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.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.AlignmentOrder;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Sequence;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.io.AnnotationFile;
50 import jalview.io.AppletFormatAdapter;
51 import jalview.io.FeaturesFile;
52 import jalview.io.TCoffeeScoreFile;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.ClustalxColourScheme;
56 import jalview.schemes.ColourSchemeI;
57 import jalview.schemes.HelixColourScheme;
58 import jalview.schemes.HydrophobicColourScheme;
59 import jalview.schemes.NucleotideColourScheme;
60 import jalview.schemes.PIDColourScheme;
61 import jalview.schemes.PurinePyrimidineColourScheme;
62 import jalview.schemes.RNAHelicesColourChooser;
63 import jalview.schemes.StrandColourScheme;
64 import jalview.schemes.TCoffeeColourScheme;
65 import jalview.schemes.TaylorColourScheme;
66 import jalview.schemes.TurnColourScheme;
67 import jalview.schemes.ZappoColourScheme;
68 import jalview.structure.StructureSelectionManager;
69 import jalview.structures.models.AAStructureBindingModel;
70 import jalview.util.MappingUtils;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
74 import java.awt.BorderLayout;
75 import java.awt.Canvas;
76 import java.awt.CheckboxMenuItem;
77 import java.awt.Color;
79 import java.awt.FontMetrics;
80 import java.awt.Frame;
81 import java.awt.Graphics;
82 import java.awt.Label;
84 import java.awt.MenuBar;
85 import java.awt.MenuItem;
86 import java.awt.event.ActionEvent;
87 import java.awt.event.ActionListener;
88 import java.awt.event.FocusEvent;
89 import java.awt.event.FocusListener;
90 import java.awt.event.ItemEvent;
91 import java.awt.event.ItemListener;
92 import java.awt.event.KeyEvent;
93 import java.awt.event.KeyListener;
94 import java.awt.event.WindowAdapter;
95 import java.awt.event.WindowEvent;
96 import java.io.IOException;
98 import java.net.URLEncoder;
99 import java.util.Arrays;
100 import java.util.Deque;
101 import java.util.HashMap;
102 import java.util.Hashtable;
103 import java.util.List;
104 import java.util.Map;
105 import java.util.StringTokenizer;
106 import java.util.Vector;
108 import javax.swing.JOptionPane;
110 import org.jmol.viewer.Viewer;
112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
113 ItemListener, KeyListener, AlignViewControllerGuiI
115 public AlignViewControllerI avc;
117 public AlignmentPanel alignPanel;
119 public AlignViewport viewport;
121 // width and height may be overridden by applet parameters
122 int frameWidth = 700;
124 int frameHeight = 500;
126 String jalviewServletURL;
129 * Flag for showing autocalculated consensus above or below other consensus
132 private boolean showAutoCalculatedAbove;
134 private SequenceAnnotationOrder annotationSortOrder;
137 * Constructor that creates the frame and adds it to the display.
144 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
147 this(al, applet, title, embedded, true);
151 * Constructor that optionally allows the frame to be displayed or only
158 * @param addToDisplay
160 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
161 boolean embedded, boolean addToDisplay)
163 this(al, null, null, applet, title, embedded, addToDisplay);
166 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
167 ColumnSelection columnSelection, JalviewLite applet,
168 String title, boolean embedded)
170 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
173 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
174 ColumnSelection columnSelection, JalviewLite applet,
175 String title, boolean embedded, boolean addToDisplay)
179 jalviewServletURL = applet.getParameter("APPLICATION_URL");
185 } catch (Exception ex)
187 ex.printStackTrace();
189 // need to get window geometry before we calculate alignment layout
195 param = applet.getParameter("windowWidth");
198 int width = Integer.parseInt(param);
201 param = applet.getParameter("windowHeight");
204 int height = Integer.parseInt(param);
205 frameHeight = height;
207 } catch (Exception ex)
211 viewport = new AlignViewport(al, applet);
213 if (hiddenSeqs != null && hiddenSeqs.length > 0)
215 viewport.hideSequence(hiddenSeqs);
217 if (columnSelection != null)
219 viewport.setColumnSelection(columnSelection);
222 alignPanel = new AlignmentPanel(this, viewport);
223 avc = new jalview.controller.AlignViewController(this, viewport,
225 viewport.updateConservation(alignPanel);
226 viewport.updateConsensus(alignPanel);
228 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
229 followMouseOverFlag.setState(viewport.isFollowHighlight());
230 showGroupConsensus.setState(viewport.isShowGroupConsensus());
231 showGroupConservation.setState(viewport.isShowGroupConservation());
232 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
233 showSequenceLogo.setState(viewport.isShowSequenceLogo());
234 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
235 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
236 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
237 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
238 showSequenceAnnotations.setState(viewport.isShowAnnotation());
240 seqLimits.setState(viewport.getShowJVSuffix());
244 String param = applet.getParameter("sortBy");
247 if (param.equalsIgnoreCase("Id"))
249 sortIDMenuItem_actionPerformed();
251 else if (param.equalsIgnoreCase("Pairwise Identity"))
253 sortPairwiseMenuItem_actionPerformed();
255 else if (param.equalsIgnoreCase("Length"))
257 sortLengthMenuItem_actionPerformed();
261 param = applet.getParameter("wrap");
264 if (param.equalsIgnoreCase("true"))
266 wrapMenuItem.setState(true);
267 wrapMenuItem_actionPerformed();
270 param = applet.getParameter("centrecolumnlabels");
273 centreColumnLabelFlag.setState(true);
274 centreColumnLabelFlag_stateChanged();
278 if (viewport.getAlignment().isNucleotide())
280 viewport.updateStrucConsensus(alignPanel);
281 if (viewport.getAlignment().hasRNAStructure())
283 RNAHelixColour.setEnabled(true);
287 RNAHelixColour.setEnabled(false);
292 RNAHelixColour.setEnabled(false);
293 purinePyrimidineColour.setEnabled(false);
295 // Some JVMS send keyevents to Top frame or lowest panel,
296 // Havent worked out why yet. So add to both this frame and seqCanvas for
298 this.addKeyListener(this);
299 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
300 alignPanel.idPanel.idCanvas.addKeyListener(this);
301 alignPanel.scalePanel.addKeyListener(this);
302 alignPanel.annotationPanel.addKeyListener(this);
303 alignPanel.annotationPanelHolder.addKeyListener(this);
304 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
305 alignPanel.alabels.addKeyListener(this);
307 setAnnotationsVisibility();
311 addToDisplay(embedded);
318 public void addToDisplay(boolean embedded)
320 createAlignFrameWindow(embedded);
322 alignPanel.adjustAnnotationHeight();
323 alignPanel.paintAlignment(true);
326 public AlignViewport getAlignViewport()
331 public SeqCanvas getSeqcanvas()
333 return alignPanel.seqPanel.seqCanvas;
337 * Load a features file onto the alignment
340 * file URL, content, or other resolvable path
342 * is protocol for accessing data referred to by file
345 public boolean parseFeaturesFile(String file, String type)
347 return parseFeaturesFile(file, type, true);
351 * Load a features file onto the alignment
354 * file URL, content, or other resolvable path
356 * is protocol for accessing data referred to by file
357 * @param autoenabledisplay
358 * when true, display features flag will be automatically enabled if
359 * features are loaded
360 * @return true if data parsed as a features file
362 public boolean parseFeaturesFile(String file, String type,
363 boolean autoenabledisplay)
365 // TODO: test if importing a features file onto an alignment which already
366 // has features with links overwrites the original links.
368 Hashtable featureLinks = new Hashtable();
369 boolean featuresFile = false;
372 featuresFile = new jalview.io.FeaturesFile(file, type).parse(viewport
373 .getAlignment(), alignPanel.seqPanel.seqCanvas
374 .getFeatureRenderer().getFeatureColours(), featureLinks,
375 true, viewport.applet.getDefaultParameter("relaxedidmatch",
377 } catch (Exception ex)
379 ex.printStackTrace();
384 if (featureLinks.size() > 0)
386 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
388 if (autoenabledisplay)
390 viewport.setShowSequenceFeatures(true);
391 sequenceFeatures.setState(true);
393 if (alignPanel.seqPanel.seqCanvas.fr != null)
395 // update the min/max ranges where necessary
396 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
398 if (viewport.featureSettings != null)
400 viewport.featureSettings.refreshTable();
402 alignPanel.paintAlignment(true);
403 statusBar.setText(MessageManager
404 .getString("label.successfully_added_features_alignment"));
410 public void keyPressed(KeyEvent evt)
412 if (viewport.cursorMode
413 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
414 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
415 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
416 && Character.isDigit(evt.getKeyChar()))
418 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
421 switch (evt.getKeyCode())
423 case 27: // escape key
424 deselectAllSequenceMenuItem_actionPerformed();
426 alignPanel.alabels.cancelDrag();
429 if (evt.isControlDown() || evt.isMetaDown())
431 cut_actionPerformed();
435 if (viewport.cursorMode && !evt.isControlDown())
437 alignPanel.seqPanel.setCursorColumn();
439 if (evt.isControlDown() || evt.isMetaDown())
441 copy_actionPerformed();
445 if (evt.isControlDown())
447 paste(evt.isShiftDown());
451 if (evt.isControlDown() || evt.isMetaDown())
453 selectAllSequenceMenuItem_actionPerformed();
456 case KeyEvent.VK_DOWN:
457 if (viewport.cursorMode)
459 alignPanel.seqPanel.moveCursor(0, 1);
463 moveSelectedSequences(false);
468 if (viewport.cursorMode)
470 alignPanel.seqPanel.moveCursor(0, -1);
474 moveSelectedSequences(true);
478 case KeyEvent.VK_LEFT:
479 if (evt.isAltDown() || !viewport.cursorMode)
481 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
485 alignPanel.seqPanel.moveCursor(-1, 0);
489 case KeyEvent.VK_RIGHT:
490 if (evt.isAltDown() || !viewport.cursorMode)
492 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
496 alignPanel.seqPanel.moveCursor(1, 0);
500 case KeyEvent.VK_SPACE:
501 if (viewport.cursorMode)
503 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
504 || evt.isShiftDown() || evt.isAltDown());
508 case KeyEvent.VK_DELETE:
509 case KeyEvent.VK_BACK_SPACE:
510 if (viewport.cursorMode)
512 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
513 || evt.isShiftDown() || evt.isAltDown());
517 cut_actionPerformed();
518 alignPanel.seqPanel.seqCanvas.repaint();
523 if (viewport.cursorMode)
525 alignPanel.seqPanel.setCursorRow();
529 if (viewport.cursorMode)
531 alignPanel.seqPanel.setCursorPosition();
535 case KeyEvent.VK_ENTER:
536 case KeyEvent.VK_COMMA:
537 if (viewport.cursorMode)
539 alignPanel.seqPanel.setCursorRowAndColumn();
544 if (viewport.cursorMode)
546 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
550 if (viewport.cursorMode)
552 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
557 viewport.cursorMode = !viewport.cursorMode;
558 statusBar.setText(MessageManager.formatMessage(
559 "label.keyboard_editing_mode",
560 new String[] { (viewport.cursorMode ? "on" : "off") }));
561 if (viewport.cursorMode)
563 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
564 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
569 if (evt.isControlDown())
571 findMenuItem_actionPerformed();
577 boolean toggleSeqs = !evt.isControlDown();
578 boolean toggleCols = !evt.isShiftDown();
579 toggleHiddenRegions(toggleSeqs, toggleCols);
583 case KeyEvent.VK_PAGE_UP:
584 if (viewport.getWrapAlignment())
586 alignPanel.scrollUp(true);
590 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
591 - viewport.endSeq + viewport.startSeq);
595 case KeyEvent.VK_PAGE_DOWN:
596 if (viewport.getWrapAlignment())
598 alignPanel.scrollUp(false);
602 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
603 + viewport.endSeq - viewport.startSeq);
608 if (evt.isControlDown())
610 undoMenuItem_actionPerformed();
615 if (evt.isControlDown())
617 redoMenuItem_actionPerformed();
622 if (evt.isControlDown())
629 if (evt.isControlDown())
631 trimAlignment(false);
636 if (evt.isControlDown())
638 if (evt.isShiftDown())
640 this.removeAllGapsMenuItem_actionPerformed();
644 removeGappedColumnMenuItem_actionPerformed();
649 if (evt.isControlDown())
653 invertColSel_actionPerformed();
657 invertSequenceMenuItem_actionPerformed();
663 if (evt.isControlDown())
665 if (evt.isShiftDown())
667 this.unGroup_actionPerformed();
671 this.createGroup_actionPerformed();
677 if (evt.isControlDown())
679 this.deleteGroups_actionPerformed();
684 if (evt.isControlDown())
691 alignPanel.paintAlignment(true);
695 * called by key handler and the hide all/show all menu items
700 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
702 boolean hide = false;
703 SequenceGroup sg = viewport.getSelectionGroup();
704 if (!toggleSeqs && !toggleCols)
706 // Hide everything by the current selection - this is a hack - we do the
707 // invert and then hide
708 // first check that there will be visible columns after the invert.
