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 cap.setText(new AppletFormatAdapter(viewport).formatSequences(
1345 e.getActionCommand(), viewport.getAlignment(),
1346 viewport.getShowJVSuffix()));
1349 public void loadAnnotations()
1351 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1352 cap.setText(MessageManager
1353 .getString("label.paste_features_annotations_Tcoffee_here"));
1354 cap.setAnnotationImport();
1355 Frame frame = new Frame();
1357 jalview.bin.JalviewLite.addFrame(frame,
1358 MessageManager.getString("action.paste_annotations"), 400, 300);
1362 public String outputAnnotations(boolean displayTextbox)
1364 String annotation = new AnnotationFile()
1365 .printAnnotationsForView(viewport);
1369 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1370 Frame frame = new Frame();
1372 jalview.bin.JalviewLite.addFrame(frame,
1373 MessageManager.getString("label.annotations"), 600, 500);
1374 cap.setText(annotation);
1380 private Map<String,Object> getDisplayedFeatureCols()
1382 if (alignPanel.getFeatureRenderer() != null
1383 && viewport.getFeaturesDisplayed()!= null)
1385 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1391 public String outputFeatures(boolean displayTextbox, String format)
1394 if (format.equalsIgnoreCase("Jalview"))
1396 features = new FeaturesFile().printJalviewFormat(viewport
1397 .getAlignment().getSequencesArray(),
1398 getDisplayedFeatureCols());
1402 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1403 .getSequencesArray(), getDisplayedFeatureCols());
1408 boolean frimport = false;
1409 if (features == null || features.equals("No Features Visible"))
1411 features = "# No features visible - paste some and import them here.";
1415 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1418 cap.setAnnotationImport();
1420 Frame frame = new Frame();
1422 jalview.bin.JalviewLite.addFrame(frame,
1423 MessageManager.getString("label.features"), 600, 500);
1424 cap.setText(features);
1428 if (features == null)
1437 void launchFullApplication()
1439 StringBuffer url = new StringBuffer(jalviewServletURL);
1441 // allow servlet parameters to be passed in applet parameter
1442 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1444 url.append(firstSep);
1447 + appendProtocol(viewport.applet.getParameter("file")));
1449 if (viewport.applet.getParameter("features") != null)
1451 url.append("&features=");
1452 url.append(appendProtocol(viewport.applet.getParameter("features")));
1455 if (viewport.applet.getParameter("annotations") != null)
1457 url.append("&annotations=");
1458 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1461 if (viewport.applet.getParameter("jnetfile") != null)
1463 url.append("&annotations=");
1464 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1467 if (viewport.applet.getParameter("defaultColour") != null)
1469 url.append("&colour="
1470 + removeWhiteSpace(viewport.applet
1471 .getParameter("defaultColour")));
1474 if (viewport.applet.getParameter("userDefinedColour") != null)
1476 url.append("&colour="
1477 + removeWhiteSpace(viewport.applet
1478 .getParameter("userDefinedColour")));
1480 if (viewport.applet.getParameter("tree") != null)
1483 + appendProtocol(viewport.applet.getParameter("tree")));
1485 if (viewport.applet.getParameter("treeFile") != null)
1488 + appendProtocol(viewport.applet.getParameter("treeFile")));
1491 showURL(url.toString(), "FULL_APP");
1494 String removeWhiteSpace(String colour)
1496 StringBuffer sb = new StringBuffer();
1497 for (int i = 0; i < colour.length(); i++)
1499 if (Character.isWhitespace(colour.charAt(i)))
1505 sb.append(colour.charAt(i));
1509 return sb.toString();
1512 String appendProtocol(String url)
1517 url = URLEncoder.encode(url);
1520 * When we finally deprecate 1.1 compatibility, we can start to use
1521 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1522 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1523 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1524 * ex.printStackTrace(); }
1526 catch (java.net.MalformedURLException ex)
1528 url = viewport.applet.getCodeBase() + url;
1533 public void closeMenuItem_actionPerformed()
1535 PaintRefresher.RemoveComponent(alignPanel);
1536 if (alignPanel.seqPanel != null
1537 && alignPanel.seqPanel.seqCanvas != null)
1539 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1541 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1543 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1546 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1561 void updateEditMenuBar()
1564 if (viewport.getHistoryList().size() > 0)
1566 undoMenuItem.setEnabled(true);
1567 CommandI command = viewport.getHistoryList().peek();
1568 undoMenuItem.setLabel(MessageManager.formatMessage(
1569 "label.undo_command", new Object[]
1570 { command.getDescription() }));
1574 undoMenuItem.setEnabled(false);
1575 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1578 if (viewport.getRedoList().size() > 0)
1580 redoMenuItem.setEnabled(true);
1582 CommandI command = viewport.getRedoList().peek();
1583 redoMenuItem.setLabel(MessageManager.formatMessage(
1584 "label.redo_command", new Object[]
1585 { command.getDescription() }));
1589 redoMenuItem.setEnabled(false);
1590 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1598 public void addHistoryItem(CommandI command)
1600 if (command.getSize() > 0)
1602 viewport.addToHistoryList(command);
1603 viewport.clearRedoList();
1604 updateEditMenuBar();
1605 viewport.updateHiddenColumns();
1610 * TODO: JAL-1104 DOCUMENT ME!
1615 protected void undoMenuItem_actionPerformed()
1617 if (viewport.getHistoryList().isEmpty())
1622 CommandI command = viewport.getHistoryList().pop();
1623 viewport.addToRedoList(command);
1624 command.undoCommand(null);
1626 AlignmentViewport originalSource = getOriginatingSource(command);
1628 if (originalSource != viewport)
1631 .println("Warning: Viewport object mismatch whilst undoing");
1633 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1634 // viewport.getColumnSelection().getHiddenColumns()
1636 updateEditMenuBar();
1637 originalSource.firePropertyChange("alignment", null, originalSource
1638 .getAlignment().getSequences());
1642 * TODO: JAL-1104 DOCUMENT ME!
