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.controller.AlignViewController;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
51 import jalview.io.AlignFile;
52 import jalview.io.AlignmentProperties;
53 import jalview.io.AnnotationFile;
54 import jalview.io.AppletFormatAdapter;
55 import jalview.io.FeaturesFile;
56 import jalview.io.NewickFile;
57 import jalview.jsdev.GenericFileAdapter;
58 import jalview.schemes.Blosum62ColourScheme;
59 import jalview.schemes.BuriedColourScheme;
60 import jalview.schemes.ClustalxColourScheme;
61 import jalview.schemes.ColourSchemeI;
62 import jalview.schemes.HelixColourScheme;
63 import jalview.schemes.HydrophobicColourScheme;
64 import jalview.schemes.NucleotideColourScheme;
65 import jalview.schemes.PIDColourScheme;
66 import jalview.schemes.PurinePyrimidineColourScheme;
67 import jalview.schemes.RNAHelicesColourChooser;
68 import jalview.schemes.RNAInteractionColourScheme;
69 import jalview.schemes.StrandColourScheme;
70 import jalview.schemes.TCoffeeColourScheme;
71 import jalview.schemes.TaylorColourScheme;
72 import jalview.schemes.TurnColourScheme;
73 import jalview.schemes.ZappoColourScheme;
74 import jalview.structure.StructureSelectionManager;
75 import jalview.structures.models.AAStructureBindingModel;
76 import jalview.util.Comparison;
77 import jalview.util.MappingUtils;
78 import jalview.util.MessageManager;
79 import jalview.viewmodel.AlignmentViewport;
81 import java.awt.BorderLayout;
82 import java.awt.Color;
84 import java.awt.FontMetrics;
85 import java.awt.Graphics;
86 import java.awt.event.ActionEvent;
87 import java.awt.event.ActionListener;
88 import java.awt.event.FocusEvent;
89 import java.awt.event.FocusListener;
90 import java.awt.event.ItemEvent;
91 import java.awt.event.ItemListener;
92 import java.awt.event.KeyEvent;
93 import java.awt.event.KeyListener;
94 import java.awt.event.WindowAdapter;
95 import java.awt.event.WindowEvent;
96 import java.io.IOException;
98 import java.net.URLEncoder;
99 import java.util.Arrays;
100 import java.util.Deque;
101 import java.util.HashMap;
102 import java.util.Hashtable;
103 import java.util.List;
104 import java.util.Map;
105 import java.util.StringTokenizer;
106 import java.util.Vector;
108 import javax.swing.JCheckBoxMenuItem;
109 import javax.swing.JFrame;
110 import javax.swing.JLabel;
111 import javax.swing.JMenu;
112 import javax.swing.JMenuBar;
113 import javax.swing.JMenuItem;
114 import javax.swing.JPanel;
116 import org.jmol.viewer.Viewer;
118 public class AlignFrame extends EmbmenuFrame implements ActionListener,
119 ItemListener, KeyListener, AlignViewControllerGuiI
121 public AlignViewControllerI avc;
123 public AlignmentPanel alignPanel;
125 public AlignViewport viewport;
127 // width and height may be overridden by applet parameters
128 int frameWidth = 700;
130 int frameHeight = 500;
132 String jalviewServletURL;
135 * Flag for showing autocalculated consensus above or below other consensus
138 private boolean showAutoCalculatedAbove;
140 private SequenceAnnotationOrder annotationSortOrder;
143 * Constructor that creates the frame and adds it to the display.
150 public AlignFrame(AlignmentI al, JalviewLite applet,
151 String title, boolean embedded)
153 this(al, applet, title, embedded, true);
157 * Constructor that optionally allows the frame to be displayed or only
164 * @param addToDisplay
166 public AlignFrame(AlignmentI al, JalviewLite applet,
167 String title, boolean embedded, boolean addToDisplay)
169 this(al, null, null, applet, title, embedded, addToDisplay);
172 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
173 ColumnSelection columnSelection, JalviewLite applet,
174 String title, boolean embedded)
176 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
179 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
180 ColumnSelection columnSelection, JalviewLite applet,
181 String title, boolean embedded, boolean addToDisplay)
185 jalviewServletURL = applet.getParameter("APPLICATION_URL");
191 } catch (Exception ex)
193 ex.printStackTrace();
195 // need to get window geometry before we calculate alignment layout
201 param = applet.getParameter("windowWidth");
204 int width = Integer.parseInt(param);
207 param = applet.getParameter("windowHeight");
210 int height = Integer.parseInt(param);
211 frameHeight = height;
213 } catch (Exception ex)
217 viewport = new AlignViewport(al, applet);
219 if (hiddenSeqs != null && hiddenSeqs.length > 0)
221 viewport.hideSequence(hiddenSeqs);
223 if (columnSelection != null)
225 viewport.setColumnSelection(columnSelection);
228 alignPanel = new AlignmentPanel(this, viewport);
229 avc = new AlignViewController(this, viewport,
231 viewport.updateConservation(alignPanel);
232 viewport.updateConsensus(alignPanel);
234 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
235 followMouseOverFlag.setState(viewport.isFollowHighlight());
236 showGroupConsensus.setState(viewport.isShowGroupConsensus());
237 showGroupConservation.setState(viewport.isShowGroupConservation());
238 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
239 showSequenceLogo.setState(viewport.isShowSequenceLogo());
240 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
241 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
242 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
243 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
244 showSequenceAnnotations.setState(viewport.isShowAnnotation());
246 seqLimits.setState(viewport.getShowJVSuffix());
250 String param = applet.getParameter("sortBy");
253 if (param.equalsIgnoreCase("Id"))
255 sortIDMenuItem_actionPerformed();
257 else if (param.equalsIgnoreCase("Pairwise Identity"))
259 sortPairwiseMenuItem_actionPerformed();
261 else if (param.equalsIgnoreCase("Length"))
263 sortLengthMenuItem_actionPerformed();
267 param = applet.getParameter("wrap");
270 if (param.equalsIgnoreCase("true"))
272 wrapMenuItem.setState(true);
273 wrapMenuItem_actionPerformed();
276 param = applet.getParameter("centrecolumnlabels");
279 centreColumnLabelFlag.setState(true);
280 centreColumnLabelFlag_stateChanged();
284 if (viewport.getAlignment().isNucleotide())
286 viewport.updateStrucConsensus(alignPanel);
287 if (viewport.getAlignment().hasRNAStructure())
289 RNAHelixColour.setEnabled(true);
293 RNAHelixColour.setEnabled(false);
298 RNAHelixColour.setEnabled(false);
299 purinePyrimidineColour.setEnabled(false);
301 // Some JVMS send keyevents to Top frame or lowest panel,
302 // Havent worked out why yet. So add to both this frame and seqCanvas for
304 this.addKeyListener(this);
305 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
306 alignPanel.idPanel.idCanvas.addKeyListener(this);
307 alignPanel.scalePanel.addKeyListener(this);
308 alignPanel.annotationPanel.addKeyListener(this);
309 alignPanel.annotationPanelHolder.addKeyListener(this);
310 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
311 alignPanel.alabels.addKeyListener(this);
315 addToDisplay(embedded);
322 public void addToDisplay(boolean embedded)
324 createAlignFrameWindow(embedded);
326 alignPanel.adjustAnnotationHeight();
327 alignPanel.paintAlignment(true);
330 public AlignViewport getAlignViewport()
335 public SeqCanvas getSeqcanvas()
337 return alignPanel.seqPanel.seqCanvas;
341 * Load a features file onto the alignment
344 * file URL, content, or other resolvable path
346 * is protocol for accessing data referred to by file
349 public boolean parseFeaturesFile(String file, String type)
351 return parseFeaturesFile(file, type, true);
355 * Load a features file onto the alignment
358 * file URL, content, or other resolvable path
360 * is protocol for accessing data referred to by file
361 * @param autoenabledisplay
362 * when true, display features flag will be automatically enabled if
363 * features are loaded
364 * @return true if data parsed as a features file
366 public boolean parseFeaturesFile(String file, String type,
367 boolean autoenabledisplay)
369 // TODO: test if importing a features file onto an alignment which already
370 // has features with links overwrites the original links.
372 Hashtable featureLinks = new Hashtable();
373 boolean featuresFile = false;
376 featuresFile = new FeaturesFile(file, type)
377 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
378 .getFeatureRenderer().getFeatureColours(), featureLinks,
379 true, viewport.applet.getDefaultParameter(
380 "relaxedidmatch", false));
381 } catch (Exception ex)
383 ex.printStackTrace();
388 if (featureLinks.size() > 0)
390 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
392 if (autoenabledisplay)
394 viewport.setShowSequenceFeatures(true);
395 sequenceFeatures.setState(true);
397 if (alignPanel.seqPanel.seqCanvas.fr != null)
399 // update the min/max ranges where necessary
400 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
402 if (viewport.featureSettings != null)
404 viewport.featureSettings.refreshTable();
406 alignPanel.paintAlignment(true);
407 statusBar.setText(MessageManager
408 .getString("label.successfully_added_features_alignment"));
414 public void keyPressed(KeyEvent evt)
416 if (viewport.cursorMode
417 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
418 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
419 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
420 && Character.isDigit(evt.getKeyChar()))
422 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
425 switch (evt.getKeyCode())
427 case 27: // escape key
428 deselectAllSequenceMenuItem_actionPerformed();
430 alignPanel.alabels.cancelDrag();
433 if (evt.isControlDown() || evt.isMetaDown())
435 cut_actionPerformed();
439 if (viewport.cursorMode && !evt.isControlDown())
441 alignPanel.seqPanel.setCursorColumn();
443 if (evt.isControlDown() || evt.isMetaDown())
445 copy_actionPerformed();
449 if (evt.isControlDown())
451 paste(evt.isShiftDown());
455 if (evt.isControlDown() || evt.isMetaDown())
457 selectAllSequenceMenuItem_actionPerformed();
460 case KeyEvent.VK_DOWN:
461 if (viewport.cursorMode)
463 alignPanel.seqPanel.moveCursor(0, 1);
467 moveSelectedSequences(false);
472 if (viewport.cursorMode)
474 alignPanel.seqPanel.moveCursor(0, -1);
478 moveSelectedSequences(true);
482 case KeyEvent.VK_LEFT:
483 if (evt.isAltDown() || !viewport.cursorMode)
485 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
489 alignPanel.seqPanel.moveCursor(-1, 0);
493 case KeyEvent.VK_RIGHT:
494 if (evt.isAltDown() || !viewport.cursorMode)
496 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
500 alignPanel.seqPanel.moveCursor(1, 0);
504 case KeyEvent.VK_SPACE:
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
508 || evt.isShiftDown() || evt.isAltDown());
512 case KeyEvent.VK_DELETE:
513 case KeyEvent.VK_BACK_SPACE:
514 if (viewport.cursorMode)
516 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
517 || evt.isShiftDown() || evt.isAltDown());
521 cut_actionPerformed();
522 alignPanel.seqPanel.seqCanvas.repaint();
527 if (viewport.cursorMode)
529 alignPanel.seqPanel.setCursorRow();
533 if (viewport.cursorMode)
535 alignPanel.seqPanel.setCursorPosition();
539 case KeyEvent.VK_ENTER:
540 case KeyEvent.VK_COMMA:
541 if (viewport.cursorMode)
543 alignPanel.seqPanel.setCursorRowAndColumn();
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
554 if (viewport.cursorMode)
556 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
561 viewport.cursorMode = !viewport.cursorMode;
562 statusBar.setText(MessageManager.formatMessage(
563 "label.keyboard_editing_mode", new String[]
564 { (viewport.cursorMode ? "on" : "off") }));
565 if (viewport.cursorMode)
567 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
568 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
573 if (evt.isControlDown())
575 findMenuItem_actionPerformed();
581 boolean toggleSeqs = !evt.isControlDown();
582 boolean toggleCols = !evt.isShiftDown();
583 toggleHiddenRegions(toggleSeqs, toggleCols);
587 case KeyEvent.VK_PAGE_UP:
588 if (viewport.getWrapAlignment())
590 alignPanel.scrollUp(true);
594 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
595 - viewport.endSeq + viewport.startSeq);
599 case KeyEvent.VK_PAGE_DOWN:
600 if (viewport.getWrapAlignment())
602 alignPanel.scrollUp(false);
606 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
607 + viewport.endSeq - viewport.startSeq);
612 if (evt.isControlDown())
614 undoMenuItem_actionPerformed();
619 if (evt.isControlDown())
621 redoMenuItem_actionPerformed();
626 if (evt.isControlDown())
633 if (evt.isControlDown())
635 trimAlignment(false);
640 if (evt.isControlDown())
642 if (evt.isShiftDown())
644 this.removeAllGapsMenuItem_actionPerformed();
648 removeGappedColumnMenuItem_actionPerformed();
653 if (evt.isControlDown())
657 invertColSel_actionPerformed();
661 invertSequenceMenuItem_actionPerformed();
667 if (evt.isControlDown())
669 if (evt.isShiftDown())
671 this.unGroup_actionPerformed();
675 this.createGroup_actionPerformed();
681 if (evt.isControlDown())
683 this.deleteGroups_actionPerformed();
688 if (evt.isControlDown())
695 alignPanel.paintAlignment(true);
699 * called by key handler and the hide all/show all menu items
704 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
706 boolean hide = false;
707 SequenceGroup sg = viewport.getSelectionGroup();
708 if (!toggleSeqs && !toggleCols)
710 // Hide everything by the current selection - this is a hack - we do the
711 // invert and then hide
712 // first check that there will be visible columns after the invert.
