2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureColourI;
29 import jalview.api.FeatureRenderer;
30 import jalview.api.FeatureSettingsControllerI;
31 import jalview.api.SequenceStructureBinding;
32 import jalview.bin.JalviewLite;
33 import jalview.commands.CommandI;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.commands.OrderCommand;
37 import jalview.commands.RemoveGapColCommand;
38 import jalview.commands.RemoveGapsCommand;
39 import jalview.commands.SlideSequencesCommand;
40 import jalview.commands.TrimRegionCommand;
41 import jalview.datamodel.Alignment;
42 import jalview.datamodel.AlignmentAnnotation;
43 import jalview.datamodel.AlignmentI;
44 import jalview.datamodel.AlignmentOrder;
45 import jalview.datamodel.ColumnSelection;
46 import jalview.datamodel.PDBEntry;
47 import jalview.datamodel.Sequence;
48 import jalview.datamodel.SequenceGroup;
49 import jalview.datamodel.SequenceI;
50 import jalview.io.AnnotationFile;
51 import jalview.io.AppletFormatAdapter;
52 import jalview.io.DataSourceType;
53 import jalview.io.FeaturesFile;
54 import jalview.io.FileFormat;
55 import jalview.io.FileFormatI;
56 import jalview.io.FileFormats;
57 import jalview.io.TCoffeeScoreFile;
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.RNAHelicesColour;
68 import jalview.schemes.StrandColourScheme;
69 import jalview.schemes.TCoffeeColourScheme;
70 import jalview.schemes.TaylorColourScheme;
71 import jalview.schemes.TurnColourScheme;
72 import jalview.schemes.ZappoColourScheme;
73 import jalview.structure.StructureSelectionManager;
74 import jalview.structures.models.AAStructureBindingModel;
75 import jalview.util.MappingUtils;
76 import jalview.util.MessageManager;
77 import jalview.viewmodel.AlignmentViewport;
79 import java.awt.BorderLayout;
80 import java.awt.Canvas;
81 import java.awt.CheckboxMenuItem;
82 import java.awt.Color;
83 import java.awt.FlowLayout;
85 import java.awt.FontMetrics;
86 import java.awt.Frame;
87 import java.awt.Graphics;
88 import java.awt.Label;
90 import java.awt.MenuBar;
91 import java.awt.MenuItem;
92 import java.awt.Panel;
93 import java.awt.event.ActionEvent;
94 import java.awt.event.ActionListener;
95 import java.awt.event.FocusEvent;
96 import java.awt.event.FocusListener;
97 import java.awt.event.ItemEvent;
98 import java.awt.event.ItemListener;
99 import java.awt.event.KeyEvent;
100 import java.awt.event.KeyListener;
101 import java.awt.event.WindowAdapter;
102 import java.awt.event.WindowEvent;
103 import java.io.IOException;
105 import java.net.URLEncoder;
106 import java.util.Arrays;
107 import java.util.Deque;
108 import java.util.HashMap;
109 import java.util.List;
110 import java.util.Map;
111 import java.util.StringTokenizer;
112 import java.util.Vector;
114 import org.jmol.viewer.Viewer;
116 public class AlignFrame extends EmbmenuFrame implements ActionListener,
117 ItemListener, KeyListener, AlignViewControllerGuiI
119 public AlignViewControllerI avc;
121 public AlignmentPanel alignPanel;
123 public AlignViewport viewport;
125 // width and height may be overridden by applet parameters
126 int frameWidth = 700;
128 int frameHeight = 500;
130 String jalviewServletURL;
133 * Flag for showing autocalculated consensus above or below other consensus
136 private boolean showAutoCalculatedAbove;
138 private SequenceAnnotationOrder annotationSortOrder;
141 * Constructor that creates the frame and adds it to the display.
148 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
151 this(al, applet, title, embedded, true);
155 * Constructor that optionally allows the frame to be displayed or only
162 * @param addToDisplay
164 public AlignFrame(AlignmentI al, JalviewLite applet, String title,
165 boolean embedded, boolean addToDisplay)
167 this(al, null, null, applet, title, embedded, addToDisplay);
170 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
171 ColumnSelection columnSelection, JalviewLite applet,
172 String title, boolean embedded)
174 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
177 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
178 ColumnSelection columnSelection, JalviewLite applet,
179 String title, boolean embedded, boolean addToDisplay)
183 jalviewServletURL = applet.getParameter("APPLICATION_URL");
189 } catch (Exception ex)
191 ex.printStackTrace();
193 // need to get window geometry before we calculate alignment layout
199 param = applet.getParameter("windowWidth");
202 int width = Integer.parseInt(param);
205 param = applet.getParameter("windowHeight");
208 int height = Integer.parseInt(param);
209 frameHeight = height;
211 } catch (Exception ex)
215 viewport = new AlignViewport(al, applet);
217 if (hiddenSeqs != null && hiddenSeqs.length > 0)
219 viewport.hideSequence(hiddenSeqs);
221 if (columnSelection != null)
223 viewport.setColumnSelection(columnSelection);
225 viewport.setScaleAboveWrapped(scaleAbove.getState());
227 alignPanel = new AlignmentPanel(this, viewport);
228 avc = new jalview.controller.AlignViewController(this, viewport,
230 viewport.updateConservation(alignPanel);
231 viewport.updateConsensus(alignPanel);
233 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
234 followMouseOverFlag.setState(viewport.isFollowHighlight());
235 showGroupConsensus.setState(viewport.isShowGroupConsensus());
236 showGroupConservation.setState(viewport.isShowGroupConservation());
237 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
238 showSequenceLogo.setState(viewport.isShowSequenceLogo());
239 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
240 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
241 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
242 showAlignmentAnnotations.setEnabled(annotationPanelMenuItem.getState());
243 showSequenceAnnotations.setEnabled(annotationPanelMenuItem.getState());
244 showAlignmentAnnotations.setState(true);
245 showSequenceAnnotations.setState(false);
247 seqLimits.setState(viewport.getShowJVSuffix());
251 String param = applet.getParameter("sortBy");
254 if (param.equalsIgnoreCase("Id"))
256 sortIDMenuItem_actionPerformed();
258 else if (param.equalsIgnoreCase("Pairwise Identity"))
260 sortPairwiseMenuItem_actionPerformed();
262 else if (param.equalsIgnoreCase("Length"))
264 sortLengthMenuItem_actionPerformed();
268 param = applet.getParameter("wrap");
271 if (param.equalsIgnoreCase("true"))
273 wrapMenuItem.setState(true);
274 wrapMenuItem_actionPerformed();
277 param = applet.getParameter("centrecolumnlabels");
280 centreColumnLabelFlag.setState(true);
281 centreColumnLabelFlag_stateChanged();
285 if (viewport.getAlignment().isNucleotide())
287 conservationMenuItem.setEnabled(false);
288 clustalColour.setEnabled(false);
289 BLOSUM62Colour.setEnabled(false);
290 zappoColour.setEnabled(false);
291 taylorColour.setEnabled(false);
292 hydrophobicityColour.setEnabled(false);
293 helixColour.setEnabled(false);
294 strandColour.setEnabled(false);
295 turnColour.setEnabled(false);
296 buriedColour.setEnabled(false);
297 viewport.updateStrucConsensus(alignPanel);
298 if (viewport.getAlignment().hasRNAStructure())
300 RNAHelixColour.setEnabled(true);
304 RNAHelixColour.setEnabled(false);
309 RNAHelixColour.setEnabled(false);
310 purinePyrimidineColour.setEnabled(false);
311 nucleotideColour.setEnabled(false);
313 // Some JVMS send keyevents to Top frame or lowest panel,
314 // Havent worked out why yet. So add to both this frame and seqCanvas for
316 this.addKeyListener(this);
317 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
318 alignPanel.idPanel.idCanvas.addKeyListener(this);
319 alignPanel.scalePanel.addKeyListener(this);
320 alignPanel.annotationPanel.addKeyListener(this);
321 alignPanel.annotationPanelHolder.addKeyListener(this);
322 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
323 alignPanel.alabels.addKeyListener(this);
325 setAnnotationsVisibility();
329 addToDisplay(embedded);
336 public void addToDisplay(boolean embedded)
338 createAlignFrameWindow(embedded);
340 alignPanel.adjustAnnotationHeight();
341 alignPanel.paintAlignment(true);
344 public AlignViewport getAlignViewport()
349 public SeqCanvas getSeqcanvas()
351 return alignPanel.seqPanel.seqCanvas;
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
363 public boolean parseFeaturesFile(String file, DataSourceType type)
365 return parseFeaturesFile(file, type, true);
369 * Load a features file onto the alignment
372 * file URL, content, or other resolvable path
374 * is protocol for accessing data referred to by file
375 * @param autoenabledisplay
376 * when true, display features flag will be automatically enabled if
377 * features are loaded
378 * @return true if data parsed as a features file
380 public boolean parseFeaturesFile(String file, DataSourceType sourceType,
381 boolean autoenabledisplay)
383 boolean featuresFile = false;
386 Map<String, FeatureColourI> colours = alignPanel.seqPanel.seqCanvas
387 .getFeatureRenderer().getFeatureColours();
388 boolean relaxedIdMatching = viewport.applet.getDefaultParameter(
389 "relaxedidmatch", false);
390 featuresFile = new FeaturesFile(file, sourceType).parse(
391 viewport.getAlignment(), colours, true, relaxedIdMatching);
392 } catch (Exception ex)
394 ex.printStackTrace();
399 if (autoenabledisplay)
401 viewport.setShowSequenceFeatures(true);
402 sequenceFeatures.setState(true);
404 if (alignPanel.seqPanel.seqCanvas.fr != null)
406 // update the min/max ranges where necessary
407 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
409 if (viewport.featureSettings != null)
411 viewport.featureSettings.refreshTable();
413 alignPanel.paintAlignment(true);
414 statusBar.setText(MessageManager
415 .getString("label.successfully_added_features_alignment"));
421 public void keyPressed(KeyEvent evt)
423 if (viewport.cursorMode
424 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
425 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
426 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
427 && Character.isDigit(evt.getKeyChar()))
429 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
432 switch (evt.getKeyCode())
434 case 27: // escape key
435 deselectAllSequenceMenuItem_actionPerformed();
437 alignPanel.alabels.cancelDrag();
440 if (evt.isControlDown() || evt.isMetaDown())
442 cut_actionPerformed();
446 if (viewport.cursorMode && !evt.isControlDown())
448 alignPanel.seqPanel.setCursorColumn();
450 if (evt.isControlDown() || evt.isMetaDown())
452 copy_actionPerformed();
456 if (evt.isControlDown())
458 paste(evt.isShiftDown());
462 if (evt.isControlDown() || evt.isMetaDown())
464 selectAllSequenceMenuItem_actionPerformed();
467 case KeyEvent.VK_DOWN:
468 if (viewport.cursorMode)
470 alignPanel.seqPanel.moveCursor(0, 1);
474 moveSelectedSequences(false);
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.moveCursor(0, -1);
485 moveSelectedSequences(true);
489 case KeyEvent.VK_LEFT:
490 if (evt.isAltDown() || !viewport.cursorMode)
492 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
496 alignPanel.seqPanel.moveCursor(-1, 0);
500 case KeyEvent.VK_RIGHT:
501 if (evt.isAltDown() || !viewport.cursorMode)
503 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
507 alignPanel.seqPanel.moveCursor(1, 0);
511 case KeyEvent.VK_SPACE:
512 if (viewport.cursorMode)
514 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
515 || evt.isShiftDown() || evt.isAltDown());
519 case KeyEvent.VK_DELETE:
520 case KeyEvent.VK_BACK_SPACE:
521 if (viewport.cursorMode)
523 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
524 || evt.isShiftDown() || evt.isAltDown());
528 cut_actionPerformed();
529 alignPanel.seqPanel.seqCanvas.repaint();
534 if (viewport.cursorMode)
536 alignPanel.seqPanel.setCursorRow();
540 if (viewport.cursorMode)
542 alignPanel.seqPanel.setCursorPosition();
546 case KeyEvent.VK_ENTER:
547 case KeyEvent.VK_COMMA:
548 if (viewport.cursorMode)
550 alignPanel.seqPanel.setCursorRowAndColumn();
555 if (viewport.cursorMode)
557 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
561 if (viewport.cursorMode)
563 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
568 viewport.cursorMode = !viewport.cursorMode;
569 statusBar.setText(MessageManager.formatMessage(
570 "label.keyboard_editing_mode",
571 new String[] { (viewport.cursorMode ? "on" : "off") }));
572 if (viewport.cursorMode)
574 alignPanel.seqPanel.seqCanvas.cursorX = viewport.getStartRes();
575 alignPanel.seqPanel.seqCanvas.cursorY = viewport.getStartSeq();
580 if (evt.isControlDown())
582 findMenuItem_actionPerformed();
588 boolean toggleSeqs = !evt.isControlDown();
589 boolean toggleCols = !evt.isShiftDown();
590 toggleHiddenRegions(toggleSeqs, toggleCols);
594 case KeyEvent.VK_PAGE_UP:
595 if (viewport.getWrapAlignment())
597 alignPanel.scrollUp(true);
601 alignPanel.setScrollValues(viewport.getStartRes(),
602 2 * viewport.getStartSeq() - viewport.getEndSeq());
606 case KeyEvent.VK_PAGE_DOWN:
607 if (viewport.getWrapAlignment())
609 alignPanel.scrollUp(false);
613 alignPanel.setScrollValues(viewport.getStartRes(),
614 viewport.getEndSeq());
619 if (evt.isControlDown())
621 undoMenuItem_actionPerformed();
626 if (evt.isControlDown())
628 redoMenuItem_actionPerformed();
633 if (evt.isControlDown())
640 if (evt.isControlDown())
642 trimAlignment(false);
647 if (evt.isControlDown())
649 if (evt.isShiftDown())
651 this.removeAllGapsMenuItem_actionPerformed();
655 removeGappedColumnMenuItem_actionPerformed();
660 if (evt.isControlDown())
664 invertColSel_actionPerformed();
668 invertSequenceMenuItem_actionPerformed();
674 if (evt.isControlDown())
676 if (evt.isShiftDown())
678 this.unGroup_actionPerformed();
682 this.createGroup_actionPerformed();
688 if (evt.isControlDown())
690 this.deleteGroups_actionPerformed();
695 if (evt.isControlDown())
702 alignPanel.paintAlignment(true);
706 * called by key handler and the hide all/show all menu items
711 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
713 boolean hide = false;
714 SequenceGroup sg = viewport.getSelectionGroup();
715 if (!toggleSeqs && !toggleCols)
717 // Hide everything by the current selection - this is a hack - we do the
718 // invert and then hide
719 // first check that there will be visible columns after the invert.