1647 protected void redoMenuItem_actionPerformed()
1649 if (viewport.getRedoList().isEmpty())
1654 CommandI command = viewport.getRedoList().pop();
1655 viewport.addToHistoryList(command);
1656 command.doCommand(null);
1658 AlignmentViewport originalSource = getOriginatingSource(command);
1660 if (originalSource != viewport)
1663 .println("Warning: Viewport object mismatch whilst re-doing");
1665 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1666 // viewport.getColumnSelection().getHiddenColumns()
1669 updateEditMenuBar();
1670 originalSource.firePropertyChange("alignment", null, originalSource
1671 .getAlignment().getSequences());
1674 AlignmentViewport getOriginatingSource(CommandI command)
1676 AlignmentViewport originalSource = null;
1677 // For sequence removal and addition, we need to fire
1678 // the property change event FROM the viewport where the
1679 // original alignment was altered
1680 AlignmentI al = null;
1681 if (command instanceof EditCommand)
1683 EditCommand editCommand = (EditCommand) command;
1684 al = editCommand.getAlignment();
1685 Vector comps = (Vector) PaintRefresher.components.get(viewport
1686 .getSequenceSetId());
1687 for (int i = 0; i < comps.size(); i++)
1689 if (comps.elementAt(i) instanceof AlignmentPanel)
1691 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1693 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1700 if (originalSource == null)
1702 // The original view is closed, we must validate
1703 // the current view against the closed view first
1706 PaintRefresher.validateSequences(al, viewport.getAlignment());
1709 originalSource = viewport;
1712 return originalSource;
1716 * Move the currently selected sequences up or down one position in the
1721 public void moveSelectedSequences(boolean up)
1723 SequenceGroup sg = viewport.getSelectionGroup();
1728 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1729 up ? null : viewport.getHiddenRepSequences(), up);
1730 alignPanel.paintAlignment(true);
1733 * Also move cDNA/protein complement sequences
1735 AlignViewportI complement = viewport.getCodingComplement();
1736 if (complement != null)
1738 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1739 viewport, complement);
1740 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1741 up ? null : complement.getHiddenRepSequences(), up);
1742 // TODO need to trigger a repaint of the complementary panel - how?
1743 // would prefer to handle in SplitFrame but it is not overriding key
1748 synchronized void slideSequences(boolean right, int size)
1750 List<SequenceI> sg = new Vector<SequenceI>();
1751 if (viewport.cursorMode)
1753 sg.add(viewport.getAlignment().getSequenceAt(
1754 alignPanel.seqPanel.seqCanvas.cursorY));
1756 else if (viewport.getSelectionGroup() != null
1757 && viewport.getSelectionGroup().getSize() != viewport
1758 .getAlignment().getHeight())
1760 sg = viewport.getSelectionGroup().getSequences(
1761 viewport.getHiddenRepSequences());
1769 Vector<SequenceI> invertGroup = new Vector();
1771 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1773 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1775 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1779 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1781 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1783 for (int i = 0; i < invertGroup.size(); i++)
1785 seqs2[i] = invertGroup.elementAt(i);
1788 SlideSequencesCommand ssc;
1791 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1792 size, viewport.getGapCharacter());
1796 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1797 size, viewport.getGapCharacter());
1800 int groupAdjustment = 0;
1801 if (ssc.getGapsInsertedBegin() && right)
1803 if (viewport.cursorMode)
1805 alignPanel.seqPanel.moveCursor(size, 0);
1809 groupAdjustment = size;
1812 else if (!ssc.getGapsInsertedBegin() && !right)
1814 if (viewport.cursorMode)
1816 alignPanel.seqPanel.moveCursor(-size, 0);
1820 groupAdjustment = -size;
1824 if (groupAdjustment != 0)
1826 viewport.getSelectionGroup().setStartRes(
1827 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1828 viewport.getSelectionGroup().setEndRes(
1829 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1832 boolean appendHistoryItem = false;
1833 Deque<CommandI> historyList = viewport.getHistoryList();
1834 if (historyList != null && historyList.size() > 0
1835 && historyList.peek() instanceof SlideSequencesCommand)
1837 appendHistoryItem = ssc
1838 .appendSlideCommand((SlideSequencesCommand) historyList
1842 if (!appendHistoryItem)
1844 addHistoryItem(ssc);
1850 static StringBuffer copiedSequences;
1852 static Vector copiedHiddenColumns;
1854 protected void copy_actionPerformed()
1856 if (viewport.getSelectionGroup() == null)
1861 SequenceGroup sg = viewport.getSelectionGroup();
1862 copiedSequences = new StringBuffer();
1863 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1864 for (int i = 0; i < sg.getSize(); i++)
1866 SequenceI seq = sg.getSequenceAt(i);
1867 int index = viewport.getAlignment().findIndex(seq);
1868 orderedSeqs.put(index, seq);
1871 int index = 0, startRes, endRes;
1874 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1876 copiedHiddenColumns = new Vector();
1877 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1878 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1880 copiedHiddenColumns.addElement(new int[]
1881 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1886 copiedHiddenColumns = null;
1889 for (int i = 0; i < sg.getSize(); i++)
1891 SequenceI seq = null;
1895 if (orderedSeqs.containsKey(index))
1897 seq = orderedSeqs.get(index);
1908 // Returns residue following index if gap
1909 startRes = seq.findPosition(sg.getStartRes());
1912 // Need to find the residue preceeding index if gap
1915 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1917 ch = seq.getCharAt(j);
1918 if (!jalview.util.Comparison.isGap((ch)))
1926 endRes += seq.getStart() - 1;
1929 copiedSequences.append(seq.getName()
1935 + seq.getSequenceAsString(sg.getStartRes(),
1936 sg.getEndRes() + 1) + "\n");
1941 protected void pasteNew_actionPerformed()
1946 protected void pasteThis_actionPerformed()
1951 void paste(boolean newAlignment)
1956 if (copiedSequences == null)
1961 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1962 Vector seqs = new Vector();
1963 while (st.hasMoreElements())
1965 String name = st.nextToken();
1966 int start = Integer.parseInt(st.nextToken());
1967 int end = Integer.parseInt(st.nextToken());
1968 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1970 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1971 for (int i = 0; i < seqs.size(); i++)
1973 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1978 String newtitle = MessageManager.getString("label.copied_sequences");
