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.TCoffeeScoreFile;
56 import jalview.schemes.Blosum62ColourScheme;
57 import jalview.schemes.BuriedColourScheme;
58 import jalview.schemes.ClustalxColourScheme;
59 import jalview.schemes.ColourSchemeI;
60 import jalview.schemes.HelixColourScheme;
61 import jalview.schemes.HydrophobicColourScheme;
62 import jalview.schemes.NucleotideColourScheme;
63 import jalview.schemes.PIDColourScheme;
64 import jalview.schemes.PurinePyrimidineColourScheme;
65 import jalview.schemes.RNAHelicesColourChooser;
66 import jalview.schemes.StrandColourScheme;
67 import jalview.schemes.TCoffeeColourScheme;
68 import jalview.schemes.TaylorColourScheme;
69 import jalview.schemes.TurnColourScheme;
70 import jalview.schemes.ZappoColourScheme;
71 import jalview.structure.StructureSelectionManager;
72 import jalview.structures.models.AAStructureBindingModel;
73 import jalview.util.MappingUtils;
74 import jalview.util.MessageManager;
75 import jalview.viewmodel.AlignmentViewport;
77 import java.awt.BorderLayout;
78 import java.awt.Canvas;
79 import java.awt.CheckboxMenuItem;
80 import java.awt.Color;
81 import java.awt.FlowLayout;
83 import java.awt.FontMetrics;
84 import java.awt.Frame;
85 import java.awt.Graphics;
86 import java.awt.Label;
88 import java.awt.MenuBar;
89 import java.awt.MenuItem;
90 import java.awt.Panel;
91 import java.awt.event.ActionEvent;
92 import java.awt.event.ActionListener;
93 import java.awt.event.FocusEvent;
94 import java.awt.event.FocusListener;
95 import java.awt.event.ItemEvent;
96 import java.awt.event.ItemListener;
97 import java.awt.event.KeyEvent;
98 import java.awt.event.KeyListener;
99 import java.awt.event.WindowAdapter;
100 import java.awt.event.WindowEvent;
101 import java.io.IOException;
103 import java.net.URLEncoder;
104 import java.util.Arrays;
105 import java.util.Deque;
106 import java.util.HashMap;
107 import java.util.List;
108 import java.util.Map;
109 import java.util.StringTokenizer;
110 import java.util.Vector;
112 import org.jmol.viewer.Viewer;
114 public class AlignFrame extends EmbmenuFrame implements ActionListener,
115 ItemListener, KeyListener, AlignViewControllerGuiI
117 public AlignViewControllerI avc;
119 public AlignmentPanel alignPanel;
121 public AlignViewport viewport;
123 // width and height may be overridden by applet parameters
124 int frameWidth = 700;
126 int frameHeight = 500;
128 String jalviewServletURL;
131 * Flag for showing autocalculated consensus above or below other consensus
134 private boolean showAutoCalculatedAbove;
136 private SequenceAnnotationOrder annotationSortOrder;
139 * Constructor that creates the frame and adds it to the display.
146 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
149 this(al, applet, title, embedded, true);
153 * Constructor that optionally allows the frame to be displayed or only
160 * @param addToDisplay
162 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
163 boolean embedded, boolean addToDisplay)
165 this(al, null, null, applet, title, embedded, addToDisplay);
168 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
169 ColumnSelection columnSelection, JalviewLite applet,
170 String title, boolean embedded)
172 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
175 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
176 ColumnSelection columnSelection, JalviewLite applet,
177 String title, boolean embedded, boolean addToDisplay)
181 jalviewServletURL = applet.getParameter("APPLICATION_URL");
187 } catch (Exception ex)
189 ex.printStackTrace();
191 // need to get window geometry before we calculate alignment layout
197 param = applet.getParameter("windowWidth");
200 int width = Integer.parseInt(param);
203 param = applet.getParameter("windowHeight");
206 int height = Integer.parseInt(param);
207 frameHeight = height;
209 } catch (Exception ex)
213 viewport = new AlignViewport(al, applet);
215 if (hiddenSeqs != null && hiddenSeqs.length > 0)
217 viewport.hideSequence(hiddenSeqs);
219 if (columnSelection != null)
221 viewport.setColumnSelection(columnSelection);
223 viewport.setScaleAboveWrapped(scaleAbove.getState());
225 alignPanel = new AlignmentPanel(this, viewport);
226 avc = new jalview.controller.AlignViewController(this, viewport,
228 viewport.updateConservation(alignPanel);
229 viewport.updateConsensus(alignPanel);
231 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
232 followMouseOverFlag.setState(viewport.isFollowHighlight());
233 showGroupConsensus.setState(viewport.isShowGroupConsensus());
234 showGroupConservation.setState(viewport.isShowGroupConservation());
235 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
236 showSequenceLogo.setState(viewport.isShowSequenceLogo());
237 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
238 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
239 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
240 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
241 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
242 showAlignmentAnnotations.setState(true);
243 showSequenceAnnotations.setState(false);
245 seqLimits.setState(viewport.getShowJVSuffix());
249 String param = applet.getParameter("sortBy");
252 if (param.equalsIgnoreCase("Id"))
254 sortIDMenuItem_actionPerformed();
256 else if (param.equalsIgnoreCase("Pairwise Identity"))
258 sortPairwiseMenuItem_actionPerformed();
260 else if (param.equalsIgnoreCase("Length"))
262 sortLengthMenuItem_actionPerformed();
266 param = applet.getParameter("wrap");
269 if (param.equalsIgnoreCase("true"))
271 wrapMenuItem.setState(true);
272 wrapMenuItem_actionPerformed();
275 param = applet.getParameter("centrecolumnlabels");
278 centreColumnLabelFlag.setState(true);
279 centreColumnLabelFlag_stateChanged();
283 if (viewport.getAlignment().isNucleotide())
285 viewport.updateStrucConsensus(alignPanel);
286 if (viewport.getAlignment().hasRNAStructure())
288 RNAHelixColour.setEnabled(true);
292 RNAHelixColour.setEnabled(false);
297 RNAHelixColour.setEnabled(false);
298 purinePyrimidineColour.setEnabled(false);
300 // Some JVMS send keyevents to Top frame or lowest panel,
301 // Havent worked out why yet. So add to both this frame and seqCanvas for
303 this.addKeyListener(this);
304 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
305 alignPanel.idPanel.idCanvas.addKeyListener(this);
306 alignPanel.scalePanel.addKeyListener(this);
307 alignPanel.annotationPanel.addKeyListener(this);
308 alignPanel.annotationPanelHolder.addKeyListener(this);
309 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
310 alignPanel.alabels.addKeyListener(this);
312 setAnnotationsVisibility();
316 addToDisplay(embedded);
323 public void addToDisplay(boolean embedded)
325 createAlignFrameWindow(embedded);
327 alignPanel.adjustAnnotationHeight();
328 alignPanel.paintAlignment(true);
331 public AlignViewport getAlignViewport()
336 public SeqCanvas getSeqcanvas()
338 return alignPanel.seqPanel.seqCanvas;
342 * Load a features file onto the alignment
345 * file URL, content, or other resolvable path
347 * is protocol for accessing data referred to by file
350 public boolean parseFeaturesFile(String file, DataSourceType type)
352 return parseFeaturesFile(file, type, true);
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
362 * @param autoenabledisplay
363 * when true, display features flag will be automatically enabled if
364 * features are loaded
365 * @return true if data parsed as a features file
367 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
368 boolean autoenabledisplay)
370 boolean featuresFile = false;
373 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
374 .getFeatureRenderer().getFeatureColours();
375 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
376 "relaxedidmatch", false);
377 featuresFile = new FeaturesFile(file, sourceType).parse(
378 viewport.getAlignment(), colours, true, relaxedIdMatching);
379 } catch (Exception ex)
381 ex.printStackTrace();
386 if (autoenabledisplay)
388 viewport.setShowSequenceFeatures(true);
389 sequenceFeatures.setState(true);
391 if (alignPanel.seqPanel.seqCanvas.fr != null)
393 // update the min/max ranges where necessary
394 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
396 if (viewport.featureSettings != null)
398 viewport.featureSettings.refreshTable();
400 alignPanel.paintAlignment(true);
401 statusBar.setText(MessageManager
402 .getString("label.successfully_added_features_alignment"));
408 public void keyPressed(KeyEvent evt)
410 if (viewport.cursorMode
411 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
412 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
413 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
414 && Character.isDigit(evt.getKeyChar()))
416 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
419 switch (evt.getKeyCode())
421 case 27: // escape key
422 deselectAllSequenceMenuItem_actionPerformed();
424 alignPanel.alabels.cancelDrag();
427 if (evt.isControlDown() || evt.isMetaDown())
429 cut_actionPerformed();
433 if (viewport.cursorMode && !evt.isControlDown())
435 alignPanel.seqPanel.setCursorColumn();
437 if (evt.isControlDown() || evt.isMetaDown())
439 copy_actionPerformed();
443 if (evt.isControlDown())
445 paste(evt.isShiftDown());
449 if (evt.isControlDown() || evt.isMetaDown())
451 selectAllSequenceMenuItem_actionPerformed();
454 case KeyEvent.VK_DOWN:
455 if (viewport.cursorMode)
457 alignPanel.seqPanel.moveCursor(0, 1);
461 moveSelectedSequences(false);
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.moveCursor(0, -1);
472 moveSelectedSequences(true);
476 case KeyEvent.VK_LEFT:
477 if (evt.isAltDown() || !viewport.cursorMode)
479 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
483 alignPanel.seqPanel.moveCursor(-1, 0);
487 case KeyEvent.VK_RIGHT:
488 if (evt.isAltDown() || !viewport.cursorMode)
490 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
494 alignPanel.seqPanel.moveCursor(1, 0);
498 case KeyEvent.VK_SPACE:
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
502 || evt.isShiftDown() || evt.isAltDown());
506 case KeyEvent.VK_DELETE:
507 case KeyEvent.VK_BACK_SPACE:
508 if (viewport.cursorMode)
510 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
511 || evt.isShiftDown() || evt.isAltDown());
515 cut_actionPerformed();
516 alignPanel.seqPanel.seqCanvas.repaint();
521 if (viewport.cursorMode)
523 alignPanel.seqPanel.setCursorRow();
527 if (viewport.cursorMode)
529 alignPanel.seqPanel.setCursorPosition();
533 case KeyEvent.VK_ENTER:
534 case KeyEvent.VK_COMMA:
535 if (viewport.cursorMode)
537 alignPanel.seqPanel.setCursorRowAndColumn();
542 if (viewport.cursorMode)
544 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
555 viewport.cursorMode = !viewport.cursorMode;
556 statusBar.setText(MessageManager.formatMessage(
557 "label.keyboard_editing_mode",
558 new String[] { (viewport.cursorMode ? "on" : "off") }));
559 if (viewport.cursorMode)
561 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
562 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
567 if (evt.isControlDown())
569 findMenuItem_actionPerformed();
575 boolean toggleSeqs = !evt.isControlDown();
576 boolean toggleCols = !evt.isShiftDown();
577 toggleHiddenRegions(toggleSeqs, toggleCols);
581 case KeyEvent.VK_PAGE_UP:
582 if (viewport.getWrapAlignment())
584 alignPanel.scrollUp(true);
588 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
589 - viewport.endSeq + viewport.startSeq);
593 case KeyEvent.VK_PAGE_DOWN:
594 if (viewport.getWrapAlignment())
596 alignPanel.scrollUp(false);
600 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
601 + viewport.endSeq - viewport.startSeq);
606 if (evt.isControlDown())
608 undoMenuItem_actionPerformed();
613 if (evt.isControlDown())
615 redoMenuItem_actionPerformed();
620 if (evt.isControlDown())
627 if (evt.isControlDown())
629 trimAlignment(false);
634 if (evt.isControlDown())
636 if (evt.isShiftDown())
638 this.removeAllGapsMenuItem_actionPerformed();
642 removeGappedColumnMenuItem_actionPerformed();
647 if (evt.isControlDown())
651 invertColSel_actionPerformed();
655 invertSequenceMenuItem_actionPerformed();
661 if (evt.isControlDown())
663 if (evt.isShiftDown())
665 this.unGroup_actionPerformed();
669 this.createGroup_actionPerformed();
675 if (evt.isControlDown())
677 this.deleteGroups_actionPerformed();
682 if (evt.isControlDown())
689 alignPanel.paintAlignment(true);
693 * called by key handler and the hide all/show all menu items
698 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
700 boolean hide = false;
701 SequenceGroup sg = viewport.getSelectionGroup();
702 if (!toggleSeqs && !toggleCols)
704 // Hide everything by the current selection - this is a hack - we do the
705 // invert and then hide
706 // first check that there will be visible columns after the invert.