720 if (viewport.hasSelectedColumns()
721 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
724 // now invert the sequence set, if required - empty selection implies
725 // that no hiding is required.
728 invertSequenceMenuItem_actionPerformed();
729 sg = viewport.getSelectionGroup();
733 viewport.expandColSelection(sg, true);
734 // finally invert the column selection and get the new sequence
735 // selection and indicate it should be hidden.
736 invertColSel_actionPerformed();
743 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
746 viewport.hideAllSelectedSeqs();
748 else if (!(toggleCols && viewport.hasSelectedColumns()))
750 viewport.showAllHiddenSeqs();
756 if (viewport.hasSelectedColumns())
758 viewport.hideSelectedColumns();
761 viewport.setSelectionGroup(sg);
766 viewport.showAllHiddenColumns();
768 viewport.sendSelection();
773 public void keyReleased(KeyEvent evt)
778 public void keyTyped(KeyEvent evt)
783 public void itemStateChanged(ItemEvent evt)
785 final Object source = evt.getSource();
786 if (source == displayNonconservedMenuItem)
788 displayNonconservedMenuItem_actionPerformed();
790 else if (source == colourTextMenuItem)
792 colourTextMenuItem_actionPerformed();
794 else if (source == wrapMenuItem)
796 wrapMenuItem_actionPerformed();
798 else if (source == scaleAbove)
800 viewport.setScaleAboveWrapped(scaleAbove.getState());
802 else if (source == scaleLeft)
804 viewport.setScaleLeftWrapped(scaleLeft.getState());
806 else if (source == scaleRight)
808 viewport.setScaleRightWrapped(scaleRight.getState());
810 else if (source == seqLimits)
812 seqLimits_itemStateChanged();
814 else if (source == viewBoxesMenuItem)
816 viewport.setShowBoxes(viewBoxesMenuItem.getState());
818 else if (source == viewTextMenuItem)
820 viewport.setShowText(viewTextMenuItem.getState());
822 else if (source == renderGapsMenuItem)
824 viewport.setRenderGaps(renderGapsMenuItem.getState());
826 else if (source == annotationPanelMenuItem)
828 boolean showAnnotations = annotationPanelMenuItem.getState();
829 showAlignmentAnnotations.setEnabled(showAnnotations);
830 showSequenceAnnotations.setEnabled(showAnnotations);
831 viewport.setShowAnnotation(showAnnotations);
832 alignPanel.setAnnotationVisible(showAnnotations);
834 else if (source == sequenceFeatures)
836 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
837 alignPanel.seqPanel.seqCanvas.repaint();
839 else if (source == showAlignmentAnnotations)
841 setAnnotationsVisibility();
843 else if (source == showSequenceAnnotations)
845 setAnnotationsVisibility();
847 else if (source == sortAnnBySequence)
849 boolean newState = sortAnnBySequence.getState();
850 sortAnnByLabel.setState(false);
851 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
852 : SequenceAnnotationOrder.NONE);
853 setViewportAnnotationOrder();
855 else if (source == sortAnnByLabel)
857 boolean newState = sortAnnByLabel.getState();
858 sortAnnBySequence.setState(false);
859 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
860 : SequenceAnnotationOrder.NONE);
861 setViewportAnnotationOrder();
863 else if (source == showAutoFirst)
865 showAutoLast.setState(!showAutoFirst.getState());
866 setShowAutoCalculatedAbove(showAutoFirst.getState());
867 setViewportAnnotationOrder();
869 else if (source == showAutoLast)
871 showAutoFirst.setState(!showAutoLast.getState());
872 setShowAutoCalculatedAbove(showAutoFirst.getState());
873 setViewportAnnotationOrder();
875 else if (source == conservationMenuItem)
877 conservationMenuItem_actionPerformed();
879 else if (source == abovePIDThreshold)
881 abovePIDThreshold_actionPerformed();
883 else if (source == applyToAllGroups)
885 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
887 else if (source == autoCalculate)
889 viewport.autoCalculateConsensus = autoCalculate.getState();
891 else if (source == sortByTree)
893 viewport.sortByTree = sortByTree.getState();
895 else if (source == this.centreColumnLabelFlag)
897 centreColumnLabelFlag_stateChanged();
899 else if (source == this.followMouseOverFlag)
901 mouseOverFlag_stateChanged();
903 else if (source == showGroupConsensus)
905 showGroupConsensus_actionPerformed();
907 else if (source == showGroupConservation)
909 showGroupConservation_actionPerformed();
911 else if (source == showSequenceLogo)
913 showSequenceLogo_actionPerformed();
915 else if (source == normSequenceLogo)
917 normSequenceLogo_actionPerformed();
919 else if (source == showConsensusHistogram)
921 showConsensusHistogram_actionPerformed();
923 else if (source == applyAutoAnnotationSettings)
925 applyAutoAnnotationSettings_actionPerformed();
927 alignPanel.paintAlignment(true);
931 * Set the visibility state of sequence-related and/or alignment-related
932 * annotations depending on checkbox selections, and repaint.
936 private void setAnnotationsVisibility()
938 boolean showForAlignment = showAlignmentAnnotations.getState();
939 boolean showForSequences = showSequenceAnnotations.getState();
940 if (alignPanel.getAlignment().getAlignmentAnnotation() != null)
942 for (AlignmentAnnotation aa : alignPanel.getAlignment()
943 .getAlignmentAnnotation())
945 boolean visible = (aa.sequenceRef == null ? showForAlignment
947 aa.visible = visible;
950 alignPanel.validateAnnotationDimensions(true);
955 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
957 this.annotationSortOrder = order;
961 * Set flags on the viewport that control annotation ordering
963 private void setViewportAnnotationOrder()
965 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
967 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
970 private void setShowAutoCalculatedAbove(boolean showAbove)
972 this.showAutoCalculatedAbove = showAbove;
975 private void mouseOverFlag_stateChanged()
977 viewport.setFollowHighlight(followMouseOverFlag.getState());
978 // TODO: could kick the scrollTo mechanism to reset view for current
982 private void centreColumnLabelFlag_stateChanged()
984 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
985 this.alignPanel.annotationPanel.repaint();
989 public void actionPerformed(ActionEvent evt)
991 viewport.applet.currentAlignFrame = this;
993 Object source = evt.getSource();
995 if (source == inputText)
997 inputText_actionPerformed();
999 else if (source == loadTree)
1001 loadTree_actionPerformed();
1003 else if (source == loadApplication)
1005 launchFullApplication();
1007 else if (source == loadAnnotations)
1011 else if (source == outputAnnotations)
1013 outputAnnotations(true);
1015 else if (source == outputFeatures)
1017 outputFeatures(true, "Jalview");
1019 else if (source == closeMenuItem)
1021 closeMenuItem_actionPerformed();
1023 else if (source == copy)
1025 copy_actionPerformed();
1027 else if (source == undoMenuItem)
1029 undoMenuItem_actionPerformed();
1031 else if (source == redoMenuItem)
1033 redoMenuItem_actionPerformed();
1035 else if (source == inputText)
1037 inputText_actionPerformed();
1039 else if (source == closeMenuItem)
1041 closeMenuItem_actionPerformed();
1043 else if (source == undoMenuItem)
1045 undoMenuItem_actionPerformed();
1047 else if (source == redoMenuItem)
1049 redoMenuItem_actionPerformed();
1051 else if (source == copy)
1053 copy_actionPerformed();
1055 else if (source == pasteNew)
1057 pasteNew_actionPerformed();
1059 else if (source == pasteThis)
1061 pasteThis_actionPerformed();
1063 else if (source == cut)
1065 cut_actionPerformed();
1067 else if (source == delete)
1069 delete_actionPerformed();
1071 else if (source == grpsFromSelection)
1073 makeGrpsFromSelection_actionPerformed();
1075 else if (source == deleteGroups)
1077 deleteGroups_actionPerformed();
1079 else if (source == selectAllSequenceMenuItem)
1081 selectAllSequenceMenuItem_actionPerformed();
1083 else if (source == deselectAllSequenceMenuItem)
1085 deselectAllSequenceMenuItem_actionPerformed();
1087 else if (source == invertSequenceMenuItem)
1089 invertSequenceMenuItem_actionPerformed();
1090 // uncomment to slave sequence selections in split frame
1091 // viewport.sendSelection();
1093 else if (source == invertColSel)
1095 viewport.invertColumnSelection();
1096 alignPanel.paintAlignment(true);
1097 viewport.sendSelection();
1099 else if (source == remove2LeftMenuItem)
1101 trimAlignment(true);
1103 else if (source == remove2RightMenuItem)
1105 trimAlignment(false);
1107 else if (source == removeGappedColumnMenuItem)
1109 removeGappedColumnMenuItem_actionPerformed();
1111 else if (source == removeAllGapsMenuItem)
1113 removeAllGapsMenuItem_actionPerformed();
1115 else if (source == findMenuItem)
1117 findMenuItem_actionPerformed();
1119 else if (source == font)
1121 new FontChooser(alignPanel);
1123 else if (source == newView)
1127 else if (source == showColumns)
1129 viewport.showAllHiddenColumns();
1130 alignPanel.paintAlignment(true);
1131 viewport.sendSelection();
1133 else if (source == showSeqs)
1135 viewport.showAllHiddenSeqs();
1136 alignPanel.paintAlignment(true);
1137 // uncomment if we want to slave sequence selections in split frame
1138 // viewport.sendSelection();
1140 else if (source == hideColumns)
1142 viewport.hideSelectedColumns();
1143 alignPanel.paintAlignment(true);
1144 viewport.sendSelection();
1146 else if (source == hideSequences
1147 && viewport.getSelectionGroup() != null)
1149 viewport.hideAllSelectedSeqs();
1150 alignPanel.paintAlignment(true);
1151 // uncomment if we want to slave sequence selections in split frame
1152 // viewport.sendSelection();
1154 else if (source == hideAllButSelection)
1156 toggleHiddenRegions(false, false);
1157 alignPanel.paintAlignment(true);
1158 viewport.sendSelection();
1160 else if (source == hideAllSelection)
1162 SequenceGroup sg = viewport.getSelectionGroup();
1163 viewport.expandColSelection(sg, false);
1164 viewport.hideAllSelectedSeqs();
1165 viewport.hideSelectedColumns();
1166 alignPanel.paintAlignment(true);
1167 viewport.sendSelection();
1169 else if (source == showAllHidden)
1171 viewport.showAllHiddenColumns();
1172 viewport.showAllHiddenSeqs();
1173 alignPanel.paintAlignment(true);
1174 viewport.sendSelection();
1176 else if (source == showGroupConsensus)
1178 showGroupConsensus_actionPerformed();
1180 else if (source == showGroupConservation)
1182 showGroupConservation_actionPerformed();
1184 else if (source == showSequenceLogo)
1186 showSequenceLogo_actionPerformed();
1188 else if (source == normSequenceLogo)
1190 normSequenceLogo_actionPerformed();
1192 else if (source == showConsensusHistogram)
1194 showConsensusHistogram_actionPerformed();
1196 else if (source == applyAutoAnnotationSettings)
1198 applyAutoAnnotationSettings_actionPerformed();
1200 else if (source == featureSettings)