1979 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1981 newtitle = getTitle();
1985 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1987 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1988 viewport.applet, newtitle, false);
1989 if (copiedHiddenColumns != null)
1991 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1993 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1994 af.viewport.hideColumns(region[0], region[1]);
1998 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2003 addSequences(newSeqs);
2006 } catch (Exception ex)
2008 } // could be anything being pasted in here
2012 void addSequences(SequenceI[] seqs)
2014 for (int i = 0; i < seqs.length; i++)
2016 viewport.getAlignment().addSequence(seqs[i]);
2020 addHistoryItem(new EditCommand(
2021 MessageManager.getString("label.add_sequences"), Action.PASTE,
2022 seqs, 0, viewport.getAlignment().getWidth(),
2023 viewport.getAlignment()));
2025 viewport.setEndSeq(viewport.getAlignment().getHeight());
2026 viewport.getAlignment().getWidth();
2027 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2032 protected void cut_actionPerformed()
2034 copy_actionPerformed();
2035 delete_actionPerformed();
2038 protected void delete_actionPerformed()
2041 SequenceGroup sg = viewport.getSelectionGroup();
2047 Vector seqs = new Vector();
2049 for (int i = 0; i < sg.getSize(); i++)
2051 seq = sg.getSequenceAt(i);
2052 seqs.addElement(seq);
2055 // If the cut affects all sequences, remove highlighted columns
2056 if (sg.getSize() == viewport.getAlignment().getHeight())
2058 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2059 sg.getEndRes() + 1);
2062 SequenceI[] cut = new SequenceI[seqs.size()];
2063 for (int i = 0; i < seqs.size(); i++)
2065 cut[i] = (SequenceI) seqs.elementAt(i);
2069 * //ADD HISTORY ITEM
2071 addHistoryItem(new EditCommand(
2072 MessageManager.getString("label.cut_sequences"), Action.CUT,
2073 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2074 viewport.getAlignment()));
2076 viewport.setSelectionGroup(null);
2077 viewport.getAlignment().deleteGroup(sg);
2079 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082 if (viewport.getAlignment().getHeight() < 1)
2084 this.setVisible(false);
2086 viewport.sendSelection();
2090 * group consensus toggled
2093 protected void showGroupConsensus_actionPerformed()
2095 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2096 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2101 * group conservation toggled.
2103 protected void showGroupConservation_actionPerformed()
2105 viewport.setShowGroupConservation(showGroupConservation.getState());
2106 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2113 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2114 * .event.ActionEvent)
2116 protected void showConsensusHistogram_actionPerformed()
2118 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2119 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2126 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2127 * .event.ActionEvent)
2129 protected void showSequenceLogo_actionPerformed()
2131 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2132 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2135 protected void normSequenceLogo_actionPerformed()
2137 showSequenceLogo.setState(true);
2138 viewport.setShowSequenceLogo(true);
2139 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2140 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2143 protected void applyAutoAnnotationSettings_actionPerformed()
2145 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2148 protected void makeGrpsFromSelection_actionPerformed()
2150 if (avc.makeGroupsFromSelection())
2152 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2153 alignPanel.updateAnnotation();
2154 alignPanel.paintAlignment(true);
2158 protected void createGroup_actionPerformed()
2163 protected void unGroup_actionPerformed()
2167 alignPanel.alignmentChanged();
2171 protected void deleteGroups_actionPerformed()
2173 if (avc.deleteGroups())
2175 alignPanel.alignmentChanged();
2179 public void selectAllSequenceMenuItem_actionPerformed()
2181 SequenceGroup sg = new SequenceGroup();
2182 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2184 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2186 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2187 viewport.setSelectionGroup(sg);
2188 alignPanel.paintAlignment(true);
2189 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2190 viewport.sendSelection();
2193 public void deselectAllSequenceMenuItem_actionPerformed()
2195 if (viewport.cursorMode)
2197 alignPanel.seqPanel.keyboardNo1 = null;
2198 alignPanel.seqPanel.keyboardNo2 = null;
2200 viewport.setSelectionGroup(null);
2201 viewport.getColumnSelection().clear();
2202 viewport.setSelectionGroup(null);
2203 alignPanel.idPanel.idCanvas.searchResults = null;
2204 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2205 alignPanel.paintAlignment(true);
2206 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2207 viewport.sendSelection();
2210 public void invertSequenceMenuItem_actionPerformed()
2212 SequenceGroup sg = viewport.getSelectionGroup();
2213 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2215 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2218 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2219 viewport.sendSelection();
2222 public void invertColSel_actionPerformed()
2224 viewport.invertColumnSelection();
2225 alignPanel.paintAlignment(true);
2226 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2227 viewport.sendSelection();
2230 void trimAlignment(boolean trimLeft)
2232 ColumnSelection colSel = viewport.getColumnSelection();
2235 if (colSel.size() > 0)
2239 column = colSel.getMin();
2243 column = colSel.getMax();
2247 if (viewport.getSelectionGroup() != null)
2249 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2250 viewport.getHiddenRepSequences());
2254 seqs = viewport.getAlignment().getSequencesArray();
2257 TrimRegionCommand trimRegion;
2260 trimRegion = new TrimRegionCommand("Remove Left",
2261 TrimRegionCommand.TRIM_LEFT, seqs, column,
2262 viewport.getAlignment(), viewport.getColumnSelection(),
2263 viewport.getSelectionGroup());
2264 viewport.setStartRes(0);
2268 trimRegion = new TrimRegionCommand("Remove Right",
2269 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2270 viewport.getAlignment(), viewport.getColumnSelection(),
2271 viewport.getSelectionGroup());
2274 statusBar.setText(MessageManager.formatMessage(
2275 "label.removed_columns", new String[]
2276 { Integer.valueOf(trimRegion.getSize()).toString() }));
2277 addHistoryItem(trimRegion);
