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.Hashtable;
106 import java.util.List;
107 import java.util.Map;
108 import java.util.StringTokenizer;
109 import java.util.Vector;
111 import org.jmol.viewer.Viewer;
113 public class AlignFrame extends EmbmenuFrame implements ActionListener,
114 ItemListener, KeyListener, AlignViewControllerGuiI
116 public AlignViewControllerI avc;
118 public AlignmentPanel alignPanel;
120 public AlignViewport viewport;
122 // width and height may be overridden by applet parameters
123 int frameWidth = 700;
125 int frameHeight = 500;
127 String jalviewServletURL;
130 * Flag for showing autocalculated consensus above or below other consensus
133 private boolean showAutoCalculatedAbove;
135 private SequenceAnnotationOrder annotationSortOrder;
138 * Constructor that creates the frame and adds it to the display.
145 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
148 this(al, applet, title, embedded, true);
152 * Constructor that optionally allows the frame to be displayed or only
159 * @param addToDisplay
161 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
162 boolean embedded, boolean addToDisplay)
164 this(al, null, null, applet, title, embedded, addToDisplay);
167 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
168 ColumnSelection columnSelection, JalviewLite applet,
169 String title, boolean embedded)
171 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
174 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
175 ColumnSelection columnSelection, JalviewLite applet,
176 String title, boolean embedded, boolean addToDisplay)
180 jalviewServletURL = applet.getParameter("APPLICATION_URL");
186 } catch (Exception ex)
188 ex.printStackTrace();
190 // need to get window geometry before we calculate alignment layout
196 param = applet.getParameter("windowWidth");
199 int width = Integer.parseInt(param);
202 param = applet.getParameter("windowHeight");
205 int height = Integer.parseInt(param);
206 frameHeight = height;
208 } catch (Exception ex)
212 viewport = new AlignViewport(al, applet);
214 if (hiddenSeqs != null && hiddenSeqs.length > 0)
216 viewport.hideSequence(hiddenSeqs);
218 if (columnSelection != null)
220 viewport.setColumnSelection(columnSelection);
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.getColumnSelection() != null
706 && viewport.getColumnSelection().getSelected() != null && viewport
707 .getColumnSelection().getSelected().size() > 0)
708 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
711 // now invert the sequence set, if required - empty selection implies
712 // that no hiding is required.
715 invertSequenceMenuItem_actionPerformed();
716 sg = viewport.getSelectionGroup();
720 viewport.expandColSelection(sg, true);
721 // finally invert the column selection and get the new sequence
722 // selection and indicate it should be hidden.
723 invertColSel_actionPerformed();
730 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
733 viewport.hideAllSelectedSeqs();
735 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
738 viewport.showAllHiddenSeqs();
744 if (viewport.getColumnSelection().getSelected().size() > 0)
746 viewport.hideSelectedColumns();
749 viewport.setSelectionGroup(sg);
754 viewport.showAllHiddenColumns();
756 viewport.sendSelection();
761 public void keyReleased(KeyEvent evt)
766 public void keyTyped(KeyEvent evt)
771 public void itemStateChanged(ItemEvent evt)
773 final Object source = evt.getSource();
774 if (source == displayNonconservedMenuItem)
776 displayNonconservedMenuItem_actionPerformed();
778 else if (source == colourTextMenuItem)
780 colourTextMenuItem_actionPerformed();
782 else if (source == wrapMenuItem)
784 wrapMenuItem_actionPerformed();
786 else if (source == scaleAbove)
788 viewport.setScaleAboveWrapped(scaleAbove.getState());
790 else if (source == scaleLeft)
792 viewport.setScaleLeftWrapped(scaleLeft.getState());
794 else if (source == scaleRight)
796 viewport.setScaleRightWrapped(scaleRight.getState());
798 else if (source == seqLimits)
800 seqLimits_itemStateChanged();
802 else if (source == viewBoxesMenuItem)
804 viewport.setShowBoxes(viewBoxesMenuItem.getState());
806 else if (source == viewTextMenuItem)
808 viewport.setShowText(viewTextMenuItem.getState());
810 else if (source == renderGapsMenuItem)
812 viewport.setRenderGaps(renderGapsMenuItem.getState());
814 else if (source == annotationPanelMenuItem)
816 boolean showAnnotations = annotationPanelMenuItem.getState();
817 showAlignmentAnnotations.setEnabled(showAnnotations);
818 showSequenceAnnotations.setEnabled(showAnnotations);
819 viewport.setShowAnnotation(showAnnotations);
820 alignPanel.setAnnotationVisible(showAnnotations);
822 else if (source == sequenceFeatures)
824 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
825 alignPanel.seqPanel.seqCanvas.repaint();
827 else if (source == showAlignmentAnnotations)
829 setAnnotationsVisibility();
831 else if (source == showSequenceAnnotations)
833 setAnnotationsVisibility();
835 else if (source == sortAnnBySequence)
837 boolean newState = sortAnnBySequence.getState();
838 sortAnnByLabel.setState(false);
839 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
840 : SequenceAnnotationOrder.NONE);
841 setViewportAnnotationOrder();
843 else if (source == sortAnnByLabel)
845 boolean newState = sortAnnByLabel.getState();
846 sortAnnBySequence.setState(false);
847 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
848 : SequenceAnnotationOrder.NONE);
849 setViewportAnnotationOrder();
851 else if (source == showAutoFirst)
853 showAutoLast.setState(!showAutoFirst.getState());
854 setShowAutoCalculatedAbove(showAutoFirst.getState());
855 setViewportAnnotationOrder();
857 else if (source == showAutoLast)
859 showAutoFirst.setState(!showAutoLast.getState());
860 setShowAutoCalculatedAbove(showAutoFirst.getState());
861 setViewportAnnotationOrder();
863 else if (source == conservationMenuItem)
865 conservationMenuItem_actionPerformed();
867 else if (source == abovePIDThreshold)
869 abovePIDThreshold_actionPerformed();
871 else if (source == applyToAllGroups)
873 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
875 else if (source == autoCalculate)
877 viewport.autoCalculateConsensus = autoCalculate.getState();
879 else if (source == sortByTree)
881 viewport.sortByTree = sortByTree.getState();
883 else if (source == this.centreColumnLabelFlag)
885 centreColumnLabelFlag_stateChanged();
887 else if (source == this.followMouseOverFlag)
889 mouseOverFlag_stateChanged();
891 else if (source == showGroupConsensus)
893 showGroupConsensus_actionPerformed();
895 else if (source == showGroupConservation)
897 showGroupConservation_actionPerformed();
899 else if (source == showSequenceLogo)
901 showSequenceLogo_actionPerformed();
903 else if (source == normSequenceLogo)
905 normSequenceLogo_actionPerformed();
907 else if (source == showConsensusHistogram)
909 showConsensusHistogram_actionPerformed();
911 else if (source == applyAutoAnnotationSettings)
913 applyAutoAnnotationSettings_actionPerformed();
915 alignPanel.paintAlignment(true);
919 * Set the visibility state of sequence-related and/or alignment-related
920 * annotations depending on checkbox selections, and repaint.
924 private void setAnnotationsVisibility()
926 boolean showForAlignment = showAlignmentAnnotations.getState();
927 boolean showForSequences = showSequenceAnnotations.getState();
928 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
930 for (AlignmentAnnotation aa : alignPanel.getAlignment()
931 .getAlignmentAnnotation())
933 boolean visible = (aa.sequenceRef == null ? showForAlignment
935 aa.visible = visible;
938 alignPanel.validateAnnotationDimensions(true);
943 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
945 this.annotationSortOrder = order;
949 * Set flags on the viewport that control annotation ordering
951 private void setViewportAnnotationOrder()
953 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
955 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
958 private void setShowAutoCalculatedAbove(boolean showAbove)
960 this.showAutoCalculatedAbove = showAbove;
963 private void mouseOverFlag_stateChanged()
965 viewport.setFollowHighlight(followMouseOverFlag.getState());
966 // TODO: could kick the scrollTo mechanism to reset view for current
970 private void centreColumnLabelFlag_stateChanged()
972 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
973 this.alignPanel.annotationPanel.repaint();
977 public void actionPerformed(ActionEvent evt)
979 viewport.applet.currentAlignFrame = this;
981 Object source = evt.getSource();
983 if (source == inputText)
985 inputText_actionPerformed();
987 else if (source == loadTree)
989 loadTree_actionPerformed();
991 else if (source == loadApplication)
993 launchFullApplication();
995 else if (source == loadAnnotations)
999 else if (source == outputAnnotations)
1001 outputAnnotations(true);
1003 else if (source == outputFeatures)
1005 outputFeatures(true, "Jalview");
1007 else if (source == closeMenuItem)
1009 closeMenuItem_actionPerformed();
1011 else if (source == copy)
1013 copy_actionPerformed();
1015 else if (source == undoMenuItem)
1017 undoMenuItem_actionPerformed();
1019 else if (source == redoMenuItem)
1021 redoMenuItem_actionPerformed();
1023 else if (source == inputText)
1025 inputText_actionPerformed();
1027 else if (source == closeMenuItem)
1029 closeMenuItem_actionPerformed();
1031 else if (source == undoMenuItem)
1033 undoMenuItem_actionPerformed();
1035 else if (source == redoMenuItem)
1037 redoMenuItem_actionPerformed();
1039 else if (source == copy)
1041 copy_actionPerformed();
1043 else if (source == pasteNew)
1045 pasteNew_actionPerformed();
1047 else if (source == pasteThis)
1049 pasteThis_actionPerformed();
1051 else if (source == cut)
1053 cut_actionPerformed();
1055 else if (source == delete)
1057 delete_actionPerformed();
1059 else if (source == grpsFromSelection)
1061 makeGrpsFromSelection_actionPerformed();
1063 else if (source == deleteGroups)
1065 deleteGroups_actionPerformed();
1067 else if (source == selectAllSequenceMenuItem)
1069 selectAllSequenceMenuItem_actionPerformed();
1071 else if (source == deselectAllSequenceMenuItem)
1073 deselectAllSequenceMenuItem_actionPerformed();
1075 else if (source == invertSequenceMenuItem)
1077 invertSequenceMenuItem_actionPerformed();
1078 // uncomment to slave sequence selections in split frame
1079 // viewport.sendSelection();
1081 else if (source == invertColSel)
1083 viewport.invertColumnSelection();
1084 alignPanel.paintAlignment(true);
1085 viewport.sendSelection();
1087 else if (source == remove2LeftMenuItem)
1089 trimAlignment(true);
1091 else if (source == remove2RightMenuItem)
1093 trimAlignment(false);
1095 else if (source == removeGappedColumnMenuItem)
1097 removeGappedColumnMenuItem_actionPerformed();
1099 else if (source == removeAllGapsMenuItem)
1101 removeAllGapsMenuItem_actionPerformed();
1103 else if (source == findMenuItem)
1105 findMenuItem_actionPerformed();
1107 else if (source == font)
1109 new FontChooser(alignPanel);
1111 else if (source == newView)
1115 else if (source == showColumns)
1117 viewport.showAllHiddenColumns();
1118 alignPanel.paintAlignment(true);
1119 viewport.sendSelection();
1121 else if (source == showSeqs)
1123 viewport.showAllHiddenSeqs();
1124 alignPanel.paintAlignment(true);
