeyListener(this);
322 alignPanel.annotationPanelHolder.addKeyListener(this);
323 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
324 alignPanel.alabels.addKeyListener(this);
326 setAnnotationsVisibility();
330 addToDisplay(embedded);
337 public void addToDisplay(boolean embedded)
339 createAlignFrameWindow(embedded);
341 alignPanel.adjustAnnotationHeight();
342 alignPanel.paintAlignment(true);
345 public AlignViewport getAlignViewport()
350 public SeqCanvas getSeqcanvas()
352 return alignPanel.seqPanel.seqCanvas;
356 * Load a features file onto the alignment
359 * file URL, content, or other resolvable path
361 * is protocol for accessing data referred to by file
364 public boolean parseFeaturesFile(String file, DataSourceType type)
366 return parseFeaturesFile(file, type, true);
370 * Load a features file onto the alignment
373 * file URL, content, or other resolvable path
375 * is protocol for accessing data referred to by file
376 * @param autoenabledisplay
377 * when true, display features flag will be automatically enabled if
378 * features are loaded
379 * @return true if data parsed as a features file
381 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
382 boolean autoenabledisplay)
384 boolean featuresFile = false;
387 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
388 .getFeatureRenderer().getFeatureColours();
389 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
390 "relaxedidmatch", false);
391 featuresFile = new FeaturesFile(file, sourceType).parse(
392 viewport.getAlignment(), colours, true, relaxedIdMatching);
393 } catch (Exception ex)
395 ex.printStackTrace();
400 if (autoenabledisplay)
402 viewport.setShowSequenceFeatures(true);
403 sequenceFeatures.setState(true);
405 if (alignPanel.seqPanel.seqCanvas.fr != null)
407 // update the min/max ranges where necessary
408 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
410 if (viewport.featureSettings != null)
412 viewport.featureSettings.refreshTable();
414 alignPanel.paintAlignment(true);
415 statusBar.setText(MessageManager
416 .getString("label.successfully_added_features_alignment"));
422 public void keyPressed(KeyEvent evt)
424 ViewportRanges ranges = viewport.getRanges();
426 if (viewport.cursorMode
427 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
428 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
429 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
430 && Character.isDigit(evt.getKeyChar()))
432 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
435 switch (evt.getKeyCode())
437 case 27: // escape key
438 deselectAllSequenceMenuItem_actionPerformed();
440 alignPanel.alabels.cancelDrag();
443 if (evt.isControlDown() || evt.isMetaDown())
445 cut_actionPerformed();
449 if (viewport.cursorMode && !evt.isControlDown())
451 alignPanel.seqPanel.setCursorColumn();
453 if (evt.isControlDown() || evt.isMetaDown())
455 copy_actionPerformed();
459 if (evt.isControlDown())
461 paste(evt.isShiftDown());
465 if (evt.isControlDown() || evt.isMetaDown())
467 selectAllSequenceMenuItem_actionPerformed();
470 case KeyEvent.VK_DOWN:
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.moveCursor(0, 1);
477 moveSelectedSequences(false);
482 if (viewport.cursorMode)
484 alignPanel.seqPanel.moveCursor(0, -1);
488 moveSelectedSequences(true);
492 case KeyEvent.VK_LEFT:
493 if (evt.isAltDown() || !viewport.cursorMode)
495 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
499 alignPanel.seqPanel.moveCursor(-1, 0);
503 case KeyEvent.VK_RIGHT:
504 if (evt.isAltDown() || !viewport.cursorMode)
506 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
510 alignPanel.seqPanel.moveCursor(1, 0);
514 case KeyEvent.VK_SPACE:
515 if (viewport.cursorMode)
517 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
518 || evt.isShiftDown() || evt.isAltDown());
522 case KeyEvent.VK_DELETE:
523 case KeyEvent.VK_BACK_SPACE:
524 if (viewport.cursorMode)
526 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
527 || evt.isShiftDown() || evt.isAltDown());
531 cut_actionPerformed();
532 alignPanel.seqPanel.seqCanvas.repaint();
537 if (viewport.cursorMode)
539 alignPanel.seqPanel.setCursorRow();
543 if (viewport.cursorMode)
545 alignPanel.seqPanel.setCursorPosition();
549 case KeyEvent.VK_ENTER:
550 case KeyEvent.VK_COMMA:
551 if (viewport.cursorMode)
553 alignPanel.seqPanel.setCursorRowAndColumn();
558 if (viewport.cursorMode)
560 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
564 if (viewport.cursorMode)
566 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
571 viewport.cursorMode = !viewport.cursorMode;
572 statusBar.setText(MessageManager.formatMessage(
573 "label.keyboard_editing_mode",
574 new String[] { (viewport.cursorMode ? "on" : "off") }));
575 if (viewport.cursorMode)
577 alignPanel.seqPanel.seqCanvas.cursorX = ranges.getStartRes();
578 alignPanel.seqPanel.seqCanvas.cursorY = ranges.getStartSeq();
583 if (evt.isControlDown())
585 findMenuItem_actionPerformed();
591 boolean toggleSeqs = !evt.isControlDown();
592 boolean toggleCols = !evt.isShiftDown();
593 toggleHiddenRegions(toggleSeqs, toggleCols);
597 case KeyEvent.VK_PAGE_UP:
598 if (viewport.getWrapAlignment())
600 alignPanel.scrollUp(true);
604 alignPanel.setScrollValues(ranges.getStartRes(),
605 2 * ranges.getStartSeq() - ranges.getEndSeq());
609 case KeyEvent.VK_PAGE_DOWN:
610 if (viewport.getWrapAlignment())
612 alignPanel.scrollUp(false);
617 .setScrollValues(ranges.getStartRes(), ranges.getEndSeq());
622 if (evt.isControlDown())
624 undoMenuItem_actionPerformed();
629 if (evt.isControlDown())
631 redoMenuItem_actionPerformed();
636 if (evt.isControlDown())
643 if (evt.isControlDown())
645 trimAlignment(false);
650 if (evt.isControlDown())
652 if (evt.isShiftDown())
654 this.removeAllGapsMenuItem_actionPerformed();
658 removeGappedColumnMenuItem_actionPerformed();
663 if (evt.isControlDown())
667 invertColSel_actionPerformed();
671 invertSequenceMenuItem_actionPerformed();
677 if (evt.isControlDown())
679 if (evt.isShiftDown())
681 this.unGroup_actionPerformed();
685 this.createGroup_actionPerformed();
691 if (evt.isControlDown())
693 this.deleteGroups_actionPerformed();
698 if (evt.isControlDown())
705 alignPanel.paintAlignment(true);
709 * called by key handler and the hide all/show all menu items
714 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
716 boolean hide = false;
717 SequenceGroup sg = viewport.getSelectionGroup();
718 if (!toggleSeqs && !toggleCols)
720 // Hide everything by the current selection - this is a hack - we do the
721 // invert and then hide
722 // first check that there will be visible columns after the invert.
723 if (viewport.hasSelectedColumns()
724 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
727 // now invert the sequence set, if required - empty selection implies
728 // that no hiding is required.
731 invertSequenceMenuItem_actionPerformed();
732 sg = viewport.getSelectionGroup();
736 viewport.expandColSelection(sg, true);
737 // finally invert the column selection and get the new sequence
738 // selection and indicate it should be hidden.
739 invertColSel_actionPerformed();
746 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
749 viewport.hideAllSelectedSeqs();
751 else if (!(toggleCols && viewport.hasSelectedColumns()))
753 viewport.showAllHiddenSeqs();
759 if (viewport.hasSelectedColumns())
761 viewport.hideSelectedColumns();
764 viewport.setSelectionGroup(sg);
769 viewport.showAllHiddenColumns();
771 viewport.sendSelection();
776 public void keyReleased(KeyEvent evt)
781 public void keyTyped(KeyEvent evt)
786 public void itemStateChanged(ItemEvent evt)
788 final Object source = evt.getSource();
789 if (source == displayNonconservedMenuItem)
791 displayNonconservedMenuItem_actionPerformed();
793 else if (source == colourTextMenuItem)
795 colourTextMenuItem_actionPerformed();
797 else if (source == wrapMenuItem)
799 wrapMenuItem_actionPerformed();
801 else if (source == scaleAbove)
803 viewport.setScaleAboveWrapped(scaleAbove.getState());
805 else if (source == scaleLeft)
807 viewport.setScaleLeftWrapped(scaleLeft.getState());
809 else if (source == scaleRight)
811 viewport.setScaleRightWrapped(scaleRight.getState());
813 else if (source == seqLimits)
815 seqLimits_itemStateChanged();
817 else if (source == viewBoxesMenuItem)
819 viewport.setShowBoxes(viewBoxesMenuItem.getState());
821 else if (source == viewTextMenuItem)
823 viewport.setShowText(viewTextMenuItem.getState());
825 else if (source == renderGapsMenuItem)
827 viewport.setRenderGaps(renderGapsMenuItem.getState());
829 else if (source == annotationPanelMenuItem)
831 boolean showAnnotations = annotationPanelMenuItem.getState();
832 showAlignmentAnnotations.setEnabled(showAnnotations);
833 showSequenceAnnotations.setEnabled(showAnnotations);
834 viewport.setShowAnnotation(showAnnotations);
835 alignPanel.setAnnotationVisible(showAnnotations);
837 else if (source == sequenceFeatures)
839 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
840 alignPanel.seqPanel.seqCanvas.repaint();
842 else if (source == showAlignmentAnnotations)
844 setAnnotationsVisibility();
846 else if (source == showSequenceAnnotations)
848 setAnnotationsVisibility();
850 else if (source == sortAnnBySequence)
852 boolean newState = sortAnnBySequence.getState();
853 sortAnnByLabel.setState(false);
854 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
855 : SequenceAnnotationOrder.NONE);
856 setViewportAnnotationOrder();
858 else if (source == sortAnnByLabel)
860 boolean newState = sortAnnByLabel.getState();
861 sortAnnBySequence.setState(false);
862 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
863 : SequenceAnnotationOrder.NONE);
864 setViewportAnnotationOrder();
866 else if (source == showAutoFirst)
868 showAutoLast.setState(!showAutoFirst.getState());
869 setShowAutoCalculatedAbove(showAutoFirst.getState());
870 setViewportAnnotationOrder();
872 else if (source == showAutoLast)
874 showAutoFirst.setState(!showAutoLast.getState());
875 setShowAutoCalculatedAbove(showAutoFirst.getState());
876 setViewportAnnotationOrder();
878 else if (source == conservationMenuItem)
880 conservationMenuItem_actionPerformed();
882 else if (source == abovePIDThreshold)
884 abovePIDThreshold_actionPerformed();
886 else if (source == applyToAllGroups)
888 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
890 else if (source == autoCalculate)
892 viewport.autoCalculateConsensus = autoCalculate.getState();
894 else if (source == sortByTree)
896 viewport.sortByTree = sortByTree.getState();
898 else if (source == this.centreColumnLabelFlag)
900 centreColumnLabelFlag_stateChanged();
902 else if (source == this.followMouseOverFlag)
904 mouseOverFlag_stateChanged();
906 else if (source == showGroupConsensus)
908 showGroupConsensus_actionPerformed();
910 else if (source == showGroupConservation)
912 showGroupConservation_actionPerformed();
914 else if (source == showSequenceLogo)
916 showSequenceLogo_actionPerformed();
918 else if (source == normSequenceLogo)
920 normSequenceLogo_actionPerformed();
922 else if (source == showConsensusHistogram)
924 showConsensusHistogram_actionPerformed();
926 else if (source == applyAutoAnnotationSettings)
928 applyAutoAnnotationSettings_actionPerformed();
930 alignPanel.paintAlignment(true);
934 * Set the visibility state of sequence-related and/or alignment-related
935 * annotations depending on checkbox selections, and repaint.