707 if (viewport.hasSelectedColumns()
708 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
711 // now invert the sequence set, if required - empty selection implies
712 // that no hiding is required.
715 invertSequenceMenuItem_actionPerformed();
716 sg = viewport.getSelectionGroup();
720 viewport.expandColSelection(sg, true);
721 // finally invert the column selection and get the new sequence
722 // selection and indicate it should be hidden.
723 invertColSel_actionPerformed();
730 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
733 viewport.hideAllSelectedSeqs();
735 else if (!(toggleCols && viewport.hasSelectedColumns()))
737 viewport.showAllHiddenSeqs();
743 if (viewport.hasSelectedColumns())
745 viewport.hideSelectedColumns();
748 viewport.setSelectionGroup(sg);
753 viewport.showAllHiddenColumns();
755 viewport.sendSelection();
760 public void keyReleased(KeyEvent evt)
765 public void keyTyped(KeyEvent evt)
770 public void itemStateChanged(ItemEvent evt)
772 final Object source = evt.getSource();
773 if (source == displayNonconservedMenuItem)
775 displayNonconservedMenuItem_actionPerformed();
777 else if (source == colourTextMenuItem)
779 colourTextMenuItem_actionPerformed();
781 else if (source == wrapMenuItem)
783 wrapMenuItem_actionPerformed();
785 else if (source == scaleAbove)
787 viewport.setScaleAboveWrapped(scaleAbove.getState());
789 else if (source == scaleLeft)
791 viewport.setScaleLeftWrapped(scaleLeft.getState());
793 else if (source == scaleRight)
795 viewport.setScaleRightWrapped(scaleRight.getState());
797 else if (source == seqLimits)
799 seqLimits_itemStateChanged();
801 else if (source == viewBoxesMenuItem)
803 viewport.setShowBoxes(viewBoxesMenuItem.getState());
805 else if (source == viewTextMenuItem)
807 viewport.setShowText(viewTextMenuItem.getState());
809 else if (source == renderGapsMenuItem)
811 viewport.setRenderGaps(renderGapsMenuItem.getState());
813 else if (source == annotationPanelMenuItem)
815 boolean showAnnotations = annotationPanelMenuItem.getState();
816 showAlignmentAnnotations.setEnabled(showAnnotations);
817 showSequenceAnnotations.setEnabled(showAnnotations);
818 viewport.setShowAnnotation(showAnnotations);
819 alignPanel.setAnnotationVisible(showAnnotations);
821 else if (source == sequenceFeatures)
823 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
824 alignPanel.seqPanel.seqCanvas.repaint();
826 else if (source == showAlignmentAnnotations)
828 setAnnotationsVisibility();
830 else if (source == showSequenceAnnotations)
832 setAnnotationsVisibility();
834 else if (source == sortAnnBySequence)
836 boolean newState = sortAnnBySequence.getState();
837 sortAnnByLabel.setState(false);
838 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
839 : SequenceAnnotationOrder.NONE);
840 setViewportAnnotationOrder();
842 else if (source == sortAnnByLabel)
844 boolean newState = sortAnnByLabel.getState();
845 sortAnnBySequence.setState(false);
846 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
847 : SequenceAnnotationOrder.NONE);
848 setViewportAnnotationOrder();
850 else if (source == showAutoFirst)
852 showAutoLast.setState(!showAutoFirst.getState());
853 setShowAutoCalculatedAbove(showAutoFirst.getState());
854 setViewportAnnotationOrder();
856 else if (source == showAutoLast)
858 showAutoFirst.setState(!showAutoLast.getState());
859 setShowAutoCalculatedAbove(showAutoFirst.getState());
860 setViewportAnnotationOrder();
862 else if (source == conservationMenuItem)
864 conservationMenuItem_actionPerformed();
866 else if (source == abovePIDThreshold)
868 abovePIDThreshold_actionPerformed();
870 else if (source == applyToAllGroups)
872 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
874 else if (source == autoCalculate)
876 viewport.autoCalculateConsensus = autoCalculate.getState();
878 else if (source == sortByTree)
880 viewport.sortByTree = sortByTree.getState();
882 else if (source == this.centreColumnLabelFlag)
884 centreColumnLabelFlag_stateChanged();
886 else if (source == this.followMouseOverFlag)
888 mouseOverFlag_stateChanged();
890 else if (source == showGroupConsensus)
892 showGroupConsensus_actionPerformed();
894 else if (source == showGroupConservation)
896 showGroupConservation_actionPerformed();
898 else if (source == showSequenceLogo)
900 showSequenceLogo_actionPerformed();
902 else if (source == normSequenceLogo)
904 normSequenceLogo_actionPerformed();
906 else if (source == showConsensusHistogram)
908 showConsensusHistogram_actionPerformed();
910 else if (source == applyAutoAnnotationSettings)
912 applyAutoAnnotationSettings_actionPerformed();
914 alignPanel.paintAlignment(true);
918 * Set the visibility state of sequence-related and/or alignment-related
919 * annotations depending on checkbox selections, and repaint.
923 private void setAnnotationsVisibility()
925 boolean showForAlignment = showAlignmentAnnotations.getState();
926 boolean showForSequences = showSequenceAnnotations.getState();
927 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
929 for (AlignmentAnnotation aa : alignPanel.getAlignment()
930 .getAlignmentAnnotation())
932 boolean visible = (aa.sequenceRef == null ? showForAlignment
934 aa.visible = visible;
937 alignPanel.validateAnnotationDimensions(true);
942 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
944 this.annotationSortOrder = order;
948 * Set flags on the viewport that control annotation ordering
950 private void setViewportAnnotationOrder()
952 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
954 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
957 private void setShowAutoCalculatedAbove(boolean showAbove)
959 this.showAutoCalculatedAbove = showAbove;
962 private void mouseOverFlag_stateChanged()
964 viewport.setFollowHighlight(followMouseOverFlag.getState());
965 // TODO: could kick the scrollTo mechanism to reset view for current
969 private void centreColumnLabelFlag_stateChanged()
971 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
972 this.alignPanel.annotationPanel.repaint();
976 public void actionPerformed(ActionEvent evt)
978 viewport.applet.currentAlignFrame = this;
980 Object source = evt.getSource();
982 if (source == inputText)
984 inputText_actionPerformed();
986 else if (source == loadTree)
988 loadTree_actionPerformed();
990 else if (source == loadApplication)
992 launchFullApplication();
994 else if (source == loadAnnotations)
998 else if (source == outputAnnotations)
1000 outputAnnotations(true);
1002 else if (source == outputFeatures)
1004 outputFeatures(true, "Jalview");
1006 else if (source == closeMenuItem)
1008 closeMenuItem_actionPerformed();
1010 else if (source == copy)
1012 copy_actionPerformed();
1014 else if (source == undoMenuItem)
1016 undoMenuItem_actionPerformed();
1018 else if (source == redoMenuItem)
1020 redoMenuItem_actionPerformed();
1022 else if (source == inputText)
1024 inputText_actionPerformed();
1026 else if (source == closeMenuItem)
1028 closeMenuItem_actionPerformed();
1030 else if (source == undoMenuItem)
1032 undoMenuItem_actionPerformed();
1034 else if (source == redoMenuItem)
1036 redoMenuItem_actionPerformed();
1038 else if (source == copy)
1040 copy_actionPerformed();
1042 else if (source == pasteNew)
1044 pasteNew_actionPerformed();
1046 else if (source == pasteThis)
1048 pasteThis_actionPerformed();
1050 else if (source == cut)
1052 cut_actionPerformed();
1054 else if (source == delete)
1056 delete_actionPerformed();
1058 else if (source == grpsFromSelection)
1060 makeGrpsFromSelection_actionPerformed();
1062 else if (source == deleteGroups)
1064 deleteGroups_actionPerformed();
1066 else if (source == selectAllSequenceMenuItem)
1068 selectAllSequenceMenuItem_actionPerformed();
1070 else if (source == deselectAllSequenceMenuItem)
1072 deselectAllSequenceMenuItem_actionPerformed();
1074 else if (source == invertSequenceMenuItem)
1076 invertSequenceMenuItem_actionPerformed();
1077 // uncomment to slave sequence selections in split frame
1078 // viewport.sendSelection();
1080 else if (source == invertColSel)
1082 viewport.invertColumnSelection();
1083 alignPanel.paintAlignment(true);
1084 viewport.sendSelection();
1086 else if (source == remove2LeftMenuItem)
1088 trimAlignment(true);
1090 else if (source == remove2RightMenuItem)
1092 trimAlignment(false);
1094 else if (source == removeGappedColumnMenuItem)
1096 removeGappedColumnMenuItem_actionPerformed();
1098 else if (source == removeAllGapsMenuItem)
1100 removeAllGapsMenuItem_actionPerformed();
1102 else if (source == findMenuItem)
1104 findMenuItem_actionPerformed();
1106 else if (source == font)
1108 new FontChooser(alignPanel);
1110 else if (source == newView)
1114 else if (source == showColumns)
1116 viewport.showAllHiddenColumns();
1117 alignPanel.paintAlignment(true);
1118 viewport.sendSelection();
1120 else if (source == showSeqs)
1122 viewport.showAllHiddenSeqs();
1123 alignPanel.paintAlignment(true);
1124 // uncomment if we want to slave sequence selections in split frame
1125 // viewport.sendSelection();
1127 else if (source == hideColumns)
1129 viewport.hideSelectedColumns();
1130 alignPanel.paintAlignment(true);
1131 viewport.sendSelection();
1133 else if (source == hideSequences
1134 && viewport.getSelectionGroup() != null)
1136 viewport.hideAllSelectedSeqs();
1137 alignPanel.paintAlignment(true);
1138 // uncomment if we want to slave sequence selections in split frame
1139 // viewport.sendSelection();
1141 else if (source == hideAllButSelection)
1143 toggleHiddenRegions(false, false);
1144 alignPanel.paintAlignment(true);
1145 viewport.sendSelection();
1147 else if (source == hideAllSelection)
1149 SequenceGroup sg = viewport.getSelectionGroup();
1150 viewport.expandColSelection(sg, false);
1151 viewport.hideAllSelectedSeqs();
1152 viewport.hideSelectedColumns();
1153 alignPanel.paintAlignment(true);
1154 viewport.sendSelection();
1156 else if (source == showAllHidden)
1158 viewport.showAllHiddenColumns();
1159 viewport.showAllHiddenSeqs();
1160 alignPanel.paintAlignment(true);
1161 viewport.sendSelection();
1163 else if (source == showGroupConsensus)
1165 showGroupConsensus_actionPerformed();
1167 else if (source == showGroupConservation)
1169 showGroupConservation_actionPerformed();
1171 else if (source == showSequenceLogo)
1173 showSequenceLogo_actionPerformed();
1175 else if (source == normSequenceLogo)
1177 normSequenceLogo_actionPerformed();
1179 else if (source == showConsensusHistogram)
1181 showConsensusHistogram_actionPerformed();