1202 new FeatureSettings(alignPanel);
1204 else if (source == alProperties)
1206 StringBuffer contents = new jalview.io.AlignmentProperties(
1207 viewport.getAlignment()).formatAsString();
1208 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1209 cap.setText(contents.toString());
1210 Frame frame = new Frame();
1212 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1213 "label.alignment_properties", new String[] { getTitle() }),
1216 else if (source == overviewMenuItem)
1218 overviewMenuItem_actionPerformed();
1220 else if (source == noColourmenuItem)
1224 else if (source == clustalColour)
1226 abovePIDThreshold.setState(false);
1227 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1229 else if (source == zappoColour)
1231 changeColour(new ZappoColourScheme());
1233 else if (source == taylorColour)
1235 changeColour(new TaylorColourScheme());
1237 else if (source == hydrophobicityColour)
1239 changeColour(new HydrophobicColourScheme());
1241 else if (source == helixColour)
1243 changeColour(new HelixColourScheme());
1245 else if (source == strandColour)
1247 changeColour(new StrandColourScheme());
1249 else if (source == turnColour)
1251 changeColour(new TurnColourScheme());
1253 else if (source == buriedColour)
1255 changeColour(new BuriedColourScheme());
1257 else if (source == nucleotideColour)
1259 changeColour(new NucleotideColourScheme());
1261 else if (source == purinePyrimidineColour)
1263 changeColour(new PurinePyrimidineColourScheme());
1265 // else if (source == RNAInteractionColour)
1267 // changeColour(new RNAInteractionColourScheme());
1269 else if (source == RNAHelixColour)
1271 changeColour(new RNAHelicesColour(viewport.getAlignment()));
1272 // new RNAHelicesColourChooser(viewport, alignPanel);
1274 else if (source == modifyPID)
1276 modifyPID_actionPerformed();
1278 else if (source == modifyConservation)
1280 modifyConservation_actionPerformed();
1282 else if (source == userDefinedColour)
1284 new UserDefinedColours(alignPanel, null);
1286 else if (source == PIDColour)
1288 changeColour(new PIDColourScheme());
1290 else if (source == BLOSUM62Colour)
1292 changeColour(new Blosum62ColourScheme());
1294 else if (source == tcoffeeColour)
1296 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1298 else if (source == annotationColour)
1300 new AnnotationColourChooser(viewport, alignPanel);
1302 else if (source == annotationColumnSelection)
1304 new AnnotationColumnChooser(viewport, alignPanel);
1306 else if (source == sortPairwiseMenuItem)
1308 sortPairwiseMenuItem_actionPerformed();
1310 else if (source == sortIDMenuItem)
1312 sortIDMenuItem_actionPerformed();
1314 else if (source == sortLengthMenuItem)
1316 sortLengthMenuItem_actionPerformed();
1318 else if (source == sortGroupMenuItem)
1320 sortGroupMenuItem_actionPerformed();
1322 else if (source == removeRedundancyMenuItem)
1324 removeRedundancyMenuItem_actionPerformed();
1326 else if (source == pairwiseAlignmentMenuItem)
1328 pairwiseAlignmentMenuItem_actionPerformed();
1330 else if (source == PCAMenuItem)
1332 PCAMenuItem_actionPerformed();
1334 else if (source == averageDistanceTreeMenuItem)
1336 averageDistanceTreeMenuItem_actionPerformed();
1338 else if (source == neighbourTreeMenuItem)
1340 neighbourTreeMenuItem_actionPerformed();
1342 else if (source == njTreeBlosumMenuItem)
1344 njTreeBlosumMenuItem_actionPerformed();
1346 else if (source == avDistanceTreeBlosumMenuItem)
1348 avTreeBlosumMenuItem_actionPerformed();
1350 else if (source == documentation)
1352 documentation_actionPerformed();
1354 else if (source == about)
1356 about_actionPerformed();
1361 public void inputText_actionPerformed()
1363 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1364 Frame frame = new Frame();
1366 jalview.bin.JalviewLite.addFrame(frame,
1367 MessageManager.getString("label.input_cut_paste"), 500, 500);
1370 protected void outputText_actionPerformed(ActionEvent e)
1372 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1373 Frame frame = new Frame();
1375 JalviewLite.addFrame(frame, MessageManager.formatMessage(
1376 "label.alignment_output_command",
1377 new Object[] { e.getActionCommand() }), 600, 500);
1379 FileFormatI fileFormat = FileFormats.getInstance().forName(
1380 e.getActionCommand());
1381 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1382 fileFormat, viewport.getAlignment(),
1383 viewport.getShowJVSuffix()));
1386 public void loadAnnotations()
1388 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1389 cap.setText(MessageManager
1390 .getString("label.paste_features_annotations_Tcoffee_here"));
1391 cap.setAnnotationImport();
1392 Frame frame = new Frame();
1394 jalview.bin.JalviewLite.addFrame(frame,
1395 MessageManager.getString("action.paste_annotations"), 400, 300);
1399 public String outputAnnotations(boolean displayTextbox)
1401 String annotation = new AnnotationFile()
1402 .printAnnotationsForView(viewport);
1406 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1407 Frame frame = new Frame();
1409 jalview.bin.JalviewLite.addFrame(frame,
1410 MessageManager.getString("label.annotations"), 600, 500);
1411 cap.setText(annotation);
1417 private Map<String, FeatureColourI> getDisplayedFeatureCols()
1419 if (alignPanel.getFeatureRenderer() != null
1420 && viewport.getFeaturesDisplayed() != null)
1422 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1428 public String outputFeatures(boolean displayTextbox, String format)
1431 FeaturesFile formatter = new FeaturesFile();
1432 if (format.equalsIgnoreCase("Jalview"))
1434 features = formatter.printJalviewFormat(viewport.getAlignment()
1435 .getSequencesArray(), getDisplayedFeatureCols());
1439 features = formatter.printGffFormat(viewport.getAlignment()
1440 .getSequencesArray(), getDisplayedFeatureCols());
1445 boolean frimport = false;
1446 if (features == null || features.equals("No Features Visible"))
1448 features = "# No features visible - paste some and import them here.";
1452 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1455 cap.setAnnotationImport();
1457 Frame frame = new Frame();
1459 jalview.bin.JalviewLite.addFrame(frame,
1460 MessageManager.getString("label.features"), 600, 500);
1461 cap.setText(features);
1465 if (features == null)
1474 void launchFullApplication()
1476 StringBuffer url = new StringBuffer(jalviewServletURL);
1478 // allow servlet parameters to be passed in applet parameter
1479 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1481 url.append(firstSep);
1484 + appendProtocol(viewport.applet.getParameter("file")));
1486 if (viewport.applet.getParameter("features") != null)
1488 url.append("&features=");
1489 url.append(appendProtocol(viewport.applet.getParameter("features")));
1492 if (viewport.applet.getParameter("annotations") != null)
1494 url.append("&annotations=");
1495 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1498 if (viewport.applet.getParameter("jnetfile") != null
1499 || viewport.applet.getParameter("jpredfile") != null)
1501 url.append("&annotations=");
1502 url.append(appendProtocol(viewport.applet.getParameter("jnetfile") != null ? viewport.applet
1503 .getParameter("jnetfile") : viewport.applet
1504 .getParameter("jpredfile")));
1507 if (viewport.applet.getParameter("defaultColour") != null)
1509 url.append("&colour="
1510 + removeWhiteSpace(viewport.applet
1511 .getParameter("defaultColour")));
1514 if (viewport.applet.getParameter("userDefinedColour") != null)
1516 url.append("&colour="
1517 + removeWhiteSpace(viewport.applet
1518 .getParameter("userDefinedColour")));
1520 if (viewport.applet.getParameter("tree") != null)
1523 + appendProtocol(viewport.applet.getParameter("tree")));
1525 if (viewport.applet.getParameter("treeFile") != null)
1528 + appendProtocol(viewport.applet.getParameter("treeFile")));
1531 showURL(url.toString(), "FULL_APP");
1534 String removeWhiteSpace(String colour)
1536 StringBuffer sb = new StringBuffer();
1537 for (int i = 0; i < colour.length(); i++)
1539 if (Character.isWhitespace(colour.charAt(i)))
1545 sb.append(colour.charAt(i));
1549 return sb.toString();
1552 String appendProtocol(String url)
1557 url = URLEncoder.encode(url);
1560 * When we finally deprecate 1.1 compatibility, we can start to use
1561 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1562 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1563 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1564 * ex.printStackTrace(); }
1566 catch (java.net.MalformedURLException ex)
1568 url = viewport.applet.getCodeBase() + url;
1573 public void closeMenuItem_actionPerformed()
1575 PaintRefresher.RemoveComponent(alignPanel);
1576 if (alignPanel.seqPanel != null
1577 && alignPanel.seqPanel.seqCanvas != null)
1579 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1581 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1583 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1586 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1601 void updateEditMenuBar()
1604 if (viewport.getHistoryList().size() > 0)
1606 undoMenuItem.setEnabled(true);
1607 CommandI command = viewport.getHistoryList().peek();
1608 undoMenuItem.setLabel(MessageManager.formatMessage(
1609 "label.undo_command",
1610 new Object[] { command.getDescription() }));
1614 undoMenuItem.setEnabled(false);
1615 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1618 if (viewport.getRedoList().size() > 0)
1620 redoMenuItem.setEnabled(true);
1622 CommandI command = viewport.getRedoList().peek();
1623 redoMenuItem.setLabel(MessageManager.formatMessage(
1624 "label.redo_command",
1625 new Object[] { command.getDescription() }));
1629 redoMenuItem.setEnabled(false);
1630 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1638 public void addHistoryItem(CommandI command)
1640 if (command.getSize() > 0)
1642 viewport.addToHistoryList(command);
1643 viewport.clearRedoList();
1644 updateEditMenuBar();
1645 viewport.updateHiddenColumns();
1650 * TODO: JAL-1104 DOCUMENT ME!
1655 protected void undoMenuItem_actionPerformed()
1657 if (viewport.getHistoryList().isEmpty())
1662 CommandI command = viewport.getHistoryList().pop();
1663 viewport.addToRedoList(command);
1664 command.undoCommand(null);
1666 AlignmentViewport originalSource = getOriginatingSource(command);
1668 if (originalSource != viewport)
1671 .println("Warning: Viewport object mismatch whilst undoing");
1673 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1674 // viewport.getColumnSelection().getHiddenColumns()
1676 updateEditMenuBar();
1677 originalSource.firePropertyChange("alignment", null, originalSource
1678 .getAlignment().getSequences());
1682 * TODO: JAL-1104 DOCUMENT ME!
