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 java.awt.BorderLayout;
24 import java.awt.Canvas;
25 import java.awt.CheckboxMenuItem;
26 import java.awt.Color;
28 import java.awt.FontMetrics;
29 import java.awt.Frame;
30 import java.awt.Graphics;
31 import java.awt.Label;
33 import java.awt.MenuBar;
34 import java.awt.MenuItem;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.FocusListener;
39 import java.awt.event.ItemEvent;
40 import java.awt.event.ItemListener;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.KeyListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.io.IOException;
47 import java.net.URLEncoder;
48 import java.util.Arrays;
49 import java.util.Deque;
50 import java.util.HashMap;
51 import java.util.Hashtable;
52 import java.util.List;
54 import java.util.StringTokenizer;
55 import java.util.Vector;
57 import jalview.analysis.AlignmentSorter;
58 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
59 import jalview.api.AlignViewControllerGuiI;
60 import jalview.api.AlignViewControllerI;
61 import jalview.api.AlignViewportI;
62 import jalview.api.FeatureRenderer;
63 import jalview.api.SequenceStructureBinding;
64 import jalview.bin.JalviewLite;
65 import jalview.commands.CommandI;
66 import jalview.commands.EditCommand;
67 import jalview.commands.EditCommand.Action;
68 import jalview.commands.OrderCommand;
69 import jalview.commands.RemoveGapColCommand;
70 import jalview.commands.RemoveGapsCommand;
71 import jalview.commands.SlideSequencesCommand;
72 import jalview.commands.TrimRegionCommand;
73 import jalview.datamodel.Alignment;
74 import jalview.datamodel.AlignmentAnnotation;
75 import jalview.datamodel.AlignmentI;
76 import jalview.datamodel.AlignmentOrder;
77 import jalview.datamodel.ColumnSelection;
78 import jalview.datamodel.PDBEntry;
79 import jalview.datamodel.Sequence;
80 import jalview.datamodel.SequenceGroup;
81 import jalview.datamodel.SequenceI;
82 import jalview.io.AnnotationFile;
83 import jalview.io.AppletFormatAdapter;
84 import jalview.io.FeaturesFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.schemes.Blosum62ColourScheme;
87 import jalview.schemes.BuriedColourScheme;
88 import jalview.schemes.ClustalxColourScheme;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.HelixColourScheme;
91 import jalview.schemes.HydrophobicColourScheme;
92 import jalview.schemes.NucleotideColourScheme;
93 import jalview.schemes.PIDColourScheme;
94 import jalview.schemes.PurinePyrimidineColourScheme;
95 import jalview.schemes.RNAHelicesColourChooser;
96 import jalview.schemes.RNAInteractionColourScheme;
97 import jalview.schemes.StrandColourScheme;
98 import jalview.schemes.TCoffeeColourScheme;
99 import jalview.schemes.TaylorColourScheme;
100 import jalview.schemes.TurnColourScheme;
101 import jalview.schemes.ZappoColourScheme;
102 import jalview.structure.StructureSelectionManager;
103 import jalview.structures.models.AAStructureBindingModel;
104 import jalview.util.MappingUtils;
105 import jalview.util.MessageManager;
106 import jalview.viewmodel.AlignmentViewport;
108 public class AlignFrame extends EmbmenuFrame implements ActionListener,
109 ItemListener, KeyListener, AlignViewControllerGuiI
111 public AlignViewControllerI avc;
113 public AlignmentPanel alignPanel;
115 public AlignViewport viewport;
117 // width and height may be overridden by applet parameters
118 int frameWidth = 700;
120 int frameHeight = 500;
122 String jalviewServletURL;
125 * Flag for showing autocalculated consensus above or below other consensus
128 private boolean showAutoCalculatedAbove;
130 private SequenceAnnotationOrder annotationSortOrder;
133 * Constructor that creates the frame and adds it to the display.
140 public AlignFrame(AlignmentI al, JalviewLite applet,
141 String title, boolean embedded)
143 this(al, applet, title, embedded, true);
147 * Constructor that optionally allows the frame to be displayed or only
154 * @param addToDisplay
156 public AlignFrame(AlignmentI al, JalviewLite applet,
157 String title, boolean embedded, boolean addToDisplay)
159 this(al, null, null, applet, title, embedded, addToDisplay);
162 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
163 ColumnSelection columnSelection, JalviewLite applet,
164 String title, boolean embedded)
166 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
169 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
170 ColumnSelection columnSelection, JalviewLite applet,
171 String title, boolean embedded, boolean addToDisplay)
175 jalviewServletURL = applet.getParameter("APPLICATION_URL");
181 } catch (Exception ex)
183 ex.printStackTrace();
185 // need to get window geometry before we calculate alignment layout
191 param = applet.getParameter("windowWidth");
194 int width = Integer.parseInt(param);
197 param = applet.getParameter("windowHeight");
200 int height = Integer.parseInt(param);
201 frameHeight = height;
203 } catch (Exception ex)
207 viewport = new AlignViewport(al, applet);
209 if (hiddenSeqs != null && hiddenSeqs.length > 0)
211 viewport.hideSequence(hiddenSeqs);
212 viewport.setHasHiddenRows(true);
214 if (columnSelection != null)
216 viewport.setColumnSelection(columnSelection);
219 alignPanel = new AlignmentPanel(this, viewport);
220 avc = new jalview.controller.AlignViewController(this, viewport,
222 viewport.updateConservation(alignPanel);
223 viewport.updateConsensus(alignPanel);
225 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
226 followMouseOverFlag.setState(viewport.isFollowHighlight());
227 showGroupConsensus.setState(viewport.isShowGroupConsensus());
228 showGroupConservation.setState(viewport.isShowGroupConservation());
229 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
230 showSequenceLogo.setState(viewport.isShowSequenceLogo());
231 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
232 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
233 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
234 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
235 showSequenceAnnotations.setState(viewport.isShowAnnotation());
237 seqLimits.setState(viewport.getShowJVSuffix());
241 String param = applet.getParameter("sortBy");
244 if (param.equalsIgnoreCase("Id"))
246 sortIDMenuItem_actionPerformed();
248 else if (param.equalsIgnoreCase("Pairwise Identity"))
250 sortPairwiseMenuItem_actionPerformed();
252 else if (param.equalsIgnoreCase("Length"))
254 sortLengthMenuItem_actionPerformed();
258 param = applet.getParameter("wrap");
261 if (param.equalsIgnoreCase("true"))
263 wrapMenuItem.setState(true);
264 wrapMenuItem_actionPerformed();
267 param = applet.getParameter("centrecolumnlabels");
270 centreColumnLabelFlag.setState(true);
271 centreColumnLabelFlag_stateChanged();
275 if (viewport.getAlignment().isNucleotide())
277 viewport.updateStrucConsensus(alignPanel);
278 if (viewport.getAlignment().hasRNAStructure())
280 RNAHelixColour.setEnabled(true);
284 RNAHelixColour.setEnabled(false);
289 RNAHelixColour.setEnabled(false);
290 purinePyrimidineColour.setEnabled(false);
292 // Some JVMS send keyevents to Top frame or lowest panel,
293 // Havent worked out why yet. So add to both this frame and seqCanvas for
295 this.addKeyListener(this);
296 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
297 alignPanel.idPanel.idCanvas.addKeyListener(this);
298 alignPanel.scalePanel.addKeyListener(this);
299 alignPanel.annotationPanel.addKeyListener(this);
300 alignPanel.annotationPanelHolder.addKeyListener(this);
301 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
302 alignPanel.alabels.addKeyListener(this);
306 addToDisplay(embedded);
313 public void addToDisplay(boolean embedded)
315 createAlignFrameWindow(embedded);
317 alignPanel.adjustAnnotationHeight();
318 alignPanel.paintAlignment(true);
321 public AlignViewport getAlignViewport()
326 public SeqCanvas getSeqcanvas()
328 return alignPanel.seqPanel.seqCanvas;
332 * Load a features file onto the alignment
335 * file URL, content, or other resolvable path
337 * is protocol for accessing data referred to by file
340 public boolean parseFeaturesFile(String file, String type)
342 return parseFeaturesFile(file, type, true);
346 * Load a features file onto the alignment
349 * file URL, content, or other resolvable path
351 * is protocol for accessing data referred to by file
352 * @param autoenabledisplay
353 * when true, display features flag will be automatically enabled if
354 * features are loaded
355 * @return true if data parsed as a features file
357 public boolean parseFeaturesFile(String file, String type,
358 boolean autoenabledisplay)
360 // TODO: test if importing a features file onto an alignment which already
361 // has features with links overwrites the original links.
363 Hashtable featureLinks = new Hashtable();
364 boolean featuresFile = false;
367 featuresFile = new jalview.io.FeaturesFile(file, type)
368 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
369 .getFeatureRenderer().getFeatureColours(), featureLinks,
370 true, viewport.applet.getDefaultParameter(
371 "relaxedidmatch", false));
372 } catch (Exception ex)
374 ex.printStackTrace();
379 if (featureLinks.size() > 0)
381 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
383 if (autoenabledisplay)
385 viewport.setShowSequenceFeatures(true);
386 sequenceFeatures.setState(true);
388 if (alignPanel.seqPanel.seqCanvas.fr != null)
390 // update the min/max ranges where necessary
391 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
393 if (viewport.featureSettings != null)
395 viewport.featureSettings.refreshTable();
397 alignPanel.paintAlignment(true);
398 statusBar.setText(MessageManager
399 .getString("label.successfully_added_features_alignment"));
405 public void keyPressed(KeyEvent evt)
407 if (viewport.cursorMode
408 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
409 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
410 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
411 && Character.isDigit(evt.getKeyChar()))
413 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
416 switch (evt.getKeyCode())
418 case 27: // escape key
419 deselectAllSequenceMenuItem_actionPerformed();
421 alignPanel.alabels.cancelDrag();
424 if (evt.isControlDown() || evt.isMetaDown())
426 cut_actionPerformed();
430 if (viewport.cursorMode && !evt.isControlDown())
432 alignPanel.seqPanel.setCursorColumn();
434 if (evt.isControlDown() || evt.isMetaDown())
436 copy_actionPerformed();
440 if (evt.isControlDown())
442 paste(evt.isShiftDown());
446 if (evt.isControlDown() || evt.isMetaDown())
448 selectAllSequenceMenuItem_actionPerformed();
451 case KeyEvent.VK_DOWN:
452 if (viewport.cursorMode)
454 alignPanel.seqPanel.moveCursor(0, 1);
458 moveSelectedSequences(false);
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.moveCursor(0, -1);
469 moveSelectedSequences(true);
473 case KeyEvent.VK_LEFT:
474 if (evt.isAltDown() || !viewport.cursorMode)
476 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
480 alignPanel.seqPanel.moveCursor(-1, 0);
484 case KeyEvent.VK_RIGHT:
485 if (evt.isAltDown() || !viewport.cursorMode)
487 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
491 alignPanel.seqPanel.moveCursor(1, 0);
495 case KeyEvent.VK_SPACE:
496 if (viewport.cursorMode)
498 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
499 || evt.isShiftDown() || evt.isAltDown());
503 case KeyEvent.VK_DELETE:
504 case KeyEvent.VK_BACK_SPACE:
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
508 || evt.isShiftDown() || evt.isAltDown());
512 cut_actionPerformed();
513 alignPanel.seqPanel.seqCanvas.repaint();
518 if (viewport.cursorMode)
520 alignPanel.seqPanel.setCursorRow();
524 if (viewport.cursorMode)
526 alignPanel.seqPanel.setCursorPosition();
530 case KeyEvent.VK_ENTER:
531 case KeyEvent.VK_COMMA:
532 if (viewport.cursorMode)
534 alignPanel.seqPanel.setCursorRowAndColumn();
539 if (viewport.cursorMode)
541 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
545 if (viewport.cursorMode)
547 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
552 viewport.cursorMode = !viewport.cursorMode;
553 statusBar.setText(MessageManager.formatMessage(
554 "label.keyboard_editing_mode", new String[]
555 { (viewport.cursorMode ? "on" : "off") }));
556 if (viewport.cursorMode)
558 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
559 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
564 if (evt.isControlDown())
566 findMenuItem_actionPerformed();
572 boolean toggleSeqs = !evt.isControlDown();
573 boolean toggleCols = !evt.isShiftDown();
574 toggleHiddenRegions(toggleSeqs, toggleCols);
578 case KeyEvent.VK_PAGE_UP:
579 if (viewport.getWrapAlignment())
581 alignPanel.scrollUp(true);
585 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
586 - viewport.endSeq + viewport.startSeq);
590 case KeyEvent.VK_PAGE_DOWN:
591 if (viewport.getWrapAlignment())
593 alignPanel.scrollUp(false);
597 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
598 + viewport.endSeq - viewport.startSeq);
603 if (evt.isControlDown())
605 undoMenuItem_actionPerformed();
610 if (evt.isControlDown())
612 redoMenuItem_actionPerformed();
617 if (evt.isControlDown())
624 if (evt.isControlDown())
626 trimAlignment(false);
631 if (evt.isControlDown())
633 if (evt.isShiftDown())
635 this.removeAllGapsMenuItem_actionPerformed();
639 removeGappedColumnMenuItem_actionPerformed();
644 if (evt.isControlDown())
648 invertColSel_actionPerformed();
652 invertSequenceMenuItem_actionPerformed();
658 if (evt.isControlDown())
660 if (evt.isShiftDown())
662 this.unGroup_actionPerformed();
666 this.createGroup_actionPerformed();
672 if (evt.isControlDown())
674 this.deleteGroups_actionPerformed();
679 if (evt.isControlDown())
686 alignPanel.paintAlignment(true);
690 * called by key handler and the hide all/show all menu items
695 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
697 boolean hide = false;
698 SequenceGroup sg = viewport.getSelectionGroup();
699 if (!toggleSeqs && !toggleCols)
701 // Hide everything by the current selection - this is a hack - we do the
702 // invert and then hide
703 // first check that there will be visible columns after the invert.