713 if ((viewport.getColumnSelection() != null
714 && viewport.getColumnSelection().getSelected() != null && viewport
715 .getColumnSelection().getSelected().size() > 0)
716 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
719 // now invert the sequence set, if required - empty selection implies
720 // that no hiding is required.
723 invertSequenceMenuItem_actionPerformed();
724 sg = viewport.getSelectionGroup();
728 viewport.expandColSelection(sg, true);
729 // finally invert the column selection and get the new sequence
730 // selection and indicate it should be hidden.
731 invertColSel_actionPerformed();
738 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
741 viewport.hideAllSelectedSeqs();
743 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
746 viewport.showAllHiddenSeqs();
752 if (viewport.getColumnSelection().getSelected().size() > 0)
754 viewport.hideSelectedColumns();
757 viewport.setSelectionGroup(sg);
762 viewport.showAllHiddenColumns();
768 public void keyReleased(KeyEvent evt)
773 public void keyTyped(KeyEvent evt)
778 public void itemStateChanged(ItemEvent evt)
780 final Object source = evt.getSource();
781 if (source == displayNonconservedMenuItem)
783 displayNonconservedMenuItem_actionPerformed();
785 else if (source == colourTextMenuItem)
787 colourTextMenuItem_actionPerformed();
789 else if (source == wrapMenuItem)
791 wrapMenuItem_actionPerformed();
793 else if (source == scaleAbove)
795 viewport.setScaleAboveWrapped(scaleAbove.getState());
797 else if (source == scaleLeft)
799 viewport.setScaleLeftWrapped(scaleLeft.getState());
801 else if (source == scaleRight)
803 viewport.setScaleRightWrapped(scaleRight.getState());
805 else if (source == seqLimits)
807 seqLimits_itemStateChanged();
809 else if (source == viewBoxesMenuItem)
811 viewport.setShowBoxes(viewBoxesMenuItem.getState());
813 else if (source == viewTextMenuItem)
815 viewport.setShowText(viewTextMenuItem.getState());
817 else if (source == renderGapsMenuItem)
819 viewport.setRenderGaps(renderGapsMenuItem.getState());
821 else if (source == annotationPanelMenuItem)
823 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
824 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
826 else if (source == sequenceFeatures)
828 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
829 alignPanel.seqPanel.seqCanvas.repaint();
831 else if (source == showAlignmentAnnotations)
833 setAnnotationsVisibility();
835 else if (source == showSequenceAnnotations)
837 setAnnotationsVisibility();
839 else if (source == sortAnnBySequence)
841 boolean newState = sortAnnBySequence.getState();
842 sortAnnByLabel.setState(false);
843 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
844 : SequenceAnnotationOrder.NONE);
845 setViewportAnnotationOrder();
847 else if (source == sortAnnByLabel)
849 boolean newState = sortAnnByLabel.getState();
850 sortAnnBySequence.setState(false);
851 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
852 : SequenceAnnotationOrder.NONE);
853 setViewportAnnotationOrder();
855 else if (source == showAutoFirst)
857 showAutoLast.setState(!showAutoFirst.getState());
858 setShowAutoCalculatedAbove(showAutoFirst.getState());
859 setViewportAnnotationOrder();
861 else if (source == showAutoLast)
863 showAutoFirst.setState(!showAutoLast.getState());
864 setShowAutoCalculatedAbove(showAutoFirst.getState());
865 setViewportAnnotationOrder();
867 else if (source == conservationMenuItem)
869 conservationMenuItem_actionPerformed();
871 else if (source == abovePIDThreshold)
873 abovePIDThreshold_actionPerformed();
875 else if (source == applyToAllGroups)
877 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
879 else if (source == autoCalculate)
881 viewport.autoCalculateConsensus = autoCalculate.getState();
883 else if (source == sortByTree)
885 viewport.sortByTree = sortByTree.getState();
887 else if (source == this.centreColumnLabelFlag)
889 centreColumnLabelFlag_stateChanged();
891 else if (source == this.followMouseOverFlag)
893 mouseOverFlag_stateChanged();
895 else if (source == showGroupConsensus)
897 showGroupConsensus_actionPerformed();
899 else if (source == showGroupConservation)
901 showGroupConservation_actionPerformed();
903 else if (source == showSequenceLogo)
905 showSequenceLogo_actionPerformed();
907 else if (source == normSequenceLogo)
909 normSequenceLogo_actionPerformed();
911 else if (source == showConsensusHistogram)
913 showConsensusHistogram_actionPerformed();
915 else if (source == applyAutoAnnotationSettings)
917 applyAutoAnnotationSettings_actionPerformed();
919 alignPanel.paintAlignment(true);
923 * Set the visibility state of sequence-related and/or alignment-related
924 * annotations depending on checkbox selections. Repaint after calling.
928 private void setAnnotationsVisibility()
930 boolean showForAlignment = showAlignmentAnnotations.getState();
931 boolean showForSequences = showSequenceAnnotations.getState();
932 for (AlignmentAnnotation aa : alignPanel.getAlignment()
933 .getAlignmentAnnotation())
935 boolean visible = (aa.sequenceRef == null ? showForAlignment
937 aa.visible = visible;
939 alignPanel.validateAnnotationDimensions(true);
944 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
946 this.annotationSortOrder = order;
950 * Set flags on the viewport that control annotation ordering
952 private void setViewportAnnotationOrder()
954 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
956 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
959 private void setShowAutoCalculatedAbove(boolean showAbove)
961 this.showAutoCalculatedAbove = showAbove;
964 private void mouseOverFlag_stateChanged()
966 viewport.setFollowHighlight(followMouseOverFlag.getState());
967 // TODO: could kick the scrollTo mechanism to reset view for current
971 private void centreColumnLabelFlag_stateChanged()
973 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
974 this.alignPanel.annotationPanel.repaint();
978 public void actionPerformed(ActionEvent evt)
980 Object source = evt.getSource();
982 if (source == inputText)
984 inputText_actionPerformed();
986 else if (source == loadTree)
988 loadTree_actionPerformed();
990 else if (source == loadApplication)
992 launchFullApplication();
994 else if (source == loadAnnotations)
998 else if (source == outputAnnotations)
1000 outputAnnotations(true);
1002 else if (source == outputFeatures)
1004 outputFeatures(true, "Jalview");
1006 else if (source == closeMenuItem)
1008 closeMenuItem_actionPerformed();
1010 else if (source == copy)
1012 copy_actionPerformed();
1014 else if (source == undoMenuItem)
1016 undoMenuItem_actionPerformed();
1018 else if (source == redoMenuItem)
1020 redoMenuItem_actionPerformed();
1022 else if (source == inputText)
1024 inputText_actionPerformed();
1026 else if (source == closeMenuItem)
1028 closeMenuItem_actionPerformed();
1030 else if (source == undoMenuItem)
1032 undoMenuItem_actionPerformed();
1034 else if (source == redoMenuItem)
1036 redoMenuItem_actionPerformed();
1038 else if (source == copy)
1040 copy_actionPerformed();
1042 else if (source == pasteNew)
1044 pasteNew_actionPerformed();
1046 else if (source == pasteThis)
1048 pasteThis_actionPerformed();
1050 else if (source == cut)
1052 cut_actionPerformed();
1054 else if (source == delete)
1056 delete_actionPerformed();
1058 else if (source == grpsFromSelection)
1060 makeGrpsFromSelection_actionPerformed();
1062 else if (source == deleteGroups)
1064 deleteGroups_actionPerformed();
1066 else if (source == selectAllSequenceMenuItem)
1068 selectAllSequenceMenuItem_actionPerformed();
1070 else if (source == deselectAllSequenceMenuItem)
1072 deselectAllSequenceMenuItem_actionPerformed();
1074 else if (source == invertSequenceMenuItem)
1076 invertSequenceMenuItem_actionPerformed();
1078 else if (source == invertColSel)
1080 viewport.invertColumnSelection();
1081 alignPanel.paintAlignment(true);
1083 else if (source == remove2LeftMenuItem)
1085 trimAlignment(true);
1087 else if (source == remove2RightMenuItem)
1089 trimAlignment(false);
1091 else if (source == removeGappedColumnMenuItem)
1093 removeGappedColumnMenuItem_actionPerformed();
1095 else if (source == removeAllGapsMenuItem)
1097 removeAllGapsMenuItem_actionPerformed();
1099 else if (source == findMenuItem)
1101 findMenuItem_actionPerformed();
1103 else if (source == font)
1105 new FontChooser(alignPanel);
1107 else if (source == newView)
1111 else if (source == showColumns)
1113 viewport.showAllHiddenColumns();
1114 alignPanel.paintAlignment(true);
1116 else if (source == showSeqs)
1118 viewport.showAllHiddenSeqs();
1119 alignPanel.paintAlignment(true);
1121 else if (source == hideColumns)
1123 viewport.hideSelectedColumns();
1124 alignPanel.paintAlignment(true);
1126 else if (source == hideSequences
1127 && viewport.getSelectionGroup() != null)
1129 viewport.hideAllSelectedSeqs();
1130 alignPanel.paintAlignment(true);
1132 else if (source == hideAllButSelection)
1134 toggleHiddenRegions(false, false);
1135 alignPanel.paintAlignment(true);
1137 else if (source == hideAllSelection)
1139 SequenceGroup sg = viewport.getSelectionGroup();
1140 viewport.expandColSelection(sg, false);
1141 viewport.hideAllSelectedSeqs();
1142 viewport.hideSelectedColumns();
1143 alignPanel.paintAlignment(true);
1145 else if (source == showAllHidden)
1147 viewport.showAllHiddenColumns();
1148 viewport.showAllHiddenSeqs();
1149 alignPanel.paintAlignment(true);
1151 else if (source == showGroupConsensus)
1153 showGroupConsensus_actionPerformed();
1155 else if (source == showGroupConservation)
1157 showGroupConservation_actionPerformed();
1159 else if (source == showSequenceLogo)
1161 showSequenceLogo_actionPerformed();
1163 else if (source == normSequenceLogo)
1165 normSequenceLogo_actionPerformed();
1167 else if (source == showConsensusHistogram)
1169 showConsensusHistogram_actionPerformed();
1171 else if (source == applyAutoAnnotationSettings)
1173 applyAutoAnnotationSettings_actionPerformed();
1175 else if (source == featureSettings)
1177 new FeatureSettings(alignPanel);
1179 else if (source == alProperties)
1181 StringBuffer contents = new AlignmentProperties(
1182 viewport.getAlignment()).formatAsString();
1183 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1184 cap.setText(contents.toString());
1185 JFrame frame = new JFrame();
1187 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1188 "label.alignment_properties", new String[]
1189 { getTitle() }), 400, 250);
1191 else if (source == overviewMenuItem)
1193 overviewMenuItem_actionPerformed();
1195 else if (source == noColourmenuItem)
1199 else if (source == clustalColour)
1201 abovePIDThreshold.setState(false);
1202 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1204 else if (source == zappoColour)
1206 changeColour(new ZappoColourScheme());
1208 else if (source == taylorColour)
1210 changeColour(new TaylorColourScheme());
1212 else if (source == hydrophobicityColour)
1214 changeColour(new HydrophobicColourScheme());
1216 else if (source == helixColour)
1218 changeColour(new HelixColourScheme());
1220 else if (source == strandColour)
1222 changeColour(new StrandColourScheme());
1224 else if (source == turnColour)
1226 changeColour(new TurnColourScheme());
1228 else if (source == buriedColour)
1230 changeColour(new BuriedColourScheme());
1232 else if (source == nucleotideColour)
