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.FeaturesFile;
53 import jalview.io.TCoffeeScoreFile;
54 import jalview.schemes.Blosum62ColourScheme;
55 import jalview.schemes.BuriedColourScheme;
56 import jalview.schemes.ClustalxColourScheme;
57 import jalview.schemes.ColourSchemeI;
58 import jalview.schemes.HelixColourScheme;
59 import jalview.schemes.HydrophobicColourScheme;
60 import jalview.schemes.NucleotideColourScheme;
61 import jalview.schemes.PIDColourScheme;
62 import jalview.schemes.PurinePyrimidineColourScheme;
63 import jalview.schemes.RNAHelicesColourChooser;
64 import jalview.schemes.StrandColourScheme;
65 import jalview.schemes.TCoffeeColourScheme;
66 import jalview.schemes.TaylorColourScheme;
67 import jalview.schemes.TurnColourScheme;
68 import jalview.schemes.ZappoColourScheme;
69 import jalview.structure.StructureSelectionManager;
70 import jalview.structures.models.AAStructureBindingModel;
71 import jalview.util.MappingUtils;
72 import jalview.util.MessageManager;
73 import jalview.viewmodel.AlignmentViewport;
75 import java.awt.BorderLayout;
76 import java.awt.Canvas;
77 import java.awt.CheckboxMenuItem;
78 import java.awt.Color;
79 import java.awt.FlowLayout;
81 import java.awt.FontMetrics;
82 import java.awt.Frame;
83 import java.awt.Graphics;
84 import java.awt.Label;
86 import java.awt.MenuBar;
87 import java.awt.MenuItem;
88 import java.awt.Panel;
89 import java.awt.event.ActionEvent;
90 import java.awt.event.ActionListener;
91 import java.awt.event.FocusEvent;
92 import java.awt.event.FocusListener;
93 import java.awt.event.ItemEvent;
94 import java.awt.event.ItemListener;
95 import java.awt.event.KeyEvent;
96 import java.awt.event.KeyListener;
97 import java.awt.event.WindowAdapter;
98 import java.awt.event.WindowEvent;
99 import java.io.IOException;
101 import java.net.URLEncoder;
102 import java.util.Arrays;
103 import java.util.Deque;
104 import java.util.HashMap;
105 import java.util.List;
106 import java.util.Map;
107 import java.util.StringTokenizer;
108 import java.util.Vector;
110 import org.jmol.viewer.Viewer;
112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
113 ItemListener, KeyListener, AlignViewControllerGuiI
115 public AlignViewControllerI avc;
117 public AlignmentPanel alignPanel;
119 public AlignViewport viewport;
121 // width and height may be overridden by applet parameters
122 int frameWidth = 700;
124 int frameHeight = 500;
126 String jalviewServletURL;
129 * Flag for showing autocalculated consensus above or below other consensus
132 private boolean showAutoCalculatedAbove;
134 private SequenceAnnotationOrder annotationSortOrder;
137 * Constructor that creates the frame and adds it to the display.
144 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
147 this(al, applet, title, embedded, true);
151 * Constructor that optionally allows the frame to be displayed or only
158 * @param addToDisplay
160 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
161 boolean embedded, boolean addToDisplay)
163 this(al, null, null, applet, title, embedded, addToDisplay);
166 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
167 ColumnSelection columnSelection, JalviewLite applet,
168 String title, boolean embedded)
170 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
173 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
174 ColumnSelection columnSelection, JalviewLite applet,
175 String title, boolean embedded, boolean addToDisplay)
179 jalviewServletURL = applet.getParameter("APPLICATION_URL");
185 } catch (Exception ex)
187 ex.printStackTrace();
189 // need to get window geometry before we calculate alignment layout
195 param = applet.getParameter("windowWidth");
198 int width = Integer.parseInt(param);
201 param = applet.getParameter("windowHeight");
204 int height = Integer.parseInt(param);
205 frameHeight = height;
207 } catch (Exception ex)
211 viewport = new AlignViewport(al, applet);
213 if (hiddenSeqs != null && hiddenSeqs.length > 0)
215 viewport.hideSequence(hiddenSeqs);
217 if (columnSelection != null)
219 viewport.setColumnSelection(columnSelection);
221 viewport.setScaleAboveWrapped(scaleAbove.getState());
223 alignPanel = new AlignmentPanel(this, viewport);
224 avc = new jalview.controller.AlignViewController(this, viewport,
226 viewport.updateConservation(alignPanel);
227 viewport.updateConsensus(alignPanel);
229 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
230 followMouseOverFlag.setState(viewport.isFollowHighlight());
231 showGroupConsensus.setState(viewport.isShowGroupConsensus());
232 showGroupConservation.setState(viewport.isShowGroupConservation());
233 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
234 showSequenceLogo.setState(viewport.isShowSequenceLogo());
235 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
236 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
237 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
238 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
239 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
240 showAlignmentAnnotations.setState(true);
241 showSequenceAnnotations.setState(false);
243 seqLimits.setState(viewport.getShowJVSuffix());
247 String param = applet.getParameter("sortBy");
250 if (param.equalsIgnoreCase("Id"))
252 sortIDMenuItem_actionPerformed();
254 else if (param.equalsIgnoreCase("Pairwise Identity"))
256 sortPairwiseMenuItem_actionPerformed();
258 else if (param.equalsIgnoreCase("Length"))
260 sortLengthMenuItem_actionPerformed();
264 param = applet.getParameter("wrap");
267 if (param.equalsIgnoreCase("true"))
269 wrapMenuItem.setState(true);
270 wrapMenuItem_actionPerformed();
273 param = applet.getParameter("centrecolumnlabels");
276 centreColumnLabelFlag.setState(true);
277 centreColumnLabelFlag_stateChanged();
281 if (viewport.getAlignment().isNucleotide())
283 viewport.updateStrucConsensus(alignPanel);
284 if (viewport.getAlignment().hasRNAStructure())
286 RNAHelixColour.setEnabled(true);
290 RNAHelixColour.setEnabled(false);
295 RNAHelixColour.setEnabled(false);
296 purinePyrimidineColour.setEnabled(false);
298 // Some JVMS send keyevents to Top frame or lowest panel,
299 // Havent worked out why yet. So add to both this frame and seqCanvas for
301 this.addKeyListener(this);
302 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
303 alignPanel.idPanel.idCanvas.addKeyListener(this);
304 alignPanel.scalePanel.addKeyListener(this);
305 alignPanel.annotationPanel.addKeyListener(this);
306 alignPanel.annotationPanelHolder.addKeyListener(this);
307 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
308 alignPanel.alabels.addKeyListener(this);
310 setAnnotationsVisibility();
314 addToDisplay(embedded);
321 public void addToDisplay(boolean embedded)
323 createAlignFrameWindow(embedded);
325 alignPanel.adjustAnnotationHeight();
326 alignPanel.paintAlignment(true);
329 public AlignViewport getAlignViewport()
334 public SeqCanvas getSeqcanvas()
336 return alignPanel.seqPanel.seqCanvas;
340 * Load a features file onto the alignment
343 * file URL, content, or other resolvable path
345 * is protocol for accessing data referred to by file
348 public boolean parseFeaturesFile(String file, String type)
350 return parseFeaturesFile(file, type, true);
354 * Load a features file onto the alignment
357 * file URL, content, or other resolvable path
359 * is protocol for accessing data referred to by file
360 * @param autoenabledisplay
361 * when true, display features flag will be automatically enabled if
362 * features are loaded
363 * @return true if data parsed as a features file
365 public boolean parseFeaturesFile(String file, String type,
366 boolean autoenabledisplay)
368 boolean featuresFile = false;
371 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
372 .getFeatureRenderer().getFeatureColours();
373 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
374 "relaxedidmatch", false);
375 featuresFile = new FeaturesFile(file, type).parse(
376 viewport.getAlignment(), colours, true, relaxedIdMatching);
377 } catch (Exception ex)
379 ex.printStackTrace();
384 if (autoenabledisplay)
386 viewport.setShowSequenceFeatures(true);
387 sequenceFeatures.setState(true);
389 if (alignPanel.seqPanel.seqCanvas.fr != null)
391 // update the min/max ranges where necessary
392 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
394 if (viewport.featureSettings != null)
396 viewport.featureSettings.refreshTable();
398 alignPanel.paintAlignment(true);
399 statusBar.setText(MessageManager
400 .getString("label.successfully_added_features_alignment"));
406 public void keyPressed(KeyEvent evt)
408 if (viewport.cursorMode
409 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
410 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
411 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
412 && Character.isDigit(evt.getKeyChar()))
414 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
