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;
78 import java.awt.FlowLayout;
80 import java.awt.FontMetrics;
81 import java.awt.Frame;
82 import java.awt.Graphics;
83 import java.awt.Label;
85 import java.awt.MenuBar;
86 import java.awt.MenuItem;
87 import java.awt.Panel;
88 import java.awt.event.ActionEvent;
89 import java.awt.event.ActionListener;
90 import java.awt.event.FocusEvent;
91 import java.awt.event.FocusListener;
92 import java.awt.event.ItemEvent;
93 import java.awt.event.ItemListener;
94 import java.awt.event.KeyEvent;
95 import java.awt.event.KeyListener;
96 import java.awt.event.WindowAdapter;
97 import java.awt.event.WindowEvent;
98 import java.io.IOException;
100 import java.net.URLEncoder;
101 import java.util.Arrays;
102 import java.util.Deque;
103 import java.util.HashMap;
104 import java.util.Hashtable;
105 import java.util.List;
106 import java.util.Map;
107 import java.util.StringTokenizer;
108 import java.util.Vector;
110 import org.jmol.viewer.Viewer;
112 public class AlignFrame extends EmbmenuFrame implements ActionListener,
113 ItemListener, KeyListener, AlignViewControllerGuiI
115 public AlignViewControllerI avc;
117 public AlignmentPanel alignPanel;
119 public AlignViewport viewport;
121 // width and height may be overridden by applet parameters
122 int frameWidth = 700;
124 int frameHeight = 500;
126 String jalviewServletURL;
129 * Flag for showing autocalculated consensus above or below other consensus
132 private boolean showAutoCalculatedAbove;
134 private SequenceAnnotationOrder annotationSortOrder;
137 * Constructor that creates the frame and adds it to the display.
144 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
147 this(al, applet, title, embedded, true);
151 * Constructor that optionally allows the frame to be displayed or only
158 * @param addToDisplay
160 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
161 boolean embedded, boolean addToDisplay)
163 this(al, null, null, applet, title, embedded, addToDisplay);
166 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
167 ColumnSelection columnSelection, JalviewLite applet,
168 String title, boolean embedded)
170 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
173 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
174 ColumnSelection columnSelection, JalviewLite applet,
175 String title, boolean embedded, boolean addToDisplay)
179 jalviewServletURL = applet.getParameter("APPLICATION_URL");
185 } catch (Exception ex)
187 ex.printStackTrace();
189 // need to get window geometry before we calculate alignment layout
195 param = applet.getParameter("windowWidth");
198 int width = Integer.parseInt(param);
201 param = applet.getParameter("windowHeight");
204 int height = Integer.parseInt(param);
205 frameHeight = height;
207 } catch (Exception ex)
211 viewport = new AlignViewport(al, applet);
213 if (hiddenSeqs != null && hiddenSeqs.length > 0)
215 viewport.hideSequence(hiddenSeqs);
217 if (columnSelection != null)
219 viewport.setColumnSelection(columnSelection);
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
2069 if (sg.getSize() == viewport.getAlignment().getHeight())
2071 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2072 .getAlignment().getWidth()) ? true : false;
2073 if (isEntireAlignWidth)
2076 String title = MessageManager.getString("label.delete_all");
2077 Panel mp = new Panel();
2078 mp.setLayout(new FlowLayout());
2079 mp.add(new Label(MessageManager.getString("warn.delete_all")));
2081 final JVDialog dialog = new JVDialog(this, title, true, 400,
2083 dialog.setMainPanel(mp);
2084 dialog.setVisible(true);
2091 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2092 sg.getEndRes() + 1);
2095 SequenceI[] cut = new SequenceI[seqs.size()];
2096 for (int i = 0; i < seqs.size(); i++)
2098 cut[i] = (SequenceI) seqs.elementAt(i);
2102 * //ADD HISTORY ITEM
2104 addHistoryItem(new EditCommand(
2105 MessageManager.getString("label.cut_sequences"), Action.CUT,
2106 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2107 viewport.getAlignment()));
2109 viewport.setSelectionGroup(null);
2110 viewport.getAlignment().deleteGroup(sg);
2112 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2115 if (viewport.getAlignment().getHeight() < 1)
2117 this.setVisible(false);
2119 viewport.sendSelection();
2123 * group consensus toggled
2126 protected void showGroupConsensus_actionPerformed()
2128 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2129 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2134 * group conservation toggled.
2136 protected void showGroupConservation_actionPerformed()
2138 viewport.setShowGroupConservation(showGroupConservation.getState());
2139 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2146 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2147 * .event.ActionEvent)
2149 protected void showConsensusHistogram_actionPerformed()
2151 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2152 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2159 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2160 * .event.ActionEvent)
2162 protected void showSequenceLogo_actionPerformed()
2164 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2165 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2168 protected void normSequenceLogo_actionPerformed()
2170 showSequenceLogo.setState(true);
2171 viewport.setShowSequenceLogo(true);
2172 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2173 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2176 protected void applyAutoAnnotationSettings_actionPerformed()
2178 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2181 protected void makeGrpsFromSelection_actionPerformed()
2183 if (avc.makeGroupsFromSelection())
2185 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2186 alignPanel.updateAnnotation();
2187 alignPanel.paintAlignment(true);
2191 protected void createGroup_actionPerformed()
2196 protected void unGroup_actionPerformed()
2200 alignPanel.alignmentChanged();
2204 protected void deleteGroups_actionPerformed()
2206 if (avc.deleteGroups())
2208 alignPanel.alignmentChanged();
2212 public void selectAllSequenceMenuItem_actionPerformed()
2214 SequenceGroup sg = new SequenceGroup();
2215 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2217 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2219 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2220 viewport.setSelectionGroup(sg);
2221 alignPanel.paintAlignment(true);
2222 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2223 viewport.sendSelection();
2226 public void deselectAllSequenceMenuItem_actionPerformed()
2228 if (viewport.cursorMode)
2230 alignPanel.seqPanel.keyboardNo1 = null;
2231 alignPanel.seqPanel.keyboardNo2 = null;
2233 viewport.setSelectionGroup(null);
2234 viewport.getColumnSelection().clear();
2235 viewport.setSelectionGroup(null);
2236 alignPanel.idPanel.idCanvas.searchResults = null;
2237 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2238 alignPanel.paintAlignment(true);
2239 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2240 viewport.sendSelection();
2243 public void invertSequenceMenuItem_actionPerformed()
2245 SequenceGroup sg = viewport.getSelectionGroup();
2246 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2248 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2251 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2252 viewport.sendSelection();
2255 public void invertColSel_actionPerformed()
2257 viewport.invertColumnSelection();
2258 alignPanel.paintAlignment(true);
2259 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2260 viewport.sendSelection();
2263 void trimAlignment(boolean trimLeft)
2265 ColumnSelection colSel = viewport.getColumnSelection();