939 private void setAnnotationsVisibility()
941 boolean showForAlignment = showAlignmentAnnotations.getState();
942 boolean showForSequences = showSequenceAnnotations.getState();
943 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
945 for (AlignmentAnnotation aa : alignPanel.getAlignment()
946 .getAlignmentAnnotation())
948 boolean visible = (aa.sequenceRef == null ? showForAlignment
950 aa.visible = visible;
953 alignPanel.validateAnnotationDimensions(true);
958 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
960 this.annotationSortOrder = order;
964 * Set flags on the viewport that control annotation ordering
966 private void setViewportAnnotationOrder()
968 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
970 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
973 private void setShowAutoCalculatedAbove(boolean showAbove)
975 this.showAutoCalculatedAbove = showAbove;
978 private void mouseOverFlag_stateChanged()
980 viewport.setFollowHighlight(followMouseOverFlag.getState());
981 // TODO: could kick the scrollTo mechanism to reset view for current
985 private void centreColumnLabelFlag_stateChanged()
987 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
988 this.alignPanel.annotationPanel.repaint();
992 public void actionPerformed(ActionEvent evt)
994 viewport.applet.currentAlignFrame = this;
996 Object source = evt.getSource();
998 if (source == inputText)
1000 inputText_actionPerformed();
1002 else if (source == loadTree)
1004 loadTree_actionPerformed();
1006 else if (source == loadApplication)
1008 launchFullApplication();
1010 else if (source == loadAnnotations)
1014 else if (source == outputAnnotations)
1016 outputAnnotations(true);
1018 else if (source == outputFeatures)
1020 outputFeatures(true, "Jalview");
1022 else if (source == closeMenuItem)
1024 closeMenuItem_actionPerformed();
1026 else if (source == copy)
1028 copy_actionPerformed();
1030 else if (source == undoMenuItem)
1032 undoMenuItem_actionPerformed();
1034 else if (source == redoMenuItem)
1036 redoMenuItem_actionPerformed();
1038 else if (source == inputText)
1040 inputText_actionPerformed();
1042 else if (source == closeMenuItem)
1044 closeMenuItem_actionPerformed();
1046 else if (source == undoMenuItem)
1048 undoMenuItem_actionPerformed();
1050 else if (source == redoMenuItem)
1052 redoMenuItem_actionPerformed();
1054 else if (source == copy)
1056 copy_actionPerformed();
1058 else if (source == pasteNew)
1060 pasteNew_actionPerformed();
1062 else if (source == pasteThis)
1064 pasteThis_actionPerformed();
1066 else if (source == cut)
1068 cut_actionPerformed();
1070 else if (source == delete)
1072 delete_actionPerformed();
1074 else if (source == grpsFromSelection)
1076 makeGrpsFromSelection_actionPerformed();
1078 else if (source == deleteGroups)
1080 deleteGroups_actionPerformed();
1082 else if (source == selectAllSequenceMenuItem)
1084 selectAllSequenceMenuItem_actionPerformed();
1086 else if (source == deselectAllSequenceMenuItem)
1088 deselectAllSequenceMenuItem_actionPerformed();
1090 else if (source == invertSequenceMenuItem)
1092 invertSequenceMenuItem_actionPerformed();
1093 // uncomment to slave sequence selections in split frame
1094 // viewport.sendSelection();
1096 else if (source == invertColSel)
1098 viewport.invertColumnSelection();
1099 alignPanel.paintAlignment(true);
1100 viewport.sendSelection();
1102 else if (source == remove2LeftMenuItem)
1104 trimAlignment(true);
1106 else if (source == remove2RightMenuItem)
1108 trimAlignment(false);
1110 else if (source == removeGappedColumnMenuItem)
1112 removeGappedColumnMenuItem_actionPerformed();
1114 else if (source == removeAllGapsMenuItem)
1116 removeAllGapsMenuItem_actionPerformed();
1118 else if (source == findMenuItem)
1120 findMenuItem_actionPerformed();
1122 else if (source == font)
1124 new FontChooser(alignPanel);
1126 else if (source == newView)
1130 else if (source == showColumns)
1132 viewport.showAllHiddenColumns();
1133 alignPanel.paintAlignment(true);
1134 viewport.sendSelection();
1136 else if (source == showSeqs)
1138 viewport.showAllHiddenSeqs();
1139 alignPanel.paintAlignment(true);
1140 // uncomment if we want to slave sequence selections in split frame
1141 // viewport.sendSelection();
1143 else if (source == hideColumns)
1145 viewport.hideSelectedColumns();
1146 alignPanel.paintAlignment(true);
1147 viewport.sendSelection();
1149 else if (source == hideSequences
1150 && viewport.getSelectionGroup() != null)
1152 viewport.hideAllSelectedSeqs();
1153 alignPanel.paintAlignment(true);
1154 // uncomment if we want to slave sequence selections in split frame
1155 // viewport.sendSelection();
1157 else if (source == hideAllButSelection)
1159 toggleHiddenRegions(false, false);
1160 alignPanel.paintAlignment(true);
1161 viewport.sendSelection();
1163 else if (source == hideAllSelection)
1165 SequenceGroup sg = viewport.getSelectionGroup();
1166 viewport.expandColSelection(sg, false);
1167 viewport.hideAllSelectedSeqs();
1168 viewport.hideSelectedColumns();
1169 alignPanel.paintAlignment(true);
1170 viewport.sendSelection();
1172 else if (source == showAllHidden)
1174 viewport.showAllHiddenColumns();
1175 viewport.showAllHiddenSeqs();
1176 alignPanel.paintAlignment(true);
1177 viewport.sendSelection();
1179 else if (source == showGroupConsensus)
1181 showGroupConsensus_actionPerformed();
1183 else if (source == showGroupConservation)
1185 showGroupConservation_actionPerformed();
1187 else if (source == showSequenceLogo)
1189 showSequenceLogo_actionPerformed();
1191 else if (source == normSequenceLogo)
1193 normSequenceLogo_actionPerformed();
1195 else if (source == showConsensusHistogram)
1197 showConsensusHistogram_actionPerformed();
1199 else if (source == applyAutoAnnotationSettings)
1201 applyAutoAnnotationSettings_actionPerformed();
1203 else if (source == featureSettings)
1205 new FeatureSettings(alignPanel);
1207 else if (source == alProperties)
1209 StringBuffer contents = new jalview.io.AlignmentProperties(
1210 viewport.getAlignment()).formatAsString();
1211 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212 cap.setText(contents.toString());
1213 Frame frame = new Frame();
1215 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1216 "label.alignment_properties", new String[] { getTitle() }),
1219 else if (source == overviewMenuItem)
1221 overviewMenuItem_actionPerformed();
1223 else if (source == noColourmenuItem)
1227 else if (source == clustalColour)
1229 abovePIDThreshold.setState(false);
1230 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1232 else if (source == zappoColour)
1234 changeColour(new ZappoColourScheme());
1236 else if (source == taylorColour)
1238 changeColour(new TaylorColourScheme());
1240 else if (source == hydrophobicityColour)
1242 changeColour(new HydrophobicColourScheme());
1244 else if (source == helixColour)
1246 changeColour(new HelixColourScheme());
1248 else if (source == strandColour)
1250 changeColour(new StrandColourScheme());
1252 else if (source == turnColour)
1254 changeColour(new TurnColourScheme());
1256 else if (source == buriedColour)
1258 changeColour(new BuriedColourScheme());
1260 else if (source == nucleotideColour)
1262 changeColour(new NucleotideColourScheme());
1264 else if (source == purinePyrimidineColour)
1266 changeColour(new PurinePyrimidineColourScheme());
1268 // else if (source == RNAInteractionColour)
1270 // changeColour(new RNAInteractionColourScheme());
1272 else if (source == RNAHelixColour)
1274 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1275 // new RNAHelicesColourChooser(viewport, alignPanel);
1277 else if (source == modifyPID)
1279 modifyPID_actionPerformed();
1281 else if (source == modifyConservation)
1283 modifyConservation_actionPerformed();
1285 else if (source == userDefinedColour)
1287 new UserDefinedColours(alignPanel, null);
1289 else if (source == PIDColour)
1291 changeColour(new PIDColourScheme());
1293 else if (source == BLOSUM62Colour)
1295 changeColour(new Blosum62ColourScheme());
1297 else if (source == tcoffeeColour)
1299 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1301 else if (source == annotationColour)
1303 new AnnotationColourChooser(viewport, alignPanel);
1305 else if (source == annotationColumnSelection)
1307 new AnnotationColumnChooser(viewport, alignPanel);
1309 else if (source == sortPairwiseMenuItem)
1311 sortPairwiseMenuItem_actionPerformed();
1313 else if (source == sortIDMenuItem)
1315 sortIDMenuItem_actionPerformed();
1317 else if (source == sortLengthMenuItem)
1319 sortLengthMenuItem_actionPerformed();
1321 else if (source == sortGroupMenuItem)
1323 sortGroupMenuItem_actionPerformed();
1325 else if (source == removeRedundancyMenuItem)
1327 removeRedundancyMenuItem_actionPerformed();
1329 else if (source == pairwiseAlignmentMenuItem)
1331 pairwiseAlignmentMenuItem_actionPerformed();
1333 else if (source == PCAMenuItem)
1335 PCAMenuItem_actionPerformed();
1337 else if (source == averageDistanceTreeMenuItem)
1339 averageDistanceTreeMenuItem_actionPerformed();
1341 else if (source == neighbourTreeMenuItem)
1343 neighbourTreeMenuItem_actionPerformed();
1345 else if (source == njTreeBlosumMenuItem)
1347 njTreeBlosumMenuItem_actionPerformed();
1349 else if (source == avDistanceTreeBlosumMenuItem)
1351 avTreeBlosumMenuItem_actionPerformed();
1353 else if (source == documentation)
1355 documentation_actionPerformed();
1357 else if (source == about)
1359 about_actionPerformed();
1364 public void inputText_actionPerformed()
1366 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1367 Frame frame = new Frame();
1369 jalview.bin.JalviewLite.addFrame(frame,
1370 MessageManager.getString("label.input_cut_paste"), 500, 500);
1373 protected void outputText_actionPerformed(ActionEvent e)
1375 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1376 Frame frame = new Frame();
1378 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1379 "label.alignment_output_command",
1380 new Object[] { e.getActionCommand() }), 600, 500);
1382 FileFormatI fileFormat = FileFormats.getInstance().forName(
1383 e.getActionCommand());
1384 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1385 fileFormat, viewport.getAlignment(),
1386 viewport.getShowJVSuffix()));
1389 public void loadAnnotations()
1391 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1392 cap.setText(MessageManager
1393 .getString("label.paste_features_annotations_Tcoffee_here"));
1394 cap.setAnnotationImport();
1395 Frame frame = new Frame();
1397 jalview.bin.JalviewLite.addFrame(frame,
1398 MessageManager.getString("action.paste_annotations"), 400, 300);
1402 public String outputAnnotations(boolean displayTextbox)
1404 String annotation = new AnnotationFile()
1405 .printAnnotationsForView(viewport);
1409 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1410 Frame frame = new Frame();
1412 jalview.bin.JalviewLite.addFrame(frame,
1413 MessageManager.getString("label.annotations"), 600, 500);
1414 cap.setText(annotation);
1420 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1422 if (alignPanel.getFeatureRenderer() != null
1423 && viewport.getFeaturesDisplayed() != null)
1425 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1431 public String outputFeatures(boolean displayTextbox, String format)
1434 FeaturesFile formatter = new FeaturesFile();
1435 if (format.equalsIgnoreCase("Jalview"))
1437 features = formatter.printJalviewFormat(viewport.getAlignment()
1438 .getSequencesArray(), getDisplayedFeatureCols());
1442 features = formatter.printGffFormat(viewport.getAlignment()
1443 .getSequencesArray(), getDisplayedFeatureCols());
1448 boolean frimport = false;
1449 if (features == null || features.equals("No Features Visible"))
1451 features = "# No features visible - paste some and import them here.";
1455 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1458 cap.setAnnotationImport();
1460 Frame frame = new Frame();
1462 jalview.bin.JalviewLite.addFrame(frame,
1463 MessageManager.getString("label.features"), 600, 500);
1464 cap.setText(features);
1468 if (features == null)
1477 void launchFullApplication()
1479 StringBuffer url = new StringBuffer(jalviewServletURL);
1481 // allow servlet parameters to be passed in applet parameter
1482 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1484 url.append(firstSep);
1487 + appendProtocol(viewport.applet.getParameter("file")));
1489 if (viewport.applet.getParameter("features") != null)
1491 url.append("&features=");
1492 url.append(appendProtocol(viewport.applet.getParameter("features")));
1495 if (viewport.applet.getParameter("annotations") != null)
1497 url.append("&annotations=");
1498 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1501 if (viewport.applet.getParameter("jnetfile") != null
1502 || viewport.applet.getParameter("jpredfile") != null)
1504 url.append("&annotations=");
1505 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1506 .getParameter("jnetfile") : viewport.applet
1507 .getParameter("jpredfile")));
1510 if (viewport.applet.getParameter("defaultColour") != null)
1512 url.append("&colour="
1513 + removeWhiteSpace(viewport.applet
1514 .getParameter("defaultColour")));