704 if ((viewport.getColumnSelection() != null
705 && viewport.getColumnSelection().getSelected() != null && viewport
706 .getColumnSelection().getSelected().size() > 0)
707 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
710 // now invert the sequence set, if required - empty selection implies
711 // that no hiding is required.
714 invertSequenceMenuItem_actionPerformed();
715 sg = viewport.getSelectionGroup();
719 viewport.expandColSelection(sg, true);
720 // finally invert the column selection and get the new sequence
721 // selection and indicate it should be hidden.
722 invertColSel_actionPerformed();
729 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
732 viewport.hideAllSelectedSeqs();
734 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
737 viewport.showAllHiddenSeqs();
743 if (viewport.getColumnSelection().getSelected().size() > 0)
745 viewport.hideSelectedColumns();
748 viewport.setSelectionGroup(sg);
753 viewport.showAllHiddenColumns();
759 public void keyReleased(KeyEvent evt)
764 public void keyTyped(KeyEvent evt)
769 public void itemStateChanged(ItemEvent evt)
771 final Object source = evt.getSource();
772 if (source == displayNonconservedMenuItem)
774 displayNonconservedMenuItem_actionPerformed();
776 else if (source == colourTextMenuItem)
778 colourTextMenuItem_actionPerformed();
780 else if (source == wrapMenuItem)
782 wrapMenuItem_actionPerformed();
784 else if (source == scaleAbove)
786 viewport.setScaleAboveWrapped(scaleAbove.getState());
788 else if (source == scaleLeft)
790 viewport.setScaleLeftWrapped(scaleLeft.getState());
792 else if (source == scaleRight)
794 viewport.setScaleRightWrapped(scaleRight.getState());
796 else if (source == seqLimits)
798 seqLimits_itemStateChanged();
800 else if (source == viewBoxesMenuItem)
802 viewport.setShowBoxes(viewBoxesMenuItem.getState());
804 else if (source == viewTextMenuItem)
806 viewport.setShowText(viewTextMenuItem.getState());
808 else if (source == renderGapsMenuItem)
810 viewport.setRenderGaps(renderGapsMenuItem.getState());
812 else if (source == annotationPanelMenuItem)
814 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
815 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
817 else if (source == sequenceFeatures)
819 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
820 alignPanel.seqPanel.seqCanvas.repaint();
822 else if (source == showAlignmentAnnotations)
824 setAnnotationsVisibility();
826 else if (source == showSequenceAnnotations)
828 setAnnotationsVisibility();
830 else if (source == sortAnnBySequence)
832 boolean newState = sortAnnBySequence.getState();
833 sortAnnByLabel.setState(false);
834 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
835 : SequenceAnnotationOrder.NONE);
836 setViewportAnnotationOrder();
838 else if (source == sortAnnByLabel)
840 boolean newState = sortAnnByLabel.getState();
841 sortAnnBySequence.setState(false);
842 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
843 : SequenceAnnotationOrder.NONE);
844 setViewportAnnotationOrder();
846 else if (source == showAutoFirst)
848 showAutoLast.setState(!showAutoFirst.getState());
849 setShowAutoCalculatedAbove(showAutoFirst.getState());
850 setViewportAnnotationOrder();
852 else if (source == showAutoLast)
854 showAutoFirst.setState(!showAutoLast.getState());
855 setShowAutoCalculatedAbove(showAutoFirst.getState());
856 setViewportAnnotationOrder();
858 else if (source == conservationMenuItem)
860 conservationMenuItem_actionPerformed();
862 else if (source == abovePIDThreshold)
864 abovePIDThreshold_actionPerformed();
866 else if (source == applyToAllGroups)
868 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
870 else if (source == autoCalculate)
872 viewport.autoCalculateConsensus = autoCalculate.getState();
874 else if (source == sortByTree)
876 viewport.sortByTree = sortByTree.getState();
878 else if (source == this.centreColumnLabelFlag)
880 centreColumnLabelFlag_stateChanged();
882 else if (source == this.followMouseOverFlag)
884 mouseOverFlag_stateChanged();
886 else if (source == showGroupConsensus)
888 showGroupConsensus_actionPerformed();
890 else if (source == showGroupConservation)
892 showGroupConservation_actionPerformed();
894 else if (source == showSequenceLogo)
896 showSequenceLogo_actionPerformed();
898 else if (source == normSequenceLogo)
900 normSequenceLogo_actionPerformed();
902 else if (source == showConsensusHistogram)
904 showConsensusHistogram_actionPerformed();
906 else if (source == applyAutoAnnotationSettings)
908 applyAutoAnnotationSettings_actionPerformed();
910 alignPanel.paintAlignment(true);
914 * Set the visibility state of sequence-related and/or alignment-related
915 * annotations depending on checkbox selections. Repaint after calling.
919 private void setAnnotationsVisibility()
921 boolean showForAlignment = showAlignmentAnnotations.getState();
922 boolean showForSequences = showSequenceAnnotations.getState();
923 for (AlignmentAnnotation aa : alignPanel.getAlignment()
924 .getAlignmentAnnotation())
926 boolean visible = (aa.sequenceRef == null ? showForAlignment
928 aa.visible = visible;
930 alignPanel.validateAnnotationDimensions(false);
933 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
935 this.annotationSortOrder = order;
939 * Set flags on the viewport that control annotation ordering
941 private void setViewportAnnotationOrder()
943 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
945 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
948 private void setShowAutoCalculatedAbove(boolean showAbove)
950 this.showAutoCalculatedAbove = showAbove;
953 private void mouseOverFlag_stateChanged()
955 viewport.setFollowHighlight(followMouseOverFlag.getState());
956 // TODO: could kick the scrollTo mechanism to reset view for current
960 private void centreColumnLabelFlag_stateChanged()
962 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
963 this.alignPanel.annotationPanel.repaint();
967 public void actionPerformed(ActionEvent evt)
969 Object source = evt.getSource();
971 if (source == inputText)
973 inputText_actionPerformed();
975 else if (source == loadTree)
977 loadTree_actionPerformed();
979 else if (source == loadApplication)
981 launchFullApplication();
983 else if (source == loadAnnotations)
987 else if (source == outputAnnotations)
989 outputAnnotations(true);
991 else if (source == outputFeatures)
993 outputFeatures(true, "Jalview");
995 else if (source == closeMenuItem)
997 closeMenuItem_actionPerformed();
999 else if (source == copy)
1001 copy_actionPerformed();
1003 else if (source == undoMenuItem)
1005 undoMenuItem_actionPerformed();
1007 else if (source == redoMenuItem)
1009 redoMenuItem_actionPerformed();
1011 else if (source == inputText)
1013 inputText_actionPerformed();
1015 else if (source == closeMenuItem)
1017 closeMenuItem_actionPerformed();
1019 else if (source == undoMenuItem)
1021 undoMenuItem_actionPerformed();
1023 else if (source == redoMenuItem)
1025 redoMenuItem_actionPerformed();
1027 else if (source == copy)
1029 copy_actionPerformed();
1031 else if (source == pasteNew)
1033 pasteNew_actionPerformed();
1035 else if (source == pasteThis)
1037 pasteThis_actionPerformed();
1039 else if (source == cut)
1041 cut_actionPerformed();
1043 else if (source == delete)
1045 delete_actionPerformed();
1047 else if (source == grpsFromSelection)
1049 makeGrpsFromSelection_actionPerformed();
1051 else if (source == deleteGroups)
1053 deleteGroups_actionPerformed();
1055 else if (source == selectAllSequenceMenuItem)
1057 selectAllSequenceMenuItem_actionPerformed();
1059 else if (source == deselectAllSequenceMenuItem)
1061 deselectAllSequenceMenuItem_actionPerformed();
1063 else if (source == invertSequenceMenuItem)
1065 invertSequenceMenuItem_actionPerformed();
1067 else if (source == invertColSel)
1069 viewport.invertColumnSelection();
1070 alignPanel.paintAlignment(true);
1072 else if (source == remove2LeftMenuItem)
1074 trimAlignment(true);
1076 else if (source == remove2RightMenuItem)
1078 trimAlignment(false);
1080 else if (source == removeGappedColumnMenuItem)
1082 removeGappedColumnMenuItem_actionPerformed();
1084 else if (source == removeAllGapsMenuItem)
1086 removeAllGapsMenuItem_actionPerformed();
1088 else if (source == findMenuItem)
1090 findMenuItem_actionPerformed();
1092 else if (source == font)
1094 new FontChooser(alignPanel);
1096 else if (source == newView)
1100 else if (source == showColumns)
1102 viewport.showAllHiddenColumns();
1103 alignPanel.paintAlignment(true);
1105 else if (source == showSeqs)
1107 viewport.showAllHiddenSeqs();
1108 alignPanel.paintAlignment(true);
1110 else if (source == hideColumns)
1112 viewport.hideSelectedColumns();
1113 alignPanel.paintAlignment(true);
1115 else if (source == hideSequences
1116 && viewport.getSelectionGroup() != null)
1118 viewport.hideAllSelectedSeqs();
1119 alignPanel.paintAlignment(true);
1121 else if (source == hideAllButSelection)
1123 toggleHiddenRegions(false, false);
1124 alignPanel.paintAlignment(true);
1126 else if (source == hideAllSelection)
1128 SequenceGroup sg = viewport.getSelectionGroup();
1129 viewport.expandColSelection(sg, false);
1130 viewport.hideAllSelectedSeqs();
1131 viewport.hideSelectedColumns();
1132 alignPanel.paintAlignment(true);
1134 else if (source == showAllHidden)
1136 viewport.showAllHiddenColumns();
1137 viewport.showAllHiddenSeqs();
1138 alignPanel.paintAlignment(true);
1140 else if (source == showGroupConsensus)
1142 showGroupConsensus_actionPerformed();
1144 else if (source == showGroupConservation)
1146 showGroupConservation_actionPerformed();
1148 else if (source == showSequenceLogo)
1150 showSequenceLogo_actionPerformed();
1152 else if (source == normSequenceLogo)
1154 normSequenceLogo_actionPerformed();
1156 else if (source == showConsensusHistogram)
1158 showConsensusHistogram_actionPerformed();
1160 else if (source == applyAutoAnnotationSettings)
1162 applyAutoAnnotationSettings_actionPerformed();
1164 else if (source == featureSettings)
1166 new FeatureSettings(alignPanel);
1168 else if (source == alProperties)
1170 StringBuffer contents = new jalview.io.AlignmentProperties(
1171 viewport.getAlignment()).formatAsString();
1172 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1173 cap.setText(contents.toString());
1174 Frame frame = new Frame();
1176 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1177 "label.alignment_properties", new String[]
1178 { getTitle() }), 400, 250);
1180 else if (source == overviewMenuItem)
1182 overviewMenuItem_actionPerformed();
1184 else if (source == noColourmenuItem)
1188 else if (source == clustalColour)
1190 abovePIDThreshold.setState(false);
1191 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1193 else if (source == zappoColour)
1195 changeColour(new ZappoColourScheme());
1197 else if (source == taylorColour)
1199 changeColour(new TaylorColourScheme());
1201 else if (source == hydrophobicityColour)
1203 changeColour(new HydrophobicColourScheme());
1205 else if (source == helixColour)
1207 changeColour(new HelixColourScheme());
1209 else if (source == strandColour)
1211 changeColour(new StrandColourScheme());
1213 else if (source == turnColour)
1215 changeColour(new TurnColourScheme());
1217 else if (source == buriedColour)
1219 changeColour(new BuriedColourScheme());
1221 else if (source == nucleotideColour)
1223 changeColour(new NucleotideColourScheme());