1234 changeColour(new NucleotideColourScheme());
1236 else if (source == purinePyrimidineColour)
1238 changeColour(new PurinePyrimidineColourScheme());
1240 else if (source == RNAInteractionColour)
1242 changeColour(new RNAInteractionColourScheme());
1244 else if (source == RNAHelixColour)
1246 new RNAHelicesColourChooser(viewport, alignPanel);
1248 else if (source == modifyPID)
1250 modifyPID_actionPerformed();
1252 else if (source == modifyConservation)
1254 modifyConservation_actionPerformed();
1256 else if (source == userDefinedColour)
1258 new UserDefinedColours(alignPanel, null);
1260 else if (source == PIDColour)
1262 changeColour(new PIDColourScheme());
1264 else if (source == BLOSUM62Colour)
1266 changeColour(new Blosum62ColourScheme());
1268 else if (source == tcoffeeColour)
1270 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1272 else if (source == annotationColour)
1274 new AnnotationColourChooser(viewport, alignPanel);
1276 else if (source == annotationColumnSelection)
1278 new AnnotationColumnChooser(viewport, alignPanel);
1280 else if (source == sortPairwiseMenuItem)
1282 sortPairwiseMenuItem_actionPerformed();
1284 else if (source == sortIDMenuItem)
1286 sortIDMenuItem_actionPerformed();
1288 else if (source == sortLengthMenuItem)
1290 sortLengthMenuItem_actionPerformed();
1292 else if (source == sortGroupMenuItem)
1294 sortGroupMenuItem_actionPerformed();
1296 else if (source == removeRedundancyMenuItem)
1298 removeRedundancyMenuItem_actionPerformed();
1300 else if (source == pairwiseAlignmentMenuItem)
1302 pairwiseAlignmentMenuItem_actionPerformed();
1304 else if (source == PCAMenuItem)
1306 PCAMenuItem_actionPerformed();
1308 else if (source == averageDistanceTreeMenuItem)
1310 averageDistanceTreeMenuItem_actionPerformed();
1312 else if (source == neighbourTreeMenuItem)
1314 neighbourTreeMenuItem_actionPerformed();
1316 else if (source == njTreeBlosumMenuItem)
1318 njTreeBlosumMenuItem_actionPerformed();
1320 else if (source == avDistanceTreeBlosumMenuItem)
1322 avTreeBlosumMenuItem_actionPerformed();
1324 else if (source == documentation)
1326 documentation_actionPerformed();
1328 else if (source == about)
1330 about_actionPerformed();
1335 public void inputText_actionPerformed()
1337 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1338 JFrame frame = new JFrame();
1340 JalviewLite.addFrame(frame,
1341 MessageManager.getString("label.input_cut_paste"), 500, 500);
1344 protected void outputText_actionPerformed(ActionEvent e)
1346 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1347 JFrame frame = new JFrame();
1349 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1350 "label.alignment_output_command", new Object[]
1351 { e.getActionCommand() }), 600, 500);
1353 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1354 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1355 e.getActionCommand(), viewport.getAlignment(),
1356 viewport.getShowJVSuffix()));
1359 public void loadAnnotations()
1361 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1362 cap.setText(MessageManager
1363 .getString("label.paste_features_annotations_Tcoffee_here"));
1364 cap.setAnnotationImport();
1365 JFrame frame = new JFrame();
1367 JalviewLite.addFrame(frame,
1368 MessageManager.getString("action.paste_annotations"), 400, 300);
1372 public String outputAnnotations(boolean displayTextbox)
1374 String annotation = new AnnotationFile()
1375 .printAnnotationsForView(viewport);
1379 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1380 JFrame frame = new JFrame();
1382 JalviewLite.addFrame(frame,
1383 MessageManager.getString("label.annotations"), 600, 500);
1384 cap.setText(annotation);
1390 private Map<String,Object> getDisplayedFeatureCols()
1392 if (alignPanel.getFeatureRenderer() != null
1393 && viewport.getFeaturesDisplayed()!= null)
1395 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1401 public String outputFeatures(boolean displayTextbox, String format)
1404 if (format.equalsIgnoreCase("Jalview"))
1406 features = new FeaturesFile().printJalviewFormat(viewport
1407 .getAlignment().getSequencesArray(),
1408 getDisplayedFeatureCols());
1412 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1413 .getSequencesArray(), getDisplayedFeatureCols());
1418 boolean frimport = false;
1419 if (features == null || features.equals("No Features Visible"))
1421 features = "# No features visible - paste some and import them here.";
1425 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1428 cap.setAnnotationImport();
1430 JFrame frame = new JFrame();
1432 JalviewLite.addFrame(frame,
1433 MessageManager.getString("label.features"), 600, 500);
1434 cap.setText(features);
1438 if (features == null)
1447 void launchFullApplication()
1449 StringBuffer url = new StringBuffer(jalviewServletURL);
1451 // allow servlet parameters to be passed in applet parameter
1452 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1454 url.append(firstSep);
1457 + appendProtocol(viewport.applet.getParameter("file")));
1459 if (viewport.applet.getParameter("features") != null)
1461 url.append("&features=");
1462 url.append(appendProtocol(viewport.applet.getParameter("features")));
1465 if (viewport.applet.getParameter("annotations") != null)
1467 url.append("&annotations=");
1468 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1471 if (viewport.applet.getParameter("jnetfile") != null)
1473 url.append("&annotations=");
1474 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1477 if (viewport.applet.getParameter("defaultColour") != null)
1479 url.append("&colour="
1480 + removeWhiteSpace(viewport.applet
1481 .getParameter("defaultColour")));
1484 if (viewport.applet.getParameter("userDefinedColour") != null)
1486 url.append("&colour="
1487 + removeWhiteSpace(viewport.applet
1488 .getParameter("userDefinedColour")));
1490 if (viewport.applet.getParameter("tree") != null)
1493 + appendProtocol(viewport.applet.getParameter("tree")));
1495 if (viewport.applet.getParameter("treeFile") != null)
1498 + appendProtocol(viewport.applet.getParameter("treeFile")));
1501 showURL(url.toString(), "FULL_APP");
1504 String removeWhiteSpace(String colour)
1506 StringBuffer sb = new StringBuffer();
1507 for (int i = 0; i < colour.length(); i++)
1509 if (Character.isWhitespace(colour.charAt(i)))
1515 sb.append(colour.charAt(i));
1519 return sb.toString();
1522 String appendProtocol(String url)
1527 url = URLEncoder.encode(url);
1530 * When we finally deprecate 1.1 compatibility, we can start to use
1531 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1532 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1533 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1534 * ex.printStackTrace(); }
1536 catch (java.net.MalformedURLException ex)
1538 url = viewport.applet.getCodeBase() + url;
1543 public void closeMenuItem_actionPerformed()
1545 PaintRefresher.RemoveComponent(alignPanel);
1546 if (alignPanel.seqPanel != null
1547 && alignPanel.seqPanel.seqCanvas != null)
1549 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1551 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1553 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1556 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1571 void updateEditMenuBar()
1574 if (viewport.getHistoryList().size() > 0)
1576 undoMenuItem.setEnabled(true);
1577 CommandI command = viewport.getHistoryList().peek();
1578 undoMenuItem.setLabel(MessageManager.formatMessage(
1579 "label.undo_command", new Object[]
1580 { command.getDescription() }));
1584 undoMenuItem.setEnabled(false);
1585 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1588 if (viewport.getRedoList().size() > 0)
1590 redoMenuItem.setEnabled(true);
1592 CommandI command = viewport.getRedoList().peek();
1593 redoMenuItem.setLabel(MessageManager.formatMessage(
1594 "label.redo_command", new Object[]
1595 { command.getDescription() }));
1599 redoMenuItem.setEnabled(false);
1600 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1608 public void addHistoryItem(CommandI command)
1610 if (command.getSize() > 0)
1612 viewport.addToHistoryList(command);
1613 viewport.clearRedoList();
1614 updateEditMenuBar();
1615 viewport.updateHiddenColumns();
1620 * TODO: JAL-1104 DOCUMENT ME!
1625 protected void undoMenuItem_actionPerformed()
1627 if (viewport.getHistoryList().isEmpty())
1632 CommandI command = viewport.getHistoryList().pop();
1633 viewport.addToRedoList(command);
1634 command.undoCommand(null);
1636 AlignmentViewport originalSource = getOriginatingSource(command);
1638 if (originalSource != viewport)
1641 .println("Warning: Viewport object mismatch whilst undoing");
1643 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1644 // viewport.getColumnSelection().getHiddenColumns()
1646 updateEditMenuBar();
1647 originalSource.firePropertyChange("alignment", null, originalSource
1648 .getAlignment().getSequences());
1652 * TODO: JAL-1104 DOCUMENT ME!
1657 protected void redoMenuItem_actionPerformed()
1659 if (viewport.getRedoList().isEmpty())
1664 CommandI command = viewport.getRedoList().pop();
1665 viewport.addToHistoryList(command);
1666 command.doCommand(null);
1668 AlignmentViewport originalSource = getOriginatingSource(command);
1670 if (originalSource != viewport)
1673 .println("Warning: Viewport object mismatch whilst re-doing");
1675 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1676 // viewport.getColumnSelection().getHiddenColumns()
1679 updateEditMenuBar();
1680 originalSource.firePropertyChange("alignment", null, originalSource
1681 .getAlignment().getSequences());
1684 AlignmentViewport getOriginatingSource(CommandI command)
1686 AlignmentViewport originalSource = null;
1687 // For sequence removal and addition, we need to fire
1688 // the property change event FROM the viewport where the
1689 // original alignment was altered
1690 AlignmentI al = null;
1691 if (command instanceof EditCommand)
1693 EditCommand editCommand = (EditCommand) command;
1694 al = editCommand.getAlignment();
1695 Vector comps = (Vector) PaintRefresher.components.get(viewport
1696 .getSequenceSetId());
1697 for (int i = 0; i < comps.size(); i++)
1699 if (comps.elementAt(i) instanceof AlignmentPanel)
1701 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1703 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1710 if (originalSource == null)
1712 // The original view is closed, we must validate
1713 // the current view against the closed view first
1716 PaintRefresher.validateSequences(al, viewport.getAlignment());
1719 originalSource = viewport;
1722 return originalSource;
1726 * Move the currently selected sequences up or down one position in the
1731 public void moveSelectedSequences(boolean up)
1733 SequenceGroup sg = viewport.getSelectionGroup();
1738 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1739 up ? null : viewport.getHiddenRepSequences(), up);
1740 alignPanel.paintAlignment(true);
1743 * Also move cDNA/protein complement sequences
1745 AlignViewportI complement = viewport.getCodingComplement();
1746 if (complement != null)
1748 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1749 viewport, complement);
1750 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1751 up ? null : complement.getHiddenRepSequences(), up);
1752 // TODO need to trigger a repaint of the complementary panel - how?