2268 if (colSel.size() > 0)
2272 column = colSel.getMin();
2276 column = colSel.getMax();
2280 if (viewport.getSelectionGroup() != null)
2282 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2283 viewport.getHiddenRepSequences());
2287 seqs = viewport.getAlignment().getSequencesArray();
2290 TrimRegionCommand trimRegion;
2293 trimRegion = new TrimRegionCommand("Remove Left",
2294 TrimRegionCommand.TRIM_LEFT, seqs, column,
2295 viewport.getAlignment(), viewport.getColumnSelection(),
2296 viewport.getSelectionGroup());
2297 viewport.setStartRes(0);
2301 trimRegion = new TrimRegionCommand("Remove Right",
2302 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2303 viewport.getAlignment(), viewport.getColumnSelection(),
2304 viewport.getSelectionGroup());
2307 statusBar.setText(MessageManager.formatMessage(
2308 "label.removed_columns",
2309 new String[] { Integer.valueOf(trimRegion.getSize())
2311 addHistoryItem(trimRegion);
2313 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2315 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2316 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2318 viewport.getAlignment().deleteGroup(sg);
2322 viewport.firePropertyChange("alignment", null, viewport
2323 .getAlignment().getSequences());
2327 public void removeGappedColumnMenuItem_actionPerformed()
2329 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2332 if (viewport.getSelectionGroup() != null)
2334 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2335 viewport.getHiddenRepSequences());
2336 start = viewport.getSelectionGroup().getStartRes();
2337 end = viewport.getSelectionGroup().getEndRes();
2341 seqs = viewport.getAlignment().getSequencesArray();
2344 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2345 "Remove Gapped Columns", seqs, start, end,
2346 viewport.getAlignment());
2348 addHistoryItem(removeGapCols);
2350 statusBar.setText(MessageManager.formatMessage(
2351 "label.removed_empty_columns",
2352 new String[] { Integer.valueOf(removeGapCols.getSize())
2355 // This is to maintain viewport position on first residue
2356 // of first sequence
2357 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2358 int startRes = seq.findPosition(viewport.startRes);
2359 // ShiftList shifts;
2360 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2361 // edit.alColumnChanges=shifts.getInverse();
2362 // if (viewport.hasHiddenColumns)
2363 // viewport.getColumnSelection().compensateForEdits(shifts);
2364 viewport.setStartRes(seq.findIndex(startRes) - 1);
2365 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2370 public void removeAllGapsMenuItem_actionPerformed()
2372 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2375 if (viewport.getSelectionGroup() != null)
2377 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2378 viewport.getHiddenRepSequences());
2379 start = viewport.getSelectionGroup().getStartRes();
2380 end = viewport.getSelectionGroup().getEndRes();
2384 seqs = viewport.getAlignment().getSequencesArray();
2387 // This is to maintain viewport position on first residue
2388 // of first sequence
2389 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2390 int startRes = seq.findPosition(viewport.startRes);
2392 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2393 viewport.getAlignment()));
2395 viewport.setStartRes(seq.findIndex(startRes) - 1);
2397 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2402 public void findMenuItem_actionPerformed()
2404 new Finder(alignPanel);
2408 * create a new view derived from the current view
2411 * @return frame for the new view
2413 public AlignFrame newView(String viewtitle)
2416 if (viewport.hasHiddenRows())
2418 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2419 .getFullAlignment().getSequencesArray());
2423 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2426 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2428 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2430 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2432 newal.addAnnotation(viewport.getAlignment()
2433 .getAlignmentAnnotation()[i]);
2438 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2440 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2441 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2442 PaintRefresher.Register(newaf.alignPanel,
2443 newaf.alignPanel.av.getSequenceSetId());
2445 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2446 newaf.alignPanel.av.getSequenceSetId());
2447 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2448 newaf.alignPanel.av.getSequenceSetId());
2450 Vector comps = (Vector) PaintRefresher.components.get(viewport
2451 .getSequenceSetId());
2453 for (int i = 0; i < comps.size(); i++)
2455 if (comps.elementAt(i) instanceof AlignmentPanel)
2461 String title = new String(this.getTitle());
2462 if (viewtitle != null)
2464 title = viewtitle + " ( " + title + ")";
2468 if (title.indexOf("(View") > -1)
2470 title = title.substring(0, title.indexOf("(View"));
2472 title += "(View " + viewSize + ")";
2475 newaf.setTitle(title.toString());
2477 newaf.viewport.setHistoryList(viewport.getHistoryList());
2478 newaf.viewport.setRedoList(viewport.getRedoList());
2484 * @return list of feature groups on the view
2486 public String[] getFeatureGroups()
2488 FeatureRenderer fr = null;
2489 if (alignPanel != null
2490 && (fr = alignPanel.getFeatureRenderer()) != null)
2492 List<String> gps = fr.getFeatureGroups();
2493 String[] _gps = gps.toArray(new String[gps.size()]);
2500 * get sequence feature groups that are hidden or shown
2506 public String[] getFeatureGroupsOfState(boolean visible)
2508 FeatureRenderer fr = null;
2509 if (alignPanel != null
2510 && (fr = alignPanel.getFeatureRenderer()) != null)
2512 List<String> gps = fr.getGroups(visible);
2513 String[] _gps = gps.toArray(new String[gps.size()]);
2520 * Change the display state for the given feature groups
2523 * list of group strings
2525 * visible or invisible
2527 public void setFeatureGroupState(String[] groups, boolean state)
2529 FeatureRenderer fr = null;
2530 this.sequenceFeatures.setState(true);
2531 viewport.setShowSequenceFeatures(true);
2532 if (alignPanel != null
2533 && (fr = alignPanel.getFeatureRenderer()) != null)
2536 fr.setGroupVisibility(Arrays.asList(groups), state);
2537 alignPanel.seqPanel.seqCanvas.repaint();
2538 if (alignPanel.overviewPanel != null)
2540 alignPanel.overviewPanel.updateOverviewImage();
2545 public void seqLimits_itemStateChanged()
2547 viewport.setShowJVSuffix(seqLimits.getState());
2548 alignPanel.fontChanged();
2549 alignPanel.paintAlignment(true);
2552 protected void colourTextMenuItem_actionPerformed()
2554 viewport.setColourText(colourTextMenuItem.getState());
2555 alignPanel.paintAlignment(true);
2558 protected void displayNonconservedMenuItem_actionPerformed()
2560 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2561 alignPanel.paintAlignment(true);
2564 protected void wrapMenuItem_actionPerformed()
2566 viewport.setWrapAlignment(wrapMenuItem.getState());
2567 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2568 scaleAbove.setEnabled(wrapMenuItem.getState());
2569 scaleLeft.setEnabled(wrapMenuItem.getState());
2570 scaleRight.setEnabled(wrapMenuItem.getState());
2571 alignPanel.paintAlignment(true);
2574 public void overviewMenuItem_actionPerformed()
2576 if (alignPanel.overviewPanel != null)
2581 Frame frame = new Frame();
2582 OverviewPanel overview = new OverviewPanel(alignPanel);
2583 frame.add(overview);
2584 // +50 must allow for applet frame window
2585 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2586 "label.overview_params", new String[] { this.getTitle() }),
2587 overview.getPreferredSize().width,