417 switch (evt.getKeyCode())
419 case 27: // escape key
420 deselectAllSequenceMenuItem_actionPerformed();
422 alignPanel.alabels.cancelDrag();
425 if (evt.isControlDown() || evt.isMetaDown())
427 cut_actionPerformed();
431 if (viewport.cursorMode && !evt.isControlDown())
433 alignPanel.seqPanel.setCursorColumn();
435 if (evt.isControlDown() || evt.isMetaDown())
437 copy_actionPerformed();
441 if (evt.isControlDown())
443 paste(evt.isShiftDown());
447 if (evt.isControlDown() || evt.isMetaDown())
449 selectAllSequenceMenuItem_actionPerformed();
452 case KeyEvent.VK_DOWN:
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.moveCursor(0, 1);
459 moveSelectedSequences(false);
464 if (viewport.cursorMode)
466 alignPanel.seqPanel.moveCursor(0, -1);
470 moveSelectedSequences(true);
474 case KeyEvent.VK_LEFT:
475 if (evt.isAltDown() || !viewport.cursorMode)
477 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
481 alignPanel.seqPanel.moveCursor(-1, 0);
485 case KeyEvent.VK_RIGHT:
486 if (evt.isAltDown() || !viewport.cursorMode)
488 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
492 alignPanel.seqPanel.moveCursor(1, 0);
496 case KeyEvent.VK_SPACE:
497 if (viewport.cursorMode)
499 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
500 || evt.isShiftDown() || evt.isAltDown());
504 case KeyEvent.VK_DELETE:
505 case KeyEvent.VK_BACK_SPACE:
506 if (viewport.cursorMode)
508 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
509 || evt.isShiftDown() || evt.isAltDown());
513 cut_actionPerformed();
514 alignPanel.seqPanel.seqCanvas.repaint();
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.setCursorRow();
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.setCursorPosition();
531 case KeyEvent.VK_ENTER:
532 case KeyEvent.VK_COMMA:
533 if (viewport.cursorMode)
535 alignPanel.seqPanel.setCursorRowAndColumn();
540 if (viewport.cursorMode)
542 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
546 if (viewport.cursorMode)
548 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
553 viewport.cursorMode = !viewport.cursorMode;
554 statusBar.setText(MessageManager.formatMessage(
555 "label.keyboard_editing_mode",
556 new String[] { (viewport.cursorMode ? "on" : "off") }));
557 if (viewport.cursorMode)
559 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
560 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
565 if (evt.isControlDown())
567 findMenuItem_actionPerformed();
573 boolean toggleSeqs = !evt.isControlDown();
574 boolean toggleCols = !evt.isShiftDown();
575 toggleHiddenRegions(toggleSeqs, toggleCols);
579 case KeyEvent.VK_PAGE_UP:
580 if (viewport.getWrapAlignment())
582 alignPanel.scrollUp(true);
586 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
587 - viewport.endSeq + viewport.startSeq);
591 case KeyEvent.VK_PAGE_DOWN:
592 if (viewport.getWrapAlignment())
594 alignPanel.scrollUp(false);
598 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
599 + viewport.endSeq - viewport.startSeq);
604 if (evt.isControlDown())
606 undoMenuItem_actionPerformed();
611 if (evt.isControlDown())
613 redoMenuItem_actionPerformed();
618 if (evt.isControlDown())
625 if (evt.isControlDown())
627 trimAlignment(false);
632 if (evt.isControlDown())
634 if (evt.isShiftDown())
636 this.removeAllGapsMenuItem_actionPerformed();
640 removeGappedColumnMenuItem_actionPerformed();
645 if (evt.isControlDown())
649 invertColSel_actionPerformed();
653 invertSequenceMenuItem_actionPerformed();
659 if (evt.isControlDown())
661 if (evt.isShiftDown())
663 this.unGroup_actionPerformed();
667 this.createGroup_actionPerformed();
673 if (evt.isControlDown())
675 this.deleteGroups_actionPerformed();
680 if (evt.isControlDown())
687 alignPanel.paintAlignment(true);
691 * called by key handler and the hide all/show all menu items
696 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
698 boolean hide = false;
699 SequenceGroup sg = viewport.getSelectionGroup();
700 if (!toggleSeqs && !toggleCols)
702 // Hide everything by the current selection - this is a hack - we do the
703 // invert and then hide
704 // first check that there will be visible columns after the invert.
705 if (viewport.hasSelectedColumns()
706 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
709 // now invert the sequence set, if required - empty selection implies
710 // that no hiding is required.
713 invertSequenceMenuItem_actionPerformed();
714 sg = viewport.getSelectionGroup();
718 viewport.expandColSelection(sg, true);
719 // finally invert the column selection and get the new sequence
720 // selection and indicate it should be hidden.
721 invertColSel_actionPerformed();
728 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
731 viewport.hideAllSelectedSeqs();
733 else if (!(toggleCols && viewport.hasSelectedColumns()))
735 viewport.showAllHiddenSeqs();
741 if (viewport.hasSelectedColumns())
743 viewport.hideSelectedColumns();
746 viewport.setSelectionGroup(sg);
751 viewport.showAllHiddenColumns();
753 viewport.sendSelection();
758 public void keyReleased(KeyEvent evt)
763 public void keyTyped(KeyEvent evt)
768 public void itemStateChanged(ItemEvent evt)
770 final Object source = evt.getSource();
771 if (source == displayNonconservedMenuItem)
773 displayNonconservedMenuItem_actionPerformed();
775 else if (source == colourTextMenuItem)
777 colourTextMenuItem_actionPerformed();
779 else if (source == wrapMenuItem)
781 wrapMenuItem_actionPerformed();
783 else if (source == scaleAbove)
785 viewport.setScaleAboveWrapped(scaleAbove.getState());
787 else if (source == scaleLeft)
789 viewport.setScaleLeftWrapped(scaleLeft.getState());
791 else if (source == scaleRight)
793 viewport.setScaleRightWrapped(scaleRight.getState());
795 else if (source == seqLimits)
797 seqLimits_itemStateChanged();
799 else if (source == viewBoxesMenuItem)
801 viewport.setShowBoxes(viewBoxesMenuItem.getState());
803 else if (source == viewTextMenuItem)
805 viewport.setShowText(viewTextMenuItem.getState());
807 else if (source == renderGapsMenuItem)
809 viewport.setRenderGaps(renderGapsMenuItem.getState());
811 else if (source == annotationPanelMenuItem)
813 boolean showAnnotations = annotationPanelMenuItem.getState();
814 showAlignmentAnnotations.setEnabled(showAnnotations);
815 showSequenceAnnotations.setEnabled(showAnnotations);
816 viewport.setShowAnnotation(showAnnotations);
817 alignPanel.setAnnotationVisible(showAnnotations);
819 else if (source == sequenceFeatures)
821 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
822 alignPanel.seqPanel.seqCanvas.repaint();
824 else if (source == showAlignmentAnnotations)
826 setAnnotationsVisibility();
828 else if (source == showSequenceAnnotations)
830 setAnnotationsVisibility();
832 else if (source == sortAnnBySequence)
834 boolean newState = sortAnnBySequence.getState();
835 sortAnnByLabel.setState(false);
836 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
837 : SequenceAnnotationOrder.NONE);
838 setViewportAnnotationOrder();
840 else if (source == sortAnnByLabel)
842 boolean newState = sortAnnByLabel.getState();
843 sortAnnBySequence.setState(false);
844 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
845 : SequenceAnnotationOrder.NONE);
846 setViewportAnnotationOrder();
848 else if (source == showAutoFirst)
850 showAutoLast.setState(!showAutoFirst.getState());
851 setShowAutoCalculatedAbove(showAutoFirst.getState());
852 setViewportAnnotationOrder();
854 else if (source == showAutoLast)
856 showAutoFirst.setState(!showAutoLast.getState());
857 setShowAutoCalculatedAbove(showAutoFirst.getState());
858 setViewportAnnotationOrder();
860 else if (source == conservationMenuItem)
862 conservationMenuItem_actionPerformed();
864 else if (source == abovePIDThreshold)
866 abovePIDThreshold_actionPerformed();
868 else if (source == applyToAllGroups)
870 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
872 else if (source == autoCalculate)
874 viewport.autoCalculateConsensus = autoCalculate.getState();
876 else if (source == sortByTree)
878 viewport.sortByTree = sortByTree.getState();
880 else if (source == this.centreColumnLabelFlag)
882 centreColumnLabelFlag_stateChanged();
884 else if (source == this.followMouseOverFlag)
886 mouseOverFlag_stateChanged();
888 else if (source == showGroupConsensus)
890 showGroupConsensus_actionPerformed();
892 else if (source == showGroupConservation)
894 showGroupConservation_actionPerformed();
896 else if (source == showSequenceLogo)
898 showSequenceLogo_actionPerformed();
900 else if (source == normSequenceLogo)
902 normSequenceLogo_actionPerformed();
904 else if (source == showConsensusHistogram)
906 showConsensusHistogram_actionPerformed();
908 else if (source == applyAutoAnnotationSettings)
910 applyAutoAnnotationSettings_actionPerformed();
912 alignPanel.paintAlignment(true);
916 * Set the visibility state of sequence-related and/or alignment-related
917 * annotations depending on checkbox selections, and repaint.