1687 protected void redoMenuItem_actionPerformed()
1689 if (viewport.getRedoList().isEmpty())
1694 CommandI command = viewport.getRedoList().pop();
1695 viewport.addToHistoryList(command);
1696 command.doCommand(null);
1698 AlignmentViewport originalSource = getOriginatingSource(command);
1700 if (originalSource != viewport)
1703 .println("Warning: Viewport object mismatch whilst re-doing");
1705 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1706 // viewport.getColumnSelection().getHiddenColumns()
1709 updateEditMenuBar();
1710 originalSource.firePropertyChange("alignment", null, originalSource
1711 .getAlignment().getSequences());
1714 AlignmentViewport getOriginatingSource(CommandI command)
1716 AlignmentViewport originalSource = null;
1717 // For sequence removal and addition, we need to fire
1718 // the property change event FROM the viewport where the
1719 // original alignment was altered
1720 AlignmentI al = null;
1721 if (command instanceof EditCommand)
1723 EditCommand editCommand = (EditCommand) command;
1724 al = editCommand.getAlignment();
1725 Vector comps = (Vector) PaintRefresher.components.get(viewport
1726 .getSequenceSetId());
1727 for (int i = 0; i < comps.size(); i++)
1729 if (comps.elementAt(i) instanceof AlignmentPanel)
1731 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1733 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1740 if (originalSource == null)
1742 // The original view is closed, we must validate
1743 // the current view against the closed view first
1746 PaintRefresher.validateSequences(al, viewport.getAlignment());
1749 originalSource = viewport;
1752 return originalSource;
1756 * Move the currently selected sequences up or down one position in the
1761 public void moveSelectedSequences(boolean up)
1763 SequenceGroup sg = viewport.getSelectionGroup();
1768 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1769 up ? null : viewport.getHiddenRepSequences(), up);
1770 alignPanel.paintAlignment(true);
1773 * Also move cDNA/protein complement sequences
1775 AlignViewportI complement = viewport.getCodingComplement();
1776 if (complement != null)
1778 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1779 viewport, complement);
1780 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1781 up ? null : complement.getHiddenRepSequences(), up);
1782 getSplitFrame().getComplement(this).alignPanel.paintAlignment(true);
1786 synchronized void slideSequences(boolean right, int size)
1788 List<SequenceI> sg = new Vector<SequenceI>();
1789 if (viewport.cursorMode)
1791 sg.add(viewport.getAlignment().getSequenceAt(
1792 alignPanel.seqPanel.seqCanvas.cursorY));
1794 else if (viewport.getSelectionGroup() != null
1795 && viewport.getSelectionGroup().getSize() != viewport
1796 .getAlignment().getHeight())
1798 sg = viewport.getSelectionGroup().getSequences(
1799 viewport.getHiddenRepSequences());
1807 Vector<SequenceI> invertGroup = new Vector();
1809 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1811 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1813 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1817 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1819 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1821 for (int i = 0; i < invertGroup.size(); i++)
1823 seqs2[i] = invertGroup.elementAt(i);
1826 SlideSequencesCommand ssc;
1829 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1830 size, viewport.getGapCharacter());
1834 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1835 size, viewport.getGapCharacter());
1838 int groupAdjustment = 0;
1839 if (ssc.getGapsInsertedBegin() && right)
1841 if (viewport.cursorMode)
1843 alignPanel.seqPanel.moveCursor(size, 0);
1847 groupAdjustment = size;
1850 else if (!ssc.getGapsInsertedBegin() && !right)
1852 if (viewport.cursorMode)
1854 alignPanel.seqPanel.moveCursor(-size, 0);
1858 groupAdjustment = -size;
1862 if (groupAdjustment != 0)
1864 viewport.getSelectionGroup().setStartRes(
1865 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1866 viewport.getSelectionGroup().setEndRes(
1867 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1870 boolean appendHistoryItem = false;
1871 Deque<CommandI> historyList = viewport.getHistoryList();
1872 if (historyList != null && historyList.size() > 0
1873 && historyList.peek() instanceof SlideSequencesCommand)
1875 appendHistoryItem = ssc
1876 .appendSlideCommand((SlideSequencesCommand) historyList
1880 if (!appendHistoryItem)
1882 addHistoryItem(ssc);
1888 static StringBuffer copiedSequences;
1890 static Vector copiedHiddenColumns;
1892 protected void copy_actionPerformed()
1894 if (viewport.getSelectionGroup() == null)
1899 SequenceGroup sg = viewport.getSelectionGroup();
1900 copiedSequences = new StringBuffer();
1901 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1902 for (int i = 0; i < sg.getSize(); i++)
1904 SequenceI seq = sg.getSequenceAt(i);
1905 int index = viewport.getAlignment().findIndex(seq);
1906 orderedSeqs.put(index, seq);
1909 int index = 0, startRes, endRes;
1912 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1914 copiedHiddenColumns = new Vector();
1915 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1916 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1918 copiedHiddenColumns.addElement(new int[] {
1919 region[0] - hiddenOffset, region[1] - hiddenOffset });
1924 copiedHiddenColumns = null;
1927 for (int i = 0; i < sg.getSize(); i++)
1929 SequenceI seq = null;
1933 if (orderedSeqs.containsKey(index))
1935 seq = orderedSeqs.get(index);
1946 // Returns residue following index if gap
1947 startRes = seq.findPosition(sg.getStartRes());
1950 // Need to find the residue preceeding index if gap
1953 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1955 ch = seq.getCharAt(j);
1956 if (!jalview.util.Comparison.isGap((ch)))
1964 endRes += seq.getStart() - 1;
1967 copiedSequences.append(seq.getName()
1973 + seq.getSequenceAsString(sg.getStartRes(),
1974 sg.getEndRes() + 1) + "\n");
1979 protected void pasteNew_actionPerformed()
1984 protected void pasteThis_actionPerformed()
1989 void paste(boolean newAlignment)
1994 if (copiedSequences == null)
1999 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
2000 Vector seqs = new Vector();
2001 while (st.hasMoreElements())
2003 String name = st.nextToken();
2004 int start = Integer.parseInt(st.nextToken());
2005 int end = Integer.parseInt(st.nextToken());
2006 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
2008 SequenceI[] newSeqs = new SequenceI[seqs.size()];
2009 for (int i = 0; i < seqs.size(); i++)
2011 newSeqs[i] = (SequenceI) seqs.elementAt(i);
2016 String newtitle = MessageManager
2017 .getString("label.copied_sequences");
2018 if (getTitle().startsWith(
2019 MessageManager.getString("label.copied_sequences")))
2021 newtitle = getTitle();
2025 newtitle = newtitle.concat(MessageManager.formatMessage(
2026 "label.from_msname", new String[] { getTitle() }));
2028 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
2029 viewport.applet, newtitle, false);
2030 if (copiedHiddenColumns != null)
2032 for (int i = 0; i < copiedHiddenColumns.size(); i++)
2034 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
2035 af.viewport.hideColumns(region[0], region[1]);
2039 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2044 addSequences(newSeqs);
2047 } catch (Exception ex)
2049 } // could be anything being pasted in here
2053 void addSequences(SequenceI[] seqs)
2055 for (int i = 0; i < seqs.length; i++)
2057 viewport.getAlignment().addSequence(seqs[i]);
2061 addHistoryItem(new EditCommand(
2062 MessageManager.getString("label.add_sequences"), Action.PASTE,
2063 seqs, 0, viewport.getAlignment().getWidth(),
2064 viewport.getAlignment()));
2066 viewport.setEndSeq(viewport.getAlignment().getHeight());
2067 viewport.getAlignment().getWidth();
2068 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2073 protected void cut_actionPerformed()
2075 copy_actionPerformed();
2076 delete_actionPerformed();
2079 protected void delete_actionPerformed()
2082 SequenceGroup sg = viewport.getSelectionGroup();
2088 Vector seqs = new Vector();
2090 for (int i = 0; i < sg.getSize(); i++)
2092 seq = sg.getSequenceAt(i);
2093 seqs.addElement(seq);
2097 * If the cut affects all sequences, warn, remove highlighted columns
2099 if (sg.getSize() == viewport.getAlignment().getHeight())
2101 boolean isEntireAlignWidth = (((sg.getEndRes() - sg.getStartRes()) + 1) == viewport
2102 .getAlignment().getWidth()) ? true : false;
2103 if (isEntireAlignWidth)
2105 String title = MessageManager.getString("label.delete_all");
2106 Panel infoPanel = new Panel();
2107 infoPanel.setLayout(new FlowLayout());
2109 .add(new Label(MessageManager.getString("warn.delete_all")));
2111 final JVDialog dialog = new JVDialog(this, title, true, 400, 200);
2112 dialog.setMainPanel(infoPanel);
2113 dialog.ok.setLabel(MessageManager.getString("action.ok"));
2114 dialog.cancel.setLabel(MessageManager.getString("action.cancel"));
2115 dialog.setVisible(true);
2122 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2123 sg.getEndRes() + 1);
2126 SequenceI[] cut = new SequenceI[seqs.size()];
2127 for (int i = 0; i < seqs.size(); i++)
2129 cut[i] = (SequenceI) seqs.elementAt(i);
2133 * //ADD HISTORY ITEM
2135 addHistoryItem(new EditCommand(
2136 MessageManager.getString("label.cut_sequences"), Action.CUT,
2137 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2138 viewport.getAlignment()));
2140 viewport.setSelectionGroup(null);
2141 viewport.getAlignment().deleteGroup(sg);
2143 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2146 if (viewport.getAlignment().getHeight() < 1)
2148 this.setVisible(false);
2150 viewport.sendSelection();
2154 * group consensus toggled
2157 protected void showGroupConsensus_actionPerformed()
2159 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2160 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2165 * group conservation toggled.
2167 protected void showGroupConservation_actionPerformed()
2169 viewport.setShowGroupConservation(showGroupConservation.getState());
2170 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2177 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2178 * .event.ActionEvent)
2180 protected void showConsensusHistogram_actionPerformed()
2182 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2183 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2190 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2191 * .event.ActionEvent)
2193 protected void showSequenceLogo_actionPerformed()
2195 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2196 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2199 protected void normSequenceLogo_actionPerformed()
2201 showSequenceLogo.setState(true);
2202 viewport.setShowSequenceLogo(true);
2203 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2204 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2207 protected void applyAutoAnnotationSettings_actionPerformed()
2209 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2212 protected void makeGrpsFromSelection_actionPerformed()
2214 if (avc.makeGroupsFromSelection())
2216 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2217 alignPanel.updateAnnotation();
2218 alignPanel.paintAlignment(true);
2222 protected void createGroup_actionPerformed()
2227 protected void unGroup_actionPerformed()
2231 alignPanel.alignmentChanged();
2235 protected void deleteGroups_actionPerformed()
2237 if (avc.deleteGroups())
2239 alignPanel.alignmentChanged();
2243 public void selectAllSequenceMenuItem_actionPerformed()
2245 SequenceGroup sg = new SequenceGroup();
2246 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2248 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2250 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2251 viewport.setSelectionGroup(sg);
2252 // JAL-2034 - should delegate to
2253 // alignPanel to decide if overview needs
2255 alignPanel.paintAlignment(false);
2256 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2257 viewport.sendSelection();
2260 public void deselectAllSequenceMenuItem_actionPerformed()
2262 if (viewport.cursorMode)
2264 alignPanel.seqPanel.keyboardNo1 = null;
2265 alignPanel.seqPanel.keyboardNo2 = null;
2267 viewport.setSelectionGroup(null);
2268 viewport.getColumnSelection().clear();
2269 viewport.setSelectionGroup(null);
2270 alignPanel.idPanel.idCanvas.searchResults = null;
2271 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2272 // JAL-2034 - should delegate to
2273 // alignPanel to decide if overview needs
2275 alignPanel.paintAlignment(false);
2276 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2277 viewport.sendSelection();
2280 public void invertSequenceMenuItem_actionPerformed()
2282 SequenceGroup sg = viewport.getSelectionGroup();
2283 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2285 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2288 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2289 viewport.sendSelection();
2292 public void invertColSel_actionPerformed()
2294 viewport.invertColumnSelection();
2295 alignPanel.paintAlignment(true);
2296 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2297 viewport.sendSelection();
2300 void trimAlignment(boolean trimLeft)
2302 ColumnSelection colSel = viewport.getColumnSelection();
2305 if (!colSel.isEmpty())
2309 column = colSel.getMin();
2313 column = colSel.getMax();
2317 if (viewport.getSelectionGroup() != null)
2319 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2320 viewport.getHiddenRepSequences());
2324 seqs = viewport.getAlignment().getSequencesArray();
2327 TrimRegionCommand trimRegion;
2330 trimRegion = new TrimRegionCommand("Remove Left", true, seqs,
2331 column, viewport.getAlignment());
2332 viewport.setStartRes(0);
2336 trimRegion = new TrimRegionCommand("Remove Right", false, seqs,
2337 column, viewport.getAlignment());
2340 statusBar.setText(MessageManager.formatMessage(
2341 "label.removed_columns",
2342 new String[] { Integer.valueOf(trimRegion.getSize())
2344 addHistoryItem(trimRegion);
2346 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2348 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2349 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2351 viewport.getAlignment().deleteGroup(sg);
2355 viewport.firePropertyChange("alignment", null, viewport
2356 .getAlignment().getSequences());
2360 public void removeGappedColumnMenuItem_actionPerformed()
2362 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2365 if (viewport.getSelectionGroup() != null)
2367 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2368 viewport.getHiddenRepSequences());
2369 start = viewport.getSelectionGroup().getStartRes();