1125 // uncomment if we want to slave sequence selections in split frame
1126 // viewport.sendSelection();
1128 else if (source == hideColumns)
1130 viewport.hideSelectedColumns();
1131 alignPanel.paintAlignment(true);
1132 viewport.sendSelection();
1134 else if (source == hideSequences
1135 && viewport.getSelectionGroup() != null)
1137 viewport.hideAllSelectedSeqs();
1138 alignPanel.paintAlignment(true);
1139 // uncomment if we want to slave sequence selections in split frame
1140 // viewport.sendSelection();
1142 else if (source == hideAllButSelection)
1144 toggleHiddenRegions(false, false);
1145 alignPanel.paintAlignment(true);
1146 viewport.sendSelection();
1148 else if (source == hideAllSelection)
1150 SequenceGroup sg = viewport.getSelectionGroup();
1151 viewport.expandColSelection(sg, false);
1152 viewport.hideAllSelectedSeqs();
1153 viewport.hideSelectedColumns();
1154 alignPanel.paintAlignment(true);
1155 viewport.sendSelection();
1157 else if (source == showAllHidden)
1159 viewport.showAllHiddenColumns();
1160 viewport.showAllHiddenSeqs();
1161 alignPanel.paintAlignment(true);
1162 viewport.sendSelection();
1164 else if (source == showGroupConsensus)
1166 showGroupConsensus_actionPerformed();
1168 else if (source == showGroupConservation)
1170 showGroupConservation_actionPerformed();
1172 else if (source == showSequenceLogo)
1174 showSequenceLogo_actionPerformed();
1176 else if (source == normSequenceLogo)
1178 normSequenceLogo_actionPerformed();
1180 else if (source == showConsensusHistogram)
1182 showConsensusHistogram_actionPerformed();
1184 else if (source == applyAutoAnnotationSettings)
1186 applyAutoAnnotationSettings_actionPerformed();
1188 else if (source == featureSettings)
1190 new FeatureSettings(alignPanel);
1192 else if (source == alProperties)
1194 StringBuffer contents = new jalview.io.AlignmentProperties(
1195 viewport.getAlignment()).formatAsString();
1196 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1197 cap.setText(contents.toString());
1198 Frame frame = new Frame();
1200 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1201 "label.alignment_properties", new String[] { getTitle() }),
1204 else if (source == overviewMenuItem)
1206 overviewMenuItem_actionPerformed();
1208 else if (source == noColourmenuItem)
1212 else if (source == clustalColour)
1214 abovePIDThreshold.setState(false);
1215 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1217 else if (source == zappoColour)
1219 changeColour(new ZappoColourScheme());
1221 else if (source == taylorColour)
1223 changeColour(new TaylorColourScheme());
1225 else if (source == hydrophobicityColour)
1227 changeColour(new HydrophobicColourScheme());
1229 else if (source == helixColour)
1231 changeColour(new HelixColourScheme());
1233 else if (source == strandColour)
1235 changeColour(new StrandColourScheme());
1237 else if (source == turnColour)
1239 changeColour(new TurnColourScheme());
1241 else if (source == buriedColour)
1243 changeColour(new BuriedColourScheme());
1245 else if (source == nucleotideColour)
1247 changeColour(new NucleotideColourScheme());
1249 else if (source == purinePyrimidineColour)
1251 changeColour(new PurinePyrimidineColourScheme());
1253 // else if (source == RNAInteractionColour)
1255 // changeColour(new RNAInteractionColourScheme());
1257 else if (source == RNAHelixColour)
1259 new RNAHelicesColourChooser(viewport, alignPanel);
1261 else if (source == modifyPID)
1263 modifyPID_actionPerformed();
1265 else if (source == modifyConservation)
1267 modifyConservation_actionPerformed();
1269 else if (source == userDefinedColour)
1271 new UserDefinedColours(alignPanel, null);
1273 else if (source == PIDColour)
1275 changeColour(new PIDColourScheme());
1277 else if (source == BLOSUM62Colour)
1279 changeColour(new Blosum62ColourScheme());
1281 else if (source == tcoffeeColour)
1283 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1285 else if (source == annotationColour)
1287 new AnnotationColourChooser(viewport, alignPanel);
1289 else if (source == annotationColumnSelection)
1291 new AnnotationColumnChooser(viewport, alignPanel);
1293 else if (source == sortPairwiseMenuItem)
1295 sortPairwiseMenuItem_actionPerformed();
1297 else if (source == sortIDMenuItem)
1299 sortIDMenuItem_actionPerformed();
1301 else if (source == sortLengthMenuItem)
1303 sortLengthMenuItem_actionPerformed();
1305 else if (source == sortGroupMenuItem)
1307 sortGroupMenuItem_actionPerformed();
1309 else if (source == removeRedundancyMenuItem)
1311 removeRedundancyMenuItem_actionPerformed();
1313 else if (source == pairwiseAlignmentMenuItem)
1315 pairwiseAlignmentMenuItem_actionPerformed();
1317 else if (source == PCAMenuItem)
1319 PCAMenuItem_actionPerformed();
1321 else if (source == averageDistanceTreeMenuItem)
1323 averageDistanceTreeMenuItem_actionPerformed();
1325 else if (source == neighbourTreeMenuItem)
1327 neighbourTreeMenuItem_actionPerformed();
1329 else if (source == njTreeBlosumMenuItem)
1331 njTreeBlosumMenuItem_actionPerformed();
1333 else if (source == avDistanceTreeBlosumMenuItem)
1335 avTreeBlosumMenuItem_actionPerformed();
1337 else if (source == documentation)
1339 documentation_actionPerformed();
1341 else if (source == about)
1343 about_actionPerformed();
1348 public void inputText_actionPerformed()
1350 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351 Frame frame = new Frame();
1353 jalview.bin.JalviewLite.addFrame(frame,
1354 MessageManager.getString("label.input_cut_paste"), 500, 500);
1357 protected void outputText_actionPerformed(ActionEvent e)
1359 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1360 Frame frame = new Frame();
1362 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1363 "label.alignment_output_command",
1364 new Object[] { e.getActionCommand() }), 600, 500);
1366 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1367 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1368 e.getActionCommand(), viewport.getAlignment(),
1369 viewport.getShowJVSuffix()));
1372 public void loadAnnotations()
1374 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1375 cap.setText(MessageManager
1376 .getString("label.paste_features_annotations_Tcoffee_here"));
1377 cap.setAnnotationImport();
1378 Frame frame = new Frame();
1380 jalview.bin.JalviewLite.addFrame(frame,
1381 MessageManager.getString("action.paste_annotations"), 400, 300);
1385 public String outputAnnotations(boolean displayTextbox)
1387 String annotation = new AnnotationFile()
1388 .printAnnotationsForView(viewport);
1392 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1393 Frame frame = new Frame();
1395 jalview.bin.JalviewLite.addFrame(frame,
1396 MessageManager.getString("label.annotations"), 600, 500);
1397 cap.setText(annotation);
1403 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1405 if (alignPanel.getFeatureRenderer() != null
1406 && viewport.getFeaturesDisplayed() != null)
1408 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1414 public String outputFeatures(boolean displayTextbox, String format)
1417 FeaturesFile formatter = new FeaturesFile();
1418 if (format.equalsIgnoreCase("Jalview"))
1420 features = formatter.printJalviewFormat(viewport
1421 .getAlignment().getSequencesArray(),
1422 getDisplayedFeatureCols());
1426 features = formatter.printGffFormat(viewport.getAlignment()
1427 .getSequencesArray(), getDisplayedFeatureCols());
1432 boolean frimport = false;
1433 if (features == null || features.equals("No Features Visible"))
1435 features = "# No features visible - paste some and import them here.";
1439 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1442 cap.setAnnotationImport();
1444 Frame frame = new Frame();
1446 jalview.bin.JalviewLite.addFrame(frame,
1447 MessageManager.getString("label.features"), 600, 500);
1448 cap.setText(features);
1452 if (features == null)
1461 void launchFullApplication()
1463 StringBuffer url = new StringBuffer(jalviewServletURL);
1465 // allow servlet parameters to be passed in applet parameter
1466 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1468 url.append(firstSep);
1471 + appendProtocol(viewport.applet.getParameter("file")));
1473 if (viewport.applet.getParameter("features") != null)
1475 url.append("&features=");
1476 url.append(appendProtocol(viewport.applet.getParameter("features")));
1479 if (viewport.applet.getParameter("annotations") != null)
1481 url.append("&annotations=");
1482 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1485 if (viewport.applet.getParameter("jnetfile") != null)
1487 url.append("&annotations=");
1488 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1491 if (viewport.applet.getParameter("defaultColour") != null)
1493 url.append("&colour="
1494 + removeWhiteSpace(viewport.applet
1495 .getParameter("defaultColour")));
1498 if (viewport.applet.getParameter("userDefinedColour") != null)
1500 url.append("&colour="
1501 + removeWhiteSpace(viewport.applet
1502 .getParameter("userDefinedColour")));
1504 if (viewport.applet.getParameter("tree") != null)
1507 + appendProtocol(viewport.applet.getParameter("tree")));
1509 if (viewport.applet.getParameter("treeFile") != null)
1512 + appendProtocol(viewport.applet.getParameter("treeFile")));
1515 showURL(url.toString(), "FULL_APP");
1518 String removeWhiteSpace(String colour)
1520 StringBuffer sb = new StringBuffer();
1521 for (int i = 0; i < colour.length(); i++)
1523 if (Character.isWhitespace(colour.charAt(i)))
1529 sb.append(colour.charAt(i));
1533 return sb.toString();
1536 String appendProtocol(String url)
1541 url = URLEncoder.encode(url);
1544 * When we finally deprecate 1.1 compatibility, we can start to use
1545 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1546 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1547 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1548 * ex.printStackTrace(); }
1550 catch (java.net.MalformedURLException ex)
1552 url = viewport.applet.getCodeBase() + url;
1557 public void closeMenuItem_actionPerformed()
1559 PaintRefresher.RemoveComponent(alignPanel);
1560 if (alignPanel.seqPanel != null
1561 && alignPanel.seqPanel.seqCanvas != null)
1563 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1565 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1567 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1570 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1585 void updateEditMenuBar()
1588 if (viewport.getHistoryList().size() > 0)
1590 undoMenuItem.setEnabled(true);
1591 CommandI command = viewport.getHistoryList().peek();
1592 undoMenuItem.setLabel(MessageManager.formatMessage(
1593 "label.undo_command",
1594 new Object[] { command.getDescription() }));
1598 undoMenuItem.setEnabled(false);
1599 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1602 if (viewport.getRedoList().size() > 0)
1604 redoMenuItem.setEnabled(true);
1606 CommandI command = viewport.getRedoList().peek();
1607 redoMenuItem.setLabel(MessageManager.formatMessage(
1608 "label.redo_command",
1609 new Object[] { command.getDescription() }));
1613 redoMenuItem.setEnabled(false);
1614 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1622 public void addHistoryItem(CommandI command)
1624 if (command.getSize() > 0)
1626 viewport.addToHistoryList(command);
1627 viewport.clearRedoList();
1628 updateEditMenuBar();
1629 viewport.updateHiddenColumns();
1634 * TODO: JAL-1104 DOCUMENT ME!