709 if ((viewport.getColumnSelection() != null
710 && viewport.getColumnSelection().getSelected() != null && viewport
711 .getColumnSelection().getSelected().size() > 0)
712 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
715 // now invert the sequence set, if required - empty selection implies
716 // that no hiding is required.
719 invertSequenceMenuItem_actionPerformed();
720 sg = viewport.getSelectionGroup();
724 viewport.expandColSelection(sg, true);
725 // finally invert the column selection and get the new sequence
726 // selection and indicate it should be hidden.
727 invertColSel_actionPerformed();
734 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
737 viewport.hideAllSelectedSeqs();
739 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
742 viewport.showAllHiddenSeqs();
748 if (viewport.getColumnSelection().getSelected().size() > 0)
750 viewport.hideSelectedColumns();
753 viewport.setSelectionGroup(sg);
758 viewport.showAllHiddenColumns();
764 public void keyReleased(KeyEvent evt)
769 public void keyTyped(KeyEvent evt)
774 public void itemStateChanged(ItemEvent evt)
776 final Object source = evt.getSource();
777 if (source == displayNonconservedMenuItem)
779 displayNonconservedMenuItem_actionPerformed();
781 else if (source == colourTextMenuItem)
783 colourTextMenuItem_actionPerformed();
785 else if (source == wrapMenuItem)
787 wrapMenuItem_actionPerformed();
789 else if (source == scaleAbove)
791 viewport.setScaleAboveWrapped(scaleAbove.getState());
793 else if (source == scaleLeft)
795 viewport.setScaleLeftWrapped(scaleLeft.getState());
797 else if (source == scaleRight)
799 viewport.setScaleRightWrapped(scaleRight.getState());
801 else if (source == seqLimits)
803 seqLimits_itemStateChanged();
805 else if (source == viewBoxesMenuItem)
807 viewport.setShowBoxes(viewBoxesMenuItem.getState());
809 else if (source == viewTextMenuItem)
811 viewport.setShowText(viewTextMenuItem.getState());
813 else if (source == renderGapsMenuItem)
815 viewport.setRenderGaps(renderGapsMenuItem.getState());
817 else if (source == annotationPanelMenuItem)
819 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
820 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
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 for (AlignmentAnnotation aa : alignPanel.getAlignment()
929 .getAlignmentAnnotation())
931 boolean visible = (aa.sequenceRef == null ? showForAlignment
933 aa.visible = visible;
935 alignPanel.validateAnnotationDimensions(true);
940 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
942 this.annotationSortOrder = order;
946 * Set flags on the viewport that control annotation ordering
948 private void setViewportAnnotationOrder()
950 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
952 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
955 private void setShowAutoCalculatedAbove(boolean showAbove)
957 this.showAutoCalculatedAbove = showAbove;
960 private void mouseOverFlag_stateChanged()
962 viewport.setFollowHighlight(followMouseOverFlag.getState());
963 // TODO: could kick the scrollTo mechanism to reset view for current
967 private void centreColumnLabelFlag_stateChanged()
969 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
970 this.alignPanel.annotationPanel.repaint();
974 public void actionPerformed(ActionEvent evt)
976 viewport.applet.currentAlignFrame = this;
978 Object source = evt.getSource();
980 if (source == inputText)
982 inputText_actionPerformed();
984 else if (source == loadTree)
986 loadTree_actionPerformed();
988 else if (source == loadApplication)
990 launchFullApplication();
992 else if (source == loadAnnotations)
996 else if (source == outputAnnotations)
998 outputAnnotations(true);
1000 else if (source == outputFeatures)
1002 outputFeatures(true, "Jalview");
1004 else if (source == closeMenuItem)
1006 closeMenuItem_actionPerformed();
1008 else if (source == copy)
1010 copy_actionPerformed();
1012 else if (source == undoMenuItem)
1014 undoMenuItem_actionPerformed();
1016 else if (source == redoMenuItem)
1018 redoMenuItem_actionPerformed();
1020 else if (source == inputText)
1022 inputText_actionPerformed();
1024 else if (source == closeMenuItem)
1026 closeMenuItem_actionPerformed();
1028 else if (source == undoMenuItem)
1030 undoMenuItem_actionPerformed();
1032 else if (source == redoMenuItem)
1034 redoMenuItem_actionPerformed();
1036 else if (source == copy)
1038 copy_actionPerformed();
1040 else if (source == pasteNew)
1042 pasteNew_actionPerformed();
1044 else if (source == pasteThis)
1046 pasteThis_actionPerformed();
1048 else if (source == cut)
1050 cut_actionPerformed();
1052 else if (source == delete)
1054 delete_actionPerformed();
1056 else if (source == grpsFromSelection)
1058 makeGrpsFromSelection_actionPerformed();
1060 else if (source == deleteGroups)
1062 deleteGroups_actionPerformed();
1064 else if (source == selectAllSequenceMenuItem)
1066 selectAllSequenceMenuItem_actionPerformed();
1068 else if (source == deselectAllSequenceMenuItem)
1070 deselectAllSequenceMenuItem_actionPerformed();
1072 else if (source == invertSequenceMenuItem)
1074 invertSequenceMenuItem_actionPerformed();
1076 else if (source == invertColSel)
1078 viewport.invertColumnSelection();
1079 alignPanel.paintAlignment(true);
1081 else if (source == remove2LeftMenuItem)
1083 trimAlignment(true);
1085 else if (source == remove2RightMenuItem)
1087 trimAlignment(false);
1089 else if (source == removeGappedColumnMenuItem)
1091 removeGappedColumnMenuItem_actionPerformed();
1093 else if (source == removeAllGapsMenuItem)
1095 removeAllGapsMenuItem_actionPerformed();
1097 else if (source == findMenuItem)
1099 findMenuItem_actionPerformed();
1101 else if (source == font)
1103 new FontChooser(alignPanel);
1105 else if (source == newView)
1109 else if (source == showColumns)
1111 viewport.showAllHiddenColumns();
1112 alignPanel.paintAlignment(true);
1114 else if (source == showSeqs)
1116 viewport.showAllHiddenSeqs();
1117 alignPanel.paintAlignment(true);
1119 else if (source == hideColumns)
1121 viewport.hideSelectedColumns();
1122 alignPanel.paintAlignment(true);
1124 else if (source == hideSequences
1125 && viewport.getSelectionGroup() != null)
1127 viewport.hideAllSelectedSeqs();
1128 alignPanel.paintAlignment(true);
1130 else if (source == hideAllButSelection)
1132 toggleHiddenRegions(false, false);
1133 alignPanel.paintAlignment(true);
1135 else if (source == hideAllSelection)
1137 SequenceGroup sg = viewport.getSelectionGroup();
1138 viewport.expandColSelection(sg, false);
1139 viewport.hideAllSelectedSeqs();
1140 viewport.hideSelectedColumns();
1141 alignPanel.paintAlignment(true);
1143 else if (source == showAllHidden)
1145 viewport.showAllHiddenColumns();
1146 viewport.showAllHiddenSeqs();
1147 alignPanel.paintAlignment(true);
1149 else if (source == showGroupConsensus)
1151 showGroupConsensus_actionPerformed();
1153 else if (source == showGroupConservation)
1155 showGroupConservation_actionPerformed();
1157 else if (source == showSequenceLogo)
1159 showSequenceLogo_actionPerformed();
1161 else if (source == normSequenceLogo)
1163 normSequenceLogo_actionPerformed();
1165 else if (source == showConsensusHistogram)
1167 showConsensusHistogram_actionPerformed();
1169 else if (source == applyAutoAnnotationSettings)
1171 applyAutoAnnotationSettings_actionPerformed();
1173 else if (source == featureSettings)
1175 new FeatureSettings(alignPanel);
1177 else if (source == alProperties)
1179 StringBuffer contents = new jalview.io.AlignmentProperties(
1180 viewport.getAlignment()).formatAsString();
1181 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1182 cap.setText(contents.toString());
1183 Frame frame = new Frame();
1185 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1186 "label.alignment_properties", new String[] { getTitle() }),
1189 else if (source == overviewMenuItem)
1191 overviewMenuItem_actionPerformed();
1193 else if (source == noColourmenuItem)
1197 else if (source == clustalColour)
1199 abovePIDThreshold.setState(false);
1200 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1202 else if (source == zappoColour)
1204 changeColour(new ZappoColourScheme());
1206 else if (source == taylorColour)
1208 changeColour(new TaylorColourScheme());
1210 else if (source == hydrophobicityColour)
1212 changeColour(new HydrophobicColourScheme());
1214 else if (source == helixColour)
1216 changeColour(new HelixColourScheme());
1218 else if (source == strandColour)
1220 changeColour(new StrandColourScheme());
1222 else if (source == turnColour)
1224 changeColour(new TurnColourScheme());
1226 else if (source == buriedColour)
1228 changeColour(new BuriedColourScheme());
1230 else if (source == nucleotideColour)
1232 changeColour(new NucleotideColourScheme());
1234 else if (source == purinePyrimidineColour)
1236 changeColour(new PurinePyrimidineColourScheme());
1238 // else if (source == RNAInteractionColour)
1240 // changeColour(new RNAInteractionColourScheme());
1242 else if (source == RNAHelixColour)
1244 new RNAHelicesColourChooser(viewport, alignPanel);
1246 else if (source == modifyPID)
1248 modifyPID_actionPerformed();
1250 else if (source == modifyConservation)
1252 modifyConservation_actionPerformed();
1254 else if (source == userDefinedColour)
1256 new UserDefinedColours(alignPanel, null);
1258 else if (source == PIDColour)
1260 changeColour(new PIDColourScheme());
1262 else if (source == BLOSUM62Colour)
1264 changeColour(new Blosum62ColourScheme());
1266 else if (source == tcoffeeColour)
1268 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1270 else if (source == annotationColour)
1272 new AnnotationColourChooser(viewport, alignPanel);
1274 else if (source == annotationColumnSelection)
1276 new AnnotationColumnChooser(viewport, alignPanel);
1278 else if (source == sortPairwiseMenuItem)
1280 sortPairwiseMenuItem_actionPerformed();
1282 else if (source == sortIDMenuItem)
1284 sortIDMenuItem_actionPerformed();
1286 else if (source == sortLengthMenuItem)
1288 sortLengthMenuItem_actionPerformed();