2588 overview.getPreferredSize().height + 50);
2591 final AlignmentPanel ap = alignPanel;
2592 frame.addWindowListener(new WindowAdapter()
2595 public void windowClosing(WindowEvent e)
2599 ap.setOverviewPanel(null);
2604 alignPanel.setOverviewPanel(overview);
2608 public void changeColour(ColourSchemeI cs)
2613 if (viewport.getAbovePIDThreshold())
2615 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2619 if (viewport.getConservationSelected())
2621 cs.setConservationApplied(true);
2622 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2627 cs.setConservationApplied(false);
2630 viewport.setGlobalColourScheme(cs);
2632 alignPanel.paintAlignment(true);
2635 protected void modifyPID_actionPerformed()
2637 if (viewport.getAbovePIDThreshold()
2638 && viewport.getGlobalColourScheme() != null)
2640 SliderPanel.setPIDSliderSource(alignPanel,
2641 viewport.getGlobalColourScheme(), "Background");
2642 SliderPanel.showPIDSlider();
2646 protected void modifyConservation_actionPerformed()
2648 if (viewport.getConservationSelected()
2649 && viewport.getGlobalColourScheme() != null)
2651 SliderPanel.setConservationSlider(alignPanel,
2652 viewport.getGlobalColourScheme(), "Background");
2653 SliderPanel.showConservationSlider();
2657 protected void conservationMenuItem_actionPerformed()
2659 viewport.setConservationSelected(conservationMenuItem.getState());
2661 viewport.setAbovePIDThreshold(false);
2662 abovePIDThreshold.setState(false);
2664 changeColour(viewport.getGlobalColourScheme());
2666 modifyConservation_actionPerformed();
2669 public void abovePIDThreshold_actionPerformed()
2671 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2673 conservationMenuItem.setState(false);
2674 viewport.setConservationSelected(false);
2676 changeColour(viewport.getGlobalColourScheme());
2678 modifyPID_actionPerformed();
2681 public void sortPairwiseMenuItem_actionPerformed()
2683 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2684 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2685 .getAlignment().getSequenceAt(0), null);
2687 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2688 viewport.getAlignment()));
2689 alignPanel.paintAlignment(true);
2692 public void sortIDMenuItem_actionPerformed()
2694 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2695 AlignmentSorter.sortByID(viewport.getAlignment());
2696 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2697 viewport.getAlignment()));
2698 alignPanel.paintAlignment(true);
2701 public void sortLengthMenuItem_actionPerformed()
2703 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2704 AlignmentSorter.sortByLength(viewport.getAlignment());
2705 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2706 viewport.getAlignment()));
2707 alignPanel.paintAlignment(true);
2710 public void sortGroupMenuItem_actionPerformed()
2712 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2713 AlignmentSorter.sortByGroup(viewport.getAlignment());
2714 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2715 viewport.getAlignment()));
2716 alignPanel.paintAlignment(true);
2720 public void removeRedundancyMenuItem_actionPerformed()
2722 new RedundancyPanel(alignPanel);
2725 public void pairwiseAlignmentMenuItem_actionPerformed()
2727 if (viewport.getSelectionGroup() != null
2728 && viewport.getSelectionGroup().getSize() > 1)
2730 Frame frame = new Frame();
2731 frame.add(new PairwiseAlignPanel(alignPanel));
2732 jalview.bin.JalviewLite.addFrame(frame,
2733 MessageManager.getString("action.pairwise_alignment"), 600,
2738 public void PCAMenuItem_actionPerformed()
2740 // are the sequences aligned?
2741 if (!viewport.getAlignment().isAligned(false))
2744 int Width = viewport.getAlignment().getWidth();
2746 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2748 current = viewport.getAlignment().getSequenceAt(i);
2750 if (current.getLength() < Width)
2752 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2755 alignPanel.paintAlignment(true);
2758 if ((viewport.getSelectionGroup() != null
2759 && viewport.getSelectionGroup().getSize() < 4 && viewport
2760 .getSelectionGroup().getSize() > 0)
2761 || viewport.getAlignment().getHeight() < 4)
2768 new PCAPanel(viewport);
2769 } catch (java.lang.OutOfMemoryError ex)
2775 public void averageDistanceTreeMenuItem_actionPerformed()
2777 NewTreePanel("AV", "PID", "Average distance tree using PID");
2780 public void neighbourTreeMenuItem_actionPerformed()
2782 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2785 protected void njTreeBlosumMenuItem_actionPerformed()
2787 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2790 protected void avTreeBlosumMenuItem_actionPerformed()
2792 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2795 void NewTreePanel(String type, String pwType, String title)
2797 // are the sequences aligned?
2798 if (!viewport.getAlignment().isAligned(false))
2801 int Width = viewport.getAlignment().getWidth();
2803 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2805 current = viewport.getAlignment().getSequenceAt(i);
2807 if (current.getLength() < Width)
2809 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2812 alignPanel.paintAlignment(true);
2816 if ((viewport.getSelectionGroup() != null && viewport
2817 .getSelectionGroup().getSize() > 1)
2818 || (viewport.getAlignment().getHeight() > 1))
2820 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2822 addTreeMenuItem(tp, title);
2824 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2828 void loadTree_actionPerformed()
2830 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2831 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2832 cap.setTreeImport();
2833 Frame frame = new Frame();
2835 jalview.bin.JalviewLite.addFrame(frame,
2836 MessageManager.getString("label.paste_newick_file"), 400, 300);
2839 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2841 TreePanel tp = new TreePanel(alignPanel, treeFile,
2842 MessageManager.getString("label.load_tree_from_file"), tree);
2843 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2844 addTreeMenuItem(tp, treeFile);
2848 * sort the alignment using the given treePanel
2851 * tree used to sort view
2853 * string used for undo event name
2855 public void sortByTree(TreePanel treePanel, String title)
2857 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2859 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2860 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2861 // HistoryItem.SORT));
2862 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2863 "label.order_by_params", new String[] { title }), oldOrder,
2864 viewport.getAlignment()));
2865 alignPanel.paintAlignment(true);
2869 * Do any automatic reordering of the alignment and add the necessary bits to
2870 * the menu structure for the new tree
2875 protected void addTreeMenuItem(final TreePanel treePanel,
2878 final MenuItem item = new MenuItem(title);
2879 sortByTreeMenu.add(item);
2880 item.addActionListener(new java.awt.event.ActionListener()
2883 public void actionPerformed(ActionEvent evt)
2885 sortByTree(treePanel, title); // treePanel.getTitle());
2889 treePanel.addWindowListener(new WindowAdapter()
2892 public void windowOpened(WindowEvent e)
2894 if (viewport.sortByTree)
2896 sortByTree(treePanel, title);
2898 super.windowOpened(e);
2902 public void windowClosing(WindowEvent e)
2904 sortByTreeMenu.remove(item);
2909 public boolean sortBy(AlignmentOrder alorder, String undoname)
2911 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2912 if (viewport.applet.debug)
2914 System.err.println("Sorting " + alorder.getOrder().size()
2915 + " in alignment '" + getTitle() + "'");
2917 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2918 if (undoname != null)