1639 protected void undoMenuItem_actionPerformed()
1641 if (viewport.getHistoryList().isEmpty())
1646 CommandI command = viewport.getHistoryList().pop();
1647 viewport.addToRedoList(command);
1648 command.undoCommand(null);
1650 AlignmentViewport originalSource = getOriginatingSource(command);
1652 if (originalSource != viewport)
1655 .println("Warning: Viewport object mismatch whilst undoing");
1657 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1658 // viewport.getColumnSelection().getHiddenColumns()
1660 updateEditMenuBar();
1661 originalSource.firePropertyChange("alignment", null, originalSource
1662 .getAlignment().getSequences());
1666 * TODO: JAL-1104 DOCUMENT ME!
1671 protected void redoMenuItem_actionPerformed()
1673 if (viewport.getRedoList().isEmpty())
1678 CommandI command = viewport.getRedoList().pop();
1679 viewport.addToHistoryList(command);
1680 command.doCommand(null);
1682 AlignmentViewport originalSource = getOriginatingSource(command);
1684 if (originalSource != viewport)
1687 .println("Warning: Viewport object mismatch whilst re-doing");
1689 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1690 // viewport.getColumnSelection().getHiddenColumns()
1693 updateEditMenuBar();
1694 originalSource.firePropertyChange("alignment", null, originalSource
1695 .getAlignment().getSequences());
1698 AlignmentViewport getOriginatingSource(CommandI command)
1700 AlignmentViewport originalSource = null;
1701 // For sequence removal and addition, we need to fire
1702 // the property change event FROM the viewport where the
1703 // original alignment was altered
1704 AlignmentI al = null;
1705 if (command instanceof EditCommand)
1707 EditCommand editCommand = (EditCommand) command;
1708 al = editCommand.getAlignment();
1709 Vector comps = (Vector) PaintRefresher.components.get(viewport
1710 .getSequenceSetId());
1711 for (int i = 0; i < comps.size(); i++)
1713 if (comps.elementAt(i) instanceof AlignmentPanel)
1715 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1717 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1724 if (originalSource == null)
1726 // The original view is closed, we must validate
1727 // the current view against the closed view first
1730 PaintRefresher.validateSequences(al, viewport.getAlignment());
1733 originalSource = viewport;
1736 return originalSource;
1740 * Move the currently selected sequences up or down one position in the
1745 public void moveSelectedSequences(boolean up)
1747 SequenceGroup sg = viewport.getSelectionGroup();
1752 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1753 up ? null : viewport.getHiddenRepSequences(), up);
1754 alignPanel.paintAlignment(true);
1757 * Also move cDNA/protein complement sequences
1759 AlignViewportI complement = viewport.getCodingComplement();
1760 if (complement != null)
1762 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1763 viewport, complement);
1764 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1765 up ? null : complement.getHiddenRepSequences(), up);
1766 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1770 synchronized void slideSequences(boolean right, int size)
1772 List<SequenceI> sg = new Vector<SequenceI>();
1773 if (viewport.cursorMode)
1775 sg.add(viewport.getAlignment().getSequenceAt(
1776 alignPanel.seqPanel.seqCanvas.cursorY));
1778 else if (viewport.getSelectionGroup() != null
1779 && viewport.getSelectionGroup().getSize() != viewport
1780 .getAlignment().getHeight())
1782 sg = viewport.getSelectionGroup().getSequences(
1783 viewport.getHiddenRepSequences());
1791 Vector<SequenceI> invertGroup = new Vector();
1793 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1795 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1797 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1801 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1803 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1805 for (int i = 0; i < invertGroup.size(); i++)
1807 seqs2[i] = invertGroup.elementAt(i);
1810 SlideSequencesCommand ssc;
1813 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1814 size, viewport.getGapCharacter());
1818 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1819 size, viewport.getGapCharacter());
1822 int groupAdjustment = 0;
1823 if (ssc.getGapsInsertedBegin() && right)
1825 if (viewport.cursorMode)
1827 alignPanel.seqPanel.moveCursor(size, 0);
1831 groupAdjustment = size;
1834 else if (!ssc.getGapsInsertedBegin() && !right)
1836 if (viewport.cursorMode)
1838 alignPanel.seqPanel.moveCursor(-size, 0);
1842 groupAdjustment = -size;
1846 if (groupAdjustment != 0)
1848 viewport.getSelectionGroup().setStartRes(
1849 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1850 viewport.getSelectionGroup().setEndRes(
1851 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1854 boolean appendHistoryItem = false;
1855 Deque<CommandI> historyList = viewport.getHistoryList();
1856 if (historyList != null && historyList.size() > 0
1857 && historyList.peek() instanceof SlideSequencesCommand)
1859 appendHistoryItem = ssc
1860 .appendSlideCommand((SlideSequencesCommand) historyList
1864 if (!appendHistoryItem)
1866 addHistoryItem(ssc);
1872 static StringBuffer copiedSequences;
1874 static Vector copiedHiddenColumns;
1876 protected void copy_actionPerformed()
1878 if (viewport.getSelectionGroup() == null)
1883 SequenceGroup sg = viewport.getSelectionGroup();
1884 copiedSequences = new StringBuffer();
1885 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1886 for (int i = 0; i < sg.getSize(); i++)
1888 SequenceI seq = sg.getSequenceAt(i);
1889 int index = viewport.getAlignment().findIndex(seq);
1890 orderedSeqs.put(index, seq);
1893 int index = 0, startRes, endRes;
1896 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1898 copiedHiddenColumns = new Vector();
1899 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1900 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1902 copiedHiddenColumns.addElement(new int[] {
1903 region[0] - hiddenOffset, region[1] - hiddenOffset });
1908 copiedHiddenColumns = null;
1911 for (int i = 0; i < sg.getSize(); i++)
1913 SequenceI seq = null;
1917 if (orderedSeqs.containsKey(index))
1919 seq = orderedSeqs.get(index);
1930 // Returns residue following index if gap
1931 startRes = seq.findPosition(sg.getStartRes());
1934 // Need to find the residue preceeding index if gap
1937 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1939 ch = seq.getCharAt(j);
1940 if (!jalview.util.Comparison.isGap((ch)))
1948 endRes += seq.getStart() - 1;
1951 copiedSequences.append(seq.getName()
1957 + seq.getSequenceAsString(sg.getStartRes(),
1958 sg.getEndRes() + 1) + "\n");
1963 protected void pasteNew_actionPerformed()
1968 protected void pasteThis_actionPerformed()
1973 void paste(boolean newAlignment)
1978 if (copiedSequences == null)
1983 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1984 Vector seqs = new Vector();
1985 while (st.hasMoreElements())
1987 String name = st.nextToken();
1988 int start = Integer.parseInt(st.nextToken());
1989 int end = Integer.parseInt(st.nextToken());
1990 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1992 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1993 for (int i = 0; i < seqs.size(); i++)
1995 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2000 String newtitle = MessageManager
2001 .getString("label.copied_sequences");
2002 if (getTitle().startsWith(
2003 MessageManager.getString("label.copied_sequences")))
2005 newtitle = getTitle();
2009 newtitle = newtitle.concat(MessageManager.formatMessage(
2010 "label.from_msname", new String[] { getTitle() }));
2012 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2013 viewport.applet, newtitle, false);
2014 if (copiedHiddenColumns != null)
2016 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2018 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2019 af.viewport.hideColumns(region[0], region[1]);
2023 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2028 addSequences(newSeqs);
2031 } catch (Exception ex)
2033 } // could be anything being pasted in here
2037 void addSequences(SequenceI[] seqs)
2039 for (int i = 0; i < seqs.length; i++)
2041 viewport.getAlignment().addSequence(seqs[i]);
2045 addHistoryItem(new EditCommand(
2046 MessageManager.getString("label.add_sequences"), Action.PASTE,
2047 seqs, 0, viewport.getAlignment().getWidth(),
2048 viewport.getAlignment()));
2050 viewport.setEndSeq(viewport.getAlignment().getHeight());
2051 viewport.getAlignment().getWidth();
2052 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2057 protected void cut_actionPerformed()
2059 copy_actionPerformed();
2060 delete_actionPerformed();
2063 protected void delete_actionPerformed()
2066 SequenceGroup sg = viewport.getSelectionGroup();
2072 Vector seqs = new Vector();
2074 for (int i = 0; i < sg.getSize(); i++)
2076 seq = sg.getSequenceAt(i);
2077 seqs.addElement(seq);
2081 * If the cut affects all sequences, warn, remove highlighted columns
2083 if (sg.getSize() == viewport.getAlignment().getHeight())
2085 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2086 .getAlignment().getWidth()) ? true : false;
2087 if (isEntireAlignWidth)
2089 String title = MessageManager.getString("label.delete_all");
2090 Panel infoPanel = new Panel();
2091 infoPanel.setLayout(new FlowLayout());
2093 .add(new Label(MessageManager.getString("warn.delete_all")));
2095 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2096 dialog.setMainPanel(infoPanel);
2097 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2098 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2099 dialog.setVisible(true);
2106 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2107 sg.getEndRes() + 1);
2110 SequenceI[] cut = new SequenceI[seqs.size()];
2111 for (int i = 0; i < seqs.size(); i++)
2113 cut[i] = (SequenceI) seqs.elementAt(i);
2117 * //ADD HISTORY ITEM
2119 addHistoryItem(new EditCommand(
2120 MessageManager.getString("label.cut_sequences"), Action.CUT,
2121 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2122 viewport.getAlignment()));
2124 viewport.setSelectionGroup(null);
2125 viewport.getAlignment().deleteGroup(sg);
2127 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2130 if (viewport.getAlignment().getHeight() < 1)
2132 this.setVisible(false);
2134 viewport.sendSelection();
2138 * group consensus toggled
2141 protected void showGroupConsensus_actionPerformed()
2143 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2144 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2149 * group conservation toggled.