1183 else if (source == applyAutoAnnotationSettings)
1185 applyAutoAnnotationSettings_actionPerformed();
1187 else if (source == featureSettings)
1189 new FeatureSettings(alignPanel);
1191 else if (source == alProperties)
1193 StringBuffer contents = new jalview.io.AlignmentProperties(
1194 viewport.getAlignment()).formatAsString();
1195 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1196 cap.setText(contents.toString());
1197 Frame frame = new Frame();
1199 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1200 "label.alignment_properties", new String[] { getTitle() }),
1203 else if (source == overviewMenuItem)
1205 overviewMenuItem_actionPerformed();
1207 else if (source == noColourmenuItem)
1211 else if (source == clustalColour)
1213 abovePIDThreshold.setState(false);
1214 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1216 else if (source == zappoColour)
1218 changeColour(new ZappoColourScheme());
1220 else if (source == taylorColour)
1222 changeColour(new TaylorColourScheme());
1224 else if (source == hydrophobicityColour)
1226 changeColour(new HydrophobicColourScheme());
1228 else if (source == helixColour)
1230 changeColour(new HelixColourScheme());
1232 else if (source == strandColour)
1234 changeColour(new StrandColourScheme());
1236 else if (source == turnColour)
1238 changeColour(new TurnColourScheme());
1240 else if (source == buriedColour)
1242 changeColour(new BuriedColourScheme());
1244 else if (source == nucleotideColour)
1246 changeColour(new NucleotideColourScheme());
1248 else if (source == purinePyrimidineColour)
1250 changeColour(new PurinePyrimidineColourScheme());
1252 // else if (source == RNAInteractionColour)
1254 // changeColour(new RNAInteractionColourScheme());
1256 else if (source == RNAHelixColour)
1258 new RNAHelicesColourChooser(viewport, alignPanel);
1260 else if (source == modifyPID)
1262 modifyPID_actionPerformed();
1264 else if (source == modifyConservation)
1266 modifyConservation_actionPerformed();
1268 else if (source == userDefinedColour)
1270 new UserDefinedColours(alignPanel, null);
1272 else if (source == PIDColour)
1274 changeColour(new PIDColourScheme());
1276 else if (source == BLOSUM62Colour)
1278 changeColour(new Blosum62ColourScheme());
1280 else if (source == tcoffeeColour)
1282 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1284 else if (source == annotationColour)
1286 new AnnotationColourChooser(viewport, alignPanel);
1288 else if (source == annotationColumnSelection)
1290 new AnnotationColumnChooser(viewport, alignPanel);
1292 else if (source == sortPairwiseMenuItem)
1294 sortPairwiseMenuItem_actionPerformed();
1296 else if (source == sortIDMenuItem)
1298 sortIDMenuItem_actionPerformed();
1300 else if (source == sortLengthMenuItem)
1302 sortLengthMenuItem_actionPerformed();
1304 else if (source == sortGroupMenuItem)
1306 sortGroupMenuItem_actionPerformed();
1308 else if (source == removeRedundancyMenuItem)
1310 removeRedundancyMenuItem_actionPerformed();
1312 else if (source == pairwiseAlignmentMenuItem)
1314 pairwiseAlignmentMenuItem_actionPerformed();
1316 else if (source == PCAMenuItem)
1318 PCAMenuItem_actionPerformed();
1320 else if (source == averageDistanceTreeMenuItem)
1322 averageDistanceTreeMenuItem_actionPerformed();
1324 else if (source == neighbourTreeMenuItem)
1326 neighbourTreeMenuItem_actionPerformed();
1328 else if (source == njTreeBlosumMenuItem)
1330 njTreeBlosumMenuItem_actionPerformed();
1332 else if (source == avDistanceTreeBlosumMenuItem)
1334 avTreeBlosumMenuItem_actionPerformed();
1336 else if (source == documentation)
1338 documentation_actionPerformed();
1340 else if (source == about)
1342 about_actionPerformed();
1347 public void inputText_actionPerformed()
1349 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1350 Frame frame = new Frame();
1352 jalview.bin.JalviewLite.addFrame(frame,
1353 MessageManager.getString("label.input_cut_paste"), 500, 500);
1356 protected void outputText_actionPerformed(ActionEvent e)
1358 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1359 Frame frame = new Frame();
1361 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1362 "label.alignment_output_command",
1363 new Object[] { e.getActionCommand() }), 600, 500);
1365 FileFormat fileFormat = FileFormat.valueOf(e.getActionCommand());
1366 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1367 fileFormat, viewport.getAlignment(),
1368 viewport.getShowJVSuffix()));
1371 public void loadAnnotations()
1373 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1374 cap.setText(MessageManager
1375 .getString("label.paste_features_annotations_Tcoffee_here"));
1376 cap.setAnnotationImport();
1377 Frame frame = new Frame();
1379 jalview.bin.JalviewLite.addFrame(frame,
1380 MessageManager.getString("action.paste_annotations"), 400, 300);
1384 public String outputAnnotations(boolean displayTextbox)
1386 String annotation = new AnnotationFile()
1387 .printAnnotationsForView(viewport);
1391 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1392 Frame frame = new Frame();
1394 jalview.bin.JalviewLite.addFrame(frame,
1395 MessageManager.getString("label.annotations"), 600, 500);
1396 cap.setText(annotation);
1402 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1404 if (alignPanel.getFeatureRenderer() != null
1405 && viewport.getFeaturesDisplayed() != null)
1407 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1413 public String outputFeatures(boolean displayTextbox, String format)
1416 FeaturesFile formatter = new FeaturesFile();
1417 if (format.equalsIgnoreCase("Jalview"))
1419 features = formatter.printJalviewFormat(viewport.getAlignment()
1420 .getSequencesArray(), getDisplayedFeatureCols());
1424 features = formatter.printGffFormat(viewport.getAlignment()
1425 .getSequencesArray(), getDisplayedFeatureCols());
1430 boolean frimport = false;
1431 if (features == null || features.equals("No Features Visible"))
1433 features = "# No features visible - paste some and import them here.";
1437 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1440 cap.setAnnotationImport();
1442 Frame frame = new Frame();
1444 jalview.bin.JalviewLite.addFrame(frame,
1445 MessageManager.getString("label.features"), 600, 500);
1446 cap.setText(features);
1450 if (features == null)
1459 void launchFullApplication()
1461 StringBuffer url = new StringBuffer(jalviewServletURL);
1463 // allow servlet parameters to be passed in applet parameter
1464 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1466 url.append(firstSep);
1469 + appendProtocol(viewport.applet.getParameter("file")));
1471 if (viewport.applet.getParameter("features") != null)
1473 url.append("&features=");
1474 url.append(appendProtocol(viewport.applet.getParameter("features")));
1477 if (viewport.applet.getParameter("annotations") != null)
1479 url.append("&annotations=");
1480 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1483 if (viewport.applet.getParameter("jnetfile") != null)
1485 url.append("&annotations=");
1486 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1489 if (viewport.applet.getParameter("defaultColour") != null)
1491 url.append("&colour="
1492 + removeWhiteSpace(viewport.applet
1493 .getParameter("defaultColour")));
1496 if (viewport.applet.getParameter("userDefinedColour") != null)
1498 url.append("&colour="
1499 + removeWhiteSpace(viewport.applet
1500 .getParameter("userDefinedColour")));
1502 if (viewport.applet.getParameter("tree") != null)
1505 + appendProtocol(viewport.applet.getParameter("tree")));
1507 if (viewport.applet.getParameter("treeFile") != null)
1510 + appendProtocol(viewport.applet.getParameter("treeFile")));
1513 showURL(url.toString(), "FULL_APP");
1516 String removeWhiteSpace(String colour)
1518 StringBuffer sb = new StringBuffer();
1519 for (int i = 0; i < colour.length(); i++)
1521 if (Character.isWhitespace(colour.charAt(i)))
1527 sb.append(colour.charAt(i));
1531 return sb.toString();
1534 String appendProtocol(String url)
1539 url = URLEncoder.encode(url);
1542 * When we finally deprecate 1.1 compatibility, we can start to use
1543 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1544 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1545 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1546 * ex.printStackTrace(); }
1548 catch (java.net.MalformedURLException ex)
1550 url = viewport.applet.getCodeBase() + url;
1555 public void closeMenuItem_actionPerformed()
1557 PaintRefresher.RemoveComponent(alignPanel);
1558 if (alignPanel.seqPanel != null
1559 && alignPanel.seqPanel.seqCanvas != null)
1561 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1563 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1565 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1568 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1583 void updateEditMenuBar()
1586 if (viewport.getHistoryList().size() > 0)
1588 undoMenuItem.setEnabled(true);
1589 CommandI command = viewport.getHistoryList().peek();
1590 undoMenuItem.setLabel(MessageManager.formatMessage(
1591 "label.undo_command",
1592 new Object[] { command.getDescription() }));
1596 undoMenuItem.setEnabled(false);
1597 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1600 if (viewport.getRedoList().size() > 0)
1602 redoMenuItem.setEnabled(true);
1604 CommandI command = viewport.getRedoList().peek();
1605 redoMenuItem.setLabel(MessageManager.formatMessage(
1606 "label.redo_command",
1607 new Object[] { command.getDescription() }));
1611 redoMenuItem.setEnabled(false);
1612 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1620 public void addHistoryItem(CommandI command)
1622 if (command.getSize() > 0)
1624 viewport.addToHistoryList(command);
1625 viewport.clearRedoList();
1626 updateEditMenuBar();
1627 viewport.updateHiddenColumns();
1632 * TODO: JAL-1104 DOCUMENT ME!
1637 protected void undoMenuItem_actionPerformed()
1639 if (viewport.getHistoryList().isEmpty())
1644 CommandI command = viewport.getHistoryList().pop();
1645 viewport.addToRedoList(command);
1646 command.undoCommand(null);
1648 AlignmentViewport originalSource = getOriginatingSource(command);
1650 if (originalSource != viewport)
1653 .println("Warning: Viewport object mismatch whilst undoing");
1655 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1656 // viewport.getColumnSelection().getHiddenColumns()
1658 updateEditMenuBar();
1659 originalSource.firePropertyChange("alignment", null, originalSource
1660 .getAlignment().getSequences());
1664 * TODO: JAL-1104 DOCUMENT ME!