1290 else if (source == sortGroupMenuItem)
1292 sortGroupMenuItem_actionPerformed();
1294 else if (source == removeRedundancyMenuItem)
1296 removeRedundancyMenuItem_actionPerformed();
1298 else if (source == pairwiseAlignmentMenuItem)
1300 pairwiseAlignmentMenuItem_actionPerformed();
1302 else if (source == PCAMenuItem)
1304 PCAMenuItem_actionPerformed();
1306 else if (source == averageDistanceTreeMenuItem)
1308 averageDistanceTreeMenuItem_actionPerformed();
1310 else if (source == neighbourTreeMenuItem)
1312 neighbourTreeMenuItem_actionPerformed();
1314 else if (source == njTreeBlosumMenuItem)
1316 njTreeBlosumMenuItem_actionPerformed();
1318 else if (source == avDistanceTreeBlosumMenuItem)
1320 avTreeBlosumMenuItem_actionPerformed();
1322 else if (source == documentation)
1324 documentation_actionPerformed();
1326 else if (source == about)
1328 about_actionPerformed();
1333 public void inputText_actionPerformed()
1335 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1336 Frame frame = new Frame();
1338 jalview.bin.JalviewLite.addFrame(frame,
1339 MessageManager.getString("label.input_cut_paste"), 500, 500);
1342 protected void outputText_actionPerformed(ActionEvent e)
1344 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1345 Frame frame = new Frame();
1347 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1348 "label.alignment_output_command",
1349 new Object[] { e.getActionCommand() }), 600, 500);
1351 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1352 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1353 e.getActionCommand(), viewport.getAlignment(),
1354 viewport.getShowJVSuffix()));
1357 public void loadAnnotations()
1359 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1360 cap.setText(MessageManager
1361 .getString("label.paste_features_annotations_Tcoffee_here"));
1362 cap.setAnnotationImport();
1363 Frame frame = new Frame();
1365 jalview.bin.JalviewLite.addFrame(frame,
1366 MessageManager.getString("action.paste_annotations"), 400, 300);
1370 public String outputAnnotations(boolean displayTextbox)
1372 String annotation = new AnnotationFile()
1373 .printAnnotationsForView(viewport);
1377 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1378 Frame frame = new Frame();
1380 jalview.bin.JalviewLite.addFrame(frame,
1381 MessageManager.getString("label.annotations"), 600, 500);
1382 cap.setText(annotation);
1388 private Map<String, Object> getDisplayedFeatureCols()
1390 if (alignPanel.getFeatureRenderer() != null
1391 && viewport.getFeaturesDisplayed() != null)
1393 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1399 public String outputFeatures(boolean displayTextbox, String format)
1402 if (format.equalsIgnoreCase("Jalview"))
1404 features = new FeaturesFile().printJalviewFormat(viewport
1405 .getAlignment().getSequencesArray(),
1406 getDisplayedFeatureCols());
1410 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1411 .getSequencesArray(), getDisplayedFeatureCols());
1416 boolean frimport = false;
1417 if (features == null || features.equals("No Features Visible"))
1419 features = "# No features visible - paste some and import them here.";
1423 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1426 cap.setAnnotationImport();
1428 Frame frame = new Frame();
1430 jalview.bin.JalviewLite.addFrame(frame,
1431 MessageManager.getString("label.features"), 600, 500);
1432 cap.setText(features);
1436 if (features == null)
1445 void launchFullApplication()
1447 StringBuffer url = new StringBuffer(jalviewServletURL);
1449 // allow servlet parameters to be passed in applet parameter
1450 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1452 url.append(firstSep);
1455 + appendProtocol(viewport.applet.getParameter("file")));
1457 if (viewport.applet.getParameter("features") != null)
1459 url.append("&features=");
1460 url.append(appendProtocol(viewport.applet.getParameter("features")));
1463 if (viewport.applet.getParameter("annotations") != null)
1465 url.append("&annotations=");
1466 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1469 if (viewport.applet.getParameter("jnetfile") != null)
1471 url.append("&annotations=");
1472 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1475 if (viewport.applet.getParameter("defaultColour") != null)
1477 url.append("&colour="
1478 + removeWhiteSpace(viewport.applet
1479 .getParameter("defaultColour")));
1482 if (viewport.applet.getParameter("userDefinedColour") != null)
1484 url.append("&colour="
1485 + removeWhiteSpace(viewport.applet
1486 .getParameter("userDefinedColour")));
1488 if (viewport.applet.getParameter("tree") != null)
1491 + appendProtocol(viewport.applet.getParameter("tree")));
1493 if (viewport.applet.getParameter("treeFile") != null)
1496 + appendProtocol(viewport.applet.getParameter("treeFile")));
1499 showURL(url.toString(), "FULL_APP");
1502 String removeWhiteSpace(String colour)
1504 StringBuffer sb = new StringBuffer();
1505 for (int i = 0; i < colour.length(); i++)
1507 if (Character.isWhitespace(colour.charAt(i)))
1513 sb.append(colour.charAt(i));
1517 return sb.toString();
1520 String appendProtocol(String url)
1525 url = URLEncoder.encode(url);
1528 * When we finally deprecate 1.1 compatibility, we can start to use
1529 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1530 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1531 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1532 * ex.printStackTrace(); }
1534 catch (java.net.MalformedURLException ex)
1536 url = viewport.applet.getCodeBase() + url;
1541 public void closeMenuItem_actionPerformed()
1543 PaintRefresher.RemoveComponent(alignPanel);
1544 if (alignPanel.seqPanel != null
1545 && alignPanel.seqPanel.seqCanvas != null)
1547 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1549 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1551 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1554 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1569 void updateEditMenuBar()
1572 if (viewport.getHistoryList().size() > 0)
1574 undoMenuItem.setEnabled(true);
1575 CommandI command = viewport.getHistoryList().peek();
1576 undoMenuItem.setLabel(MessageManager.formatMessage(
1577 "label.undo_command",
1578 new Object[] { command.getDescription() }));
1582 undoMenuItem.setEnabled(false);
1583 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1586 if (viewport.getRedoList().size() > 0)
1588 redoMenuItem.setEnabled(true);
1590 CommandI command = viewport.getRedoList().peek();
1591 redoMenuItem.setLabel(MessageManager.formatMessage(
1592 "label.redo_command",
1593 new Object[] { command.getDescription() }));
1597 redoMenuItem.setEnabled(false);
1598 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1606 public void addHistoryItem(CommandI command)
1608 if (command.getSize() > 0)
1610 viewport.addToHistoryList(command);
1611 viewport.clearRedoList();
1612 updateEditMenuBar();
1613 viewport.updateHiddenColumns();
1618 * TODO: JAL-1104 DOCUMENT ME!
1623 protected void undoMenuItem_actionPerformed()
1625 if (viewport.getHistoryList().isEmpty())
1630 CommandI command = viewport.getHistoryList().pop();
1631 viewport.addToRedoList(command);
1632 command.undoCommand(null);
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1636 if (originalSource != viewport)
1639 .println("Warning: Viewport object mismatch whilst undoing");
1641 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1642 // viewport.getColumnSelection().getHiddenColumns()
1644 updateEditMenuBar();
1645 originalSource.firePropertyChange("alignment", null, originalSource
1646 .getAlignment().getSequences());
1650 * TODO: JAL-1104 DOCUMENT ME!
1655 protected void redoMenuItem_actionPerformed()
1657 if (viewport.getRedoList().isEmpty())
1662 CommandI command = viewport.getRedoList().pop();
1663 viewport.addToHistoryList(command);
1664 command.doCommand(null);
1666 AlignmentViewport originalSource = getOriginatingSource(command);
1668 if (originalSource != viewport)
1671 .println("Warning: Viewport object mismatch whilst re-doing");
1673 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1674 // viewport.getColumnSelection().getHiddenColumns()
1677 updateEditMenuBar();
1678 originalSource.firePropertyChange("alignment", null, originalSource
1679 .getAlignment().getSequences());
1682 AlignmentViewport getOriginatingSource(CommandI command)
1684 AlignmentViewport originalSource = null;
1685 // For sequence removal and addition, we need to fire
1686 // the property change event FROM the viewport where the
1687 // original alignment was altered
1688 AlignmentI al = null;
1689 if (command instanceof EditCommand)
1691 EditCommand editCommand = (EditCommand) command;
1692 al = editCommand.getAlignment();
1693 Vector comps = (Vector) PaintRefresher.components.get(viewport
1694 .getSequenceSetId());
1695 for (int i = 0; i < comps.size(); i++)
1697 if (comps.elementAt(i) instanceof AlignmentPanel)
1699 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1701 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1708 if (originalSource == null)
1710 // The original view is closed, we must validate
1711 // the current view against the closed view first
1714 PaintRefresher.validateSequences(al, viewport.getAlignment());
1717 originalSource = viewport;
1720 return originalSource;
1724 * Move the currently selected sequences up or down one position in the
1729 public void moveSelectedSequences(boolean up)
1731 SequenceGroup sg = viewport.getSelectionGroup();
1736 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1737 up ? null : viewport.getHiddenRepSequences(), up);
1738 alignPanel.paintAlignment(true);
1741 * Also move cDNA/protein complement sequences
1743 AlignViewportI complement = viewport.getCodingComplement();
1744 if (complement != null)
1746 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1747 viewport, complement);
1748 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1749 up ? null : complement.getHiddenRepSequences(), up);
1750 // TODO need to trigger a repaint of the complementary panel - how?