2151 protected void showGroupConservation_actionPerformed()
2153 viewport.setShowGroupConservation(showGroupConservation.getState());
2154 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2161 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2162 * .event.ActionEvent)
2164 protected void showConsensusHistogram_actionPerformed()
2166 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2167 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2174 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2175 * .event.ActionEvent)
2177 protected void showSequenceLogo_actionPerformed()
2179 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2180 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2183 protected void normSequenceLogo_actionPerformed()
2185 showSequenceLogo.setState(true);
2186 viewport.setShowSequenceLogo(true);
2187 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2188 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2191 protected void applyAutoAnnotationSettings_actionPerformed()
2193 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2196 protected void makeGrpsFromSelection_actionPerformed()
2198 if (avc.makeGroupsFromSelection())
2200 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2201 alignPanel.updateAnnotation();
2202 alignPanel.paintAlignment(true);
2206 protected void createGroup_actionPerformed()
2211 protected void unGroup_actionPerformed()
2215 alignPanel.alignmentChanged();
2219 protected void deleteGroups_actionPerformed()
2221 if (avc.deleteGroups())
2223 alignPanel.alignmentChanged();
2227 public void selectAllSequenceMenuItem_actionPerformed()
2229 SequenceGroup sg = new SequenceGroup();
2230 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2232 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2234 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2235 viewport.setSelectionGroup(sg);
2236 alignPanel.paintAlignment(true);
2237 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2238 viewport.sendSelection();
2241 public void deselectAllSequenceMenuItem_actionPerformed()
2243 if (viewport.cursorMode)
2245 alignPanel.seqPanel.keyboardNo1 = null;
2246 alignPanel.seqPanel.keyboardNo2 = null;
2248 viewport.setSelectionGroup(null);
2249 viewport.getColumnSelection().clear();
2250 viewport.setSelectionGroup(null);
2251 alignPanel.idPanel.idCanvas.searchResults = null;
2252 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2253 alignPanel.paintAlignment(true);
2254 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2255 viewport.sendSelection();
2258 public void invertSequenceMenuItem_actionPerformed()
2260 SequenceGroup sg = viewport.getSelectionGroup();
2261 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2263 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2266 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2267 viewport.sendSelection();
2270 public void invertColSel_actionPerformed()
2272 viewport.invertColumnSelection();
2273 alignPanel.paintAlignment(true);
2274 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2275 viewport.sendSelection();
2278 void trimAlignment(boolean trimLeft)
2280 ColumnSelection colSel = viewport.getColumnSelection();
2283 if (!colSel.isEmpty())
2287 column = colSel.getMin();
2291 column = colSel.getMax();
2295 if (viewport.getSelectionGroup() != null)
2297 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2298 viewport.getHiddenRepSequences());
2302 seqs = viewport.getAlignment().getSequencesArray();
2305 TrimRegionCommand trimRegion;
2308 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2309 column, viewport.getAlignment());
2310 viewport.setStartRes(0);
2314 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2315 column, viewport.getAlignment());
2318 statusBar.setText(MessageManager.formatMessage(
2319 "label.removed_columns",
2320 new String[] { Integer.valueOf(trimRegion.getSize())
2322 addHistoryItem(trimRegion);
2324 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2326 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2327 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2329 viewport.getAlignment().deleteGroup(sg);
2333 viewport.firePropertyChange("alignment", null, viewport
2334 .getAlignment().getSequences());
2338 public void removeGappedColumnMenuItem_actionPerformed()
2340 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2343 if (viewport.getSelectionGroup() != null)
2345 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2346 viewport.getHiddenRepSequences());
2347 start = viewport.getSelectionGroup().getStartRes();
2348 end = viewport.getSelectionGroup().getEndRes();
2352 seqs = viewport.getAlignment().getSequencesArray();
2355 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2356 "Remove Gapped Columns", seqs, start, end,
2357 viewport.getAlignment());
2359 addHistoryItem(removeGapCols);
2361 statusBar.setText(MessageManager.formatMessage(
2362 "label.removed_empty_columns",
2363 new String[] { Integer.valueOf(removeGapCols.getSize())
2366 // This is to maintain viewport position on first residue
2367 // of first sequence
2368 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2369 int startRes = seq.findPosition(viewport.startRes);
2370 // ShiftList shifts;
2371 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2372 // edit.alColumnChanges=shifts.getInverse();
2373 // if (viewport.hasHiddenColumns)
2374 // viewport.getColumnSelection().compensateForEdits(shifts);
2375 viewport.setStartRes(seq.findIndex(startRes) - 1);
2376 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2381 public void removeAllGapsMenuItem_actionPerformed()
2383 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2386 if (viewport.getSelectionGroup() != null)
2388 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2389 viewport.getHiddenRepSequences());
2390 start = viewport.getSelectionGroup().getStartRes();
2391 end = viewport.getSelectionGroup().getEndRes();
2395 seqs = viewport.getAlignment().getSequencesArray();
2398 // This is to maintain viewport position on first residue
2399 // of first sequence
2400 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2401 int startRes = seq.findPosition(viewport.startRes);
2403 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2404 viewport.getAlignment()));
2406 viewport.setStartRes(seq.findIndex(startRes) - 1);
2408 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2413 public void findMenuItem_actionPerformed()
2415 new Finder(alignPanel);
2419 * create a new view derived from the current view
2422 * @return frame for the new view
2424 public AlignFrame newView(String viewtitle)
2427 if (viewport.hasHiddenRows())
2429 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2430 .getFullAlignment().getSequencesArray());
2434 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2437 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2439 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2441 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2443 newal.addAnnotation(viewport.getAlignment()
2444 .getAlignmentAnnotation()[i]);
2449 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2451 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2452 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2453 PaintRefresher.Register(newaf.alignPanel,
2454 newaf.alignPanel.av.getSequenceSetId());
2456 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2457 newaf.alignPanel.av.getSequenceSetId());
2458 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2459 newaf.alignPanel.av.getSequenceSetId());
2461 Vector comps = (Vector) PaintRefresher.components.get(viewport
2462 .getSequenceSetId());
2464 for (int i = 0; i < comps.size(); i++)
2466 if (comps.elementAt(i) instanceof AlignmentPanel)
2472 String title = new String(this.getTitle());
2473 if (viewtitle != null)
2475 title = viewtitle + " ( " + title + ")";
2479 if (title.indexOf("(View") > -1)
2481 title = title.substring(0, title.indexOf("(View"));
2483 title += "(View " + viewSize + ")";
2486 newaf.setTitle(title.toString());
2488 newaf.viewport.setHistoryList(viewport.getHistoryList());
2489 newaf.viewport.setRedoList(viewport.getRedoList());
2495 * @return list of feature groups on the view
2497 public String[] getFeatureGroups()
2499 FeatureRenderer fr = null;
2500 if (alignPanel != null
2501 && (fr = alignPanel.getFeatureRenderer()) != null)
2503 List<String> gps = fr.getFeatureGroups();
2504 String[] _gps = gps.toArray(new String[gps.size()]);
2511 * get sequence feature groups that are hidden or shown
2517 public String[] getFeatureGroupsOfState(boolean visible)
2519 FeatureRenderer fr = null;
2520 if (alignPanel != null
2521 && (fr = alignPanel.getFeatureRenderer()) != null)
2523 List<String> gps = fr.getGroups(visible);
2524 String[] _gps = gps.toArray(new String[gps.size()]);
2531 * Change the display state for the given feature groups
2534 * list of group strings
2536 * visible or invisible
2538 public void setFeatureGroupState(String[] groups, boolean state)
2540 FeatureRenderer fr = null;
2541 this.sequenceFeatures.setState(true);
2542 viewport.setShowSequenceFeatures(true);
2543 if (alignPanel != null
2544 && (fr = alignPanel.getFeatureRenderer()) != null)
2547 fr.setGroupVisibility(Arrays.asList(groups), state);
2548 alignPanel.seqPanel.seqCanvas.repaint();
2549 if (alignPanel.overviewPanel != null)
2551 alignPanel.overviewPanel.updateOverviewImage();
2556 public void seqLimits_itemStateChanged()
2558 viewport.setShowJVSuffix(seqLimits.getState());
2559 alignPanel.fontChanged();
2560 alignPanel.paintAlignment(true);
2563 protected void colourTextMenuItem_actionPerformed()
2565 viewport.setColourText(colourTextMenuItem.getState());
2566 alignPanel.paintAlignment(true);
2569 protected void displayNonconservedMenuItem_actionPerformed()
2571 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2572 alignPanel.paintAlignment(true);
2575 protected void wrapMenuItem_actionPerformed()
2577 viewport.setWrapAlignment(wrapMenuItem.getState());
2578 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2579 scaleAbove.setEnabled(wrapMenuItem.getState());
2580 scaleLeft.setEnabled(wrapMenuItem.getState());
2581 scaleRight.setEnabled(wrapMenuItem.getState());
2582 alignPanel.paintAlignment(true);
2585 public void overviewMenuItem_actionPerformed()
2587 if (alignPanel.overviewPanel != null)
2592 Frame frame = new Frame();
2593 OverviewPanel overview = new OverviewPanel(alignPanel);
2594 frame.add(overview);
2595 // +50 must allow for applet frame window
2596 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2597 "label.overview_params", new String[] { this.getTitle() }),
2598 overview.getPreferredSize().width,
2599 overview.getPreferredSize().height + 50);
2602 final AlignmentPanel ap = alignPanel;
2603 frame.addWindowListener(new WindowAdapter()
2606 public void windowClosing(WindowEvent e)
2610 ap.setOverviewPanel(null);
2615 alignPanel.setOverviewPanel(overview);
2620 public void changeColour(ColourSchemeI cs)
2625 if (viewport.getAbovePIDThreshold())
2627 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2631 if (viewport.getConservationSelected())
2633 cs.setConservationApplied(true);
2634 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2639 cs.setConservationApplied(false);
2642 viewport.setGlobalColourScheme(cs);
2644 alignPanel.paintAlignment(true);
2647 protected void modifyPID_actionPerformed()
2649 if (viewport.getAbovePIDThreshold()
2650 && viewport.getGlobalColourScheme() != null)
2652 SliderPanel.setPIDSliderSource(alignPanel,
2653 viewport.getGlobalColourScheme(), "Background");
2654 SliderPanel.showPIDSlider();
2658 protected void modifyConservation_actionPerformed()
2660 if (viewport.getConservationSelected()
2661 && viewport.getGlobalColourScheme() != null)
2663 SliderPanel.setConservationSlider(alignPanel,
2664 viewport.getGlobalColourScheme(), "Background");
2665 SliderPanel.showConservationSlider();
2669 protected void conservationMenuItem_actionPerformed()
2671 viewport.setConservationSelected(conservationMenuItem.getState());
2673 viewport.setAbovePIDThreshold(false);
2674 abovePIDThreshold.setState(false);
2676 changeColour(viewport.getGlobalColourScheme());
2678 modifyConservation_actionPerformed();
2681 public void abovePIDThreshold_actionPerformed()
2683 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2685 conservationMenuItem.setState(false);
2686 viewport.setConservationSelected(false);
2688 changeColour(viewport.getGlobalColourScheme());
2690 modifyPID_actionPerformed();
2693 public void sortPairwiseMenuItem_actionPerformed()
2695 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2696 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2697 .getAlignment().getSequenceAt(0), null);
2699 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2700 viewport.getAlignment()));
2701 alignPanel.paintAlignment(true);
2704 public void sortIDMenuItem_actionPerformed()
2706 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2707 AlignmentSorter.sortByID(viewport.getAlignment());
2708 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2709 viewport.getAlignment()));
2710 alignPanel.paintAlignment(true);
2713 public void sortLengthMenuItem_actionPerformed()
2715 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2716 AlignmentSorter.sortByLength(viewport.getAlignment());
2717 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2718 viewport.getAlignment()));
2719 alignPanel.paintAlignment(true);
2722 public void sortGroupMenuItem_actionPerformed()
2724 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2725 AlignmentSorter.sortByGroup(viewport.getAlignment());
2726 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2727 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2732 public void removeRedundancyMenuItem_actionPerformed()
2734 new RedundancyPanel(alignPanel);
2737 public void pairwiseAlignmentMenuItem_actionPerformed()
2739 if (viewport.getSelectionGroup() != null
2740 && viewport.getSelectionGroup().getSize() > 1)
2742 Frame frame = new Frame();
2743 frame.add(new PairwiseAlignPanel(alignPanel));
2744 jalview.bin.JalviewLite.addFrame(frame,
2745 MessageManager.getString("action.pairwise_alignment"), 600,
2750 public void PCAMenuItem_actionPerformed()
2752 // are the sequences aligned?