1669 protected void redoMenuItem_actionPerformed()
1671 if (viewport.getRedoList().isEmpty())
1676 CommandI command = viewport.getRedoList().pop();
1677 viewport.addToHistoryList(command);
1678 command.doCommand(null);
1680 AlignmentViewport originalSource = getOriginatingSource(command);
1682 if (originalSource != viewport)
1685 .println("Warning: Viewport object mismatch whilst re-doing");
1687 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1688 // viewport.getColumnSelection().getHiddenColumns()
1691 updateEditMenuBar();
1692 originalSource.firePropertyChange("alignment", null, originalSource
1693 .getAlignment().getSequences());
1696 AlignmentViewport getOriginatingSource(CommandI command)
1698 AlignmentViewport originalSource = null;
1699 // For sequence removal and addition, we need to fire
1700 // the property change event FROM the viewport where the
1701 // original alignment was altered
1702 AlignmentI al = null;
1703 if (command instanceof EditCommand)
1705 EditCommand editCommand = (EditCommand) command;
1706 al = editCommand.getAlignment();
1707 Vector comps = (Vector) PaintRefresher.components.get(viewport
1708 .getSequenceSetId());
1709 for (int i = 0; i < comps.size(); i++)
1711 if (comps.elementAt(i) instanceof AlignmentPanel)
1713 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1715 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1722 if (originalSource == null)
1724 // The original view is closed, we must validate
1725 // the current view against the closed view first
1728 PaintRefresher.validateSequences(al, viewport.getAlignment());
1731 originalSource = viewport;
1734 return originalSource;
1738 * Move the currently selected sequences up or down one position in the
1743 public void moveSelectedSequences(boolean up)
1745 SequenceGroup sg = viewport.getSelectionGroup();
1750 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1751 up ? null : viewport.getHiddenRepSequences(), up);
1752 alignPanel.paintAlignment(true);
1755 * Also move cDNA/protein complement sequences
1757 AlignViewportI complement = viewport.getCodingComplement();
1758 if (complement != null)
1760 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1761 viewport, complement);
1762 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1763 up ? null : complement.getHiddenRepSequences(), up);
1764 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1768 synchronized void slideSequences(boolean right, int size)
1770 List<SequenceI> sg = new Vector<SequenceI>();
1771 if (viewport.cursorMode)
1773 sg.add(viewport.getAlignment().getSequenceAt(
1774 alignPanel.seqPanel.seqCanvas.cursorY));
1776 else if (viewport.getSelectionGroup() != null
1777 && viewport.getSelectionGroup().getSize() != viewport
1778 .getAlignment().getHeight())
1780 sg = viewport.getSelectionGroup().getSequences(
1781 viewport.getHiddenRepSequences());
1789 Vector<SequenceI> invertGroup = new Vector();
1791 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1793 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1795 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1799 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1801 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1803 for (int i = 0; i < invertGroup.size(); i++)
1805 seqs2[i] = invertGroup.elementAt(i);
1808 SlideSequencesCommand ssc;
1811 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1812 size, viewport.getGapCharacter());
1816 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1817 size, viewport.getGapCharacter());
1820 int groupAdjustment = 0;
1821 if (ssc.getGapsInsertedBegin() && right)
1823 if (viewport.cursorMode)
1825 alignPanel.seqPanel.moveCursor(size, 0);
1829 groupAdjustment = size;
1832 else if (!ssc.getGapsInsertedBegin() && !right)
1834 if (viewport.cursorMode)
1836 alignPanel.seqPanel.moveCursor(-size, 0);
1840 groupAdjustment = -size;
1844 if (groupAdjustment != 0)
1846 viewport.getSelectionGroup().setStartRes(
1847 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1848 viewport.getSelectionGroup().setEndRes(
1849 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1852 boolean appendHistoryItem = false;
1853 Deque<CommandI> historyList = viewport.getHistoryList();
1854 if (historyList != null && historyList.size() > 0
1855 && historyList.peek() instanceof SlideSequencesCommand)
1857 appendHistoryItem = ssc
1858 .appendSlideCommand((SlideSequencesCommand) historyList
1862 if (!appendHistoryItem)
1864 addHistoryItem(ssc);
1870 static StringBuffer copiedSequences;
1872 static Vector copiedHiddenColumns;
1874 protected void copy_actionPerformed()
1876 if (viewport.getSelectionGroup() == null)
1881 SequenceGroup sg = viewport.getSelectionGroup();
1882 copiedSequences = new StringBuffer();
1883 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1884 for (int i = 0; i < sg.getSize(); i++)
1886 SequenceI seq = sg.getSequenceAt(i);
1887 int index = viewport.getAlignment().findIndex(seq);
1888 orderedSeqs.put(index, seq);
1891 int index = 0, startRes, endRes;
1894 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1896 copiedHiddenColumns = new Vector();
1897 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1898 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1900 copiedHiddenColumns.addElement(new int[] {
1901 region[0] - hiddenOffset, region[1] - hiddenOffset });
1906 copiedHiddenColumns = null;
1909 for (int i = 0; i < sg.getSize(); i++)
1911 SequenceI seq = null;
1915 if (orderedSeqs.containsKey(index))
1917 seq = orderedSeqs.get(index);
1928 // Returns residue following index if gap
1929 startRes = seq.findPosition(sg.getStartRes());
1932 // Need to find the residue preceeding index if gap
1935 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1937 ch = seq.getCharAt(j);
1938 if (!jalview.util.Comparison.isGap((ch)))
1946 endRes += seq.getStart() - 1;
1949 copiedSequences.append(seq.getName()
1955 + seq.getSequenceAsString(sg.getStartRes(),
1956 sg.getEndRes() + 1) + "\n");
1961 protected void pasteNew_actionPerformed()
1966 protected void pasteThis_actionPerformed()
1971 void paste(boolean newAlignment)
1976 if (copiedSequences == null)
1981 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1982 Vector seqs = new Vector();
1983 while (st.hasMoreElements())
1985 String name = st.nextToken();
1986 int start = Integer.parseInt(st.nextToken());
1987 int end = Integer.parseInt(st.nextToken());
1988 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1990 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1991 for (int i = 0; i < seqs.size(); i++)
1993 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1998 String newtitle = MessageManager
1999 .getString("label.copied_sequences");
2000 if (getTitle().startsWith(
2001 MessageManager.getString("label.copied_sequences")))
2003 newtitle = getTitle();
2007 newtitle = newtitle.concat(MessageManager.formatMessage(
2008 "label.from_msname", new String[] { getTitle() }));
2010 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2011 viewport.applet, newtitle, false);
2012 if (copiedHiddenColumns != null)
2014 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2016 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2017 af.viewport.hideColumns(region[0], region[1]);
2021 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2026 addSequences(newSeqs);
2029 } catch (Exception ex)
2031 } // could be anything being pasted in here
2035 void addSequences(SequenceI[] seqs)
2037 for (int i = 0; i < seqs.length; i++)
2039 viewport.getAlignment().addSequence(seqs[i]);
2043 addHistoryItem(new EditCommand(
2044 MessageManager.getString("label.add_sequences"), Action.PASTE,
2045 seqs, 0, viewport.getAlignment().getWidth(),
2046 viewport.getAlignment()));
2048 viewport.setEndSeq(viewport.getAlignment().getHeight());
2049 viewport.getAlignment().getWidth();
2050 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2055 protected void cut_actionPerformed()
2057 copy_actionPerformed();
2058 delete_actionPerformed();
2061 protected void delete_actionPerformed()
2064 SequenceGroup sg = viewport.getSelectionGroup();
2070 Vector seqs = new Vector();
2072 for (int i = 0; i < sg.getSize(); i++)
2074 seq = sg.getSequenceAt(i);
2075 seqs.addElement(seq);
2079 * If the cut affects all sequences, warn, remove highlighted columns
2081 if (sg.getSize() == viewport.getAlignment().getHeight())
2083 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2084 .getAlignment().getWidth()) ? true : false;
2085 if (isEntireAlignWidth)
2087 String title = MessageManager.getString("label.delete_all");
2088 Panel infoPanel = new Panel();
2089 infoPanel.setLayout(new FlowLayout());
2091 .add(new Label(MessageManager.getString("warn.delete_all")));
2093 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2094 dialog.setMainPanel(infoPanel);
2095 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2096 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2097 dialog.setVisible(true);
2104 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2105 sg.getEndRes() + 1);
2108 SequenceI[] cut = new SequenceI[seqs.size()];
2109 for (int i = 0; i < seqs.size(); i++)
2111 cut[i] = (SequenceI) seqs.elementAt(i);
2115 * //ADD HISTORY ITEM
2117 addHistoryItem(new EditCommand(
2118 MessageManager.getString("label.cut_sequences"), Action.CUT,
2119 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2120 viewport.getAlignment()));
2122 viewport.setSelectionGroup(null);
2123 viewport.getAlignment().deleteGroup(sg);
2125 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2128 if (viewport.getAlignment().getHeight() < 1)
2130 this.setVisible(false);
2132 viewport.sendSelection();
2136 * group consensus toggled
2139 protected void showGroupConsensus_actionPerformed()
2141 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2142 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2147 * group conservation toggled.
2149 protected void showGroupConservation_actionPerformed()
2151 viewport.setShowGroupConservation(showGroupConservation.getState());
2152 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2159 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2160 * .event.ActionEvent)
2162 protected void showConsensusHistogram_actionPerformed()
2164 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2165 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2172 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2173 * .event.ActionEvent)
2175 protected void showSequenceLogo_actionPerformed()
2177 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2178 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 protected void normSequenceLogo_actionPerformed()
2183 showSequenceLogo.setState(true);
2184 viewport.setShowSequenceLogo(true);
2185 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2186 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2189 protected void applyAutoAnnotationSettings_actionPerformed()
2191 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2194 protected void makeGrpsFromSelection_actionPerformed()
2196 if (avc.makeGroupsFromSelection())
2198 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2199 alignPanel.updateAnnotation();
2200 alignPanel.paintAlignment(true);
2204 protected void createGroup_actionPerformed()
2209 protected void unGroup_actionPerformed()
2213 alignPanel.alignmentChanged();
2217 protected void deleteGroups_actionPerformed()
2219 if (avc.deleteGroups())
2221 alignPanel.alignmentChanged();
2225 public void selectAllSequenceMenuItem_actionPerformed()
2227 SequenceGroup sg = new SequenceGroup();
2228 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2230 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2232 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2233 viewport.setSelectionGroup(sg);
2234 // JAL-2034 - should delegate to
2235 // alignPanel to decide if overview needs
2237 alignPanel.paintAlignment(false);
2238 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2239 viewport.sendSelection();
2242 public void deselectAllSequenceMenuItem_actionPerformed()
2244 if (viewport.cursorMode)
2246 alignPanel.seqPanel.keyboardNo1 = null;
2247 alignPanel.seqPanel.keyboardNo2 = null;
2249 viewport.setSelectionGroup(null);
2250 viewport.getColumnSelection().clear();
2251 viewport.setSelectionGroup(null);
2252 alignPanel.idPanel.idCanvas.searchResults = null;
2253 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2254 // JAL-2034 - should delegate to
2255 // alignPanel to decide if overview needs
2257 alignPanel.paintAlignment(false);
2258 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2259 viewport.sendSelection();
2262 public void invertSequenceMenuItem_actionPerformed()
2264 SequenceGroup sg = viewport.getSelectionGroup();
2265 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2267 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2270 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2271 viewport.sendSelection();
2274 public void invertColSel_actionPerformed()
2276 viewport.invertColumnSelection();
2277 alignPanel.paintAlignment(true);
2278 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2279 viewport.sendSelection();
2282 void trimAlignment(boolean trimLeft)
2284 ColumnSelection colSel = viewport.getColumnSelection();
2287 if (!colSel.isEmpty())
2291 column = colSel.getMin();
2295 column = colSel.getMax();
2299 if (viewport.getSelectionGroup() != null)
2301 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2302 viewport.getHiddenRepSequences());
2306 seqs = viewport.getAlignment().getSequencesArray();
2309 TrimRegionCommand trimRegion;
2312 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2313 column, viewport.getAlignment());
2314 viewport.setStartRes(0);
2318 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2319 column, viewport.getAlignment());
2322 statusBar.setText(MessageManager.formatMessage(
2323 "label.removed_columns",
2324 new String[] { Integer.valueOf(trimRegion.getSize())
2326 addHistoryItem(trimRegion);
2328 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2330 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2331 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2333 viewport.getAlignment().deleteGroup(sg);
2337 viewport.firePropertyChange("alignment", null, viewport
2338 .getAlignment().getSequences());
2342 public void removeGappedColumnMenuItem_actionPerformed()
2344 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2347 if (viewport.getSelectionGroup() != null)
2349 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2350 viewport.getHiddenRepSequences());