1225 else if (source == purinePyrimidineColour)
1227 changeColour(new PurinePyrimidineColourScheme());
1229 else if (source == RNAInteractionColour)
1231 changeColour(new RNAInteractionColourScheme());
1233 else if (source == RNAHelixColour)
1235 new RNAHelicesColourChooser(viewport, alignPanel);
1237 else if (source == modifyPID)
1239 modifyPID_actionPerformed();
1241 else if (source == modifyConservation)
1243 modifyConservation_actionPerformed();
1245 else if (source == userDefinedColour)
1247 new UserDefinedColours(alignPanel, null);
1249 else if (source == PIDColour)
1251 changeColour(new PIDColourScheme());
1253 else if (source == BLOSUM62Colour)
1255 changeColour(new Blosum62ColourScheme());
1257 else if (source == tcoffeeColour)
1259 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1261 else if (source == annotationColour)
1263 new AnnotationColourChooser(viewport, alignPanel);
1265 else if (source == annotationColumnSelection)
1267 new AnnotationColumnChooser(viewport, alignPanel);
1269 else if (source == sortPairwiseMenuItem)
1271 sortPairwiseMenuItem_actionPerformed();
1273 else if (source == sortIDMenuItem)
1275 sortIDMenuItem_actionPerformed();
1277 else if (source == sortLengthMenuItem)
1279 sortLengthMenuItem_actionPerformed();
1281 else if (source == sortGroupMenuItem)
1283 sortGroupMenuItem_actionPerformed();
1285 else if (source == removeRedundancyMenuItem)
1287 removeRedundancyMenuItem_actionPerformed();
1289 else if (source == pairwiseAlignmentMenuItem)
1291 pairwiseAlignmentMenuItem_actionPerformed();
1293 else if (source == PCAMenuItem)
1295 PCAMenuItem_actionPerformed();
1297 else if (source == averageDistanceTreeMenuItem)
1299 averageDistanceTreeMenuItem_actionPerformed();
1301 else if (source == neighbourTreeMenuItem)
1303 neighbourTreeMenuItem_actionPerformed();
1305 else if (source == njTreeBlosumMenuItem)
1307 njTreeBlosumMenuItem_actionPerformed();
1309 else if (source == avDistanceTreeBlosumMenuItem)
1311 avTreeBlosumMenuItem_actionPerformed();
1313 else if (source == documentation)
1315 documentation_actionPerformed();
1317 else if (source == about)
1319 about_actionPerformed();
1324 public void inputText_actionPerformed()
1326 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1327 Frame frame = new Frame();
1329 jalview.bin.JalviewLite.addFrame(frame,
1330 MessageManager.getString("label.input_cut_paste"), 500, 500);
1333 protected void outputText_actionPerformed(ActionEvent e)
1335 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1336 Frame frame = new Frame();
1338 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1339 "label.alignment_output_command", new Object[]
1340 { e.getActionCommand() }), 600, 500);
1342 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1343 viewport.setFeatureRenderer(fr);
1344 viewport.setIncludeHiddenRegion(false);
1345 cap.setText(new AppletFormatAdapter(viewport).formatSequences(
1346 e.getActionCommand(), viewport.getAlignment(),
1347 viewport.getShowJVSuffix()));
1350 public void loadAnnotations()
1352 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1353 cap.setText(MessageManager
1354 .getString("label.paste_features_annotations_Tcoffee_here"));
1355 cap.setAnnotationImport();
1356 Frame frame = new Frame();
1358 jalview.bin.JalviewLite.addFrame(frame,
1359 MessageManager.getString("action.paste_annotations"), 400, 300);
1363 public String outputAnnotations(boolean displayTextbox)
1365 String annotation = new AnnotationFile()
1366 .printAnnotationsForView(viewport);
1370 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1371 Frame frame = new Frame();
1373 jalview.bin.JalviewLite.addFrame(frame,
1374 MessageManager.getString("label.annotations"), 600, 500);
1375 cap.setText(annotation);
1381 private Map<String,Object> getDisplayedFeatureCols()
1383 if (alignPanel.getFeatureRenderer() != null
1384 && viewport.getFeaturesDisplayed()!= null)
1386 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1392 public String outputFeatures(boolean displayTextbox, String format)
1395 if (format.equalsIgnoreCase("Jalview"))
1397 features = new FeaturesFile().printJalviewFormat(viewport
1398 .getAlignment().getSequencesArray(),
1399 getDisplayedFeatureCols());
1403 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1404 .getSequencesArray(), getDisplayedFeatureCols());
1409 boolean frimport = false;
1410 if (features == null || features.equals("No Features Visible"))
1412 features = "# No features visible - paste some and import them here.";
1416 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1419 cap.setAnnotationImport();
1421 Frame frame = new Frame();
1423 jalview.bin.JalviewLite.addFrame(frame,
1424 MessageManager.getString("label.features"), 600, 500);
1425 cap.setText(features);
1429 if (features == null)
1438 void launchFullApplication()
1440 StringBuffer url = new StringBuffer(jalviewServletURL);
1442 // allow servlet parameters to be passed in applet parameter
1443 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1445 url.append(firstSep);
1448 + appendProtocol(viewport.applet.getParameter("file")));
1450 if (viewport.applet.getParameter("features") != null)
1452 url.append("&features=");
1453 url.append(appendProtocol(viewport.applet.getParameter("features")));
1456 if (viewport.applet.getParameter("annotations") != null)
1458 url.append("&annotations=");
1459 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1462 if (viewport.applet.getParameter("jnetfile") != null)
1464 url.append("&annotations=");
1465 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1468 if (viewport.applet.getParameter("defaultColour") != null)
1470 url.append("&colour="
1471 + removeWhiteSpace(viewport.applet
1472 .getParameter("defaultColour")));
1475 if (viewport.applet.getParameter("userDefinedColour") != null)
1477 url.append("&colour="
1478 + removeWhiteSpace(viewport.applet
1479 .getParameter("userDefinedColour")));
1481 if (viewport.applet.getParameter("tree") != null)
1484 + appendProtocol(viewport.applet.getParameter("tree")));
1486 if (viewport.applet.getParameter("treeFile") != null)
1489 + appendProtocol(viewport.applet.getParameter("treeFile")));
1492 showURL(url.toString(), "FULL_APP");
1495 String removeWhiteSpace(String colour)
1497 StringBuffer sb = new StringBuffer();
1498 for (int i = 0; i < colour.length(); i++)
1500 if (Character.isWhitespace(colour.charAt(i)))
1506 sb.append(colour.charAt(i));
1510 return sb.toString();
1513 String appendProtocol(String url)
1518 url = URLEncoder.encode(url);
1521 * When we finally deprecate 1.1 compatibility, we can start to use
1522 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1523 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1524 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1525 * ex.printStackTrace(); }
1527 catch (java.net.MalformedURLException ex)
1529 url = viewport.applet.getCodeBase() + url;
1534 public void closeMenuItem_actionPerformed()
1536 PaintRefresher.RemoveComponent(alignPanel);
1537 if (alignPanel.seqPanel != null
1538 && alignPanel.seqPanel.seqCanvas != null)
1540 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1542 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1544 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1547 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1562 void updateEditMenuBar()
1565 if (viewport.getHistoryList().size() > 0)
1567 undoMenuItem.setEnabled(true);
1568 CommandI command = viewport.getHistoryList().peek();
1569 undoMenuItem.setLabel(MessageManager.formatMessage(
1570 "label.undo_command", new Object[]
1571 { command.getDescription() }));
1575 undoMenuItem.setEnabled(false);
1576 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1579 if (viewport.getRedoList().size() > 0)
1581 redoMenuItem.setEnabled(true);
1583 CommandI command = viewport.getRedoList().peek();
1584 redoMenuItem.setLabel(MessageManager.formatMessage(
1585 "label.redo_command", new Object[]
1586 { command.getDescription() }));
1590 redoMenuItem.setEnabled(false);
1591 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1599 public void addHistoryItem(CommandI command)
1601 if (command.getSize() > 0)
1603 viewport.addToHistoryList(command);
1604 viewport.clearRedoList();
1605 updateEditMenuBar();
1606 viewport.updateHiddenColumns();
1611 * TODO: JAL-1104 DOCUMENT ME!
1616 protected void undoMenuItem_actionPerformed()
1618 if (viewport.getHistoryList().isEmpty())
1623 CommandI command = viewport.getHistoryList().pop();
1624 viewport.addToRedoList(command);
1625 command.undoCommand(null);
1627 AlignmentViewport originalSource = getOriginatingSource(command);
1629 if (originalSource != viewport)
1632 .println("Warning: Viewport object mismatch whilst undoing");
1634 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1635 // viewport.getColumnSelection().getHiddenColumns()
1637 updateEditMenuBar();
1638 originalSource.firePropertyChange("alignment", null, originalSource
1639 .getAlignment().getSequences());
1643 * TODO: JAL-1104 DOCUMENT ME!
1648 protected void redoMenuItem_actionPerformed()
1650 if (viewport.getRedoList().isEmpty())
1655 CommandI command = viewport.getRedoList().pop();
1656 viewport.addToHistoryList(command);
1657 command.doCommand(null);
1659 AlignmentViewport originalSource = getOriginatingSource(command);
1661 if (originalSource != viewport)
1664 .println("Warning: Viewport object mismatch whilst re-doing");
1666 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1667 // viewport.getColumnSelection().getHiddenColumns()
1670 updateEditMenuBar();
1671 originalSource.firePropertyChange("alignment", null, originalSource
1672 .getAlignment().getSequences());
1675 AlignmentViewport getOriginatingSource(CommandI command)
1677 AlignmentViewport originalSource = null;
1678 // For sequence removal and addition, we need to fire
1679 // the property change event FROM the viewport where the
1680 // original alignment was altered
1681 AlignmentI al = null;
1682 if (command instanceof EditCommand)
1684 EditCommand editCommand = (EditCommand) command;
1685 al = editCommand.getAlignment();
1686 Vector comps = (Vector) PaintRefresher.components.get(viewport
1687 .getSequenceSetId());
1688 for (int i = 0; i < comps.size(); i++)
1690 if (comps.elementAt(i) instanceof AlignmentPanel)
1692 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1694 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1701 if (originalSource == null)
1703 // The original view is closed, we must validate
1704 // the current view against the closed view first
1707 PaintRefresher.validateSequences(al, viewport.getAlignment());
1710 originalSource = viewport;
1713 return originalSource;
1717 * Move the currently selected sequences up or down one position in the
1722 public void moveSelectedSequences(boolean up)
1724 SequenceGroup sg = viewport.getSelectionGroup();
1729 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1730 up ? null : viewport.getHiddenRepSequences(), up);
1731 alignPanel.paintAlignment(true);
1734 * Also move cDNA/protein complement sequences
1736 AlignViewportI complement = viewport.getCodingComplement();
1737 if (complement != null)
1739 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1740 viewport, complement);
1741 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1742 up ? null : complement.getHiddenRepSequences(), up);
1743 // TODO need to trigger a repaint of the complementary panel - how?