1517 if (viewport.applet.getParameter("userDefinedColour") != null)
1519 url.append("&colour="
1520 + removeWhiteSpace(viewport.applet
1521 .getParameter("userDefinedColour")));
1523 if (viewport.applet.getParameter("tree") != null)
1526 + appendProtocol(viewport.applet.getParameter("tree")));
1528 if (viewport.applet.getParameter("treeFile") != null)
1531 + appendProtocol(viewport.applet.getParameter("treeFile")));
1534 showURL(url.toString(), "FULL_APP");
1537 String removeWhiteSpace(String colour)
1539 StringBuffer sb = new StringBuffer();
1540 for (int i = 0; i < colour.length(); i++)
1542 if (Character.isWhitespace(colour.charAt(i)))
1548 sb.append(colour.charAt(i));
1552 return sb.toString();
1555 String appendProtocol(String url)
1560 url = URLEncoder.encode(url);
1563 * When we finally deprecate 1.1 compatibility, we can start to use
1564 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1565 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1566 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1567 * ex.printStackTrace(); }
1569 catch (java.net.MalformedURLException ex)
1571 url = viewport.applet.getCodeBase() + url;
1576 public void closeMenuItem_actionPerformed()
1578 PaintRefresher.RemoveComponent(alignPanel);
1579 if (alignPanel.seqPanel != null
1580 && alignPanel.seqPanel.seqCanvas != null)
1582 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1584 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1586 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1589 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1604 void updateEditMenuBar()
1607 if (viewport.getHistoryList().size() > 0)
1609 undoMenuItem.setEnabled(true);
1610 CommandI command = viewport.getHistoryList().peek();
1611 undoMenuItem.setLabel(MessageManager.formatMessage(
1612 "label.undo_command",
1613 new Object[] { command.getDescription() }));
1617 undoMenuItem.setEnabled(false);
1618 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1621 if (viewport.getRedoList().size() > 0)
1623 redoMenuItem.setEnabled(true);
1625 CommandI command = viewport.getRedoList().peek();
1626 redoMenuItem.setLabel(MessageManager.formatMessage(
1627 "label.redo_command",
1628 new Object[] { command.getDescription() }));
1632 redoMenuItem.setEnabled(false);
1633 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1641 public void addHistoryItem(CommandI command)
1643 if (command.getSize() > 0)
1645 viewport.addToHistoryList(command);
1646 viewport.clearRedoList();
1647 updateEditMenuBar();
1648 viewport.updateHiddenColumns();
1653 * TODO: JAL-1104 DOCUMENT ME!
1658 protected void undoMenuItem_actionPerformed()
1660 if (viewport.getHistoryList().isEmpty())
1665 CommandI command = viewport.getHistoryList().pop();
1666 viewport.addToRedoList(command);
1667 command.undoCommand(null);
1669 AlignmentViewport originalSource = getOriginatingSource(command);
1671 if (originalSource != viewport)
1674 .println("Warning: Viewport object mismatch whilst undoing");
1676 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1677 // viewport.getColumnSelection().getHiddenColumns()
1679 updateEditMenuBar();
1680 originalSource.firePropertyChange("alignment", null, originalSource
1681 .getAlignment().getSequences());
1685 * TODO: JAL-1104 DOCUMENT ME!
1690 protected void redoMenuItem_actionPerformed()
1692 if (viewport.getRedoList().isEmpty())
1697 CommandI command = viewport.getRedoList().pop();
1698 viewport.addToHistoryList(command);
1699 command.doCommand(null);
1701 AlignmentViewport originalSource = getOriginatingSource(command);
1703 if (originalSource != viewport)
1706 .println("Warning: Viewport object mismatch whilst re-doing");
1708 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1709 // viewport.getColumnSelection().getHiddenColumns()
1712 updateEditMenuBar();
1713 originalSource.firePropertyChange("alignment", null, originalSource
1714 .getAlignment().getSequences());
1717 AlignmentViewport getOriginatingSource(CommandI command)
1719 AlignmentViewport originalSource = null;
1720 // For sequence removal and addition, we need to fire
1721 // the property change event FROM the viewport where the
1722 // original alignment was altered
1723 AlignmentI al = null;
1724 if (command instanceof EditCommand)
1726 EditCommand editCommand = (EditCommand) command;
1727 al = editCommand.getAlignment();
1728 Vector comps = (Vector) PaintRefresher.components.get(viewport
1729 .getSequenceSetId());
1730 for (int i = 0; i < comps.size(); i++)
1732 if (comps.elementAt(i) instanceof AlignmentPanel)
1734 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1736 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1743 if (originalSource == null)
1745 // The original view is closed, we must validate
1746 // the current view against the closed view first
1749 PaintRefresher.validateSequences(al, viewport.getAlignment());
1752 originalSource = viewport;
1755 return originalSource;
1759 * Move the currently selected sequences up or down one position in the
1764 public void moveSelectedSequences(boolean up)
1766 SequenceGroup sg = viewport.getSelectionGroup();
1771 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1772 up ? null : viewport.getHiddenRepSequences(), up);
1773 alignPanel.paintAlignment(true);
1776 * Also move cDNA/protein complement sequences
1778 AlignViewportI complement = viewport.getCodingComplement();
1779 if (complement != null)
1781 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1782 viewport, complement);
1783 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1784 up ? null : complement.getHiddenRepSequences(), up);
1785 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1789 synchronized void slideSequences(boolean right, int size)
1791 List<SequenceI> sg = new Vector<SequenceI>();
1792 if (viewport.cursorMode)
1794 sg.add(viewport.getAlignment().getSequenceAt(
1795 alignPanel.seqPanel.seqCanvas.cursorY));
1797 else if (viewport.getSelectionGroup() != null
1798 && viewport.getSelectionGroup().getSize() != viewport
1799 .getAlignment().getHeight())
1801 sg = viewport.getSelectionGroup().getSequences(
1802 viewport.getHiddenRepSequences());
1810 Vector<SequenceI> invertGroup = new Vector();
1812 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1814 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1816 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1820 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1822 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1824 for (int i = 0; i < invertGroup.size(); i++)
1826 seqs2[i] = invertGroup.elementAt(i);
1829 SlideSequencesCommand ssc;
1832 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1833 size, viewport.getGapCharacter());
1837 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1838 size, viewport.getGapCharacter());
1841 int groupAdjustment = 0;
1842 if (ssc.getGapsInsertedBegin() && right)
1844 if (viewport.cursorMode)
1846 alignPanel.seqPanel.moveCursor(size, 0);
1850 groupAdjustment = size;
1853 else if (!ssc.getGapsInsertedBegin() && !right)
1855 if (viewport.cursorMode)
1857 alignPanel.seqPanel.moveCursor(-size, 0);
1861 groupAdjustment = -size;
1865 if (groupAdjustment != 0)
1867 viewport.getSelectionGroup().setStartRes(
1868 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1869 viewport.getSelectionGroup().setEndRes(
1870 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1873 boolean appendHistoryItem = false;
1874 Deque<CommandI> historyList = viewport.getHistoryList();
1875 if (historyList != null && historyList.size() > 0
1876 && historyList.peek() instanceof SlideSequencesCommand)
1878 appendHistoryItem = ssc
1879 .appendSlideCommand((SlideSequencesCommand) historyList
1883 if (!appendHistoryItem)
1885 addHistoryItem(ssc);
1891 static StringBuffer copiedSequences;
1893 static Vector copiedHiddenColumns;
1895 protected void copy_actionPerformed()
1897 if (viewport.getSelectionGroup() == null)
1902 SequenceGroup sg = viewport.getSelectionGroup();
1903 copiedSequences = new StringBuffer();
1904 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1905 for (int i = 0; i < sg.getSize(); i++)
1907 SequenceI seq = sg.getSequenceAt(i);
1908 int index = viewport.getAlignment().findIndex(seq);
1909 orderedSeqs.put(index, seq);
1912 int index = 0, startRes, endRes;
1915 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1917 copiedHiddenColumns = new Vector();
1918 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1919 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1921 copiedHiddenColumns.addElement(new int[] {
1922 region[0] - hiddenOffset, region[1] - hiddenOffset });
1927 copiedHiddenColumns = null;
1930 for (int i = 0; i < sg.getSize(); i++)
1932 SequenceI seq = null;
1936 if (orderedSeqs.containsKey(index))
1938 seq = orderedSeqs.get(index);
1949 // Returns residue following index if gap
1950 startRes = seq.findPosition(sg.getStartRes());
1953 // Need to find the residue preceeding index if gap
1956 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1958 ch = seq.getCharAt(j);
1959 if (!jalview.util.Comparison.isGap((ch)))
1967 endRes += seq.getStart() - 1;
1970 copiedSequences.append(seq.getName()
1976 + seq.getSequenceAsString(sg.getStartRes(),
1977 sg.getEndRes() + 1) + "\n");
1982 protected void pasteNew_actionPerformed()
1987 protected void pasteThis_actionPerformed()
1992 void paste(boolean newAlignment)
1997 if (copiedSequences == null)
2002 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2003 Vector seqs = new Vector();
2004 while (st.hasMoreElements())
2006 String name = st.nextToken();
2007 int start = Integer.parseInt(st.nextToken());
2008 int end = Integer.parseInt(st.nextToken());
2009 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2011 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2012 for (int i = 0; i < seqs.size(); i++)
2014 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2019 String newtitle = MessageManager
2020 .getString("label.copied_sequences");
2021 if (getTitle().startsWith(
2022 MessageManager.getString("label.copied_sequences")))
2024 newtitle = getTitle();
2028 newtitle = newtitle.concat(MessageManager.formatMessage(
2029 "label.from_msname", new String[] { getTitle() }));
2031 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2032 viewport.applet, newtitle, false);
2033 if (copiedHiddenColumns != null)
2035 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2037 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2038 af.viewport.hideColumns(region[0], region[1]);
2042 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2047 addSequences(newSeqs);
2050 } catch (Exception ex)
2052 } // could be anything being pasted in here
2056 void addSequences(SequenceI[] seqs)
2058 for (int i = 0; i < seqs.length; i++)
2060 viewport.getAlignment().addSequence(seqs[i]);
2064 addHistoryItem(new EditCommand(
2065 MessageManager.getString("label.add_sequences"), Action.PASTE,
2066 seqs, 0, viewport.getAlignment().getWidth(),
2067 viewport.getAlignment()));
2069 viewport.getRanges().setEndSeq(viewport.getAlignment().getHeight());
2070 viewport.getAlignment().getWidth();
2071 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2076 protected void cut_actionPerformed()
2078 copy_actionPerformed();
2079 delete_actionPerformed();
2082 protected void delete_actionPerformed()
2085 SequenceGroup sg = viewport.getSelectionGroup();
2091 Vector seqs = new Vector();
2093 for (int i = 0; i < sg.getSize(); i++)
2095 seq = sg.getSequenceAt(i);
2096 seqs.addElement(seq);
2100 * If the cut affects all sequences, warn, remove highlighted columns
2102 if (sg.getSize() == viewport.getAlignment().getHeight())
2104 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2105 .getAlignment().getWidth()) ? true : false;
2106 if (isEntireAlignWidth)
2108 String title = MessageManager.getString("label.delete_all");
2109 Panel infoPanel = new Panel();
2110 infoPanel.setLayout(new FlowLayout());
2112 .add(new Label(MessageManager.getString("warn.delete_all")));
2114 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2115 dialog.setMainPanel(infoPanel);
2116 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2117 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2118 dialog.setVisible(true);
2125 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2126 sg.getEndRes() + 1);
2129 SequenceI[] cut = new SequenceI[seqs.size()];
2130 for (int i = 0; i < seqs.size(); i++)
2132 cut[i] = (SequenceI) seqs.elementAt(i);
2136 * //ADD HISTORY ITEM
2138 addHistoryItem(new EditCommand(
2139 MessageManager.getString("label.cut_sequences"), Action.CUT,
2140 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2141 viewport.getAlignment()));
2143 viewport.setSelectionGroup(null);
2144 viewport.getAlignment().deleteGroup(sg);
2146 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2149 if (viewport.getAlignment().getHeight() < 1)
2151 this.setVisible(false);
2153 viewport.sendSelection();
2157 * group consensus toggled
2160 protected void showGroupConsensus_actionPerformed()
2162 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2163 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168 * group conservation toggled.