2920 addHistoryItem(new OrderCommand(undoname, oldOrder,
2921 viewport.getAlignment()));
2923 alignPanel.paintAlignment(true);
2927 protected void documentation_actionPerformed()
2929 alignPanel.av.applet.openJalviewHelpUrl();
2932 protected void about_actionPerformed()
2935 class AboutPanel extends Canvas
2941 public AboutPanel(String version, String builddate)
2943 this.version = version;
2944 this.builddate = builddate;
2948 public void paint(Graphics g)
2950 g.setColor(Color.white);
2951 g.fillRect(0, 0, getSize().width, getSize().height);
2952 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2953 FontMetrics fm = g.getFontMetrics();
2954 int fh = fm.getHeight();
2956 g.setColor(Color.black);
2957 // TODO: update this text for each release or centrally store it for
2958 // lite and application
2959 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2960 g.drawString(MessageManager.formatMessage(
2961 "label.jalviewLite_release", new String[] { version }), x,
2963 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2964 g.drawString(MessageManager.formatMessage(
2965 "label.jaview_build_date", new String[] { builddate }), x,
2967 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2968 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2970 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2971 x + 50, y += fh + 8);
2973 MessageManager.getString("label.jalview_dev_managers"), x,
2975 g.drawString(MessageManager
2976 .getString("label.jalview_distribution_lists"), x, y += fh);
2977 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2980 MessageManager.getString("label.jalview_cite_1_authors"),
2983 MessageManager.getString("label.jalview_cite_1_title"), x,
2985 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2990 Frame frame = new Frame();
2991 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2993 jalview.bin.JalviewLite.addFrame(frame,
2994 MessageManager.getString("label.jalview"), 580, 220);
2998 public void showURL(String url, String target)
3000 if (viewport.applet == null)
3002 System.out.println("Not running as applet - no browser available.");
3006 viewport.applet.showURL(url, target);
3010 // ////////////////////////////////////////////////////////////////////////////////
3011 // JBuilder Graphics here
3013 MenuBar alignFrameMenuBar = new MenuBar();
3015 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3017 MenuItem loadApplication = new MenuItem(
3018 MessageManager.getString("label.view_full_application"));
3020 MenuItem loadTree = new MenuItem(
3021 MessageManager.getString("label.load_associated_tree"));
3023 MenuItem loadAnnotations = new MenuItem(
3024 MessageManager.getString("label.load_features_annotations"));
3026 MenuItem outputFeatures = new MenuItem(
3027 MessageManager.getString("label.export_features"));
3029 MenuItem outputAnnotations = new MenuItem(
3030 MessageManager.getString("label.export_annotations"));
3032 MenuItem closeMenuItem = new MenuItem(
3033 MessageManager.getString("action.close"));
3035 MenuItem selectAllSequenceMenuItem = new MenuItem(
3036 MessageManager.getString("action.select_all"));
3038 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3039 MessageManager.getString("action.deselect_all"));
3041 MenuItem invertSequenceMenuItem = new MenuItem(
3042 MessageManager.getString("action.invert_selection"));
3044 MenuItem remove2LeftMenuItem = new MenuItem();
3046 MenuItem remove2RightMenuItem = new MenuItem();
3048 MenuItem removeGappedColumnMenuItem = new MenuItem();
3050 MenuItem removeAllGapsMenuItem = new MenuItem();
3052 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3054 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3056 MenuItem sortPairwiseMenuItem = new MenuItem();
3058 MenuItem sortIDMenuItem = new MenuItem();
3060 MenuItem sortLengthMenuItem = new MenuItem();
3062 MenuItem sortGroupMenuItem = new MenuItem();
3064 MenuItem removeRedundancyMenuItem = new MenuItem();
3066 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3068 MenuItem PCAMenuItem = new MenuItem();
3070 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3072 MenuItem neighbourTreeMenuItem = new MenuItem();
3074 BorderLayout borderLayout1 = new BorderLayout();
3076 public Label statusBar = new Label();
3078 MenuItem clustalColour = new MenuItem();
3080 MenuItem zappoColour = new MenuItem();
3082 MenuItem taylorColour = new MenuItem();
3084 MenuItem hydrophobicityColour = new MenuItem();
3086 MenuItem helixColour = new MenuItem();
3088 MenuItem strandColour = new MenuItem();
3090 MenuItem turnColour = new MenuItem();
3092 MenuItem buriedColour = new MenuItem();
3094 MenuItem purinePyrimidineColour = new MenuItem();
3096 // MenuItem RNAInteractionColour = new MenuItem();
3098 MenuItem RNAHelixColour = new MenuItem();
3100 MenuItem userDefinedColour = new MenuItem();
3102 MenuItem PIDColour = new MenuItem();
3104 MenuItem BLOSUM62Colour = new MenuItem();
3106 MenuItem tcoffeeColour = new MenuItem();
3108 MenuItem njTreeBlosumMenuItem = new MenuItem();
3110 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3112 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3114 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3116 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3118 MenuItem alProperties = new MenuItem(
3119 MessageManager.getString("label.alignment_props"));
3121 MenuItem overviewMenuItem = new MenuItem();
3123 MenuItem undoMenuItem = new MenuItem();
3125 MenuItem redoMenuItem = new MenuItem();
3127 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3129 MenuItem noColourmenuItem = new MenuItem();
3131 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3133 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3135 MenuItem findMenuItem = new MenuItem();
3137 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3139 MenuItem nucleotideColour = new MenuItem();
3141 MenuItem deleteGroups = new MenuItem();
3143 MenuItem grpsFromSelection = new MenuItem();
3145 MenuItem createGroup = new MenuItem();
3147 MenuItem unGroup = new MenuItem();
3149 MenuItem delete = new MenuItem();
3151 MenuItem copy = new MenuItem();
3153 MenuItem cut = new MenuItem();
3155 Menu pasteMenu = new Menu();
3157 MenuItem pasteNew = new MenuItem();
3159 MenuItem pasteThis = new MenuItem();
3161 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3163 MenuItem font = new MenuItem();
3165 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3167 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3169 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3171 MenuItem modifyPID = new MenuItem();
3173 MenuItem modifyConservation = new MenuItem();
3175 CheckboxMenuItem autoCalculate = null;
3177 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3178 "Sort Alignment With New Tree", true);
3180 Menu sortByTreeMenu = new Menu();
3182 MenuItem inputText = new MenuItem();
3184 MenuItem documentation = new MenuItem();
3186 MenuItem about = new MenuItem();
3188 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3190 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3192 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3194 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3196 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3198 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3200 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3202 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3204 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3207 * Initialise menus and other items
3211 private void jbInit() throws Exception
3213 setMenuBar(alignFrameMenuBar);
3216 * Configure File menu items and actions
3219 .setLabel(MessageManager.getString("label.input_from_textbox"));
3220 inputText.addActionListener(this);