1744 // would prefer to handle in SplitFrame but it is not overriding key
1749 synchronized void slideSequences(boolean right, int size)
1751 List<SequenceI> sg = new Vector<SequenceI>();
1752 if (viewport.cursorMode)
1754 sg.add(viewport.getAlignment().getSequenceAt(
1755 alignPanel.seqPanel.seqCanvas.cursorY));
1757 else if (viewport.getSelectionGroup() != null
1758 && viewport.getSelectionGroup().getSize() != viewport
1759 .getAlignment().getHeight())
1761 sg = viewport.getSelectionGroup().getSequences(
1762 viewport.getHiddenRepSequences());
1770 Vector<SequenceI> invertGroup = new Vector();
1772 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1774 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1776 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1780 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1782 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1784 for (int i = 0; i < invertGroup.size(); i++)
1786 seqs2[i] = invertGroup.elementAt(i);
1789 SlideSequencesCommand ssc;
1792 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1793 size, viewport.getGapCharacter());
1797 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1798 size, viewport.getGapCharacter());
1801 int groupAdjustment = 0;
1802 if (ssc.getGapsInsertedBegin() && right)
1804 if (viewport.cursorMode)
1806 alignPanel.seqPanel.moveCursor(size, 0);
1810 groupAdjustment = size;
1813 else if (!ssc.getGapsInsertedBegin() && !right)
1815 if (viewport.cursorMode)
1817 alignPanel.seqPanel.moveCursor(-size, 0);
1821 groupAdjustment = -size;
1825 if (groupAdjustment != 0)
1827 viewport.getSelectionGroup().setStartRes(
1828 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1829 viewport.getSelectionGroup().setEndRes(
1830 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1833 boolean appendHistoryItem = false;
1834 Deque<CommandI> historyList = viewport.getHistoryList();
1835 if (historyList != null && historyList.size() > 0
1836 && historyList.peek() instanceof SlideSequencesCommand)
1838 appendHistoryItem = ssc
1839 .appendSlideCommand((SlideSequencesCommand) historyList
1843 if (!appendHistoryItem)
1845 addHistoryItem(ssc);
1851 static StringBuffer copiedSequences;
1853 static Vector copiedHiddenColumns;
1855 protected void copy_actionPerformed()
1857 if (viewport.getSelectionGroup() == null)
1862 SequenceGroup sg = viewport.getSelectionGroup();
1863 copiedSequences = new StringBuffer();
1864 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1865 for (int i = 0; i < sg.getSize(); i++)
1867 SequenceI seq = sg.getSequenceAt(i);
1868 int index = viewport.getAlignment().findIndex(seq);
1869 orderedSeqs.put(index, seq);
1872 int index = 0, startRes, endRes;
1875 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1877 copiedHiddenColumns = new Vector();
1878 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1879 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1881 copiedHiddenColumns.addElement(new int[]
1882 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1887 copiedHiddenColumns = null;
1890 for (int i = 0; i < sg.getSize(); i++)
1892 SequenceI seq = null;
1896 if (orderedSeqs.containsKey(index))
1898 seq = orderedSeqs.get(index);
1909 // Returns residue following index if gap
1910 startRes = seq.findPosition(sg.getStartRes());
1913 // Need to find the residue preceeding index if gap
1916 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1918 ch = seq.getCharAt(j);
1919 if (!jalview.util.Comparison.isGap((ch)))
1927 endRes += seq.getStart() - 1;
1930 copiedSequences.append(seq.getName()
1936 + seq.getSequenceAsString(sg.getStartRes(),
1937 sg.getEndRes() + 1) + "\n");
1942 protected void pasteNew_actionPerformed()
1947 protected void pasteThis_actionPerformed()
1952 void paste(boolean newAlignment)
1957 if (copiedSequences == null)
1962 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1963 Vector seqs = new Vector();
1964 while (st.hasMoreElements())
1966 String name = st.nextToken();
1967 int start = Integer.parseInt(st.nextToken());
1968 int end = Integer.parseInt(st.nextToken());
1969 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1971 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1972 for (int i = 0; i < seqs.size(); i++)
1974 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1979 String newtitle = MessageManager.getString("label.copied_sequences");
1980 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1982 newtitle = getTitle();
1986 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1988 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1989 viewport.applet, newtitle, false);
1990 if (copiedHiddenColumns != null)
1992 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1994 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1995 af.viewport.hideColumns(region[0], region[1]);
1999 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2004 addSequences(newSeqs);
2007 } catch (Exception ex)
2009 } // could be anything being pasted in here
2013 void addSequences(SequenceI[] seqs)
2015 for (int i = 0; i < seqs.length; i++)
2017 viewport.getAlignment().addSequence(seqs[i]);
2021 addHistoryItem(new EditCommand(
2022 MessageManager.getString("label.add_sequences"), Action.PASTE,
2023 seqs, 0, viewport.getAlignment().getWidth(),
2024 viewport.getAlignment()));
2026 viewport.setEndSeq(viewport.getAlignment().getHeight());
2027 viewport.getAlignment().getWidth();
2028 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2033 protected void cut_actionPerformed()
2035 copy_actionPerformed();
2036 delete_actionPerformed();
2039 protected void delete_actionPerformed()
2042 SequenceGroup sg = viewport.getSelectionGroup();
2048 Vector seqs = new Vector();
2050 for (int i = 0; i < sg.getSize(); i++)
2052 seq = sg.getSequenceAt(i);
2053 seqs.addElement(seq);
2056 // If the cut affects all sequences, remove highlighted columns
2057 if (sg.getSize() == viewport.getAlignment().getHeight())
2059 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2060 sg.getEndRes() + 1);
2063 SequenceI[] cut = new SequenceI[seqs.size()];
2064 for (int i = 0; i < seqs.size(); i++)
2066 cut[i] = (SequenceI) seqs.elementAt(i);
2070 * //ADD HISTORY ITEM
2072 addHistoryItem(new EditCommand(
2073 MessageManager.getString("label.cut_sequences"), Action.CUT,
2074 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2075 viewport.getAlignment()));
2077 viewport.setSelectionGroup(null);
2078 viewport.getAlignment().deleteGroup(sg);
2080 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2083 if (viewport.getAlignment().getHeight() < 1)
2085 this.setVisible(false);
2087 viewport.sendSelection();
2091 * group consensus toggled
2094 protected void showGroupConsensus_actionPerformed()
2096 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2097 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2102 * group conservation toggled.
2104 protected void showGroupConservation_actionPerformed()
2106 viewport.setShowGroupConservation(showGroupConservation.getState());
2107 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2114 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2115 * .event.ActionEvent)
2117 protected void showConsensusHistogram_actionPerformed()
2119 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2120 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2127 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2128 * .event.ActionEvent)
2130 protected void showSequenceLogo_actionPerformed()
2132 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2133 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2136 protected void normSequenceLogo_actionPerformed()
2138 showSequenceLogo.setState(true);
2139 viewport.setShowSequenceLogo(true);
2140 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2141 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2144 protected void applyAutoAnnotationSettings_actionPerformed()
2146 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2149 protected void makeGrpsFromSelection_actionPerformed()
2151 if (avc.makeGroupsFromSelection())
2153 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2154 alignPanel.updateAnnotation();
2155 alignPanel.paintAlignment(true);
2159 protected void createGroup_actionPerformed()
2164 protected void unGroup_actionPerformed()
2168 alignPanel.alignmentChanged();
2172 protected void deleteGroups_actionPerformed()
2174 if (avc.deleteGroups())
2176 alignPanel.alignmentChanged();
2180 public void selectAllSequenceMenuItem_actionPerformed()
2182 SequenceGroup sg = new SequenceGroup();
2183 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2185 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2187 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2188 viewport.setSelectionGroup(sg);
2189 alignPanel.paintAlignment(true);
2190 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2191 viewport.sendSelection();
2194 public void deselectAllSequenceMenuItem_actionPerformed()
2196 if (viewport.cursorMode)
2198 alignPanel.seqPanel.keyboardNo1 = null;
2199 alignPanel.seqPanel.keyboardNo2 = null;
2201 viewport.setSelectionGroup(null);
2202 viewport.getColumnSelection().clear();
2203 viewport.setSelectionGroup(null);
2204 alignPanel.idPanel.idCanvas.searchResults = null;
2205 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2206 alignPanel.paintAlignment(true);
2207 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2208 viewport.sendSelection();
2211 public void invertSequenceMenuItem_actionPerformed()
2213 SequenceGroup sg = viewport.getSelectionGroup();
2214 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2216 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2219 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2220 viewport.sendSelection();
2223 public void invertColSel_actionPerformed()
2225 viewport.invertColumnSelection();
2226 alignPanel.paintAlignment(true);
2227 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2228 viewport.sendSelection();
2231 void trimAlignment(boolean trimLeft)
2233 ColumnSelection colSel = viewport.getColumnSelection();
2236 if (colSel.size() > 0)
2240 column = colSel.getMin();
2244 column = colSel.getMax();
2248 if (viewport.getSelectionGroup() != null)
2250 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2251 viewport.getHiddenRepSequences());
2255 seqs = viewport.getAlignment().getSequencesArray();
2258 TrimRegionCommand trimRegion;
2261 trimRegion = new TrimRegionCommand("Remove Left",
2262 TrimRegionCommand.TRIM_LEFT, seqs, column,
2263 viewport.getAlignment(), viewport.getColumnSelection(),
2264 viewport.getSelectionGroup());
2265 viewport.setStartRes(0);
2269 trimRegion = new TrimRegionCommand("Remove Right",
2270 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2271 viewport.getAlignment(), viewport.getColumnSelection(),
2272 viewport.getSelectionGroup());
2275 statusBar.setText(MessageManager.formatMessage(
2276 "label.removed_columns", new String[]
2277 { Integer.valueOf(trimRegion.getSize()).toString() }));
2278 addHistoryItem(trimRegion);
2280 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2282 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2283 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2285 viewport.getAlignment().deleteGroup(sg);
2289 viewport.firePropertyChange("alignment", null, viewport
2290 .getAlignment().getSequences());
2294 public void removeGappedColumnMenuItem_actionPerformed()
2296 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2299 if (viewport.getSelectionGroup() != null)
2301 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2302 viewport.getHiddenRepSequences());
2303 start = viewport.getSelectionGroup().getStartRes();
2304 end = viewport.getSelectionGroup().getEndRes();
2308 seqs = viewport.getAlignment().getSequencesArray();
2311 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2312 "Remove Gapped Columns", seqs, start, end,
2313 viewport.getAlignment());
2315 addHistoryItem(removeGapCols);
2317 statusBar.setText(MessageManager.formatMessage(
2318 "label.removed_empty_columns", new String[]
2319 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2321 // This is to maintain viewport position on first residue
2322 // of first sequence
2323 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2324 int startRes = seq.findPosition(viewport.startRes);
2325 // ShiftList shifts;
2326 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2327 // edit.alColumnChanges=shifts.getInverse();
2328 // if (viewport.hasHiddenColumns)
2329 // viewport.getColumnSelection().compensateForEdits(shifts);
2330 viewport.setStartRes(seq.findIndex(startRes) - 1);
2331 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2336 public void removeAllGapsMenuItem_actionPerformed()
2338 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2341 if (viewport.getSelectionGroup() != null)
2343 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2344 viewport.getHiddenRepSequences());
2345 start = viewport.getSelectionGroup().getStartRes();