2753 if (!viewport.getAlignment().isAligned(false))
2756 int Width = viewport.getAlignment().getWidth();
2758 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2760 current = viewport.getAlignment().getSequenceAt(i);
2762 if (current.getLength() < Width)
2764 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2767 alignPanel.paintAlignment(true);
2770 if ((viewport.getSelectionGroup() != null
2771 && viewport.getSelectionGroup().getSize() < 4 && viewport
2772 .getSelectionGroup().getSize() > 0)
2773 || viewport.getAlignment().getHeight() < 4)
2780 new PCAPanel(viewport);
2781 } catch (java.lang.OutOfMemoryError ex)
2787 public void averageDistanceTreeMenuItem_actionPerformed()
2789 NewTreePanel("AV", "PID", "Average distance tree using PID");
2792 public void neighbourTreeMenuItem_actionPerformed()
2794 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2797 protected void njTreeBlosumMenuItem_actionPerformed()
2799 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2802 protected void avTreeBlosumMenuItem_actionPerformed()
2804 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2807 void NewTreePanel(String type, String pwType, String title)
2809 // are the sequences aligned?
2810 if (!viewport.getAlignment().isAligned(false))
2813 int Width = viewport.getAlignment().getWidth();
2815 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2817 current = viewport.getAlignment().getSequenceAt(i);
2819 if (current.getLength() < Width)
2821 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2824 alignPanel.paintAlignment(true);
2828 if ((viewport.getSelectionGroup() != null && viewport
2829 .getSelectionGroup().getSize() > 1)
2830 || (viewport.getAlignment().getHeight() > 1))
2832 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2834 addTreeMenuItem(tp, title);
2836 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2840 void loadTree_actionPerformed()
2842 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2843 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2844 cap.setTreeImport();
2845 Frame frame = new Frame();
2847 jalview.bin.JalviewLite.addFrame(frame,
2848 MessageManager.getString("label.paste_newick_file"), 400, 300);
2851 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2853 TreePanel tp = new TreePanel(alignPanel, treeFile,
2854 MessageManager.getString("label.load_tree_from_file"), tree);
2855 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2856 addTreeMenuItem(tp, treeFile);
2860 * sort the alignment using the given treePanel
2863 * tree used to sort view
2865 * string used for undo event name
2867 public void sortByTree(TreePanel treePanel, String title)
2869 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2871 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2872 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2873 // HistoryItem.SORT));
2874 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2875 "label.order_by_params", new String[] { title }), oldOrder,
2876 viewport.getAlignment()));
2877 alignPanel.paintAlignment(true);
2881 * Do any automatic reordering of the alignment and add the necessary bits to
2882 * the menu structure for the new tree
2887 protected void addTreeMenuItem(final TreePanel treePanel,
2890 final MenuItem item = new MenuItem(title);
2891 sortByTreeMenu.add(item);
2892 item.addActionListener(new java.awt.event.ActionListener()
2895 public void actionPerformed(ActionEvent evt)
2897 sortByTree(treePanel, title); // treePanel.getTitle());
2901 treePanel.addWindowListener(new WindowAdapter()
2904 public void windowOpened(WindowEvent e)
2906 if (viewport.sortByTree)
2908 sortByTree(treePanel, title);
2910 super.windowOpened(e);
2914 public void windowClosing(WindowEvent e)
2916 sortByTreeMenu.remove(item);
2921 public boolean sortBy(AlignmentOrder alorder, String undoname)
2923 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2924 if (viewport.applet.debug)
2926 System.err.println("Sorting " + alorder.getOrder().size()
2927 + " in alignment '" + getTitle() + "'");
2929 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2930 if (undoname != null)
2932 addHistoryItem(new OrderCommand(undoname, oldOrder,
2933 viewport.getAlignment()));
2935 alignPanel.paintAlignment(true);
2939 protected void documentation_actionPerformed()
2941 alignPanel.av.applet.openJalviewHelpUrl();
2944 protected void about_actionPerformed()
2947 class AboutPanel extends Canvas
2953 public AboutPanel(String version, String builddate)
2955 this.version = version;
2956 this.builddate = builddate;
2960 public void paint(Graphics g)
2962 g.setColor(Color.white);
2963 g.fillRect(0, 0, getSize().width, getSize().height);
2964 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2965 FontMetrics fm = g.getFontMetrics();
2966 int fh = fm.getHeight();
2968 g.setColor(Color.black);
2969 // TODO: update this text for each release or centrally store it for
2970 // lite and application
2971 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2972 g.drawString(MessageManager.formatMessage(
2973 "label.jalviewLite_release", new String[] { version }), x,
2975 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2976 g.drawString(MessageManager.formatMessage(
2977 "label.jaview_build_date", new String[] { builddate }), x,
2979 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2980 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2982 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2983 x + 50, y += fh + 8);
2985 MessageManager.getString("label.jalview_dev_managers"), x,
2987 g.drawString(MessageManager
2988 .getString("label.jalview_distribution_lists"), x, y += fh);
2989 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2992 MessageManager.getString("label.jalview_cite_1_authors"),
2995 MessageManager.getString("label.jalview_cite_1_title"), x,
2997 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3002 Frame frame = new Frame();
3003 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3005 jalview.bin.JalviewLite.addFrame(frame,
3006 MessageManager.getString("label.jalview"), 580, 220);
3010 public void showURL(String url, String target)
3012 if (viewport.applet == null)
3014 System.out.println("Not running as applet - no browser available.");
3018 viewport.applet.showURL(url, target);
3022 // ////////////////////////////////////////////////////////////////////////////////
3023 // JBuilder Graphics here
3025 MenuBar alignFrameMenuBar = new MenuBar();
3027 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3029 MenuItem loadApplication = new MenuItem(
3030 MessageManager.getString("label.view_full_application"));
3032 MenuItem loadTree = new MenuItem(
3033 MessageManager.getString("label.load_associated_tree"));
3035 MenuItem loadAnnotations = new MenuItem(
3036 MessageManager.getString("label.load_features_annotations"));
3038 MenuItem outputFeatures = new MenuItem(
3039 MessageManager.getString("label.export_features"));
3041 MenuItem outputAnnotations = new MenuItem(
3042 MessageManager.getString("label.export_annotations"));
3044 MenuItem closeMenuItem = new MenuItem(
3045 MessageManager.getString("action.close"));
3047 MenuItem selectAllSequenceMenuItem = new MenuItem(
3048 MessageManager.getString("action.select_all"));
3050 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3051 MessageManager.getString("action.deselect_all"));
3053 MenuItem invertSequenceMenuItem = new MenuItem(
3054 MessageManager.getString("action.invert_selection"));
3056 MenuItem remove2LeftMenuItem = new MenuItem();
3058 MenuItem remove2RightMenuItem = new MenuItem();
3060 MenuItem removeGappedColumnMenuItem = new MenuItem();
3062 MenuItem removeAllGapsMenuItem = new MenuItem();
3064 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3066 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3068 MenuItem sortPairwiseMenuItem = new MenuItem();
3070 MenuItem sortIDMenuItem = new MenuItem();
3072 MenuItem sortLengthMenuItem = new MenuItem();
3074 MenuItem sortGroupMenuItem = new MenuItem();
3076 MenuItem removeRedundancyMenuItem = new MenuItem();
3078 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3080 MenuItem PCAMenuItem = new MenuItem();
3082 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3084 MenuItem neighbourTreeMenuItem = new MenuItem();
3086 BorderLayout borderLayout1 = new BorderLayout();
3088 public Label statusBar = new Label();
3090 MenuItem clustalColour = new MenuItem();
3092 MenuItem zappoColour = new MenuItem();
3094 MenuItem taylorColour = new MenuItem();
3096 MenuItem hydrophobicityColour = new MenuItem();
3098 MenuItem helixColour = new MenuItem();
3100 MenuItem strandColour = new MenuItem();
3102 MenuItem turnColour = new MenuItem();
3104 MenuItem buriedColour = new MenuItem();
3106 MenuItem purinePyrimidineColour = new MenuItem();
3108 // MenuItem RNAInteractionColour = new MenuItem();
3110 MenuItem RNAHelixColour = new MenuItem();
3112 MenuItem userDefinedColour = new MenuItem();
3114 MenuItem PIDColour = new MenuItem();
3116 MenuItem BLOSUM62Colour = new MenuItem();
3118 MenuItem tcoffeeColour = new MenuItem();
3120 MenuItem njTreeBlosumMenuItem = new MenuItem();
3122 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3124 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3126 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3128 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3130 MenuItem alProperties = new MenuItem(
3131 MessageManager.getString("label.alignment_props"));
3133 MenuItem overviewMenuItem = new MenuItem();
3135 MenuItem undoMenuItem = new MenuItem();
3137 MenuItem redoMenuItem = new MenuItem();
3139 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3141 MenuItem noColourmenuItem = new MenuItem();
3143 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3145 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3147 MenuItem findMenuItem = new MenuItem();
3149 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3151 MenuItem nucleotideColour = new MenuItem();
3153 MenuItem deleteGroups = new MenuItem();
3155 MenuItem grpsFromSelection = new MenuItem();
3157 MenuItem createGroup = new MenuItem();
3159 MenuItem unGroup = new MenuItem();
3161 MenuItem delete = new MenuItem();
3163 MenuItem copy = new MenuItem();
3165 MenuItem cut = new MenuItem();
3167 Menu pasteMenu = new Menu();
3169 MenuItem pasteNew = new MenuItem();
3171 MenuItem pasteThis = new MenuItem();
3173 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3175 MenuItem font = new MenuItem();
3177 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3179 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3181 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3183 MenuItem modifyPID = new MenuItem();
3185 MenuItem modifyConservation = new MenuItem();
3187 CheckboxMenuItem autoCalculate = null;
3189 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3190 "Sort Alignment With New Tree", true);
3192 Menu sortByTreeMenu = new Menu();
3194 MenuItem inputText = new MenuItem();
3196 MenuItem documentation = new MenuItem();
3198 MenuItem about = new MenuItem();