1751 // would prefer to handle in SplitFrame but it is not overriding key
1756 synchronized void slideSequences(boolean right, int size)
1758 List<SequenceI> sg = new Vector<SequenceI>();
1759 if (viewport.cursorMode)
1761 sg.add(viewport.getAlignment().getSequenceAt(
1762 alignPanel.seqPanel.seqCanvas.cursorY));
1764 else if (viewport.getSelectionGroup() != null
1765 && viewport.getSelectionGroup().getSize() != viewport
1766 .getAlignment().getHeight())
1768 sg = viewport.getSelectionGroup().getSequences(
1769 viewport.getHiddenRepSequences());
1777 Vector<SequenceI> invertGroup = new Vector();
1779 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1781 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1783 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1787 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1789 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1791 for (int i = 0; i < invertGroup.size(); i++)
1793 seqs2[i] = invertGroup.elementAt(i);
1796 SlideSequencesCommand ssc;
1799 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1800 size, viewport.getGapCharacter());
1804 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1805 size, viewport.getGapCharacter());
1808 int groupAdjustment = 0;
1809 if (ssc.getGapsInsertedBegin() && right)
1811 if (viewport.cursorMode)
1813 alignPanel.seqPanel.moveCursor(size, 0);
1817 groupAdjustment = size;
1820 else if (!ssc.getGapsInsertedBegin() && !right)
1822 if (viewport.cursorMode)
1824 alignPanel.seqPanel.moveCursor(-size, 0);
1828 groupAdjustment = -size;
1832 if (groupAdjustment != 0)
1834 viewport.getSelectionGroup().setStartRes(
1835 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1836 viewport.getSelectionGroup().setEndRes(
1837 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1840 boolean appendHistoryItem = false;
1841 Deque<CommandI> historyList = viewport.getHistoryList();
1842 if (historyList != null && historyList.size() > 0
1843 && historyList.peek() instanceof SlideSequencesCommand)
1845 appendHistoryItem = ssc
1846 .appendSlideCommand((SlideSequencesCommand) historyList
1850 if (!appendHistoryItem)
1852 addHistoryItem(ssc);
1858 static StringBuffer copiedSequences;
1860 static Vector copiedHiddenColumns;
1862 protected void copy_actionPerformed()
1864 if (viewport.getSelectionGroup() == null)
1869 SequenceGroup sg = viewport.getSelectionGroup();
1870 copiedSequences = new StringBuffer();
1871 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1872 for (int i = 0; i < sg.getSize(); i++)
1874 SequenceI seq = sg.getSequenceAt(i);
1875 int index = viewport.getAlignment().findIndex(seq);
1876 orderedSeqs.put(index, seq);
1879 int index = 0, startRes, endRes;
1882 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1884 copiedHiddenColumns = new Vector();
1885 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1886 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1888 copiedHiddenColumns.addElement(new int[] {
1889 region[0] - hiddenOffset, region[1] - hiddenOffset });
1894 copiedHiddenColumns = null;
1897 for (int i = 0; i < sg.getSize(); i++)
1899 SequenceI seq = null;
1903 if (orderedSeqs.containsKey(index))
1905 seq = orderedSeqs.get(index);
1916 // Returns residue following index if gap
1917 startRes = seq.findPosition(sg.getStartRes());
1920 // Need to find the residue preceeding index if gap
1923 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1925 ch = seq.getCharAt(j);
1926 if (!jalview.util.Comparison.isGap((ch)))
1934 endRes += seq.getStart() - 1;
1937 copiedSequences.append(seq.getName()
1943 + seq.getSequenceAsString(sg.getStartRes(),
1944 sg.getEndRes() + 1) + "\n");
1949 protected void pasteNew_actionPerformed()
1954 protected void pasteThis_actionPerformed()
1959 void paste(boolean newAlignment)
1964 if (copiedSequences == null)
1969 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1970 Vector seqs = new Vector();
1971 while (st.hasMoreElements())
1973 String name = st.nextToken();
1974 int start = Integer.parseInt(st.nextToken());
1975 int end = Integer.parseInt(st.nextToken());
1976 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1978 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1979 for (int i = 0; i < seqs.size(); i++)
1981 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1986 String newtitle = MessageManager
1987 .getString("label.copied_sequences");
1988 if (getTitle().startsWith(
1989 MessageManager.getString("label.copied_sequences")))
1991 newtitle = getTitle();
1995 newtitle = newtitle.concat(MessageManager.formatMessage(
1996 "label.from_msname", new String[] { getTitle() }));
1998 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1999 viewport.applet, newtitle, false);
2000 if (copiedHiddenColumns != null)
2002 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2004 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2005 af.viewport.hideColumns(region[0], region[1]);
2009 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2014 addSequences(newSeqs);
2017 } catch (Exception ex)
2019 } // could be anything being pasted in here
2023 void addSequences(SequenceI[] seqs)
2025 for (int i = 0; i < seqs.length; i++)
2027 viewport.getAlignment().addSequence(seqs[i]);
2031 addHistoryItem(new EditCommand(
2032 MessageManager.getString("label.add_sequences"), Action.PASTE,
2033 seqs, 0, viewport.getAlignment().getWidth(),
2034 viewport.getAlignment()));
2036 viewport.setEndSeq(viewport.getAlignment().getHeight());
2037 viewport.getAlignment().getWidth();
2038 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2043 protected void cut_actionPerformed()
2045 copy_actionPerformed();
2046 delete_actionPerformed();
2049 protected void delete_actionPerformed()
2052 SequenceGroup sg = viewport.getSelectionGroup();
2058 Vector seqs = new Vector();
2060 for (int i = 0; i < sg.getSize(); i++)
2062 seq = sg.getSequenceAt(i);
2063 seqs.addElement(seq);
2067 * If the cut affects all sequences, warn, remove highlighted columns
2068 */if (sg.getSize() == viewport.getAlignment().getHeight())
2070 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2071 .getAlignment().getWidth()) ? true : false;
2072 if (isEntireAlignWidth)
2074 int confirm = JOptionPane.showConfirmDialog(this,
2075 MessageManager.getString("warn.delete_all"), // $NON-NLS-1$
2076 MessageManager.getString("label.delete_all"), // $NON-NLS-1$
2077 JOptionPane.OK_CANCEL_OPTION);
2079 if (confirm == JOptionPane.CANCEL_OPTION
2080 || confirm == JOptionPane.CLOSED_OPTION)
2085 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2086 sg.getEndRes() + 1);
2089 SequenceI[] cut = new SequenceI[seqs.size()];
2090 for (int i = 0; i < seqs.size(); i++)
2092 cut[i] = (SequenceI) seqs.elementAt(i);
2096 * //ADD HISTORY ITEM
2098 addHistoryItem(new EditCommand(
2099 MessageManager.getString("label.cut_sequences"), Action.CUT,
2100 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2101 viewport.getAlignment()));
2103 viewport.setSelectionGroup(null);
2104 viewport.getAlignment().deleteGroup(sg);
2106 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2109 if (viewport.getAlignment().getHeight() < 1)
2111 this.setVisible(false);
2113 viewport.sendSelection();
2117 * group consensus toggled
2120 protected void showGroupConsensus_actionPerformed()
2122 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2123 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2128 * group conservation toggled.
2130 protected void showGroupConservation_actionPerformed()
2132 viewport.setShowGroupConservation(showGroupConservation.getState());
2133 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2140 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2141 * .event.ActionEvent)
2143 protected void showConsensusHistogram_actionPerformed()
2145 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2146 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2154 * .event.ActionEvent)
2156 protected void showSequenceLogo_actionPerformed()
2158 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2159 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2162 protected void normSequenceLogo_actionPerformed()
2164 showSequenceLogo.setState(true);
2165 viewport.setShowSequenceLogo(true);
2166 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2167 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2170 protected void applyAutoAnnotationSettings_actionPerformed()
2172 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2175 protected void makeGrpsFromSelection_actionPerformed()
2177 if (avc.makeGroupsFromSelection())
2179 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2180 alignPanel.updateAnnotation();
2181 alignPanel.paintAlignment(true);
2185 protected void createGroup_actionPerformed()
2190 protected void unGroup_actionPerformed()
2194 alignPanel.alignmentChanged();
2198 protected void deleteGroups_actionPerformed()
2200 if (avc.deleteGroups())
2202 alignPanel.alignmentChanged();
2206 public void selectAllSequenceMenuItem_actionPerformed()
2208 SequenceGroup sg = new SequenceGroup();
2209 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2211 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2213 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2214 viewport.setSelectionGroup(sg);
2215 alignPanel.paintAlignment(true);
2216 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2217 viewport.sendSelection();
2220 public void deselectAllSequenceMenuItem_actionPerformed()
2222 if (viewport.cursorMode)
2224 alignPanel.seqPanel.keyboardNo1 = null;
2225 alignPanel.seqPanel.keyboardNo2 = null;
2227 viewport.setSelectionGroup(null);
2228 viewport.getColumnSelection().clear();
2229 viewport.setSelectionGroup(null);
2230 alignPanel.idPanel.idCanvas.searchResults = null;
2231 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2232 alignPanel.paintAlignment(true);
2233 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2234 viewport.sendSelection();
2237 public void invertSequenceMenuItem_actionPerformed()
2239 SequenceGroup sg = viewport.getSelectionGroup();
2240 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2242 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2245 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2246 viewport.sendSelection();
2249 public void invertColSel_actionPerformed()
2251 viewport.invertColumnSelection();
2252 alignPanel.paintAlignment(true);
2253 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2254 viewport.sendSelection();
2257 void trimAlignment(boolean trimLeft)
2259 ColumnSelection colSel = viewport.getColumnSelection();
2262 if (colSel.size() > 0)
2266 column = colSel.getMin();
2270 column = colSel.getMax();
2274 if (viewport.getSelectionGroup() != null)
2276 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2277 viewport.getHiddenRepSequences());
2281 seqs = viewport.getAlignment().getSequencesArray();
2284 TrimRegionCommand trimRegion;
2287 trimRegion = new TrimRegionCommand("Remove Left",
2288 TrimRegionCommand.TRIM_LEFT, seqs, column,
2289 viewport.getAlignment(), viewport.getColumnSelection(),
2290 viewport.getSelectionGroup());
2291 viewport.setStartRes(0);
2295 trimRegion = new TrimRegionCommand("Remove Right",
2296 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2297 viewport.getAlignment(), viewport.getColumnSelection(),
2298 viewport.getSelectionGroup());
2301 statusBar.setText(MessageManager.formatMessage(
2302 "label.removed_columns",
2303 new String[] { Integer.valueOf(trimRegion.getSize())
2305 addHistoryItem(trimRegion);
2307 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2309 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2310 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2312 viewport.getAlignment().deleteGroup(sg);
2316 viewport.firePropertyChange("alignment", null, viewport
2317 .getAlignment().getSequences());
2321 public void removeGappedColumnMenuItem_actionPerformed()
2323 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2326 if (viewport.getSelectionGroup() != null)
2328 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2329 viewport.getHiddenRepSequences());
2330 start = viewport.getSelectionGroup().getStartRes();
2331 end = viewport.getSelectionGroup().getEndRes();
2335 seqs = viewport.getAlignment().getSequencesArray();
2338 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2339 "Remove Gapped Columns", seqs, start, end,
2340 viewport.getAlignment());
2342 addHistoryItem(removeGapCols);
2344 statusBar.setText(MessageManager.formatMessage(
2345 "label.removed_empty_columns",
2346 new String[] { Integer.valueOf(removeGapCols.getSize())
2349 // This is to maintain viewport position on first residue
2350 // of first sequence
2351 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2352 int startRes = seq.findPosition(viewport.startRes);
2353 // ShiftList shifts;
2354 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2355 // edit.alColumnChanges=shifts.getInverse();
2356 // if (viewport.hasHiddenColumns)
2357 // viewport.getColumnSelection().compensateForEdits(shifts);
2358 viewport.setStartRes(seq.findIndex(startRes) - 1);
2359 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2364 public void removeAllGapsMenuItem_actionPerformed()
2366 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2369 if (viewport.getSelectionGroup() != null)
2371 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2372 viewport.getHiddenRepSequences());
2373 start = viewport.getSelectionGroup().getStartRes();
2374 end = viewport.getSelectionGroup().getEndRes();
2378 seqs = viewport.getAlignment().getSequencesArray();
2381 // This is to maintain viewport position on first residue
2382 // of first sequence
2383 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2384 int startRes = seq.findPosition(viewport.startRes);
2386 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2387 viewport.getAlignment()));
2389 viewport.setStartRes(seq.findIndex(startRes) - 1);