2346 end = viewport.getSelectionGroup().getEndRes();
2350 seqs = viewport.getAlignment().getSequencesArray();
2353 // This is to maintain viewport position on first residue
2354 // of first sequence
2355 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2356 int startRes = seq.findPosition(viewport.startRes);
2358 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2359 viewport.getAlignment()));
2361 viewport.setStartRes(seq.findIndex(startRes) - 1);
2363 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2368 public void findMenuItem_actionPerformed()
2370 new Finder(alignPanel);
2374 * create a new view derived from the current view
2377 * @return frame for the new view
2379 public AlignFrame newView(String viewtitle)
2382 if (viewport.hasHiddenRows())
2384 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2385 .getFullAlignment().getSequencesArray());
2389 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2392 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2394 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2396 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2398 newal.addAnnotation(viewport.getAlignment()
2399 .getAlignmentAnnotation()[i]);
2404 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2406 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2407 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2408 PaintRefresher.Register(newaf.alignPanel,
2409 newaf.alignPanel.av.getSequenceSetId());
2411 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2412 newaf.alignPanel.av.getSequenceSetId());
2413 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2414 newaf.alignPanel.av.getSequenceSetId());
2416 Vector comps = (Vector) PaintRefresher.components.get(viewport
2417 .getSequenceSetId());
2419 for (int i = 0; i < comps.size(); i++)
2421 if (comps.elementAt(i) instanceof AlignmentPanel)
2427 String title = new String(this.getTitle());
2428 if (viewtitle != null)
2430 title = viewtitle + " ( " + title + ")";
2434 if (title.indexOf("(View") > -1)
2436 title = title.substring(0, title.indexOf("(View"));
2438 title += "(View " + viewSize + ")";
2441 newaf.setTitle(title.toString());
2443 newaf.viewport.setHistoryList(viewport.getHistoryList());
2444 newaf.viewport.setRedoList(viewport.getRedoList());
2450 * @return list of feature groups on the view
2452 public String[] getFeatureGroups()
2454 FeatureRenderer fr = null;
2455 if (alignPanel != null
2456 && (fr = alignPanel.getFeatureRenderer()) != null)
2458 List<String> gps = fr.getFeatureGroups();
2459 String[] _gps = gps.toArray(new String[gps.size()]);
2466 * get sequence feature groups that are hidden or shown
2472 public String[] getFeatureGroupsOfState(boolean visible)
2474 FeatureRenderer fr = null;
2475 if (alignPanel != null
2476 && (fr = alignPanel.getFeatureRenderer()) != null)
2478 List<String> gps = fr.getGroups(visible);
2479 String[] _gps = gps.toArray(new String[gps.size()]);
2486 * Change the display state for the given feature groups
2489 * list of group strings
2491 * visible or invisible
2493 public void setFeatureGroupState(String[] groups, boolean state)
2495 FeatureRenderer fr = null;
2496 this.sequenceFeatures.setState(true);
2497 viewport.setShowSequenceFeatures(true);
2498 if (alignPanel != null
2499 && (fr = alignPanel.getFeatureRenderer()) != null)
2502 fr.setGroupVisibility(Arrays.asList(groups), state);
2503 alignPanel.seqPanel.seqCanvas.repaint();
2504 if (alignPanel.overviewPanel != null)
2506 alignPanel.overviewPanel.updateOverviewImage();
2511 public void seqLimits_itemStateChanged()
2513 viewport.setShowJVSuffix(seqLimits.getState());
2514 alignPanel.fontChanged();
2515 alignPanel.paintAlignment(true);
2518 protected void colourTextMenuItem_actionPerformed()
2520 viewport.setColourText(colourTextMenuItem.getState());
2521 alignPanel.paintAlignment(true);
2524 protected void displayNonconservedMenuItem_actionPerformed()
2526 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2527 alignPanel.paintAlignment(true);
2530 protected void wrapMenuItem_actionPerformed()
2532 viewport.setWrapAlignment(wrapMenuItem.getState());
2533 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2534 scaleAbove.setEnabled(wrapMenuItem.getState());
2535 scaleLeft.setEnabled(wrapMenuItem.getState());
2536 scaleRight.setEnabled(wrapMenuItem.getState());
2537 alignPanel.paintAlignment(true);
2540 public void overviewMenuItem_actionPerformed()
2542 if (alignPanel.overviewPanel != null)
2547 Frame frame = new Frame();
2548 OverviewPanel overview = new OverviewPanel(alignPanel);
2549 frame.add(overview);
2550 // +50 must allow for applet frame window
2551 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2552 "label.overview_params", new String[]
2553 { this.getTitle() }), overview.getPreferredSize().width,
2554 overview.getPreferredSize().height + 50);
2557 final AlignmentPanel ap = alignPanel;
2558 frame.addWindowListener(new WindowAdapter()
2561 public void windowClosing(WindowEvent e)
2565 ap.setOverviewPanel(null);
2570 alignPanel.setOverviewPanel(overview);
2574 public void changeColour(ColourSchemeI cs)
2580 if (viewport.getAbovePIDThreshold())
2582 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2586 if (viewport.getConservationSelected())
2588 cs.setConservationApplied(true);
2589 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2594 cs.setConservationApplied(false);
2597 viewport.setGlobalColourScheme(cs);
2599 if (alignPanel.getOverviewPanel() != null)
2601 alignPanel.getOverviewPanel().updateOverviewImage();
2604 jalview.structure.StructureSelectionManager
2605 .getStructureSelectionManager(viewport.applet)
2606 .sequenceColoursChanged(alignPanel);
2608 alignPanel.paintAlignment(true);
2611 protected void modifyPID_actionPerformed()
2613 if (viewport.getAbovePIDThreshold()
2614 && viewport.getGlobalColourScheme() != null)
2616 SliderPanel.setPIDSliderSource(alignPanel,
2617 viewport.getGlobalColourScheme(), "Background");
2618 SliderPanel.showPIDSlider();
2622 protected void modifyConservation_actionPerformed()
2624 if (viewport.getConservationSelected()
2625 && viewport.getGlobalColourScheme() != null)
2627 SliderPanel.setConservationSlider(alignPanel,
2628 viewport.getGlobalColourScheme(), "Background");
2629 SliderPanel.showConservationSlider();
2633 protected void conservationMenuItem_actionPerformed()
2635 viewport.setConservationSelected(conservationMenuItem.getState());
2637 viewport.setAbovePIDThreshold(false);
2638 abovePIDThreshold.setState(false);
2640 changeColour(viewport.getGlobalColourScheme());
2642 modifyConservation_actionPerformed();
2645 public void abovePIDThreshold_actionPerformed()
2647 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2649 conservationMenuItem.setState(false);
2650 viewport.setConservationSelected(false);
2652 changeColour(viewport.getGlobalColourScheme());
2654 modifyPID_actionPerformed();
2657 public void sortPairwiseMenuItem_actionPerformed()
2659 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2660 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2661 .getAlignment().getSequenceAt(0), null);
2663 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2664 viewport.getAlignment()));
2665 alignPanel.paintAlignment(true);
2668 public void sortIDMenuItem_actionPerformed()
2670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2671 AlignmentSorter.sortByID(viewport.getAlignment());
2672 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2673 viewport.getAlignment()));
2674 alignPanel.paintAlignment(true);
2677 public void sortLengthMenuItem_actionPerformed()
2679 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2680 AlignmentSorter.sortByLength(viewport.getAlignment());
2681 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2682 viewport.getAlignment()));
2683 alignPanel.paintAlignment(true);
2686 public void sortGroupMenuItem_actionPerformed()
2688 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2689 AlignmentSorter.sortByGroup(viewport.getAlignment());
2690 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2691 viewport.getAlignment()));
2692 alignPanel.paintAlignment(true);
2696 public void removeRedundancyMenuItem_actionPerformed()
2698 new RedundancyPanel(alignPanel);
2701 public void pairwiseAlignmentMenuItem_actionPerformed()
2703 if (viewport.getSelectionGroup() != null
2704 && viewport.getSelectionGroup().getSize() > 1)
2706 Frame frame = new Frame();
2707 frame.add(new PairwiseAlignPanel(alignPanel));
2708 jalview.bin.JalviewLite.addFrame(frame,
2709 MessageManager.getString("action.pairwise_alignment"), 600,
2714 public void PCAMenuItem_actionPerformed()
2716 // are the sequences aligned?
2717 if (!viewport.getAlignment().isAligned(false))
2720 int Width = viewport.getAlignment().getWidth();
2722 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2724 current = viewport.getAlignment().getSequenceAt(i);
2726 if (current.getLength() < Width)
2728 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2731 alignPanel.paintAlignment(true);
2734 if ((viewport.getSelectionGroup() != null
2735 && viewport.getSelectionGroup().getSize() < 4 && viewport
2736 .getSelectionGroup().getSize() > 0)
2737 || viewport.getAlignment().getHeight() < 4)
2744 new PCAPanel(viewport);
2745 } catch (java.lang.OutOfMemoryError ex)
2751 public void averageDistanceTreeMenuItem_actionPerformed()
2753 NewTreePanel("AV", "PID", "Average distance tree using PID");
2756 public void neighbourTreeMenuItem_actionPerformed()
2758 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2761 protected void njTreeBlosumMenuItem_actionPerformed()
2763 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2766 protected void avTreeBlosumMenuItem_actionPerformed()
2768 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2771 void NewTreePanel(String type, String pwType, String title)
2773 // are the sequences aligned?
2774 if (!viewport.getAlignment().isAligned(false))
2777 int Width = viewport.getAlignment().getWidth();
2779 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2781 current = viewport.getAlignment().getSequenceAt(i);
2783 if (current.getLength() < Width)
2785 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2788 alignPanel.paintAlignment(true);
2792 if ((viewport.getSelectionGroup() != null && viewport
2793 .getSelectionGroup().getSize() > 1)
2794 || (viewport.getAlignment().getHeight() > 1))
2796 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2798 addTreeMenuItem(tp, title);
2800 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2804 void loadTree_actionPerformed()
2806 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2807 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2808 cap.setTreeImport();
2809 Frame frame = new Frame();
2811 jalview.bin.JalviewLite.addFrame(frame,
2812 MessageManager.getString("label.paste_newick_file"), 400, 300);
2815 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2817 TreePanel tp = new TreePanel(alignPanel, treeFile,
2818 MessageManager.getString("label.load_tree_from_file"), tree);
2819 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2820 addTreeMenuItem(tp, treeFile);
2824 * sort the alignment using the given treePanel
2827 * tree used to sort view
2829 * string used for undo event name
2831 public void sortByTree(TreePanel treePanel, String title)
2833 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2835 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2836 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2837 // HistoryItem.SORT));
2838 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2839 "label.order_by_params", new String[]
2840 { title }), oldOrder, viewport.getAlignment()));
2841 alignPanel.paintAlignment(true);
2845 * Do any automatic reordering of the alignment and add the necessary bits to
2846 * the menu structure for the new tree
2851 protected void addTreeMenuItem(final TreePanel treePanel,
2854 final MenuItem item = new MenuItem(title);
2855 sortByTreeMenu.add(item);
2856 item.addActionListener(new java.awt.event.ActionListener()
2859 public void actionPerformed(ActionEvent evt)
2861 sortByTree(treePanel, title); // treePanel.getTitle());
2865 treePanel.addWindowListener(new WindowAdapter()
2868 public void windowOpened(WindowEvent e)
2870 if (viewport.sortByTree)
2872 sortByTree(treePanel, title);
2874 super.windowOpened(e);
2878 public void windowClosing(WindowEvent e)
2880 sortByTreeMenu.remove(item);
2885 public boolean sortBy(AlignmentOrder alorder, String undoname)
2887 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2888 if (viewport.applet.debug)
2890 System.err.println("Sorting " + alorder.getOrder().size()
2891 + " in alignment '" + getTitle() + "'");
2893 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2894 if (undoname != null)
2896 addHistoryItem(new OrderCommand(undoname, oldOrder,
2897 viewport.getAlignment()));
2899 alignPanel.paintAlignment(true);
2903 protected void documentation_actionPerformed()