2170 protected void showGroupConservation_actionPerformed()
2172 viewport.setShowGroupConservation(showGroupConservation.getState());
2173 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2180 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2181 * .event.ActionEvent)
2183 protected void showConsensusHistogram_actionPerformed()
2185 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2186 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2193 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2194 * .event.ActionEvent)
2196 protected void showSequenceLogo_actionPerformed()
2198 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2199 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2202 protected void normSequenceLogo_actionPerformed()
2204 showSequenceLogo.setState(true);
2205 viewport.setShowSequenceLogo(true);
2206 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2207 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2210 protected void applyAutoAnnotationSettings_actionPerformed()
2212 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2215 protected void makeGrpsFromSelection_actionPerformed()
2217 if (avc.makeGroupsFromSelection())
2219 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2220 alignPanel.updateAnnotation();
2221 alignPanel.paintAlignment(true);
2225 protected void createGroup_actionPerformed()
2230 protected void unGroup_actionPerformed()
2234 alignPanel.alignmentChanged();
2238 protected void deleteGroups_actionPerformed()
2240 if (avc.deleteGroups())
2242 alignPanel.alignmentChanged();
2246 public void selectAllSequenceMenuItem_actionPerformed()
2248 SequenceGroup sg = new SequenceGroup();
2249 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2251 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2253 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2254 viewport.setSelectionGroup(sg);
2255 // JAL-2034 - should delegate to
2256 // alignPanel to decide if overview needs
2258 alignPanel.paintAlignment(false);
2259 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2260 viewport.sendSelection();
2263 public void deselectAllSequenceMenuItem_actionPerformed()
2265 if (viewport.cursorMode)
2267 alignPanel.seqPanel.keyboardNo1 = null;
2268 alignPanel.seqPanel.keyboardNo2 = null;
2270 viewport.setSelectionGroup(null);
2271 viewport.getColumnSelection().clear();
2272 viewport.setSelectionGroup(null);
2273 alignPanel.idPanel.idCanvas.searchResults = null;
2274 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2275 // JAL-2034 - should delegate to
2276 // alignPanel to decide if overview needs
2278 alignPanel.paintAlignment(false);
2279 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2280 viewport.sendSelection();
2283 public void invertSequenceMenuItem_actionPerformed()
2285 SequenceGroup sg = viewport.getSelectionGroup();
2286 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2288 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2291 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2292 viewport.sendSelection();
2295 public void invertColSel_actionPerformed()
2297 viewport.invertColumnSelection();
2298 alignPanel.paintAlignment(true);
2299 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2300 viewport.sendSelection();
2303 void trimAlignment(boolean trimLeft)
2305 AlignmentI al = viewport.getAlignment();
2306 ViewportRanges ranges = viewport.getRanges();
2307 ColumnSelection colSel = viewport.getColumnSelection();
2310 if (!colSel.isEmpty())
2314 column = colSel.getMin();
2318 column = colSel.getMax();
2322 if (viewport.getSelectionGroup() != null)
2324 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2325 viewport.getHiddenRepSequences());
2329 seqs = al.getSequencesArray();
2332 TrimRegionCommand trimRegion;
2335 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2337 ranges.setStartRes(0);
2341 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2345 statusBar.setText(MessageManager.formatMessage(
2346 "label.removed_columns",
2347 new String[] { Integer.valueOf(trimRegion.getSize())
2349 addHistoryItem(trimRegion);
2351 for (SequenceGroup sg : al.getGroups())
2353 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2354 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2360 viewport.firePropertyChange("alignment", null, al.getSequences());
2364 public void removeGappedColumnMenuItem_actionPerformed()
2366 AlignmentI al = viewport.getAlignment();
2367 ViewportRanges ranges = viewport.getRanges();
2369 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2372 if (viewport.getSelectionGroup() != null)
2374 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2375 viewport.getHiddenRepSequences());
2376 start = viewport.getSelectionGroup().getStartRes();
2377 end = viewport.getSelectionGroup().getEndRes();
2381 seqs = viewport.getAlignment().getSequencesArray();
2384 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2385 "Remove Gapped Columns", seqs, start, end,
2386 viewport.getAlignment());
2388 addHistoryItem(removeGapCols);
2390 statusBar.setText(MessageManager.formatMessage(
2391 "label.removed_empty_columns",
2392 new String[] { Integer.valueOf(removeGapCols.getSize())
2395 // This is to maintain viewport position on first residue
2396 // of first sequence
2397 SequenceI seq = al.getSequenceAt(0);
2398 int startRes = seq.findPosition(ranges.getStartRes());
2399 // ShiftList shifts;
2400 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2401 // edit.alColumnChanges=shifts.getInverse();
2402 // if (viewport.hasHiddenColumns)
2403 // viewport.getColumnSelection().compensateForEdits(shifts);
2404 ranges.setStartRes(seq.findIndex(startRes) - 1);
2405 viewport.firePropertyChange("alignment", null, al.getSequences());
2409 public void removeAllGapsMenuItem_actionPerformed()
2411 AlignmentI al = viewport.getAlignment();
2412 ViewportRanges ranges = viewport.getRanges();
2414 int end = ranges.getAbsoluteAlignmentWidth() - 1;
2417 if (viewport.getSelectionGroup() != null)
2419 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2420 viewport.getHiddenRepSequences());
2421 start = viewport.getSelectionGroup().getStartRes();
2422 end = viewport.getSelectionGroup().getEndRes();
2426 seqs = viewport.getAlignment().getSequencesArray();
2429 // This is to maintain viewport position on first residue
2430 // of first sequence
2431 SequenceI seq = al.getSequenceAt(0);
2432 int startRes = seq.findPosition(ranges.getStartRes());
2434 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2437 ranges.setStartRes(seq.findIndex(startRes) - 1);
2439 viewport.firePropertyChange("alignment", null, al.getSequences());
2443 public void findMenuItem_actionPerformed()
2445 new Finder(alignPanel);
2449 * create a new view derived from the current view
2452 * @return frame for the new view
2454 public AlignFrame newView(String viewtitle)
2457 if (viewport.hasHiddenRows())
2459 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2460 .getFullAlignment().getSequencesArray());
2464 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2467 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2469 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2471 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2473 newal.addAnnotation(viewport.getAlignment()
2474 .getAlignmentAnnotation()[i]);
2479 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2481 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2482 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2483 PaintRefresher.Register(newaf.alignPanel,
2484 newaf.alignPanel.av.getSequenceSetId());
2486 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2487 newaf.alignPanel.av.getSequenceSetId());
2488 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2489 newaf.alignPanel.av.getSequenceSetId());
2491 Vector comps = (Vector) PaintRefresher.components.get(viewport
2492 .getSequenceSetId());
2494 for (int i = 0; i < comps.size(); i++)
2496 if (comps.elementAt(i) instanceof AlignmentPanel)
2502 String title = new String(this.getTitle());
2503 if (viewtitle != null)
2505 title = viewtitle + " ( " + title + ")";
2509 if (title.indexOf("(View") > -1)
2511 title = title.substring(0, title.indexOf("(View"));
2513 title += "(View " + viewSize + ")";
2516 newaf.setTitle(title.toString());
2518 newaf.viewport.setHistoryList(viewport.getHistoryList());
2519 newaf.viewport.setRedoList(viewport.getRedoList());
2525 * @return list of feature groups on the view
2527 public String[] getFeatureGroups()
2529 FeatureRenderer fr = null;
2530 if (alignPanel != null
2531 && (fr = alignPanel.getFeatureRenderer()) != null)
2533 List<String> gps = fr.getFeatureGroups();
2534 String[] _gps = gps.toArray(new String[gps.size()]);
2541 * get sequence feature groups that are hidden or shown
2547 public String[] getFeatureGroupsOfState(boolean visible)
2549 FeatureRenderer fr = null;
2550 if (alignPanel != null
2551 && (fr = alignPanel.getFeatureRenderer()) != null)
2553 List<String> gps = fr.getGroups(visible);
2554 String[] _gps = gps.toArray(new String[gps.size()]);
2561 * Change the display state for the given feature groups
2564 * list of group strings
2566 * visible or invisible
2568 public void setFeatureGroupState(String[] groups, boolean state)
2570 FeatureRenderer fr = null;
2571 this.sequenceFeatures.setState(true);
2572 viewport.setShowSequenceFeatures(true);
2573 if (alignPanel != null
2574 && (fr = alignPanel.getFeatureRenderer()) != null)
2577 fr.setGroupVisibility(Arrays.asList(groups), state);
2578 alignPanel.seqPanel.seqCanvas.repaint();
2579 if (alignPanel.overviewPanel != null)
2581 alignPanel.overviewPanel.updateOverviewImage();
2586 public void seqLimits_itemStateChanged()
2588 viewport.setShowJVSuffix(seqLimits.getState());
2589 alignPanel.fontChanged();
2590 alignPanel.paintAlignment(true);
2593 protected void colourTextMenuItem_actionPerformed()
2595 viewport.setColourText(colourTextMenuItem.getState());
2596 alignPanel.paintAlignment(true);
2599 protected void displayNonconservedMenuItem_actionPerformed()
2601 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2602 alignPanel.paintAlignment(true);
2605 protected void wrapMenuItem_actionPerformed()
2607 viewport.setWrapAlignment(wrapMenuItem.getState());
2608 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2609 scaleAbove.setEnabled(wrapMenuItem.getState());
2610 scaleLeft.setEnabled(wrapMenuItem.getState());
2611 scaleRight.setEnabled(wrapMenuItem.getState());
2612 alignPanel.paintAlignment(true);
2615 public void overviewMenuItem_actionPerformed()
2617 if (alignPanel.overviewPanel != null)
2622 Frame frame = new Frame();
2623 OverviewPanel overview = new OverviewPanel(alignPanel);
2624 frame.add(overview);
2625 // +50 must allow for applet frame window
2626 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2627 "label.overview_params", new String[] { this.getTitle() }),
2628 overview.getPreferredSize().width,
2629 overview.getPreferredSize().height + 50);
2632 final AlignmentPanel ap = alignPanel;
2633 frame.addWindowListener(new WindowAdapter()
2636 public void windowClosing(WindowEvent e)
2640 ap.setOverviewPanel(null);
2645 alignPanel.setOverviewPanel(overview);
2650 public void changeColour(ColourSchemeI cs)
2652 viewport.setGlobalColourScheme(cs);
2654 alignPanel.paintAlignment(true);
2657 protected void modifyPID_actionPerformed()
2659 if (viewport.getAbovePIDThreshold()
2660 && viewport.getGlobalColourScheme() != null)
2662 SliderPanel.setPIDSliderSource(alignPanel,
2663 viewport.getResidueShading(), alignPanel.getViewName());
2664 SliderPanel.showPIDSlider();
2668 protected void modifyConservation_actionPerformed()
2670 if (viewport.getConservationSelected()
2671 && viewport.getGlobalColourScheme() != null)
2673 SliderPanel.setConservationSlider(alignPanel,
2674 viewport.getResidueShading(), alignPanel.getViewName());
2675 SliderPanel.showConservationSlider();
2679 protected void conservationMenuItem_actionPerformed()
2681 boolean selected = conservationMenuItem.getState();
2682 modifyConservation.setEnabled(selected);
2683 viewport.setConservationSelected(selected);
2685 // viewport.setAbovePIDThreshold(false);
2686 // abovePIDThreshold.setState(false);
2688 changeColour(viewport.getGlobalColourScheme());
2692 modifyConservation_actionPerformed();
2696 SliderPanel.hideConservationSlider();
2700 public void abovePIDThreshold_actionPerformed()
2702 boolean selected = abovePIDThreshold.getState();
2703 modifyPID.setEnabled(selected);
2704 viewport.setAbovePIDThreshold(selected);
2705 // conservationMenuItem.setState(false);
2706 // viewport.setConservationSelected(false);
2708 changeColour(viewport.getGlobalColourScheme());
2712 modifyPID_actionPerformed();
2716 SliderPanel.hidePIDSlider();
2720 public void sortPairwiseMenuItem_actionPerformed()
2722 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2723 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2724 .getAlignment().getSequenceAt(0), null);
2726 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2727 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2731 public void sortIDMenuItem_actionPerformed()
2733 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2734 AlignmentSorter.sortByID(viewport.getAlignment());
2735 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2736 viewport.getAlignment()));
2737 alignPanel.paintAlignment(true);
2740 public void sortLengthMenuItem_actionPerformed()
2742 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2743 AlignmentSorter.sortByLength(viewport.getAlignment());
2744 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2745 viewport.getAlignment()));
2746 alignPanel.paintAlignment(true);
2749 public void sortGroupMenuItem_actionPerformed()
2751 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2752 AlignmentSorter.sortByGroup(viewport.getAlignment());
2753 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2754 viewport.getAlignment()));
2755 alignPanel.paintAlignment(true);
2759 public void removeRedundancyMenuItem_actionPerformed()
2761 new RedundancyPanel(alignPanel);
2764 public void pairwiseAlignmentMenuItem_actionPerformed()
2766 if (viewport.getSelectionGroup() != null
2767 && viewport.getSelectionGroup().getSize() > 1)
2769 Frame frame = new Frame();
2770 frame.add(new PairwiseAlignPanel(alignPanel));
2771 jalview.bin.JalviewLite.addFrame(frame,
2772 MessageManager.getString("action.pairwise_alignment"), 600,
2777 public void PCAMenuItem_actionPerformed()
2779 // are the sequences aligned?