921 private void setAnnotationsVisibility()
923 boolean showForAlignment = showAlignmentAnnotations.getState();
924 boolean showForSequences = showSequenceAnnotations.getState();
925 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
927 for (AlignmentAnnotation aa : alignPanel.getAlignment()
928 .getAlignmentAnnotation())
930 boolean visible = (aa.sequenceRef == null ? showForAlignment
932 aa.visible = visible;
935 alignPanel.validateAnnotationDimensions(true);
940 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
942 this.annotationSortOrder = order;
946 * Set flags on the viewport that control annotation ordering
948 private void setViewportAnnotationOrder()
950 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
952 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
955 private void setShowAutoCalculatedAbove(boolean showAbove)
957 this.showAutoCalculatedAbove = showAbove;
960 private void mouseOverFlag_stateChanged()
962 viewport.setFollowHighlight(followMouseOverFlag.getState());
963 // TODO: could kick the scrollTo mechanism to reset view for current
967 private void centreColumnLabelFlag_stateChanged()
969 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
970 this.alignPanel.annotationPanel.repaint();
974 public void actionPerformed(ActionEvent evt)
976 viewport.applet.currentAlignFrame = this;
978 Object source = evt.getSource();
980 if (source == inputText)
982 inputText_actionPerformed();
984 else if (source == loadTree)
986 loadTree_actionPerformed();
988 else if (source == loadApplication)
990 launchFullApplication();
992 else if (source == loadAnnotations)
996 else if (source == outputAnnotations)
998 outputAnnotations(true);
1000 else if (source == outputFeatures)
1002 outputFeatures(true, "Jalview");
1004 else if (source == closeMenuItem)
1006 closeMenuItem_actionPerformed();
1008 else if (source == copy)
1010 copy_actionPerformed();
1012 else if (source == undoMenuItem)
1014 undoMenuItem_actionPerformed();
1016 else if (source == redoMenuItem)
1018 redoMenuItem_actionPerformed();
1020 else if (source == inputText)
1022 inputText_actionPerformed();
1024 else if (source == closeMenuItem)
1026 closeMenuItem_actionPerformed();
1028 else if (source == undoMenuItem)
1030 undoMenuItem_actionPerformed();
1032 else if (source == redoMenuItem)
1034 redoMenuItem_actionPerformed();
1036 else if (source == copy)
1038 copy_actionPerformed();
1040 else if (source == pasteNew)
1042 pasteNew_actionPerformed();
1044 else if (source == pasteThis)
1046 pasteThis_actionPerformed();
1048 else if (source == cut)
1050 cut_actionPerformed();
1052 else if (source == delete)
1054 delete_actionPerformed();
1056 else if (source == grpsFromSelection)
1058 makeGrpsFromSelection_actionPerformed();
1060 else if (source == deleteGroups)
1062 deleteGroups_actionPerformed();
1064 else if (source == selectAllSequenceMenuItem)
1066 selectAllSequenceMenuItem_actionPerformed();
1068 else if (source == deselectAllSequenceMenuItem)
1070 deselectAllSequenceMenuItem_actionPerformed();
1072 else if (source == invertSequenceMenuItem)
1074 invertSequenceMenuItem_actionPerformed();
1075 // uncomment to slave sequence selections in split frame
1076 // viewport.sendSelection();
1078 else if (source == invertColSel)
1080 viewport.invertColumnSelection();
1081 alignPanel.paintAlignment(true);
1082 viewport.sendSelection();
1084 else if (source == remove2LeftMenuItem)
1086 trimAlignment(true);
1088 else if (source == remove2RightMenuItem)
1090 trimAlignment(false);
1092 else if (source == removeGappedColumnMenuItem)
1094 removeGappedColumnMenuItem_actionPerformed();
1096 else if (source == removeAllGapsMenuItem)
1098 removeAllGapsMenuItem_actionPerformed();
1100 else if (source == findMenuItem)
1102 findMenuItem_actionPerformed();
1104 else if (source == font)
1106 new FontChooser(alignPanel);
1108 else if (source == newView)
1112 else if (source == showColumns)
1114 viewport.showAllHiddenColumns();
1115 alignPanel.paintAlignment(true);
1116 viewport.sendSelection();
1118 else if (source == showSeqs)
1120 viewport.showAllHiddenSeqs();
1121 alignPanel.paintAlignment(true);
1122 // uncomment if we want to slave sequence selections in split frame
1123 // viewport.sendSelection();
1125 else if (source == hideColumns)
1127 viewport.hideSelectedColumns();
1128 alignPanel.paintAlignment(true);
1129 viewport.sendSelection();
1131 else if (source == hideSequences
1132 && viewport.getSelectionGroup() != null)
1134 viewport.hideAllSelectedSeqs();
1135 alignPanel.paintAlignment(true);
1136 // uncomment if we want to slave sequence selections in split frame
1137 // viewport.sendSelection();
1139 else if (source == hideAllButSelection)
1141 toggleHiddenRegions(false, false);
1142 alignPanel.paintAlignment(true);
1143 viewport.sendSelection();
1145 else if (source == hideAllSelection)
1147 SequenceGroup sg = viewport.getSelectionGroup();
1148 viewport.expandColSelection(sg, false);
1149 viewport.hideAllSelectedSeqs();
1150 viewport.hideSelectedColumns();
1151 alignPanel.paintAlignment(true);
1152 viewport.sendSelection();
1154 else if (source == showAllHidden)
1156 viewport.showAllHiddenColumns();
1157 viewport.showAllHiddenSeqs();
1158 alignPanel.paintAlignment(true);
1159 viewport.sendSelection();
1161 else if (source == showGroupConsensus)
1163 showGroupConsensus_actionPerformed();
1165 else if (source == showGroupConservation)
1167 showGroupConservation_actionPerformed();
1169 else if (source == showSequenceLogo)
1171 showSequenceLogo_actionPerformed();
1173 else if (source == normSequenceLogo)
1175 normSequenceLogo_actionPerformed();
1177 else if (source == showConsensusHistogram)
1179 showConsensusHistogram_actionPerformed();
1181 else if (source == applyAutoAnnotationSettings)
1183 applyAutoAnnotationSettings_actionPerformed();
1185 else if (source == featureSettings)
1187 new FeatureSettings(alignPanel);
1189 else if (source == alProperties)
1191 StringBuffer contents = new jalview.io.AlignmentProperties(
1192 viewport.getAlignment()).formatAsString();
1193 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1194 cap.setText(contents.toString());
1195 Frame frame = new Frame();
1197 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1198 "label.alignment_properties", new String[] { getTitle() }),
1201 else if (source == overviewMenuItem)
1203 overviewMenuItem_actionPerformed();
1205 else if (source == noColourmenuItem)
1209 else if (source == clustalColour)
1211 abovePIDThreshold.setState(false);
1212 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1214 else if (source == zappoColour)
1216 changeColour(new ZappoColourScheme());
1218 else if (source == taylorColour)
1220 changeColour(new TaylorColourScheme());
1222 else if (source == hydrophobicityColour)
1224 changeColour(new HydrophobicColourScheme());
1226 else if (source == helixColour)
1228 changeColour(new HelixColourScheme());
1230 else if (source == strandColour)
1232 changeColour(new StrandColourScheme());
1234 else if (source == turnColour)
1236 changeColour(new TurnColourScheme());
1238 else if (source == buriedColour)
1240 changeColour(new BuriedColourScheme());
1242 else if (source == nucleotideColour)
1244 changeColour(new NucleotideColourScheme());
1246 else if (source == purinePyrimidineColour)
1248 changeColour(new PurinePyrimidineColourScheme());
1250 // else if (source == RNAInteractionColour)
1252 // changeColour(new RNAInteractionColourScheme());
1254 else if (source == RNAHelixColour)
1256 new RNAHelicesColourChooser(viewport, alignPanel);
1258 else if (source == modifyPID)
1260 modifyPID_actionPerformed();
1262 else if (source == modifyConservation)
1264 modifyConservation_actionPerformed();
1266 else if (source == userDefinedColour)
1268 new UserDefinedColours(alignPanel, null);
1270 else if (source == PIDColour)
1272 changeColour(new PIDColourScheme());
1274 else if (source == BLOSUM62Colour)
1276 changeColour(new Blosum62ColourScheme());
1278 else if (source == tcoffeeColour)
1280 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1282 else if (source == annotationColour)