1753 // would prefer to handle in SplitFrame but it is not overriding key
1758 synchronized void slideSequences(boolean right, int size)
1760 List<SequenceI> sg = new Vector<SequenceI>();
1761 if (viewport.cursorMode)
1763 sg.add(viewport.getAlignment().getSequenceAt(
1764 alignPanel.seqPanel.seqCanvas.cursorY));
1766 else if (viewport.getSelectionGroup() != null
1767 && viewport.getSelectionGroup().getSize() != viewport
1768 .getAlignment().getHeight())
1770 sg = viewport.getSelectionGroup().getSequences(
1771 viewport.getHiddenRepSequences());
1779 Vector<SequenceI> invertGroup = new Vector();
1781 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1783 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1785 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1789 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1791 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1793 for (int i = 0; i < invertGroup.size(); i++)
1795 seqs2[i] = invertGroup.elementAt(i);
1798 SlideSequencesCommand ssc;
1801 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1802 size, viewport.getGapCharacter());
1806 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1807 size, viewport.getGapCharacter());
1810 int groupAdjustment = 0;
1811 if (ssc.getGapsInsertedBegin() && right)
1813 if (viewport.cursorMode)
1815 alignPanel.seqPanel.moveCursor(size, 0);
1819 groupAdjustment = size;
1822 else if (!ssc.getGapsInsertedBegin() && !right)
1824 if (viewport.cursorMode)
1826 alignPanel.seqPanel.moveCursor(-size, 0);
1830 groupAdjustment = -size;
1834 if (groupAdjustment != 0)
1836 viewport.getSelectionGroup().setStartRes(
1837 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1838 viewport.getSelectionGroup().setEndRes(
1839 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1842 boolean appendHistoryItem = false;
1843 Deque<CommandI> historyList = viewport.getHistoryList();
1844 if (historyList != null && historyList.size() > 0
1845 && historyList.peek() instanceof SlideSequencesCommand)
1847 appendHistoryItem = ssc
1848 .appendSlideCommand((SlideSequencesCommand) historyList
1852 if (!appendHistoryItem)
1854 addHistoryItem(ssc);
1860 static StringBuffer copiedSequences;
1862 static Vector copiedHiddenColumns;
1864 protected void copy_actionPerformed()
1866 if (viewport.getSelectionGroup() == null)
1871 SequenceGroup sg = viewport.getSelectionGroup();
1872 copiedSequences = new StringBuffer();
1873 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1874 for (int i = 0; i < sg.getSize(); i++)
1876 SequenceI seq = sg.getSequenceAt(i);
1877 int index = viewport.getAlignment().findIndex(seq);
1878 orderedSeqs.put(index, seq);
1881 int index = 0, startRes, endRes;
1884 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1886 copiedHiddenColumns = new Vector();
1887 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1888 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1890 copiedHiddenColumns.addElement(new int[]
1891 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1896 copiedHiddenColumns = null;
1899 for (int i = 0; i < sg.getSize(); i++)
1901 SequenceI seq = null;
1905 if (orderedSeqs.containsKey(index))
1907 seq = orderedSeqs.get(index);
1918 // Returns residue following index if gap
1919 startRes = seq.findPosition(sg.getStartRes());
1922 // Need to find the residue preceeding index if gap
1925 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1927 ch = seq.getCharAt(j);
1928 if (!Comparison.isGap((ch)))
1936 endRes += seq.getStart() - 1;
1939 copiedSequences.append(seq.getName()
1945 + seq.getSequenceAsString(sg.getStartRes(),
1946 sg.getEndRes() + 1) + "\n");
1951 protected void pasteNew_actionPerformed()
1956 protected void pasteThis_actionPerformed()
1961 void paste(boolean newAlignment)
1966 if (copiedSequences == null)
1971 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1972 Vector seqs = new Vector();
1973 while (st.hasMoreElements())
1975 String name = st.nextToken();
1976 int start = Integer.parseInt(st.nextToken());
1977 int end = Integer.parseInt(st.nextToken());
1978 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1980 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1981 for (int i = 0; i < seqs.size(); i++)
1983 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1988 String newtitle = MessageManager.getString("label.copied_sequences");
1989 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1991 newtitle = getTitle();
1995 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1997 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1998 viewport.applet, newtitle, false);
1999 if (copiedHiddenColumns != null)
2001 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2003 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2004 af.viewport.hideColumns(region[0], region[1]);
2008 JalviewLite.addFrame(af, newtitle, frameWidth,
2013 addSequences(newSeqs);
2016 } catch (Exception ex)
2018 } // could be anything being pasted in here
2022 void addSequences(SequenceI[] seqs)
2024 for (int i = 0; i < seqs.length; i++)
2026 viewport.getAlignment().addSequence(seqs[i]);
2030 addHistoryItem(new EditCommand(
2031 MessageManager.getString("label.add_sequences"), Action.PASTE,
2032 seqs, 0, viewport.getAlignment().getWidth(),
2033 viewport.getAlignment()));
2035 viewport.setEndSeq(viewport.getAlignment().getHeight());
2036 viewport.getAlignment().getWidth();
2037 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2042 protected void cut_actionPerformed()
2044 copy_actionPerformed();
2045 delete_actionPerformed();
2048 protected void delete_actionPerformed()
2051 SequenceGroup sg = viewport.getSelectionGroup();
2057 Vector seqs = new Vector();
2059 for (int i = 0; i < sg.getSize(); i++)
2061 seq = sg.getSequenceAt(i);
2062 seqs.addElement(seq);
2065 // If the cut affects all sequences, remove highlighted columns
2066 if (sg.getSize() == viewport.getAlignment().getHeight())
2068 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2069 sg.getEndRes() + 1);
2072 SequenceI[] cut = new SequenceI[seqs.size()];
2073 for (int i = 0; i < seqs.size(); i++)
2075 cut[i] = (SequenceI) seqs.elementAt(i);
2079 * //ADD HISTORY ITEM
2081 addHistoryItem(new EditCommand(
2082 MessageManager.getString("label.cut_sequences"), Action.CUT,
2083 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2084 viewport.getAlignment()));
2086 viewport.setSelectionGroup(null);
2087 viewport.getAlignment().deleteGroup(sg);
2089 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2092 if (viewport.getAlignment().getHeight() < 1)
2094 this.setVisible(false);
2096 viewport.sendSelection();
2100 * group consensus toggled
2103 protected void showGroupConsensus_actionPerformed()
2105 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2106 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2111 * group conservation toggled.
2113 protected void showGroupConservation_actionPerformed()
2115 viewport.setShowGroupConservation(showGroupConservation.getState());
2116 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2123 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2124 * .event.ActionEvent)
2126 protected void showConsensusHistogram_actionPerformed()
2128 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2129 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2136 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2137 * .event.ActionEvent)
2139 protected void showSequenceLogo_actionPerformed()
2141 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2142 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145 protected void normSequenceLogo_actionPerformed()
2147 showSequenceLogo.setState(true);
2148 viewport.setShowSequenceLogo(true);
2149 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2150 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2153 protected void applyAutoAnnotationSettings_actionPerformed()
2155 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2158 protected void makeGrpsFromSelection_actionPerformed()
2160 if (avc.makeGroupsFromSelection())
2162 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2163 alignPanel.updateAnnotation();
2164 alignPanel.paintAlignment(true);
2168 protected void createGroup_actionPerformed()
2173 protected void unGroup_actionPerformed()
2177 alignPanel.alignmentChanged();
2181 protected void deleteGroups_actionPerformed()
2183 if (avc.deleteGroups())
2185 alignPanel.alignmentChanged();
2189 public void selectAllSequenceMenuItem_actionPerformed()
2191 SequenceGroup sg = new SequenceGroup();
2192 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2194 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2196 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2197 viewport.setSelectionGroup(sg);
2198 alignPanel.paintAlignment(true);
2199 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2200 viewport.sendSelection();
2203 public void deselectAllSequenceMenuItem_actionPerformed()
2205 if (viewport.cursorMode)
2207 alignPanel.seqPanel.keyboardNo1 = null;
2208 alignPanel.seqPanel.keyboardNo2 = null;
2210 viewport.setSelectionGroup(null);
2211 viewport.getColumnSelection().clear();
2212 viewport.setSelectionGroup(null);
2213 alignPanel.idPanel.idCanvas.searchResults = null;
2214 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2215 alignPanel.paintAlignment(true);
2216 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2217 viewport.sendSelection();
2220 public void invertSequenceMenuItem_actionPerformed()
2222 SequenceGroup sg = viewport.getSelectionGroup();
2223 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2225 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2228 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2229 viewport.sendSelection();
2232 public void invertColSel_actionPerformed()
2234 viewport.invertColumnSelection();
2235 alignPanel.paintAlignment(true);
2236 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2237 viewport.sendSelection();
2240 void trimAlignment(boolean trimLeft)
2242 ColumnSelection colSel = viewport.getColumnSelection();
2245 if (colSel.size() > 0)
2249 column = colSel.getMin();
2253 column = colSel.getMax();
2257 if (viewport.getSelectionGroup() != null)
2259 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2260 viewport.getHiddenRepSequences());
2264 seqs = viewport.getAlignment().getSequencesArray();
2267 TrimRegionCommand trimRegion;
2270 trimRegion = new TrimRegionCommand("Remove Left",
2271 TrimRegionCommand.TRIM_LEFT, seqs, column,
2272 viewport.getAlignment(), viewport.getColumnSelection(),
2273 viewport.getSelectionGroup());
2274 viewport.setStartRes(0);
2278 trimRegion = new TrimRegionCommand("Remove Right",
2279 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2280 viewport.getAlignment(), viewport.getColumnSelection(),
2281 viewport.getSelectionGroup());
2284 statusBar.setText(MessageManager.formatMessage(
2285 "label.removed_columns", new String[]
2286 { Integer.valueOf(trimRegion.getSize()).toString() }));
2287 addHistoryItem(trimRegion);
2289 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2291 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2292 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2294 viewport.getAlignment().deleteGroup(sg);
2298 viewport.firePropertyChange("alignment", null, viewport
2299 .getAlignment().getSequences());
2303 public void removeGappedColumnMenuItem_actionPerformed()
2305 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2308 if (viewport.getSelectionGroup() != null)
2310 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2311 viewport.getHiddenRepSequences());
2312 start = viewport.getSelectionGroup().getStartRes();
2313 end = viewport.getSelectionGroup().getEndRes();
2317 seqs = viewport.getAlignment().getSequencesArray();
2320 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2321 "Remove Gapped Columns", seqs, start, end,
2322 viewport.getAlignment());
2324 addHistoryItem(removeGapCols);
2326 statusBar.setText(MessageManager.formatMessage(
2327 "label.removed_empty_columns", new String[]
2328 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2330 // This is to maintain viewport position on first residue
2331 // of first sequence
2332 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2333 int startRes = seq.findPosition(viewport.startRes);
2334 // ShiftList shifts;
2335 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2336 // edit.alColumnChanges=shifts.getInverse();
2337 // if (viewport.hasHiddenColumns)
2338 // viewport.getColumnSelection().compensateForEdits(shifts);
2339 viewport.setStartRes(seq.findIndex(startRes) - 1);
2340 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2345 public void removeAllGapsMenuItem_actionPerformed()
2347 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2350 if (viewport.getSelectionGroup() != null)
2352 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2353 viewport.getHiddenRepSequences());
2354 start = viewport.getSelectionGroup().getStartRes();
2355 end = viewport.getSelectionGroup().getEndRes();
2359 seqs = viewport.getAlignment().getSequencesArray();
2362 // This is to maintain viewport position on first residue
2363 // of first sequence
2364 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2365 int startRes = seq.findPosition(viewport.startRes);
2367 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2368 viewport.getAlignment()));
2370 viewport.setStartRes(seq.findIndex(startRes) - 1);
2372 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2377 public void findMenuItem_actionPerformed()
2379 new Finder(alignPanel);
2383 * create a new view derived from the current view
2386 * @return frame for the new view
2388 public AlignFrame newView(String viewtitle)
2391 if (viewport.hasHiddenRows())
2393 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2394 .getFullAlignment().getSequencesArray());