2905 alignPanel.av.applet.openJalviewHelpUrl();
2908 protected void about_actionPerformed()
2911 class AboutPanel extends Canvas
2917 public AboutPanel(String version, String builddate)
2919 this.version = version;
2920 this.builddate = builddate;
2924 public void paint(Graphics g)
2926 g.setColor(Color.white);
2927 g.fillRect(0, 0, getSize().width, getSize().height);
2928 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2929 FontMetrics fm = g.getFontMetrics();
2930 int fh = fm.getHeight();
2932 g.setColor(Color.black);
2933 // TODO: update this text for each release or centrally store it for
2934 // lite and application
2935 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2936 g.drawString(MessageManager.formatMessage(
2937 "label.jalviewLite_release", new String[]
2938 { version }), x, y += fh);
2939 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2940 g.drawString(MessageManager.formatMessage(
2941 "label.jaview_build_date", new String[]
2942 { builddate }), x, y += fh);
2943 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2944 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2946 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2947 x + 50, y += fh + 8);
2949 MessageManager.getString("label.jalview_dev_managers"), x,
2951 g.drawString(MessageManager
2952 .getString("label.jalview_distribution_lists"), x, y += fh);
2953 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2956 MessageManager.getString("label.jalview_cite_1_authors"),
2959 MessageManager.getString("label.jalview_cite_1_title"), x,
2961 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2966 Frame frame = new Frame();
2967 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2969 jalview.bin.JalviewLite.addFrame(frame,
2970 MessageManager.getString("label.jalview"), 580, 220);
2974 public void showURL(String url, String target)
2976 if (viewport.applet == null)
2978 System.out.println("Not running as applet - no browser available.");
2982 viewport.applet.showURL(url, target);
2986 // ////////////////////////////////////////////////////////////////////////////////
2987 // JBuilder Graphics here
2989 MenuBar alignFrameMenuBar = new MenuBar();
2991 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2993 MenuItem loadApplication = new MenuItem(
2994 MessageManager.getString("label.view_full_application"));
2996 MenuItem loadTree = new MenuItem(
2997 MessageManager.getString("label.load_associated_tree"));
2999 MenuItem loadAnnotations = new MenuItem(
3000 MessageManager.getString("label.load_features_annotations"));
3002 MenuItem outputFeatures = new MenuItem(
3003 MessageManager.getString("label.export_features").concat("..."));
3005 MenuItem outputAnnotations = new MenuItem(
3006 MessageManager.getString("label.export_annotations").concat("..."));
3008 MenuItem closeMenuItem = new MenuItem(
3009 MessageManager.getString("action.close"));
3011 MenuItem selectAllSequenceMenuItem = new MenuItem(
3012 MessageManager.getString("action.select_all"));
3014 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3015 MessageManager.getString("action.deselect_all"));
3017 MenuItem invertSequenceMenuItem = new MenuItem(
3018 MessageManager.getString("action.invert_selection"));
3020 MenuItem remove2LeftMenuItem = new MenuItem();
3022 MenuItem remove2RightMenuItem = new MenuItem();
3024 MenuItem removeGappedColumnMenuItem = new MenuItem();
3026 MenuItem removeAllGapsMenuItem = new MenuItem();
3028 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3030 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3032 MenuItem sortPairwiseMenuItem = new MenuItem();
3034 MenuItem sortIDMenuItem = new MenuItem();
3036 MenuItem sortLengthMenuItem = new MenuItem();
3038 MenuItem sortGroupMenuItem = new MenuItem();
3040 MenuItem removeRedundancyMenuItem = new MenuItem();
3042 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3044 MenuItem PCAMenuItem = new MenuItem();
3046 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3048 MenuItem neighbourTreeMenuItem = new MenuItem();
3050 BorderLayout borderLayout1 = new BorderLayout();
3052 public Label statusBar = new Label();
3054 MenuItem clustalColour = new MenuItem();
3056 MenuItem zappoColour = new MenuItem();
3058 MenuItem taylorColour = new MenuItem();
3060 MenuItem hydrophobicityColour = new MenuItem();
3062 MenuItem helixColour = new MenuItem();
3064 MenuItem strandColour = new MenuItem();
3066 MenuItem turnColour = new MenuItem();
3068 MenuItem buriedColour = new MenuItem();
3070 MenuItem purinePyrimidineColour = new MenuItem();
3072 MenuItem RNAInteractionColour = new MenuItem();
3074 MenuItem RNAHelixColour = new MenuItem();
3076 MenuItem userDefinedColour = new MenuItem();
3078 MenuItem PIDColour = new MenuItem();
3080 MenuItem BLOSUM62Colour = new MenuItem();
3082 MenuItem tcoffeeColour = new MenuItem();
3084 MenuItem njTreeBlosumMenuItem = new MenuItem();
3086 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3088 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3090 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3092 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3094 MenuItem alProperties = new MenuItem(
3095 MessageManager.getString("label.alignment_props"));
3097 MenuItem overviewMenuItem = new MenuItem();
3099 MenuItem undoMenuItem = new MenuItem();
3101 MenuItem redoMenuItem = new MenuItem();
3103 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3105 MenuItem noColourmenuItem = new MenuItem();
3107 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3109 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3111 MenuItem findMenuItem = new MenuItem();
3113 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3115 MenuItem nucleotideColour = new MenuItem();
3117 MenuItem deleteGroups = new MenuItem();
3119 MenuItem grpsFromSelection = new MenuItem();
3121 MenuItem createGroup = new MenuItem();
3123 MenuItem unGroup = new MenuItem();
3125 MenuItem delete = new MenuItem();
3127 MenuItem copy = new MenuItem();
3129 MenuItem cut = new MenuItem();
3131 Menu pasteMenu = new Menu();
3133 MenuItem pasteNew = new MenuItem();
3135 MenuItem pasteThis = new MenuItem();
3137 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3139 MenuItem font = new MenuItem();
3141 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3143 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3145 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3147 MenuItem modifyPID = new MenuItem();
3149 MenuItem modifyConservation = new MenuItem();
3151 CheckboxMenuItem autoCalculate = null;
3153 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3154 "Sort Alignment With New Tree", true);
3156 Menu sortByTreeMenu = new Menu();
3158 MenuItem inputText = new MenuItem();
3160 MenuItem documentation = new MenuItem();
3162 MenuItem about = new MenuItem();
3164 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3166 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3168 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3170 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3172 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3174 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3176 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3178 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3180 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3183 * Initialise menus and other items
3187 private void jbInit() throws Exception
3189 setMenuBar(alignFrameMenuBar);
3192 * Configure File menu items and actions
3195 .setLabel(MessageManager.getString("label.input_from_textbox"));
3196 inputText.addActionListener(this);
3197 Menu outputTextboxMenu = new Menu(
3198 MessageManager.getString("label.out_to_textbox"));
3199 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3202 MenuItem item = new MenuItem(
3203 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3205 item.addActionListener(new java.awt.event.ActionListener()
3208 public void actionPerformed(ActionEvent e)
3210 outputText_actionPerformed(e);
3214 outputTextboxMenu.add(item);
3216 closeMenuItem.addActionListener(this);
3217 loadApplication.addActionListener(this);
3218 loadTree.addActionListener(this);
3219 loadAnnotations.addActionListener(this);
3220 outputFeatures.addActionListener(this);
3221 outputAnnotations.addActionListener(this);
3224 * Configure Edit menu items and actions
3226 undoMenuItem.setEnabled(false);
3227 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3228 undoMenuItem.addActionListener(this);
3229 redoMenuItem.setEnabled(false);
3230 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3231 redoMenuItem.addActionListener(this);
3232 copy.setLabel(MessageManager.getString("action.copy"));
3233 copy.addActionListener(this);
3234 cut.setLabel(MessageManager.getString("action.cut"));
3235 cut.addActionListener(this);
3236 delete.setLabel(MessageManager.getString("action.delete"));
3237 delete.addActionListener(this);
3238 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3239 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3240 pasteNew.addActionListener(this);
3241 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3242 pasteThis.addActionListener(this);
3243 remove2LeftMenuItem.setLabel(MessageManager
3244 .getString("action.remove_left"));
3245 remove2LeftMenuItem.addActionListener(this);
3246 remove2RightMenuItem.setLabel(MessageManager
3247 .getString("action.remove_right"));
3248 remove2RightMenuItem.addActionListener(this);
3249 removeGappedColumnMenuItem.setLabel(MessageManager
3250 .getString("action.remove_empty_columns"));
3251 removeGappedColumnMenuItem.addActionListener(this);
3252 removeAllGapsMenuItem.setLabel(MessageManager
3253 .getString("action.remove_all_gaps"));
3254 removeAllGapsMenuItem.addActionListener(this);
3255 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3256 "action.remove_redundancy").concat("..."));
3257 removeRedundancyMenuItem.addActionListener(this);
3260 * Configure Select menu items and actions
3262 findMenuItem.setLabel(MessageManager.getString("action.find"));
3263 findMenuItem.addActionListener(this);
3264 selectAllSequenceMenuItem.addActionListener(this);
3265 deselectAllSequenceMenuItem.addActionListener(this);
3266 invertSequenceMenuItem.setLabel(MessageManager
3267 .getString("action.invert_sequence_selection"));
3268 invertSequenceMenuItem.addActionListener(this);
3269 invertColSel.setLabel(MessageManager
3270 .getString("action.invert_column_selection"));
3271 invertColSel.addActionListener(this);
3272 deleteGroups.setLabel(MessageManager
3273 .getString("action.undefine_groups"));
3274 deleteGroups.addActionListener(this);
3275 grpsFromSelection.setLabel(MessageManager
3276 .getString("action.make_groups_selection"));
3277 grpsFromSelection.addActionListener(this);
3278 createGroup.setLabel(MessageManager.getString("action.create_group"));
3279 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3280 annotationColumnSelection.setLabel("Select by Annotation");
3281 annotationColumnSelection.addActionListener(this);
3284 * Configure View menu items and actions
3286 newView.setLabel(MessageManager.getString("action.new_view"));
3287 newView.addActionListener(this);
3288 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3289 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3290 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3291 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3293 .setLabel(MessageManager.getString("label.selected_columns"));
3294 hideSequences.setLabel(MessageManager
3295 .getString("label.selected_sequences"));
3296 hideAllButSelection.setLabel(MessageManager
3297 .getString("label.all_but_selected_region"));
3298 hideAllSelection.setLabel(MessageManager
3299 .getString("label.selected_region"));
3300 showAllHidden.setLabel(MessageManager
3301 .getString("label.all_sequences_columns"));
3302 showColumns.addActionListener(this);
3303 showSeqs.addActionListener(this);
3304 hideColumns.addActionListener(this);
3305 hideSequences.addActionListener(this);
3306 hideAllButSelection.addActionListener(this);
3307 hideAllSelection.addActionListener(this);
3308 showAllHidden.addActionListener(this);
3309 featureSettings.setLabel(MessageManager
3310 .getString("label.feature_settings"));
3311 featureSettings.addActionListener(this);
3312 sequenceFeatures.setLabel(MessageManager
3313 .getString("label.show_sequence_features"));
3314 sequenceFeatures.addItemListener(this);
3315 sequenceFeatures.setState(false);
3316 followMouseOverFlag.setLabel(MessageManager
3317 .getString("label.automatic_scrolling"));
3318 followMouseOverFlag.addItemListener(this);
3319 alProperties.addActionListener(this);
3320 overviewMenuItem.setLabel(MessageManager
3321 .getString("label.overview_window"));
3322 overviewMenuItem.addActionListener(this);
3325 * Configure Annotations menu items and actions
3327 annotationPanelMenuItem.setLabel(MessageManager
3328 .getString("label.show_annotations"));
3329 annotationPanelMenuItem.addItemListener(this);