1284 new AnnotationColourChooser(viewport, alignPanel);
1286 else if (source == annotationColumnSelection)
1288 new AnnotationColumnChooser(viewport, alignPanel);
1290 else if (source == sortPairwiseMenuItem)
1292 sortPairwiseMenuItem_actionPerformed();
1294 else if (source == sortIDMenuItem)
1296 sortIDMenuItem_actionPerformed();
1298 else if (source == sortLengthMenuItem)
1300 sortLengthMenuItem_actionPerformed();
1302 else if (source == sortGroupMenuItem)
1304 sortGroupMenuItem_actionPerformed();
1306 else if (source == removeRedundancyMenuItem)
1308 removeRedundancyMenuItem_actionPerformed();
1310 else if (source == pairwiseAlignmentMenuItem)
1312 pairwiseAlignmentMenuItem_actionPerformed();
1314 else if (source == PCAMenuItem)
1316 PCAMenuItem_actionPerformed();
1318 else if (source == averageDistanceTreeMenuItem)
1320 averageDistanceTreeMenuItem_actionPerformed();
1322 else if (source == neighbourTreeMenuItem)
1324 neighbourTreeMenuItem_actionPerformed();
1326 else if (source == njTreeBlosumMenuItem)
1328 njTreeBlosumMenuItem_actionPerformed();
1330 else if (source == avDistanceTreeBlosumMenuItem)
1332 avTreeBlosumMenuItem_actionPerformed();
1334 else if (source == documentation)
1336 documentation_actionPerformed();
1338 else if (source == about)
1340 about_actionPerformed();
1345 public void inputText_actionPerformed()
1347 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1348 Frame frame = new Frame();
1350 jalview.bin.JalviewLite.addFrame(frame,
1351 MessageManager.getString("label.input_cut_paste"), 500, 500);
1354 protected void outputText_actionPerformed(ActionEvent e)
1356 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1357 Frame frame = new Frame();
1359 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1360 "label.alignment_output_command",
1361 new Object[] { e.getActionCommand() }), 600, 500);
1363 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1364 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1365 e.getActionCommand(), viewport.getAlignment(),
1366 viewport.getShowJVSuffix()));
1369 public void loadAnnotations()
1371 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1372 cap.setText(MessageManager
1373 .getString("label.paste_features_annotations_Tcoffee_here"));
1374 cap.setAnnotationImport();
1375 Frame frame = new Frame();
1377 jalview.bin.JalviewLite.addFrame(frame,
1378 MessageManager.getString("action.paste_annotations"), 400, 300);
1382 public String outputAnnotations(boolean displayTextbox)
1384 String annotation = new AnnotationFile()
1385 .printAnnotationsForView(viewport);
1389 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1390 Frame frame = new Frame();
1392 jalview.bin.JalviewLite.addFrame(frame,
1393 MessageManager.getString("label.annotations"), 600, 500);
1394 cap.setText(annotation);
1400 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1402 if (alignPanel.getFeatureRenderer() != null
1403 && viewport.getFeaturesDisplayed() != null)
1405 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1411 public String outputFeatures(boolean displayTextbox, String format)
1414 FeaturesFile formatter = new FeaturesFile();
1415 if (format.equalsIgnoreCase("Jalview"))
1417 features = formatter.printJalviewFormat(viewport.getAlignment()
1418 .getSequencesArray(), getDisplayedFeatureCols());
1422 features = formatter.printGffFormat(viewport.getAlignment()
1423 .getSequencesArray(), getDisplayedFeatureCols());
1428 boolean frimport = false;
1429 if (features == null || features.equals("No Features Visible"))
1431 features = "# No features visible - paste some and import them here.";
1435 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1438 cap.setAnnotationImport();
1440 Frame frame = new Frame();
1442 jalview.bin.JalviewLite.addFrame(frame,
1443 MessageManager.getString("label.features"), 600, 500);
1444 cap.setText(features);
1448 if (features == null)
1457 void launchFullApplication()
1459 StringBuffer url = new StringBuffer(jalviewServletURL);
1461 // allow servlet parameters to be passed in applet parameter
1462 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1464 url.append(firstSep);
1467 + appendProtocol(viewport.applet.getParameter("file")));
1469 if (viewport.applet.getParameter("features") != null)
1471 url.append("&features=");
1472 url.append(appendProtocol(viewport.applet.getParameter("features")));
1475 if (viewport.applet.getParameter("annotations") != null)
1477 url.append("&annotations=");
1478 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1481 if (viewport.applet.getParameter("jnetfile") != null)
1483 url.append("&annotations=");
1484 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1487 if (viewport.applet.getParameter("defaultColour") != null)
1489 url.append("&colour="
1490 + removeWhiteSpace(viewport.applet
1491 .getParameter("defaultColour")));
1494 if (viewport.applet.getParameter("userDefinedColour") != null)
1496 url.append("&colour="
1497 + removeWhiteSpace(viewport.applet
1498 .getParameter("userDefinedColour")));
1500 if (viewport.applet.getParameter("tree") != null)
1503 + appendProtocol(viewport.applet.getParameter("tree")));
1505 if (viewport.applet.getParameter("treeFile") != null)
1508 + appendProtocol(viewport.applet.getParameter("treeFile")));
1511 showURL(url.toString(), "FULL_APP");
1514 String removeWhiteSpace(String colour)
1516 StringBuffer sb = new StringBuffer();
1517 for (int i = 0; i < colour.length(); i++)
1519 if (Character.isWhitespace(colour.charAt(i)))
1525 sb.append(colour.charAt(i));
1529 return sb.toString();
1532 String appendProtocol(String url)
1537 url = URLEncoder.encode(url);
1540 * When we finally deprecate 1.1 compatibility, we can start to use
1541 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1542 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1543 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1544 * ex.printStackTrace(); }
1546 catch (java.net.MalformedURLException ex)
1548 url = viewport.applet.getCodeBase() + url;
1553 public void closeMenuItem_actionPerformed()
1555 PaintRefresher.RemoveComponent(alignPanel);
1556 if (alignPanel.seqPanel != null
1557 && alignPanel.seqPanel.seqCanvas != null)
1559 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1561 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1563 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1566 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1581 void updateEditMenuBar()
1584 if (viewport.getHistoryList().size() > 0)
1586 undoMenuItem.setEnabled(true);
1587 CommandI command = viewport.getHistoryList().peek();
1588 undoMenuItem.setLabel(MessageManager.formatMessage(
1589 "label.undo_command",
1590 new Object[] { command.getDescription() }));
1594 undoMenuItem.setEnabled(false);
1595 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1598 if (viewport.getRedoList().size() > 0)
1600 redoMenuItem.setEnabled(true);
1602 CommandI command = viewport.getRedoList().peek();
1603 redoMenuItem.setLabel(MessageManager.formatMessage(
1604 "label.redo_command",
1605 new Object[] { command.getDescription() }));
1609 redoMenuItem.setEnabled(false);
1610 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1618 public void addHistoryItem(CommandI command)
1620 if (command.getSize() > 0)
1622 viewport.addToHistoryList(command);
1623 viewport.clearRedoList();
1624 updateEditMenuBar();
1625 viewport.updateHiddenColumns();
1630 * TODO: JAL-1104 DOCUMENT ME!
1635 protected void undoMenuItem_actionPerformed()
1637 if (viewport.getHistoryList().isEmpty())
1642 CommandI command = viewport.getHistoryList().pop();
1643 viewport.addToRedoList(command);
1644 command.undoCommand(null);
1646 AlignmentViewport originalSource = getOriginatingSource(command);
1648 if (originalSource != viewport)
1651 .println("Warning: Viewport object mismatch whilst undoing");
1653 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1654 // viewport.getColumnSelection().getHiddenColumns()
1656 updateEditMenuBar();
1657 originalSource.firePropertyChange("alignment", null, originalSource
1658 .getAlignment().getSequences());
1662 * TODO: JAL-1104 DOCUMENT ME!