2398 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2401 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2403 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2405 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2407 newal.addAnnotation(viewport.getAlignment()
2408 .getAlignmentAnnotation()[i]);
2413 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2415 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2416 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2417 PaintRefresher.Register(newaf.alignPanel,
2418 newaf.alignPanel.av.getSequenceSetId());
2420 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2421 newaf.alignPanel.av.getSequenceSetId());
2422 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2423 newaf.alignPanel.av.getSequenceSetId());
2425 Vector comps = (Vector) PaintRefresher.components.get(viewport
2426 .getSequenceSetId());
2428 for (int i = 0; i < comps.size(); i++)
2430 if (comps.elementAt(i) instanceof AlignmentPanel)
2436 String title = new String(this.getTitle());
2437 if (viewtitle != null)
2439 title = viewtitle + " ( " + title + ")";
2443 if (title.indexOf("(View") > -1)
2445 title = title.substring(0, title.indexOf("(View"));
2447 title += "(View " + viewSize + ")";
2450 newaf.setTitle(title.toString());
2452 newaf.viewport.setHistoryList(viewport.getHistoryList());
2453 newaf.viewport.setRedoList(viewport.getRedoList());
2459 * @return list of feature groups on the view
2461 public String[] getFeatureGroups()
2463 FeatureRenderer fr = null;
2464 if (alignPanel != null
2465 && (fr = alignPanel.getFeatureRenderer()) != null)
2467 List<String> gps = fr.getFeatureGroups();
2468 String[] _gps = gps.toArray(new String[gps.size()]);
2475 * get sequence feature groups that are hidden or shown
2481 public String[] getFeatureGroupsOfState(boolean visible)
2483 FeatureRenderer fr = null;
2484 if (alignPanel != null
2485 && (fr = alignPanel.getFeatureRenderer()) != null)
2487 List<String> gps = fr.getGroups(visible);
2488 String[] _gps = gps.toArray(new String[gps.size()]);
2495 * Change the display state for the given feature groups
2498 * list of group strings
2500 * visible or invisible
2502 public void setFeatureGroupState(String[] groups, boolean state)
2504 FeatureRenderer fr = null;
2505 this.sequenceFeatures.setState(true);
2506 viewport.setShowSequenceFeatures(true);
2507 if (alignPanel != null
2508 && (fr = alignPanel.getFeatureRenderer()) != null)
2511 fr.setGroupVisibility(Arrays.asList(groups), state);
2512 alignPanel.seqPanel.seqCanvas.repaint();
2513 if (alignPanel.overviewPanel != null)
2515 alignPanel.overviewPanel.updateOverviewImage();
2520 public void seqLimits_itemStateChanged()
2522 viewport.setShowJVSuffix(seqLimits.getState());
2523 alignPanel.fontChanged();
2524 alignPanel.paintAlignment(true);
2527 protected void colourTextMenuItem_actionPerformed()
2529 viewport.setColourText(colourTextMenuItem.getState());
2530 alignPanel.paintAlignment(true);
2533 protected void displayNonconservedMenuItem_actionPerformed()
2535 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2536 alignPanel.paintAlignment(true);
2539 protected void wrapMenuItem_actionPerformed()
2541 viewport.setWrapAlignment(wrapMenuItem.getState());
2542 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2543 scaleAbove.setEnabled(wrapMenuItem.getState());
2544 scaleLeft.setEnabled(wrapMenuItem.getState());
2545 scaleRight.setEnabled(wrapMenuItem.getState());
2546 alignPanel.paintAlignment(true);
2549 public void overviewMenuItem_actionPerformed()
2551 if (alignPanel.overviewPanel != null)
2556 JFrame frame = new JFrame();
2557 OverviewPanel overview = new OverviewPanel(alignPanel);
2558 frame.add(overview);
2559 // +50 must allow for applet frame window
2560 JalviewLite.addFrame(frame, MessageManager.formatMessage(
2561 "label.overview_params", new String[]
2562 { this.getTitle() }), overview.getPreferredSize().width,
2563 overview.getPreferredSize().height + 50);
2566 final AlignmentPanel ap = alignPanel;
2567 frame.addWindowListener(new WindowAdapter()
2570 public void windowClosing(WindowEvent e)
2574 ap.setOverviewPanel(null);
2579 alignPanel.setOverviewPanel(overview);
2583 public void changeColour(ColourSchemeI cs)
2589 if (viewport.getAbovePIDThreshold())
2591 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2595 if (viewport.getConservationSelected())
2597 cs.setConservationApplied(true);
2598 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2603 cs.setConservationApplied(false);
2606 viewport.setGlobalColourScheme(cs);
2608 if (alignPanel.getOverviewPanel() != null)
2610 alignPanel.getOverviewPanel().updateOverviewImage();
2613 StructureSelectionManager.getStructureSelectionManager(viewport.applet)
2614 .sequenceColoursChanged(alignPanel);
2616 alignPanel.paintAlignment(true);
2619 protected void modifyPID_actionPerformed()
2621 if (viewport.getAbovePIDThreshold()
2622 && viewport.getGlobalColourScheme() != null)
2624 SliderPanel.setPIDSliderSource(alignPanel,
2625 viewport.getGlobalColourScheme(), "Background");
2626 SliderPanel.showPIDSlider();
2630 protected void modifyConservation_actionPerformed()
2632 if (viewport.getConservationSelected()
2633 && viewport.getGlobalColourScheme() != null)
2635 SliderPanel.setConservationSlider(alignPanel,
2636 viewport.getGlobalColourScheme(), "Background");
2637 SliderPanel.showConservationSlider();
2641 protected void conservationMenuItem_actionPerformed()
2643 viewport.setConservationSelected(conservationMenuItem.getState());
2645 viewport.setAbovePIDThreshold(false);
2646 abovePIDThreshold.setState(false);
2648 changeColour(viewport.getGlobalColourScheme());
2650 modifyConservation_actionPerformed();
2653 public void abovePIDThreshold_actionPerformed()
2655 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2657 conservationMenuItem.setState(false);
2658 viewport.setConservationSelected(false);
2660 changeColour(viewport.getGlobalColourScheme());
2662 modifyPID_actionPerformed();
2665 public void sortPairwiseMenuItem_actionPerformed()
2667 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2668 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2669 .getAlignment().getSequenceAt(0), null);
2671 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2672 viewport.getAlignment()));
2673 alignPanel.paintAlignment(true);
2676 public void sortIDMenuItem_actionPerformed()
2678 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2679 AlignmentSorter.sortByID(viewport.getAlignment());
2680 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2681 viewport.getAlignment()));
2682 alignPanel.paintAlignment(true);
2685 public void sortLengthMenuItem_actionPerformed()
2687 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688 AlignmentSorter.sortByLength(viewport.getAlignment());
2689 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2690 viewport.getAlignment()));
2691 alignPanel.paintAlignment(true);
2694 public void sortGroupMenuItem_actionPerformed()
2696 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2697 AlignmentSorter.sortByGroup(viewport.getAlignment());
2698 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2699 viewport.getAlignment()));
2700 alignPanel.paintAlignment(true);
2704 public void removeRedundancyMenuItem_actionPerformed()
2706 new RedundancyPanel(alignPanel);
2709 public void pairwiseAlignmentMenuItem_actionPerformed()
2711 if (viewport.getSelectionGroup() != null
2712 && viewport.getSelectionGroup().getSize() > 1)
2714 JFrame frame = new JFrame();
2715 frame.add(new PairwiseAlignPanel(alignPanel));
2716 JalviewLite.addFrame(frame,
2717 MessageManager.getString("action.pairwise_alignment"), 600,
2722 public void PCAMenuItem_actionPerformed()
2724 // are the sequences aligned?
2725 if (!viewport.getAlignment().isAligned(false))
2728 int Width = viewport.getAlignment().getWidth();
2730 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2732 current = viewport.getAlignment().getSequenceAt(i);
2734 if (current.getLength() < Width)
2736 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2739 alignPanel.paintAlignment(true);
2742 if ((viewport.getSelectionGroup() != null
2743 && viewport.getSelectionGroup().getSize() < 4 && viewport
2744 .getSelectionGroup().getSize() > 0)
2745 || viewport.getAlignment().getHeight() < 4)
2752 new PCAPanel(viewport);
2753 } catch (java.lang.OutOfMemoryError ex)
2759 public void averageDistanceTreeMenuItem_actionPerformed()
2761 NewTreePanel("AV", "PID", "Average distance tree using PID");
2764 public void neighbourTreeMenuItem_actionPerformed()
2766 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2769 protected void njTreeBlosumMenuItem_actionPerformed()
2771 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2774 protected void avTreeBlosumMenuItem_actionPerformed()
2776 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2779 void NewTreePanel(String type, String pwType, String title)
2781 // are the sequences aligned?
2782 if (!viewport.getAlignment().isAligned(false))
2785 int Width = viewport.getAlignment().getWidth();
2787 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2789 current = viewport.getAlignment().getSequenceAt(i);
2791 if (current.getLength() < Width)
2793 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2796 alignPanel.paintAlignment(true);
2800 if ((viewport.getSelectionGroup() != null && viewport
2801 .getSelectionGroup().getSize() > 1)
2802 || (viewport.getAlignment().getHeight() > 1))
2804 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2806 addTreeMenuItem(tp, title);
2808 JalviewLite.addFrame(tp, title, 600, 500);
2812 void loadTree_actionPerformed()
2814 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2815 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2816 cap.setTreeImport();
2817 JFrame frame = new JFrame();
2819 JalviewLite.addFrame(frame,
2820 MessageManager.getString("label.paste_newick_file"), 400, 300);
2823 public void loadTree(NewickFile tree, String treeFile)
2825 TreePanel tp = new TreePanel(alignPanel, treeFile,
2826 MessageManager.getString("label.load_tree_from_file"), tree);
2827 JalviewLite.addFrame(tp, treeFile, 600, 500);
2828 addTreeMenuItem(tp, treeFile);
2832 * sort the alignment using the given treePanel
2835 * tree used to sort view
2837 * string used for undo event name
2839 public void sortByTree(TreePanel treePanel, String title)
2841 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2843 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2844 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2845 // HistoryItem.SORT));
2846 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2847 "label.order_by_params", new String[]
2848 { title }), oldOrder, viewport.getAlignment()));
2849 alignPanel.paintAlignment(true);
2853 * Do any automatic reordering of the alignment and add the necessary bits to
2854 * the menu structure for the new tree
2859 protected void addTreeMenuItem(final TreePanel treePanel,
2862 final JMenuItem item = new JMenuItem(title);
2863 sortByTreeMenu.add(item);
2864 item.addActionListener(new java.awt.event.ActionListener()
2867 public void actionPerformed(ActionEvent evt)
2869 sortByTree(treePanel, title); // treePanel.getTitle());
2873 treePanel.addWindowListener(new WindowAdapter()
2876 public void windowOpened(WindowEvent e)
2878 if (viewport.sortByTree)
2880 sortByTree(treePanel, title);
2882 super.windowOpened(e);
2886 public void windowClosing(WindowEvent e)
2888 sortByTreeMenu.remove(item);
2893 public boolean sortBy(AlignmentOrder alorder, String undoname)
2895 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2896 if (JalviewLite.debug)
2898 System.err.println("Sorting " + alorder.getOrder().size()
2899 + " in alignment '" + getTitle() + "'");
2901 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2902 if (undoname != null)
2904 addHistoryItem(new OrderCommand(undoname, oldOrder,
2905 viewport.getAlignment()));
2907 alignPanel.paintAlignment(true);
2911 protected void documentation_actionPerformed()
2913 alignPanel.av.applet.openJalviewHelpUrl();
2916 protected void about_actionPerformed()
2919 class AboutPanel extends JPanel
2925 public AboutPanel(String version, String builddate)
2927 this.version = version;
2928 this.builddate = builddate;
2932 public void paint(Graphics g)
2934 g.setColor(Color.white);
2935 g.fillRect(0, 0, getSize().width, getSize().height);
2936 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2937 FontMetrics fm = g.getFontMetrics();
2938 int fh = fm.getHeight();
2940 g.setColor(Color.black);
2941 // TODO: update this text for each release or centrally store it for
2942 // lite and application
2943 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2944 g.drawString(MessageManager.formatMessage(
2945 "label.jalviewLite_release", new String[]
2946 { version }), x, y += fh);
2947 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2948 g.drawString(MessageManager.formatMessage(
2949 "label.jaview_build_date", new String[]
2950 { builddate }), x, y += fh);
2951 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2952 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2954 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2955 x + 50, y += fh + 8);
2957 MessageManager.getString("label.jalview_dev_managers"), x,
2959 g.drawString(MessageManager
2960 .getString("label.jalview_distribution_lists"), x, y += fh);
2961 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2964 MessageManager.getString("label.jalview_cite_1_authors"),
2967 MessageManager.getString("label.jalview_cite_1_title"), x,
2969 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2974 JFrame frame = new JFrame();
2975 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2977 JalviewLite.addFrame(frame,
2978 MessageManager.getString("label.jalview"), 580, 220);
2982 public void showURL(String url, String target)
2984 if (viewport.applet == null)
2986 System.out.println("Not running as applet - no browser available.");
2990 viewport.applet.showURL(url, target);