2351 start = viewport.getSelectionGroup().getStartRes();
2352 end = viewport.getSelectionGroup().getEndRes();
2356 seqs = viewport.getAlignment().getSequencesArray();
2359 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2360 "Remove Gapped Columns", seqs, start, end,
2361 viewport.getAlignment());
2363 addHistoryItem(removeGapCols);
2365 statusBar.setText(MessageManager.formatMessage(
2366 "label.removed_empty_columns",
2367 new String[] { Integer.valueOf(removeGapCols.getSize())
2370 // This is to maintain viewport position on first residue
2371 // of first sequence
2372 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2373 int startRes = seq.findPosition(viewport.startRes);
2374 // ShiftList shifts;
2375 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2376 // edit.alColumnChanges=shifts.getInverse();
2377 // if (viewport.hasHiddenColumns)
2378 // viewport.getColumnSelection().compensateForEdits(shifts);
2379 viewport.setStartRes(seq.findIndex(startRes) - 1);
2380 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2385 public void removeAllGapsMenuItem_actionPerformed()
2387 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2390 if (viewport.getSelectionGroup() != null)
2392 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2393 viewport.getHiddenRepSequences());
2394 start = viewport.getSelectionGroup().getStartRes();
2395 end = viewport.getSelectionGroup().getEndRes();
2399 seqs = viewport.getAlignment().getSequencesArray();
2402 // This is to maintain viewport position on first residue
2403 // of first sequence
2404 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2405 int startRes = seq.findPosition(viewport.startRes);
2407 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2408 viewport.getAlignment()));
2410 viewport.setStartRes(seq.findIndex(startRes) - 1);
2412 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2417 public void findMenuItem_actionPerformed()
2419 new Finder(alignPanel);
2423 * create a new view derived from the current view
2426 * @return frame for the new view
2428 public AlignFrame newView(String viewtitle)
2431 if (viewport.hasHiddenRows())
2433 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2434 .getFullAlignment().getSequencesArray());
2438 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2441 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2443 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2445 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2447 newal.addAnnotation(viewport.getAlignment()
2448 .getAlignmentAnnotation()[i]);
2453 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2455 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2456 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2457 PaintRefresher.Register(newaf.alignPanel,
2458 newaf.alignPanel.av.getSequenceSetId());
2460 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2461 newaf.alignPanel.av.getSequenceSetId());
2462 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2463 newaf.alignPanel.av.getSequenceSetId());
2465 Vector comps = (Vector) PaintRefresher.components.get(viewport
2466 .getSequenceSetId());
2468 for (int i = 0; i < comps.size(); i++)
2470 if (comps.elementAt(i) instanceof AlignmentPanel)
2476 String title = new String(this.getTitle());
2477 if (viewtitle != null)
2479 title = viewtitle + " ( " + title + ")";
2483 if (title.indexOf("(View") > -1)
2485 title = title.substring(0, title.indexOf("(View"));
2487 title += "(View " + viewSize + ")";
2490 newaf.setTitle(title.toString());
2492 newaf.viewport.setHistoryList(viewport.getHistoryList());
2493 newaf.viewport.setRedoList(viewport.getRedoList());
2499 * @return list of feature groups on the view
2501 public String[] getFeatureGroups()
2503 FeatureRenderer fr = null;
2504 if (alignPanel != null
2505 && (fr = alignPanel.getFeatureRenderer()) != null)
2507 List<String> gps = fr.getFeatureGroups();
2508 String[] _gps = gps.toArray(new String[gps.size()]);
2515 * get sequence feature groups that are hidden or shown
2521 public String[] getFeatureGroupsOfState(boolean visible)
2523 FeatureRenderer fr = null;
2524 if (alignPanel != null
2525 && (fr = alignPanel.getFeatureRenderer()) != null)
2527 List<String> gps = fr.getGroups(visible);
2528 String[] _gps = gps.toArray(new String[gps.size()]);
2535 * Change the display state for the given feature groups
2538 * list of group strings
2540 * visible or invisible
2542 public void setFeatureGroupState(String[] groups, boolean state)
2544 FeatureRenderer fr = null;
2545 this.sequenceFeatures.setState(true);
2546 viewport.setShowSequenceFeatures(true);
2547 if (alignPanel != null
2548 && (fr = alignPanel.getFeatureRenderer()) != null)
2551 fr.setGroupVisibility(Arrays.asList(groups), state);
2552 alignPanel.seqPanel.seqCanvas.repaint();
2553 if (alignPanel.overviewPanel != null)
2555 alignPanel.overviewPanel.updateOverviewImage();
2560 public void seqLimits_itemStateChanged()
2562 viewport.setShowJVSuffix(seqLimits.getState());
2563 alignPanel.fontChanged();
2564 alignPanel.paintAlignment(true);
2567 protected void colourTextMenuItem_actionPerformed()
2569 viewport.setColourText(colourTextMenuItem.getState());
2570 alignPanel.paintAlignment(true);
2573 protected void displayNonconservedMenuItem_actionPerformed()
2575 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2576 alignPanel.paintAlignment(true);
2579 protected void wrapMenuItem_actionPerformed()
2581 viewport.setWrapAlignment(wrapMenuItem.getState());
2582 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2583 scaleAbove.setEnabled(wrapMenuItem.getState());
2584 scaleLeft.setEnabled(wrapMenuItem.getState());
2585 scaleRight.setEnabled(wrapMenuItem.getState());
2586 alignPanel.paintAlignment(true);
2589 public void overviewMenuItem_actionPerformed()
2591 if (alignPanel.overviewPanel != null)
2596 Frame frame = new Frame();
2597 OverviewPanel overview = new OverviewPanel(alignPanel);
2598 frame.add(overview);
2599 // +50 must allow for applet frame window
2600 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2601 "label.overview_params", new String[] { this.getTitle() }),
2602 overview.getPreferredSize().width,
2603 overview.getPreferredSize().height + 50);
2606 final AlignmentPanel ap = alignPanel;
2607 frame.addWindowListener(new WindowAdapter()
2610 public void windowClosing(WindowEvent e)
2614 ap.setOverviewPanel(null);
2619 alignPanel.setOverviewPanel(overview);
2624 public void changeColour(ColourSchemeI cs)
2629 if (viewport.getAbovePIDThreshold())
2631 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2635 if (viewport.getConservationSelected())
2637 cs.setConservationApplied(true);
2638 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2643 cs.setConservationApplied(false);
2646 viewport.setGlobalColourScheme(cs);
2648 alignPanel.paintAlignment(true);
2651 protected void modifyPID_actionPerformed()
2653 if (viewport.getAbovePIDThreshold()
2654 && viewport.getGlobalColourScheme() != null)
2656 SliderPanel.setPIDSliderSource(alignPanel,
2657 viewport.getGlobalColourScheme(), "Background");
2658 SliderPanel.showPIDSlider();
2662 protected void modifyConservation_actionPerformed()
2664 if (viewport.getConservationSelected()
2665 && viewport.getGlobalColourScheme() != null)
2667 SliderPanel.setConservationSlider(alignPanel,
2668 viewport.getGlobalColourScheme(), "Background");
2669 SliderPanel.showConservationSlider();
2673 protected void conservationMenuItem_actionPerformed()
2675 viewport.setConservationSelected(conservationMenuItem.getState());
2677 viewport.setAbovePIDThreshold(false);
2678 abovePIDThreshold.setState(false);
2680 changeColour(viewport.getGlobalColourScheme());
2682 modifyConservation_actionPerformed();
2685 public void abovePIDThreshold_actionPerformed()
2687 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2689 conservationMenuItem.setState(false);
2690 viewport.setConservationSelected(false);
2692 changeColour(viewport.getGlobalColourScheme());
2694 modifyPID_actionPerformed();
2697 public void sortPairwiseMenuItem_actionPerformed()
2699 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2700 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2701 .getAlignment().getSequenceAt(0), null);
2703 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2704 viewport.getAlignment()));
2705 alignPanel.paintAlignment(true);
2708 public void sortIDMenuItem_actionPerformed()
2710 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2711 AlignmentSorter.sortByID(viewport.getAlignment());
2712 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2713 viewport.getAlignment()));
2714 alignPanel.paintAlignment(true);
2717 public void sortLengthMenuItem_actionPerformed()
2719 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2720 AlignmentSorter.sortByLength(viewport.getAlignment());
2721 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2722 viewport.getAlignment()));
2723 alignPanel.paintAlignment(true);
2726 public void sortGroupMenuItem_actionPerformed()
2728 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2729 AlignmentSorter.sortByGroup(viewport.getAlignment());
2730 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2731 viewport.getAlignment()));
2732 alignPanel.paintAlignment(true);
2736 public void removeRedundancyMenuItem_actionPerformed()
2738 new RedundancyPanel(alignPanel);
2741 public void pairwiseAlignmentMenuItem_actionPerformed()
2743 if (viewport.getSelectionGroup() != null
2744 && viewport.getSelectionGroup().getSize() > 1)
2746 Frame frame = new Frame();
2747 frame.add(new PairwiseAlignPanel(alignPanel));
2748 jalview.bin.JalviewLite.addFrame(frame,
2749 MessageManager.getString("action.pairwise_alignment"), 600,
2754 public void PCAMenuItem_actionPerformed()
2756 // are the sequences aligned?
2757 if (!viewport.getAlignment().isAligned(false))
2760 int Width = viewport.getAlignment().getWidth();
2762 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2764 current = viewport.getAlignment().getSequenceAt(i);
2766 if (current.getLength() < Width)
2768 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2771 alignPanel.paintAlignment(true);
2774 if ((viewport.getSelectionGroup() != null
2775 && viewport.getSelectionGroup().getSize() < 4 && viewport
2776 .getSelectionGroup().getSize() > 0)
2777 || viewport.getAlignment().getHeight() < 4)
2784 new PCAPanel(viewport);
2785 } catch (java.lang.OutOfMemoryError ex)
2791 public void averageDistanceTreeMenuItem_actionPerformed()
2793 NewTreePanel("AV", "PID", "Average distance tree using PID");
2796 public void neighbourTreeMenuItem_actionPerformed()
2798 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2801 protected void njTreeBlosumMenuItem_actionPerformed()
2803 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2806 protected void avTreeBlosumMenuItem_actionPerformed()
2808 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2811 void NewTreePanel(String type, String pwType, String title)
2813 // are the sequences aligned?
2814 if (!viewport.getAlignment().isAligned(false))
2817 int Width = viewport.getAlignment().getWidth();
2819 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2821 current = viewport.getAlignment().getSequenceAt(i);
2823 if (current.getLength() < Width)
2825 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2828 alignPanel.paintAlignment(true);
2832 if ((viewport.getSelectionGroup() != null && viewport
2833 .getSelectionGroup().getSize() > 1)
2834 || (viewport.getAlignment().getHeight() > 1))
2836 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2838 addTreeMenuItem(tp, title);
2840 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2844 void loadTree_actionPerformed()
2846 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2847 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2848 cap.setTreeImport();
2849 Frame frame = new Frame();
2851 jalview.bin.JalviewLite.addFrame(frame,
2852 MessageManager.getString("label.paste_newick_file"), 400, 300);
2855 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2857 TreePanel tp = new TreePanel(alignPanel, treeFile,
2858 MessageManager.getString("label.load_tree_from_file"), tree);
2859 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2860 addTreeMenuItem(tp, treeFile);
2864 * sort the alignment using the given treePanel
2867 * tree used to sort view
2869 * string used for undo event name
2871 public void sortByTree(TreePanel treePanel, String title)
2873 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2875 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2876 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2877 // HistoryItem.SORT));
2878 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2879 "label.order_by_params", new String[] { title }), oldOrder,
2880 viewport.getAlignment()));
2881 alignPanel.paintAlignment(true);
2885 * Do any automatic reordering of the alignment and add the necessary bits to
2886 * the menu structure for the new tree
2891 protected void addTreeMenuItem(final TreePanel treePanel,
2894 final MenuItem item = new MenuItem(title);
2895 sortByTreeMenu.add(item);
2896 item.addActionListener(new java.awt.event.ActionListener()
2899 public void actionPerformed(ActionEvent evt)
2901 sortByTree(treePanel, title); // treePanel.getTitle());
2905 treePanel.addWindowListener(new WindowAdapter()
2908 public void windowOpened(WindowEvent e)
2910 if (viewport.sortByTree)
2912 sortByTree(treePanel, title);
2914 super.windowOpened(e);
2918 public void windowClosing(WindowEvent e)
2920 sortByTreeMenu.remove(item);
2925 public boolean sortBy(AlignmentOrder alorder, String undoname)
2927 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2928 if (viewport.applet.debug)
2930 System.err.println("Sorting " + alorder.getOrder().size()
2931 + " in alignment '" + getTitle() + "'");
2933 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2934 if (undoname != null)
2936 addHistoryItem(new OrderCommand(undoname, oldOrder,
2937 viewport.getAlignment()));
2939 alignPanel.paintAlignment(true);
2943 protected void documentation_actionPerformed()
2945 alignPanel.av.applet.openJalviewHelpUrl();
2948 protected void about_actionPerformed()
2951 class AboutPanel extends Canvas
2957 public AboutPanel(String version, String builddate)
2959 this.version = version;
2960 this.builddate = builddate;
2964 public void paint(Graphics g)
2966 g.setColor(Color.white);
2967 g.fillRect(0, 0, getSize().width, getSize().height);
2968 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2969 FontMetrics fm = g.getFontMetrics();