1667 protected void redoMenuItem_actionPerformed()
1669 if (viewport.getRedoList().isEmpty())
1674 CommandI command = viewport.getRedoList().pop();
1675 viewport.addToHistoryList(command);
1676 command.doCommand(null);
1678 AlignmentViewport originalSource = getOriginatingSource(command);
1680 if (originalSource != viewport)
1683 .println("Warning: Viewport object mismatch whilst re-doing");
1685 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1686 // viewport.getColumnSelection().getHiddenColumns()
1689 updateEditMenuBar();
1690 originalSource.firePropertyChange("alignment", null, originalSource
1691 .getAlignment().getSequences());
1694 AlignmentViewport getOriginatingSource(CommandI command)
1696 AlignmentViewport originalSource = null;
1697 // For sequence removal and addition, we need to fire
1698 // the property change event FROM the viewport where the
1699 // original alignment was altered
1700 AlignmentI al = null;
1701 if (command instanceof EditCommand)
1703 EditCommand editCommand = (EditCommand) command;
1704 al = editCommand.getAlignment();
1705 Vector comps = (Vector) PaintRefresher.components.get(viewport
1706 .getSequenceSetId());
1707 for (int i = 0; i < comps.size(); i++)
1709 if (comps.elementAt(i) instanceof AlignmentPanel)
1711 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1713 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1720 if (originalSource == null)
1722 // The original view is closed, we must validate
1723 // the current view against the closed view first
1726 PaintRefresher.validateSequences(al, viewport.getAlignment());
1729 originalSource = viewport;
1732 return originalSource;
1736 * Move the currently selected sequences up or down one position in the
1741 public void moveSelectedSequences(boolean up)
1743 SequenceGroup sg = viewport.getSelectionGroup();
1748 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1749 up ? null : viewport.getHiddenRepSequences(), up);
1750 alignPanel.paintAlignment(true);
1753 * Also move cDNA/protein complement sequences
1755 AlignViewportI complement = viewport.getCodingComplement();
1756 if (complement != null)
1758 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1759 viewport, complement);
1760 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1761 up ? null : complement.getHiddenRepSequences(), up);
1762 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1766 synchronized void slideSequences(boolean right, int size)
1768 List<SequenceI> sg = new Vector<SequenceI>();
1769 if (viewport.cursorMode)
1771 sg.add(viewport.getAlignment().getSequenceAt(
1772 alignPanel.seqPanel.seqCanvas.cursorY));
1774 else if (viewport.getSelectionGroup() != null
1775 && viewport.getSelectionGroup().getSize() != viewport
1776 .getAlignment().getHeight())
1778 sg = viewport.getSelectionGroup().getSequences(
1779 viewport.getHiddenRepSequences());
1787 Vector<SequenceI> invertGroup = new Vector();
1789 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1791 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1793 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1797 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1799 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1801 for (int i = 0; i < invertGroup.size(); i++)
1803 seqs2[i] = invertGroup.elementAt(i);
1806 SlideSequencesCommand ssc;
1809 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1810 size, viewport.getGapCharacter());
1814 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1815 size, viewport.getGapCharacter());
1818 int groupAdjustment = 0;
1819 if (ssc.getGapsInsertedBegin() && right)
1821 if (viewport.cursorMode)
1823 alignPanel.seqPanel.moveCursor(size, 0);
1827 groupAdjustment = size;
1830 else if (!ssc.getGapsInsertedBegin() && !right)
1832 if (viewport.cursorMode)
1834 alignPanel.seqPanel.moveCursor(-size, 0);
1838 groupAdjustment = -size;
1842 if (groupAdjustment != 0)
1844 viewport.getSelectionGroup().setStartRes(
1845 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1846 viewport.getSelectionGroup().setEndRes(
1847 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1850 boolean appendHistoryItem = false;
1851 Deque<CommandI> historyList = viewport.getHistoryList();
1852 if (historyList != null && historyList.size() > 0
1853 && historyList.peek() instanceof SlideSequencesCommand)
1855 appendHistoryItem = ssc
1856 .appendSlideCommand((SlideSequencesCommand) historyList
1860 if (!appendHistoryItem)
1862 addHistoryItem(ssc);
1868 static StringBuffer copiedSequences;
1870 static Vector copiedHiddenColumns;
1872 protected void copy_actionPerformed()
1874 if (viewport.getSelectionGroup() == null)
1879 SequenceGroup sg = viewport.getSelectionGroup();
1880 copiedSequences = new StringBuffer();
1881 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1882 for (int i = 0; i < sg.getSize(); i++)
1884 SequenceI seq = sg.getSequenceAt(i);
1885 int index = viewport.getAlignment().findIndex(seq);
1886 orderedSeqs.put(index, seq);
1889 int index = 0, startRes, endRes;
1892 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1894 copiedHiddenColumns = new Vector();
1895 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1896 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1898 copiedHiddenColumns.addElement(new int[] {
1899 region[0] - hiddenOffset, region[1] - hiddenOffset });
1904 copiedHiddenColumns = null;
1907 for (int i = 0; i < sg.getSize(); i++)
1909 SequenceI seq = null;
1913 if (orderedSeqs.containsKey(index))
1915 seq = orderedSeqs.get(index);
1926 // Returns residue following index if gap
1927 startRes = seq.findPosition(sg.getStartRes());
1930 // Need to find the residue preceeding index if gap
1933 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1935 ch = seq.getCharAt(j);
1936 if (!jalview.util.Comparison.isGap((ch)))
1944 endRes += seq.getStart() - 1;
1947 copiedSequences.append(seq.getName()
1953 + seq.getSequenceAsString(sg.getStartRes(),
1954 sg.getEndRes() + 1) + "\n");
1959 protected void pasteNew_actionPerformed()
1964 protected void pasteThis_actionPerformed()
1969 void paste(boolean newAlignment)
1974 if (copiedSequences == null)
1979 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1980 Vector seqs = new Vector();
1981 while (st.hasMoreElements())
1983 String name = st.nextToken();
1984 int start = Integer.parseInt(st.nextToken());
1985 int end = Integer.parseInt(st.nextToken());
1986 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1988 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1989 for (int i = 0; i < seqs.size(); i++)
1991 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1996 String newtitle = MessageManager
1997 .getString("label.copied_sequences");
1998 if (getTitle().startsWith(
1999 MessageManager.getString("label.copied_sequences")))
2001 newtitle = getTitle();
2005 newtitle = newtitle.concat(MessageManager.formatMessage(
2006 "label.from_msname", new String[] { getTitle() }));
2008 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2009 viewport.applet, newtitle, false);
2010 if (copiedHiddenColumns != null)
2012 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2014 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2015 af.viewport.hideColumns(region[0], region[1]);
2019 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2024 addSequences(newSeqs);
2027 } catch (Exception ex)
2029 } // could be anything being pasted in here
2033 void addSequences(SequenceI[] seqs)
2035 for (int i = 0; i < seqs.length; i++)
2037 viewport.getAlignment().addSequence(seqs[i]);
2041 addHistoryItem(new EditCommand(
2042 MessageManager.getString("label.add_sequences"), Action.PASTE,
2043 seqs, 0, viewport.getAlignment().getWidth(),
2044 viewport.getAlignment()));
2046 viewport.setEndSeq(viewport.getAlignment().getHeight());
2047 viewport.getAlignment().getWidth();
2048 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2053 protected void cut_actionPerformed()
2055 copy_actionPerformed();
2056 delete_actionPerformed();
2059 protected void delete_actionPerformed()
2062 SequenceGroup sg = viewport.getSelectionGroup();
2068 Vector seqs = new Vector();
2070 for (int i = 0; i < sg.getSize(); i++)
2072 seq = sg.getSequenceAt(i);
2073 seqs.addElement(seq);
2077 * If the cut affects all sequences, warn, remove highlighted columns
2079 if (sg.getSize() == viewport.getAlignment().getHeight())
2081 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2082 .getAlignment().getWidth()) ? true : false;
2083 if (isEntireAlignWidth)
2085 String title = MessageManager.getString("label.delete_all");
2086 Panel infoPanel = new Panel();
2087 infoPanel.setLayout(new FlowLayout());
2089 .add(new Label(MessageManager.getString("warn.delete_all")));
2091 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2092 dialog.setMainPanel(infoPanel);
2093 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2094 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2095 dialog.setVisible(true);
2102 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2103 sg.getEndRes() + 1);
2106 SequenceI[] cut = new SequenceI[seqs.size()];
2107 for (int i = 0; i < seqs.size(); i++)
2109 cut[i] = (SequenceI) seqs.elementAt(i);
2113 * //ADD HISTORY ITEM
2115 addHistoryItem(new EditCommand(
2116 MessageManager.getString("label.cut_sequences"), Action.CUT,
2117 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2118 viewport.getAlignment()));
2120 viewport.setSelectionGroup(null);
2121 viewport.getAlignment().deleteGroup(sg);
2123 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2126 if (viewport.getAlignment().getHeight() < 1)
2128 this.setVisible(false);
2130 viewport.sendSelection();
2134 * group consensus toggled
2137 protected void showGroupConsensus_actionPerformed()
2139 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2140 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145 * group conservation toggled.