2370 end = viewport.getSelectionGroup().getEndRes();
2374 seqs = viewport.getAlignment().getSequencesArray();
2377 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2378 "Remove Gapped Columns", seqs, start, end,
2379 viewport.getAlignment());
2381 addHistoryItem(removeGapCols);
2383 statusBar.setText(MessageManager.formatMessage(
2384 "label.removed_empty_columns",
2385 new String[] { Integer.valueOf(removeGapCols.getSize())
2388 // This is to maintain viewport position on first residue
2389 // of first sequence
2390 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2391 int startRes = seq.findPosition(viewport.getStartRes());
2392 // ShiftList shifts;
2393 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2394 // edit.alColumnChanges=shifts.getInverse();
2395 // if (viewport.hasHiddenColumns)
2396 // viewport.getColumnSelection().compensateForEdits(shifts);
2397 viewport.setStartRes(seq.findIndex(startRes) - 1);
2398 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2403 public void removeAllGapsMenuItem_actionPerformed()
2405 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2408 if (viewport.getSelectionGroup() != null)
2410 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2411 viewport.getHiddenRepSequences());
2412 start = viewport.getSelectionGroup().getStartRes();
2413 end = viewport.getSelectionGroup().getEndRes();
2417 seqs = viewport.getAlignment().getSequencesArray();
2420 // This is to maintain viewport position on first residue
2421 // of first sequence
2422 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2423 int startRes = seq.findPosition(viewport.getStartRes());
2425 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2426 viewport.getAlignment()));
2428 viewport.setStartRes(seq.findIndex(startRes) - 1);
2430 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2435 public void findMenuItem_actionPerformed()
2437 new Finder(alignPanel);
2441 * create a new view derived from the current view
2444 * @return frame for the new view
2446 public AlignFrame newView(String viewtitle)
2449 if (viewport.hasHiddenRows())
2451 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2452 .getFullAlignment().getSequencesArray());
2456 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2459 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2461 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2463 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2465 newal.addAnnotation(viewport.getAlignment()
2466 .getAlignmentAnnotation()[i]);
2471 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2473 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2474 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2475 PaintRefresher.Register(newaf.alignPanel,
2476 newaf.alignPanel.av.getSequenceSetId());
2478 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2479 newaf.alignPanel.av.getSequenceSetId());
2480 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2481 newaf.alignPanel.av.getSequenceSetId());
2483 Vector comps = (Vector) PaintRefresher.components.get(viewport
2484 .getSequenceSetId());
2486 for (int i = 0; i < comps.size(); i++)
2488 if (comps.elementAt(i) instanceof AlignmentPanel)
2494 String title = new String(this.getTitle());
2495 if (viewtitle != null)
2497 title = viewtitle + " ( " + title + ")";
2501 if (title.indexOf("(View") > -1)
2503 title = title.substring(0, title.indexOf("(View"));
2505 title += "(View " + viewSize + ")";
2508 newaf.setTitle(title.toString());
2510 newaf.viewport.setHistoryList(viewport.getHistoryList());
2511 newaf.viewport.setRedoList(viewport.getRedoList());
2517 * @return list of feature groups on the view
2519 public String[] getFeatureGroups()
2521 FeatureRenderer fr = null;
2522 if (alignPanel != null
2523 && (fr = alignPanel.getFeatureRenderer()) != null)
2525 List<String> gps = fr.getFeatureGroups();
2526 String[] _gps = gps.toArray(new String[gps.size()]);
2533 * get sequence feature groups that are hidden or shown
2539 public String[] getFeatureGroupsOfState(boolean visible)
2541 FeatureRenderer fr = null;
2542 if (alignPanel != null
2543 && (fr = alignPanel.getFeatureRenderer()) != null)
2545 List<String> gps = fr.getGroups(visible);
2546 String[] _gps = gps.toArray(new String[gps.size()]);
2553 * Change the display state for the given feature groups
2556 * list of group strings
2558 * visible or invisible
2560 public void setFeatureGroupState(String[] groups, boolean state)
2562 FeatureRenderer fr = null;
2563 this.sequenceFeatures.setState(true);
2564 viewport.setShowSequenceFeatures(true);
2565 if (alignPanel != null
2566 && (fr = alignPanel.getFeatureRenderer()) != null)
2569 fr.setGroupVisibility(Arrays.asList(groups), state);
2570 alignPanel.seqPanel.seqCanvas.repaint();
2571 if (alignPanel.overviewPanel != null)
2573 alignPanel.overviewPanel.updateOverviewImage();
2578 public void seqLimits_itemStateChanged()
2580 viewport.setShowJVSuffix(seqLimits.getState());
2581 alignPanel.fontChanged();
2582 alignPanel.paintAlignment(true);
2585 protected void colourTextMenuItem_actionPerformed()
2587 viewport.setColourText(colourTextMenuItem.getState());
2588 alignPanel.paintAlignment(true);
2591 protected void displayNonconservedMenuItem_actionPerformed()
2593 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2594 alignPanel.paintAlignment(true);
2597 protected void wrapMenuItem_actionPerformed()
2599 viewport.setWrapAlignment(wrapMenuItem.getState());
2600 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2601 scaleAbove.setEnabled(wrapMenuItem.getState());
2602 scaleLeft.setEnabled(wrapMenuItem.getState());
2603 scaleRight.setEnabled(wrapMenuItem.getState());
2604 alignPanel.paintAlignment(true);
2607 public void overviewMenuItem_actionPerformed()
2609 if (alignPanel.overviewPanel != null)
2614 Frame frame = new Frame();
2615 OverviewPanel overview = new OverviewPanel(alignPanel);
2616 frame.add(overview);
2617 // +50 must allow for applet frame window
2618 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2619 "label.overview_params", new String[] { this.getTitle() }),
2620 overview.getPreferredSize().width,
2621 overview.getPreferredSize().height + 50);
2624 final AlignmentPanel ap = alignPanel;
2625 frame.addWindowListener(new WindowAdapter()
2628 public void windowClosing(WindowEvent e)
2632 ap.setOverviewPanel(null);
2637 alignPanel.setOverviewPanel(overview);
2642 public void changeColour(ColourSchemeI cs)
2644 viewport.setGlobalColourScheme(cs);
2646 alignPanel.paintAlignment(true);
2649 protected void modifyPID_actionPerformed()
2651 if (viewport.getAbovePIDThreshold()
2652 && viewport.getGlobalColourScheme() != null)
2654 SliderPanel.setPIDSliderSource(alignPanel,
2655 viewport.getResidueShading(), alignPanel.getViewName());
2656 SliderPanel.showPIDSlider();
2660 protected void modifyConservation_actionPerformed()
2662 if (viewport.getConservationSelected()
2663 && viewport.getGlobalColourScheme() != null)
2665 SliderPanel.setConservationSlider(alignPanel,
2666 viewport.getResidueShading(), alignPanel.getViewName());
2667 SliderPanel.showConservationSlider();
2671 protected void conservationMenuItem_actionPerformed()
2673 boolean selected = conservationMenuItem.getState();
2674 modifyConservation.setEnabled(selected);
2675 viewport.setConservationSelected(selected);
2677 // viewport.setAbovePIDThreshold(false);
2678 // abovePIDThreshold.setState(false);
2680 changeColour(viewport.getGlobalColourScheme());
2684 modifyConservation_actionPerformed();
2688 SliderPanel.hideConservationSlider();
2692 public void abovePIDThreshold_actionPerformed()
2694 boolean selected = abovePIDThreshold.getState();
2695 modifyPID.setEnabled(selected);
2696 viewport.setAbovePIDThreshold(selected);
2697 // conservationMenuItem.setState(false);
2698 // viewport.setConservationSelected(false);
2700 changeColour(viewport.getGlobalColourScheme());
2704 modifyPID_actionPerformed();
2708 SliderPanel.hidePIDSlider();
2712 public void sortPairwiseMenuItem_actionPerformed()
2714 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2715 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2716 .getAlignment().getSequenceAt(0), null);
2718 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2719 viewport.getAlignment()));
2720 alignPanel.paintAlignment(true);
2723 public void sortIDMenuItem_actionPerformed()
2725 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2726 AlignmentSorter.sortByID(viewport.getAlignment());
2727 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2728 viewport.getAlignment()));
2729 alignPanel.paintAlignment(true);
2732 public void sortLengthMenuItem_actionPerformed()
2734 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2735 AlignmentSorter.sortByLength(viewport.getAlignment());
2736 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2737 viewport.getAlignment()));
2738 alignPanel.paintAlignment(true);
2741 public void sortGroupMenuItem_actionPerformed()
2743 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2744 AlignmentSorter.sortByGroup(viewport.getAlignment());
2745 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2746 viewport.getAlignment()));
2747 alignPanel.paintAlignment(true);
2751 public void removeRedundancyMenuItem_actionPerformed()
2753 new RedundancyPanel(alignPanel);
2756 public void pairwiseAlignmentMenuItem_actionPerformed()
2758 if (viewport.getSelectionGroup() != null
2759 && viewport.getSelectionGroup().getSize() > 1)
2761 Frame frame = new Frame();
2762 frame.add(new PairwiseAlignPanel(alignPanel));
2763 jalview.bin.JalviewLite.addFrame(frame,
2764 MessageManager.getString("action.pairwise_alignment"), 600,
2769 public void PCAMenuItem_actionPerformed()
2771 // are the sequences aligned?
2772 if (!viewport.getAlignment().isAligned(false))
2775 int Width = viewport.getAlignment().getWidth();
2777 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2779 current = viewport.getAlignment().getSequenceAt(i);
2781 if (current.getLength() < Width)
2783 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2786 alignPanel.paintAlignment(true);
2789 if ((viewport.getSelectionGroup() != null
2790 && viewport.getSelectionGroup().getSize() < 4 && viewport
2791 .getSelectionGroup().getSize() > 0)
2792 || viewport.getAlignment().getHeight() < 4)
2799 new PCAPanel(viewport);
2800 } catch (java.lang.OutOfMemoryError ex)
2806 public void averageDistanceTreeMenuItem_actionPerformed()
2808 NewTreePanel("AV", "PID", "Average distance tree using PID");
2811 public void neighbourTreeMenuItem_actionPerformed()
2813 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2816 protected void njTreeBlosumMenuItem_actionPerformed()
2818 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2821 protected void avTreeBlosumMenuItem_actionPerformed()
2823 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2826 void NewTreePanel(String type, String pwType, String title)
2828 // are the sequences aligned?
2829 if (!viewport.getAlignment().isAligned(false))
2832 int Width = viewport.getAlignment().getWidth();
2834 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2836 current = viewport.getAlignment().getSequenceAt(i);
2838 if (current.getLength() < Width)
2840 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2843 alignPanel.paintAlignment(true);
2847 if ((viewport.getSelectionGroup() != null && viewport
2848 .getSelectionGroup().getSize() > 1)
2849 || (viewport.getAlignment().getHeight() > 1))
2851 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2853 addTreeMenuItem(tp, title);
2855 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2859 void loadTree_actionPerformed()
2861 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2862 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2863 cap.setTreeImport();
2864 Frame frame = new Frame();
2866 jalview.bin.JalviewLite.addFrame(frame,
2867 MessageManager.getString("label.paste_newick_file"), 400, 300);
2870 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2872 TreePanel tp = new TreePanel(alignPanel, treeFile,
2873 MessageManager.getString("label.load_tree_from_file"), tree);
2874 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2875 addTreeMenuItem(tp, treeFile);
2879 * sort the alignment using the given treePanel
2882 * tree used to sort view
2884 * string used for undo event name
2886 public void sortByTree(TreePanel treePanel, String title)
2888 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2890 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2891 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2892 // HistoryItem.SORT));
2893 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2894 "label.order_by_params", new String[] { title }), oldOrder,
2895 viewport.getAlignment()));
2896 alignPanel.paintAlignment(true);
2900 * Do any automatic reordering of the alignment and add the necessary bits to
2901 * the menu structure for the new tree
2906 protected void addTreeMenuItem(final TreePanel treePanel,
2909 final MenuItem item = new MenuItem(title);
2910 sortByTreeMenu.add(item);
2911 item.addActionListener(new java.awt.event.ActionListener()
2914 public void actionPerformed(ActionEvent evt)
2916 sortByTree(treePanel, title); // treePanel.getTitle());
2920 treePanel.addWindowListener(new WindowAdapter()
2923 public void windowOpened(WindowEvent e)
2925 if (viewport.sortByTree)
2927 sortByTree(treePanel, title);
2929 super.windowOpened(e);
2933 public void windowClosing(WindowEvent e)
2935 sortByTreeMenu.remove(item);
2940 public boolean sortBy(AlignmentOrder alorder, String undoname)
2942 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2943 if (viewport.applet.debug)
2945 System.err.println("Sorting " + alorder.getOrder().size()
2946 + " in alignment '" + getTitle() + "'");
2948 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2949 if (undoname != null)
2951 addHistoryItem(new OrderCommand(undoname, oldOrder,
2952 viewport.getAlignment()));
2954 alignPanel.paintAlignment(true);
2958 protected void documentation_actionPerformed()
2960 alignPanel.av.applet.openJalviewHelpUrl();
2963 protected void about_actionPerformed()
2966 class AboutPanel extends Canvas
2972 public AboutPanel(String version, String builddate)
2974 this.version = version;
2975 this.builddate = builddate;
2979 public void paint(Graphics g)
2981 g.setColor(Color.white);
2982 g.fillRect(0, 0, getSize().width, getSize().height);
2983 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2984 FontMetrics fm = g.getFontMetrics();
2985 int fh = fm.getHeight();
2987 g.setColor(Color.black);
2988 // TODO: update this text for each release or centrally store it for
2989 // lite and application