2994 // ////////////////////////////////////////////////////////////////////////////////
2995 // JBuilder Graphics here
2997 JMenuBar alignFrameMenuBar = new JMenuBar();
2999 JMenu fileMenu = new JMenu(MessageManager.getString("action.file"));
3001 JMenuItem loadApplication = new JMenuItem(
3002 MessageManager.getString("label.view_full_application"));
3004 JMenuItem loadTree = new JMenuItem(
3005 MessageManager.getString("label.load_associated_tree"));
3007 JMenuItem loadAnnotations = new JMenuItem(
3008 MessageManager.getString("label.load_features_annotations"));
3010 JMenuItem outputFeatures = new JMenuItem(
3011 MessageManager.getString("label.export_features").concat("..."));
3013 JMenuItem outputAnnotations = new JMenuItem(
3014 MessageManager.getString("label.export_annotations").concat("..."));
3016 JMenuItem closeMenuItem = new JMenuItem(
3017 MessageManager.getString("action.close"));
3019 JMenuItem selectAllSequenceMenuItem = new JMenuItem(
3020 MessageManager.getString("action.select_all"));
3022 JMenuItem deselectAllSequenceMenuItem = new JMenuItem(
3023 MessageManager.getString("action.deselect_all"));
3025 JMenuItem invertSequenceMenuItem = new JMenuItem(
3026 MessageManager.getString("action.invert_selection"));
3028 JMenuItem remove2LeftMenuItem = new JMenuItem();
3030 JMenuItem remove2RightMenuItem = new JMenuItem();
3032 JMenuItem removeGappedColumnMenuItem = new JMenuItem();
3034 JMenuItem removeAllGapsMenuItem = new JMenuItem();
3036 JCheckBoxMenuItem viewBoxesMenuItem = new JCheckBoxMenuItem();
3038 JCheckBoxMenuItem viewTextMenuItem = new JCheckBoxMenuItem();
3040 JMenuItem sortPairwiseMenuItem = new JMenuItem();
3042 JMenuItem sortIDMenuItem = new JMenuItem();
3044 JMenuItem sortLengthMenuItem = new JMenuItem();
3046 JMenuItem sortGroupMenuItem = new JMenuItem();
3048 JMenuItem removeRedundancyMenuItem = new JMenuItem();
3050 JMenuItem pairwiseAlignmentMenuItem = new JMenuItem();
3052 JMenuItem PCAMenuItem = new JMenuItem();
3054 JMenuItem averageDistanceTreeMenuItem = new JMenuItem();
3056 JMenuItem neighbourTreeMenuItem = new JMenuItem();
3058 BorderLayout borderLayout1 = new BorderLayout();
3060 public JLabel statusBar = new JLabel();
3062 JMenuItem clustalColour = new JMenuItem();
3064 JMenuItem zappoColour = new JMenuItem();
3066 JMenuItem taylorColour = new JMenuItem();
3068 JMenuItem hydrophobicityColour = new JMenuItem();
3070 JMenuItem helixColour = new JMenuItem();
3072 JMenuItem strandColour = new JMenuItem();
3074 JMenuItem turnColour = new JMenuItem();
3076 JMenuItem buriedColour = new JMenuItem();
3078 JMenuItem purinePyrimidineColour = new JMenuItem();
3080 JMenuItem RNAInteractionColour = new JMenuItem();
3082 JMenuItem RNAHelixColour = new JMenuItem();
3084 JMenuItem userDefinedColour = new JMenuItem();
3086 JMenuItem PIDColour = new JMenuItem();
3088 JMenuItem BLOSUM62Colour = new JMenuItem();
3090 JMenuItem tcoffeeColour = new JMenuItem();
3092 JMenuItem njTreeBlosumMenuItem = new JMenuItem();
3094 JMenuItem avDistanceTreeBlosumMenuItem = new JMenuItem();
3096 JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
3098 JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
3100 JCheckBoxMenuItem displayNonconservedMenuItem = new JCheckBoxMenuItem();
3102 JMenuItem alProperties = new JMenuItem(
3103 MessageManager.getString("label.alignment_props"));
3105 JMenuItem overviewMenuItem = new JMenuItem();
3107 JMenuItem undoMenuItem = new JMenuItem();
3109 JMenuItem redoMenuItem = new JMenuItem();
3111 JCheckBoxMenuItem conservationMenuItem = new JCheckBoxMenuItem();
3113 JMenuItem noColourmenuItem = new JMenuItem();
3115 JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
3117 JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
3119 JMenuItem findMenuItem = new JMenuItem();
3121 JCheckBoxMenuItem abovePIDThreshold = new JCheckBoxMenuItem();
3123 JMenuItem nucleotideColour = new JMenuItem();
3125 JMenuItem deleteGroups = new JMenuItem();
3127 JMenuItem grpsFromSelection = new JMenuItem();
3129 JMenuItem createGroup = new JMenuItem();
3131 JMenuItem unGroup = new JMenuItem();
3133 JMenuItem delete = new JMenuItem();
3135 JMenuItem copy = new JMenuItem();
3137 JMenuItem cut = new JMenuItem();
3139 JMenu pasteMenu = new JMenu();
3141 JMenuItem pasteNew = new JMenuItem();
3143 JMenuItem pasteThis = new JMenuItem();
3145 JCheckBoxMenuItem applyToAllGroups = new JCheckBoxMenuItem();
3147 JMenuItem font = new JMenuItem();
3149 JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
3151 JCheckBoxMenuItem scaleLeft = new JCheckBoxMenuItem();
3153 JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
3155 JMenuItem modifyPID = new JMenuItem();
3157 JMenuItem modifyConservation = new JMenuItem();
3159 JCheckBoxMenuItem autoCalculate = null;
3161 JCheckBoxMenuItem sortByTree = new JCheckBoxMenuItem(
3162 "Sort Alignment With New Tree", true);
3164 JMenu sortByTreeMenu = new JMenu();
3166 JMenuItem inputText = new JMenuItem();
3168 JMenuItem documentation = new JMenuItem();
3170 JMenuItem about = new JMenuItem();
3172 JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
3174 JCheckBoxMenuItem centreColumnLabelFlag = new JCheckBoxMenuItem();
3176 JCheckBoxMenuItem followMouseOverFlag = new JCheckBoxMenuItem();
3178 JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem();
3180 JCheckBoxMenuItem applyAutoAnnotationSettings = new JCheckBoxMenuItem();
3182 JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem();
3184 JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem();
3186 JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem();
3188 JCheckBoxMenuItem normSequenceLogo = new JCheckBoxMenuItem();
3191 * Initialise menus and other items
3195 private void jbInit() throws Exception
3197 setJMenuBar(alignFrameMenuBar);
3200 * Configure File menu items and actions
3203 .setLabel(MessageManager.getString("label.input_from_textbox"));
3204 inputText.addActionListener(this);
3205 JMenu outputTextboxMenu = new JMenu(
3206 MessageManager.getString("label.out_to_textbox"));
3207 for (int i = 0; i < AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3210 JMenuItem item = new JMenuItem(AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3212 item.addActionListener(new java.awt.event.ActionListener()
3215 public void actionPerformed(ActionEvent e)
3217 outputText_actionPerformed(e);
3221 outputTextboxMenu.add(item);
3223 closeMenuItem.addActionListener(this);
3224 loadApplication.addActionListener(this);
3225 loadTree.addActionListener(this);
3226 loadAnnotations.addActionListener(this);
3227 outputFeatures.addActionListener(this);
3228 outputAnnotations.addActionListener(this);
3231 * Configure Edit menu items and actions
3233 undoMenuItem.setEnabled(false);
3234 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3235 undoMenuItem.addActionListener(this);
3236 redoMenuItem.setEnabled(false);
3237 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3238 redoMenuItem.addActionListener(this);
3239 copy.setLabel(MessageManager.getString("action.copy"));
3240 copy.addActionListener(this);
3241 cut.setLabel(MessageManager.getString("action.cut"));
3242 cut.addActionListener(this);
3243 delete.setLabel(MessageManager.getString("action.delete"));
3244 delete.addActionListener(this);
3245 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3246 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3247 pasteNew.addActionListener(this);
3248 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3249 pasteThis.addActionListener(this);
3250 remove2LeftMenuItem.setLabel(MessageManager
3251 .getString("action.remove_left"));
3252 remove2LeftMenuItem.addActionListener(this);
3253 remove2RightMenuItem.setLabel(MessageManager
3254 .getString("action.remove_right"));
3255 remove2RightMenuItem.addActionListener(this);
3256 removeGappedColumnMenuItem.setLabel(MessageManager
3257 .getString("action.remove_empty_columns"));
3258 removeGappedColumnMenuItem.addActionListener(this);
3259 removeAllGapsMenuItem.setLabel(MessageManager
3260 .getString("action.remove_all_gaps"));
3261 removeAllGapsMenuItem.addActionListener(this);
3262 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3263 "action.remove_redundancy").concat("..."));
3264 removeRedundancyMenuItem.addActionListener(this);
3267 * Configure Select menu items and actions
3269 findMenuItem.setLabel(MessageManager.getString("action.find"));
3270 findMenuItem.addActionListener(this);
3271 selectAllSequenceMenuItem.addActionListener(this);
3272 deselectAllSequenceMenuItem.addActionListener(this);
3273 invertSequenceMenuItem.setLabel(MessageManager
3274 .getString("action.invert_sequence_selection"));
3275 invertSequenceMenuItem.addActionListener(this);
3276 invertColSel.setLabel(MessageManager
3277 .getString("action.invert_column_selection"));
3278 invertColSel.addActionListener(this);
3279 deleteGroups.setLabel(MessageManager
3280 .getString("action.undefine_groups"));
3281 deleteGroups.addActionListener(this);
3282 grpsFromSelection.setLabel(MessageManager
3283 .getString("action.make_groups_selection"));
3284 grpsFromSelection.addActionListener(this);
3285 createGroup.setLabel(MessageManager.getString("action.create_group"));
3286 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3287 annotationColumnSelection.setLabel("Select by Annotation");
3288 annotationColumnSelection.addActionListener(this);
3291 * Configure View menu items and actions
3293 newView.setLabel(MessageManager.getString("action.new_view"));
3294 newView.addActionListener(this);
3295 JMenu showMenu = new JMenu(MessageManager.getString("action.show"));
3296 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3297 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3298 JMenu hideMenu = new JMenu(MessageManager.getString("action.hide"));
3300 .setLabel(MessageManager.getString("label.selected_columns"));
3301 hideSequences.setLabel(MessageManager
3302 .getString("label.selected_sequences"));
3303 hideAllButSelection.setLabel(MessageManager
3304 .getString("label.all_but_selected_region"));
3305 hideAllSelection.setLabel(MessageManager
3306 .getString("label.selected_region"));
3307 showAllHidden.setLabel(MessageManager
3308 .getString("label.all_sequences_columns"));
3309 showColumns.addActionListener(this);
3310 showSeqs.addActionListener(this);
3311 hideColumns.addActionListener(this);
3312 hideSequences.addActionListener(this);
3313 hideAllButSelection.addActionListener(this);
3314 hideAllSelection.addActionListener(this);
3315 showAllHidden.addActionListener(this);
3316 featureSettings.setLabel(MessageManager
3317 .getString("label.feature_settings"));
3318 featureSettings.addActionListener(this);
3319 sequenceFeatures.setLabel(MessageManager
3320 .getString("label.show_sequence_features"));
3321 sequenceFeatures.addItemListener(this);
3322 sequenceFeatures.setState(false);
3323 followMouseOverFlag.setLabel(MessageManager
3324 .getString("label.automatic_scrolling"));
3325 followMouseOverFlag.addItemListener(this);
3326 alProperties.addActionListener(this);
3327 overviewMenuItem.setLabel(MessageManager
3328 .getString("label.overview_window"));
3329 overviewMenuItem.addActionListener(this);
3332 * Configure Annotations menu items and actions
3334 annotationPanelMenuItem.setLabel(MessageManager
3335 .getString("label.show_annotations"));
3336 annotationPanelMenuItem.addItemListener(this);
3337 showGroupConsensus.setLabel(MessageManager
3338 .getString("label.group_consensus"));
3339 showGroupConservation.setLabel(MessageManager
3340 .getString("label.group_conservation"));
3341 showConsensusHistogram.setLabel(MessageManager
3342 .getString("label.show_consensus_histogram"));
3343 showSequenceLogo.setLabel(MessageManager
3344 .getString("label.show_consensus_logo"));
3345 normSequenceLogo.setLabel(MessageManager
3346 .getString("label.norm_consensus_logo"));
3347 applyAutoAnnotationSettings.setLabel(MessageManager
3348 .getString("label.apply_all_groups"));
3349 applyAutoAnnotationSettings.setState(true);
3350 JMenu autoAnnMenu = new JMenu(
3351 MessageManager.getString("label.autocalculated_annotation"));
3352 showGroupConsensus.addItemListener(this);
3353 showGroupConservation.addItemListener(this);
3354 showConsensusHistogram.addItemListener(this);
3355 showSequenceLogo.addItemListener(this);
3356 normSequenceLogo.addItemListener(this);
3357 applyAutoAnnotationSettings.addItemListener(this);
3358 showAlignmentAnnotations = new JCheckBoxMenuItem(
3359 MessageManager.getString("label.show_all_al_annotations"));
3360 showSequenceAnnotations = new JCheckBoxMenuItem(
3361 MessageManager.getString("label.show_all_seq_annotations"));
3362 sortAnnBySequence = new JCheckBoxMenuItem(
3363 MessageManager.getString("label.sort_annotations_by_sequence"));
3364 sortAnnByLabel = new JCheckBoxMenuItem(
3365 MessageManager.getString("label.sort_annotations_by_label"));
3366 showAutoFirst = new JCheckBoxMenuItem(
3367 MessageManager.getString("label.show_first"));
3368 showAutoLast = new JCheckBoxMenuItem(
3369 MessageManager.getString("label.show_last"));
3370 showAlignmentAnnotations.addItemListener(this);
3371 showSequenceAnnotations.addItemListener(this);
3372 sortAnnBySequence.addItemListener(this);
3373 sortAnnByLabel.addItemListener(this);
3374 showAutoFirst.addItemListener(this);
3375 showAutoLast.addItemListener(this);
3378 * Configure Format menu items and actions
3380 font.setLabel(MessageManager.getString("action.font"));
3381 font.addActionListener(this);
3382 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3383 scaleAbove.setState(true);
3384 scaleAbove.setEnabled(false);
3385 scaleAbove.addItemListener(this);
3386 scaleLeft.setEnabled(false);
3387 scaleLeft.setState(true);
3388 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3389 scaleLeft.addItemListener(this);
3390 scaleRight.setEnabled(false);
3391 scaleRight.setState(true);
3392 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3393 scaleRight.addItemListener(this);