2391 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2396 public void findMenuItem_actionPerformed()
2398 new Finder(alignPanel);
2402 * create a new view derived from the current view
2405 * @return frame for the new view
2407 public AlignFrame newView(String viewtitle)
2410 if (viewport.hasHiddenRows())
2412 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2413 .getFullAlignment().getSequencesArray());
2417 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2420 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2422 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2424 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2426 newal.addAnnotation(viewport.getAlignment()
2427 .getAlignmentAnnotation()[i]);
2432 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2434 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2435 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2436 PaintRefresher.Register(newaf.alignPanel,
2437 newaf.alignPanel.av.getSequenceSetId());
2439 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2440 newaf.alignPanel.av.getSequenceSetId());
2441 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2442 newaf.alignPanel.av.getSequenceSetId());
2444 Vector comps = (Vector) PaintRefresher.components.get(viewport
2445 .getSequenceSetId());
2447 for (int i = 0; i < comps.size(); i++)
2449 if (comps.elementAt(i) instanceof AlignmentPanel)
2455 String title = new String(this.getTitle());
2456 if (viewtitle != null)
2458 title = viewtitle + " ( " + title + ")";
2462 if (title.indexOf("(View") > -1)
2464 title = title.substring(0, title.indexOf("(View"));
2466 title += "(View " + viewSize + ")";
2469 newaf.setTitle(title.toString());
2471 newaf.viewport.setHistoryList(viewport.getHistoryList());
2472 newaf.viewport.setRedoList(viewport.getRedoList());
2478 * @return list of feature groups on the view
2480 public String[] getFeatureGroups()
2482 FeatureRenderer fr = null;
2483 if (alignPanel != null
2484 && (fr = alignPanel.getFeatureRenderer()) != null)
2486 List<String> gps = fr.getFeatureGroups();
2487 String[] _gps = gps.toArray(new String[gps.size()]);
2494 * get sequence feature groups that are hidden or shown
2500 public String[] getFeatureGroupsOfState(boolean visible)
2502 FeatureRenderer fr = null;
2503 if (alignPanel != null
2504 && (fr = alignPanel.getFeatureRenderer()) != null)
2506 List<String> gps = fr.getGroups(visible);
2507 String[] _gps = gps.toArray(new String[gps.size()]);
2514 * Change the display state for the given feature groups
2517 * list of group strings
2519 * visible or invisible
2521 public void setFeatureGroupState(String[] groups, boolean state)
2523 FeatureRenderer fr = null;
2524 this.sequenceFeatures.setState(true);
2525 viewport.setShowSequenceFeatures(true);
2526 if (alignPanel != null
2527 && (fr = alignPanel.getFeatureRenderer()) != null)
2530 fr.setGroupVisibility(Arrays.asList(groups), state);
2531 alignPanel.seqPanel.seqCanvas.repaint();
2532 if (alignPanel.overviewPanel != null)
2534 alignPanel.overviewPanel.updateOverviewImage();
2539 public void seqLimits_itemStateChanged()
2541 viewport.setShowJVSuffix(seqLimits.getState());
2542 alignPanel.fontChanged();
2543 alignPanel.paintAlignment(true);
2546 protected void colourTextMenuItem_actionPerformed()
2548 viewport.setColourText(colourTextMenuItem.getState());
2549 alignPanel.paintAlignment(true);
2552 protected void displayNonconservedMenuItem_actionPerformed()
2554 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2555 alignPanel.paintAlignment(true);
2558 protected void wrapMenuItem_actionPerformed()
2560 viewport.setWrapAlignment(wrapMenuItem.getState());
2561 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2562 scaleAbove.setEnabled(wrapMenuItem.getState());
2563 scaleLeft.setEnabled(wrapMenuItem.getState());
2564 scaleRight.setEnabled(wrapMenuItem.getState());
2565 alignPanel.paintAlignment(true);
2568 public void overviewMenuItem_actionPerformed()
2570 if (alignPanel.overviewPanel != null)
2575 Frame frame = new Frame();
2576 OverviewPanel overview = new OverviewPanel(alignPanel);
2577 frame.add(overview);
2578 // +50 must allow for applet frame window
2579 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2580 "label.overview_params", new String[] { this.getTitle() }),
2581 overview.getPreferredSize().width,
2582 overview.getPreferredSize().height + 50);
2585 final AlignmentPanel ap = alignPanel;
2586 frame.addWindowListener(new WindowAdapter()
2589 public void windowClosing(WindowEvent e)
2593 ap.setOverviewPanel(null);
2598 alignPanel.setOverviewPanel(overview);
2602 public void changeColour(ColourSchemeI cs)
2607 if (viewport.getAbovePIDThreshold())
2609 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2613 if (viewport.getConservationSelected())
2615 cs.setConservationApplied(true);
2616 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2621 cs.setConservationApplied(false);
2624 viewport.setGlobalColourScheme(cs);
2626 alignPanel.paintAlignment(true);
2629 protected void modifyPID_actionPerformed()
2631 if (viewport.getAbovePIDThreshold()
2632 && viewport.getGlobalColourScheme() != null)
2634 SliderPanel.setPIDSliderSource(alignPanel,
2635 viewport.getGlobalColourScheme(), "Background");
2636 SliderPanel.showPIDSlider();
2640 protected void modifyConservation_actionPerformed()
2642 if (viewport.getConservationSelected()
2643 && viewport.getGlobalColourScheme() != null)
2645 SliderPanel.setConservationSlider(alignPanel,
2646 viewport.getGlobalColourScheme(), "Background");
2647 SliderPanel.showConservationSlider();
2651 protected void conservationMenuItem_actionPerformed()
2653 viewport.setConservationSelected(conservationMenuItem.getState());
2655 viewport.setAbovePIDThreshold(false);
2656 abovePIDThreshold.setState(false);
2658 changeColour(viewport.getGlobalColourScheme());
2660 modifyConservation_actionPerformed();
2663 public void abovePIDThreshold_actionPerformed()
2665 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2667 conservationMenuItem.setState(false);
2668 viewport.setConservationSelected(false);
2670 changeColour(viewport.getGlobalColourScheme());
2672 modifyPID_actionPerformed();
2675 public void sortPairwiseMenuItem_actionPerformed()
2677 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2678 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2679 .getAlignment().getSequenceAt(0), null);
2681 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2682 viewport.getAlignment()));
2683 alignPanel.paintAlignment(true);
2686 public void sortIDMenuItem_actionPerformed()
2688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2689 AlignmentSorter.sortByID(viewport.getAlignment());
2690 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2691 viewport.getAlignment()));
2692 alignPanel.paintAlignment(true);
2695 public void sortLengthMenuItem_actionPerformed()
2697 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2698 AlignmentSorter.sortByLength(viewport.getAlignment());
2699 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2700 viewport.getAlignment()));
2701 alignPanel.paintAlignment(true);
2704 public void sortGroupMenuItem_actionPerformed()
2706 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2707 AlignmentSorter.sortByGroup(viewport.getAlignment());
2708 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2709 viewport.getAlignment()));
2710 alignPanel.paintAlignment(true);
2714 public void removeRedundancyMenuItem_actionPerformed()
2716 new RedundancyPanel(alignPanel);
2719 public void pairwiseAlignmentMenuItem_actionPerformed()
2721 if (viewport.getSelectionGroup() != null
2722 && viewport.getSelectionGroup().getSize() > 1)
2724 Frame frame = new Frame();
2725 frame.add(new PairwiseAlignPanel(alignPanel));
2726 jalview.bin.JalviewLite.addFrame(frame,
2727 MessageManager.getString("action.pairwise_alignment"), 600,
2732 public void PCAMenuItem_actionPerformed()
2734 // are the sequences aligned?
2735 if (!viewport.getAlignment().isAligned(false))
2738 int Width = viewport.getAlignment().getWidth();
2740 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2742 current = viewport.getAlignment().getSequenceAt(i);
2744 if (current.getLength() < Width)
2746 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2749 alignPanel.paintAlignment(true);
2752 if ((viewport.getSelectionGroup() != null
2753 && viewport.getSelectionGroup().getSize() < 4 && viewport
2754 .getSelectionGroup().getSize() > 0)
2755 || viewport.getAlignment().getHeight() < 4)
2762 new PCAPanel(viewport);
2763 } catch (java.lang.OutOfMemoryError ex)
2769 public void averageDistanceTreeMenuItem_actionPerformed()
2771 NewTreePanel("AV", "PID", "Average distance tree using PID");
2774 public void neighbourTreeMenuItem_actionPerformed()
2776 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2779 protected void njTreeBlosumMenuItem_actionPerformed()
2781 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2784 protected void avTreeBlosumMenuItem_actionPerformed()
2786 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2789 void NewTreePanel(String type, String pwType, String title)
2791 // are the sequences aligned?
2792 if (!viewport.getAlignment().isAligned(false))
2795 int Width = viewport.getAlignment().getWidth();
2797 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2799 current = viewport.getAlignment().getSequenceAt(i);
2801 if (current.getLength() < Width)
2803 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2806 alignPanel.paintAlignment(true);
2810 if ((viewport.getSelectionGroup() != null && viewport
2811 .getSelectionGroup().getSize() > 1)
2812 || (viewport.getAlignment().getHeight() > 1))
2814 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2816 addTreeMenuItem(tp, title);
2818 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2822 void loadTree_actionPerformed()
2824 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2825 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2826 cap.setTreeImport();
2827 Frame frame = new Frame();
2829 jalview.bin.JalviewLite.addFrame(frame,
2830 MessageManager.getString("label.paste_newick_file"), 400, 300);
2833 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2835 TreePanel tp = new TreePanel(alignPanel, treeFile,
2836 MessageManager.getString("label.load_tree_from_file"), tree);
2837 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2838 addTreeMenuItem(tp, treeFile);
2842 * sort the alignment using the given treePanel
2845 * tree used to sort view
2847 * string used for undo event name
2849 public void sortByTree(TreePanel treePanel, String title)
2851 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2853 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2854 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2855 // HistoryItem.SORT));
2856 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2857 "label.order_by_params", new String[] { title }), oldOrder,
2858 viewport.getAlignment()));
2859 alignPanel.paintAlignment(true);
2863 * Do any automatic reordering of the alignment and add the necessary bits to
2864 * the menu structure for the new tree
2869 protected void addTreeMenuItem(final TreePanel treePanel,
2872 final MenuItem item = new MenuItem(title);
2873 sortByTreeMenu.add(item);
2874 item.addActionListener(new java.awt.event.ActionListener()
2877 public void actionPerformed(ActionEvent evt)
2879 sortByTree(treePanel, title); // treePanel.getTitle());
2883 treePanel.addWindowListener(new WindowAdapter()
2886 public void windowOpened(WindowEvent e)
2888 if (viewport.sortByTree)
2890 sortByTree(treePanel, title);
2892 super.windowOpened(e);
2896 public void windowClosing(WindowEvent e)
2898 sortByTreeMenu.remove(item);
2903 public boolean sortBy(AlignmentOrder alorder, String undoname)
2905 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2906 if (viewport.applet.debug)
2908 System.err.println("Sorting " + alorder.getOrder().size()
2909 + " in alignment '" + getTitle() + "'");
2911 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2912 if (undoname != null)
2914 addHistoryItem(new OrderCommand(undoname, oldOrder,
2915 viewport.getAlignment()));
2917 alignPanel.paintAlignment(true);
2921 protected void documentation_actionPerformed()
2923 alignPanel.av.applet.openJalviewHelpUrl();
2926 protected void about_actionPerformed()
2929 class AboutPanel extends Canvas
2935 public AboutPanel(String version, String builddate)
2937 this.version = version;
2938 this.builddate = builddate;
2942 public void paint(Graphics g)
2944 g.setColor(Color.white);
2945 g.fillRect(0, 0, getSize().width, getSize().height);
2946 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2947 FontMetrics fm = g.getFontMetrics();
2948 int fh = fm.getHeight();
2950 g.setColor(Color.black);
2951 // TODO: update this text for each release or centrally store it for
2952 // lite and application
2953 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2954 g.drawString(MessageManager.formatMessage(
2955 "label.jalviewLite_release", new String[] { version }), x,
2957 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2958 g.drawString(MessageManager.formatMessage(
2959 "label.jaview_build_date", new String[] { builddate }), x,
2961 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2962 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2964 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2965 x + 50, y += fh + 8);
2967 MessageManager.getString("label.jalview_dev_managers"), x,
2969 g.drawString(MessageManager
2970 .getString("label.jalview_distribution_lists"), x, y += fh);
2971 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2974 MessageManager.getString("label.jalview_cite_1_authors"),
2977 MessageManager.getString("label.jalview_cite_1_title"), x,
2979 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2984 Frame frame = new Frame();
2985 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2987 jalview.bin.JalviewLite.addFrame(frame,