2780 if (!viewport.getAlignment().isAligned(false))
2783 int Width = viewport.getAlignment().getWidth();
2785 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2787 current = viewport.getAlignment().getSequenceAt(i);
2789 if (current.getLength() < Width)
2791 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2794 alignPanel.paintAlignment(true);
2797 if ((viewport.getSelectionGroup() != null
2798 && viewport.getSelectionGroup().getSize() < 4 && viewport
2799 .getSelectionGroup().getSize() > 0)
2800 || viewport.getAlignment().getHeight() < 4)
2807 new PCAPanel(viewport);
2808 } catch (java.lang.OutOfMemoryError ex)
2814 public void averageDistanceTreeMenuItem_actionPerformed()
2816 NewTreePanel("AV", "PID", "Average distance tree using PID");
2819 public void neighbourTreeMenuItem_actionPerformed()
2821 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2824 protected void njTreeBlosumMenuItem_actionPerformed()
2826 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2829 protected void avTreeBlosumMenuItem_actionPerformed()
2831 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2834 void NewTreePanel(String type, String pwType, String title)
2836 // are the sequences aligned?
2837 if (!viewport.getAlignment().isAligned(false))
2840 int Width = viewport.getAlignment().getWidth();
2842 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2844 current = viewport.getAlignment().getSequenceAt(i);
2846 if (current.getLength() < Width)
2848 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2851 alignPanel.paintAlignment(true);
2855 if ((viewport.getSelectionGroup() != null && viewport
2856 .getSelectionGroup().getSize() > 1)
2857 || (viewport.getAlignment().getHeight() > 1))
2859 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2861 addTreeMenuItem(tp, title);
2863 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2867 void loadTree_actionPerformed()
2869 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2870 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2871 cap.setTreeImport();
2872 Frame frame = new Frame();
2874 jalview.bin.JalviewLite.addFrame(frame,
2875 MessageManager.getString("label.paste_newick_file"), 400, 300);
2878 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2880 TreePanel tp = new TreePanel(alignPanel, treeFile,
2881 MessageManager.getString("label.load_tree_from_file"), tree);
2882 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2883 addTreeMenuItem(tp, treeFile);
2887 * sort the alignment using the given treePanel
2890 * tree used to sort view
2892 * string used for undo event name
2894 public void sortByTree(TreePanel treePanel, String title)
2896 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2898 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2899 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2900 // HistoryItem.SORT));
2901 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2902 "label.order_by_params", new String[] { title }), oldOrder,
2903 viewport.getAlignment()));
2904 alignPanel.paintAlignment(true);
2908 * Do any automatic reordering of the alignment and add the necessary bits to
2909 * the menu structure for the new tree
2914 protected void addTreeMenuItem(final TreePanel treePanel,
2917 final MenuItem item = new MenuItem(title);
2918 sortByTreeMenu.add(item);
2919 item.addActionListener(new java.awt.event.ActionListener()
2922 public void actionPerformed(ActionEvent evt)
2924 sortByTree(treePanel, title); // treePanel.getTitle());
2928 treePanel.addWindowListener(new WindowAdapter()
2931 public void windowOpened(WindowEvent e)
2933 if (viewport.sortByTree)
2935 sortByTree(treePanel, title);
2937 super.windowOpened(e);
2941 public void windowClosing(WindowEvent e)
2943 sortByTreeMenu.remove(item);
2948 public boolean sortBy(AlignmentOrder alorder, String undoname)
2950 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2951 if (viewport.applet.debug)
2953 System.err.println("Sorting " + alorder.getOrder().size()
2954 + " in alignment '" + getTitle() + "'");
2956 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2957 if (undoname != null)
2959 addHistoryItem(new OrderCommand(undoname, oldOrder,
2960 viewport.getAlignment()));
2962 alignPanel.paintAlignment(true);
2966 protected void documentation_actionPerformed()
2968 alignPanel.av.applet.openJalviewHelpUrl();
2971 protected void about_actionPerformed()
2974 class AboutPanel extends Canvas
2980 public AboutPanel(String version, String builddate)
2982 this.version = version;
2983 this.builddate = builddate;
2987 public void paint(Graphics g)
2989 g.setColor(Color.white);
2990 g.fillRect(0, 0, getSize().width, getSize().height);
2991 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2992 FontMetrics fm = g.getFontMetrics();
2993 int fh = fm.getHeight();
2995 g.setColor(Color.black);
2996 // TODO: update this text for each release or centrally store it for
2997 // lite and application
2998 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2999 g.drawString(MessageManager.formatMessage(
3000 "label.jalviewLite_release", new String[] { version }), x,
3002 g.setFont(new Font("Helvetica", Font.BOLD, 12));
3003 g.drawString(MessageManager.formatMessage(
3004 "label.jaview_build_date", new String[] { builddate }), x,
3006 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
3007 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3009 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3010 x + 50, y += fh + 8);
3012 MessageManager.getString("label.jalview_dev_managers"), x,
3014 g.drawString(MessageManager
3015 .getString("label.jalview_distribution_lists"), x, y += fh);
3016 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3019 MessageManager.getString("label.jalview_cite_1_authors"),
3022 MessageManager.getString("label.jalview_cite_1_title"), x,
3024 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3029 Frame frame = new Frame();
3030 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3032 jalview.bin.JalviewLite.addFrame(frame,
3033 MessageManager.getString("label.jalview"), 580, 220);
3037 public void showURL(String url, String target)
3039 if (viewport.applet == null)
3041 System.out.println("Not running as applet - no browser available.");
3045 viewport.applet.showURL(url, target);
3049 // ////////////////////////////////////////////////////////////////////////////////
3050 // JBuilder Graphics here
3052 MenuBar alignFrameMenuBar = new MenuBar();
3054 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3056 MenuItem loadApplication = new MenuItem(
3057 MessageManager.getString("label.view_full_application"));
3059 MenuItem loadTree = new MenuItem(
3060 MessageManager.getString("label.load_associated_tree"));
3062 MenuItem loadAnnotations = new MenuItem(
3063 MessageManager.getString("label.load_features_annotations"));
3065 MenuItem outputFeatures = new MenuItem(
3066 MessageManager.getString("label.export_features"));
3068 MenuItem outputAnnotations = new MenuItem(
3069 MessageManager.getString("label.export_annotations"));
3071 MenuItem closeMenuItem = new MenuItem(
3072 MessageManager.getString("action.close"));
3074 MenuItem selectAllSequenceMenuItem = new MenuItem(
3075 MessageManager.getString("action.select_all"));
3077 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3078 MessageManager.getString("action.deselect_all"));
3080 MenuItem invertSequenceMenuItem = new MenuItem(
3081 MessageManager.getString("action.invert_selection"));
3083 MenuItem remove2LeftMenuItem = new MenuItem();
3085 MenuItem remove2RightMenuItem = new MenuItem();
3087 MenuItem removeGappedColumnMenuItem = new MenuItem();
3089 MenuItem removeAllGapsMenuItem = new MenuItem();
3091 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3093 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3095 MenuItem sortPairwiseMenuItem = new MenuItem();
3097 MenuItem sortIDMenuItem = new MenuItem();
3099 MenuItem sortLengthMenuItem = new MenuItem();
3101 MenuItem sortGroupMenuItem = new MenuItem();
3103 MenuItem removeRedundancyMenuItem = new MenuItem();
3105 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3107 MenuItem PCAMenuItem = new MenuItem();
3109 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3111 MenuItem neighbourTreeMenuItem = new MenuItem();
3113 BorderLayout borderLayout1 = new BorderLayout();
3115 public Label statusBar = new Label();
3117 MenuItem clustalColour = new MenuItem();
3119 MenuItem zappoColour = new MenuItem();
3121 MenuItem taylorColour = new MenuItem();
3123 MenuItem hydrophobicityColour = new MenuItem();
3125 MenuItem helixColour = new MenuItem();
3127 MenuItem strandColour = new MenuItem();
3129 MenuItem turnColour = new MenuItem();
3131 MenuItem buriedColour = new MenuItem();
3133 MenuItem purinePyrimidineColour = new MenuItem();
3135 // MenuItem RNAInteractionColour = new MenuItem();
3137 MenuItem RNAHelixColour = new MenuItem();
3139 MenuItem userDefinedColour = new MenuItem();
3141 MenuItem PIDColour = new MenuItem();
3143 MenuItem BLOSUM62Colour = new MenuItem();
3145 MenuItem tcoffeeColour = new MenuItem();
3147 MenuItem njTreeBlosumMenuItem = new MenuItem();
3149 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3151 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3153 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3155 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3157 MenuItem alProperties = new MenuItem(
3158 MessageManager.getString("label.alignment_props"));
3160 MenuItem overviewMenuItem = new MenuItem();
3162 MenuItem undoMenuItem = new MenuItem();
3164 MenuItem redoMenuItem = new MenuItem();
3166 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3168 MenuItem noColourmenuItem = new MenuItem();
3170 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3172 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3174 MenuItem findMenuItem = new MenuItem();
3176 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3178 MenuItem nucleotideColour = new MenuItem();
3180 MenuItem deleteGroups = new MenuItem();
3182 MenuItem grpsFromSelection = new MenuItem();
3184 MenuItem createGroup = new MenuItem();
3186 MenuItem unGroup = new MenuItem();
3188 MenuItem delete = new MenuItem();
3190 MenuItem copy = new MenuItem();
3192 MenuItem cut = new MenuItem();
3194 Menu pasteMenu = new Menu();
3196 MenuItem pasteNew = new MenuItem();
3198 MenuItem pasteThis = new MenuItem();
3200 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3202 MenuItem font = new MenuItem();
3204 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3206 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3208 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3210 MenuItem modifyPID = new MenuItem();
3212 MenuItem modifyConservation = new MenuItem();
3214 CheckboxMenuItem autoCalculate = null;
3216 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3217 "Sort Alignment With New Tree", true);
3219 Menu sortByTreeMenu = new Menu();
3221 MenuItem inputText = new MenuItem();
3223 MenuItem documentation = new MenuItem();
3225 MenuItem about = new MenuItem();
3227 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3229 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3231 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3233 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3235 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3237 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3239 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3241 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3243 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3246 * Initialise menus and other items