3221 Menu outputTextboxMenu = new Menu(
3222 MessageManager.getString("label.out_to_textbox"));
3223 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3226 MenuItem item = new MenuItem(
3227 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3229 item.addActionListener(new java.awt.event.ActionListener()
3232 public void actionPerformed(ActionEvent e)
3234 outputText_actionPerformed(e);
3238 outputTextboxMenu.add(item);
3240 closeMenuItem.addActionListener(this);
3241 loadApplication.addActionListener(this);
3242 loadTree.addActionListener(this);
3243 loadAnnotations.addActionListener(this);
3244 outputFeatures.addActionListener(this);
3245 outputAnnotations.addActionListener(this);
3248 * Configure Edit menu items and actions
3250 undoMenuItem.setEnabled(false);
3251 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3252 undoMenuItem.addActionListener(this);
3253 redoMenuItem.setEnabled(false);
3254 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3255 redoMenuItem.addActionListener(this);
3256 copy.setLabel(MessageManager.getString("action.copy"));
3257 copy.addActionListener(this);
3258 cut.setLabel(MessageManager.getString("action.cut"));
3259 cut.addActionListener(this);
3260 delete.setLabel(MessageManager.getString("action.delete"));
3261 delete.addActionListener(this);
3262 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3263 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3264 pasteNew.addActionListener(this);
3265 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3266 pasteThis.addActionListener(this);
3267 remove2LeftMenuItem.setLabel(MessageManager
3268 .getString("action.remove_left"));
3269 remove2LeftMenuItem.addActionListener(this);
3270 remove2RightMenuItem.setLabel(MessageManager
3271 .getString("action.remove_right"));
3272 remove2RightMenuItem.addActionListener(this);
3273 removeGappedColumnMenuItem.setLabel(MessageManager
3274 .getString("action.remove_empty_columns"));
3275 removeGappedColumnMenuItem.addActionListener(this);
3276 removeAllGapsMenuItem.setLabel(MessageManager
3277 .getString("action.remove_all_gaps"));
3278 removeAllGapsMenuItem.addActionListener(this);
3279 removeRedundancyMenuItem.setLabel(MessageManager
3280 .getString("action.remove_redundancy"));
3281 removeRedundancyMenuItem.addActionListener(this);
3284 * Configure Select menu items and actions
3286 findMenuItem.setLabel(MessageManager.getString("action.find"));
3287 findMenuItem.addActionListener(this);
3288 selectAllSequenceMenuItem.addActionListener(this);
3289 deselectAllSequenceMenuItem.addActionListener(this);
3290 invertSequenceMenuItem.setLabel(MessageManager
3291 .getString("action.invert_sequence_selection"));
3292 invertSequenceMenuItem.addActionListener(this);
3293 invertColSel.setLabel(MessageManager
3294 .getString("action.invert_column_selection"));
3295 invertColSel.addActionListener(this);
3296 deleteGroups.setLabel(MessageManager
3297 .getString("action.undefine_groups"));
3298 deleteGroups.addActionListener(this);
3299 grpsFromSelection.setLabel(MessageManager
3300 .getString("action.make_groups_selection"));
3301 grpsFromSelection.addActionListener(this);
3302 createGroup.setLabel(MessageManager.getString("action.create_group"));
3303 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3304 annotationColumnSelection.setLabel(MessageManager
3305 .getString("action.select_by_annotation"));
3306 annotationColumnSelection.addActionListener(this);
3309 * Configure View menu items and actions
3311 newView.setLabel(MessageManager.getString("action.new_view"));
3312 newView.addActionListener(this);
3313 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3314 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3315 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3316 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3318 .setLabel(MessageManager.getString("label.selected_columns"));
3319 hideSequences.setLabel(MessageManager
3320 .getString("label.selected_sequences"));
3321 hideAllButSelection.setLabel(MessageManager
3322 .getString("label.all_but_selected_region"));
3323 hideAllSelection.setLabel(MessageManager
3324 .getString("label.selected_region"));
3325 showAllHidden.setLabel(MessageManager
3326 .getString("label.all_sequences_columns"));
3327 showColumns.addActionListener(this);
3328 showSeqs.addActionListener(this);
3329 hideColumns.addActionListener(this);
3330 hideSequences.addActionListener(this);
3331 hideAllButSelection.addActionListener(this);
3332 hideAllSelection.addActionListener(this);
3333 showAllHidden.addActionListener(this);
3334 featureSettings.setLabel(MessageManager
3335 .getString("action.feature_settings"));
3336 featureSettings.addActionListener(this);
3337 sequenceFeatures.setLabel(MessageManager
3338 .getString("label.show_sequence_features"));
3339 sequenceFeatures.addItemListener(this);
3340 sequenceFeatures.setState(false);
3341 followMouseOverFlag.setLabel(MessageManager
3342 .getString("label.automatic_scrolling"));
3343 followMouseOverFlag.addItemListener(this);
3344 alProperties.addActionListener(this);
3345 overviewMenuItem.setLabel(MessageManager
3346 .getString("label.overview_window"));
3347 overviewMenuItem.addActionListener(this);
3350 * Configure Annotations menu items and actions
3352 annotationPanelMenuItem.setLabel(MessageManager
3353 .getString("label.show_annotations"));
3354 annotationPanelMenuItem.addItemListener(this);
3355 showGroupConsensus.setLabel(MessageManager
3356 .getString("label.group_consensus"));
3357 showGroupConservation.setLabel(MessageManager
3358 .getString("label.group_conservation"));
3359 showConsensusHistogram.setLabel(MessageManager
3360 .getString("label.show_consensus_histogram"));
3361 showSequenceLogo.setLabel(MessageManager
3362 .getString("label.show_consensus_logo"));
3363 normSequenceLogo.setLabel(MessageManager
3364 .getString("label.norm_consensus_logo"));
3365 applyAutoAnnotationSettings.setLabel(MessageManager
3366 .getString("label.apply_all_groups"));
3367 applyAutoAnnotationSettings.setState(true);
3368 Menu autoAnnMenu = new Menu(
3369 MessageManager.getString("label.autocalculated_annotation"));
3370 showGroupConsensus.addItemListener(this);
3371 showGroupConservation.addItemListener(this);
3372 showConsensusHistogram.addItemListener(this);
3373 showSequenceLogo.addItemListener(this);
3374 normSequenceLogo.addItemListener(this);
3375 applyAutoAnnotationSettings.addItemListener(this);
3376 showAlignmentAnnotations = new CheckboxMenuItem(
3377 MessageManager.getString("label.show_all_al_annotations"));
3378 showSequenceAnnotations = new CheckboxMenuItem(
3379 MessageManager.getString("label.show_all_seq_annotations"));
3380 sortAnnBySequence = new CheckboxMenuItem(
3381 MessageManager.getString("label.sort_annotations_by_sequence"));
3382 sortAnnByLabel = new CheckboxMenuItem(
3383 MessageManager.getString("label.sort_annotations_by_label"));
3384 showAutoFirst = new CheckboxMenuItem(
3385 MessageManager.getString("label.show_first"));
3386 showAutoFirst.setState(false); // pending applet parameter
3387 setShowAutoCalculatedAbove(showAutoFirst.getState());
3388 showAutoLast = new CheckboxMenuItem(
3389 MessageManager.getString("label.show_last"));
3390 showAutoLast.setState(!showAutoFirst.getState());
3391 showAlignmentAnnotations.addItemListener(this);
3392 showSequenceAnnotations.addItemListener(this);
3393 sortAnnBySequence.addItemListener(this);
3394 sortAnnByLabel.addItemListener(this);
3395 showAutoFirst.addItemListener(this);
3396 showAutoLast.addItemListener(this);
3399 * Configure Format menu items and actions
3401 font.setLabel(MessageManager.getString("action.font"));
3402 font.addActionListener(this);