2279 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2281 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2282 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2284 viewport.getAlignment().deleteGroup(sg);
2288 viewport.firePropertyChange("alignment", null, viewport
2289 .getAlignment().getSequences());
2293 public void removeGappedColumnMenuItem_actionPerformed()
2295 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2298 if (viewport.getSelectionGroup() != null)
2300 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2301 viewport.getHiddenRepSequences());
2302 start = viewport.getSelectionGroup().getStartRes();
2303 end = viewport.getSelectionGroup().getEndRes();
2307 seqs = viewport.getAlignment().getSequencesArray();
2310 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2311 "Remove Gapped Columns", seqs, start, end,
2312 viewport.getAlignment());
2314 addHistoryItem(removeGapCols);
2316 statusBar.setText(MessageManager.formatMessage(
2317 "label.removed_empty_columns", new String[]
2318 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2320 // This is to maintain viewport position on first residue
2321 // of first sequence
2322 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2323 int startRes = seq.findPosition(viewport.startRes);
2324 // ShiftList shifts;
2325 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2326 // edit.alColumnChanges=shifts.getInverse();
2327 // if (viewport.hasHiddenColumns)
2328 // viewport.getColumnSelection().compensateForEdits(shifts);
2329 viewport.setStartRes(seq.findIndex(startRes) - 1);
2330 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2335 public void removeAllGapsMenuItem_actionPerformed()
2337 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2340 if (viewport.getSelectionGroup() != null)
2342 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2343 viewport.getHiddenRepSequences());
2344 start = viewport.getSelectionGroup().getStartRes();
2345 end = viewport.getSelectionGroup().getEndRes();
2349 seqs = viewport.getAlignment().getSequencesArray();
2352 // This is to maintain viewport position on first residue
2353 // of first sequence
2354 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2355 int startRes = seq.findPosition(viewport.startRes);
2357 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2358 viewport.getAlignment()));
2360 viewport.setStartRes(seq.findIndex(startRes) - 1);
2362 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2367 public void findMenuItem_actionPerformed()
2369 new Finder(alignPanel);
2373 * create a new view derived from the current view
2376 * @return frame for the new view
2378 public AlignFrame newView(String viewtitle)
2381 if (viewport.hasHiddenRows())
2383 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2384 .getFullAlignment().getSequencesArray());
2388 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2391 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2393 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2395 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2397 newal.addAnnotation(viewport.getAlignment()
2398 .getAlignmentAnnotation()[i]);
2403 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2405 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2406 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2407 PaintRefresher.Register(newaf.alignPanel,
2408 newaf.alignPanel.av.getSequenceSetId());
2410 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2411 newaf.alignPanel.av.getSequenceSetId());
2412 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2413 newaf.alignPanel.av.getSequenceSetId());
2415 Vector comps = (Vector) PaintRefresher.components.get(viewport
2416 .getSequenceSetId());
2418 for (int i = 0; i < comps.size(); i++)
2420 if (comps.elementAt(i) instanceof AlignmentPanel)
2426 String title = new String(this.getTitle());
2427 if (viewtitle != null)
2429 title = viewtitle + " ( " + title + ")";
2433 if (title.indexOf("(View") > -1)
2435 title = title.substring(0, title.indexOf("(View"));
2437 title += "(View " + viewSize + ")";
2440 newaf.setTitle(title.toString());
2442 newaf.viewport.setHistoryList(viewport.getHistoryList());
2443 newaf.viewport.setRedoList(viewport.getRedoList());
2449 * @return list of feature groups on the view
2451 public String[] getFeatureGroups()
2453 FeatureRenderer fr = null;
2454 if (alignPanel != null
2455 && (fr = alignPanel.getFeatureRenderer()) != null)
2457 List<String> gps = fr.getFeatureGroups();
2458 String[] _gps = gps.toArray(new String[gps.size()]);
2465 * get sequence feature groups that are hidden or shown
2471 public String[] getFeatureGroupsOfState(boolean visible)
2473 FeatureRenderer fr = null;
2474 if (alignPanel != null
2475 && (fr = alignPanel.getFeatureRenderer()) != null)
2477 List<String> gps = fr.getGroups(visible);
2478 String[] _gps = gps.toArray(new String[gps.size()]);
2485 * Change the display state for the given feature groups
2488 * list of group strings
2490 * visible or invisible
2492 public void setFeatureGroupState(String[] groups, boolean state)
2494 FeatureRenderer fr = null;
2495 this.sequenceFeatures.setState(true);
2496 viewport.setShowSequenceFeatures(true);
2497 if (alignPanel != null
2498 && (fr = alignPanel.getFeatureRenderer()) != null)
2501 fr.setGroupVisibility(Arrays.asList(groups), state);
2502 alignPanel.seqPanel.seqCanvas.repaint();
2503 if (alignPanel.overviewPanel != null)
2505 alignPanel.overviewPanel.updateOverviewImage();
2510 public void seqLimits_itemStateChanged()
2512 viewport.setShowJVSuffix(seqLimits.getState());
2513 alignPanel.fontChanged();
2514 alignPanel.paintAlignment(true);
2517 protected void colourTextMenuItem_actionPerformed()
2519 viewport.setColourText(colourTextMenuItem.getState());
2520 alignPanel.paintAlignment(true);
2523 protected void displayNonconservedMenuItem_actionPerformed()
2525 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2526 alignPanel.paintAlignment(true);
2529 protected void wrapMenuItem_actionPerformed()
2531 viewport.setWrapAlignment(wrapMenuItem.getState());
2532 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2533 scaleAbove.setEnabled(wrapMenuItem.getState());
2534 scaleLeft.setEnabled(wrapMenuItem.getState());
2535 scaleRight.setEnabled(wrapMenuItem.getState());
2536 alignPanel.paintAlignment(true);
2539 public void overviewMenuItem_actionPerformed()
2541 if (alignPanel.overviewPanel != null)
2546 Frame frame = new Frame();
2547 OverviewPanel overview = new OverviewPanel(alignPanel);
2548 frame.add(overview);
2549 // +50 must allow for applet frame window
2550 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2551 "label.overview_params", new String[]
2552 { this.getTitle() }), overview.getPreferredSize().width,
2553 overview.getPreferredSize().height + 50);
2556 final AlignmentPanel ap = alignPanel;