3250 private void jbInit() throws Exception
3252 setMenuBar(alignFrameMenuBar);
3255 * Configure File menu items and actions
3258 .setLabel(MessageManager.getString("label.input_from_textbox"));
3259 inputText.addActionListener(this);
3260 Menu outputTextboxMenu = new Menu(
3261 MessageManager.getString("label.out_to_textbox"));
3262 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3264 MenuItem item = new MenuItem(ff);
3266 item.addActionListener(new java.awt.event.ActionListener()
3269 public void actionPerformed(ActionEvent e)
3271 outputText_actionPerformed(e);
3275 outputTextboxMenu.add(item);
3277 closeMenuItem.addActionListener(this);
3278 loadApplication.addActionListener(this);
3279 loadTree.addActionListener(this);
3280 loadAnnotations.addActionListener(this);
3281 outputFeatures.addActionListener(this);
3282 outputAnnotations.addActionListener(this);
3285 * Configure Edit menu items and actions
3287 undoMenuItem.setEnabled(false);
3288 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3289 undoMenuItem.addActionListener(this);
3290 redoMenuItem.setEnabled(false);
3291 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3292 redoMenuItem.addActionListener(this);
3293 copy.setLabel(MessageManager.getString("action.copy"));
3294 copy.addActionListener(this);
3295 cut.setLabel(MessageManager.getString("action.cut"));
3296 cut.addActionListener(this);
3297 delete.setLabel(MessageManager.getString("action.delete"));
3298 delete.addActionListener(this);
3299 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3300 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3301 pasteNew.addActionListener(this);
3302 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3303 pasteThis.addActionListener(this);
3304 remove2LeftMenuItem.setLabel(MessageManager
3305 .getString("action.remove_left"));
3306 remove2LeftMenuItem.addActionListener(this);
3307 remove2RightMenuItem.setLabel(MessageManager
3308 .getString("action.remove_right"));
3309 remove2RightMenuItem.addActionListener(this);
3310 removeGappedColumnMenuItem.setLabel(MessageManager
3311 .getString("action.remove_empty_columns"));
3312 removeGappedColumnMenuItem.addActionListener(this);
3313 removeAllGapsMenuItem.setLabel(MessageManager
3314 .getString("action.remove_all_gaps"));
3315 removeAllGapsMenuItem.addActionListener(this);
3316 removeRedundancyMenuItem.setLabel(MessageManager
3317 .getString("action.remove_redundancy"));
3318 removeRedundancyMenuItem.addActionListener(this);
3321 * Configure Select menu items and actions
3323 findMenuItem.setLabel(MessageManager.getString("action.find"));
3324 findMenuItem.addActionListener(this);
3325 selectAllSequenceMenuItem.addActionListener(this);
3326 deselectAllSequenceMenuItem.addActionListener(this);
3327 invertSequenceMenuItem.setLabel(MessageManager
3328 .getString("action.invert_sequence_selection"));
3329 invertSequenceMenuItem.addActionListener(this);
3330 invertColSel.setLabel(MessageManager
3331 .getString("action.invert_column_selection"));
3332 invertColSel.addActionListener(this);
3333 deleteGroups.setLabel(MessageManager
3334 .getString("action.undefine_groups"));
3335 deleteGroups.addActionListener(this);
3336 grpsFromSelection.setLabel(MessageManager
3337 .getString("action.make_groups_selection"));
3338 grpsFromSelection.addActionListener(this);
3339 createGroup.setLabel(MessageManager.getString("action.create_group"));
3340 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3341 annotationColumnSelection.setLabel(MessageManager
3342 .getString("action.select_by_annotation"));
3343 annotationColumnSelection.addActionListener(this);
3346 * Configure View menu items and actions
3348 newView.setLabel(MessageManager.getString("action.new_view"));
3349 newView.addActionListener(this);
3350 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3351 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3352 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3353 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3355 .setLabel(MessageManager.getString("label.selected_columns"));
3356 hideSequences.setLabel(MessageManager
3357 .getString("label.selected_sequences"));
3358 hideAllButSelection.setLabel(MessageManager
3359 .getString("label.all_but_selected_region"));
3360 hideAllSelection.setLabel(MessageManager
3361 .getString("label.selected_region"));
3362 showAllHidden.setLabel(MessageManager
3363 .getString("label.all_sequences_columns"));
3364 showColumns.addActionListener(this);
3365 showSeqs.addActionListener(this);
3366 hideColumns.addActionListener(this);
3367 hideSequences.addActionListener(this);
3368 hideAllButSelection.addActionListener(this);
3369 hideAllSelection.addActionListener(this);
3370 showAllHidden.addActionListener(this);
3371 featureSettings.setLabel(MessageManager
3372 .getString("action.feature_settings"));
3373 featureSettings.addActionListener(this);
3374 sequenceFeatures.setLabel(MessageManager
3375 .getString("label.show_sequence_features"));
3376 sequenceFeatures.addItemListener(this);
3377 sequenceFeatures.setState(false);
3378 followMouseOverFlag.setLabel(MessageManager
3379 .getString("label.automatic_scrolling"));
3380 followMouseOverFlag.addItemListener(this);
3381 alProperties.addActionListener(this);
3382 overviewMenuItem.setLabel(MessageManager
3383 .getString("label.overview_window"));
3384 overviewMenuItem.addActionListener(this);
3387 * Configure Annotations menu items and actions
3389 annotationPanelMenuItem.setLabel(MessageManager
3390 .getString("label.show_annotations"));
3391 annotationPanelMenuItem.addItemListener(this);
3392 showGroupConsensus.setLabel(MessageManager
3393 .getString("label.group_consensus"));
3394 showGroupConservation.setLabel(MessageManager
3395 .getString("label.group_conservation"));
3396 showConsensusHistogram.setLabel(MessageManager
3397 .getString("label.show_consensus_histogram"));
3398 showSequenceLogo.setLabel(MessageManager
3399 .getString("label.show_consensus_logo"));
3400 normSequenceLogo.setLabel(MessageManager
3401 .getString("label.norm_consensus_logo"));
3402 applyAutoAnnotationSettings.setLabel(MessageManager
3403 .getString("label.apply_all_groups"));
3404 applyAutoAnnotationSettings.setState(true);
3405 Menu autoAnnMenu = new Menu(
3406 MessageManager.getString("label.autocalculated_annotation"));
3407 showGroupConsensus.addItemListener(this);
3408 showGroupConservation.addItemListener(this);
3409 showConsensusHistogram.addItemListener(this);
3410 showSequenceLogo.addItemListener(this);
3411 normSequenceLogo.addItemListener(this);
3412 applyAutoAnnotationSettings.addItemListener(this);
3413 showAlignmentAnnotations = new CheckboxMenuItem(
3414 MessageManager.getString("label.show_all_al_annotations"));
3415 showSequenceAnnotations = new CheckboxMenuItem(
3416 MessageManager.getString("label.show_all_seq_annotations"));
3417 sortAnnBySequence = new CheckboxMenuItem(
3418 MessageManager.getString("label.sort_annotations_by_sequence"));
3419 sortAnnByLabel = new CheckboxMenuItem(
3420 MessageManager.getString("label.sort_annotations_by_label"));
3421 showAutoFirst = new CheckboxMenuItem(
3422 MessageManager.getString("label.show_first"));
3423 showAutoFirst.setState(false); // pending applet parameter
3424 setShowAutoCalculatedAbove(showAutoFirst.getState());
3425 showAutoLast = new CheckboxMenuItem(
3426 MessageManager.getString("label.show_last"));
3427 showAutoLast.setState(!showAutoFirst.getState());
3428 showAlignmentAnnotations.addItemListener(this);
3429 showSequenceAnnotations.addItemListener(this);
3430 sortAnnBySequence.addItemListener(this);
3431 sortAnnByLabel.addItemListener(this);
3432 showAutoFirst.addItemListener(this);
3433 showAutoLast.addItemListener(this);
3436 * Configure Format menu items and actions
3438 font.setLabel(MessageManager.getString("action.font"));
3439 font.addActionListener(this);
3440 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3441 scaleAbove.setState(true);
3442 scaleAbove.setEnabled(false);
3443 scaleAbove.addItemListener(this);
3444 scaleLeft.setEnabled(false);
3445 scaleLeft.setState(true);
3446 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3447 scaleLeft.addItemListener(this);
3448 scaleRight.setEnabled(false);
3449 scaleRight.setState(true);
3450 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3451 scaleRight.addItemListener(this);
3452 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3453 viewBoxesMenuItem.setState(true);
3454 viewBoxesMenuItem.addItemListener(this);
3455 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3456 viewTextMenuItem.setState(true);
3457 viewTextMenuItem.addItemListener(this);
3458 colourTextMenuItem.setLabel(MessageManager
3459 .getString("label.colour_text"));
3460 colourTextMenuItem.addItemListener(this);
3461 displayNonconservedMenuItem.setLabel(MessageManager
3462 .getString("label.show_non_conserved"));
3463 displayNonconservedMenuItem.addItemListener(this);
3464 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3465 wrapMenuItem.addItemListener(this);
3466 renderGapsMenuItem.setLabel(MessageManager
3467 .getString("action.show_gaps"));
3468 renderGapsMenuItem.setState(true);
3469 renderGapsMenuItem.addItemListener(this);
3470 centreColumnLabelFlag.setLabel(MessageManager
3471 .getString("label.centre_column_labels"));
3472 centreColumnLabelFlag.addItemListener(this);
3473 seqLimits.setState(true);
3474 seqLimits.setLabel(MessageManager
3475 .getString("label.show_sequence_limits"));
3476 seqLimits.addItemListener(this);
3479 * Configure Colour menu items and actions
3481 applyToAllGroups.setLabel(MessageManager
3482 .getString("label.apply_colour_to_all_groups"));
3483 applyToAllGroups.setState(true);
3484 applyToAllGroups.addItemListener(this);
3485 clustalColour.setLabel(MessageManager
3486 .getString("label.colourScheme_clustal"));
3487 clustalColour.addActionListener(this);
3488 zappoColour.setLabel(MessageManager
3489 .getString("label.colourScheme_zappo"));
3490 zappoColour.addActionListener(this);
3491 taylorColour.setLabel(MessageManager
3492 .getString("label.colourScheme_taylor"));
3493 taylorColour.addActionListener(this);
3494 hydrophobicityColour.setLabel(MessageManager
3495 .getString("label.colourScheme_hydrophobic"));
3496 hydrophobicityColour.addActionListener(this);
3497 helixColour.setLabel(MessageManager
3498 .getString("label.colourScheme_helix_propensity"));
3499 helixColour.addActionListener(this);
3500 strandColour.setLabel(MessageManager
3501 .getString("label.colourScheme_strand_propensity"));
3502 strandColour.addActionListener(this);
3503 turnColour.setLabel(MessageManager
3504 .getString("label.colourScheme_turn_propensity"));
3505 turnColour.addActionListener(this);
3506 buriedColour.setLabel(MessageManager
3507 .getString("label.colourScheme_buried_index"));
3508 buriedColour.addActionListener(this);
3509 purinePyrimidineColour.setLabel(MessageManager
3510 .getString("label.colourScheme_purine/pyrimidine"));
3511 purinePyrimidineColour.addActionListener(this);
3512 // RNAInteractionColour.setLabel(MessageManager
3513 // .getString("label.rna_interaction"));
3514 // RNAInteractionColour.addActionListener(this);
3515 RNAHelixColour.setLabel(MessageManager