2990 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2991 g.drawString(MessageManager.formatMessage(
2992 "label.jalviewLite_release", new String[] { version }), x,
2994 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2995 g.drawString(MessageManager.formatMessage(
2996 "label.jaview_build_date", new String[] { builddate }), x,
2998 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2999 g.drawString(MessageManager.getString("label.jalview_authors_1"),
3001 g.drawString(MessageManager.getString("label.jalview_authors_2"),
3002 x + 50, y += fh + 8);
3004 MessageManager.getString("label.jalview_dev_managers"), x,
3006 g.drawString(MessageManager
3007 .getString("label.jalview_distribution_lists"), x, y += fh);
3008 g.drawString(MessageManager.getString("label.jalview_please_cite"),
3011 MessageManager.getString("label.jalview_cite_1_authors"),
3014 MessageManager.getString("label.jalview_cite_1_title"), x,
3016 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
3021 Frame frame = new Frame();
3022 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
3024 jalview.bin.JalviewLite.addFrame(frame,
3025 MessageManager.getString("label.jalview"), 580, 220);
3029 public void showURL(String url, String target)
3031 if (viewport.applet == null)
3033 System.out.println("Not running as applet - no browser available.");
3037 viewport.applet.showURL(url, target);
3041 // ////////////////////////////////////////////////////////////////////////////////
3042 // JBuilder Graphics here
3044 MenuBar alignFrameMenuBar = new MenuBar();
3046 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
3048 MenuItem loadApplication = new MenuItem(
3049 MessageManager.getString("label.view_full_application"));
3051 MenuItem loadTree = new MenuItem(
3052 MessageManager.getString("label.load_associated_tree"));
3054 MenuItem loadAnnotations = new MenuItem(
3055 MessageManager.getString("label.load_features_annotations"));
3057 MenuItem outputFeatures = new MenuItem(
3058 MessageManager.getString("label.export_features"));
3060 MenuItem outputAnnotations = new MenuItem(
3061 MessageManager.getString("label.export_annotations"));
3063 MenuItem closeMenuItem = new MenuItem(
3064 MessageManager.getString("action.close"));
3066 MenuItem selectAllSequenceMenuItem = new MenuItem(
3067 MessageManager.getString("action.select_all"));
3069 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3070 MessageManager.getString("action.deselect_all"));
3072 MenuItem invertSequenceMenuItem = new MenuItem(
3073 MessageManager.getString("action.invert_selection"));
3075 MenuItem remove2LeftMenuItem = new MenuItem();
3077 MenuItem remove2RightMenuItem = new MenuItem();
3079 MenuItem removeGappedColumnMenuItem = new MenuItem();
3081 MenuItem removeAllGapsMenuItem = new MenuItem();
3083 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3085 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3087 MenuItem sortPairwiseMenuItem = new MenuItem();
3089 MenuItem sortIDMenuItem = new MenuItem();
3091 MenuItem sortLengthMenuItem = new MenuItem();
3093 MenuItem sortGroupMenuItem = new MenuItem();
3095 MenuItem removeRedundancyMenuItem = new MenuItem();
3097 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3099 MenuItem PCAMenuItem = new MenuItem();
3101 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3103 MenuItem neighbourTreeMenuItem = new MenuItem();
3105 BorderLayout borderLayout1 = new BorderLayout();
3107 public Label statusBar = new Label();
3109 MenuItem clustalColour = new MenuItem();
3111 MenuItem zappoColour = new MenuItem();
3113 MenuItem taylorColour = new MenuItem();
3115 MenuItem hydrophobicityColour = new MenuItem();
3117 MenuItem helixColour = new MenuItem();
3119 MenuItem strandColour = new MenuItem();
3121 MenuItem turnColour = new MenuItem();
3123 MenuItem buriedColour = new MenuItem();
3125 MenuItem purinePyrimidineColour = new MenuItem();
3127 // MenuItem RNAInteractionColour = new MenuItem();
3129 MenuItem RNAHelixColour = new MenuItem();
3131 MenuItem userDefinedColour = new MenuItem();
3133 MenuItem PIDColour = new MenuItem();
3135 MenuItem BLOSUM62Colour = new MenuItem();
3137 MenuItem tcoffeeColour = new MenuItem();
3139 MenuItem njTreeBlosumMenuItem = new MenuItem();
3141 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3143 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3145 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3147 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3149 MenuItem alProperties = new MenuItem(
3150 MessageManager.getString("label.alignment_props"));
3152 MenuItem overviewMenuItem = new MenuItem();
3154 MenuItem undoMenuItem = new MenuItem();
3156 MenuItem redoMenuItem = new MenuItem();
3158 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3160 MenuItem noColourmenuItem = new MenuItem();
3162 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3164 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3166 MenuItem findMenuItem = new MenuItem();
3168 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3170 MenuItem nucleotideColour = new MenuItem();
3172 MenuItem deleteGroups = new MenuItem();
3174 MenuItem grpsFromSelection = new MenuItem();
3176 MenuItem createGroup = new MenuItem();
3178 MenuItem unGroup = new MenuItem();
3180 MenuItem delete = new MenuItem();
3182 MenuItem copy = new MenuItem();
3184 MenuItem cut = new MenuItem();
3186 Menu pasteMenu = new Menu();
3188 MenuItem pasteNew = new MenuItem();
3190 MenuItem pasteThis = new MenuItem();
3192 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3194 MenuItem font = new MenuItem();
3196 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3198 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3200 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3202 MenuItem modifyPID = new MenuItem();
3204 MenuItem modifyConservation = new MenuItem();
3206 CheckboxMenuItem autoCalculate = null;
3208 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3209 "Sort Alignment With New Tree", true);
3211 Menu sortByTreeMenu = new Menu();
3213 MenuItem inputText = new MenuItem();
3215 MenuItem documentation = new MenuItem();
3217 MenuItem about = new MenuItem();
3219 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3221 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3223 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3225 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3227 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3229 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3231 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3233 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3235 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3238 * Initialise menus and other items
3242 private void jbInit() throws Exception
3244 setMenuBar(alignFrameMenuBar);
3247 * Configure File menu items and actions
3250 .setLabel(MessageManager.getString("label.input_from_textbox"));
3251 inputText.addActionListener(this);
3252 Menu outputTextboxMenu = new Menu(
3253 MessageManager.getString("label.out_to_textbox"));
3254 for (String ff : FileFormats.getInstance().getWritableFormats(true))
3256 MenuItem item = new MenuItem(ff);
3258 item.addActionListener(new java.awt.event.ActionListener()
3261 public void actionPerformed(ActionEvent e)
3263 outputText_actionPerformed(e);
3267 outputTextboxMenu.add(item);
3269 closeMenuItem.addActionListener(this);
3270 loadApplication.addActionListener(this);
3271 loadTree.addActionListener(this);
3272 loadAnnotations.addActionListener(this);
3273 outputFeatures.addActionListener(this);
3274 outputAnnotations.addActionListener(this);
3277 * Configure Edit menu items and actions
3279 undoMenuItem.setEnabled(false);
3280 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3281 undoMenuItem.addActionListener(this);
3282 redoMenuItem.setEnabled(false);
3283 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3284 redoMenuItem.addActionListener(this);
3285 copy.setLabel(MessageManager.getString("action.copy"));
3286 copy.addActionListener(this);
3287 cut.setLabel(MessageManager.getString("action.cut"));
3288 cut.addActionListener(this);
3289 delete.setLabel(MessageManager.getString("action.delete"));
3290 delete.addActionListener(this);
3291 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3292 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3293 pasteNew.addActionListener(this);
3294 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3295 pasteThis.addActionListener(this);
3296 remove2LeftMenuItem.setLabel(MessageManager
3297 .getString("action.remove_left"));
3298 remove2LeftMenuItem.addActionListener(this);
3299 remove2RightMenuItem.setLabel(MessageManager
3300 .getString("action.remove_right"));
3301 remove2RightMenuItem.addActionListener(this);
3302 removeGappedColumnMenuItem.setLabel(MessageManager
3303 .getString("action.remove_empty_columns"));
3304 removeGappedColumnMenuItem.addActionListener(this);
3305 removeAllGapsMenuItem.setLabel(MessageManager
3306 .getString("action.remove_all_gaps"));
3307 removeAllGapsMenuItem.addActionListener(this);
3308 removeRedundancyMenuItem.setLabel(MessageManager
3309 .getString("action.remove_redundancy"));
3310 removeRedundancyMenuItem.addActionListener(this);
3313 * Configure Select menu items and actions
3315 findMenuItem.setLabel(MessageManager.getString("action.find"));
3316 findMenuItem.addActionListener(this);
3317 selectAllSequenceMenuItem.addActionListener(this);
3318 deselectAllSequenceMenuItem.addActionListener(this);
3319 invertSequenceMenuItem.setLabel(MessageManager
3320 .getString("action.invert_sequence_selection"));
3321 invertSequenceMenuItem.addActionListener(this);
3322 invertColSel.setLabel(MessageManager
3323 .getString("action.invert_column_selection"));
3324 invertColSel.addActionListener(this);
3325 deleteGroups.setLabel(MessageManager
3326 .getString("action.undefine_groups"));
3327 deleteGroups.addActionListener(this);
3328 grpsFromSelection.setLabel(MessageManager
3329 .getString("action.make_groups_selection"));
3330 grpsFromSelection.addActionListener(this);
3331 createGroup.setLabel(MessageManager.getString("action.create_group"));
3332 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3333 annotationColumnSelection.setLabel(MessageManager
3334 .getString("action.select_by_annotation"));
3335 annotationColumnSelection.addActionListener(this);
3338 * Configure View menu items and actions
3340 newView.setLabel(MessageManager.getString("action.new_view"));
3341 newView.addActionListener(this);
3342 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3343 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3344 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3345 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3347 .setLabel(MessageManager.getString("label.selected_columns"));
3348 hideSequences.setLabel(MessageManager
3349 .getString("label.selected_sequences"));
3350 hideAllButSelection.setLabel(MessageManager
3351 .getString("label.all_but_selected_region"));
3352 hideAllSelection.setLabel(MessageManager
3353 .getString("label.selected_region"));
3354 showAllHidden.setLabel(MessageManager
3355 .getString("label.all_sequences_columns"));
3356 showColumns.addActionListener(this);
3357 showSeqs.addActionListener(this);
3358 hideColumns.addActionListener(this);
3359 hideSequences.addActionListener(this);
3360 hideAllButSelection.addActionListener(this);
3361 hideAllSelection.addActionListener(this);
3362 showAllHidden.addActionListener(this);
3363 featureSettings.setLabel(MessageManager
3364 .getString("action.feature_settings"));
3365 featureSettings.addActionListener(this);
3366 sequenceFeatures.setLabel(MessageManager
3367 .getString("label.show_sequence_features"));
3368 sequenceFeatures.addItemListener(this);
3369 sequenceFeatures.setState(false);
3370 followMouseOverFlag.setLabel(MessageManager
3371 .getString("label.automatic_scrolling"));
3372 followMouseOverFlag.addItemListener(this);
3373 alProperties.addActionListener(this);
3374 overviewMenuItem.setLabel(MessageManager
3375 .getString("label.overview_window"));
3376 overviewMenuItem.addActionListener(this);
3379 * Configure Annotations menu items and actions
3381 annotationPanelMenuItem.setLabel(MessageManager
3382 .getString("label.show_annotations"));
3383 annotationPanelMenuItem.addItemListener(this);
3384 showGroupConsensus.setLabel(MessageManager
3385 .getString("label.group_consensus"));
3386 showGroupConservation.setLabel(MessageManager
3387 .getString("label.group_conservation"));
3388 showConsensusHistogram.setLabel(MessageManager
3389 .getString("label.show_consensus_histogram"));
3390 showSequenceLogo.setLabel(MessageManager
3391 .getString("label.show_consensus_logo"));
3392 normSequenceLogo.setLabel(MessageManager
3393 .getString("label.norm_consensus_logo"));
3394 applyAutoAnnotationSettings.setLabel(MessageManager
3395 .getString("label.apply_all_groups"));
3396 applyAutoAnnotationSettings.setState(true);
3397 Menu autoAnnMenu = new Menu(
3398 MessageManager.getString("label.autocalculated_annotation"));
3399 showGroupConsensus.addItemListener(this);
3400 showGroupConservation.addItemListener(this);
3401 showConsensusHistogram.addItemListener(this);
3402 showSequenceLogo.addItemListener(this);
3403 normSequenceLogo.addItemListener(this);
3404 applyAutoAnnotationSettings.addItemListener(this);
3405 showAlignmentAnnotations = new CheckboxMenuItem(
3406 MessageManager.getString("label.show_all_al_annotations"));
3407 showSequenceAnnotations = new CheckboxMenuItem(
3408 MessageManager.getString("label.show_all_seq_annotations"));
3409 sortAnnBySequence = new CheckboxMenuItem(
3410 MessageManager.getString("label.sort_annotations_by_sequence"));
3411 sortAnnByLabel = new CheckboxMenuItem(
3412 MessageManager.getString("label.sort_annotations_by_label"));
3413 showAutoFirst = new CheckboxMenuItem(
3414 MessageManager.getString("label.show_first"));
3415 showAutoFirst.setState(false); // pending applet parameter
3416 setShowAutoCalculatedAbove(showAutoFirst.getState());
3417 showAutoLast = new CheckboxMenuItem(
3418 MessageManager.getString("label.show_last"));
3419 showAutoLast.setState(!showAutoFirst.getState());
3420 showAlignmentAnnotations.addItemListener(this);
3421 showSequenceAnnotations.addItemListener(this);
3422 sortAnnBySequence.addItemListener(this);
3423 sortAnnByLabel.addItemListener(this);
3424 showAutoFirst.addItemListener(this);
3425 showAutoLast.addItemListener(this);
3428 * Configure Format menu items and actions
3430 font.setLabel(MessageManager.getString("action.font"));
3431 font.addActionListener(this);
3432 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3433 scaleAbove.setState(true);