3200 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3202 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3204 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3206 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3208 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3210 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3212 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3214 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3216 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3219 * Initialise menus and other items
3223 private void jbInit() throws Exception
3225 setMenuBar(alignFrameMenuBar);
3228 * Configure File menu items and actions
3231 .setLabel(MessageManager.getString("label.input_from_textbox"));
3232 inputText.addActionListener(this);
3233 Menu outputTextboxMenu = new Menu(
3234 MessageManager.getString("label.out_to_textbox"));
3235 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3238 MenuItem item = new MenuItem(
3239 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3241 item.addActionListener(new java.awt.event.ActionListener()
3244 public void actionPerformed(ActionEvent e)
3246 outputText_actionPerformed(e);
3250 outputTextboxMenu.add(item);
3252 closeMenuItem.addActionListener(this);
3253 loadApplication.addActionListener(this);
3254 loadTree.addActionListener(this);
3255 loadAnnotations.addActionListener(this);
3256 outputFeatures.addActionListener(this);
3257 outputAnnotations.addActionListener(this);
3260 * Configure Edit menu items and actions
3262 undoMenuItem.setEnabled(false);
3263 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3264 undoMenuItem.addActionListener(this);
3265 redoMenuItem.setEnabled(false);
3266 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3267 redoMenuItem.addActionListener(this);
3268 copy.setLabel(MessageManager.getString("action.copy"));
3269 copy.addActionListener(this);
3270 cut.setLabel(MessageManager.getString("action.cut"));
3271 cut.addActionListener(this);
3272 delete.setLabel(MessageManager.getString("action.delete"));
3273 delete.addActionListener(this);
3274 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3275 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3276 pasteNew.addActionListener(this);
3277 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3278 pasteThis.addActionListener(this);
3279 remove2LeftMenuItem.setLabel(MessageManager
3280 .getString("action.remove_left"));
3281 remove2LeftMenuItem.addActionListener(this);
3282 remove2RightMenuItem.setLabel(MessageManager
3283 .getString("action.remove_right"));
3284 remove2RightMenuItem.addActionListener(this);
3285 removeGappedColumnMenuItem.setLabel(MessageManager
3286 .getString("action.remove_empty_columns"));
3287 removeGappedColumnMenuItem.addActionListener(this);
3288 removeAllGapsMenuItem.setLabel(MessageManager
3289 .getString("action.remove_all_gaps"));
3290 removeAllGapsMenuItem.addActionListener(this);
3291 removeRedundancyMenuItem.setLabel(MessageManager
3292 .getString("action.remove_redundancy"));
3293 removeRedundancyMenuItem.addActionListener(this);
3296 * Configure Select menu items and actions
3298 findMenuItem.setLabel(MessageManager.getString("action.find"));
3299 findMenuItem.addActionListener(this);
3300 selectAllSequenceMenuItem.addActionListener(this);
3301 deselectAllSequenceMenuItem.addActionListener(this);
3302 invertSequenceMenuItem.setLabel(MessageManager
3303 .getString("action.invert_sequence_selection"));
3304 invertSequenceMenuItem.addActionListener(this);
3305 invertColSel.setLabel(MessageManager
3306 .getString("action.invert_column_selection"));
3307 invertColSel.addActionListener(this);
3308 deleteGroups.setLabel(MessageManager
3309 .getString("action.undefine_groups"));
3310 deleteGroups.addActionListener(this);
3311 grpsFromSelection.setLabel(MessageManager
3312 .getString("action.make_groups_selection"));
3313 grpsFromSelection.addActionListener(this);
3314 createGroup.setLabel(MessageManager.getString("action.create_group"));
3315 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3316 annotationColumnSelection.setLabel(MessageManager
3317 .getString("action.select_by_annotation"));
3318 annotationColumnSelection.addActionListener(this);
3321 * Configure View menu items and actions
3323 newView.setLabel(MessageManager.getString("action.new_view"));
3324 newView.addActionListener(this);
3325 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3326 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3327 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3328 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3330 .setLabel(MessageManager.getString("label.selected_columns"));
3331 hideSequences.setLabel(MessageManager
3332 .getString("label.selected_sequences"));
3333 hideAllButSelection.setLabel(MessageManager
3334 .getString("label.all_but_selected_region"));
3335 hideAllSelection.setLabel(MessageManager
3336 .getString("label.selected_region"));
3337 showAllHidden.setLabel(MessageManager
3338 .getString("label.all_sequences_columns"));
3339 showColumns.addActionListener(this);
3340 showSeqs.addActionListener(this);
3341 hideColumns.addActionListener(this);
3342 hideSequences.addActionListener(this);
3343 hideAllButSelection.addActionListener(this);
3344 hideAllSelection.addActionListener(this);
3345 showAllHidden.addActionListener(this);
3346 featureSettings.setLabel(MessageManager
3347 .getString("action.feature_settings"));
3348 featureSettings.addActionListener(this);
3349 sequenceFeatures.setLabel(MessageManager
3350 .getString("label.show_sequence_features"));
3351 sequenceFeatures.addItemListener(this);
3352 sequenceFeatures.setState(false);
3353 followMouseOverFlag.setLabel(MessageManager
3354 .getString("label.automatic_scrolling"));
3355 followMouseOverFlag.addItemListener(this);
3356 alProperties.addActionListener(this);
3357 overviewMenuItem.setLabel(MessageManager
3358 .getString("label.overview_window"));
3359 overviewMenuItem.addActionListener(this);
3362 * Configure Annotations menu items and actions
3364 annotationPanelMenuItem.setLabel(MessageManager
3365 .getString("label.show_annotations"));
3366 annotationPanelMenuItem.addItemListener(this);
3367 showGroupConsensus.setLabel(MessageManager
3368 .getString("label.group_consensus"));
3369 showGroupConservation.setLabel(MessageManager
3370 .getString("label.group_conservation"));
3371 showConsensusHistogram.setLabel(MessageManager
3372 .getString("label.show_consensus_histogram"));
3373 showSequenceLogo.setLabel(MessageManager
3374 .getString("label.show_consensus_logo"));
3375 normSequenceLogo.setLabel(MessageManager
3376 .getString("label.norm_consensus_logo"));
3377 applyAutoAnnotationSettings.setLabel(MessageManager
3378 .getString("label.apply_all_groups"));
3379 applyAutoAnnotationSettings.setState(true);
3380 Menu autoAnnMenu = new Menu(
3381 MessageManager.getString("label.autocalculated_annotation"));
3382 showGroupConsensus.addItemListener(this);
3383 showGroupConservation.addItemListener(this);
3384 showConsensusHistogram.addItemListener(this);
3385 showSequenceLogo.addItemListener(this);
3386 normSequenceLogo.addItemListener(this);
3387 applyAutoAnnotationSettings.addItemListener(this);
3388 showAlignmentAnnotations = new CheckboxMenuItem(
3389 MessageManager.getString("label.show_all_al_annotations"));
3390 showSequenceAnnotations = new CheckboxMenuItem(
3391 MessageManager.getString("label.show_all_seq_annotations"));
3392 sortAnnBySequence = new CheckboxMenuItem(
3393 MessageManager.getString("label.sort_annotations_by_sequence"));
3394 sortAnnByLabel = new CheckboxMenuItem(
3395 MessageManager.getString("label.sort_annotations_by_label"));
3396 showAutoFirst = new CheckboxMenuItem(
3397 MessageManager.getString("label.show_first"));
3398 showAutoFirst.setState(false); // pending applet parameter
3399 setShowAutoCalculatedAbove(showAutoFirst.getState());
3400 showAutoLast = new CheckboxMenuItem(
3401 MessageManager.getString("label.show_last"));
3402 showAutoLast.setState(!showAutoFirst.getState());
3403 showAlignmentAnnotations.addItemListener(this);
3404 showSequenceAnnotations.addItemListener(this);
3405 sortAnnBySequence.addItemListener(this);
3406 sortAnnByLabel.addItemListener(this);
3407 showAutoFirst.addItemListener(this);
3408 showAutoLast.addItemListener(this);
3411 * Configure Format menu items and actions
3413 font.setLabel(MessageManager.getString("action.font"));
3414 font.addActionListener(this);
3415 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3416 scaleAbove.setState(true);
3417 scaleAbove.setEnabled(false);
3418 scaleAbove.addItemListener(this);
3419 scaleLeft.setEnabled(false);
3420 scaleLeft.setState(true);
3421 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3422 scaleLeft.addItemListener(this);
3423 scaleRight.setEnabled(false);
3424 scaleRight.setState(true);
3425 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3426 scaleRight.addItemListener(this);
3427 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3428 viewBoxesMenuItem.setState(true);
3429 viewBoxesMenuItem.addItemListener(this);
3430 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3431 viewTextMenuItem.setState(true);
3432 viewTextMenuItem.addItemListener(this);
3433 colourTextMenuItem.setLabel(MessageManager
3434 .getString("label.colour_text"));
3435 colourTextMenuItem.addItemListener(this);
3436 displayNonconservedMenuItem.setLabel(MessageManager
3437 .getString("label.show_non_conversed"));
3438 displayNonconservedMenuItem.addItemListener(this);
3439 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3440 wrapMenuItem.addItemListener(this);
3441 renderGapsMenuItem.setLabel(MessageManager
3442 .getString("action.show_gaps"));
3443 renderGapsMenuItem.setState(true);
3444 renderGapsMenuItem.addItemListener(this);
3445 centreColumnLabelFlag.setLabel(MessageManager
3446 .getString("label.centre_column_labels"));
3447 centreColumnLabelFlag.addItemListener(this);
3448 seqLimits.setState(true);
3449 seqLimits.setLabel(MessageManager
3450 .getString("label.show_sequence_limits"));
3451 seqLimits.addItemListener(this);
3454 * Configure Colour menu items and actions
3456 applyToAllGroups.setLabel(MessageManager
3457 .getString("label.apply_colour_to_all_groups"));
3458 applyToAllGroups.setState(true);
3459 applyToAllGroups.addItemListener(this);
3460 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3461 clustalColour.addActionListener(this);
3462 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3463 zappoColour.addActionListener(this);
3464 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3465 taylorColour.addActionListener(this);
3466 hydrophobicityColour.setLabel(MessageManager
3467 .getString("label.hydrophobicity"));
3468 hydrophobicityColour.addActionListener(this);
3470 .setLabel(MessageManager.getString("label.helix_propensity"));
3471 helixColour.addActionListener(this);
3472 strandColour.setLabel(MessageManager
3473 .getString("label.strand_propensity"));
3474 strandColour.addActionListener(this);
3475 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3476 turnColour.addActionListener(this);
3477 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3478 buriedColour.addActionListener(this);
3479 purinePyrimidineColour.setLabel(MessageManager
3480 .getString("label.purine_pyrimidine"));
3481 purinePyrimidineColour.addActionListener(this);
3482 // RNAInteractionColour.setLabel(MessageManager
3483 // .getString("label.rna_interaction"));