2557 frame.addWindowListener(new WindowAdapter()
2560 public void windowClosing(WindowEvent e)
2564 ap.setOverviewPanel(null);
2569 alignPanel.setOverviewPanel(overview);
2573 public void changeColour(ColourSchemeI cs)
2579 if (viewport.getAbovePIDThreshold())
2581 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2585 if (viewport.getConservationSelected())
2587 cs.setConservationApplied(true);
2588 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2593 cs.setConservationApplied(false);
2596 viewport.setGlobalColourScheme(cs);
2598 if (alignPanel.getOverviewPanel() != null)
2600 alignPanel.getOverviewPanel().updateOverviewImage();
2603 jalview.structure.StructureSelectionManager
2604 .getStructureSelectionManager(viewport.applet)
2605 .sequenceColoursChanged(alignPanel);
2607 alignPanel.paintAlignment(true);
2610 protected void modifyPID_actionPerformed()
2612 if (viewport.getAbovePIDThreshold()
2613 && viewport.getGlobalColourScheme() != null)
2615 SliderPanel.setPIDSliderSource(alignPanel,
2616 viewport.getGlobalColourScheme(), "Background");
2617 SliderPanel.showPIDSlider();
2621 protected void modifyConservation_actionPerformed()
2623 if (viewport.getConservationSelected()
2624 && viewport.getGlobalColourScheme() != null)
2626 SliderPanel.setConservationSlider(alignPanel,
2627 viewport.getGlobalColourScheme(), "Background");
2628 SliderPanel.showConservationSlider();
2632 protected void conservationMenuItem_actionPerformed()
2634 viewport.setConservationSelected(conservationMenuItem.getState());
2636 viewport.setAbovePIDThreshold(false);
2637 abovePIDThreshold.setState(false);
2639 changeColour(viewport.getGlobalColourScheme());
2641 modifyConservation_actionPerformed();
2644 public void abovePIDThreshold_actionPerformed()
2646 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2648 conservationMenuItem.setState(false);
2649 viewport.setConservationSelected(false);
2651 changeColour(viewport.getGlobalColourScheme());
2653 modifyPID_actionPerformed();
2656 public void sortPairwiseMenuItem_actionPerformed()
2658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2659 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2660 .getAlignment().getSequenceAt(0), null);
2662 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2663 viewport.getAlignment()));
2664 alignPanel.paintAlignment(true);
2667 public void sortIDMenuItem_actionPerformed()
2669 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2670 AlignmentSorter.sortByID(viewport.getAlignment());
2671 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2672 viewport.getAlignment()));
2673 alignPanel.paintAlignment(true);
2676 public void sortLengthMenuItem_actionPerformed()
2678 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2679 AlignmentSorter.sortByLength(viewport.getAlignment());
2680 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2681 viewport.getAlignment()));
2682 alignPanel.paintAlignment(true);
2685 public void sortGroupMenuItem_actionPerformed()
2687 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2688 AlignmentSorter.sortByGroup(viewport.getAlignment());
2689 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2690 viewport.getAlignment()));
2691 alignPanel.paintAlignment(true);
2695 public void removeRedundancyMenuItem_actionPerformed()
2697 new RedundancyPanel(alignPanel);
2700 public void pairwiseAlignmentMenuItem_actionPerformed()
2702 if (viewport.getSelectionGroup() != null
2703 && viewport.getSelectionGroup().getSize() > 1)
2705 Frame frame = new Frame();
2706 frame.add(new PairwiseAlignPanel(alignPanel));
2707 jalview.bin.JalviewLite.addFrame(frame,
2708 MessageManager.getString("action.pairwise_alignment"), 600,
2713 public void PCAMenuItem_actionPerformed()
2715 // are the sequences aligned?
2716 if (!viewport.getAlignment().isAligned(false))
2719 int Width = viewport.getAlignment().getWidth();
2721 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2723 current = viewport.getAlignment().getSequenceAt(i);
2725 if (current.getLength() < Width)
2727 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2730 alignPanel.paintAlignment(true);
2733 if ((viewport.getSelectionGroup() != null
2734 && viewport.getSelectionGroup().getSize() < 4 && viewport
2735 .getSelectionGroup().getSize() > 0)
2736 || viewport.getAlignment().getHeight() < 4)
2743 new PCAPanel(viewport);
2744 } catch (java.lang.OutOfMemoryError ex)
2750 public void averageDistanceTreeMenuItem_actionPerformed()
2752 NewTreePanel("AV", "PID", "Average distance tree using PID");
2755 public void neighbourTreeMenuItem_actionPerformed()
2757 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2760 protected void njTreeBlosumMenuItem_actionPerformed()
2762 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2765 protected void avTreeBlosumMenuItem_actionPerformed()
2767 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2770 void NewTreePanel(String type, String pwType, String title)
2772 // are the sequences aligned?
2773 if (!viewport.getAlignment().isAligned(false))
2776 int Width = viewport.getAlignment().getWidth();
2778 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2780 current = viewport.getAlignment().getSequenceAt(i);
2782 if (current.getLength() < Width)
2784 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2787 alignPanel.paintAlignment(true);
2791 if ((viewport.getSelectionGroup() != null && viewport
2792 .getSelectionGroup().getSize() > 1)
2793 || (viewport.getAlignment().getHeight() > 1))
2795 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2797 addTreeMenuItem(tp, title);
2799 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2803 void loadTree_actionPerformed()
2805 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2806 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2807 cap.setTreeImport();
2808 Frame frame = new Frame();
2810 jalview.bin.JalviewLite.addFrame(frame,
2811 MessageManager.getString("label.paste_newick_file"), 400, 300);
2814 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2816 TreePanel tp = new TreePanel(alignPanel, treeFile,
2817 MessageManager.getString("label.load_tree_from_file"), tree);
2818 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2819 addTreeMenuItem(tp, treeFile);
2823 * sort the alignment using the given treePanel
2826 * tree used to sort view
2828 * string used for undo event name
2830 public void sortByTree(TreePanel treePanel, String title)
2832 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2834 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2835 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2836 // HistoryItem.SORT));
2837 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2838 "label.order_by_params", new String[]
2839 { title }), oldOrder, viewport.getAlignment()));