3434 scaleAbove.setEnabled(false);
3435 scaleAbove.addItemListener(this);
3436 scaleLeft.setEnabled(false);
3437 scaleLeft.setState(true);
3438 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3439 scaleLeft.addItemListener(this);
3440 scaleRight.setEnabled(false);
3441 scaleRight.setState(true);
3442 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3443 scaleRight.addItemListener(this);
3444 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3445 viewBoxesMenuItem.setState(true);
3446 viewBoxesMenuItem.addItemListener(this);
3447 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3448 viewTextMenuItem.setState(true);
3449 viewTextMenuItem.addItemListener(this);
3450 colourTextMenuItem.setLabel(MessageManager
3451 .getString("label.colour_text"));
3452 colourTextMenuItem.addItemListener(this);
3453 displayNonconservedMenuItem.setLabel(MessageManager
3454 .getString("label.show_non_conserved"));
3455 displayNonconservedMenuItem.addItemListener(this);
3456 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3457 wrapMenuItem.addItemListener(this);
3458 renderGapsMenuItem.setLabel(MessageManager
3459 .getString("action.show_gaps"));
3460 renderGapsMenuItem.setState(true);
3461 renderGapsMenuItem.addItemListener(this);
3462 centreColumnLabelFlag.setLabel(MessageManager
3463 .getString("label.centre_column_labels"));
3464 centreColumnLabelFlag.addItemListener(this);
3465 seqLimits.setState(true);
3466 seqLimits.setLabel(MessageManager
3467 .getString("label.show_sequence_limits"));
3468 seqLimits.addItemListener(this);
3471 * Configure Colour menu items and actions
3473 applyToAllGroups.setLabel(MessageManager
3474 .getString("label.apply_colour_to_all_groups"));
3475 applyToAllGroups.setState(true);
3476 applyToAllGroups.addItemListener(this);
3477 clustalColour.setLabel(MessageManager
3478 .getString("label.colourScheme_clustal"));
3479 clustalColour.addActionListener(this);
3480 zappoColour.setLabel(MessageManager
3481 .getString("label.colourScheme_zappo"));
3482 zappoColour.addActionListener(this);
3483 taylorColour.setLabel(MessageManager
3484 .getString("label.colourScheme_taylor"));
3485 taylorColour.addActionListener(this);
3486 hydrophobicityColour.setLabel(MessageManager
3487 .getString("label.colourScheme_hydrophobic"));
3488 hydrophobicityColour.addActionListener(this);
3489 helixColour.setLabel(MessageManager
3490 .getString("label.colourScheme_helix_propensity"));
3491 helixColour.addActionListener(this);
3492 strandColour.setLabel(MessageManager
3493 .getString("label.colourScheme_strand_propensity"));
3494 strandColour.addActionListener(this);
3495 turnColour.setLabel(MessageManager
3496 .getString("label.colourScheme_turn_propensity"));
3497 turnColour.addActionListener(this);
3498 buriedColour.setLabel(MessageManager
3499 .getString("label.colourScheme_buried_index"));
3500 buriedColour.addActionListener(this);
3501 purinePyrimidineColour.setLabel(MessageManager
3502 .getString("label.colourScheme_purine/pyrimidine"));
3503 purinePyrimidineColour.addActionListener(this);
3504 // RNAInteractionColour.setLabel(MessageManager
3505 // .getString("label.rna_interaction"));
3506 // RNAInteractionColour.addActionListener(this);
3507 RNAHelixColour.setLabel(MessageManager
3508 .getString("label.colourScheme_rna_helices"));
3509 RNAHelixColour.addActionListener(this);
3510 userDefinedColour.setLabel(MessageManager
3511 .getString("action.user_defined"));
3512 userDefinedColour.addActionListener(this);
3513 PIDColour.setLabel(MessageManager
3514 .getString("label.colourScheme_%_identity"));
3515 PIDColour.addActionListener(this);
3516 BLOSUM62Colour.setLabel(MessageManager
3517 .getString("label.colourScheme_blosum62"));
3518 BLOSUM62Colour.addActionListener(this);
3519 tcoffeeColour.setLabel(MessageManager
3520 .getString("label.colourScheme_t-coffee_scores"));
3521 // it will be enabled only if a score file is provided
3522 tcoffeeColour.setEnabled(false);
3523 tcoffeeColour.addActionListener(this);
3524 conservationMenuItem.setLabel(MessageManager
3525 .getString("action.by_conservation"));
3526 conservationMenuItem.addItemListener(this);
3527 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3528 noColourmenuItem.addActionListener(this);
3529 abovePIDThreshold.setLabel(MessageManager
3530 .getString("label.above_identity_threshold"));
3531 abovePIDThreshold.addItemListener(this);
3532 nucleotideColour.setLabel(MessageManager
3533 .getString("label.colourScheme_nucleotide"));
3534 nucleotideColour.addActionListener(this);
3535 modifyPID.setLabel(MessageManager
3536 .getString("label.modify_identity_threshold"));
3537 modifyPID.setEnabled(abovePIDThreshold.getState());
3538 modifyPID.addActionListener(this);
3539 modifyConservation.setLabel(MessageManager
3540 .getString("label.modify_conservation_threshold"));
3541 modifyConservation.setEnabled(conservationMenuItem.getState());
3542 modifyConservation.addActionListener(this);
3543 annotationColour.setLabel(MessageManager
3544 .getString("action.by_annotation"));
3545 annotationColour.addActionListener(this);
3548 * Configure Calculate menu items and actions
3550 sortPairwiseMenuItem.setLabel(MessageManager
3551 .getString("action.by_pairwise_id"));
3552 sortPairwiseMenuItem.addActionListener(this);
3553 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3554 sortIDMenuItem.addActionListener(this);
3555 sortLengthMenuItem.setLabel(MessageManager
3556 .getString("action.by_length"));
3557 sortLengthMenuItem.addActionListener(this);
3558 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3559 sortGroupMenuItem.addActionListener(this);
3560 pairwiseAlignmentMenuItem.setLabel(MessageManager
3561 .getString("action.pairwise_alignment"));
3562 pairwiseAlignmentMenuItem.addActionListener(this);
3563 PCAMenuItem.setLabel(MessageManager
3564 .getString("label.principal_component_analysis"));
3565 PCAMenuItem.addActionListener(this);
3566 autoCalculate = new CheckboxMenuItem(
3567 MessageManager.getString("label.autocalculate_consensus"), true);
3568 averageDistanceTreeMenuItem.setLabel(MessageManager
3569 .getString("label.average_distance_identity"));
3570 averageDistanceTreeMenuItem.addActionListener(this);
3571 neighbourTreeMenuItem.setLabel(MessageManager
3572 .getString("label.neighbour_joining_identity"));
3573 neighbourTreeMenuItem.addActionListener(this);
3574 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3575 .getString("label.average_distance_blosum62"));
3576 avDistanceTreeBlosumMenuItem.addActionListener(this);
3577 njTreeBlosumMenuItem.setLabel(MessageManager
3578 .getString("label.neighbour_blosum62"));
3579 njTreeBlosumMenuItem.addActionListener(this);
3580 sortByTreeMenu.setLabel(MessageManager
3581 .getString("action.by_tree_order"));
3582 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3583 Menu calculateTreeMenu = new Menu(
3584 MessageManager.getString("action.calculate_tree"));
3585 autoCalculate.addItemListener(this);
3586 sortByTree.addItemListener(this);
3589 * Configure Help menu items and actions
3591 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3592 documentation.setLabel(MessageManager.getString("label.documentation"));
3593 documentation.addActionListener(this);
3594 about.setLabel(MessageManager.getString("label.about"));
3595 about.addActionListener(this);
3598 * Add top level menus to frame
3600 alignFrameMenuBar.add(fileMenu);
3601 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3602 alignFrameMenuBar.add(editMenu);
3603 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3604 alignFrameMenuBar.add(selectMenu);
3605 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3606 alignFrameMenuBar.add(viewMenu);
3607 Menu annotationsMenu = new Menu(
3608 MessageManager.getString("action.annotations"));
3609 alignFrameMenuBar.add(annotationsMenu);
3610 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3611 alignFrameMenuBar.add(formatMenu);
3612 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3613 alignFrameMenuBar.add(colourMenu);
3614 Menu calculateMenu = new Menu(
3615 MessageManager.getString("action.calculate"));
3616 alignFrameMenuBar.add(calculateMenu);
3617 alignFrameMenuBar.add(helpMenu);
3622 fileMenu.add(inputText);
3623 fileMenu.add(loadTree);
3624 fileMenu.add(loadAnnotations);
3625 fileMenu.addSeparator();
3626 fileMenu.add(outputTextboxMenu);
3627 fileMenu.add(outputFeatures);
3628 fileMenu.add(outputAnnotations);
3629 if (jalviewServletURL != null)
3631 fileMenu.add(loadApplication);
3633 fileMenu.addSeparator();
3634 fileMenu.add(closeMenuItem);
3639 editMenu.add(undoMenuItem);
3640 editMenu.add(redoMenuItem);
3643 pasteMenu.add(pasteNew);
3644 pasteMenu.add(pasteThis);
3645 editMenu.add(pasteMenu);
3646 editMenu.add(delete);
3647 editMenu.addSeparator();
3648 editMenu.add(remove2LeftMenuItem);
3649 editMenu.add(remove2RightMenuItem);
3650 editMenu.add(removeGappedColumnMenuItem);
3651 editMenu.add(removeAllGapsMenuItem);
3652 editMenu.add(removeRedundancyMenuItem);
3657 selectMenu.add(findMenuItem);
3658 selectMenu.addSeparator();
3659 selectMenu.add(selectAllSequenceMenuItem);
3660 selectMenu.add(deselectAllSequenceMenuItem);
3661 selectMenu.add(invertSequenceMenuItem);
3662 selectMenu.add(invertColSel);
3663 selectMenu.add(createGroup);
3664 selectMenu.add(unGroup);
3665 selectMenu.add(grpsFromSelection);
3666 selectMenu.add(deleteGroups);
3667 selectMenu.add(annotationColumnSelection);
3672 viewMenu.add(newView);
3673 viewMenu.addSeparator();
3674 showMenu.add(showColumns);
3675 showMenu.add(showSeqs);
3676 showMenu.add(showAllHidden);
3677 viewMenu.add(showMenu);
3678 hideMenu.add(hideColumns);
3679 hideMenu.add(hideSequences);
3680 hideMenu.add(hideAllSelection);
3681 hideMenu.add(hideAllButSelection);
3682 viewMenu.add(hideMenu);
3683 viewMenu.addSeparator();
3684 viewMenu.add(followMouseOverFlag);
3685 viewMenu.addSeparator();
3686 viewMenu.add(sequenceFeatures);
3687 viewMenu.add(featureSettings);
3688 viewMenu.addSeparator();
3689 viewMenu.add(alProperties);
3690 viewMenu.addSeparator();
3691 viewMenu.add(overviewMenuItem);
3696 annotationsMenu.add(annotationPanelMenuItem);
3697 annotationsMenu.addSeparator();
3698 annotationsMenu.add(showAlignmentAnnotations);
3699 annotationsMenu.add(showSequenceAnnotations);
3700 annotationsMenu.add(sortAnnBySequence);
3701 annotationsMenu.add(sortAnnByLabel);
3702 annotationsMenu.addSeparator();
3703 autoAnnMenu.add(showAutoFirst);
3704 autoAnnMenu.add(showAutoLast);
3705 autoAnnMenu.addSeparator();
3706 autoAnnMenu.add(applyAutoAnnotationSettings);
3707 autoAnnMenu.add(showConsensusHistogram);
3708 autoAnnMenu.add(showSequenceLogo);
3709 autoAnnMenu.add(normSequenceLogo);
3710 autoAnnMenu.addSeparator();
3711 autoAnnMenu.add(showGroupConservation);
3712 autoAnnMenu.add(showGroupConsensus);
3713 annotationsMenu.add(autoAnnMenu);
3718 formatMenu.add(font);
3719 formatMenu.add(seqLimits);
3720 formatMenu.add(wrapMenuItem);
3721 formatMenu.add(scaleAbove);
3722 formatMenu.add(scaleLeft);
3723 formatMenu.add(scaleRight);
3724 formatMenu.add(viewBoxesMenuItem);
3725 formatMenu.add(viewTextMenuItem);
3726 formatMenu.add(colourTextMenuItem);
3727 formatMenu.add(displayNonconservedMenuItem);
3728 formatMenu.add(renderGapsMenuItem);
3729 formatMenu.add(centreColumnLabelFlag);
3734 colourMenu.add(applyToAllGroups);
3735 colourMenu.addSeparator();
3736 colourMenu.add(noColourmenuItem);
3737 colourMenu.add(clustalColour);
3738 colourMenu.add(BLOSUM62Colour);
3739 colourMenu.add(PIDColour);
3740 colourMenu.add(zappoColour);
3741 colourMenu.add(taylorColour);
3742 colourMenu.add(hydrophobicityColour);
3743 colourMenu.add(helixColour);
3744 colourMenu.add(strandColour);
3745 colourMenu.add(turnColour);
3746 colourMenu.add(buriedColour);
3747 colourMenu.add(nucleotideColour);
3748 colourMenu.add(purinePyrimidineColour);
3749 // colourMenu.add(RNAInteractionColour);
3750 colourMenu.add(tcoffeeColour);
3751 colourMenu.add(userDefinedColour);
3752 colourMenu.addSeparator();
3753 colourMenu.add(conservationMenuItem);
3754 colourMenu.add(modifyConservation);
3755 colourMenu.add(abovePIDThreshold);
3756 colourMenu.add(modifyPID);
3757 colourMenu.add(annotationColour);
3758 colourMenu.add(RNAHelixColour);
3763 sortMenu.add(sortIDMenuItem);
3764 sortMenu.add(sortLengthMenuItem);
3765 sortMenu.add(sortByTreeMenu);
3766 sortMenu.add(sortGroupMenuItem);
3767 sortMenu.add(sortPairwiseMenuItem);
3768 calculateMenu.add(sortMenu);
3769 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3770 calculateTreeMenu.add(neighbourTreeMenuItem);
3771 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3772 calculateTreeMenu.add(njTreeBlosumMenuItem);
3773 calculateMenu.add(calculateTreeMenu);
3774 calculateMenu.addSeparator();
3775 calculateMenu.add(pairwiseAlignmentMenuItem);
3776 calculateMenu.add(PCAMenuItem);
3777 calculateMenu.add(autoCalculate);
3778 calculateMenu.add(sortByTree);
3783 helpMenu.add(documentation);
3784 helpMenu.add(about);
3789 statusBar.setBackground(Color.white);
3790 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3791 statusBar.setText(MessageManager.getString("label.status_bar"));
3792 this.add(statusBar, BorderLayout.SOUTH);
3796 public void setStatus(String string)
3798 statusBar.setText(string);
3801 MenuItem featureSettings = new MenuItem();
3803 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3805 MenuItem annotationColour = new MenuItem();
3807 MenuItem annotationColumnSelection = new MenuItem();
3809 MenuItem invertColSel = new MenuItem();
3811 MenuItem showColumns = new MenuItem();
3813 MenuItem showSeqs = new MenuItem();
3815 MenuItem hideColumns = new MenuItem();
3817 MenuItem hideSequences = new MenuItem();
3819 MenuItem hideAllButSelection = new MenuItem();
3821 MenuItem hideAllSelection = new MenuItem();
3823 MenuItem showAllHidden = new MenuItem();
3825 MenuItem newView = new MenuItem();
3827 private CheckboxMenuItem showAlignmentAnnotations;
3829 private CheckboxMenuItem showSequenceAnnotations;
3831 private CheckboxMenuItem sortAnnBySequence;
3833 private CheckboxMenuItem sortAnnByLabel;
3835 private CheckboxMenuItem showAutoFirst;
3837 private CheckboxMenuItem showAutoLast;
3839 private SplitFrame splitFrame;
3842 * Attach the alignFrame panels after embedding menus, if necessary. This used
3843 * to be called setEmbedded, but is now creates the dropdown menus in a
3844 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3846 * @param reallyEmbedded
3847 * true to attach the view to the applet area on the page rather than
3850 public void createAlignFrameWindow(boolean reallyEmbedded)
3854 embedAlignFrameInApplet(viewport.applet);
3859 // test and embed menu bar if necessary.