3403 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3404 scaleAbove.setState(true);
3405 scaleAbove.setEnabled(false);
3406 scaleAbove.addItemListener(this);
3407 scaleLeft.setEnabled(false);
3408 scaleLeft.setState(true);
3409 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3410 scaleLeft.addItemListener(this);
3411 scaleRight.setEnabled(false);
3412 scaleRight.setState(true);
3413 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3414 scaleRight.addItemListener(this);
3415 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3416 viewBoxesMenuItem.setState(true);
3417 viewBoxesMenuItem.addItemListener(this);
3418 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3419 viewTextMenuItem.setState(true);
3420 viewTextMenuItem.addItemListener(this);
3421 colourTextMenuItem.setLabel(MessageManager
3422 .getString("label.colour_text"));
3423 colourTextMenuItem.addItemListener(this);
3424 displayNonconservedMenuItem.setLabel(MessageManager
3425 .getString("label.show_non_conversed"));
3426 displayNonconservedMenuItem.addItemListener(this);
3427 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3428 wrapMenuItem.addItemListener(this);
3429 renderGapsMenuItem.setLabel(MessageManager
3430 .getString("action.show_gaps"));
3431 renderGapsMenuItem.setState(true);
3432 renderGapsMenuItem.addItemListener(this);
3433 centreColumnLabelFlag.setLabel(MessageManager
3434 .getString("label.centre_column_labels"));
3435 centreColumnLabelFlag.addItemListener(this);
3436 seqLimits.setState(true);
3437 seqLimits.setLabel(MessageManager
3438 .getString("label.show_sequence_limits"));
3439 seqLimits.addItemListener(this);
3442 * Configure Colour menu items and actions
3444 applyToAllGroups.setLabel(MessageManager
3445 .getString("label.apply_colour_to_all_groups"));
3446 applyToAllGroups.setState(true);
3447 applyToAllGroups.addItemListener(this);
3448 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3449 clustalColour.addActionListener(this);
3450 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3451 zappoColour.addActionListener(this);
3452 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3453 taylorColour.addActionListener(this);
3454 hydrophobicityColour.setLabel(MessageManager
3455 .getString("label.hydrophobicity"));
3456 hydrophobicityColour.addActionListener(this);
3458 .setLabel(MessageManager.getString("label.helix_propensity"));
3459 helixColour.addActionListener(this);
3460 strandColour.setLabel(MessageManager
3461 .getString("label.strand_propensity"));
3462 strandColour.addActionListener(this);
3463 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3464 turnColour.addActionListener(this);
3465 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3466 buriedColour.addActionListener(this);
3467 purinePyrimidineColour.setLabel(MessageManager
3468 .getString("label.purine_pyrimidine"));
3469 purinePyrimidineColour.addActionListener(this);
3470 // RNAInteractionColour.setLabel(MessageManager
3471 // .getString("label.rna_interaction"));
3472 // RNAInteractionColour.addActionListener(this);
3473 RNAHelixColour.setLabel(MessageManager
3474 .getString("action.by_rna_helixes"));
3475 RNAHelixColour.addActionListener(this);
3476 userDefinedColour.setLabel(MessageManager
3477 .getString("action.user_defined"));
3478 userDefinedColour.addActionListener(this);
3479 PIDColour.setLabel(MessageManager
3480 .getString("label.percentage_identity"));
3481 PIDColour.addActionListener(this);
3482 BLOSUM62Colour.setLabel(MessageManager
3483 .getString("label.blosum62_score"));
3484 BLOSUM62Colour.addActionListener(this);
3486 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3487 // it will be enabled only if a score file is provided
3488 tcoffeeColour.setEnabled(false);
3489 tcoffeeColour.addActionListener(this);
3490 conservationMenuItem.setLabel(MessageManager
3491 .getString("action.by_conservation"));
3492 conservationMenuItem.addItemListener(this);
3493 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3494 noColourmenuItem.addActionListener(this);
3495 abovePIDThreshold.setLabel(MessageManager
3496 .getString("label.above_identity_threshold"));
3497 abovePIDThreshold.addItemListener(this);
3498 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3499 nucleotideColour.addActionListener(this);
3500 modifyPID.setLabel(MessageManager
3501 .getString("label.modify_identity_thereshold"));
3502 modifyPID.addActionListener(this);
3503 modifyConservation.setLabel(MessageManager
3504 .getString("label.modify_conservation_thereshold"));
3505 modifyConservation.addActionListener(this);
3506 annotationColour.setLabel(MessageManager
3507 .getString("action.by_annotation"));
3508 annotationColour.addActionListener(this);
3511 * Configure Calculate menu items and actions
3513 sortPairwiseMenuItem.setLabel(MessageManager
3514 .getString("action.by_pairwise_id"));
3515 sortPairwiseMenuItem.addActionListener(this);
3516 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3517 sortIDMenuItem.addActionListener(this);
3518 sortLengthMenuItem.setLabel(MessageManager
3519 .getString("action.by_length"));
3520 sortLengthMenuItem.addActionListener(this);
3521 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3522 sortGroupMenuItem.addActionListener(this);
3523 pairwiseAlignmentMenuItem.setLabel(MessageManager
3524 .getString("action.pairwise_alignment"));
3525 pairwiseAlignmentMenuItem.addActionListener(this);
3526 PCAMenuItem.setLabel(MessageManager
3527 .getString("label.principal_component_analysis"));
3528 PCAMenuItem.addActionListener(this);
3529 autoCalculate = new CheckboxMenuItem(
3530 MessageManager.getString("label.autocalculate_consensus"), true);
3531 averageDistanceTreeMenuItem.setLabel(MessageManager
3532 .getString("label.average_distance_identity"));
3533 averageDistanceTreeMenuItem.addActionListener(this);
3534 neighbourTreeMenuItem.setLabel(MessageManager
3535 .getString("label.neighbour_joining_identity"));
3536 neighbourTreeMenuItem.addActionListener(this);
3537 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3538 .getString("label.average_distance_bloslum62"));
3539 avDistanceTreeBlosumMenuItem.addActionListener(this);
3540 njTreeBlosumMenuItem.setLabel(MessageManager
3541 .getString("label.neighbour_blosum62"));
3542 njTreeBlosumMenuItem.addActionListener(this);
3543 sortByTreeMenu.setLabel(MessageManager
3544 .getString("action.by_tree_order"));
3545 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3546 Menu calculateTreeMenu = new Menu(
3547 MessageManager.getString("action.calculate_tree"));
3548 autoCalculate.addItemListener(this);
3549 sortByTree.addItemListener(this);
3552 * Configure Help menu items and actions
3554 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3555 documentation.setLabel(MessageManager.getString("label.documentation"));
3556 documentation.addActionListener(this);
3557 about.setLabel(MessageManager.getString("label.about"));
3558 about.addActionListener(this);
3561 * Add top level menus to frame
3563 alignFrameMenuBar.add(fileMenu);
3564 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3565 alignFrameMenuBar.add(editMenu);
3566 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3567 alignFrameMenuBar.add(selectMenu);
3568 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3569 alignFrameMenuBar.add(viewMenu);
3570 Menu annotationsMenu = new Menu(
3571 MessageManager.getString("action.annotations"));
3572 alignFrameMenuBar.add(annotationsMenu);
3573 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3574 alignFrameMenuBar.add(formatMenu);
3575 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3576 alignFrameMenuBar.add(colourMenu);
3577 Menu calculateMenu = new Menu(
3578 MessageManager.getString("action.calculate"));