2840 alignPanel.paintAlignment(true);
2844 * Do any automatic reordering of the alignment and add the necessary bits to
2845 * the menu structure for the new tree
2850 protected void addTreeMenuItem(final TreePanel treePanel,
2853 final MenuItem item = new MenuItem(title);
2854 sortByTreeMenu.add(item);
2855 item.addActionListener(new java.awt.event.ActionListener()
2858 public void actionPerformed(ActionEvent evt)
2860 sortByTree(treePanel, title); // treePanel.getTitle());
2864 treePanel.addWindowListener(new WindowAdapter()
2867 public void windowOpened(WindowEvent e)
2869 if (viewport.sortByTree)
2871 sortByTree(treePanel, title);
2873 super.windowOpened(e);
2877 public void windowClosing(WindowEvent e)
2879 sortByTreeMenu.remove(item);
2884 public boolean sortBy(AlignmentOrder alorder, String undoname)
2886 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2887 if (viewport.applet.debug)
2889 System.err.println("Sorting " + alorder.getOrder().size()
2890 + " in alignment '" + getTitle() + "'");
2892 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2893 if (undoname != null)
2895 addHistoryItem(new OrderCommand(undoname, oldOrder,
2896 viewport.getAlignment()));
2898 alignPanel.paintAlignment(true);
2902 protected void documentation_actionPerformed()
2904 alignPanel.av.applet.openJalviewHelpUrl();
2907 protected void about_actionPerformed()
2910 class AboutPanel extends Canvas
2916 public AboutPanel(String version, String builddate)
2918 this.version = version;
2919 this.builddate = builddate;
2923 public void paint(Graphics g)
2925 g.setColor(Color.white);
2926 g.fillRect(0, 0, getSize().width, getSize().height);
2927 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2928 FontMetrics fm = g.getFontMetrics();
2929 int fh = fm.getHeight();
2931 g.setColor(Color.black);
2932 // TODO: update this text for each release or centrally store it for
2933 // lite and application
2934 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2935 g.drawString(MessageManager.formatMessage(
2936 "label.jalviewLite_release", new String[]
2937 { version }), x, y += fh);
2938 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2939 g.drawString(MessageManager.formatMessage(
2940 "label.jaview_build_date", new String[]
2941 { builddate }), x, y += fh);
2942 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2943 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2945 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2946 x + 50, y += fh + 8);
2948 MessageManager.getString("label.jalview_dev_managers"), x,
2950 g.drawString(MessageManager
2951 .getString("label.jalview_distribution_lists"), x, y += fh);
2952 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2955 MessageManager.getString("label.jalview_cite_1_authors"),
2958 MessageManager.getString("label.jalview_cite_1_title"), x,
2960 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2965 Frame frame = new Frame();
2966 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2968 jalview.bin.JalviewLite.addFrame(frame,
2969 MessageManager.getString("label.jalview"), 580, 220);
2973 public void showURL(String url, String target)
2975 if (viewport.applet == null)
2977 System.out.println("Not running as applet - no browser available.");
2981 viewport.applet.showURL(url, target);
2985 // ////////////////////////////////////////////////////////////////////////////////
2986 // JBuilder Graphics here
2988 MenuBar alignFrameMenuBar = new MenuBar();
2990 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2992 MenuItem loadApplication = new MenuItem(
2993 MessageManager.getString("label.view_full_application"));
2995 MenuItem loadTree = new MenuItem(
2996 MessageManager.getString("label.load_associated_tree"));
2998 MenuItem loadAnnotations = new MenuItem(
2999 MessageManager.getString("label.load_features_annotations"));
3001 MenuItem outputFeatures = new MenuItem(
3002 MessageManager.getString("label.export_features").concat("..."));
3004 MenuItem outputAnnotations = new MenuItem(
3005 MessageManager.getString("label.export_annotations").concat("..."));
3007 MenuItem closeMenuItem = new MenuItem(
3008 MessageManager.getString("action.close"));
3010 MenuItem selectAllSequenceMenuItem = new MenuItem(
3011 MessageManager.getString("action.select_all"));
3013 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3014 MessageManager.getString("action.deselect_all"));
3016 MenuItem invertSequenceMenuItem = new MenuItem(
3017 MessageManager.getString("action.invert_selection"));
3019 MenuItem remove2LeftMenuItem = new MenuItem();
3021 MenuItem remove2RightMenuItem = new MenuItem();
3023 MenuItem removeGappedColumnMenuItem = new MenuItem();
3025 MenuItem removeAllGapsMenuItem = new MenuItem();
3027 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3029 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3031 MenuItem sortPairwiseMenuItem = new MenuItem();
3033 MenuItem sortIDMenuItem = new MenuItem();
3035 MenuItem sortLengthMenuItem = new MenuItem();
3037 MenuItem sortGroupMenuItem = new MenuItem();
3039 MenuItem removeRedundancyMenuItem = new MenuItem();
3041 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3043 MenuItem PCAMenuItem = new MenuItem();
3045 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3047 MenuItem neighbourTreeMenuItem = new MenuItem();
3049 BorderLayout borderLayout1 = new BorderLayout();
3051 public Label statusBar = new Label();
3053 MenuItem clustalColour = new MenuItem();
3055 MenuItem zappoColour = new MenuItem();
3057 MenuItem taylorColour = new MenuItem();
3059 MenuItem hydrophobicityColour = new MenuItem();
3061 MenuItem helixColour = new MenuItem();
3063 MenuItem strandColour = new MenuItem();
3065 MenuItem turnColour = new MenuItem();
3067 MenuItem buriedColour = new MenuItem();
3069 MenuItem purinePyrimidineColour = new MenuItem();
3071 MenuItem RNAInteractionColour = new MenuItem();
3073 MenuItem RNAHelixColour = new MenuItem();
3075 MenuItem userDefinedColour = new MenuItem();
3077 MenuItem PIDColour = new MenuItem();
3079 MenuItem BLOSUM62Colour = new MenuItem();
3081 MenuItem tcoffeeColour = new MenuItem();
3083 MenuItem njTreeBlosumMenuItem = new MenuItem();
3085 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3087 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3089 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3091 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3093 MenuItem alProperties = new MenuItem(
3094 MessageManager.getString("label.alignment_props"));
3096 MenuItem overviewMenuItem = new MenuItem();
3098 MenuItem undoMenuItem = new MenuItem();
3100 MenuItem redoMenuItem = new MenuItem();
3102 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3104 MenuItem noColourmenuItem = new MenuItem();