2970 int fh = fm.getHeight();
2972 g.setColor(Color.black);
2973 // TODO: update this text for each release or centrally store it for
2974 // lite and application
2975 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2976 g.drawString(MessageManager.formatMessage(
2977 "label.jalviewLite_release", new String[] { version }), x,
2979 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2980 g.drawString(MessageManager.formatMessage(
2981 "label.jaview_build_date", new String[] { builddate }), x,
2983 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2984 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2986 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2987 x + 50, y += fh + 8);
2989 MessageManager.getString("label.jalview_dev_managers"), x,
2991 g.drawString(MessageManager
2992 .getString("label.jalview_distribution_lists"), x, y += fh);
2993 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2996 MessageManager.getString("label.jalview_cite_1_authors"),
2999 MessageManager.getString("label.jalview_cite_1_title"), x,
3001 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3006 Frame frame = new Frame();
3007 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3009 jalview.bin.JalviewLite.addFrame(frame,
3010 MessageManager.getString("label.jalview"), 580, 220);
3014 public void showURL(String url, String target)
3016 if (viewport.applet == null)
3018 System.out.println("Not running as applet - no browser available.");
3022 viewport.applet.showURL(url, target);
3026 // ////////////////////////////////////////////////////////////////////////////////
3027 // JBuilder Graphics here
3029 MenuBar alignFrameMenuBar = new MenuBar();
3031 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3033 MenuItem loadApplication = new MenuItem(
3034 MessageManager.getString("label.view_full_application"));
3036 MenuItem loadTree = new MenuItem(
3037 MessageManager.getString("label.load_associated_tree"));
3039 MenuItem loadAnnotations = new MenuItem(
3040 MessageManager.getString("label.load_features_annotations"));
3042 MenuItem outputFeatures = new MenuItem(
3043 MessageManager.getString("label.export_features"));
3045 MenuItem outputAnnotations = new MenuItem(
3046 MessageManager.getString("label.export_annotations"));
3048 MenuItem closeMenuItem = new MenuItem(
3049 MessageManager.getString("action.close"));
3051 MenuItem selectAllSequenceMenuItem = new MenuItem(
3052 MessageManager.getString("action.select_all"));
3054 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3055 MessageManager.getString("action.deselect_all"));
3057 MenuItem invertSequenceMenuItem = new MenuItem(
3058 MessageManager.getString("action.invert_selection"));
3060 MenuItem remove2LeftMenuItem = new MenuItem();
3062 MenuItem remove2RightMenuItem = new MenuItem();
3064 MenuItem removeGappedColumnMenuItem = new MenuItem();
3066 MenuItem removeAllGapsMenuItem = new MenuItem();
3068 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3070 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3072 MenuItem sortPairwiseMenuItem = new MenuItem();
3074 MenuItem sortIDMenuItem = new MenuItem();
3076 MenuItem sortLengthMenuItem = new MenuItem();
3078 MenuItem sortGroupMenuItem = new MenuItem();
3080 MenuItem removeRedundancyMenuItem = new MenuItem();
3082 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3084 MenuItem PCAMenuItem = new MenuItem();
3086 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3088 MenuItem neighbourTreeMenuItem = new MenuItem();
3090 BorderLayout borderLayout1 = new BorderLayout();
3092 public Label statusBar = new Label();
3094 MenuItem clustalColour = new MenuItem();
3096 MenuItem zappoColour = new MenuItem();
3098 MenuItem taylorColour = new MenuItem();
3100 MenuItem hydrophobicityColour = new MenuItem();
3102 MenuItem helixColour = new MenuItem();
3104 MenuItem strandColour = new MenuItem();
3106 MenuItem turnColour = new MenuItem();
3108 MenuItem buriedColour = new MenuItem();
3110 MenuItem purinePyrimidineColour = new MenuItem();
3112 // MenuItem RNAInteractionColour = new MenuItem();
3114 MenuItem RNAHelixColour = new MenuItem();
3116 MenuItem userDefinedColour = new MenuItem();
3118 MenuItem PIDColour = new MenuItem();
3120 MenuItem BLOSUM62Colour = new MenuItem();
3122 MenuItem tcoffeeColour = new MenuItem();
3124 MenuItem njTreeBlosumMenuItem = new MenuItem();
3126 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3128 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3130 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3132 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3134 MenuItem alProperties = new MenuItem(
3135 MessageManager.getString("label.alignment_props"));
3137 MenuItem overviewMenuItem = new MenuItem();
3139 MenuItem undoMenuItem = new MenuItem();
3141 MenuItem redoMenuItem = new MenuItem();
3143 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3145 MenuItem noColourmenuItem = new MenuItem();
3147 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3149 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3151 MenuItem findMenuItem = new MenuItem();
3153 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3155 MenuItem nucleotideColour = new MenuItem();
3157 MenuItem deleteGroups = new MenuItem();
3159 MenuItem grpsFromSelection = new MenuItem();
3161 MenuItem createGroup = new MenuItem();
3163 MenuItem unGroup = new MenuItem();
3165 MenuItem delete = new MenuItem();
3167 MenuItem copy = new MenuItem();
3169 MenuItem cut = new MenuItem();
3171 Menu pasteMenu = new Menu();
3173 MenuItem pasteNew = new MenuItem();
3175 MenuItem pasteThis = new MenuItem();
3177 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3179 MenuItem font = new MenuItem();
3181 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3183 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3185 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3187 MenuItem modifyPID = new MenuItem();
3189 MenuItem modifyConservation = new MenuItem();
3191 CheckboxMenuItem autoCalculate = null;
3193 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3194 "Sort Alignment With New Tree", true);
3196 Menu sortByTreeMenu = new Menu();
3198 MenuItem inputText = new MenuItem();
3200 MenuItem documentation = new MenuItem();
3202 MenuItem about = new MenuItem();
3204 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3206 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3208 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3210 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3212 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3214 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3216 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3218 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3220 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3223 * Initialise menus and other items
3227 private void jbInit() throws Exception
3229 setMenuBar(alignFrameMenuBar);
3232 * Configure File menu items and actions
3235 .setLabel(MessageManager.getString("label.input_from_textbox"));
3236 inputText.addActionListener(this);
3237 Menu outputTextboxMenu = new Menu(
3238 MessageManager.getString("label.out_to_textbox"));
3239 for (String ff : FileFormat.getWritableFormats(true))
3241 MenuItem item = new MenuItem(ff);
3243 item.addActionListener(new java.awt.event.ActionListener()
3246 public void actionPerformed(ActionEvent e)
3248 outputText_actionPerformed(e);
3252 outputTextboxMenu.add(item);
3254 closeMenuItem.addActionListener(this);
3255 loadApplication.addActionListener(this);
3256 loadTree.addActionListener(this);
3257 loadAnnotations.addActionListener(this);
3258 outputFeatures.addActionListener(this);
3259 outputAnnotations.addActionListener(this);
3262 * Configure Edit menu items and actions
3264 undoMenuItem.setEnabled(false);
3265 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3266 undoMenuItem.addActionListener(this);
3267 redoMenuItem.setEnabled(false);
3268 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3269 redoMenuItem.addActionListener(this);
3270 copy.setLabel(MessageManager.getString("action.copy"));
3271 copy.addActionListener(this);
3272 cut.setLabel(MessageManager.getString("action.cut"));
3273 cut.addActionListener(this);
3274 delete.setLabel(MessageManager.getString("action.delete"));
3275 delete.addActionListener(this);
3276 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3277 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3278 pasteNew.addActionListener(this);
3279 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3280 pasteThis.addActionListener(this);
3281 remove2LeftMenuItem.setLabel(MessageManager
3282 .getString("action.remove_left"));
3283 remove2LeftMenuItem.addActionListener(this);
3284 remove2RightMenuItem.setLabel(MessageManager
3285 .getString("action.remove_right"));
3286 remove2RightMenuItem.addActionListener(this);
3287 removeGappedColumnMenuItem.setLabel(MessageManager
3288 .getString("action.remove_empty_columns"));
3289 removeGappedColumnMenuItem.addActionListener(this);
3290 removeAllGapsMenuItem.setLabel(MessageManager
3291 .getString("action.remove_all_gaps"));
3292 removeAllGapsMenuItem.addActionListener(this);
3293 removeRedundancyMenuItem.setLabel(MessageManager
3294 .getString("action.remove_redundancy"));
3295 removeRedundancyMenuItem.addActionListener(this);
3298 * Configure Select menu items and actions
3300 findMenuItem.setLabel(MessageManager.getString("action.find"));
3301 findMenuItem.addActionListener(this);
3302 selectAllSequenceMenuItem.addActionListener(this);
3303 deselectAllSequenceMenuItem.addActionListener(this);
3304 invertSequenceMenuItem.setLabel(MessageManager
3305 .getString("action.invert_sequence_selection"));
3306 invertSequenceMenuItem.addActionListener(this);
3307 invertColSel.setLabel(MessageManager
3308 .getString("action.invert_column_selection"));
3309 invertColSel.addActionListener(this);
3310 deleteGroups.setLabel(MessageManager
3311 .getString("action.undefine_groups"));
3312 deleteGroups.addActionListener(this);
3313 grpsFromSelection.setLabel(MessageManager
3314 .getString("action.make_groups_selection"));
3315 grpsFromSelection.addActionListener(this);
3316 createGroup.setLabel(MessageManager.getString("action.create_group"));
3317 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3318 annotationColumnSelection.setLabel(MessageManager
3319 .getString("action.select_by_annotation"));
3320 annotationColumnSelection.addActionListener(this);
3323 * Configure View menu items and actions
3325 newView.setLabel(MessageManager.getString("action.new_view"));
3326 newView.addActionListener(this);
3327 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3328 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3329 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3330 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3332 .setLabel(MessageManager.getString("label.selected_columns"));
3333 hideSequences.setLabel(MessageManager
3334 .getString("label.selected_sequences"));
3335 hideAllButSelection.setLabel(MessageManager
3336 .getString("label.all_but_selected_region"));
3337 hideAllSelection.setLabel(MessageManager
3338 .getString("label.selected_region"));
3339 showAllHidden.setLabel(MessageManager
3340 .getString("label.all_sequences_columns"));
3341 showColumns.addActionListener(this);
3342 showSeqs.addActionListener(this);
3343 hideColumns.addActionListener(this);
3344 hideSequences.addActionListener(this);
3345 hideAllButSelection.addActionListener(this);
3346 hideAllSelection.addActionListener(this);
3347 showAllHidden.addActionListener(this);
3348 featureSettings.setLabel(MessageManager
3349 .getString("action.feature_settings"));
3350 featureSettings.addActionListener(this);
3351 sequenceFeatures.setLabel(MessageManager
3352 .getString("label.show_sequence_features"));
3353 sequenceFeatures.addItemListener(this);
3354 sequenceFeatures.setState(false);
3355 followMouseOverFlag.setLabel(MessageManager
3356 .getString("label.automatic_scrolling"));
3357 followMouseOverFlag.addItemListener(this);
3358 alProperties.addActionListener(this);
3359 overviewMenuItem.setLabel(MessageManager
3360 .getString("label.overview_window"));
3361 overviewMenuItem.addActionListener(this);
3364 * Configure Annotations menu items and actions
3366 annotationPanelMenuItem.setLabel(MessageManager
3367 .getString("label.show_annotations"));
3368 annotationPanelMenuItem.addItemListener(this);
3369 showGroupConsensus.setLabel(MessageManager
3370 .getString("label.group_consensus"));
3371 showGroupConservation.setLabel(MessageManager
3372 .getString("label.group_conservation"));
3373 showConsensusHistogram.setLabel(MessageManager
3374 .getString("label.show_consensus_histogram"));
3375 showSequenceLogo.setLabel(MessageManager
3376 .getString("label.show_consensus_logo"));
3377 normSequenceLogo.setLabel(MessageManager
3378 .getString("label.norm_consensus_logo"));
3379 applyAutoAnnotationSettings.setLabel(MessageManager
3380 .getString("label.apply_all_groups"));
3381 applyAutoAnnotationSettings.setState(true);
3382 Menu autoAnnMenu = new Menu(
3383 MessageManager.getString("label.autocalculated_annotation"));
3384 showGroupConsensus.addItemListener(this);
3385 showGroupConservation.addItemListener(this);
3386 showConsensusHistogram.addItemListener(this);
3387 showSequenceLogo.addItemListener(this);
3388 normSequenceLogo.addItemListener(this);
3389 applyAutoAnnotationSettings.addItemListener(this);
3390 showAlignmentAnnotations = new CheckboxMenuItem(
3391 MessageManager.getString("label.show_all_al_annotations"));
3392 showSequenceAnnotations = new CheckboxMenuItem(
3393 MessageManager.getString("label.show_all_seq_annotations"));
3394 sortAnnBySequence = new CheckboxMenuItem(
3395 MessageManager.getString("label.sort_annotations_by_sequence"));
3396 sortAnnByLabel = new CheckboxMenuItem(
3397 MessageManager.getString("label.sort_annotations_by_label"));
3398 showAutoFirst = new CheckboxMenuItem(
3399 MessageManager.getString("label.show_first"));
3400 showAutoFirst.setState(false); // pending applet parameter
3401 setShowAutoCalculatedAbove(showAutoFirst.getState());
3402 showAutoLast = new CheckboxMenuItem(
3403 MessageManager.getString("label.show_last"));
3404 showAutoLast.setState(!showAutoFirst.getState());
3405 showAlignmentAnnotations.addItemListener(this);
3406 showSequenceAnnotations.addItemListener(this);
3407 sortAnnBySequence.addItemListener(this);
3408 sortAnnByLabel.addItemListener(this);