3330 showGroupConsensus.setLabel(MessageManager
3331 .getString("label.group_consensus"));
3332 showGroupConservation.setLabel(MessageManager
3333 .getString("label.group_conservation"));
3334 showConsensusHistogram.setLabel(MessageManager
3335 .getString("label.show_consensus_histogram"));
3336 showSequenceLogo.setLabel(MessageManager
3337 .getString("label.show_consensus_logo"));
3338 normSequenceLogo.setLabel(MessageManager
3339 .getString("label.norm_consensus_logo"));
3340 applyAutoAnnotationSettings.setLabel(MessageManager
3341 .getString("label.apply_all_groups"));
3342 applyAutoAnnotationSettings.setState(true);
3343 Menu autoAnnMenu = new Menu(
3344 MessageManager.getString("label.autocalculated_annotation"));
3345 showGroupConsensus.addItemListener(this);
3346 showGroupConservation.addItemListener(this);
3347 showConsensusHistogram.addItemListener(this);
3348 showSequenceLogo.addItemListener(this);
3349 normSequenceLogo.addItemListener(this);
3350 applyAutoAnnotationSettings.addItemListener(this);
3351 showAlignmentAnnotations = new CheckboxMenuItem(
3352 MessageManager.getString("label.show_all_al_annotations"));
3353 showSequenceAnnotations = new CheckboxMenuItem(
3354 MessageManager.getString("label.show_all_seq_annotations"));
3355 sortAnnBySequence = new CheckboxMenuItem(
3356 MessageManager.getString("label.sort_annotations_by_sequence"));
3357 sortAnnByLabel = new CheckboxMenuItem(
3358 MessageManager.getString("label.sort_annotations_by_label"));
3359 showAutoFirst = new CheckboxMenuItem(
3360 MessageManager.getString("label.show_first"));
3361 showAutoLast = new CheckboxMenuItem(
3362 MessageManager.getString("label.show_last"));
3363 showAlignmentAnnotations.addItemListener(this);
3364 showSequenceAnnotations.addItemListener(this);
3365 sortAnnBySequence.addItemListener(this);
3366 sortAnnByLabel.addItemListener(this);
3367 showAutoFirst.addItemListener(this);
3368 showAutoLast.addItemListener(this);
3371 * Configure Format menu items and actions
3373 font.setLabel(MessageManager.getString("action.font"));
3374 font.addActionListener(this);
3375 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3376 scaleAbove.setState(true);
3377 scaleAbove.setEnabled(false);
3378 scaleAbove.addItemListener(this);
3379 scaleLeft.setEnabled(false);
3380 scaleLeft.setState(true);
3381 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3382 scaleLeft.addItemListener(this);
3383 scaleRight.setEnabled(false);
3384 scaleRight.setState(true);
3385 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3386 scaleRight.addItemListener(this);
3387 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3388 viewBoxesMenuItem.setState(true);
3389 viewBoxesMenuItem.addItemListener(this);
3390 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3391 viewTextMenuItem.setState(true);
3392 viewTextMenuItem.addItemListener(this);
3393 colourTextMenuItem.setLabel(MessageManager
3394 .getString("label.colour_text"));
3395 colourTextMenuItem.addItemListener(this);
3396 displayNonconservedMenuItem.setLabel(MessageManager
3397 .getString("label.show_non_conversed"));
3398 displayNonconservedMenuItem.addItemListener(this);
3399 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3400 wrapMenuItem.addItemListener(this);
3401 renderGapsMenuItem.setLabel(MessageManager
3402 .getString("action.show_gaps"));
3403 renderGapsMenuItem.setState(true);
3404 renderGapsMenuItem.addItemListener(this);
3405 centreColumnLabelFlag.setLabel(MessageManager
3406 .getString("label.centre_column_labels"));
3407 centreColumnLabelFlag.addItemListener(this);
3408 seqLimits.setState(true);
3409 seqLimits.setLabel(MessageManager
3410 .getString("label.show_sequence_limits"));
3411 seqLimits.addItemListener(this);
3414 * Configure Colour menu items and actions
3416 applyToAllGroups.setLabel(MessageManager
3417 .getString("label.apply_colour_to_all_groups"));
3418 applyToAllGroups.setState(true);
3419 applyToAllGroups.addItemListener(this);
3420 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3421 clustalColour.addActionListener(this);
3422 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3423 zappoColour.addActionListener(this);
3424 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3425 taylorColour.addActionListener(this);
3426 hydrophobicityColour.setLabel(MessageManager
3427 .getString("label.hydrophobicity"));
3428 hydrophobicityColour.addActionListener(this);
3430 .setLabel(MessageManager.getString("label.helix_propensity"));
3431 helixColour.addActionListener(this);
3432 strandColour.setLabel(MessageManager
3433 .getString("label.strand_propensity"));
3434 strandColour.addActionListener(this);
3435 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3436 turnColour.addActionListener(this);
3437 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3438 buriedColour.addActionListener(this);
3439 purinePyrimidineColour.setLabel(MessageManager
3440 .getString("label.purine_pyrimidine"));
3441 purinePyrimidineColour.addActionListener(this);
3442 RNAInteractionColour.setLabel(MessageManager
3443 .getString("label.rna_interaction"));
3444 RNAInteractionColour.addActionListener(this);
3445 RNAHelixColour.setLabel(MessageManager
3446 .getString("action.by_rna_helixes"));
3447 RNAHelixColour.addActionListener(this);
3448 userDefinedColour.setLabel(MessageManager
3449 .getString("action.user_defined"));
3450 userDefinedColour.addActionListener(this);
3451 PIDColour.setLabel(MessageManager
3452 .getString("label.percentage_identity"));
3453 PIDColour.addActionListener(this);
3454 BLOSUM62Colour.setLabel(MessageManager
3455 .getString("label.blosum62_score"));
3456 BLOSUM62Colour.addActionListener(this);
3458 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3459 // it will be enabled only if a score file is provided
3460 tcoffeeColour.setEnabled(false);
3461 tcoffeeColour.addActionListener(this);
3462 conservationMenuItem.setLabel(MessageManager
3463 .getString("action.by_conservation"));
3464 conservationMenuItem.addItemListener(this);
3465 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3466 noColourmenuItem.addActionListener(this);
3467 abovePIDThreshold.setLabel(MessageManager
3468 .getString("label.above_identity_threshold"));
3469 abovePIDThreshold.addItemListener(this);
3470 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3471 nucleotideColour.addActionListener(this);
3472 modifyPID.setLabel(MessageManager
3473 .getString("label.modify_identity_thereshold"));
3474 modifyPID.addActionListener(this);
3475 modifyConservation.setLabel(MessageManager
3476 .getString("label.modify_conservation_thereshold"));
3477 modifyConservation.addActionListener(this);
3478 annotationColour.setLabel(MessageManager
3479 .getString("action.by_annotation"));
3480 annotationColour.addActionListener(this);
3483 * Configure Calculate menu items and actions
3485 sortPairwiseMenuItem.setLabel(MessageManager
3486 .getString("action.by_pairwise_id"));
3487 sortPairwiseMenuItem.addActionListener(this);
3488 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3489 sortIDMenuItem.addActionListener(this);
3490 sortLengthMenuItem.setLabel(MessageManager
3491 .getString("action.by_length"));
3492 sortLengthMenuItem.addActionListener(this);
3493 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3494 sortGroupMenuItem.addActionListener(this);
3495 pairwiseAlignmentMenuItem.setLabel(MessageManager
3496 .getString("action.pairwise_alignment"));
3497 pairwiseAlignmentMenuItem.addActionListener(this);
3498 PCAMenuItem.setLabel(MessageManager
3499 .getString("label.principal_component_analysis"));
3500 PCAMenuItem.addActionListener(this);
3501 autoCalculate = new CheckboxMenuItem(
3502 MessageManager.getString("label.autocalculate_consensus"), true);
3503 averageDistanceTreeMenuItem.setLabel(MessageManager
3504 .getString("label.average_distance_identity"));
3505 averageDistanceTreeMenuItem.addActionListener(this);
3506 neighbourTreeMenuItem.setLabel(MessageManager
3507 .getString("label.neighbour_joining_identity"));
3508 neighbourTreeMenuItem.addActionListener(this);
3509 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3510 .getString("label.average_distance_bloslum62"));
3511 avDistanceTreeBlosumMenuItem.addActionListener(this);
3512 njTreeBlosumMenuItem.setLabel(MessageManager
3513 .getString("label.neighbour_blosum62"));
3514 njTreeBlosumMenuItem.addActionListener(this);
3515 sortByTreeMenu.setLabel(MessageManager
3516 .getString("action.by_tree_order"));
3517 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3518 Menu calculateTreeMenu = new Menu(
3519 MessageManager.getString("action.calculate_tree"));
3520 autoCalculate.addItemListener(this);
3521 sortByTree.addItemListener(this);
3524 * Configure Help menu items and actions
3526 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3527 documentation.setLabel(MessageManager.getString("label.documentation"));
3528 documentation.addActionListener(this);
3529 about.setLabel(MessageManager.getString("label.about"));
3530 about.addActionListener(this);
3533 * Add top level menus to frame
3535 alignFrameMenuBar.add(fileMenu);
3536 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3537 alignFrameMenuBar.add(editMenu);
3538 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3539 alignFrameMenuBar.add(selectMenu);
3540 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3541 alignFrameMenuBar.add(viewMenu);
3542 Menu annotationsMenu = new Menu(
3543 MessageManager.getString("action.annotations"));
3544 alignFrameMenuBar.add(annotationsMenu);
3545 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3546 alignFrameMenuBar.add(formatMenu);
3547 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3548 alignFrameMenuBar.add(colourMenu);
3549 Menu calculateMenu = new Menu(
3550 MessageManager.getString("action.calculate"));
3551 alignFrameMenuBar.add(calculateMenu);
3552 alignFrameMenuBar.add(helpMenu);
3557 fileMenu.add(inputText);
3558 fileMenu.add(loadTree);
3559 fileMenu.add(loadAnnotations);
3560 fileMenu.addSeparator();
3561 fileMenu.add(outputTextboxMenu);
3562 fileMenu.add(outputFeatures);
3563 fileMenu.add(outputAnnotations);
3564 if (jalviewServletURL != null)
3566 fileMenu.add(loadApplication);
3568 fileMenu.addSeparator();
3569 fileMenu.add(closeMenuItem);
3574 editMenu.add(undoMenuItem);
3575 editMenu.add(redoMenuItem);
3578 pasteMenu.add(pasteNew);
3579 pasteMenu.add(pasteThis);
3580 editMenu.add(pasteMenu);
3581 editMenu.add(delete);
3582 editMenu.addSeparator();
3583 editMenu.add(remove2LeftMenuItem);
3584 editMenu.add(remove2RightMenuItem);
3585 editMenu.add(removeGappedColumnMenuItem);
3586 editMenu.add(removeAllGapsMenuItem);
3587 editMenu.add(removeRedundancyMenuItem);
3592 selectMenu.add(findMenuItem);
3593 selectMenu.addSeparator();
3594 selectMenu.add(selectAllSequenceMenuItem);
3595 selectMenu.add(deselectAllSequenceMenuItem);
3596 selectMenu.add(invertSequenceMenuItem);
3597 selectMenu.add(invertColSel);
3598 selectMenu.add(createGroup);
3599 selectMenu.add(unGroup);
3600 selectMenu.add(grpsFromSelection);
3601 selectMenu.add(deleteGroups);
3602 selectMenu.add(annotationColumnSelection);
3607 viewMenu.add(newView);
3608 viewMenu.addSeparator();
3609 showMenu.add(showColumns);
3610 showMenu.add(showSeqs);
3611 showMenu.add(showAllHidden);
3612 viewMenu.add(showMenu);
3613 hideMenu.add(hideColumns);
3614 hideMenu.add(hideSequences);
3615 hideMenu.add(hideAllSelection);
3616 hideMenu.add(hideAllButSelection);
3617 viewMenu.add(hideMenu);
3618 viewMenu.addSeparator();
3619 viewMenu.add(followMouseOverFlag);
3620 viewMenu.addSeparator();
3621 viewMenu.add(sequenceFeatures);
3622 viewMenu.add(featureSettings);
3623 viewMenu.addSeparator();
3624 viewMenu.add(alProperties);
3625 viewMenu.addSeparator();
3626 viewMenu.add(overviewMenuItem);
3631 annotationsMenu.add(annotationPanelMenuItem);
3632 annotationsMenu.addSeparator();
3633 annotationsMenu.add(showAlignmentAnnotations);
3634 annotationsMenu.add(showSequenceAnnotations);
3635 annotationsMenu.add(sortAnnBySequence);
3636 annotationsMenu.add(sortAnnByLabel);
3637 annotationsMenu.addSeparator();
3638 autoAnnMenu.add(showAutoFirst);
3639 autoAnnMenu.add(showAutoLast);
3640 autoAnnMenu.addSeparator();
3641 autoAnnMenu.add(applyAutoAnnotationSettings);
3642 autoAnnMenu.add(showConsensusHistogram);
3643 autoAnnMenu.add(showSequenceLogo);
3644 autoAnnMenu.add(normSequenceLogo);
3645 autoAnnMenu.addSeparator();
3646 autoAnnMenu.add(showGroupConservation);
3647 autoAnnMenu.add(showGroupConsensus);
3648 annotationsMenu.add(autoAnnMenu);
3653 formatMenu.add(font);
3654 formatMenu.add(seqLimits);
3655 formatMenu.add(wrapMenuItem);
3656 formatMenu.add(scaleAbove);
3657 formatMenu.add(scaleLeft);
3658 formatMenu.add(scaleRight);
3659 formatMenu.add(viewBoxesMenuItem);
3660 formatMenu.add(viewTextMenuItem);
3661 formatMenu.add(colourTextMenuItem);
3662 formatMenu.add(displayNonconservedMenuItem);
3663 formatMenu.add(renderGapsMenuItem);