3106 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3108 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3110 MenuItem findMenuItem = new MenuItem();
3112 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3114 MenuItem nucleotideColour = new MenuItem();
3116 MenuItem deleteGroups = new MenuItem();
3118 MenuItem grpsFromSelection = new MenuItem();
3120 MenuItem createGroup = new MenuItem();
3122 MenuItem unGroup = new MenuItem();
3124 MenuItem delete = new MenuItem();
3126 MenuItem copy = new MenuItem();
3128 MenuItem cut = new MenuItem();
3130 Menu pasteMenu = new Menu();
3132 MenuItem pasteNew = new MenuItem();
3134 MenuItem pasteThis = new MenuItem();
3136 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3138 MenuItem font = new MenuItem();
3140 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3142 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3144 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3146 MenuItem modifyPID = new MenuItem();
3148 MenuItem modifyConservation = new MenuItem();
3150 CheckboxMenuItem autoCalculate = null;
3152 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3153 "Sort Alignment With New Tree", true);
3155 Menu sortByTreeMenu = new Menu();
3157 MenuItem inputText = new MenuItem();
3159 MenuItem documentation = new MenuItem();
3161 MenuItem about = new MenuItem();
3163 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3165 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3167 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3169 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3171 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3173 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3175 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3177 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3179 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3182 * Initialise menus and other items
3186 private void jbInit() throws Exception
3188 setMenuBar(alignFrameMenuBar);
3191 * Configure File menu items and actions
3194 .setLabel(MessageManager.getString("label.input_from_textbox"));
3195 inputText.addActionListener(this);
3196 Menu outputTextboxMenu = new Menu(
3197 MessageManager.getString("label.out_to_textbox"));
3198 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3201 MenuItem item = new MenuItem(
3202 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3204 item.addActionListener(new java.awt.event.ActionListener()
3207 public void actionPerformed(ActionEvent e)
3209 outputText_actionPerformed(e);
3213 outputTextboxMenu.add(item);
3215 closeMenuItem.addActionListener(this);
3216 loadApplication.addActionListener(this);
3217 loadTree.addActionListener(this);
3218 loadAnnotations.addActionListener(this);
3219 outputFeatures.addActionListener(this);
3220 outputAnnotations.addActionListener(this);
3223 * Configure Edit menu items and actions
3225 undoMenuItem.setEnabled(false);
3226 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3227 undoMenuItem.addActionListener(this);
3228 redoMenuItem.setEnabled(false);
3229 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3230 redoMenuItem.addActionListener(this);
3231 copy.setLabel(MessageManager.getString("action.copy"));
3232 copy.addActionListener(this);
3233 cut.setLabel(MessageManager.getString("action.cut"));
3234 cut.addActionListener(this);
3235 delete.setLabel(MessageManager.getString("action.delete"));
3236 delete.addActionListener(this);
3237 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3238 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3239 pasteNew.addActionListener(this);
3240 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3241 pasteThis.addActionListener(this);
3242 remove2LeftMenuItem.setLabel(MessageManager
3243 .getString("action.remove_left"));
3244 remove2LeftMenuItem.addActionListener(this);
3245 remove2RightMenuItem.setLabel(MessageManager
3246 .getString("action.remove_right"));
3247 remove2RightMenuItem.addActionListener(this);
3248 removeGappedColumnMenuItem.setLabel(MessageManager
3249 .getString("action.remove_empty_columns"));
3250 removeGappedColumnMenuItem.addActionListener(this);
3251 removeAllGapsMenuItem.setLabel(MessageManager
3252 .getString("action.remove_all_gaps"));
3253 removeAllGapsMenuItem.addActionListener(this);
3254 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3255 "action.remove_redundancy").concat("..."));
3256 removeRedundancyMenuItem.addActionListener(this);
3259 * Configure Select menu items and actions
3261 findMenuItem.setLabel(MessageManager.getString("action.find"));
3262 findMenuItem.addActionListener(this);
3263 selectAllSequenceMenuItem.addActionListener(this);
3264 deselectAllSequenceMenuItem.addActionListener(this);
3265 invertSequenceMenuItem.setLabel(MessageManager
3266 .getString("action.invert_sequence_selection"));
3267 invertSequenceMenuItem.addActionListener(this);
3268 invertColSel.setLabel(MessageManager
3269 .getString("action.invert_column_selection"));
3270 invertColSel.addActionListener(this);
3271 deleteGroups.setLabel(MessageManager
3272 .getString("action.undefine_groups"));
3273 deleteGroups.addActionListener(this);
3274 grpsFromSelection.setLabel(MessageManager
3275 .getString("action.make_groups_selection"));
3276 grpsFromSelection.addActionListener(this);
3277 createGroup.setLabel(MessageManager.getString("action.create_group"));
3278 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3279 annotationColumnSelection.setLabel("Select by Annotation");
3280 annotationColumnSelection.addActionListener(this);
3283 * Configure View menu items and actions
3285 newView.setLabel(MessageManager.getString("action.new_view"));
3286 newView.addActionListener(this);
3287 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3288 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3289 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3290 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3292 .setLabel(MessageManager.getString("label.selected_columns"));
3293 hideSequences.setLabel(MessageManager
3294 .getString("label.selected_sequences"));
3295 hideAllButSelection.setLabel(MessageManager
3296 .getString("label.all_but_selected_region"));
3297 hideAllSelection.setLabel(MessageManager
3298 .getString("label.selected_region"));
3299 showAllHidden.setLabel(MessageManager
3300 .getString("label.all_sequences_columns"));
3301 showColumns.addActionListener(this);
3302 showSeqs.addActionListener(this);
3303 hideColumns.addActionListener(this);
3304 hideSequences.addActionListener(this);
3305 hideAllButSelection.addActionListener(this);
3306 hideAllSelection.addActionListener(this);
3307 showAllHidden.addActionListener(this);
3308 featureSettings.setLabel(MessageManager