3516 .getString("label.colourScheme_rna_helices"));
3517 RNAHelixColour.addActionListener(this);
3518 userDefinedColour.setLabel(MessageManager
3519 .getString("action.user_defined"));
3520 userDefinedColour.addActionListener(this);
3521 PIDColour.setLabel(MessageManager
3522 .getString("label.colourScheme_%_identity"));
3523 PIDColour.addActionListener(this);
3524 BLOSUM62Colour.setLabel(MessageManager
3525 .getString("label.colourScheme_blosum62"));
3526 BLOSUM62Colour.addActionListener(this);
3527 tcoffeeColour.setLabel(MessageManager
3528 .getString("label.colourScheme_t-coffee_scores"));
3529 // it will be enabled only if a score file is provided
3530 tcoffeeColour.setEnabled(false);
3531 tcoffeeColour.addActionListener(this);
3532 conservationMenuItem.setLabel(MessageManager
3533 .getString("action.by_conservation"));
3534 conservationMenuItem.addItemListener(this);
3535 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3536 noColourmenuItem.addActionListener(this);
3537 abovePIDThreshold.setLabel(MessageManager
3538 .getString("label.above_identity_threshold"));
3539 abovePIDThreshold.addItemListener(this);
3540 nucleotideColour.setLabel(MessageManager
3541 .getString("label.colourScheme_nucleotide"));
3542 nucleotideColour.addActionListener(this);
3543 modifyPID.setLabel(MessageManager
3544 .getString("label.modify_identity_threshold"));
3545 modifyPID.setEnabled(abovePIDThreshold.getState());
3546 modifyPID.addActionListener(this);
3547 modifyConservation.setLabel(MessageManager
3548 .getString("label.modify_conservation_threshold"));
3549 modifyConservation.setEnabled(conservationMenuItem.getState());
3550 modifyConservation.addActionListener(this);
3551 annotationColour.setLabel(MessageManager
3552 .getString("action.by_annotation"));
3553 annotationColour.addActionListener(this);
3556 * Configure Calculate menu items and actions
3558 sortPairwiseMenuItem.setLabel(MessageManager
3559 .getString("action.by_pairwise_id"));
3560 sortPairwiseMenuItem.addActionListener(this);
3561 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3562 sortIDMenuItem.addActionListener(this);
3563 sortLengthMenuItem.setLabel(MessageManager
3564 .getString("action.by_length"));
3565 sortLengthMenuItem.addActionListener(this);
3566 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3567 sortGroupMenuItem.addActionListener(this);
3568 pairwiseAlignmentMenuItem.setLabel(MessageManager
3569 .getString("action.pairwise_alignment"));
3570 pairwiseAlignmentMenuItem.addActionListener(this);
3571 PCAMenuItem.setLabel(MessageManager
3572 .getString("label.principal_component_analysis"));
3573 PCAMenuItem.addActionListener(this);
3574 autoCalculate = new CheckboxMenuItem(
3575 MessageManager.getString("label.autocalculate_consensus"), true);
3576 averageDistanceTreeMenuItem.setLabel(MessageManager
3577 .getString("label.average_distance_identity"));
3578 averageDistanceTreeMenuItem.addActionListener(this);
3579 neighbourTreeMenuItem.setLabel(MessageManager
3580 .getString("label.neighbour_joining_identity"));
3581 neighbourTreeMenuItem.addActionListener(this);
3582 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3583 .getString("label.average_distance_blosum62"));
3584 avDistanceTreeBlosumMenuItem.addActionListener(this);
3585 njTreeBlosumMenuItem.setLabel(MessageManager
3586 .getString("label.neighbour_blosum62"));
3587 njTreeBlosumMenuItem.addActionListener(this);
3588 sortByTreeMenu.setLabel(MessageManager
3589 .getString("action.by_tree_order"));
3590 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3591 Menu calculateTreeMenu = new Menu(
3592 MessageManager.getString("action.calculate_tree"));
3593 autoCalculate.addItemListener(this);
3594 sortByTree.addItemListener(this);
3597 * Configure Help menu items and actions
3599 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3600 documentation.setLabel(MessageManager.getString("label.documentation"));
3601 documentation.addActionListener(this);
3602 about.setLabel(MessageManager.getString("label.about"));
3603 about.addActionListener(this);
3606 * Add top level menus to frame
3608 alignFrameMenuBar.add(fileMenu);
3609 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3610 alignFrameMenuBar.add(editMenu);
3611 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3612 alignFrameMenuBar.add(selectMenu);
3613 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3614 alignFrameMenuBar.add(viewMenu);
3615 Menu annotationsMenu = new Menu(
3616 MessageManager.getString("action.annotations"));
3617 alignFrameMenuBar.add(annotationsMenu);
3618 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3619 alignFrameMenuBar.add(formatMenu);
3620 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3621 alignFrameMenuBar.add(colourMenu);
3622 Menu calculateMenu = new Menu(
3623 MessageManager.getString("action.calculate"));
3624 alignFrameMenuBar.add(calculateMenu);
3625 alignFrameMenuBar.add(helpMenu);
3630 fileMenu.add(inputText);
3631 fileMenu.add(loadTree);
3632 fileMenu.add(loadAnnotations);
3633 fileMenu.addSeparator();
3634 fileMenu.add(outputTextboxMenu);
3635 fileMenu.add(outputFeatures);
3636 fileMenu.add(outputAnnotations);
3637 if (jalviewServletURL != null)
3639 fileMenu.add(loadApplication);
3641 fileMenu.addSeparator();
3642 fileMenu.add(closeMenuItem);
3647 editMenu.add(undoMenuItem);
3648 editMenu.add(redoMenuItem);
3651 pasteMenu.add(pasteNew);
3652 pasteMenu.add(pasteThis);
3653 editMenu.add(pasteMenu);
3654 editMenu.add(delete);
3655 editMenu.addSeparator();
3656 editMenu.add(remove2LeftMenuItem);
3657 editMenu.add(remove2RightMenuItem);
3658 editMenu.add(removeGappedColumnMenuItem);
3659 editMenu.add(removeAllGapsMenuItem);
3660 editMenu.add(removeRedundancyMenuItem);
3665 selectMenu.add(findMenuItem);
3666 selectMenu.addSeparator();
3667 selectMenu.add(selectAllSequenceMenuItem);
3668 selectMenu.add(deselectAllSequenceMenuItem);
3669 selectMenu.add(invertSequenceMenuItem);
3670 selectMenu.add(invertColSel);
3671 selectMenu.add(createGroup);
3672 selectMenu.add(unGroup);
3673 selectMenu.add(grpsFromSelection);
3674 selectMenu.add(deleteGroups);
3675 selectMenu.add(annotationColumnSelection);
3680 viewMenu.add(newView);
3681 viewMenu.addSeparator();
3682 showMenu.add(showColumns);
3683 showMenu.add(showSeqs);
3684 showMenu.add(showAllHidden);
3685 viewMenu.add(showMenu);
3686 hideMenu.add(hideColumns);
3687 hideMenu.add(hideSequences);
3688 hideMenu.add(hideAllSelection);
3689 hideMenu.add(hideAllButSelection);
3690 viewMenu.add(hideMenu);
3691 viewMenu.addSeparator();
3692 viewMenu.add(followMouseOverFlag);
3693 viewMenu.addSeparator();
3694 viewMenu.add(sequenceFeatures);
3695 viewMenu.add(featureSettings);
3696 viewMenu.addSeparator();
3697 viewMenu.add(alProperties);
3698 viewMenu.addSeparator();
3699 viewMenu.add(overviewMenuItem);
3704 annotationsMenu.add(annotationPanelMenuItem);
3705 annotationsMenu.addSeparator();
3706 annotationsMenu.add(showAlignmentAnnotations);
3707 annotationsMenu.add(showSequenceAnnotations);
3708 annotationsMenu.add(sortAnnBySequence);
3709 annotationsMenu.add(sortAnnByLabel);
3710 annotationsMenu.addSeparator();
3711 autoAnnMenu.add(showAutoFirst);
3712 autoAnnMenu.add(showAutoLast);
3713 autoAnnMenu.addSeparator();
3714 autoAnnMenu.add(applyAutoAnnotationSettings);
3715 autoAnnMenu.add(showConsensusHistogram);
3716 autoAnnMenu.add(showSequenceLogo);
3717 autoAnnMenu.add(normSequenceLogo);
3718 autoAnnMenu.addSeparator();
3719 autoAnnMenu.add(showGroupConservation);
3720 autoAnnMenu.add(showGroupConsensus);
3721 annotationsMenu.add(autoAnnMenu);
3726 formatMenu.add(font);
3727 formatMenu.add(seqLimits);
3728 formatMenu.add(wrapMenuItem);
3729 formatMenu.add(scaleAbove);
3730 formatMenu.add(scaleLeft);
3731 formatMenu.add(scaleRight);
3732 formatMenu.add(viewBoxesMenuItem);
3733 formatMenu.add(viewTextMenuItem);
3734 formatMenu.add(colourTextMenuItem);
3735 formatMenu.add(displayNonconservedMenuItem);
3736 formatMenu.add(renderGapsMenuItem);
3737 formatMenu.add(centreColumnLabelFlag);
3742 colourMenu.add(applyToAllGroups);
3743 colourMenu.addSeparator();
3744 colourMenu.add(noColourmenuItem);
3745 colourMenu.add(clustalColour);
3746 colourMenu.add(BLOSUM62Colour);
3747 colourMenu.add(PIDColour);
3748 colourMenu.add(zappoColour);
3749 colourMenu.add(taylorColour);
3750 colourMenu.add(hydrophobicityColour);
3751 colourMenu.add(helixColour);
3752 colourMenu.add(strandColour);
3753 colourMenu.add(turnColour);
3754 colourMenu.add(buriedColour);
3755 colourMenu.add(nucleotideColour);
3756 colourMenu.add(purinePyrimidineColour);
3757 // colourMenu.add(RNAInteractionColour);
3758 colourMenu.add(tcoffeeColour);
3759 colourMenu.add(userDefinedColour);
3760 colourMenu.addSeparator();
3761 colourMenu.add(conservationMenuItem);
3762 colourMenu.add(modifyConservation);
3763 colourMenu.add(abovePIDThreshold);
3764 colourMenu.add(modifyPID);
3765 colourMenu.add(annotationColour);
3766 colourMenu.add(RNAHelixColour);
3771 sortMenu.add(sortIDMenuItem);
3772 sortMenu.add(sortLengthMenuItem);
3773 sortMenu.add(sortByTreeMenu);
3774 sortMenu.add(sortGroupMenuItem);
3775 sortMenu.add(sortPairwiseMenuItem);
3776 calculateMenu.add(sortMenu);
3777 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3778 calculateTreeMenu.add(neighbourTreeMenuItem);
3779 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3780 calculateTreeMenu.add(njTreeBlosumMenuItem);
3781 calculateMenu.add(calculateTreeMenu);
3782 calculateMenu.addSeparator();
3783 calculateMenu.add(pairwiseAlignmentMenuItem);
3784 calculateMenu.add(PCAMenuItem);
3785 calculateMenu.add(autoCalculate);
3786 calculateMenu.add(sortByTree);
3791 helpMenu.add(documentation);
3792 helpMenu.add(about);
3797 statusBar.setBackground(Color.white);
3798 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3799 statusBar.setText(MessageManager.getString("label.status_bar"));
3800 this.add(statusBar, BorderLayout.SOUTH);
3804 public void setStatus(String string)
3806 statusBar.setText(string);
3809 MenuItem featureSettings = new MenuItem();
3811 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3813 MenuItem annotationColour = new MenuItem();
3815 MenuItem annotationColumnSelection = new MenuItem();
3817 MenuItem invertColSel = new MenuItem();
3819 MenuItem showColumns = new MenuItem();
3821 MenuItem showSeqs = new MenuItem();
3823 MenuItem hideColumns = new MenuItem();
3825 MenuItem hideSequences = new MenuItem();
3827 MenuItem hideAllButSelection = new MenuItem();
3829 MenuItem hideAllSelection = new MenuItem();
3831 MenuItem showAllHidden = new MenuItem();
3833 MenuItem newView = new MenuItem();
3835 private CheckboxMenuItem showAlignmentAnnotations;
3837 private CheckboxMenuItem showSequenceAnnotations;
3839 private CheckboxMenuItem sortAnnBySequence;
3841 private CheckboxMenuItem sortAnnByLabel;
3843 private CheckboxMenuItem showAutoFirst;
3845 private CheckboxMenuItem showAutoLast;
3847 private SplitFrame splitFrame;
3850 * Attach the alignFrame panels after embedding menus, if necessary. This used
3851 * to be called setEmbedded, but is now creates the dropdown menus in a
3852 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3854 * @param reallyEmbedded
3855 * true to attach the view to the applet area on the page rather than
3858 public void createAlignFrameWindow(boolean reallyEmbedded)
3862 embedAlignFrameInApplet(viewport.applet);
3867 // test and embed menu bar if necessary.