2988 MessageManager.getString("label.jalview"), 580, 220);
2992 public void showURL(String url, String target)
2994 if (viewport.applet == null)
2996 System.out.println("Not running as applet - no browser available.");
3000 viewport.applet.showURL(url, target);
3004 // ////////////////////////////////////////////////////////////////////////////////
3005 // JBuilder Graphics here
3007 MenuBar alignFrameMenuBar = new MenuBar();
3009 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3011 MenuItem loadApplication = new MenuItem(
3012 MessageManager.getString("label.view_full_application"));
3014 MenuItem loadTree = new MenuItem(
3015 MessageManager.getString("label.load_associated_tree"));
3017 MenuItem loadAnnotations = new MenuItem(
3018 MessageManager.getString("label.load_features_annotations"));
3020 MenuItem outputFeatures = new MenuItem(
3021 MessageManager.getString("label.export_features"));
3023 MenuItem outputAnnotations = new MenuItem(
3024 MessageManager.getString("label.export_annotations"));
3026 MenuItem closeMenuItem = new MenuItem(
3027 MessageManager.getString("action.close"));
3029 MenuItem selectAllSequenceMenuItem = new MenuItem(
3030 MessageManager.getString("action.select_all"));
3032 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3033 MessageManager.getString("action.deselect_all"));
3035 MenuItem invertSequenceMenuItem = new MenuItem(
3036 MessageManager.getString("action.invert_selection"));
3038 MenuItem remove2LeftMenuItem = new MenuItem();
3040 MenuItem remove2RightMenuItem = new MenuItem();
3042 MenuItem removeGappedColumnMenuItem = new MenuItem();
3044 MenuItem removeAllGapsMenuItem = new MenuItem();
3046 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3048 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3050 MenuItem sortPairwiseMenuItem = new MenuItem();
3052 MenuItem sortIDMenuItem = new MenuItem();
3054 MenuItem sortLengthMenuItem = new MenuItem();
3056 MenuItem sortGroupMenuItem = new MenuItem();
3058 MenuItem removeRedundancyMenuItem = new MenuItem();
3060 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3062 MenuItem PCAMenuItem = new MenuItem();
3064 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3066 MenuItem neighbourTreeMenuItem = new MenuItem();
3068 BorderLayout borderLayout1 = new BorderLayout();
3070 public Label statusBar = new Label();
3072 MenuItem clustalColour = new MenuItem();
3074 MenuItem zappoColour = new MenuItem();
3076 MenuItem taylorColour = new MenuItem();
3078 MenuItem hydrophobicityColour = new MenuItem();
3080 MenuItem helixColour = new MenuItem();
3082 MenuItem strandColour = new MenuItem();
3084 MenuItem turnColour = new MenuItem();
3086 MenuItem buriedColour = new MenuItem();
3088 MenuItem purinePyrimidineColour = new MenuItem();
3090 // MenuItem RNAInteractionColour = new MenuItem();
3092 MenuItem RNAHelixColour = new MenuItem();
3094 MenuItem userDefinedColour = new MenuItem();
3096 MenuItem PIDColour = new MenuItem();
3098 MenuItem BLOSUM62Colour = new MenuItem();
3100 MenuItem tcoffeeColour = new MenuItem();
3102 MenuItem njTreeBlosumMenuItem = new MenuItem();
3104 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3106 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3108 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3110 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3112 MenuItem alProperties = new MenuItem(
3113 MessageManager.getString("label.alignment_props"));
3115 MenuItem overviewMenuItem = new MenuItem();
3117 MenuItem undoMenuItem = new MenuItem();
3119 MenuItem redoMenuItem = new MenuItem();
3121 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3123 MenuItem noColourmenuItem = new MenuItem();
3125 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3127 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3129 MenuItem findMenuItem = new MenuItem();
3131 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3133 MenuItem nucleotideColour = new MenuItem();
3135 MenuItem deleteGroups = new MenuItem();
3137 MenuItem grpsFromSelection = new MenuItem();
3139 MenuItem createGroup = new MenuItem();
3141 MenuItem unGroup = new MenuItem();
3143 MenuItem delete = new MenuItem();
3145 MenuItem copy = new MenuItem();
3147 MenuItem cut = new MenuItem();
3149 Menu pasteMenu = new Menu();
3151 MenuItem pasteNew = new MenuItem();
3153 MenuItem pasteThis = new MenuItem();
3155 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3157 MenuItem font = new MenuItem();
3159 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3161 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3163 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3165 MenuItem modifyPID = new MenuItem();
3167 MenuItem modifyConservation = new MenuItem();
3169 CheckboxMenuItem autoCalculate = null;
3171 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3172 "Sort Alignment With New Tree", true);
3174 Menu sortByTreeMenu = new Menu();
3176 MenuItem inputText = new MenuItem();
3178 MenuItem documentation = new MenuItem();
3180 MenuItem about = new MenuItem();
3182 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3184 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3186 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3188 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3190 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3192 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3194 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3196 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3198 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3201 * Initialise menus and other items
3205 private void jbInit() throws Exception
3207 setMenuBar(alignFrameMenuBar);
3210 * Configure File menu items and actions
3213 .setLabel(MessageManager.getString("label.input_from_textbox"));
3214 inputText.addActionListener(this);
3215 Menu outputTextboxMenu = new Menu(
3216 MessageManager.getString("label.out_to_textbox"));
3217 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3220 MenuItem item = new MenuItem(
3221 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3223 item.addActionListener(new java.awt.event.ActionListener()
3226 public void actionPerformed(ActionEvent e)
3228 outputText_actionPerformed(e);
3232 outputTextboxMenu.add(item);
3234 closeMenuItem.addActionListener(this);
3235 loadApplication.addActionListener(this);
3236 loadTree.addActionListener(this);
3237 loadAnnotations.addActionListener(this);
3238 outputFeatures.addActionListener(this);
3239 outputAnnotations.addActionListener(this);
3242 * Configure Edit menu items and actions
3244 undoMenuItem.setEnabled(false);
3245 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3246 undoMenuItem.addActionListener(this);
3247 redoMenuItem.setEnabled(false);
3248 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3249 redoMenuItem.addActionListener(this);
3250 copy.setLabel(MessageManager.getString("action.copy"));
3251 copy.addActionListener(this);
3252 cut.setLabel(MessageManager.getString("action.cut"));
3253 cut.addActionListener(this);
3254 delete.setLabel(MessageManager.getString("action.delete"));
3255 delete.addActionListener(this);
3256 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3257 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3258 pasteNew.addActionListener(this);
3259 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3260 pasteThis.addActionListener(this);
3261 remove2LeftMenuItem.setLabel(MessageManager
3262 .getString("action.remove_left"));
3263 remove2LeftMenuItem.addActionListener(this);
3264 remove2RightMenuItem.setLabel(MessageManager
3265 .getString("action.remove_right"));
3266 remove2RightMenuItem.addActionListener(this);
3267 removeGappedColumnMenuItem.setLabel(MessageManager
3268 .getString("action.remove_empty_columns"));
3269 removeGappedColumnMenuItem.addActionListener(this);
3270 removeAllGapsMenuItem.setLabel(MessageManager
3271 .getString("action.remove_all_gaps"));
3272 removeAllGapsMenuItem.addActionListener(this);
3273 removeRedundancyMenuItem.setLabel(MessageManager
3274 .getString("action.remove_redundancy"));
3275 removeRedundancyMenuItem.addActionListener(this);
3278 * Configure Select menu items and actions
3280 findMenuItem.setLabel(MessageManager.getString("action.find"));
3281 findMenuItem.addActionListener(this);
3282 selectAllSequenceMenuItem.addActionListener(this);
3283 deselectAllSequenceMenuItem.addActionListener(this);
3284 invertSequenceMenuItem.setLabel(MessageManager
3285 .getString("action.invert_sequence_selection"));
3286 invertSequenceMenuItem.addActionListener(this);
3287 invertColSel.setLabel(MessageManager
3288 .getString("action.invert_column_selection"));
3289 invertColSel.addActionListener(this);
3290 deleteGroups.setLabel(MessageManager
3291 .getString("action.undefine_groups"));
3292 deleteGroups.addActionListener(this);
3293 grpsFromSelection.setLabel(MessageManager
3294 .getString("action.make_groups_selection"));
3295 grpsFromSelection.addActionListener(this);
3296 createGroup.setLabel(MessageManager.getString("action.create_group"));
3297 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3298 annotationColumnSelection.setLabel(MessageManager
3299 .getString("action.select_by_annotation"));
3300 annotationColumnSelection.addActionListener(this);
3303 * Configure View menu items and actions
3305 newView.setLabel(MessageManager.getString("action.new_view"));
3306 newView.addActionListener(this);
3307 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3308 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3309 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3310 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3312 .setLabel(MessageManager.getString("label.selected_columns"));
3313 hideSequences.setLabel(MessageManager
3314 .getString("label.selected_sequences"));
3315 hideAllButSelection.setLabel(MessageManager
3316 .getString("label.all_but_selected_region"));
3317 hideAllSelection.setLabel(MessageManager
3318 .getString("label.selected_region"));
3319 showAllHidden.setLabel(MessageManager
3320 .getString("label.all_sequences_columns"));
3321 showColumns.addActionListener(this);
3322 showSeqs.addActionListener(this);
3323 hideColumns.addActionListener(this);
3324 hideSequences.addActionListener(this);
3325 hideAllButSelection.addActionListener(this);
3326 hideAllSelection.addActionListener(this);
3327 showAllHidden.addActionListener(this);
3328 featureSettings.setLabel(MessageManager
3329 .getString("action.feature_settings"));
3330 featureSettings.addActionListener(this);
3331 sequenceFeatures.setLabel(MessageManager
3332 .getString("label.show_sequence_features"));
3333 sequenceFeatures.addItemListener(this);
3334 sequenceFeatures.setState(false);
3335 followMouseOverFlag.setLabel(MessageManager
3336 .getString("label.automatic_scrolling"));
3337 followMouseOverFlag.addItemListener(this);
3338 alProperties.addActionListener(this);
3339 overviewMenuItem.setLabel(MessageManager
3340 .getString("label.overview_window"));
3341 overviewMenuItem.addActionListener(this);
3344 * Configure Annotations menu items and actions
3346 annotationPanelMenuItem.setLabel(MessageManager
3347 .getString("label.show_annotations"));
3348 annotationPanelMenuItem.addItemListener(this);
3349 showGroupConsensus.setLabel(MessageManager
3350 .getString("label.group_consensus"));
3351 showGroupConservation.setLabel(MessageManager
3352 .getString("label.group_conservation"));
3353 showConsensusHistogram.setLabel(MessageManager
3354 .getString("label.show_consensus_histogram"));
3355 showSequenceLogo.setLabel(MessageManager
3356 .getString("label.show_consensus_logo"));
3357 normSequenceLogo.setLabel(MessageManager
3358 .getString("label.norm_consensus_logo"));
3359 applyAutoAnnotationSettings.setLabel(MessageManager
3360 .getString("label.apply_all_groups"));
3361 applyAutoAnnotationSettings.setState(true);
3362 Menu autoAnnMenu = new Menu(
3363 MessageManager.getString("label.autocalculated_annotation"));
3364 showGroupConsensus.addItemListener(this);
3365 showGroupConservation.addItemListener(this);
3366 showConsensusHistogram.addItemListener(this);
3367 showSequenceLogo.addItemListener(this);
3368 normSequenceLogo.addItemListener(this);
3369 applyAutoAnnotationSettings.addItemListener(this);
3370 showAlignmentAnnotations = new CheckboxMenuItem(
3371 MessageManager.getString("label.show_all_al_annotations"));
3372 showSequenceAnnotations = new CheckboxMenuItem(
3373 MessageManager.getString("label.show_all_seq_annotations"));
3374 sortAnnBySequence = new CheckboxMenuItem(
3375 MessageManager.getString("label.sort_annotations_by_sequence"));
3376 sortAnnByLabel = new CheckboxMenuItem(
3377 MessageManager.getString("label.sort_annotations_by_label"));
3378 showAutoFirst = new CheckboxMenuItem(
3379 MessageManager.getString("label.show_first"));
3380 showAutoFirst.setState(false); // pending applet parameter
3381 setShowAutoCalculatedAbove(showAutoFirst.getState());
3382 showAutoLast = new CheckboxMenuItem(
3383 MessageManager.getString("label.show_last"));
3384 showAutoLast.setState(!showAutoFirst.getState());
3385 showAlignmentAnnotations.addItemListener(this);
3386 showSequenceAnnotations.addItemListener(this);
3387 sortAnnBySequence.addItemListener(this);
3388 sortAnnByLabel.addItemListener(this);
3389 showAutoFirst.addItemListener(this);
3390 showAutoLast.addItemListener(this);
3393 * Configure Format menu items and actions
3395 font.setLabel(MessageManager.getString("action.font"));
3396 font.addActionListener(this);
3397 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3398 scaleAbove.setState(true);
3399 scaleAbove.setEnabled(false);
3400 scaleAbove.addItemListener(this);
3401 scaleLeft.setEnabled(false);
3402 scaleLeft.setState(true);
3403 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3404 scaleLeft.addItemListener(this);
3405 scaleRight.setEnabled(false);
3406 scaleRight.setState(true);