3664 formatMenu.add(centreColumnLabelFlag);
3669 colourMenu.add(applyToAllGroups);
3670 colourMenu.addSeparator();
3671 colourMenu.add(noColourmenuItem);
3672 colourMenu.add(clustalColour);
3673 colourMenu.add(BLOSUM62Colour);
3674 colourMenu.add(PIDColour);
3675 colourMenu.add(zappoColour);
3676 colourMenu.add(taylorColour);
3677 colourMenu.add(hydrophobicityColour);
3678 colourMenu.add(helixColour);
3679 colourMenu.add(strandColour);
3680 colourMenu.add(turnColour);
3681 colourMenu.add(buriedColour);
3682 colourMenu.add(nucleotideColour);
3683 colourMenu.add(purinePyrimidineColour);
3684 // colourMenu.add(RNAInteractionColour);
3685 colourMenu.add(tcoffeeColour);
3686 colourMenu.add(userDefinedColour);
3687 colourMenu.addSeparator();
3688 colourMenu.add(conservationMenuItem);
3689 colourMenu.add(modifyConservation);
3690 colourMenu.add(abovePIDThreshold);
3691 colourMenu.add(modifyPID);
3692 colourMenu.add(annotationColour);
3693 colourMenu.add(RNAHelixColour);
3698 sortMenu.add(sortIDMenuItem);
3699 sortMenu.add(sortLengthMenuItem);
3700 sortMenu.add(sortByTreeMenu);
3701 sortMenu.add(sortGroupMenuItem);
3702 sortMenu.add(sortPairwiseMenuItem);
3703 calculateMenu.add(sortMenu);
3704 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3705 calculateTreeMenu.add(neighbourTreeMenuItem);
3706 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3707 calculateTreeMenu.add(njTreeBlosumMenuItem);
3708 calculateMenu.add(calculateTreeMenu);
3709 calculateMenu.addSeparator();
3710 calculateMenu.add(pairwiseAlignmentMenuItem);
3711 calculateMenu.add(PCAMenuItem);
3712 calculateMenu.add(autoCalculate);
3713 calculateMenu.add(sortByTree);
3718 helpMenu.add(documentation);
3719 helpMenu.add(about);
3724 statusBar.setBackground(Color.white);
3725 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3726 statusBar.setText(MessageManager.getString("label.status_bar"));
3727 this.add(statusBar, BorderLayout.SOUTH);
3730 public void setStatus(String string)
3732 statusBar.setText(string);
3735 MenuItem featureSettings = new MenuItem();
3737 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3739 MenuItem annotationColour = new MenuItem();
3741 MenuItem annotationColumnSelection = new MenuItem();
3743 MenuItem invertColSel = new MenuItem();
3745 MenuItem showColumns = new MenuItem();
3747 MenuItem showSeqs = new MenuItem();
3749 MenuItem hideColumns = new MenuItem();
3751 MenuItem hideSequences = new MenuItem();
3753 MenuItem hideAllButSelection = new MenuItem();
3755 MenuItem hideAllSelection = new MenuItem();
3757 MenuItem showAllHidden = new MenuItem();
3759 MenuItem newView = new MenuItem();
3761 private CheckboxMenuItem showAlignmentAnnotations;
3763 private CheckboxMenuItem showSequenceAnnotations;
3765 private CheckboxMenuItem sortAnnBySequence;
3767 private CheckboxMenuItem sortAnnByLabel;
3769 private CheckboxMenuItem showAutoFirst;
3771 private CheckboxMenuItem showAutoLast;
3773 private SplitFrame splitFrame;
3776 * Attach the alignFrame panels after embedding menus, if necessary. This used
3777 * to be called setEmbedded, but is now creates the dropdown menus in a
3778 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3780 * @param reallyEmbedded
3781 * true to attach the view to the applet area on the page rather than
3784 public void createAlignFrameWindow(boolean reallyEmbedded)
3788 embedAlignFrameInApplet(viewport.applet);
3793 // test and embed menu bar if necessary.
3795 if (embedMenuIfNeeded(alignPanel))
3798 * adjust for status bar height too. ? pointless as overridden by layout
3801 alignPanel.setSize(getSize().width,
3802 getSize().height - statusBar.getHeight());
3804 add(statusBar, BorderLayout.SOUTH);
3805 add(alignPanel, BorderLayout.CENTER);
3806 // and register with the applet so it can pass external API calls to us
3807 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3814 * Add the components of this AlignFrame to the applet container.
3818 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3821 // Explicitly build the embedded menu panel for the on-page applet
3823 // view cannot be closed if its actually on the page
3824 fileMenu.remove(closeMenuItem);
3825 fileMenu.remove(3); // Remove Separator
3826 // construct embedded menu, using default font
3827 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3828 // and actually add the components to the applet area
3829 theApplet.setLayout(new BorderLayout());
3830 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3831 theApplet.add(statusBar, BorderLayout.SOUTH);
3832 // TODO should size be left to the layout manager?
3833 alignPanel.setSize(theApplet.getSize().width,
3834 theApplet.getSize().height - embeddedMenu.getHeight()
3835 - statusBar.getHeight());
3836 theApplet.add(alignPanel, BorderLayout.CENTER);
3837 final AlignFrame me = this;
3838 theApplet.addFocusListener(new FocusListener()
3842 public void focusLost(FocusEvent e)
3844 if (theApplet.currentAlignFrame == me)
3846 theApplet.currentAlignFrame = null;
3851 public void focusGained(FocusEvent e)
3853 theApplet.currentAlignFrame = me;
3856 theApplet.validate();
3860 * create a new binding between structures in an existing jmol viewer instance
3861 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3862 * this does not open a new Jmol window, or modify the display of the
3863 * structures in the original jmol window. Note This method doesn't work
3864 * without an additional javascript library to exchange messages between the
3865 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3868 * JmolViewer instance
3869 * @param sequenceIds
3870 * - sequence Ids to search for associations
3872 public SequenceStructureBinding addStructureViewInstance(
3873 Object jmolviewer, String[] sequenceIds)
3875 org.jmol.api.JmolViewer viewer = null;
3878 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3879 } catch (ClassCastException ex)
3881 System.err.println("Unsupported viewer object :"
3882 + jmolviewer.getClass());
3886 System.err.println("Can't use this object as a structure viewer:"
3887 + jmolviewer.getClass());
3890 SequenceI[] seqs = null;
3891 if (sequenceIds == null || sequenceIds.length == 0)
3893 seqs = viewport.getAlignment().getSequencesArray();
3897 Vector sqi = new Vector();
3898 AlignmentI al = viewport.getAlignment();
3899 for (int sid = 0; sid < sequenceIds.length; sid++)
3901 SequenceI sq = al.findName(sequenceIds[sid]);
3909 seqs = new SequenceI[sqi.size()];
3910 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3912 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3920 AAStructureBindingModel jmv = null;
3921 // TODO: search for a jmv that involves viewer
3923 { // create a new viewer/jalview binding.
3924 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3932 * bind a pdb file to a sequence in the current view
3935 * - sequenceId within the dataset.
3936 * @param pdbEntryString
3937 * - the short name for the PDB file
3939 * - pdb file - either a URL or a valid PDB file.
3940 * @return true if binding was as success TODO: consider making an exception
3941 * structure for indicating when PDB parsing or sequenceId location
3944 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3947 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3948 boolean needtoadd = false;
3949 if (toaddpdb != null)
3951 Vector pdbe = toaddpdb.getPDBId();
3952 PDBEntry pdbentry = null;
3953 if (pdbe != null && pdbe.size() > 0)
3955 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3957 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3958 if (!pdbentry.getId().equals(pdbEntryString)
3959 && !pdbentry.getFile().equals(pdbFile))
3969 if (pdbentry == null)
3971 pdbentry = new PDBEntry();
3972 pdbentry.setId(pdbEntryString);
3973 pdbentry.setFile(pdbFile);
3974 needtoadd = true; // add this new entry to sequence.
3976 // resolve data source
3977 // TODO: this code should be a refactored to an io package
3978 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3979 if (protocol == null)
3985 // make a note of the access mode and add
3986 if (pdbentry.getProperty() == null)
3988 pdbentry.setProperty(new Hashtable());
3990 pdbentry.getProperty().put("protocol", protocol);
3991 toaddpdb.addPDBId(pdbentry);
3992 alignPanel.getStructureSelectionManager()
3993 .registerPDBEntry(pdbentry);
3999 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4003 Vector sequences = new Vector();
4004 for (int i = 0; i < seqs.length; i++)
4006 if (seqs[i] != null)
4008 sequences.addElement(new Object[]
4009 { seqs[i], (chains != null) ? chains[i] : null });
4012 seqs = new SequenceI[sequences.size()];
4013 chains = new String[sequences.size()];
4014 for (int i = 0, isize = sequences.size(); i < isize; i++)
4016 Object[] oj = (Object[]) sequences.elementAt(i);
4018 seqs[i] = (SequenceI) oj[0];
4019 chains[i] = (String) oj[1];
4027 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4028 SequenceI[] seqs, String[] chains, String protocol)
4030 // Scrub any null sequences from the array
4031 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4032 seqs = (SequenceI[]) sqch[0];
4033 chains = (String[]) sqch[1];
4034 if (seqs == null || seqs.length == 0)
4037 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4039 if (protocol == null || protocol.trim().length() == 0
4040 || protocol.equals("null"))
4042 protocol = (String) pdb.getProperty().get("protocol");
4043 if (protocol == null)
4045 System.err.println("Couldn't work out protocol to open structure: "
4050 if (applet.useXtrnalSviewer)
4052 // register the association(s) and quit, don't create any windows.
4053 if (StructureSelectionManager.getStructureSelectionManager(applet)
4054 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4056 System.err.println("Failed to map " + pdb.getFile() + " ("
4057 + protocol + ") to any sequences");
4061 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4063 // can only do alignments with Jmol
4064 // find the last jmol window assigned to this alignment
4065 jalview.appletgui.AppletJmol ajm = null, tajm;
4066 Vector jmols = applet
4067 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4068 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4070 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4071 if (tajm.ap.alignFrame == this)
4080 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4081 // try and add the pdb structure
4086 // otherwise, create a new window
4087 if (applet.jmolAvailable)
4089 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4091 applet.lastFrameX += 40;
4092 applet.lastFrameY += 40;
4096 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4101 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4102 SequenceI[][] seqs, String[][] chains, String[] protocols)
4104 // TODO Auto-generated method stub
4105 System.err.println("Aligned Structure View: Not yet implemented.");
4109 * modify the current selection, providing the user has not made a selection
4113 * - sequences from this alignment
4115 * - columns to be selected on the alignment
4117 public void select(SequenceGroup sel, ColumnSelection csel)
4119 alignPanel.seqPanel.selection(sel, csel, null);
4122 public void scrollTo(int row, int column)
4124 alignPanel.seqPanel.scrollTo(row, column);
4127 public void scrollToRow(int row)
4129 alignPanel.seqPanel.scrollToRow(row);
4132 public void scrollToColumn(int column)
4134 alignPanel.seqPanel.scrollToColumn(column);
4138 * @return the alignments unique ID.
4140 public String getSequenceSetId()
4142 return viewport.getSequenceSetId();
4146 * Load the (T-Coffee) score file from the specified url
4149 * File/URL/T-COFFEE score file contents
4150 * @throws IOException
4151 * @return true if alignment was annotated with data from source
4153 public boolean loadScoreFile(String source) throws IOException
4156 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4157 AppletFormatAdapter.checkProtocol(source));
4158 if (!file.isValid())
4160 // TODO: raise dialog for gui
4161 System.err.println("Problems parsing T-Coffee scores: "
4162 + file.getWarningMessage());
4163 System.err.println("Origin was:\n" + source);
4168 * check that the score matrix matches the alignment dimensions
4171 if ((aln = viewport.getAlignment()) != null
4172 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4175 // TODO: raise a dialog box here rather than bomb out.
4177 .println("The scores matrix does not match the alignment dimensions");
4181 // TODO add parameter to indicate if matching should be done
4182 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4184 alignPanel.fontChanged();
4185 tcoffeeColour.setEnabled(true);
4186 // switch to this color
4187 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4192 System.err.println("Problems resolving T-Coffee scores:");
4193 if (file.getWarningMessage() != null)
4195 System.err.println(file.getWarningMessage());
4201 public SplitFrame getSplitFrame()
4203 return this.splitFrame;
4206 public void setSplitFrame(SplitFrame sf)
4208 this.splitFrame = sf;