3484 // RNAInteractionColour.addActionListener(this);
3485 RNAHelixColour.setLabel(MessageManager
3486 .getString("action.by_rna_helixes"));
3487 RNAHelixColour.addActionListener(this);
3488 userDefinedColour.setLabel(MessageManager
3489 .getString("action.user_defined"));
3490 userDefinedColour.addActionListener(this);
3491 PIDColour.setLabel(MessageManager
3492 .getString("label.percentage_identity"));
3493 PIDColour.addActionListener(this);
3494 BLOSUM62Colour.setLabel(MessageManager
3495 .getString("label.blosum62_score"));
3496 BLOSUM62Colour.addActionListener(this);
3498 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3499 // it will be enabled only if a score file is provided
3500 tcoffeeColour.setEnabled(false);
3501 tcoffeeColour.addActionListener(this);
3502 conservationMenuItem.setLabel(MessageManager
3503 .getString("action.by_conservation"));
3504 conservationMenuItem.addItemListener(this);
3505 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3506 noColourmenuItem.addActionListener(this);
3507 abovePIDThreshold.setLabel(MessageManager
3508 .getString("label.above_identity_threshold"));
3509 abovePIDThreshold.addItemListener(this);
3510 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3511 nucleotideColour.addActionListener(this);
3512 modifyPID.setLabel(MessageManager
3513 .getString("label.modify_identity_thereshold"));
3514 modifyPID.addActionListener(this);
3515 modifyConservation.setLabel(MessageManager
3516 .getString("label.modify_conservation_thereshold"));
3517 modifyConservation.addActionListener(this);
3518 annotationColour.setLabel(MessageManager
3519 .getString("action.by_annotation"));
3520 annotationColour.addActionListener(this);
3523 * Configure Calculate menu items and actions
3525 sortPairwiseMenuItem.setLabel(MessageManager
3526 .getString("action.by_pairwise_id"));
3527 sortPairwiseMenuItem.addActionListener(this);
3528 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3529 sortIDMenuItem.addActionListener(this);
3530 sortLengthMenuItem.setLabel(MessageManager
3531 .getString("action.by_length"));
3532 sortLengthMenuItem.addActionListener(this);
3533 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3534 sortGroupMenuItem.addActionListener(this);
3535 pairwiseAlignmentMenuItem.setLabel(MessageManager
3536 .getString("action.pairwise_alignment"));
3537 pairwiseAlignmentMenuItem.addActionListener(this);
3538 PCAMenuItem.setLabel(MessageManager
3539 .getString("label.principal_component_analysis"));
3540 PCAMenuItem.addActionListener(this);
3541 autoCalculate = new CheckboxMenuItem(
3542 MessageManager.getString("label.autocalculate_consensus"), true);
3543 averageDistanceTreeMenuItem.setLabel(MessageManager
3544 .getString("label.average_distance_identity"));
3545 averageDistanceTreeMenuItem.addActionListener(this);
3546 neighbourTreeMenuItem.setLabel(MessageManager
3547 .getString("label.neighbour_joining_identity"));
3548 neighbourTreeMenuItem.addActionListener(this);
3549 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3550 .getString("label.average_distance_bloslum62"));
3551 avDistanceTreeBlosumMenuItem.addActionListener(this);
3552 njTreeBlosumMenuItem.setLabel(MessageManager
3553 .getString("label.neighbour_blosum62"));
3554 njTreeBlosumMenuItem.addActionListener(this);
3555 sortByTreeMenu.setLabel(MessageManager
3556 .getString("action.by_tree_order"));
3557 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3558 Menu calculateTreeMenu = new Menu(
3559 MessageManager.getString("action.calculate_tree"));
3560 autoCalculate.addItemListener(this);
3561 sortByTree.addItemListener(this);
3564 * Configure Help menu items and actions
3566 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3567 documentation.setLabel(MessageManager.getString("label.documentation"));
3568 documentation.addActionListener(this);
3569 about.setLabel(MessageManager.getString("label.about"));
3570 about.addActionListener(this);
3573 * Add top level menus to frame
3575 alignFrameMenuBar.add(fileMenu);
3576 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3577 alignFrameMenuBar.add(editMenu);
3578 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3579 alignFrameMenuBar.add(selectMenu);
3580 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3581 alignFrameMenuBar.add(viewMenu);
3582 Menu annotationsMenu = new Menu(
3583 MessageManager.getString("action.annotations"));
3584 alignFrameMenuBar.add(annotationsMenu);
3585 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3586 alignFrameMenuBar.add(formatMenu);
3587 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3588 alignFrameMenuBar.add(colourMenu);
3589 Menu calculateMenu = new Menu(
3590 MessageManager.getString("action.calculate"));
3591 alignFrameMenuBar.add(calculateMenu);
3592 alignFrameMenuBar.add(helpMenu);
3597 fileMenu.add(inputText);
3598 fileMenu.add(loadTree);
3599 fileMenu.add(loadAnnotations);
3600 fileMenu.addSeparator();
3601 fileMenu.add(outputTextboxMenu);
3602 fileMenu.add(outputFeatures);
3603 fileMenu.add(outputAnnotations);
3604 if (jalviewServletURL != null)
3606 fileMenu.add(loadApplication);
3608 fileMenu.addSeparator();
3609 fileMenu.add(closeMenuItem);
3614 editMenu.add(undoMenuItem);
3615 editMenu.add(redoMenuItem);
3618 pasteMenu.add(pasteNew);
3619 pasteMenu.add(pasteThis);
3620 editMenu.add(pasteMenu);
3621 editMenu.add(delete);
3622 editMenu.addSeparator();
3623 editMenu.add(remove2LeftMenuItem);
3624 editMenu.add(remove2RightMenuItem);
3625 editMenu.add(removeGappedColumnMenuItem);
3626 editMenu.add(removeAllGapsMenuItem);
3627 editMenu.add(removeRedundancyMenuItem);
3632 selectMenu.add(findMenuItem);
3633 selectMenu.addSeparator();
3634 selectMenu.add(selectAllSequenceMenuItem);
3635 selectMenu.add(deselectAllSequenceMenuItem);
3636 selectMenu.add(invertSequenceMenuItem);
3637 selectMenu.add(invertColSel);
3638 selectMenu.add(createGroup);
3639 selectMenu.add(unGroup);
3640 selectMenu.add(grpsFromSelection);
3641 selectMenu.add(deleteGroups);
3642 selectMenu.add(annotationColumnSelection);
3647 viewMenu.add(newView);
3648 viewMenu.addSeparator();
3649 showMenu.add(showColumns);
3650 showMenu.add(showSeqs);
3651 showMenu.add(showAllHidden);
3652 viewMenu.add(showMenu);
3653 hideMenu.add(hideColumns);
3654 hideMenu.add(hideSequences);
3655 hideMenu.add(hideAllSelection);
3656 hideMenu.add(hideAllButSelection);
3657 viewMenu.add(hideMenu);
3658 viewMenu.addSeparator();
3659 viewMenu.add(followMouseOverFlag);
3660 viewMenu.addSeparator();
3661 viewMenu.add(sequenceFeatures);
3662 viewMenu.add(featureSettings);
3663 viewMenu.addSeparator();
3664 viewMenu.add(alProperties);
3665 viewMenu.addSeparator();
3666 viewMenu.add(overviewMenuItem);
3671 annotationsMenu.add(annotationPanelMenuItem);
3672 annotationsMenu.addSeparator();
3673 annotationsMenu.add(showAlignmentAnnotations);
3674 annotationsMenu.add(showSequenceAnnotations);
3675 annotationsMenu.add(sortAnnBySequence);
3676 annotationsMenu.add(sortAnnByLabel);
3677 annotationsMenu.addSeparator();
3678 autoAnnMenu.add(showAutoFirst);
3679 autoAnnMenu.add(showAutoLast);
3680 autoAnnMenu.addSeparator();
3681 autoAnnMenu.add(applyAutoAnnotationSettings);
3682 autoAnnMenu.add(showConsensusHistogram);
3683 autoAnnMenu.add(showSequenceLogo);
3684 autoAnnMenu.add(normSequenceLogo);
3685 autoAnnMenu.addSeparator();
3686 autoAnnMenu.add(showGroupConservation);
3687 autoAnnMenu.add(showGroupConsensus);
3688 annotationsMenu.add(autoAnnMenu);
3693 formatMenu.add(font);
3694 formatMenu.add(seqLimits);
3695 formatMenu.add(wrapMenuItem);
3696 formatMenu.add(scaleAbove);
3697 formatMenu.add(scaleLeft);
3698 formatMenu.add(scaleRight);
3699 formatMenu.add(viewBoxesMenuItem);
3700 formatMenu.add(viewTextMenuItem);
3701 formatMenu.add(colourTextMenuItem);
3702 formatMenu.add(displayNonconservedMenuItem);
3703 formatMenu.add(renderGapsMenuItem);
3704 formatMenu.add(centreColumnLabelFlag);
3709 colourMenu.add(applyToAllGroups);
3710 colourMenu.addSeparator();
3711 colourMenu.add(noColourmenuItem);
3712 colourMenu.add(clustalColour);
3713 colourMenu.add(BLOSUM62Colour);
3714 colourMenu.add(PIDColour);
3715 colourMenu.add(zappoColour);
3716 colourMenu.add(taylorColour);
3717 colourMenu.add(hydrophobicityColour);
3718 colourMenu.add(helixColour);
3719 colourMenu.add(strandColour);
3720 colourMenu.add(turnColour);
3721 colourMenu.add(buriedColour);
3722 colourMenu.add(nucleotideColour);
3723 colourMenu.add(purinePyrimidineColour);
3724 // colourMenu.add(RNAInteractionColour);
3725 colourMenu.add(tcoffeeColour);
3726 colourMenu.add(userDefinedColour);
3727 colourMenu.addSeparator();
3728 colourMenu.add(conservationMenuItem);
3729 colourMenu.add(modifyConservation);
3730 colourMenu.add(abovePIDThreshold);
3731 colourMenu.add(modifyPID);
3732 colourMenu.add(annotationColour);
3733 colourMenu.add(RNAHelixColour);
3738 sortMenu.add(sortIDMenuItem);
3739 sortMenu.add(sortLengthMenuItem);
3740 sortMenu.add(sortByTreeMenu);
3741 sortMenu.add(sortGroupMenuItem);
3742 sortMenu.add(sortPairwiseMenuItem);
3743 calculateMenu.add(sortMenu);
3744 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3745 calculateTreeMenu.add(neighbourTreeMenuItem);
3746 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3747 calculateTreeMenu.add(njTreeBlosumMenuItem);
3748 calculateMenu.add(calculateTreeMenu);
3749 calculateMenu.addSeparator();
3750 calculateMenu.add(pairwiseAlignmentMenuItem);
3751 calculateMenu.add(PCAMenuItem);
3752 calculateMenu.add(autoCalculate);
3753 calculateMenu.add(sortByTree);
3758 helpMenu.add(documentation);
3759 helpMenu.add(about);
3764 statusBar.setBackground(Color.white);
3765 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3766 statusBar.setText(MessageManager.getString("label.status_bar"));
3767 this.add(statusBar, BorderLayout.SOUTH);
3771 public void setStatus(String string)
3773 statusBar.setText(string);
3776 MenuItem featureSettings = new MenuItem();
3778 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3780 MenuItem annotationColour = new MenuItem();
3782 MenuItem annotationColumnSelection = new MenuItem();
3784 MenuItem invertColSel = new MenuItem();
3786 MenuItem showColumns = new MenuItem();
3788 MenuItem showSeqs = new MenuItem();
3790 MenuItem hideColumns = new MenuItem();
3792 MenuItem hideSequences = new MenuItem();
3794 MenuItem hideAllButSelection = new MenuItem();
3796 MenuItem hideAllSelection = new MenuItem();
3798 MenuItem showAllHidden = new MenuItem();
3800 MenuItem newView = new MenuItem();
3802 private CheckboxMenuItem showAlignmentAnnotations;
3804 private CheckboxMenuItem showSequenceAnnotations;
3806 private CheckboxMenuItem sortAnnBySequence;
3808 private CheckboxMenuItem sortAnnByLabel;
3810 private CheckboxMenuItem showAutoFirst;
3812 private CheckboxMenuItem showAutoLast;
3814 private SplitFrame splitFrame;
3817 * Attach the alignFrame panels after embedding menus, if necessary. This used
3818 * to be called setEmbedded, but is now creates the dropdown menus in a
3819 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3821 * @param reallyEmbedded
3822 * true to attach the view to the applet area on the page rather than
3825 public void createAlignFrameWindow(boolean reallyEmbedded)
3829 embedAlignFrameInApplet(viewport.applet);
3834 // test and embed menu bar if necessary.