3409 showAutoFirst.addItemListener(this);
3410 showAutoLast.addItemListener(this);
3413 * Configure Format menu items and actions
3415 font.setLabel(MessageManager.getString("action.font"));
3416 font.addActionListener(this);
3417 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3418 scaleAbove.setState(true);
3419 scaleAbove.setEnabled(false);
3420 scaleAbove.addItemListener(this);
3421 scaleLeft.setEnabled(false);
3422 scaleLeft.setState(true);
3423 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3424 scaleLeft.addItemListener(this);
3425 scaleRight.setEnabled(false);
3426 scaleRight.setState(true);
3427 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3428 scaleRight.addItemListener(this);
3429 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3430 viewBoxesMenuItem.setState(true);
3431 viewBoxesMenuItem.addItemListener(this);
3432 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3433 viewTextMenuItem.setState(true);
3434 viewTextMenuItem.addItemListener(this);
3435 colourTextMenuItem.setLabel(MessageManager
3436 .getString("label.colour_text"));
3437 colourTextMenuItem.addItemListener(this);
3438 displayNonconservedMenuItem.setLabel(MessageManager
3439 .getString("label.show_non_conversed"));
3440 displayNonconservedMenuItem.addItemListener(this);
3441 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3442 wrapMenuItem.addItemListener(this);
3443 renderGapsMenuItem.setLabel(MessageManager
3444 .getString("action.show_gaps"));
3445 renderGapsMenuItem.setState(true);
3446 renderGapsMenuItem.addItemListener(this);
3447 centreColumnLabelFlag.setLabel(MessageManager
3448 .getString("label.centre_column_labels"));
3449 centreColumnLabelFlag.addItemListener(this);
3450 seqLimits.setState(true);
3451 seqLimits.setLabel(MessageManager
3452 .getString("label.show_sequence_limits"));
3453 seqLimits.addItemListener(this);
3456 * Configure Colour menu items and actions
3458 applyToAllGroups.setLabel(MessageManager
3459 .getString("label.apply_colour_to_all_groups"));
3460 applyToAllGroups.setState(true);
3461 applyToAllGroups.addItemListener(this);
3462 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3463 clustalColour.addActionListener(this);
3464 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3465 zappoColour.addActionListener(this);
3466 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3467 taylorColour.addActionListener(this);
3468 hydrophobicityColour.setLabel(MessageManager
3469 .getString("label.hydrophobicity"));
3470 hydrophobicityColour.addActionListener(this);
3472 .setLabel(MessageManager.getString("label.helix_propensity"));
3473 helixColour.addActionListener(this);
3474 strandColour.setLabel(MessageManager
3475 .getString("label.strand_propensity"));
3476 strandColour.addActionListener(this);
3477 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3478 turnColour.addActionListener(this);
3479 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3480 buriedColour.addActionListener(this);
3481 purinePyrimidineColour.setLabel(MessageManager
3482 .getString("label.purine_pyrimidine"));
3483 purinePyrimidineColour.addActionListener(this);
3484 // RNAInteractionColour.setLabel(MessageManager
3485 // .getString("label.rna_interaction"));
3486 // RNAInteractionColour.addActionListener(this);
3487 RNAHelixColour.setLabel(MessageManager
3488 .getString("action.by_rna_helixes"));
3489 RNAHelixColour.addActionListener(this);
3490 userDefinedColour.setLabel(MessageManager
3491 .getString("action.user_defined"));
3492 userDefinedColour.addActionListener(this);
3493 PIDColour.setLabel(MessageManager
3494 .getString("label.percentage_identity"));
3495 PIDColour.addActionListener(this);
3496 BLOSUM62Colour.setLabel(MessageManager
3497 .getString("label.blosum62_score"));
3498 BLOSUM62Colour.addActionListener(this);
3500 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3501 // it will be enabled only if a score file is provided
3502 tcoffeeColour.setEnabled(false);
3503 tcoffeeColour.addActionListener(this);
3504 conservationMenuItem.setLabel(MessageManager
3505 .getString("action.by_conservation"));
3506 conservationMenuItem.addItemListener(this);
3507 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3508 noColourmenuItem.addActionListener(this);
3509 abovePIDThreshold.setLabel(MessageManager
3510 .getString("label.above_identity_threshold"));
3511 abovePIDThreshold.addItemListener(this);
3512 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3513 nucleotideColour.addActionListener(this);
3514 modifyPID.setLabel(MessageManager
3515 .getString("label.modify_identity_threshold"));
3516 modifyPID.addActionListener(this);
3517 modifyConservation.setLabel(MessageManager
3518 .getString("label.modify_conservation_threshold"));
3519 modifyConservation.addActionListener(this);
3520 annotationColour.setLabel(MessageManager
3521 .getString("action.by_annotation"));
3522 annotationColour.addActionListener(this);
3525 * Configure Calculate menu items and actions
3527 sortPairwiseMenuItem.setLabel(MessageManager
3528 .getString("action.by_pairwise_id"));
3529 sortPairwiseMenuItem.addActionListener(this);
3530 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3531 sortIDMenuItem.addActionListener(this);
3532 sortLengthMenuItem.setLabel(MessageManager
3533 .getString("action.by_length"));
3534 sortLengthMenuItem.addActionListener(this);
3535 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3536 sortGroupMenuItem.addActionListener(this);
3537 pairwiseAlignmentMenuItem.setLabel(MessageManager
3538 .getString("action.pairwise_alignment"));
3539 pairwiseAlignmentMenuItem.addActionListener(this);
3540 PCAMenuItem.setLabel(MessageManager
3541 .getString("label.principal_component_analysis"));
3542 PCAMenuItem.addActionListener(this);
3543 autoCalculate = new CheckboxMenuItem(
3544 MessageManager.getString("label.autocalculate_consensus"), true);
3545 averageDistanceTreeMenuItem.setLabel(MessageManager
3546 .getString("label.average_distance_identity"));
3547 averageDistanceTreeMenuItem.addActionListener(this);
3548 neighbourTreeMenuItem.setLabel(MessageManager
3549 .getString("label.neighbour_joining_identity"));
3550 neighbourTreeMenuItem.addActionListener(this);
3551 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3552 .getString("label.average_distance_bloslum62"));
3553 avDistanceTreeBlosumMenuItem.addActionListener(this);
3554 njTreeBlosumMenuItem.setLabel(MessageManager
3555 .getString("label.neighbour_blosum62"));
3556 njTreeBlosumMenuItem.addActionListener(this);
3557 sortByTreeMenu.setLabel(MessageManager
3558 .getString("action.by_tree_order"));
3559 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3560 Menu calculateTreeMenu = new Menu(
3561 MessageManager.getString("action.calculate_tree"));
3562 autoCalculate.addItemListener(this);
3563 sortByTree.addItemListener(this);
3566 * Configure Help menu items and actions
3568 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3569 documentation.setLabel(MessageManager.getString("label.documentation"));
3570 documentation.addActionListener(this);
3571 about.setLabel(MessageManager.getString("label.about"));
3572 about.addActionListener(this);
3575 * Add top level menus to frame
3577 alignFrameMenuBar.add(fileMenu);
3578 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3579 alignFrameMenuBar.add(editMenu);
3580 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3581 alignFrameMenuBar.add(selectMenu);
3582 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3583 alignFrameMenuBar.add(viewMenu);
3584 Menu annotationsMenu = new Menu(
3585 MessageManager.getString("action.annotations"));
3586 alignFrameMenuBar.add(annotationsMenu);
3587 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3588 alignFrameMenuBar.add(formatMenu);
3589 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3590 alignFrameMenuBar.add(colourMenu);
3591 Menu calculateMenu = new Menu(
3592 MessageManager.getString("action.calculate"));
3593 alignFrameMenuBar.add(calculateMenu);
3594 alignFrameMenuBar.add(helpMenu);
3599 fileMenu.add(inputText);
3600 fileMenu.add(loadTree);
3601 fileMenu.add(loadAnnotations);
3602 fileMenu.addSeparator();
3603 fileMenu.add(outputTextboxMenu);
3604 fileMenu.add(outputFeatures);
3605 fileMenu.add(outputAnnotations);
3606 if (jalviewServletURL != null)
3608 fileMenu.add(loadApplication);
3610 fileMenu.addSeparator();
3611 fileMenu.add(closeMenuItem);
3616 editMenu.add(undoMenuItem);
3617 editMenu.add(redoMenuItem);
3620 pasteMenu.add(pasteNew);
3621 pasteMenu.add(pasteThis);
3622 editMenu.add(pasteMenu);
3623 editMenu.add(delete);
3624 editMenu.addSeparator();
3625 editMenu.add(remove2LeftMenuItem);
3626 editMenu.add(remove2RightMenuItem);
3627 editMenu.add(removeGappedColumnMenuItem);
3628 editMenu.add(removeAllGapsMenuItem);
3629 editMenu.add(removeRedundancyMenuItem);
3634 selectMenu.add(findMenuItem);
3635 selectMenu.addSeparator();
3636 selectMenu.add(selectAllSequenceMenuItem);
3637 selectMenu.add(deselectAllSequenceMenuItem);
3638 selectMenu.add(invertSequenceMenuItem);
3639 selectMenu.add(invertColSel);
3640 selectMenu.add(createGroup);
3641 selectMenu.add(unGroup);
3642 selectMenu.add(grpsFromSelection);
3643 selectMenu.add(deleteGroups);
3644 selectMenu.add(annotationColumnSelection);
3649 viewMenu.add(newView);
3650 viewMenu.addSeparator();
3651 showMenu.add(showColumns);
3652 showMenu.add(showSeqs);
3653 showMenu.add(showAllHidden);
3654 viewMenu.add(showMenu);
3655 hideMenu.add(hideColumns);
3656 hideMenu.add(hideSequences);
3657 hideMenu.add(hideAllSelection);
3658 hideMenu.add(hideAllButSelection);
3659 viewMenu.add(hideMenu);
3660 viewMenu.addSeparator();
3661 viewMenu.add(followMouseOverFlag);
3662 viewMenu.addSeparator();
3663 viewMenu.add(sequenceFeatures);
3664 viewMenu.add(featureSettings);
3665 viewMenu.addSeparator();
3666 viewMenu.add(alProperties);
3667 viewMenu.addSeparator();
3668 viewMenu.add(overviewMenuItem);
3673 annotationsMenu.add(annotationPanelMenuItem);
3674 annotationsMenu.addSeparator();
3675 annotationsMenu.add(showAlignmentAnnotations);
3676 annotationsMenu.add(showSequenceAnnotations);
3677 annotationsMenu.add(sortAnnBySequence);
3678 annotationsMenu.add(sortAnnByLabel);
3679 annotationsMenu.addSeparator();
3680 autoAnnMenu.add(showAutoFirst);
3681 autoAnnMenu.add(showAutoLast);
3682 autoAnnMenu.addSeparator();
3683 autoAnnMenu.add(applyAutoAnnotationSettings);
3684 autoAnnMenu.add(showConsensusHistogram);
3685 autoAnnMenu.add(showSequenceLogo);
3686 autoAnnMenu.add(normSequenceLogo);
3687 autoAnnMenu.addSeparator();
3688 autoAnnMenu.add(showGroupConservation);
3689 autoAnnMenu.add(showGroupConsensus);
3690 annotationsMenu.add(autoAnnMenu);
3695 formatMenu.add(font);
3696 formatMenu.add(seqLimits);
3697 formatMenu.add(wrapMenuItem);
3698 formatMenu.add(scaleAbove);
3699 formatMenu.add(scaleLeft);
3700 formatMenu.add(scaleRight);
3701 formatMenu.add(viewBoxesMenuItem);
3702 formatMenu.add(viewTextMenuItem);
3703 formatMenu.add(colourTextMenuItem);
3704 formatMenu.add(displayNonconservedMenuItem);
3705 formatMenu.add(renderGapsMenuItem);
3706 formatMenu.add(centreColumnLabelFlag);
3711 colourMenu.add(applyToAllGroups);
3712 colourMenu.addSeparator();
3713 colourMenu.add(noColourmenuItem);
3714 colourMenu.add(clustalColour);
3715 colourMenu.add(BLOSUM62Colour);
3716 colourMenu.add(PIDColour);
3717 colourMenu.add(zappoColour);
3718 colourMenu.add(taylorColour);
3719 colourMenu.add(hydrophobicityColour);
3720 colourMenu.add(helixColour);
3721 colourMenu.add(strandColour);
3722 colourMenu.add(turnColour);
3723 colourMenu.add(buriedColour);
3724 colourMenu.add(nucleotideColour);
3725 colourMenu.add(purinePyrimidineColour);
3726 // colourMenu.add(RNAInteractionColour);
3727 colourMenu.add(tcoffeeColour);
3728 colourMenu.add(userDefinedColour);
3729 colourMenu.addSeparator();
3730 colourMenu.add(conservationMenuItem);
3731 colourMenu.add(modifyConservation);
3732 colourMenu.add(abovePIDThreshold);
3733 colourMenu.add(modifyPID);
3734 colourMenu.add(annotationColour);
3735 colourMenu.add(RNAHelixColour);
3740 sortMenu.add(sortIDMenuItem);
3741 sortMenu.add(sortLengthMenuItem);
3742 sortMenu.add(sortByTreeMenu);
3743 sortMenu.add(sortGroupMenuItem);
3744 sortMenu.add(sortPairwiseMenuItem);
3745 calculateMenu.add(sortMenu);
3746 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3747 calculateTreeMenu.add(neighbourTreeMenuItem);
3748 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3749 calculateTreeMenu.add(njTreeBlosumMenuItem);
3750 calculateMenu.add(calculateTreeMenu);
3751 calculateMenu.addSeparator();
3752 calculateMenu.add(pairwiseAlignmentMenuItem);
3753 calculateMenu.add(PCAMenuItem);
3754 calculateMenu.add(autoCalculate);
3755 calculateMenu.add(sortByTree);
3760 helpMenu.add(documentation);
3761 helpMenu.add(about);
3766 statusBar.setBackground(Color.white);
3767 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3768 statusBar.setText(MessageManager.getString("label.status_bar"));
3769 this.add(statusBar, BorderLayout.SOUTH);
3773 public void setStatus(String string)
3775 statusBar.setText(string);
3778 MenuItem featureSettings = new MenuItem();
3780 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3782 MenuItem annotationColour = new MenuItem();
3784 MenuItem annotationColumnSelection = new MenuItem();
3786 MenuItem invertColSel = new MenuItem();
3788 MenuItem showColumns = new MenuItem();
3790 MenuItem showSeqs = new MenuItem();
3792 MenuItem hideColumns = new MenuItem();
3794 MenuItem hideSequences = new MenuItem();
3796 MenuItem hideAllButSelection = new MenuItem();
3798 MenuItem hideAllSelection = new MenuItem();
3800 MenuItem showAllHidden = new MenuItem();
3802 MenuItem newView = new MenuItem();
3804 private CheckboxMenuItem showAlignmentAnnotations;
3806 private CheckboxMenuItem showSequenceAnnotations;
3808 private CheckboxMenuItem sortAnnBySequence;
3810 private CheckboxMenuItem sortAnnByLabel;
3812 private CheckboxMenuItem showAutoFirst;
3814 private CheckboxMenuItem showAutoLast;
3816 private SplitFrame splitFrame;
3819 * Attach the alignFrame panels after embedding menus, if necessary. This used
3820 * to be called setEmbedded, but is now creates the dropdown menus in a
3821 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3823 * @param reallyEmbedded
3824 * true to attach the view to the applet area on the page rather than
3827 public void createAlignFrameWindow(boolean reallyEmbedded)
3831 embedAlignFrameInApplet(viewport.applet);
3836 // test and embed menu bar if necessary.