3394 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3395 viewBoxesMenuItem.setState(true);
3396 viewBoxesMenuItem.addItemListener(this);
3397 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3398 viewTextMenuItem.setState(true);
3399 viewTextMenuItem.addItemListener(this);
3400 colourTextMenuItem.setLabel(MessageManager
3401 .getString("label.colour_text"));
3402 colourTextMenuItem.addItemListener(this);
3403 displayNonconservedMenuItem.setLabel(MessageManager
3404 .getString("label.show_non_conversed"));
3405 displayNonconservedMenuItem.addItemListener(this);
3406 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3407 wrapMenuItem.addItemListener(this);
3408 renderGapsMenuItem.setLabel(MessageManager
3409 .getString("action.show_gaps"));
3410 renderGapsMenuItem.setState(true);
3411 renderGapsMenuItem.addItemListener(this);
3412 centreColumnLabelFlag.setLabel(MessageManager
3413 .getString("label.centre_column_labels"));
3414 centreColumnLabelFlag.addItemListener(this);
3415 seqLimits.setState(true);
3416 seqLimits.setLabel(MessageManager
3417 .getString("label.show_sequence_limits"));
3418 seqLimits.addItemListener(this);
3421 * Configure Colour menu items and actions
3423 applyToAllGroups.setLabel(MessageManager
3424 .getString("label.apply_colour_to_all_groups"));
3425 applyToAllGroups.setState(true);
3426 applyToAllGroups.addItemListener(this);
3427 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3428 clustalColour.addActionListener(this);
3429 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3430 zappoColour.addActionListener(this);
3431 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3432 taylorColour.addActionListener(this);
3433 hydrophobicityColour.setLabel(MessageManager
3434 .getString("label.hydrophobicity"));
3435 hydrophobicityColour.addActionListener(this);
3437 .setLabel(MessageManager.getString("label.helix_propensity"));
3438 helixColour.addActionListener(this);
3439 strandColour.setLabel(MessageManager
3440 .getString("label.strand_propensity"));
3441 strandColour.addActionListener(this);
3442 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3443 turnColour.addActionListener(this);
3444 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3445 buriedColour.addActionListener(this);
3446 purinePyrimidineColour.setLabel(MessageManager
3447 .getString("label.purine_pyrimidine"));
3448 purinePyrimidineColour.addActionListener(this);
3449 RNAInteractionColour.setLabel(MessageManager
3450 .getString("label.rna_interaction"));
3451 RNAInteractionColour.addActionListener(this);
3452 RNAHelixColour.setLabel(MessageManager
3453 .getString("action.by_rna_helixes"));
3454 RNAHelixColour.addActionListener(this);
3455 userDefinedColour.setLabel(MessageManager
3456 .getString("action.user_defined"));
3457 userDefinedColour.addActionListener(this);
3458 PIDColour.setLabel(MessageManager
3459 .getString("label.percentage_identity"));
3460 PIDColour.addActionListener(this);
3461 BLOSUM62Colour.setLabel(MessageManager
3462 .getString("label.blosum62_score"));
3463 BLOSUM62Colour.addActionListener(this);
3465 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3466 // it will be enabled only if a score file is provided
3467 tcoffeeColour.setEnabled(false);
3468 tcoffeeColour.addActionListener(this);
3469 conservationMenuItem.setLabel(MessageManager
3470 .getString("action.by_conservation"));
3471 conservationMenuItem.addItemListener(this);
3472 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3473 noColourmenuItem.addActionListener(this);
3474 abovePIDThreshold.setLabel(MessageManager
3475 .getString("label.above_identity_threshold"));
3476 abovePIDThreshold.addItemListener(this);
3477 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3478 nucleotideColour.addActionListener(this);
3479 modifyPID.setLabel(MessageManager
3480 .getString("label.modify_identity_thereshold"));
3481 modifyPID.addActionListener(this);
3482 modifyConservation.setLabel(MessageManager
3483 .getString("label.modify_conservation_thereshold"));
3484 modifyConservation.addActionListener(this);
3485 annotationColour.setLabel(MessageManager
3486 .getString("action.by_annotation"));
3487 annotationColour.addActionListener(this);
3490 * Configure Calculate menu items and actions
3492 sortPairwiseMenuItem.setLabel(MessageManager
3493 .getString("action.by_pairwise_id"));
3494 sortPairwiseMenuItem.addActionListener(this);
3495 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3496 sortIDMenuItem.addActionListener(this);
3497 sortLengthMenuItem.setLabel(MessageManager
3498 .getString("action.by_length"));
3499 sortLengthMenuItem.addActionListener(this);
3500 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3501 sortGroupMenuItem.addActionListener(this);
3502 pairwiseAlignmentMenuItem.setLabel(MessageManager
3503 .getString("action.pairwise_alignment"));
3504 pairwiseAlignmentMenuItem.addActionListener(this);
3505 PCAMenuItem.setLabel(MessageManager
3506 .getString("label.principal_component_analysis"));
3507 PCAMenuItem.addActionListener(this);
3508 autoCalculate = new JCheckBoxMenuItem(
3509 MessageManager.getString("label.autocalculate_consensus"), true);
3510 averageDistanceTreeMenuItem.setLabel(MessageManager
3511 .getString("label.average_distance_identity"));
3512 averageDistanceTreeMenuItem.addActionListener(this);
3513 neighbourTreeMenuItem.setLabel(MessageManager
3514 .getString("label.neighbour_joining_identity"));
3515 neighbourTreeMenuItem.addActionListener(this);
3516 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3517 .getString("label.average_distance_bloslum62"));
3518 avDistanceTreeBlosumMenuItem.addActionListener(this);
3519 njTreeBlosumMenuItem.setLabel(MessageManager
3520 .getString("label.neighbour_blosum62"));
3521 njTreeBlosumMenuItem.addActionListener(this);
3522 sortByTreeMenu.setLabel(MessageManager
3523 .getString("action.by_tree_order"));
3524 JMenu sortMenu = new JMenu(MessageManager.getString("action.sort"));
3525 JMenu calculateTreeMenu = new JMenu(
3526 MessageManager.getString("action.calculate_tree"));
3527 autoCalculate.addItemListener(this);
3528 sortByTree.addItemListener(this);
3531 * Configure Help menu items and actions
3533 JMenu helpMenu = new JMenu(MessageManager.getString("action.help"));
3534 documentation.setLabel(MessageManager.getString("label.documentation"));
3535 documentation.addActionListener(this);
3536 about.setLabel(MessageManager.getString("label.about"));
3537 about.addActionListener(this);
3540 * Add top level menus to frame
3542 alignFrameMenuBar.add(fileMenu);
3543 JMenu editMenu = new JMenu(MessageManager.getString("action.edit"));
3544 alignFrameMenuBar.add(editMenu);
3545 JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
3546 alignFrameMenuBar.add(selectMenu);
3547 JMenu viewMenu = new JMenu(MessageManager.getString("action.view"));
3548 alignFrameMenuBar.add(viewMenu);
3549 JMenu annotationsMenu = new JMenu(
3550 MessageManager.getString("action.annotations"));
3551 alignFrameMenuBar.add(annotationsMenu);
3552 JMenu formatMenu = new JMenu(MessageManager.getString("action.format"));
3553 alignFrameMenuBar.add(formatMenu);
3554 JMenu colourMenu = new JMenu(MessageManager.getString("action.colour"));
3555 alignFrameMenuBar.add(colourMenu);
3556 JMenu calculateMenu = new JMenu(
3557 MessageManager.getString("action.calculate"));
3558 alignFrameMenuBar.add(calculateMenu);
3559 alignFrameMenuBar.add(helpMenu);
3564 fileMenu.add(inputText);
3565 fileMenu.add(loadTree);
3566 fileMenu.add(loadAnnotations);
3567 fileMenu.addSeparator();
3568 fileMenu.add(outputTextboxMenu);
3569 fileMenu.add(outputFeatures);
3570 fileMenu.add(outputAnnotations);
3571 if (jalviewServletURL != null)
3573 fileMenu.add(loadApplication);
3575 fileMenu.addSeparator();
3576 fileMenu.add(closeMenuItem);
3581 editMenu.add(undoMenuItem);
3582 editMenu.add(redoMenuItem);
3585 pasteMenu.add(pasteNew);
3586 pasteMenu.add(pasteThis);
3587 editMenu.add(pasteMenu);
3588 editMenu.add(delete);
3589 editMenu.addSeparator();
3590 editMenu.add(remove2LeftMenuItem);
3591 editMenu.add(remove2RightMenuItem);
3592 editMenu.add(removeGappedColumnMenuItem);
3593 editMenu.add(removeAllGapsMenuItem);
3594 editMenu.add(removeRedundancyMenuItem);
3599 selectMenu.add(findMenuItem);
3600 selectMenu.addSeparator();
3601 selectMenu.add(selectAllSequenceMenuItem);
3602 selectMenu.add(deselectAllSequenceMenuItem);
3603 selectMenu.add(invertSequenceMenuItem);
3604 selectMenu.add(invertColSel);
3605 selectMenu.add(createGroup);
3606 selectMenu.add(unGroup);
3607 selectMenu.add(grpsFromSelection);
3608 selectMenu.add(deleteGroups);
3609 selectMenu.add(annotationColumnSelection);
3614 viewMenu.add(newView);
3615 viewMenu.addSeparator();
3616 showMenu.add(showColumns);
3617 showMenu.add(showSeqs);
3618 showMenu.add(showAllHidden);
3619 viewMenu.add(showMenu);
3620 hideMenu.add(hideColumns);
3621 hideMenu.add(hideSequences);
3622 hideMenu.add(hideAllSelection);
3623 hideMenu.add(hideAllButSelection);
3624 viewMenu.add(hideMenu);
3625 viewMenu.addSeparator();
3626 viewMenu.add(followMouseOverFlag);
3627 viewMenu.addSeparator();
3628 viewMenu.add(sequenceFeatures);
3629 viewMenu.add(featureSettings);
3630 viewMenu.addSeparator();
3631 viewMenu.add(alProperties);
3632 viewMenu.addSeparator();
3633 viewMenu.add(overviewMenuItem);
3638 annotationsMenu.add(annotationPanelMenuItem);
3639 annotationsMenu.addSeparator();
3640 annotationsMenu.add(showAlignmentAnnotations);
3641 annotationsMenu.add(showSequenceAnnotations);
3642 annotationsMenu.add(sortAnnBySequence);
3643 annotationsMenu.add(sortAnnByLabel);
3644 annotationsMenu.addSeparator();
3645 autoAnnMenu.add(showAutoFirst);
3646 autoAnnMenu.add(showAutoLast);
3647 autoAnnMenu.addSeparator();
3648 autoAnnMenu.add(applyAutoAnnotationSettings);
3649 autoAnnMenu.add(showConsensusHistogram);
3650 autoAnnMenu.add(showSequenceLogo);
3651 autoAnnMenu.add(normSequenceLogo);
3652 autoAnnMenu.addSeparator();
3653 autoAnnMenu.add(showGroupConservation);
3654 autoAnnMenu.add(showGroupConsensus);
3655 annotationsMenu.add(autoAnnMenu);
3660 formatMenu.add(font);
3661 formatMenu.add(seqLimits);
3662 formatMenu.add(wrapMenuItem);
3663 formatMenu.add(scaleAbove);
3664 formatMenu.add(scaleLeft);
3665 formatMenu.add(scaleRight);
3666 formatMenu.add(viewBoxesMenuItem);
3667 formatMenu.add(viewTextMenuItem);
3668 formatMenu.add(colourTextMenuItem);
3669 formatMenu.add(displayNonconservedMenuItem);
3670 formatMenu.add(renderGapsMenuItem);
3671 formatMenu.add(centreColumnLabelFlag);
3676 colourMenu.add(applyToAllGroups);
3677 colourMenu.addSeparator();
3678 colourMenu.add(noColourmenuItem);
3679 colourMenu.add(clustalColour);
3680 colourMenu.add(BLOSUM62Colour);
3681 colourMenu.add(PIDColour);
3682 colourMenu.add(zappoColour);
3683 colourMenu.add(taylorColour);
3684 colourMenu.add(hydrophobicityColour);
3685 colourMenu.add(helixColour);
3686 colourMenu.add(strandColour);
3687 colourMenu.add(turnColour);
3688 colourMenu.add(buriedColour);
3689 colourMenu.add(nucleotideColour);
3690 colourMenu.add(purinePyrimidineColour);
3691 // colourMenu.add(RNAInteractionColour);
3692 colourMenu.add(tcoffeeColour);
3693 colourMenu.add(userDefinedColour);
3694 colourMenu.addSeparator();
3695 colourMenu.add(conservationMenuItem);
3696 colourMenu.add(modifyConservation);
3697 colourMenu.add(abovePIDThreshold);
3698 colourMenu.add(modifyPID);
3699 colourMenu.add(annotationColour);
3700 colourMenu.add(RNAHelixColour);
3705 sortMenu.add(sortIDMenuItem);
3706 sortMenu.add(sortLengthMenuItem);
3707 sortMenu.add(sortByTreeMenu);
3708 sortMenu.add(sortGroupMenuItem);
3709 sortMenu.add(sortPairwiseMenuItem);
3710 calculateMenu.add(sortMenu);
3711 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3712 calculateTreeMenu.add(neighbourTreeMenuItem);
3713 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3714 calculateTreeMenu.add(njTreeBlosumMenuItem);
3715 calculateMenu.add(calculateTreeMenu);
3716 calculateMenu.addSeparator();
3717 calculateMenu.add(pairwiseAlignmentMenuItem);
3718 calculateMenu.add(PCAMenuItem);
3719 calculateMenu.add(autoCalculate);
3720 calculateMenu.add(sortByTree);
3725 helpMenu.add(documentation);
3726 helpMenu.add(about);
3731 statusBar.setBackground(Color.white);
3732 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3733 statusBar.setText(MessageManager.getString("label.status_bar"));
3734 this.add(statusBar, BorderLayout.SOUTH);
3737 public void setStatus(String string)
3739 statusBar.setText(string);
3742 JMenuItem featureSettings = new JMenuItem();
3744 JCheckBoxMenuItem sequenceFeatures = new JCheckBoxMenuItem();
3746 JMenuItem annotationColour = new JMenuItem();
3748 JMenuItem annotationColumnSelection = new JMenuItem();
3750 JMenuItem invertColSel = new JMenuItem();
3752 JMenuItem showColumns = new JMenuItem();
3754 JMenuItem showSeqs = new JMenuItem();
3756 JMenuItem hideColumns = new JMenuItem();
3758 JMenuItem hideSequences = new JMenuItem();
3760 JMenuItem hideAllButSelection = new JMenuItem();
3762 JMenuItem hideAllSelection = new JMenuItem();
3764 JMenuItem showAllHidden = new JMenuItem();
3766 JMenuItem newView = new JMenuItem();
3768 private JCheckBoxMenuItem showAlignmentAnnotations;
3770 private JCheckBoxMenuItem showSequenceAnnotations;
3772 private JCheckBoxMenuItem sortAnnBySequence;
3774 private JCheckBoxMenuItem sortAnnByLabel;
3776 private JCheckBoxMenuItem showAutoFirst;
3778 private JCheckBoxMenuItem showAutoLast;
3780 private SplitFrame splitFrame;
3783 * Attach the alignFrame panels after embedding menus, if necessary. This used
3784 * to be called setEmbedded, but is now creates the dropdown menus in a
3785 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3787 * @param reallyEmbedded
3788 * true to attach the view to the applet area on the page rather than
3791 public void createAlignFrameWindow(boolean reallyEmbedded)
3795 embedAlignFrameInApplet(viewport.applet);
3800 // test and embed menu bar if necessary.