3836 if (embedMenuIfNeeded(alignPanel))
3839 * adjust for status bar height too. ? pointless as overridden by layout
3842 alignPanel.setSize(getSize().width,
3843 getSize().height - statusBar.getHeight());
3845 add(statusBar, BorderLayout.SOUTH);
3846 add(alignPanel, BorderLayout.CENTER);
3847 // and register with the applet so it can pass external API calls to us
3848 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3854 * Add the components of this AlignFrame to the applet container.
3858 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3861 // Explicitly build the embedded menu panel for the on-page applet
3863 // view cannot be closed if its actually on the page
3864 fileMenu.remove(closeMenuItem);
3865 fileMenu.remove(3); // Remove Separator
3866 // construct embedded menu, using default font
3867 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3868 // and actually add the components to the applet area
3869 theApplet.setLayout(new BorderLayout());
3870 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3871 theApplet.add(statusBar, BorderLayout.SOUTH);
3872 // TODO should size be left to the layout manager?
3873 alignPanel.setSize(theApplet.getSize().width,
3874 theApplet.getSize().height - embeddedMenu.getHeight()
3875 - statusBar.getHeight());
3876 theApplet.add(alignPanel, BorderLayout.CENTER);
3877 final AlignFrame me = this;
3878 theApplet.addFocusListener(new FocusListener()
3882 public void focusLost(FocusEvent e)
3884 if (theApplet.currentAlignFrame == me)
3886 theApplet.currentAlignFrame = null;
3891 public void focusGained(FocusEvent e)
3893 theApplet.currentAlignFrame = me;
3896 theApplet.validate();
3900 * create a new binding between structures in an existing jmol viewer instance
3901 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3902 * this does not open a new Jmol window, or modify the display of the
3903 * structures in the original jmol window. Note This method doesn't work
3904 * without an additional javascript library to exchange messages between the
3905 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3908 * JmolViewer instance
3909 * @param sequenceIds
3910 * - sequence Ids to search for associations
3912 public SequenceStructureBinding addStructureViewInstance(
3913 Object jmolviewer, String[] sequenceIds)
3915 Viewer viewer = null;
3918 viewer = (Viewer) jmolviewer;
3919 } catch (ClassCastException ex)
3921 System.err.println("Unsupported viewer object :"
3922 + jmolviewer.getClass());
3926 System.err.println("Can't use this object as a structure viewer:"
3927 + jmolviewer.getClass());
3930 SequenceI[] seqs = null;
3931 if (sequenceIds == null || sequenceIds.length == 0)
3933 seqs = viewport.getAlignment().getSequencesArray();
3937 Vector sqi = new Vector();
3938 AlignmentI al = viewport.getAlignment();
3939 for (int sid = 0; sid < sequenceIds.length; sid++)
3941 SequenceI sq = al.findName(sequenceIds[sid]);
3949 seqs = new SequenceI[sqi.size()];
3950 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3952 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3960 AAStructureBindingModel jmv = null;
3961 // TODO: search for a jmv that involves viewer
3963 { // create a new viewer/jalview binding.
3964 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3971 * bind a pdb file to a sequence in the current view
3974 * - sequenceId within the dataset.
3975 * @param pdbEntryString
3976 * - the short name for the PDB file
3978 * - pdb file - either a URL or a valid PDB file.
3979 * @return true if binding was as success TODO: consider making an exception
3980 * structure for indicating when PDB parsing or sequenceId location
3983 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3986 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3987 boolean needtoadd = false;
3988 if (toaddpdb != null)
3990 Vector pdbe = toaddpdb.getAllPDBEntries();
3991 PDBEntry pdbentry = null;
3992 if (pdbe != null && pdbe.size() > 0)
3994 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3996 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3997 if (!pdbentry.getId().equals(pdbEntryString)
3998 && !pdbentry.getFile().equals(pdbFile))
4008 if (pdbentry == null)
4010 pdbentry = new PDBEntry();
4011 pdbentry.setId(pdbEntryString);
4012 pdbentry.setFile(pdbFile);
4013 needtoadd = true; // add this new entry to sequence.
4015 // resolve data source
4016 // TODO: this code should be a refactored to an io package
4017 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4018 if (protocol == null)
4024 // make a note of the access mode and add
4025 if (pdbentry.getProperty() == null)
4027 pdbentry.setProperty(new Hashtable());
4029 pdbentry.getProperty().put("protocol", protocol);
4030 toaddpdb.addPDBId(pdbentry);
4031 alignPanel.getStructureSelectionManager()
4032 .registerPDBEntry(pdbentry);
4038 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4042 Vector sequences = new Vector();
4043 for (int i = 0; i < seqs.length; i++)
4045 if (seqs[i] != null)
4047 sequences.addElement(new Object[] { seqs[i],
4048 (chains != null) ? chains[i] : null });
4051 seqs = new SequenceI[sequences.size()];
4052 chains = new String[sequences.size()];
4053 for (int i = 0, isize = sequences.size(); i < isize; i++)
4055 Object[] oj = (Object[]) sequences.elementAt(i);
4057 seqs[i] = (SequenceI) oj[0];
4058 chains[i] = (String) oj[1];
4061 return new Object[] { seqs, chains };
4065 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4066 SequenceI[] seqs, String[] chains, String protocol)
4068 // Scrub any null sequences from the array
4069 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4070 seqs = (SequenceI[]) sqch[0];
4071 chains = (String[]) sqch[1];
4072 if (seqs == null || seqs.length == 0)
4075 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4077 if (protocol == null || protocol.trim().length() == 0
4078 || protocol.equals("null"))
4080 protocol = (String) pdb.getProperty().get("protocol");
4081 if (protocol == null)
4083 System.err.println("Couldn't work out protocol to open structure: "
4088 if (applet.useXtrnalSviewer)
4090 // register the association(s) and quit, don't create any windows.
4091 if (StructureSelectionManager.getStructureSelectionManager(applet)
4092 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4094 System.err.println("Failed to map " + pdb.getFile() + " ("
4095 + protocol + ") to any sequences");
4099 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4101 // can only do alignments with Jmol
4102 // find the last jmol window assigned to this alignment
4103 jalview.appletgui.AppletJmol ajm = null, tajm;
4104 Vector jmols = applet
4105 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4106 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4108 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4109 if (tajm.ap.alignFrame == this)
4118 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4119 // try and add the pdb structure
4124 // otherwise, create a new window
4125 if (applet.jmolAvailable)
4127 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4129 applet.lastFrameX += 40;
4130 applet.lastFrameY += 40;
4134 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4139 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4140 SequenceI[][] seqs, String[][] chains, String[] protocols)
4142 // TODO Auto-generated method stub
4143 System.err.println("Aligned Structure View: Not yet implemented.");
4147 * modify the current selection, providing the user has not made a selection
4151 * - sequences from this alignment
4153 * - columns to be selected on the alignment
4155 public void select(SequenceGroup sel, ColumnSelection csel)
4157 alignPanel.seqPanel.selection(sel, csel, null);
4160 public void scrollTo(int row, int column)
4162 alignPanel.seqPanel.scrollTo(row, column);
4165 public void scrollToRow(int row)
4167 alignPanel.seqPanel.scrollToRow(row);
4170 public void scrollToColumn(int column)
4172 alignPanel.seqPanel.scrollToColumn(column);
4176 * @return the alignments unique ID.
4178 public String getSequenceSetId()
4180 return viewport.getSequenceSetId();
4184 * Load the (T-Coffee) score file from the specified url
4187 * File/URL/T-COFFEE score file contents
4188 * @throws IOException
4189 * @return true if alignment was annotated with data from source
4191 public boolean loadScoreFile(String source) throws IOException
4194 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4195 AppletFormatAdapter.checkProtocol(source));
4196 if (!file.isValid())
4198 // TODO: raise dialog for gui
4199 System.err.println("Problems parsing T-Coffee scores: "
4200 + file.getWarningMessage());
4201 System.err.println("Origin was:\n" + source);
4206 * check that the score matrix matches the alignment dimensions
4209 if ((aln = viewport.getAlignment()) != null
4210 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4213 // TODO: raise a dialog box here rather than bomb out.
4215 .println("The scores matrix does not match the alignment dimensions");
4219 // TODO add parameter to indicate if matching should be done
4220 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4222 alignPanel.fontChanged();
4223 tcoffeeColour.setEnabled(true);
4224 // switch to this color
4225 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4230 System.err.println("Problems resolving T-Coffee scores:");
4231 if (file.getWarningMessage() != null)
4233 System.err.println(file.getWarningMessage());
4239 public SplitFrame getSplitFrame()
4241 return this.splitFrame;
4244 public void setSplitFrame(SplitFrame sf)
4246 this.splitFrame = sf;
4249 // may not need this
4251 public void setShowSeqFeatures(boolean b)
4253 // showSeqFeatures.setSelected(b);
4254 viewport.setShowSequenceFeatures(b);
4259 public void setMenusForViewport()
4261 // setMenusFromViewport(viewport);
4266 public void refreshFeatureUI(boolean enableIfNecessary)
4268 if (enableIfNecessary)
4270 sequenceFeatures.setState(true);
4271 alignPanel.av.setShowSequenceFeatures(true);
4276 public FeatureSettingsControllerI getFeatureSettingsUI()
4278 return alignPanel.av.featureSettings;