2147 protected void showGroupConservation_actionPerformed()
2149 viewport.setShowGroupConservation(showGroupConservation.getState());
2150 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2157 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2158 * .event.ActionEvent)
2160 protected void showConsensusHistogram_actionPerformed()
2162 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2163 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2171 * .event.ActionEvent)
2173 protected void showSequenceLogo_actionPerformed()
2175 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2176 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2179 protected void normSequenceLogo_actionPerformed()
2181 showSequenceLogo.setState(true);
2182 viewport.setShowSequenceLogo(true);
2183 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2184 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2187 protected void applyAutoAnnotationSettings_actionPerformed()
2189 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2192 protected void makeGrpsFromSelection_actionPerformed()
2194 if (avc.makeGroupsFromSelection())
2196 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2197 alignPanel.updateAnnotation();
2198 alignPanel.paintAlignment(true);
2202 protected void createGroup_actionPerformed()
2207 protected void unGroup_actionPerformed()
2211 alignPanel.alignmentChanged();
2215 protected void deleteGroups_actionPerformed()
2217 if (avc.deleteGroups())
2219 alignPanel.alignmentChanged();
2223 public void selectAllSequenceMenuItem_actionPerformed()
2225 SequenceGroup sg = new SequenceGroup();
2226 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2228 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2230 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2231 viewport.setSelectionGroup(sg);
2232 // JAL-2034 - should delegate to
2233 // alignPanel to decide if overview needs
2235 alignPanel.paintAlignment(false);
2236 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2237 viewport.sendSelection();
2240 public void deselectAllSequenceMenuItem_actionPerformed()
2242 if (viewport.cursorMode)
2244 alignPanel.seqPanel.keyboardNo1 = null;
2245 alignPanel.seqPanel.keyboardNo2 = null;
2247 viewport.setSelectionGroup(null);
2248 viewport.getColumnSelection().clear();
2249 viewport.setSelectionGroup(null);
2250 alignPanel.idPanel.idCanvas.searchResults = null;
2251 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2252 // JAL-2034 - should delegate to
2253 // alignPanel to decide if overview needs
2255 alignPanel.paintAlignment(false);
2256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257 viewport.sendSelection();
2260 public void invertSequenceMenuItem_actionPerformed()
2262 SequenceGroup sg = viewport.getSelectionGroup();
2263 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2265 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2268 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2269 viewport.sendSelection();
2272 public void invertColSel_actionPerformed()
2274 viewport.invertColumnSelection();
2275 alignPanel.paintAlignment(true);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277 viewport.sendSelection();
2280 void trimAlignment(boolean trimLeft)
2282 ColumnSelection colSel = viewport.getColumnSelection();
2285 if (!colSel.isEmpty())
2289 column = colSel.getMin();
2293 column = colSel.getMax();
2297 if (viewport.getSelectionGroup() != null)
2299 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2300 viewport.getHiddenRepSequences());
2304 seqs = viewport.getAlignment().getSequencesArray();
2307 TrimRegionCommand trimRegion;
2310 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2311 column, viewport.getAlignment());
2312 viewport.setStartRes(0);
2316 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2317 column, viewport.getAlignment());
2320 statusBar.setText(MessageManager.formatMessage(
2321 "label.removed_columns",
2322 new String[] { Integer.valueOf(trimRegion.getSize())
2324 addHistoryItem(trimRegion);
2326 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2328 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2329 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2331 viewport.getAlignment().deleteGroup(sg);
2335 viewport.firePropertyChange("alignment", null, viewport
2336 .getAlignment().getSequences());
2340 public void removeGappedColumnMenuItem_actionPerformed()
2342 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2345 if (viewport.getSelectionGroup() != null)
2347 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2348 viewport.getHiddenRepSequences());
2349 start = viewport.getSelectionGroup().getStartRes();
2350 end = viewport.getSelectionGroup().getEndRes();
2354 seqs = viewport.getAlignment().getSequencesArray();
2357 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2358 "Remove Gapped Columns", seqs, start, end,
2359 viewport.getAlignment());
2361 addHistoryItem(removeGapCols);
2363 statusBar.setText(MessageManager.formatMessage(
2364 "label.removed_empty_columns",
2365 new String[] { Integer.valueOf(removeGapCols.getSize())
2368 // This is to maintain viewport position on first residue
2369 // of first sequence
2370 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2371 int startRes = seq.findPosition(viewport.startRes);
2372 // ShiftList shifts;
2373 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2374 // edit.alColumnChanges=shifts.getInverse();
2375 // if (viewport.hasHiddenColumns)
2376 // viewport.getColumnSelection().compensateForEdits(shifts);
2377 viewport.setStartRes(seq.findIndex(startRes) - 1);
2378 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2383 public void removeAllGapsMenuItem_actionPerformed()
2385 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2388 if (viewport.getSelectionGroup() != null)
2390 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2391 viewport.getHiddenRepSequences());
2392 start = viewport.getSelectionGroup().getStartRes();
2393 end = viewport.getSelectionGroup().getEndRes();
2397 seqs = viewport.getAlignment().getSequencesArray();
2400 // This is to maintain viewport position on first residue
2401 // of first sequence
2402 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2403 int startRes = seq.findPosition(viewport.startRes);
2405 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2406 viewport.getAlignment()));
2408 viewport.setStartRes(seq.findIndex(startRes) - 1);
2410 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2415 public void findMenuItem_actionPerformed()
2417 new Finder(alignPanel);
2421 * create a new view derived from the current view
2424 * @return frame for the new view
2426 public AlignFrame newView(String viewtitle)
2429 if (viewport.hasHiddenRows())
2431 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2432 .getFullAlignment().getSequencesArray());
2436 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2439 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2441 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2443 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2445 newal.addAnnotation(viewport.getAlignment()
2446 .getAlignmentAnnotation()[i]);
2451 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2453 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2454 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2455 PaintRefresher.Register(newaf.alignPanel,
2456 newaf.alignPanel.av.getSequenceSetId());
2458 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2459 newaf.alignPanel.av.getSequenceSetId());
2460 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2461 newaf.alignPanel.av.getSequenceSetId());
2463 Vector comps = (Vector) PaintRefresher.components.get(viewport
2464 .getSequenceSetId());
2466 for (int i = 0; i < comps.size(); i++)
2468 if (comps.elementAt(i) instanceof AlignmentPanel)
2474 String title = new String(this.getTitle());
2475 if (viewtitle != null)
2477 title = viewtitle + " ( " + title + ")";
2481 if (title.indexOf("(View") > -1)
2483 title = title.substring(0, title.indexOf("(View"));
2485 title += "(View " + viewSize + ")";
2488 newaf.setTitle(title.toString());
2490 newaf.viewport.setHistoryList(viewport.getHistoryList());
2491 newaf.viewport.setRedoList(viewport.getRedoList());
2497 * @return list of feature groups on the view
2499 public String[] getFeatureGroups()
2501 FeatureRenderer fr = null;
2502 if (alignPanel != null
2503 && (fr = alignPanel.getFeatureRenderer()) != null)
2505 List<String> gps = fr.getFeatureGroups();
2506 String[] _gps = gps.toArray(new String[gps.size()]);
2513 * get sequence feature groups that are hidden or shown
2519 public String[] getFeatureGroupsOfState(boolean visible)
2521 FeatureRenderer fr = null;
2522 if (alignPanel != null
2523 && (fr = alignPanel.getFeatureRenderer()) != null)
2525 List<String> gps = fr.getGroups(visible);
2526 String[] _gps = gps.toArray(new String[gps.size()]);
2533 * Change the display state for the given feature groups
2536 * list of group strings
2538 * visible or invisible
2540 public void setFeatureGroupState(String[] groups, boolean state)
2542 FeatureRenderer fr = null;
2543 this.sequenceFeatures.setState(true);
2544 viewport.setShowSequenceFeatures(true);
2545 if (alignPanel != null
2546 && (fr = alignPanel.getFeatureRenderer()) != null)
2549 fr.setGroupVisibility(Arrays.asList(groups), state);
2550 alignPanel.seqPanel.seqCanvas.repaint();
2551 if (alignPanel.overviewPanel != null)
2553 alignPanel.overviewPanel.updateOverviewImage();
2558 public void seqLimits_itemStateChanged()
2560 viewport.setShowJVSuffix(seqLimits.getState());
2561 alignPanel.fontChanged();
2562 alignPanel.paintAlignment(true);
2565 protected void colourTextMenuItem_actionPerformed()
2567 viewport.setColourText(colourTextMenuItem.getState());
2568 alignPanel.paintAlignment(true);
2571 protected void displayNonconservedMenuItem_actionPerformed()
2573 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2574 alignPanel.paintAlignment(true);
2577 protected void wrapMenuItem_actionPerformed()
2579 viewport.setWrapAlignment(wrapMenuItem.getState());
2580 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2581 scaleAbove.setEnabled(wrapMenuItem.getState());
2582 scaleLeft.setEnabled(wrapMenuItem.getState());
2583 scaleRight.setEnabled(wrapMenuItem.getState());
2584 alignPanel.paintAlignment(true);
2587 public void overviewMenuItem_actionPerformed()
2589 if (alignPanel.overviewPanel != null)
2594 Frame frame = new Frame();
2595 OverviewPanel overview = new OverviewPanel(alignPanel);
2596 frame.add(overview);
2597 // +50 must allow for applet frame window
2598 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2599 "label.overview_params", new String[] { this.getTitle() }),
2600 overview.getPreferredSize().width,
2601 overview.getPreferredSize().height + 50);
2604 final AlignmentPanel ap = alignPanel;
2605 frame.addWindowListener(new WindowAdapter()
2608 public void windowClosing(WindowEvent e)
2612 ap.setOverviewPanel(null);
2617 alignPanel.setOverviewPanel(overview);
2622 public void changeColour(ColourSchemeI cs)
2627 if (viewport.getAbovePIDThreshold())
2629 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2633 if (viewport.getConservationSelected())
2635 cs.setConservationApplied(true);
2636 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2641 cs.setConservationApplied(false);
2644 viewport.setGlobalColourScheme(cs);
2646 alignPanel.paintAlignment(true);
2649 protected void modifyPID_actionPerformed()
2651 if (viewport.getAbovePIDThreshold()
2652 && viewport.getGlobalColourScheme() != null)
2654 SliderPanel.setPIDSliderSource(alignPanel,
2655 viewport.getGlobalColourScheme(), "Background");
2656 SliderPanel.showPIDSlider();
2660 protected void modifyConservation_actionPerformed()
2662 if (viewport.getConservationSelected()
2663 && viewport.getGlobalColourScheme() != null)
2665 SliderPanel.setConservationSlider(alignPanel,
2666 viewport.getGlobalColourScheme(), "Background");
2667 SliderPanel.showConservationSlider();
2671 protected void conservationMenuItem_actionPerformed()
2673 viewport.setConservationSelected(conservationMenuItem.getState());
2675 viewport.setAbovePIDThreshold(false);
2676 abovePIDThreshold.setState(false);
2678 changeColour(viewport.getGlobalColourScheme());
2680 modifyConservation_actionPerformed();
2683 public void abovePIDThreshold_actionPerformed()
2685 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2687 conservationMenuItem.setState(false);
2688 viewport.setConservationSelected(false);
2690 changeColour(viewport.getGlobalColourScheme());
2692 modifyPID_actionPerformed();
2695 public void sortPairwiseMenuItem_actionPerformed()
2697 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2698 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2699 .getAlignment().getSequenceAt(0), null);
2701 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2702 viewport.getAlignment()));
2703 alignPanel.paintAlignment(true);
2706 public void sortIDMenuItem_actionPerformed()
2708 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2709 AlignmentSorter.sortByID(viewport.getAlignment());
2710 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2711 viewport.getAlignment()));
2712 alignPanel.paintAlignment(true);
2715 public void sortLengthMenuItem_actionPerformed()
2717 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2718 AlignmentSorter.sortByLength(viewport.getAlignment());
2719 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2720 viewport.getAlignment()));
2721 alignPanel.paintAlignment(true);
2724 public void sortGroupMenuItem_actionPerformed()
2726 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2727 AlignmentSorter.sortByGroup(viewport.getAlignment());
2728 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2729 viewport.getAlignment()));
2730 alignPanel.paintAlignment(true);
2734 public void removeRedundancyMenuItem_actionPerformed()
2736 new RedundancyPanel(alignPanel);
2739 public void pairwiseAlignmentMenuItem_actionPerformed()
2741 if (viewport.getSelectionGroup() != null
2742 && viewport.getSelectionGroup().getSize() > 1)
2744 Frame frame = new Frame();
2745 frame.add(new PairwiseAlignPanel(alignPanel));
2746 jalview.bin.JalviewLite.addFrame(frame,
2747 MessageManager.getString("action.pairwise_alignment"), 600,
2752 public void PCAMenuItem_actionPerformed()
2754 // are the sequences aligned?