3407 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3408 scaleRight.addItemListener(this);
3409 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3410 viewBoxesMenuItem.setState(true);
3411 viewBoxesMenuItem.addItemListener(this);
3412 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3413 viewTextMenuItem.setState(true);
3414 viewTextMenuItem.addItemListener(this);
3415 colourTextMenuItem.setLabel(MessageManager
3416 .getString("label.colour_text"));
3417 colourTextMenuItem.addItemListener(this);
3418 displayNonconservedMenuItem.setLabel(MessageManager
3419 .getString("label.show_non_conversed"));
3420 displayNonconservedMenuItem.addItemListener(this);
3421 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3422 wrapMenuItem.addItemListener(this);
3423 renderGapsMenuItem.setLabel(MessageManager
3424 .getString("action.show_gaps"));
3425 renderGapsMenuItem.setState(true);
3426 renderGapsMenuItem.addItemListener(this);
3427 centreColumnLabelFlag.setLabel(MessageManager
3428 .getString("label.centre_column_labels"));
3429 centreColumnLabelFlag.addItemListener(this);
3430 seqLimits.setState(true);
3431 seqLimits.setLabel(MessageManager
3432 .getString("label.show_sequence_limits"));
3433 seqLimits.addItemListener(this);
3436 * Configure Colour menu items and actions
3438 applyToAllGroups.setLabel(MessageManager
3439 .getString("label.apply_colour_to_all_groups"));
3440 applyToAllGroups.setState(true);
3441 applyToAllGroups.addItemListener(this);
3442 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3443 clustalColour.addActionListener(this);
3444 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3445 zappoColour.addActionListener(this);
3446 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3447 taylorColour.addActionListener(this);
3448 hydrophobicityColour.setLabel(MessageManager
3449 .getString("label.hydrophobicity"));
3450 hydrophobicityColour.addActionListener(this);
3452 .setLabel(MessageManager.getString("label.helix_propensity"));
3453 helixColour.addActionListener(this);
3454 strandColour.setLabel(MessageManager
3455 .getString("label.strand_propensity"));
3456 strandColour.addActionListener(this);
3457 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3458 turnColour.addActionListener(this);
3459 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3460 buriedColour.addActionListener(this);
3461 purinePyrimidineColour.setLabel(MessageManager
3462 .getString("label.purine_pyrimidine"));
3463 purinePyrimidineColour.addActionListener(this);
3464 // RNAInteractionColour.setLabel(MessageManager
3465 // .getString("label.rna_interaction"));
3466 // RNAInteractionColour.addActionListener(this);
3467 RNAHelixColour.setLabel(MessageManager
3468 .getString("action.by_rna_helixes"));
3469 RNAHelixColour.addActionListener(this);
3470 userDefinedColour.setLabel(MessageManager
3471 .getString("action.user_defined"));
3472 userDefinedColour.addActionListener(this);
3473 PIDColour.setLabel(MessageManager
3474 .getString("label.percentage_identity"));
3475 PIDColour.addActionListener(this);
3476 BLOSUM62Colour.setLabel(MessageManager
3477 .getString("label.blosum62_score"));
3478 BLOSUM62Colour.addActionListener(this);
3480 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3481 // it will be enabled only if a score file is provided
3482 tcoffeeColour.setEnabled(false);
3483 tcoffeeColour.addActionListener(this);
3484 conservationMenuItem.setLabel(MessageManager
3485 .getString("action.by_conservation"));
3486 conservationMenuItem.addItemListener(this);
3487 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3488 noColourmenuItem.addActionListener(this);
3489 abovePIDThreshold.setLabel(MessageManager
3490 .getString("label.above_identity_threshold"));
3491 abovePIDThreshold.addItemListener(this);
3492 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3493 nucleotideColour.addActionListener(this);
3494 modifyPID.setLabel(MessageManager
3495 .getString("label.modify_identity_thereshold"));
3496 modifyPID.addActionListener(this);
3497 modifyConservation.setLabel(MessageManager
3498 .getString("label.modify_conservation_thereshold"));
3499 modifyConservation.addActionListener(this);
3500 annotationColour.setLabel(MessageManager
3501 .getString("action.by_annotation"));
3502 annotationColour.addActionListener(this);
3505 * Configure Calculate menu items and actions
3507 sortPairwiseMenuItem.setLabel(MessageManager
3508 .getString("action.by_pairwise_id"));
3509 sortPairwiseMenuItem.addActionListener(this);
3510 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3511 sortIDMenuItem.addActionListener(this);
3512 sortLengthMenuItem.setLabel(MessageManager
3513 .getString("action.by_length"));
3514 sortLengthMenuItem.addActionListener(this);
3515 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3516 sortGroupMenuItem.addActionListener(this);
3517 pairwiseAlignmentMenuItem.setLabel(MessageManager
3518 .getString("action.pairwise_alignment"));
3519 pairwiseAlignmentMenuItem.addActionListener(this);
3520 PCAMenuItem.setLabel(MessageManager
3521 .getString("label.principal_component_analysis"));
3522 PCAMenuItem.addActionListener(this);
3523 autoCalculate = new CheckboxMenuItem(
3524 MessageManager.getString("label.autocalculate_consensus"), true);
3525 averageDistanceTreeMenuItem.setLabel(MessageManager
3526 .getString("label.average_distance_identity"));
3527 averageDistanceTreeMenuItem.addActionListener(this);
3528 neighbourTreeMenuItem.setLabel(MessageManager
3529 .getString("label.neighbour_joining_identity"));
3530 neighbourTreeMenuItem.addActionListener(this);
3531 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3532 .getString("label.average_distance_bloslum62"));
3533 avDistanceTreeBlosumMenuItem.addActionListener(this);
3534 njTreeBlosumMenuItem.setLabel(MessageManager
3535 .getString("label.neighbour_blosum62"));
3536 njTreeBlosumMenuItem.addActionListener(this);
3537 sortByTreeMenu.setLabel(MessageManager
3538 .getString("action.by_tree_order"));
3539 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3540 Menu calculateTreeMenu = new Menu(
3541 MessageManager.getString("action.calculate_tree"));
3542 autoCalculate.addItemListener(this);
3543 sortByTree.addItemListener(this);
3546 * Configure Help menu items and actions
3548 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3549 documentation.setLabel(MessageManager.getString("label.documentation"));
3550 documentation.addActionListener(this);
3551 about.setLabel(MessageManager.getString("label.about"));
3552 about.addActionListener(this);
3555 * Add top level menus to frame
3557 alignFrameMenuBar.add(fileMenu);
3558 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3559 alignFrameMenuBar.add(editMenu);
3560 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3561 alignFrameMenuBar.add(selectMenu);
3562 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3563 alignFrameMenuBar.add(viewMenu);
3564 Menu annotationsMenu = new Menu(
3565 MessageManager.getString("action.annotations"));
3566 alignFrameMenuBar.add(annotationsMenu);
3567 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3568 alignFrameMenuBar.add(formatMenu);
3569 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3570 alignFrameMenuBar.add(colourMenu);
3571 Menu calculateMenu = new Menu(
3572 MessageManager.getString("action.calculate"));
3573 alignFrameMenuBar.add(calculateMenu);
3574 alignFrameMenuBar.add(helpMenu);
3579 fileMenu.add(inputText);
3580 fileMenu.add(loadTree);
3581 fileMenu.add(loadAnnotations);
3582 fileMenu.addSeparator();
3583 fileMenu.add(outputTextboxMenu);
3584 fileMenu.add(outputFeatures);
3585 fileMenu.add(outputAnnotations);
3586 if (jalviewServletURL != null)
3588 fileMenu.add(loadApplication);
3590 fileMenu.addSeparator();
3591 fileMenu.add(closeMenuItem);
3596 editMenu.add(undoMenuItem);
3597 editMenu.add(redoMenuItem);
3600 pasteMenu.add(pasteNew);
3601 pasteMenu.add(pasteThis);
3602 editMenu.add(pasteMenu);
3603 editMenu.add(delete);
3604 editMenu.addSeparator();
3605 editMenu.add(remove2LeftMenuItem);
3606 editMenu.add(remove2RightMenuItem);
3607 editMenu.add(removeGappedColumnMenuItem);
3608 editMenu.add(removeAllGapsMenuItem);
3609 editMenu.add(removeRedundancyMenuItem);
3614 selectMenu.add(findMenuItem);
3615 selectMenu.addSeparator();
3616 selectMenu.add(selectAllSequenceMenuItem);
3617 selectMenu.add(deselectAllSequenceMenuItem);
3618 selectMenu.add(invertSequenceMenuItem);
3619 selectMenu.add(invertColSel);
3620 selectMenu.add(createGroup);
3621 selectMenu.add(unGroup);
3622 selectMenu.add(grpsFromSelection);
3623 selectMenu.add(deleteGroups);
3624 selectMenu.add(annotationColumnSelection);
3629 viewMenu.add(newView);
3630 viewMenu.addSeparator();
3631 showMenu.add(showColumns);
3632 showMenu.add(showSeqs);
3633 showMenu.add(showAllHidden);
3634 viewMenu.add(showMenu);
3635 hideMenu.add(hideColumns);
3636 hideMenu.add(hideSequences);
3637 hideMenu.add(hideAllSelection);
3638 hideMenu.add(hideAllButSelection);
3639 viewMenu.add(hideMenu);
3640 viewMenu.addSeparator();
3641 viewMenu.add(followMouseOverFlag);
3642 viewMenu.addSeparator();
3643 viewMenu.add(sequenceFeatures);
3644 viewMenu.add(featureSettings);
3645 viewMenu.addSeparator();
3646 viewMenu.add(alProperties);
3647 viewMenu.addSeparator();
3648 viewMenu.add(overviewMenuItem);
3653 annotationsMenu.add(annotationPanelMenuItem);
3654 annotationsMenu.addSeparator();
3655 annotationsMenu.add(showAlignmentAnnotations);
3656 annotationsMenu.add(showSequenceAnnotations);
3657 annotationsMenu.add(sortAnnBySequence);
3658 annotationsMenu.add(sortAnnByLabel);
3659 annotationsMenu.addSeparator();
3660 autoAnnMenu.add(showAutoFirst);
3661 autoAnnMenu.add(showAutoLast);
3662 autoAnnMenu.addSeparator();
3663 autoAnnMenu.add(applyAutoAnnotationSettings);
3664 autoAnnMenu.add(showConsensusHistogram);
3665 autoAnnMenu.add(showSequenceLogo);
3666 autoAnnMenu.add(normSequenceLogo);
3667 autoAnnMenu.addSeparator();
3668 autoAnnMenu.add(showGroupConservation);
3669 autoAnnMenu.add(showGroupConsensus);
3670 annotationsMenu.add(autoAnnMenu);
3675 formatMenu.add(font);
3676 formatMenu.add(seqLimits);
3677 formatMenu.add(wrapMenuItem);
3678 formatMenu.add(scaleAbove);
3679 formatMenu.add(scaleLeft);
3680 formatMenu.add(scaleRight);
3681 formatMenu.add(viewBoxesMenuItem);
3682 formatMenu.add(viewTextMenuItem);
3683 formatMenu.add(colourTextMenuItem);
3684 formatMenu.add(displayNonconservedMenuItem);
3685 formatMenu.add(renderGapsMenuItem);
3686 formatMenu.add(centreColumnLabelFlag);
3691 colourMenu.add(applyToAllGroups);
3692 colourMenu.addSeparator();
3693 colourMenu.add(noColourmenuItem);
3694 colourMenu.add(clustalColour);
3695 colourMenu.add(BLOSUM62Colour);
3696 colourMenu.add(PIDColour);
3697 colourMenu.add(zappoColour);
3698 colourMenu.add(taylorColour);
3699 colourMenu.add(hydrophobicityColour);
3700 colourMenu.add(helixColour);
3701 colourMenu.add(strandColour);
3702 colourMenu.add(turnColour);
3703 colourMenu.add(buriedColour);
3704 colourMenu.add(nucleotideColour);
3705 colourMenu.add(purinePyrimidineColour);
3706 // colourMenu.add(RNAInteractionColour);
3707 colourMenu.add(tcoffeeColour);
3708 colourMenu.add(userDefinedColour);
3709 colourMenu.addSeparator();
3710 colourMenu.add(conservationMenuItem);
3711 colourMenu.add(modifyConservation);
3712 colourMenu.add(abovePIDThreshold);
3713 colourMenu.add(modifyPID);
3714 colourMenu.add(annotationColour);
3715 colourMenu.add(RNAHelixColour);
3720 sortMenu.add(sortIDMenuItem);
3721 sortMenu.add(sortLengthMenuItem);
3722 sortMenu.add(sortByTreeMenu);
3723 sortMenu.add(sortGroupMenuItem);
3724 sortMenu.add(sortPairwiseMenuItem);
3725 calculateMenu.add(sortMenu);
3726 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3727 calculateTreeMenu.add(neighbourTreeMenuItem);
3728 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3729 calculateTreeMenu.add(njTreeBlosumMenuItem);
3730 calculateMenu.add(calculateTreeMenu);
3731 calculateMenu.addSeparator();
3732 calculateMenu.add(pairwiseAlignmentMenuItem);
3733 calculateMenu.add(PCAMenuItem);
3734 calculateMenu.add(autoCalculate);
3735 calculateMenu.add(sortByTree);
3740 helpMenu.add(documentation);
3741 helpMenu.add(about);
3746 statusBar.setBackground(Color.white);
3747 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3748 statusBar.setText(MessageManager.getString("label.status_bar"));
3749 this.add(statusBar, BorderLayout.SOUTH);
3752 public void setStatus(String string)
3754 statusBar.setText(string);
3757 MenuItem featureSettings = new MenuItem();
3759 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3761 MenuItem annotationColour = new MenuItem();
3763 MenuItem annotationColumnSelection = new MenuItem();
3765 MenuItem invertColSel = new MenuItem();
3767 MenuItem showColumns = new MenuItem();
3769 MenuItem showSeqs = new MenuItem();
3771 MenuItem hideColumns = new MenuItem();
3773 MenuItem hideSequences = new MenuItem();
3775 MenuItem hideAllButSelection = new MenuItem();
3777 MenuItem hideAllSelection = new MenuItem();
3779 MenuItem showAllHidden = new MenuItem();
3781 MenuItem newView = new MenuItem();
3783 private CheckboxMenuItem showAlignmentAnnotations;
3785 private CheckboxMenuItem showSequenceAnnotations;
3787 private CheckboxMenuItem sortAnnBySequence;
3789 private CheckboxMenuItem sortAnnByLabel;
3791 private CheckboxMenuItem showAutoFirst;
3793 private CheckboxMenuItem showAutoLast;
3795 private SplitFrame splitFrame;
3798 * Attach the alignFrame panels after embedding menus, if necessary. This used
3799 * to be called setEmbedded, but is now creates the dropdown menus in a
3800 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3802 * @param reallyEmbedded
3803 * true to attach the view to the applet area on the page rather than
3806 public void createAlignFrameWindow(boolean reallyEmbedded)
3810 embedAlignFrameInApplet(viewport.applet);
3815 // test and embed menu bar if necessary.