3838 if (embedMenuIfNeeded(alignPanel))
3841 * adjust for status bar height too. ? pointless as overridden by layout
3844 alignPanel.setSize(getSize().width,
3845 getSize().height - statusBar.getHeight());
3847 add(statusBar, BorderLayout.SOUTH);
3848 add(alignPanel, BorderLayout.CENTER);
3849 // and register with the applet so it can pass external API calls to us
3850 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3856 * Add the components of this AlignFrame to the applet container.
3860 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3863 // Explicitly build the embedded menu panel for the on-page applet
3865 // view cannot be closed if its actually on the page
3866 fileMenu.remove(closeMenuItem);
3867 fileMenu.remove(3); // Remove Separator
3868 // construct embedded menu, using default font
3869 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3870 // and actually add the components to the applet area
3871 theApplet.setLayout(new BorderLayout());
3872 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3873 theApplet.add(statusBar, BorderLayout.SOUTH);
3874 // TODO should size be left to the layout manager?
3875 alignPanel.setSize(theApplet.getSize().width,
3876 theApplet.getSize().height - embeddedMenu.getHeight()
3877 - statusBar.getHeight());
3878 theApplet.add(alignPanel, BorderLayout.CENTER);
3879 final AlignFrame me = this;
3880 theApplet.addFocusListener(new FocusListener()
3884 public void focusLost(FocusEvent e)
3886 if (theApplet.currentAlignFrame == me)
3888 theApplet.currentAlignFrame = null;
3893 public void focusGained(FocusEvent e)
3895 theApplet.currentAlignFrame = me;
3898 theApplet.validate();
3902 * create a new binding between structures in an existing jmol viewer instance
3903 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3904 * this does not open a new Jmol window, or modify the display of the
3905 * structures in the original jmol window. Note This method doesn't work
3906 * without an additional javascript library to exchange messages between the
3907 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3910 * JmolViewer instance
3911 * @param sequenceIds
3912 * - sequence Ids to search for associations
3914 public SequenceStructureBinding addStructureViewInstance(
3915 Object jmolviewer, String[] sequenceIds)
3917 Viewer viewer = null;
3920 viewer = (Viewer) jmolviewer;
3921 } catch (ClassCastException ex)
3923 System.err.println("Unsupported viewer object :"
3924 + jmolviewer.getClass());
3928 System.err.println("Can't use this object as a structure viewer:"
3929 + jmolviewer.getClass());
3932 SequenceI[] seqs = null;
3933 if (sequenceIds == null || sequenceIds.length == 0)
3935 seqs = viewport.getAlignment().getSequencesArray();
3939 Vector sqi = new Vector();
3940 AlignmentI al = viewport.getAlignment();
3941 for (int sid = 0; sid < sequenceIds.length; sid++)
3943 SequenceI sq = al.findName(sequenceIds[sid]);
3951 seqs = new SequenceI[sqi.size()];
3952 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3954 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3962 AAStructureBindingModel jmv = null;
3963 // TODO: search for a jmv that involves viewer
3965 { // create a new viewer/jalview binding.
3966 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3973 * bind a pdb file to a sequence in the current view
3976 * - sequenceId within the dataset.
3977 * @param pdbEntryString
3978 * - the short name for the PDB file
3980 * - pdb file - either a URL or a valid PDB file.
3981 * @return true if binding was as success TODO: consider making an exception
3982 * structure for indicating when PDB parsing or sequenceId location
3985 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3988 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3989 boolean needtoadd = false;
3990 if (toaddpdb != null)
3992 Vector pdbe = toaddpdb.getAllPDBEntries();
3993 PDBEntry pdbentry = null;
3994 if (pdbe != null && pdbe.size() > 0)
3996 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3998 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3999 if (!pdbentry.getId().equals(pdbEntryString)
4000 && !pdbentry.getFile().equals(pdbFile))
4010 if (pdbentry == null)
4012 pdbentry = new PDBEntry();
4013 pdbentry.setId(pdbEntryString);
4014 pdbentry.setFile(pdbFile);
4015 needtoadd = true; // add this new entry to sequence.
4017 // resolve data source
4018 // TODO: this code should be a refactored to an io package
4019 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4020 pdbFile, FileFormat.PDB);
4021 if (protocol == null)
4027 pdbentry.setProperty("protocol", protocol);
4028 toaddpdb.addPDBId(pdbentry);
4029 alignPanel.getStructureSelectionManager()
4030 .registerPDBEntry(pdbentry);
4036 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4040 Vector sequences = new Vector();
4041 for (int i = 0; i < seqs.length; i++)
4043 if (seqs[i] != null)
4045 sequences.addElement(new Object[] { seqs[i],
4046 (chains != null) ? chains[i] : null });
4049 seqs = new SequenceI[sequences.size()];
4050 chains = new String[sequences.size()];
4051 for (int i = 0, isize = sequences.size(); i < isize; i++)
4053 Object[] oj = (Object[]) sequences.elementAt(i);
4055 seqs[i] = (SequenceI) oj[0];
4056 chains[i] = (String) oj[1];
4059 return new Object[] { seqs, chains };
4063 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4064 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4066 // Scrub any null sequences from the array
4067 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4068 seqs = (SequenceI[]) sqch[0];
4069 chains = (String[]) sqch[1];
4070 if (seqs == null || seqs.length == 0)
4073 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4075 if (protocol == null)
4077 String sourceType = (String) pdb.getProperty("protocol");
4080 protocol = DataSourceType.valueOf(sourceType);
4081 } catch (IllegalArgumentException e)
4085 if (protocol == null)
4087 System.err.println("Couldn't work out protocol to open structure: "
4092 if (applet.useXtrnalSviewer)
4094 // register the association(s) and quit, don't create any windows.
4095 if (StructureSelectionManager.getStructureSelectionManager(applet)
4096 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4098 System.err.println("Failed to map " + pdb.getFile() + " ("
4099 + protocol + ") to any sequences");
4103 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4105 // can only do alignments with Jmol
4106 // find the last jmol window assigned to this alignment
4107 AppletJmol ajm = null, tajm;
4108 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4109 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4111 tajm = (AppletJmol) jmols.elementAt(i);
4112 if (tajm.ap.alignFrame == this)
4121 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4122 // try and add the pdb structure
4127 // otherwise, create a new window
4128 if (applet.jmolAvailable)
4130 new AppletJmol(pdb, seqs, chains, alignPanel,
4132 applet.lastFrameX += 40;
4133 applet.lastFrameY += 40;
4137 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4142 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4143 SequenceI[][] seqs, String[][] chains, String[] protocols)
4145 // TODO Auto-generated method stub
4146 System.err.println("Aligned Structure View: Not yet implemented.");
4150 * modify the current selection, providing the user has not made a selection
4154 * - sequences from this alignment
4156 * - columns to be selected on the alignment
4158 public void select(SequenceGroup sel, ColumnSelection csel)
4160 alignPanel.seqPanel.selection(sel, csel, null);
4163 public void scrollTo(int row, int column)
4165 alignPanel.seqPanel.scrollTo(row, column);
4168 public void scrollToRow(int row)
4170 alignPanel.seqPanel.scrollToRow(row);
4173 public void scrollToColumn(int column)
4175 alignPanel.seqPanel.scrollToColumn(column);
4179 * @return the alignments unique ID.
4181 public String getSequenceSetId()
4183 return viewport.getSequenceSetId();
4187 * Load the (T-Coffee) score file from the specified url
4190 * File/URL/T-COFFEE score file contents
4191 * @throws IOException
4192 * @return true if alignment was annotated with data from source
4194 public boolean loadScoreFile(String source) throws IOException
4197 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4198 AppletFormatAdapter.checkProtocol(source));
4199 if (!file.isValid())
4201 // TODO: raise dialog for gui
4202 System.err.println("Problems parsing T-Coffee scores: "
4203 + file.getWarningMessage());
4204 System.err.println("Origin was:\n" + source);
4209 * check that the score matrix matches the alignment dimensions
4212 if ((aln = viewport.getAlignment()) != null
4213 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4216 // TODO: raise a dialog box here rather than bomb out.
4218 .println("The scores matrix does not match the alignment dimensions");
4222 // TODO add parameter to indicate if matching should be done
4223 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4225 alignPanel.fontChanged();
4226 tcoffeeColour.setEnabled(true);
4227 // switch to this color
4228 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4233 System.err.println("Problems resolving T-Coffee scores:");
4234 if (file.getWarningMessage() != null)
4236 System.err.println(file.getWarningMessage());
4242 public SplitFrame getSplitFrame()
4244 return this.splitFrame;
4247 public void setSplitFrame(SplitFrame sf)
4249 this.splitFrame = sf;
4252 // may not need this
4254 public void setShowSeqFeatures(boolean b)
4256 // showSeqFeatures.setSelected(b);
4257 viewport.setShowSequenceFeatures(b);
4262 public void setMenusForViewport()
4264 // setMenusFromViewport(viewport);
4269 public void refreshFeatureUI(boolean enableIfNecessary)
4271 if (enableIfNecessary)
4273 sequenceFeatures.setState(true);
4274 alignPanel.av.setShowSequenceFeatures(true);
4279 public FeatureSettingsControllerI getFeatureSettingsUI()
4281 return alignPanel.av.featureSettings;