2755 if (!viewport.getAlignment().isAligned(false))
2758 int Width = viewport.getAlignment().getWidth();
2760 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2762 current = viewport.getAlignment().getSequenceAt(i);
2764 if (current.getLength() < Width)
2766 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2769 alignPanel.paintAlignment(true);
2772 if ((viewport.getSelectionGroup() != null
2773 && viewport.getSelectionGroup().getSize() < 4 && viewport
2774 .getSelectionGroup().getSize() > 0)
2775 || viewport.getAlignment().getHeight() < 4)
2782 new PCAPanel(viewport);
2783 } catch (java.lang.OutOfMemoryError ex)
2789 public void averageDistanceTreeMenuItem_actionPerformed()
2791 NewTreePanel("AV", "PID", "Average distance tree using PID");
2794 public void neighbourTreeMenuItem_actionPerformed()
2796 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2799 protected void njTreeBlosumMenuItem_actionPerformed()
2801 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2804 protected void avTreeBlosumMenuItem_actionPerformed()
2806 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2809 void NewTreePanel(String type, String pwType, String title)
2811 // are the sequences aligned?
2812 if (!viewport.getAlignment().isAligned(false))
2815 int Width = viewport.getAlignment().getWidth();
2817 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2819 current = viewport.getAlignment().getSequenceAt(i);
2821 if (current.getLength() < Width)
2823 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2826 alignPanel.paintAlignment(true);
2830 if ((viewport.getSelectionGroup() != null && viewport
2831 .getSelectionGroup().getSize() > 1)
2832 || (viewport.getAlignment().getHeight() > 1))
2834 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2836 addTreeMenuItem(tp, title);
2838 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2842 void loadTree_actionPerformed()
2844 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2845 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2846 cap.setTreeImport();
2847 Frame frame = new Frame();
2849 jalview.bin.JalviewLite.addFrame(frame,
2850 MessageManager.getString("label.paste_newick_file"), 400, 300);
2853 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2855 TreePanel tp = new TreePanel(alignPanel, treeFile,
2856 MessageManager.getString("label.load_tree_from_file"), tree);
2857 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2858 addTreeMenuItem(tp, treeFile);
2862 * sort the alignment using the given treePanel
2865 * tree used to sort view
2867 * string used for undo event name
2869 public void sortByTree(TreePanel treePanel, String title)
2871 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2873 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2874 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2875 // HistoryItem.SORT));
2876 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2877 "label.order_by_params", new String[] { title }), oldOrder,
2878 viewport.getAlignment()));
2879 alignPanel.paintAlignment(true);
2883 * Do any automatic reordering of the alignment and add the necessary bits to
2884 * the menu structure for the new tree
2889 protected void addTreeMenuItem(final TreePanel treePanel,
2892 final MenuItem item = new MenuItem(title);
2893 sortByTreeMenu.add(item);
2894 item.addActionListener(new java.awt.event.ActionListener()
2897 public void actionPerformed(ActionEvent evt)
2899 sortByTree(treePanel, title); // treePanel.getTitle());
2903 treePanel.addWindowListener(new WindowAdapter()
2906 public void windowOpened(WindowEvent e)
2908 if (viewport.sortByTree)
2910 sortByTree(treePanel, title);
2912 super.windowOpened(e);
2916 public void windowClosing(WindowEvent e)
2918 sortByTreeMenu.remove(item);
2923 public boolean sortBy(AlignmentOrder alorder, String undoname)
2925 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2926 if (viewport.applet.debug)
2928 System.err.println("Sorting " + alorder.getOrder().size()
2929 + " in alignment '" + getTitle() + "'");
2931 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2932 if (undoname != null)
2934 addHistoryItem(new OrderCommand(undoname, oldOrder,
2935 viewport.getAlignment()));
2937 alignPanel.paintAlignment(true);
2941 protected void documentation_actionPerformed()
2943 alignPanel.av.applet.openJalviewHelpUrl();
2946 protected void about_actionPerformed()
2949 class AboutPanel extends Canvas
2955 public AboutPanel(String version, String builddate)
2957 this.version = version;
2958 this.builddate = builddate;
2962 public void paint(Graphics g)
2964 g.setColor(Color.white);
2965 g.fillRect(0, 0, getSize().width, getSize().height);
2966 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2967 FontMetrics fm = g.getFontMetrics();
2968 int fh = fm.getHeight();
2970 g.setColor(Color.black);
2971 // TODO: update this text for each release or centrally store it for
2972 // lite and application
2973 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2974 g.drawString(MessageManager.formatMessage(
2975 "label.jalviewLite_release", new String[] { version }), x,
2977 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2978 g.drawString(MessageManager.formatMessage(
2979 "label.jaview_build_date", new String[] { builddate }), x,
2981 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2982 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2984 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2985 x + 50, y += fh + 8);
2987 MessageManager.getString("label.jalview_dev_managers"), x,
2989 g.drawString(MessageManager
2990 .getString("label.jalview_distribution_lists"), x, y += fh);
2991 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2994 MessageManager.getString("label.jalview_cite_1_authors"),
2997 MessageManager.getString("label.jalview_cite_1_title"), x,
2999 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3004 Frame frame = new Frame();
3005 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3007 jalview.bin.JalviewLite.addFrame(frame,
3008 MessageManager.getString("label.jalview"), 580, 220);
3012 public void showURL(String url, String target)
3014 if (viewport.applet == null)
3016 System.out.println("Not running as applet - no browser available.");
3020 viewport.applet.showURL(url, target);
3024 // ////////////////////////////////////////////////////////////////////////////////
3025 // JBuilder Graphics here
3027 MenuBar alignFrameMenuBar = new MenuBar();
3029 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3031 MenuItem loadApplication = new MenuItem(
3032 MessageManager.getString("label.view_full_application"));
3034 MenuItem loadTree = new MenuItem(
3035 MessageManager.getString("label.load_associated_tree"));
3037 MenuItem loadAnnotations = new MenuItem(
3038 MessageManager.getString("label.load_features_annotations"));
3040 MenuItem outputFeatures = new MenuItem(
3041 MessageManager.getString("label.export_features"));
3043 MenuItem outputAnnotations = new MenuItem(
3044 MessageManager.getString("label.export_annotations"));
3046 MenuItem closeMenuItem = new MenuItem(
3047 MessageManager.getString("action.close"));
3049 MenuItem selectAllSequenceMenuItem = new MenuItem(
3050 MessageManager.getString("action.select_all"));
3052 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3053 MessageManager.getString("action.deselect_all"));
3055 MenuItem invertSequenceMenuItem = new MenuItem(
3056 MessageManager.getString("action.invert_selection"));
3058 MenuItem remove2LeftMenuItem = new MenuItem();
3060 MenuItem remove2RightMenuItem = new MenuItem();
3062 MenuItem removeGappedColumnMenuItem = new MenuItem();
3064 MenuItem removeAllGapsMenuItem = new MenuItem();
3066 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3068 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3070 MenuItem sortPairwiseMenuItem = new MenuItem();
3072 MenuItem sortIDMenuItem = new MenuItem();
3074 MenuItem sortLengthMenuItem = new MenuItem();
3076 MenuItem sortGroupMenuItem = new MenuItem();
3078 MenuItem removeRedundancyMenuItem = new MenuItem();
3080 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3082 MenuItem PCAMenuItem = new MenuItem();
3084 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3086 MenuItem neighbourTreeMenuItem = new MenuItem();
3088 BorderLayout borderLayout1 = new BorderLayout();
3090 public Label statusBar = new Label();
3092 MenuItem clustalColour = new MenuItem();
3094 MenuItem zappoColour = new MenuItem();
3096 MenuItem taylorColour = new MenuItem();
3098 MenuItem hydrophobicityColour = new MenuItem();
3100 MenuItem helixColour = new MenuItem();
3102 MenuItem strandColour = new MenuItem();
3104 MenuItem turnColour = new MenuItem();
3106 MenuItem buriedColour = new MenuItem();
3108 MenuItem purinePyrimidineColour = new MenuItem();
3110 // MenuItem RNAInteractionColour = new MenuItem();