3802 if (embedMenuIfNeeded(alignPanel))
3805 * adjust for status bar height too. ? pointless as overridden by layout
3808 alignPanel.setSize(getSize().width,
3809 getSize().height - statusBar.getHeight());
3811 add(statusBar, BorderLayout.SOUTH);
3812 add(alignPanel, BorderLayout.CENTER);
3813 // and register with the applet so it can pass external API calls to us
3814 JalviewLite.addFrame(this, this.getTitle(),
3821 * Add the components of this AlignFrame to the applet container.
3825 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3828 // Explicitly build the embedded menu panel for the on-page applet
3830 // view cannot be closed if its actually on the page
3831 fileMenu.remove(closeMenuItem);
3832 fileMenu.remove(3); // Remove Separator
3833 // construct embedded menu, using default font
3834 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3835 // and actually add the components to the applet area
3836 theApplet.setLayout(new BorderLayout());
3837 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3838 theApplet.add(statusBar, BorderLayout.SOUTH);
3839 // TODO should size be left to the layout manager?
3840 alignPanel.setSize(theApplet.getSize().width,
3841 theApplet.getSize().height - embeddedMenu.getHeight()
3842 - statusBar.getHeight());
3843 theApplet.add(alignPanel, BorderLayout.CENTER);
3844 final AlignFrame me = this;
3845 theApplet.addFocusListener(new FocusListener()
3849 public void focusLost(FocusEvent e)
3851 if (theApplet.currentAlignFrame == me)
3853 theApplet.currentAlignFrame = null;
3858 public void focusGained(FocusEvent e)
3860 theApplet.currentAlignFrame = me;
3863 theApplet.validate();
3867 * create a new binding between structures in an existing jmol viewer instance
3868 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3869 * this does not open a new Jmol window, or modify the display of the
3870 * structures in the original jmol window. Note This method doesn't work
3871 * without an additional javascript library to exchange messages between the
3872 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3875 * JmolViewer instance
3876 * @param sequenceIds
3877 * - sequence Ids to search for associations
3879 public SequenceStructureBinding addStructureViewInstance(
3880 Object jmolviewer, String[] sequenceIds)
3882 Viewer viewer = null;
3885 viewer = (Viewer) jmolviewer;
3886 } catch (ClassCastException ex)
3888 System.err.println("Unsupported viewer object :"
3889 + jmolviewer.getClass());
3893 System.err.println("Can't use this object as a structure viewer:"
3894 + jmolviewer.getClass());
3897 SequenceI[] seqs = null;
3898 if (sequenceIds == null || sequenceIds.length == 0)
3900 seqs = viewport.getAlignment().getSequencesArray();
3904 Vector sqi = new Vector();
3905 AlignmentI al = viewport.getAlignment();
3906 for (int sid = 0; sid < sequenceIds.length; sid++)
3908 SequenceI sq = al.findName(sequenceIds[sid]);
3916 seqs = new SequenceI[sqi.size()];
3917 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3919 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3927 AAStructureBindingModel jmv = null;
3928 // TODO: search for a jmv that involves viewer
3930 { // create a new viewer/jalview binding.
3931 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3939 * bind a pdb file to a sequence in the current view
3942 * - sequenceId within the dataset.
3943 * @param pdbEntryString
3944 * - the short name for the PDB file
3946 * - pdb file - either a URL or a valid PDB file.
3947 * @return true if binding was as success TODO: consider making an exception
3948 * structure for indicating when PDB parsing or sequenceId location
3951 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3954 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3955 boolean needtoadd = false;
3956 if (toaddpdb != null)
3958 Vector pdbe = toaddpdb.getPDBId();
3959 PDBEntry pdbentry = null;
3960 if (pdbe != null && pdbe.size() > 0)
3962 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3964 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3965 if (!pdbentry.getId().equals(pdbEntryString)
3966 && !pdbentry.getFile().equals(pdbFile))
3976 if (pdbentry == null)
3978 pdbentry = new PDBEntry();
3979 pdbentry.setId(pdbEntryString);
3980 pdbentry.setFile(pdbFile);
3981 needtoadd = true; // add this new entry to sequence.
3983 // resolve data source
3984 // TODO: this code should be a refactored to an io package
3985 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3986 if (protocol == null)
3992 // make a note of the access mode and add
3993 if (pdbentry.getProperty() == null)
3995 pdbentry.setProperty(new Hashtable());
3997 pdbentry.getProperty().put("protocol", protocol);
3998 toaddpdb.addPDBId(pdbentry);
3999 alignPanel.getStructureSelectionManager()
4000 .registerPDBEntry(pdbentry);
4006 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4010 Vector sequences = new Vector();
4011 for (int i = 0; i < seqs.length; i++)
4013 if (seqs[i] != null)
4015 sequences.addElement(new Object[]
4016 { seqs[i], (chains != null) ? chains[i] : null });
4019 seqs = new SequenceI[sequences.size()];
4020 chains = new String[sequences.size()];
4021 for (int i = 0, isize = sequences.size(); i < isize; i++)
4023 Object[] oj = (Object[]) sequences.elementAt(i);
4025 seqs[i] = (SequenceI) oj[0];
4026 chains[i] = (String) oj[1];
4034 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4035 SequenceI[] seqs, String[] chains, String protocol)
4037 // Scrub any null sequences from the array
4038 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4039 seqs = (SequenceI[]) sqch[0];
4040 chains = (String[]) sqch[1];
4041 if (seqs == null || seqs.length == 0)
4044 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4046 if (protocol == null || protocol.trim().length() == 0
4047 || protocol.equals("null"))
4049 protocol = (String) pdb.getProperty().get("protocol");
4050 if (protocol == null)
4052 System.err.println("Couldn't work out protocol to open structure: "
4057 if (applet.useXtrnalSviewer)
4059 // register the association(s) and quit, don't create any windows.
4060 if (StructureSelectionManager.getStructureSelectionManager(applet)
4061 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4063 System.err.println("Failed to map " + pdb.getFile() + " ("
4064 + protocol + ") to any sequences");
4068 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4070 // can only do alignments with Jmol
4071 // find the last jmol window assigned to this alignment
4072 AppletJmol ajm = null, tajm;
4073 Vector jmols = applet
4074 .getAppletWindow(AppletJmol.class);
4075 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4077 tajm = (AppletJmol) jmols.elementAt(i);
4078 if (tajm.ap.alignFrame == this)
4087 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4088 // try and add the pdb structure
4093 // otherwise, create a new window
4094 // if (applet.jmolAvailable)
4096 new AppletJmol(pdb, seqs, chains, alignPanel, protocol);
4097 applet.lastFrameX += 40;
4098 applet.lastFrameY += 40;
4102 // new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4107 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4108 SequenceI[][] seqs, String[][] chains, String[] protocols)
4110 // TODO Auto-generated method stub
4111 System.err.println("Aligned Structure View: Not yet implemented.");
4115 * modify the current selection, providing the user has not made a selection
4119 * - sequences from this alignment
4121 * - columns to be selected on the alignment
4123 public void select(SequenceGroup sel, ColumnSelection csel)
4125 alignPanel.seqPanel.selection(sel, csel, null);
4128 public void scrollTo(int row, int column)
4130 alignPanel.seqPanel.scrollTo(row, column);
4133 public void scrollToRow(int row)
4135 alignPanel.seqPanel.scrollToRow(row);
4138 public void scrollToColumn(int column)
4140 alignPanel.seqPanel.scrollToColumn(column);
4144 * @return the alignments unique ID.
4146 public String getSequenceSetId()
4148 return viewport.getSequenceSetId();
4152 * Load the (T-Coffee) score file from the specified url
4155 * File/URL/T-COFFEE score file contents
4156 * @throws IOException
4157 * @return true if alignment was annotated with data from source
4159 public boolean loadScoreFile(String source) throws IOException
4162 AlignFile file = GenericFileAdapter.newTCoffeeScoreFile(source,
4163 AppletFormatAdapter.checkProtocol(source));
4164 if (!file.isValid())
4166 // TODO: raise dialog for gui
4167 System.err.println("Problems parsing T-Coffee scores: "
4168 + file.getWarningMessage());
4169 System.err.println("Origin was:\n" + source);
4174 * check that the score matrix matches the alignment dimensions
4177 if ((aln = viewport.getAlignment()) != null
4178 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4181 // TODO: raise a dialog box here rather than bomb out.
4183 .println("The scores matrix does not match the alignment dimensions");
4187 // TODO add parameter to indicate if matching should be done
4188 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4190 alignPanel.fontChanged();
4191 tcoffeeColour.setEnabled(true);
4192 // switch to this color
4193 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4198 System.err.println("Problems resolving T-Coffee scores:");
4199 if (file.getWarningMessage() != null)
4201 System.err.println(file.getWarningMessage());
4207 public SplitFrame getSplitFrame()
4209 return this.splitFrame;
4212 public void setSplitFrame(SplitFrame sf)
4214 this.splitFrame = sf;
4217 // may not need this
4219 public void setShowSeqFeatures(boolean b)
4221 // showSeqFeatures.setSelected(b);
4222 viewport.setShowSequenceFeatures(b);
4227 public void setMenusForViewport()
4229 // setMenusFromViewport(viewport);
4233 public void refreshFeatureUI(boolean enableIfNecessary)
4235 if (enableIfNecessary)
4237 sequenceFeatures.setState(true);
4238 alignPanel.av.setShowSequenceFeatures(true);
4243 public FeatureSettingsControllerI getFeatureSettingsUI()
4245 return alignPanel.av.featureSettings;