3579 alignFrameMenuBar.add(calculateMenu);
3580 alignFrameMenuBar.add(helpMenu);
3585 fileMenu.add(inputText);
3586 fileMenu.add(loadTree);
3587 fileMenu.add(loadAnnotations);
3588 fileMenu.addSeparator();
3589 fileMenu.add(outputTextboxMenu);
3590 fileMenu.add(outputFeatures);
3591 fileMenu.add(outputAnnotations);
3592 if (jalviewServletURL != null)
3594 fileMenu.add(loadApplication);
3596 fileMenu.addSeparator();
3597 fileMenu.add(closeMenuItem);
3602 editMenu.add(undoMenuItem);
3603 editMenu.add(redoMenuItem);
3606 pasteMenu.add(pasteNew);
3607 pasteMenu.add(pasteThis);
3608 editMenu.add(pasteMenu);
3609 editMenu.add(delete);
3610 editMenu.addSeparator();
3611 editMenu.add(remove2LeftMenuItem);
3612 editMenu.add(remove2RightMenuItem);
3613 editMenu.add(removeGappedColumnMenuItem);
3614 editMenu.add(removeAllGapsMenuItem);
3615 editMenu.add(removeRedundancyMenuItem);
3620 selectMenu.add(findMenuItem);
3621 selectMenu.addSeparator();
3622 selectMenu.add(selectAllSequenceMenuItem);
3623 selectMenu.add(deselectAllSequenceMenuItem);
3624 selectMenu.add(invertSequenceMenuItem);
3625 selectMenu.add(invertColSel);
3626 selectMenu.add(createGroup);
3627 selectMenu.add(unGroup);
3628 selectMenu.add(grpsFromSelection);
3629 selectMenu.add(deleteGroups);
3630 selectMenu.add(annotationColumnSelection);
3635 viewMenu.add(newView);
3636 viewMenu.addSeparator();
3637 showMenu.add(showColumns);
3638 showMenu.add(showSeqs);
3639 showMenu.add(showAllHidden);
3640 viewMenu.add(showMenu);
3641 hideMenu.add(hideColumns);
3642 hideMenu.add(hideSequences);
3643 hideMenu.add(hideAllSelection);
3644 hideMenu.add(hideAllButSelection);
3645 viewMenu.add(hideMenu);
3646 viewMenu.addSeparator();
3647 viewMenu.add(followMouseOverFlag);
3648 viewMenu.addSeparator();
3649 viewMenu.add(sequenceFeatures);
3650 viewMenu.add(featureSettings);
3651 viewMenu.addSeparator();
3652 viewMenu.add(alProperties);
3653 viewMenu.addSeparator();
3654 viewMenu.add(overviewMenuItem);
3659 annotationsMenu.add(annotationPanelMenuItem);
3660 annotationsMenu.addSeparator();
3661 annotationsMenu.add(showAlignmentAnnotations);
3662 annotationsMenu.add(showSequenceAnnotations);
3663 annotationsMenu.add(sortAnnBySequence);
3664 annotationsMenu.add(sortAnnByLabel);
3665 annotationsMenu.addSeparator();
3666 autoAnnMenu.add(showAutoFirst);
3667 autoAnnMenu.add(showAutoLast);
3668 autoAnnMenu.addSeparator();
3669 autoAnnMenu.add(applyAutoAnnotationSettings);
3670 autoAnnMenu.add(showConsensusHistogram);
3671 autoAnnMenu.add(showSequenceLogo);
3672 autoAnnMenu.add(normSequenceLogo);
3673 autoAnnMenu.addSeparator();
3674 autoAnnMenu.add(showGroupConservation);
3675 autoAnnMenu.add(showGroupConsensus);
3676 annotationsMenu.add(autoAnnMenu);
3681 formatMenu.add(font);
3682 formatMenu.add(seqLimits);
3683 formatMenu.add(wrapMenuItem);
3684 formatMenu.add(scaleAbove);
3685 formatMenu.add(scaleLeft);
3686 formatMenu.add(scaleRight);
3687 formatMenu.add(viewBoxesMenuItem);
3688 formatMenu.add(viewTextMenuItem);
3689 formatMenu.add(colourTextMenuItem);
3690 formatMenu.add(displayNonconservedMenuItem);
3691 formatMenu.add(renderGapsMenuItem);
3692 formatMenu.add(centreColumnLabelFlag);
3697 colourMenu.add(applyToAllGroups);
3698 colourMenu.addSeparator();
3699 colourMenu.add(noColourmenuItem);
3700 colourMenu.add(clustalColour);
3701 colourMenu.add(BLOSUM62Colour);
3702 colourMenu.add(PIDColour);
3703 colourMenu.add(zappoColour);
3704 colourMenu.add(taylorColour);
3705 colourMenu.add(hydrophobicityColour);
3706 colourMenu.add(helixColour);
3707 colourMenu.add(strandColour);
3708 colourMenu.add(turnColour);
3709 colourMenu.add(buriedColour);
3710 colourMenu.add(nucleotideColour);
3711 colourMenu.add(purinePyrimidineColour);
3712 // colourMenu.add(RNAInteractionColour);
3713 colourMenu.add(tcoffeeColour);
3714 colourMenu.add(userDefinedColour);
3715 colourMenu.addSeparator();
3716 colourMenu.add(conservationMenuItem);
3717 colourMenu.add(modifyConservation);
3718 colourMenu.add(abovePIDThreshold);
3719 colourMenu.add(modifyPID);
3720 colourMenu.add(annotationColour);
3721 colourMenu.add(RNAHelixColour);
3726 sortMenu.add(sortIDMenuItem);
3727 sortMenu.add(sortLengthMenuItem);
3728 sortMenu.add(sortByTreeMenu);
3729 sortMenu.add(sortGroupMenuItem);
3730 sortMenu.add(sortPairwiseMenuItem);
3731 calculateMenu.add(sortMenu);
3732 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3733 calculateTreeMenu.add(neighbourTreeMenuItem);
3734 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3735 calculateTreeMenu.add(njTreeBlosumMenuItem);
3736 calculateMenu.add(calculateTreeMenu);
3737 calculateMenu.addSeparator();
3738 calculateMenu.add(pairwiseAlignmentMenuItem);
3739 calculateMenu.add(PCAMenuItem);
3740 calculateMenu.add(autoCalculate);
3741 calculateMenu.add(sortByTree);
3746 helpMenu.add(documentation);
3747 helpMenu.add(about);
3752 statusBar.setBackground(Color.white);
3753 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3754 statusBar.setText(MessageManager.getString("label.status_bar"));
3755 this.add(statusBar, BorderLayout.SOUTH);
3758 public void setStatus(String string)
3760 statusBar.setText(string);
3763 MenuItem featureSettings = new MenuItem();
3765 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3767 MenuItem annotationColour = new MenuItem();
3769 MenuItem annotationColumnSelection = new MenuItem();
3771 MenuItem invertColSel = new MenuItem();
3773 MenuItem showColumns = new MenuItem();
3775 MenuItem showSeqs = new MenuItem();
3777 MenuItem hideColumns = new MenuItem();
3779 MenuItem hideSequences = new MenuItem();
3781 MenuItem hideAllButSelection = new MenuItem();
3783 MenuItem hideAllSelection = new MenuItem();
3785 MenuItem showAllHidden = new MenuItem();
3787 MenuItem newView = new MenuItem();
3789 private CheckboxMenuItem showAlignmentAnnotations;
3791 private CheckboxMenuItem showSequenceAnnotations;
3793 private CheckboxMenuItem sortAnnBySequence;
3795 private CheckboxMenuItem sortAnnByLabel;
3797 private CheckboxMenuItem showAutoFirst;
3799 private CheckboxMenuItem showAutoLast;
3801 private SplitFrame splitFrame;
3804 * Attach the alignFrame panels after embedding menus, if necessary. This used
3805 * to be called setEmbedded, but is now creates the dropdown menus in a
3806 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3808 * @param reallyEmbedded
3809 * true to attach the view to the applet area on the page rather than
3812 public void createAlignFrameWindow(boolean reallyEmbedded)
3816 embedAlignFrameInApplet(viewport.applet);
3821 // test and embed menu bar if necessary.
3823 if (embedMenuIfNeeded(alignPanel))
3826 * adjust for status bar height too. ? pointless as overridden by layout
3829 alignPanel.setSize(getSize().width,
3830 getSize().height - statusBar.getHeight());
3832 add(statusBar, BorderLayout.SOUTH);
3833 add(alignPanel, BorderLayout.CENTER);
3834 // and register with the applet so it can pass external API calls to us
3835 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3841 * Add the components of this AlignFrame to the applet container.
3845 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3848 // Explicitly build the embedded menu panel for the on-page applet
3850 // view cannot be closed if its actually on the page
3851 fileMenu.remove(closeMenuItem);
3852 fileMenu.remove(3); // Remove Separator
3853 // construct embedded menu, using default font
3854 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3855 // and actually add the components to the applet area
3856 theApplet.setLayout(new BorderLayout());
3857 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3858 theApplet.add(statusBar, BorderLayout.SOUTH);
3859 // TODO should size be left to the layout manager?