3869 if (embedMenuIfNeeded(alignPanel))
3872 * adjust for status bar height too. ? pointless as overridden by layout
3875 alignPanel.setSize(getSize().width,
3876 getSize().height - statusBar.getHeight());
3878 add(statusBar, BorderLayout.SOUTH);
3879 add(alignPanel, BorderLayout.CENTER);
3880 // and register with the applet so it can pass external API calls to us
3881 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3887 * Add the components of this AlignFrame to the applet container.
3891 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3894 // Explicitly build the embedded menu panel for the on-page applet
3896 // view cannot be closed if its actually on the page
3897 fileMenu.remove(closeMenuItem);
3898 fileMenu.remove(3); // Remove Separator
3899 // construct embedded menu, using default font
3900 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3901 // and actually add the components to the applet area
3902 theApplet.setLayout(new BorderLayout());
3903 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3904 theApplet.add(statusBar, BorderLayout.SOUTH);
3905 // TODO should size be left to the layout manager?
3906 alignPanel.setSize(theApplet.getSize().width,
3907 theApplet.getSize().height - embeddedMenu.getHeight()
3908 - statusBar.getHeight());
3909 theApplet.add(alignPanel, BorderLayout.CENTER);
3910 final AlignFrame me = this;
3911 theApplet.addFocusListener(new FocusListener()
3915 public void focusLost(FocusEvent e)
3917 if (theApplet.currentAlignFrame == me)
3919 theApplet.currentAlignFrame = null;
3924 public void focusGained(FocusEvent e)
3926 theApplet.currentAlignFrame = me;
3929 theApplet.validate();
3933 * create a new binding between structures in an existing jmol viewer instance
3934 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3935 * this does not open a new Jmol window, or modify the display of the
3936 * structures in the original jmol window. Note This method doesn't work
3937 * without an additional javascript library to exchange messages between the
3938 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3941 * JmolViewer instance
3942 * @param sequenceIds
3943 * - sequence Ids to search for associations
3945 public SequenceStructureBinding addStructureViewInstance(
3946 Object jmolviewer, String[] sequenceIds)
3948 Viewer viewer = null;
3951 viewer = (Viewer) jmolviewer;
3952 } catch (ClassCastException ex)
3954 System.err.println("Unsupported viewer object :"
3955 + jmolviewer.getClass());
3959 System.err.println("Can't use this object as a structure viewer:"
3960 + jmolviewer.getClass());
3963 SequenceI[] seqs = null;
3964 if (sequenceIds == null || sequenceIds.length == 0)
3966 seqs = viewport.getAlignment().getSequencesArray();
3970 Vector sqi = new Vector();
3971 AlignmentI al = viewport.getAlignment();
3972 for (int sid = 0; sid < sequenceIds.length; sid++)
3974 SequenceI sq = al.findName(sequenceIds[sid]);
3982 seqs = new SequenceI[sqi.size()];
3983 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3985 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3993 AAStructureBindingModel jmv = null;
3994 // TODO: search for a jmv that involves viewer
3996 { // create a new viewer/jalview binding.
3997 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
4004 * bind a pdb file to a sequence in the current view
4007 * - sequenceId within the dataset.
4008 * @param pdbEntryString
4009 * - the short name for the PDB file
4011 * - pdb file - either a URL or a valid PDB file.
4012 * @return true if binding was as success TODO: consider making an exception
4013 * structure for indicating when PDB parsing or sequenceId location
4016 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4019 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4020 boolean needtoadd = false;
4021 if (toaddpdb != null)
4023 Vector pdbe = toaddpdb.getAllPDBEntries();
4024 PDBEntry pdbentry = null;
4025 if (pdbe != null && pdbe.size() > 0)
4027 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4029 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4030 if (!pdbentry.getId().equals(pdbEntryString)
4031 && !pdbentry.getFile().equals(pdbFile))
4041 if (pdbentry == null)
4043 pdbentry = new PDBEntry();
4044 pdbentry.setId(pdbEntryString);
4045 pdbentry.setFile(pdbFile);
4046 needtoadd = true; // add this new entry to sequence.
4048 // resolve data source
4049 // TODO: this code should be a refactored to an io package
4050 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4051 pdbFile, FileFormat.PDB);
4052 if (protocol == null)
4058 pdbentry.setProperty("protocol", protocol);
4059 toaddpdb.addPDBId(pdbentry);
4060 alignPanel.getStructureSelectionManager()
4061 .registerPDBEntry(pdbentry);
4067 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4071 Vector sequences = new Vector();
4072 for (int i = 0; i < seqs.length; i++)
4074 if (seqs[i] != null)
4076 sequences.addElement(new Object[] { seqs[i],
4077 (chains != null) ? chains[i] : null });
4080 seqs = new SequenceI[sequences.size()];
4081 chains = new String[sequences.size()];
4082 for (int i = 0, isize = sequences.size(); i < isize; i++)
4084 Object[] oj = (Object[]) sequences.elementAt(i);
4086 seqs[i] = (SequenceI) oj[0];
4087 chains[i] = (String) oj[1];
4090 return new Object[] { seqs, chains };
4094 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4095 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4097 // Scrub any null sequences from the array
4098 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4099 seqs = (SequenceI[]) sqch[0];
4100 chains = (String[]) sqch[1];
4101 if (seqs == null || seqs.length == 0)
4104 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4106 if (protocol == null)
4108 String sourceType = (String) pdb.getProperty("protocol");
4111 protocol = DataSourceType.valueOf(sourceType);
4112 } catch (IllegalArgumentException e)
4116 if (protocol == null)
4118 System.err.println("Couldn't work out protocol to open structure: "
4123 if (applet.useXtrnalSviewer)
4125 // register the association(s) and quit, don't create any windows.
4126 if (StructureSelectionManager.getStructureSelectionManager(applet)
4127 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4129 System.err.println("Failed to map " + pdb.getFile() + " ("
4130 + protocol + ") to any sequences");
4134 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4136 // can only do alignments with Jmol
4137 // find the last jmol window assigned to this alignment
4138 AppletJmol ajm = null, tajm;
4139 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4140 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4142 tajm = (AppletJmol) jmols.elementAt(i);
4143 if (tajm.ap.alignFrame == this)
4152 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4153 // try and add the pdb structure
4158 // otherwise, create a new window
4159 if (applet.jmolAvailable)
4161 new AppletJmol(pdb, seqs, chains, alignPanel,
4163 applet.lastFrameX += 40;
4164 applet.lastFrameY += 40;
4168 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4173 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4174 SequenceI[][] seqs, String[][] chains, String[] protocols)
4176 // TODO Auto-generated method stub
4177 System.err.println("Aligned Structure View: Not yet implemented.");
4181 * modify the current selection, providing the user has not made a selection
4185 * - sequences from this alignment
4187 * - columns to be selected on the alignment
4189 public void select(SequenceGroup sel, ColumnSelection csel)
4191 alignPanel.seqPanel.selection(sel, csel, null);
4194 public void scrollTo(int row, int column)
4196 alignPanel.seqPanel.scrollTo(row, column);
4199 public void scrollToRow(int row)
4201 alignPanel.seqPanel.scrollToRow(row);
4204 public void scrollToColumn(int column)
4206 alignPanel.seqPanel.scrollToColumn(column);
4210 * @return the alignments unique ID.
4212 public String getSequenceSetId()
4214 return viewport.getSequenceSetId();
4218 * Load the (T-Coffee) score file from the specified url
4221 * File/URL/T-COFFEE score file contents
4222 * @throws IOException
4223 * @return true if alignment was annotated with data from source
4225 public boolean loadScoreFile(String source) throws IOException
4228 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4229 AppletFormatAdapter.checkProtocol(source));
4230 if (!file.isValid())
4232 // TODO: raise dialog for gui
4233 System.err.println("Problems parsing T-Coffee scores: "
4234 + file.getWarningMessage());
4235 System.err.println("Origin was:\n" + source);
4240 * check that the score matrix matches the alignment dimensions
4243 if ((aln = viewport.getAlignment()) != null
4244 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4247 // TODO: raise a dialog box here rather than bomb out.
4249 .println("The scores matrix does not match the alignment dimensions");
4253 // TODO add parameter to indicate if matching should be done
4254 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4256 alignPanel.fontChanged();
4257 tcoffeeColour.setEnabled(true);
4258 // switch to this color
4259 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4264 System.err.println("Problems resolving T-Coffee scores:");
4265 if (file.getWarningMessage() != null)
4267 System.err.println(file.getWarningMessage());
4273 public SplitFrame getSplitFrame()
4275 return this.splitFrame;
4278 public void setSplitFrame(SplitFrame sf)
4280 this.splitFrame = sf;
4283 // may not need this
4285 public void setShowSeqFeatures(boolean b)
4287 // showSeqFeatures.setSelected(b);
4288 viewport.setShowSequenceFeatures(b);
4293 public void setMenusForViewport()
4295 // setMenusFromViewport(viewport);
4300 public void refreshFeatureUI(boolean enableIfNecessary)
4302 if (enableIfNecessary)
4304 sequenceFeatures.setState(true);
4305 alignPanel.av.setShowSequenceFeatures(true);
4310 public FeatureSettingsControllerI getFeatureSettingsUI()
4312 return alignPanel.av.featureSettings;