3817 if (embedMenuIfNeeded(alignPanel))
3820 * adjust for status bar height too. ? pointless as overridden by layout
3823 alignPanel.setSize(getSize().width,
3824 getSize().height - statusBar.getHeight());
3826 add(statusBar, BorderLayout.SOUTH);
3827 add(alignPanel, BorderLayout.CENTER);
3828 // and register with the applet so it can pass external API calls to us
3829 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3835 * Add the components of this AlignFrame to the applet container.
3839 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3842 // Explicitly build the embedded menu panel for the on-page applet
3844 // view cannot be closed if its actually on the page
3845 fileMenu.remove(closeMenuItem);
3846 fileMenu.remove(3); // Remove Separator
3847 // construct embedded menu, using default font
3848 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3849 // and actually add the components to the applet area
3850 theApplet.setLayout(new BorderLayout());
3851 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3852 theApplet.add(statusBar, BorderLayout.SOUTH);
3853 // TODO should size be left to the layout manager?
3854 alignPanel.setSize(theApplet.getSize().width,
3855 theApplet.getSize().height - embeddedMenu.getHeight()
3856 - statusBar.getHeight());
3857 theApplet.add(alignPanel, BorderLayout.CENTER);
3858 final AlignFrame me = this;
3859 theApplet.addFocusListener(new FocusListener()
3863 public void focusLost(FocusEvent e)
3865 if (theApplet.currentAlignFrame == me)
3867 theApplet.currentAlignFrame = null;
3872 public void focusGained(FocusEvent e)
3874 theApplet.currentAlignFrame = me;
3877 theApplet.validate();
3881 * create a new binding between structures in an existing jmol viewer instance
3882 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3883 * this does not open a new Jmol window, or modify the display of the
3884 * structures in the original jmol window. Note This method doesn't work
3885 * without an additional javascript library to exchange messages between the
3886 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3889 * JmolViewer instance
3890 * @param sequenceIds
3891 * - sequence Ids to search for associations
3893 public SequenceStructureBinding addStructureViewInstance(
3894 Object jmolviewer, String[] sequenceIds)
3896 Viewer viewer = null;
3899 viewer = (Viewer) jmolviewer;
3900 } catch (ClassCastException ex)
3902 System.err.println("Unsupported viewer object :"
3903 + jmolviewer.getClass());
3907 System.err.println("Can't use this object as a structure viewer:"
3908 + jmolviewer.getClass());
3911 SequenceI[] seqs = null;
3912 if (sequenceIds == null || sequenceIds.length == 0)
3914 seqs = viewport.getAlignment().getSequencesArray();
3918 Vector sqi = new Vector();
3919 AlignmentI al = viewport.getAlignment();
3920 for (int sid = 0; sid < sequenceIds.length; sid++)
3922 SequenceI sq = al.findName(sequenceIds[sid]);
3930 seqs = new SequenceI[sqi.size()];
3931 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3933 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3941 AAStructureBindingModel jmv = null;
3942 // TODO: search for a jmv that involves viewer
3944 { // create a new viewer/jalview binding.
3945 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3952 * bind a pdb file to a sequence in the current view
3955 * - sequenceId within the dataset.
3956 * @param pdbEntryString
3957 * - the short name for the PDB file
3959 * - pdb file - either a URL or a valid PDB file.
3960 * @return true if binding was as success TODO: consider making an exception
3961 * structure for indicating when PDB parsing or sequenceId location
3964 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3967 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3968 boolean needtoadd = false;
3969 if (toaddpdb != null)
3971 Vector pdbe = toaddpdb.getAllPDBEntries();
3972 PDBEntry pdbentry = null;
3973 if (pdbe != null && pdbe.size() > 0)
3975 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3977 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3978 if (!pdbentry.getId().equals(pdbEntryString)
3979 && !pdbentry.getFile().equals(pdbFile))
3989 if (pdbentry == null)
3991 pdbentry = new PDBEntry();
3992 pdbentry.setId(pdbEntryString);
3993 pdbentry.setFile(pdbFile);
3994 needtoadd = true; // add this new entry to sequence.
3996 // resolve data source
3997 // TODO: this code should be a refactored to an io package
3998 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3999 if (protocol == null)
4005 // make a note of the access mode and add
4006 if (pdbentry.getProperty() == null)
4008 pdbentry.setProperty(new Hashtable());
4010 pdbentry.getProperty().put("protocol", protocol);
4011 toaddpdb.addPDBId(pdbentry);
4012 alignPanel.getStructureSelectionManager()
4013 .registerPDBEntry(pdbentry);
4019 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4023 Vector sequences = new Vector();
4024 for (int i = 0; i < seqs.length; i++)
4026 if (seqs[i] != null)
4028 sequences.addElement(new Object[] { seqs[i],
4029 (chains != null) ? chains[i] : null });
4032 seqs = new SequenceI[sequences.size()];
4033 chains = new String[sequences.size()];
4034 for (int i = 0, isize = sequences.size(); i < isize; i++)
4036 Object[] oj = (Object[]) sequences.elementAt(i);
4038 seqs[i] = (SequenceI) oj[0];
4039 chains[i] = (String) oj[1];
4042 return new Object[] { seqs, chains };
4046 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4047 SequenceI[] seqs, String[] chains, String protocol)
4049 // Scrub any null sequences from the array
4050 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4051 seqs = (SequenceI[]) sqch[0];
4052 chains = (String[]) sqch[1];
4053 if (seqs == null || seqs.length == 0)
4056 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4058 if (protocol == null || protocol.trim().length() == 0
4059 || protocol.equals("null"))
4061 protocol = (String) pdb.getProperty().get("protocol");
4062 if (protocol == null)
4064 System.err.println("Couldn't work out protocol to open structure: "
4069 if (applet.useXtrnalSviewer)
4071 // register the association(s) and quit, don't create any windows.
4072 if (StructureSelectionManager.getStructureSelectionManager(applet)
4073 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4075 System.err.println("Failed to map " + pdb.getFile() + " ("
4076 + protocol + ") to any sequences");
4080 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4082 // can only do alignments with Jmol
4083 // find the last jmol window assigned to this alignment
4084 jalview.appletgui.AppletJmol ajm = null, tajm;
4085 Vector jmols = applet
4086 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4087 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4089 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4090 if (tajm.ap.alignFrame == this)
4099 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4100 // try and add the pdb structure
4105 // otherwise, create a new window
4106 if (applet.jmolAvailable)
4108 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4110 applet.lastFrameX += 40;
4111 applet.lastFrameY += 40;
4115 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4120 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4121 SequenceI[][] seqs, String[][] chains, String[] protocols)
4123 // TODO Auto-generated method stub
4124 System.err.println("Aligned Structure View: Not yet implemented.");
4128 * modify the current selection, providing the user has not made a selection
4132 * - sequences from this alignment
4134 * - columns to be selected on the alignment
4136 public void select(SequenceGroup sel, ColumnSelection csel)
4138 alignPanel.seqPanel.selection(sel, csel, null);
4141 public void scrollTo(int row, int column)
4143 alignPanel.seqPanel.scrollTo(row, column);
4146 public void scrollToRow(int row)
4148 alignPanel.seqPanel.scrollToRow(row);
4151 public void scrollToColumn(int column)
4153 alignPanel.seqPanel.scrollToColumn(column);
4157 * @return the alignments unique ID.
4159 public String getSequenceSetId()
4161 return viewport.getSequenceSetId();
4165 * Load the (T-Coffee) score file from the specified url
4168 * File/URL/T-COFFEE score file contents
4169 * @throws IOException
4170 * @return true if alignment was annotated with data from source
4172 public boolean loadScoreFile(String source) throws IOException
4175 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4176 AppletFormatAdapter.checkProtocol(source));
4177 if (!file.isValid())
4179 // TODO: raise dialog for gui
4180 System.err.println("Problems parsing T-Coffee scores: "
4181 + file.getWarningMessage());
4182 System.err.println("Origin was:\n" + source);
4187 * check that the score matrix matches the alignment dimensions
4190 if ((aln = viewport.getAlignment()) != null
4191 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4194 // TODO: raise a dialog box here rather than bomb out.
4196 .println("The scores matrix does not match the alignment dimensions");
4200 // TODO add parameter to indicate if matching should be done
4201 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4203 alignPanel.fontChanged();
4204 tcoffeeColour.setEnabled(true);
4205 // switch to this color
4206 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4211 System.err.println("Problems resolving T-Coffee scores:");
4212 if (file.getWarningMessage() != null)
4214 System.err.println(file.getWarningMessage());
4220 public SplitFrame getSplitFrame()
4222 return this.splitFrame;
4225 public void setSplitFrame(SplitFrame sf)
4227 this.splitFrame = sf;
4230 // may not need this
4232 public void setShowSeqFeatures(boolean b)
4234 // showSeqFeatures.setSelected(b);
4235 viewport.setShowSequenceFeatures(b);
4240 public void setMenusForViewport()
4242 // setMenusFromViewport(viewport);
4247 public void refreshFeatureUI(boolean enableIfNecessary)
4249 if (enableIfNecessary)
4251 sequenceFeatures.setState(true);
4252 alignPanel.av.setShowSequenceFeatures(true);
4257 public FeatureSettingsControllerI getFeatureSettingsUI()
4259 return alignPanel.av.featureSettings;