3860 alignPanel.setSize(theApplet.getSize().width,
3861 theApplet.getSize().height - embeddedMenu.getHeight()
3862 - statusBar.getHeight());
3863 theApplet.add(alignPanel, BorderLayout.CENTER);
3864 final AlignFrame me = this;
3865 theApplet.addFocusListener(new FocusListener()
3869 public void focusLost(FocusEvent e)
3871 if (theApplet.currentAlignFrame == me)
3873 theApplet.currentAlignFrame = null;
3878 public void focusGained(FocusEvent e)
3880 theApplet.currentAlignFrame = me;
3883 theApplet.validate();
3887 * create a new binding between structures in an existing jmol viewer instance
3888 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3889 * this does not open a new Jmol window, or modify the display of the
3890 * structures in the original jmol window. Note This method doesn't work
3891 * without an additional javascript library to exchange messages between the
3892 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3895 * JmolViewer instance
3896 * @param sequenceIds
3897 * - sequence Ids to search for associations
3899 public SequenceStructureBinding addStructureViewInstance(
3900 Object jmolviewer, String[] sequenceIds)
3902 Viewer viewer = null;
3905 viewer = (Viewer) jmolviewer;
3906 } catch (ClassCastException ex)
3908 System.err.println("Unsupported viewer object :"
3909 + jmolviewer.getClass());
3913 System.err.println("Can't use this object as a structure viewer:"
3914 + jmolviewer.getClass());
3917 SequenceI[] seqs = null;
3918 if (sequenceIds == null || sequenceIds.length == 0)
3920 seqs = viewport.getAlignment().getSequencesArray();
3924 Vector sqi = new Vector();
3925 AlignmentI al = viewport.getAlignment();
3926 for (int sid = 0; sid < sequenceIds.length; sid++)
3928 SequenceI sq = al.findName(sequenceIds[sid]);
3936 seqs = new SequenceI[sqi.size()];
3937 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3939 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3947 AAStructureBindingModel jmv = null;
3948 // TODO: search for a jmv that involves viewer
3950 { // create a new viewer/jalview binding.
3951 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3958 * bind a pdb file to a sequence in the current view
3961 * - sequenceId within the dataset.
3962 * @param pdbEntryString
3963 * - the short name for the PDB file
3965 * - pdb file - either a URL or a valid PDB file.
3966 * @return true if binding was as success TODO: consider making an exception
3967 * structure for indicating when PDB parsing or sequenceId location
3970 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3973 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3974 boolean needtoadd = false;
3975 if (toaddpdb != null)
3977 Vector pdbe = toaddpdb.getAllPDBEntries();
3978 PDBEntry pdbentry = null;
3979 if (pdbe != null && pdbe.size() > 0)
3981 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3983 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3984 if (!pdbentry.getId().equals(pdbEntryString)
3985 && !pdbentry.getFile().equals(pdbFile))
3995 if (pdbentry == null)
3997 pdbentry = new PDBEntry();
3998 pdbentry.setId(pdbEntryString);
3999 pdbentry.setFile(pdbFile);
4000 needtoadd = true; // add this new entry to sequence.
4002 // resolve data source
4003 // TODO: this code should be a refactored to an io package
4004 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
4005 if (protocol == null)
4011 // make a note of the access mode and add
4012 if (pdbentry.getProperty() == null)
4014 pdbentry.setProperty(new Hashtable());
4016 pdbentry.getProperty().put("protocol", protocol);
4017 toaddpdb.addPDBId(pdbentry);
4018 alignPanel.getStructureSelectionManager()
4019 .registerPDBEntry(pdbentry);
4025 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4029 Vector sequences = new Vector();
4030 for (int i = 0; i < seqs.length; i++)
4032 if (seqs[i] != null)
4034 sequences.addElement(new Object[] { seqs[i],
4035 (chains != null) ? chains[i] : null });
4038 seqs = new SequenceI[sequences.size()];
4039 chains = new String[sequences.size()];
4040 for (int i = 0, isize = sequences.size(); i < isize; i++)
4042 Object[] oj = (Object[]) sequences.elementAt(i);
4044 seqs[i] = (SequenceI) oj[0];
4045 chains[i] = (String) oj[1];
4048 return new Object[] { seqs, chains };
4052 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4053 SequenceI[] seqs, String[] chains, String protocol)
4055 // Scrub any null sequences from the array
4056 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4057 seqs = (SequenceI[]) sqch[0];
4058 chains = (String[]) sqch[1];
4059 if (seqs == null || seqs.length == 0)
4062 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4064 if (protocol == null || protocol.trim().length() == 0
4065 || protocol.equals("null"))
4067 protocol = (String) pdb.getProperty().get("protocol");
4068 if (protocol == null)
4070 System.err.println("Couldn't work out protocol to open structure: "
4075 if (applet.useXtrnalSviewer)
4077 // register the association(s) and quit, don't create any windows.
4078 if (StructureSelectionManager.getStructureSelectionManager(applet)
4079 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4081 System.err.println("Failed to map " + pdb.getFile() + " ("
4082 + protocol + ") to any sequences");
4086 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4088 // can only do alignments with Jmol
4089 // find the last jmol window assigned to this alignment
4090 jalview.appletgui.AppletJmol ajm = null, tajm;
4091 Vector jmols = applet
4092 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4093 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4095 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4096 if (tajm.ap.alignFrame == this)
4105 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4106 // try and add the pdb structure
4111 // otherwise, create a new window
4112 if (applet.jmolAvailable)
4114 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4116 applet.lastFrameX += 40;
4117 applet.lastFrameY += 40;
4121 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4126 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4127 SequenceI[][] seqs, String[][] chains, String[] protocols)
4129 // TODO Auto-generated method stub
4130 System.err.println("Aligned Structure View: Not yet implemented.");
4134 * modify the current selection, providing the user has not made a selection
4138 * - sequences from this alignment
4140 * - columns to be selected on the alignment
4142 public void select(SequenceGroup sel, ColumnSelection csel)
4144 alignPanel.seqPanel.selection(sel, csel, null);
4147 public void scrollTo(int row, int column)
4149 alignPanel.seqPanel.scrollTo(row, column);
4152 public void scrollToRow(int row)
4154 alignPanel.seqPanel.scrollToRow(row);
4157 public void scrollToColumn(int column)
4159 alignPanel.seqPanel.scrollToColumn(column);
4163 * @return the alignments unique ID.
4165 public String getSequenceSetId()
4167 return viewport.getSequenceSetId();
4171 * Load the (T-Coffee) score file from the specified url
4174 * File/URL/T-COFFEE score file contents
4175 * @throws IOException
4176 * @return true if alignment was annotated with data from source
4178 public boolean loadScoreFile(String source) throws IOException
4181 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4182 AppletFormatAdapter.checkProtocol(source));
4183 if (!file.isValid())
4185 // TODO: raise dialog for gui
4186 System.err.println("Problems parsing T-Coffee scores: "
4187 + file.getWarningMessage());
4188 System.err.println("Origin was:\n" + source);
4193 * check that the score matrix matches the alignment dimensions
4196 if ((aln = viewport.getAlignment()) != null
4197 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4200 // TODO: raise a dialog box here rather than bomb out.
4202 .println("The scores matrix does not match the alignment dimensions");
4206 // TODO add parameter to indicate if matching should be done
4207 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4209 alignPanel.fontChanged();
4210 tcoffeeColour.setEnabled(true);
4211 // switch to this color
4212 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4217 System.err.println("Problems resolving T-Coffee scores:");
4218 if (file.getWarningMessage() != null)
4220 System.err.println(file.getWarningMessage());
4226 public SplitFrame getSplitFrame()
4228 return this.splitFrame;
4231 public void setSplitFrame(SplitFrame sf)
4233 this.splitFrame = sf;
4236 // may not need this
4238 public void setShowSeqFeatures(boolean b)
4240 // showSeqFeatures.setSelected(b);
4241 viewport.setShowSequenceFeatures(b);
4246 public void setMenusForViewport()
4248 // setMenusFromViewport(viewport);
4253 public void refreshFeatureUI(boolean enableIfNecessary)
4255 if (enableIfNecessary)
4257 sequenceFeatures.setState(true);
4258 alignPanel.av.setShowSequenceFeatures(true);
4263 public FeatureSettingsControllerI getFeatureSettingsUI()
4265 return alignPanel.av.featureSettings;