3861 if (embedMenuIfNeeded(alignPanel))
3864 * adjust for status bar height too. ? pointless as overridden by layout
3867 alignPanel.setSize(getSize().width,
3868 getSize().height - statusBar.getHeight());
3870 add(statusBar, BorderLayout.SOUTH);
3871 add(alignPanel, BorderLayout.CENTER);
3872 // and register with the applet so it can pass external API calls to us
3873 jalview.bin.JalviewLite.addFrame(this, this.getTitle(), frameWidth,
3879 * Add the components of this AlignFrame to the applet container.
3883 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3886 // Explicitly build the embedded menu panel for the on-page applet
3888 // view cannot be closed if its actually on the page
3889 fileMenu.remove(closeMenuItem);
3890 fileMenu.remove(3); // Remove Separator
3891 // construct embedded menu, using default font
3892 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3893 // and actually add the components to the applet area
3894 theApplet.setLayout(new BorderLayout());
3895 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3896 theApplet.add(statusBar, BorderLayout.SOUTH);
3897 // TODO should size be left to the layout manager?
3898 alignPanel.setSize(theApplet.getSize().width,
3899 theApplet.getSize().height - embeddedMenu.getHeight()
3900 - statusBar.getHeight());
3901 theApplet.add(alignPanel, BorderLayout.CENTER);
3902 final AlignFrame me = this;
3903 theApplet.addFocusListener(new FocusListener()
3907 public void focusLost(FocusEvent e)
3909 if (theApplet.currentAlignFrame == me)
3911 theApplet.currentAlignFrame = null;
3916 public void focusGained(FocusEvent e)
3918 theApplet.currentAlignFrame = me;
3921 theApplet.validate();
3925 * create a new binding between structures in an existing jmol viewer instance
3926 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3927 * this does not open a new Jmol window, or modify the display of the
3928 * structures in the original jmol window. Note This method doesn't work
3929 * without an additional javascript library to exchange messages between the
3930 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3933 * JmolViewer instance
3934 * @param sequenceIds
3935 * - sequence Ids to search for associations
3937 public SequenceStructureBinding addStructureViewInstance(
3938 Object jmolviewer, String[] sequenceIds)
3940 Viewer viewer = null;
3943 viewer = (Viewer) jmolviewer;
3944 } catch (ClassCastException ex)
3946 System.err.println("Unsupported viewer object :"
3947 + jmolviewer.getClass());
3951 System.err.println("Can't use this object as a structure viewer:"
3952 + jmolviewer.getClass());
3955 SequenceI[] seqs = null;
3956 if (sequenceIds == null || sequenceIds.length == 0)
3958 seqs = viewport.getAlignment().getSequencesArray();
3962 Vector sqi = new Vector();
3963 AlignmentI al = viewport.getAlignment();
3964 for (int sid = 0; sid < sequenceIds.length; sid++)
3966 SequenceI sq = al.findName(sequenceIds[sid]);
3974 seqs = new SequenceI[sqi.size()];
3975 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3977 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3985 AAStructureBindingModel jmv = null;
3986 // TODO: search for a jmv that involves viewer
3988 { // create a new viewer/jalview binding.
3989 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][] { seqs });
3996 * bind a pdb file to a sequence in the current view
3999 * - sequenceId within the dataset.
4000 * @param pdbEntryString
4001 * - the short name for the PDB file
4003 * - pdb file - either a URL or a valid PDB file.
4004 * @return true if binding was as success TODO: consider making an exception
4005 * structure for indicating when PDB parsing or sequenceId location
4008 public boolean addPdbFile(String sequenceId, String pdbEntryString,
4011 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
4012 boolean needtoadd = false;
4013 if (toaddpdb != null)
4015 Vector pdbe = toaddpdb.getAllPDBEntries();
4016 PDBEntry pdbentry = null;
4017 if (pdbe != null && pdbe.size() > 0)
4019 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
4021 pdbentry = (PDBEntry) pdbe.elementAt(pe);
4022 if (!pdbentry.getId().equals(pdbEntryString)
4023 && !pdbentry.getFile().equals(pdbFile))
4033 if (pdbentry == null)
4035 pdbentry = new PDBEntry();
4036 pdbentry.setId(pdbEntryString);
4037 pdbentry.setFile(pdbFile);
4038 needtoadd = true; // add this new entry to sequence.
4040 // resolve data source
4041 // TODO: this code should be a refactored to an io package
4042 DataSourceType protocol = AppletFormatAdapter.resolveProtocol(
4043 pdbFile, FileFormat.PDB);
4044 if (protocol == null)
4050 pdbentry.setProperty("protocol", protocol);
4051 toaddpdb.addPDBId(pdbentry);
4052 alignPanel.getStructureSelectionManager()
4053 .registerPDBEntry(pdbentry);
4059 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4063 Vector sequences = new Vector();
4064 for (int i = 0; i < seqs.length; i++)
4066 if (seqs[i] != null)
4068 sequences.addElement(new Object[] { seqs[i],
4069 (chains != null) ? chains[i] : null });
4072 seqs = new SequenceI[sequences.size()];
4073 chains = new String[sequences.size()];
4074 for (int i = 0, isize = sequences.size(); i < isize; i++)
4076 Object[] oj = (Object[]) sequences.elementAt(i);
4078 seqs[i] = (SequenceI) oj[0];
4079 chains[i] = (String) oj[1];
4082 return new Object[] { seqs, chains };
4086 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4087 SequenceI[] seqs, String[] chains, DataSourceType protocol)
4089 // Scrub any null sequences from the array
4090 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4091 seqs = (SequenceI[]) sqch[0];
4092 chains = (String[]) sqch[1];
4093 if (seqs == null || seqs.length == 0)
4096 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4098 if (protocol == null)
4100 String sourceType = (String) pdb.getProperty("protocol");
4103 protocol = DataSourceType.valueOf(sourceType);
4104 } catch (IllegalArgumentException e)
4108 if (protocol == null)
4110 System.err.println("Couldn't work out protocol to open structure: "
4115 if (applet.useXtrnalSviewer)
4117 // register the association(s) and quit, don't create any windows.
4118 if (StructureSelectionManager.getStructureSelectionManager(applet)
4119 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4121 System.err.println("Failed to map " + pdb.getFile() + " ("
4122 + protocol + ") to any sequences");
4126 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4128 // can only do alignments with Jmol
4129 // find the last jmol window assigned to this alignment
4130 AppletJmol ajm = null, tajm;
4131 Vector jmols = applet.getAppletWindow(AppletJmol.class);
4132 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4134 tajm = (AppletJmol) jmols.elementAt(i);
4135 if (tajm.ap.alignFrame == this)
4144 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4145 // try and add the pdb structure
4150 // otherwise, create a new window
4151 if (applet.jmolAvailable)
4153 new AppletJmol(pdb, seqs, chains, alignPanel,
4155 applet.lastFrameX += 40;
4156 applet.lastFrameY += 40;
4160 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4165 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4166 SequenceI[][] seqs, String[][] chains, String[] protocols)
4168 // TODO Auto-generated method stub
4169 System.err.println("Aligned Structure View: Not yet implemented.");
4173 * modify the current selection, providing the user has not made a selection
4177 * - sequences from this alignment
4179 * - columns to be selected on the alignment
4181 public void select(SequenceGroup sel, ColumnSelection csel)
4183 alignPanel.seqPanel.selection(sel, csel, null);
4186 public void scrollTo(int row, int column)
4188 alignPanel.seqPanel.scrollTo(row, column);
4191 public void scrollToRow(int row)
4193 alignPanel.seqPanel.scrollToRow(row);
4196 public void scrollToColumn(int column)
4198 alignPanel.seqPanel.scrollToColumn(column);
4202 * @return the alignments unique ID.
4204 public String getSequenceSetId()
4206 return viewport.getSequenceSetId();
4210 * Load the (T-Coffee) score file from the specified url
4213 * File/URL/T-COFFEE score file contents
4214 * @throws IOException
4215 * @return true if alignment was annotated with data from source
4217 public boolean loadScoreFile(String source) throws IOException
4220 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4221 AppletFormatAdapter.checkProtocol(source));
4222 if (!file.isValid())
4224 // TODO: raise dialog for gui
4225 System.err.println("Problems parsing T-Coffee scores: "
4226 + file.getWarningMessage());
4227 System.err.println("Origin was:\n" + source);
4232 * check that the score matrix matches the alignment dimensions
4235 if ((aln = viewport.getAlignment()) != null
4236 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4239 // TODO: raise a dialog box here rather than bomb out.
4241 .println("The scores matrix does not match the alignment dimensions");
4245 // TODO add parameter to indicate if matching should be done
4246 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4248 alignPanel.fontChanged();
4249 tcoffeeColour.setEnabled(true);
4250 // switch to this color
4251 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4256 System.err.println("Problems resolving T-Coffee scores:");
4257 if (file.getWarningMessage() != null)
4259 System.err.println(file.getWarningMessage());
4265 public SplitFrame getSplitFrame()
4267 return this.splitFrame;
4270 public void setSplitFrame(SplitFrame sf)
4272 this.splitFrame = sf;
4275 // may not need this
4277 public void setShowSeqFeatures(boolean b)
4279 // showSeqFeatures.setSelected(b);
4280 viewport.setShowSequenceFeatures(b);
4285 public void setMenusForViewport()
4287 // setMenusFromViewport(viewport);
4292 public void refreshFeatureUI(boolean enableIfNecessary)
4294 if (enableIfNecessary)
4296 sequenceFeatures.setState(true);
4297 alignPanel.av.setShowSequenceFeatures(true);
4302 public FeatureSettingsControllerI getFeatureSettingsUI()
4304 return alignPanel.av.featureSettings;