3112 MenuItem RNAHelixColour = new MenuItem();
3114 MenuItem userDefinedColour = new MenuItem();
3116 MenuItem PIDColour = new MenuItem();
3118 MenuItem BLOSUM62Colour = new MenuItem();
3120 MenuItem tcoffeeColour = new MenuItem();
3122 MenuItem njTreeBlosumMenuItem = new MenuItem();
3124 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3126 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3128 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3130 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3132 MenuItem alProperties = new MenuItem(
3133 MessageManager.getString("label.alignment_props"));
3135 MenuItem overviewMenuItem = new MenuItem();
3137 MenuItem undoMenuItem = new MenuItem();
3139 MenuItem redoMenuItem = new MenuItem();
3141 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3143 MenuItem noColourmenuItem = new MenuItem();
3145 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3147 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3149 MenuItem findMenuItem = new MenuItem();
3151 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3153 MenuItem nucleotideColour = new MenuItem();
3155 MenuItem deleteGroups = new MenuItem();
3157 MenuItem grpsFromSelection = new MenuItem();
3159 MenuItem createGroup = new MenuItem();
3161 MenuItem unGroup = new MenuItem();
3163 MenuItem delete = new MenuItem();
3165 MenuItem copy = new MenuItem();
3167 MenuItem cut = new MenuItem();
3169 Menu pasteMenu = new Menu();
3171 MenuItem pasteNew = new MenuItem();
3173 MenuItem pasteThis = new MenuItem();
3175 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3177 MenuItem font = new MenuItem();
3179 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3181 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3183 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3185 MenuItem modifyPID = new MenuItem();
3187 MenuItem modifyConservation = new MenuItem();
3189 CheckboxMenuItem autoCalculate = null;
3191 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3192 "Sort Alignment With New Tree", true);
3194 Menu sortByTreeMenu = new Menu();
3196 MenuItem inputText = new MenuItem();
3198 MenuItem documentation = new MenuItem();
3200 MenuItem about = new MenuItem();
3202 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3204 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3206 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3208 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3210 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3212 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3214 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3216 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3218 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3221 * Initialise menus and other items
3225 private void jbInit() throws Exception
3227 setMenuBar(alignFrameMenuBar);
3230 * Configure File menu items and actions
3233 .setLabel(MessageManager.getString("label.input_from_textbox"));
3234 inputText.addActionListener(this);
3235 Menu outputTextboxMenu = new Menu(
3236 MessageManager.getString("label.out_to_textbox"));
3237 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3240 MenuItem item = new MenuItem(
3241 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
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 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4020 if (protocol == null)
4026 pdbentry.setProperty("protocol", protocol);
4027 toaddpdb.addPDBId(pdbentry);
4028 alignPanel.getStructureSelectionManager()
4029 .registerPDBEntry(pdbentry);
4035 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4039 Vector sequences = new Vector();
4040 for (int i = 0; i < seqs.length; i++)
4042 if (seqs[i] != null)
4044 sequences.addElement(new Object[] { seqs[i],
4045 (chains != null) ? chains[i] : null });
4048 seqs = new SequenceI[sequences.size()];
4049 chains = new String[sequences.size()];
4050 for (int i = 0, isize = sequences.size(); i < isize; i++)
4052 Object[] oj = (Object[]) sequences.elementAt(i);
4054 seqs[i] = (SequenceI) oj[0];
4055 chains[i] = (String) oj[1];
4058 return new Object[] { seqs, chains };
4062 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4063 SequenceI[] seqs, String[] chains, String protocol)
4065 // Scrub any null sequences from the array
4066 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4067 seqs = (SequenceI[]) sqch[0];
4068 chains = (String[]) sqch[1];
4069 if (seqs == null || seqs.length == 0)
4072 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4074 if (protocol == null || protocol.trim().length() == 0
4075 || protocol.equals("null"))
4077 protocol = (String) pdb.getProperty("protocol");
4078 if (protocol == null)
4080 System.err.println("Couldn't work out protocol to open structure: "
4085 if (applet.useXtrnalSviewer)
4087 // register the association(s) and quit, don't create any windows.
4088 if (StructureSelectionManager.getStructureSelectionManager(applet)
4089 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4091 System.err.println("Failed to map " + pdb.getFile() + " ("
4092 + protocol + ") to any sequences");
4096 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4098 // can only do alignments with Jmol
4099 // find the last jmol window assigned to this alignment
4100 jalview.appletgui.AppletJmol ajm = null, tajm;
4101 Vector jmols = applet
4102 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4103 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4105 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4106 if (tajm.ap.alignFrame == this)
4115 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4116 // try and add the pdb structure
4121 // otherwise, create a new window
4122 if (applet.jmolAvailable)
4124 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4126 applet.lastFrameX += 40;
4127 applet.lastFrameY += 40;
4131 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4136 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4137 SequenceI[][] seqs, String[][] chains, String[] protocols)
4139 // TODO Auto-generated method stub
4140 System.err.println("Aligned Structure View: Not yet implemented.");
4144 * modify the current selection, providing the user has not made a selection
4148 * - sequences from this alignment
4150 * - columns to be selected on the alignment
4152 public void select(SequenceGroup sel, ColumnSelection csel)
4154 alignPanel.seqPanel.selection(sel, csel, null);
4157 public void scrollTo(int row, int column)
4159 alignPanel.seqPanel.scrollTo(row, column);
4162 public void scrollToRow(int row)
4164 alignPanel.seqPanel.scrollToRow(row);
4167 public void scrollToColumn(int column)
4169 alignPanel.seqPanel.scrollToColumn(column);
4173 * @return the alignments unique ID.
4175 public String getSequenceSetId()
4177 return viewport.getSequenceSetId();
4181 * Load the (T-Coffee) score file from the specified url
4184 * File/URL/T-COFFEE score file contents
4185 * @throws IOException
4186 * @return true if alignment was annotated with data from source
4188 public boolean loadScoreFile(String source) throws IOException
4191 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4192 AppletFormatAdapter.checkProtocol(source));
4193 if (!file.isValid())
4195 // TODO: raise dialog for gui
4196 System.err.println("Problems parsing T-Coffee scores: "
4197 + file.getWarningMessage());
4198 System.err.println("Origin was:\n" + source);
4203 * check that the score matrix matches the alignment dimensions
4206 if ((aln = viewport.getAlignment()) != null
4207 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4210 // TODO: raise a dialog box here rather than bomb out.
4212 .println("The scores matrix does not match the alignment dimensions");
4216 // TODO add parameter to indicate if matching should be done
4217 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4219 alignPanel.fontChanged();
4220 tcoffeeColour.setEnabled(true);
4221 // switch to this color
4222 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4227 System.err.println("Problems resolving T-Coffee scores:");
4228 if (file.getWarningMessage() != null)
4230 System.err.println(file.getWarningMessage());
4236 public SplitFrame getSplitFrame()
4238 return this.splitFrame;
4241 public void setSplitFrame(SplitFrame sf)
4243 this.splitFrame = sf;
4246 // may not need this
4248 public void setShowSeqFeatures(boolean b)
4250 // showSeqFeatures.setSelected(b);
4251 viewport.setShowSequenceFeatures(b);
4256 public void setMenusForViewport()
4258 // setMenusFromViewport(viewport);
4263 public void refreshFeatureUI(boolean enableIfNecessary)
4265 if (enableIfNecessary)
4267 sequenceFeatures.setState(true);
4268 alignPanel.av.setShowSequenceFeatures(true);
4273 public FeatureSettingsControllerI getFeatureSettingsUI()
4275 return alignPanel.av.featureSettings;