3309 .getString("label.feature_settings"));
3310 featureSettings.addActionListener(this);
3311 sequenceFeatures.setLabel(MessageManager
3312 .getString("label.show_sequence_features"));
3313 sequenceFeatures.addItemListener(this);
3314 sequenceFeatures.setState(false);
3315 followMouseOverFlag.setLabel(MessageManager
3316 .getString("label.automatic_scrolling"));
3317 followMouseOverFlag.addItemListener(this);
3318 alProperties.addActionListener(this);
3319 overviewMenuItem.setLabel(MessageManager
3320 .getString("label.overview_window"));
3321 overviewMenuItem.addActionListener(this);
3324 * Configure Annotations menu items and actions
3326 annotationPanelMenuItem.setLabel(MessageManager
3327 .getString("label.show_annotations"));
3328 annotationPanelMenuItem.addItemListener(this);
3329 showGroupConsensus.setLabel(MessageManager
3330 .getString("label.group_consensus"));
3331 showGroupConservation.setLabel(MessageManager
3332 .getString("label.group_conservation"));
3333 showConsensusHistogram.setLabel(MessageManager
3334 .getString("label.show_consensus_histogram"));
3335 showSequenceLogo.setLabel(MessageManager
3336 .getString("label.show_consensus_logo"));
3337 normSequenceLogo.setLabel(MessageManager
3338 .getString("label.norm_consensus_logo"));
3339 applyAutoAnnotationSettings.setLabel(MessageManager
3340 .getString("label.apply_all_groups"));
3341 applyAutoAnnotationSettings.setState(true);
3342 Menu autoAnnMenu = new Menu(
3343 MessageManager.getString("label.autocalculated_annotation"));
3344 showGroupConsensus.addItemListener(this);
3345 showGroupConservation.addItemListener(this);
3346 showConsensusHistogram.addItemListener(this);
3347 showSequenceLogo.addItemListener(this);
3348 normSequenceLogo.addItemListener(this);
3349 applyAutoAnnotationSettings.addItemListener(this);
3350 showAlignmentAnnotations = new CheckboxMenuItem(
3351 MessageManager.getString("label.show_all_al_annotations"));
3352 showSequenceAnnotations = new CheckboxMenuItem(
3353 MessageManager.getString("label.show_all_seq_annotations"));
3354 sortAnnBySequence = new CheckboxMenuItem(
3355 MessageManager.getString("label.sort_annotations_by_sequence"));
3356 sortAnnByLabel = new CheckboxMenuItem(
3357 MessageManager.getString("label.sort_annotations_by_label"));
3358 showAutoFirst = new CheckboxMenuItem(
3359 MessageManager.getString("label.show_first"));
3360 showAutoLast = new CheckboxMenuItem(
3361 MessageManager.getString("label.show_last"));
3362 showAlignmentAnnotations.addItemListener(this);
3363 showSequenceAnnotations.addItemListener(this);
3364 sortAnnBySequence.addItemListener(this);
3365 sortAnnByLabel.addItemListener(this);
3366 showAutoFirst.addItemListener(this);
3367 showAutoLast.addItemListener(this);
3370 * Configure Format menu items and actions
3372 font.setLabel(MessageManager.getString("action.font"));
3373 font.addActionListener(this);
3374 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3375 scaleAbove.setState(true);
3376 scaleAbove.setEnabled(false);
3377 scaleAbove.addItemListener(this);
3378 scaleLeft.setEnabled(false);
3379 scaleLeft.setState(true);
3380 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3381 scaleLeft.addItemListener(this);
3382 scaleRight.setEnabled(false);
3383 scaleRight.setState(true);
3384 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3385 scaleRight.addItemListener(this);
3386 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3387 viewBoxesMenuItem.setState(true);
3388 viewBoxesMenuItem.addItemListener(this);
3389 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3390 viewTextMenuItem.setState(true);
3391 viewTextMenuItem.addItemListener(this);
3392 colourTextMenuItem.setLabel(MessageManager
3393 .getString("label.colour_text"));
3394 colourTextMenuItem.addItemListener(this);
3395 displayNonconservedMenuItem.setLabel(MessageManager
3396 .getString("label.show_non_conversed"));
3397 displayNonconservedMenuItem.addItemListener(this);
3398 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3399 wrapMenuItem.addItemListener(this);
3400 renderGapsMenuItem.setLabel(MessageManager
3401 .getString("action.show_gaps"));
3402 renderGapsMenuItem.setState(true);
3403 renderGapsMenuItem.addItemListener(this);
3404 centreColumnLabelFlag.setLabel(MessageManager
3405 .getString("label.centre_column_labels"));
3406 centreColumnLabelFlag.addItemListener(this);
3407 seqLimits.setState(true);
3408 seqLimits.setLabel(MessageManager
3409 .getString("label.show_sequence_limits"));
3410 seqLimits.addItemListener(this);
3413 * Configure Colour menu items and actions
3415 applyToAllGroups.setLabel(MessageManager
3416 .getString("label.apply_colour_to_all_groups"));
3417 applyToAllGroups.setState(true);
3418 applyToAllGroups.addItemListener(this);
3419 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3420 clustalColour.addActionListener(this);
3421 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3422 zappoColour.addActionListener(this);
3423 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3424 taylorColour.addActionListener(this);
3425 hydrophobicityColour.setLabel(MessageManager
3426 .getString("label.hydrophobicity"));
3427 hydrophobicityColour.addActionListener(this);
3429 .setLabel(MessageManager.getString("label.helix_propensity"));
3430 helixColour.addActionListener(this);
3431 strandColour.setLabel(MessageManager
3432 .getString("label.strand_propensity"));
3433 strandColour.addActionListener(this);
3434 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3435 turnColour.addActionListener(this);
3436 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3437 buriedColour.addActionListener(this);
3438 purinePyrimidineColour.setLabel(MessageManager
3439 .getString("label.purine_pyrimidine"));
3440 purinePyrimidineColour.addActionListener(this);
3441 RNAInteractionColour.setLabel(MessageManager
3442 .getString("label.rna_interaction"));
3443 RNAInteractionColour.addActionListener(this);
3444 RNAHelixColour.setLabel(MessageManager
3445 .getString("action.by_rna_helixes"));
3446 RNAHelixColour.addActionListener(this);
3447 userDefinedColour.setLabel(MessageManager
3448 .getString("action.user_defined"));
3449 userDefinedColour.addActionListener(this);
3450 PIDColour.setLabel(MessageManager
3451 .getString("label.percentage_identity"));
3452 PIDColour.addActionListener(this);
3453 BLOSUM62Colour.setLabel(MessageManager
3454 .getString("label.blosum62_score"));
3455 BLOSUM62Colour.addActionListener(this);
3457 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3458 // it will be enabled only if a score file is provided
3459 tcoffeeColour.setEnabled(false);
3460 tcoffeeColour.addActionListener(this);
3461 conservationMenuItem.setLabel(MessageManager
3462 .getString("action.by_conservation"));
3463 conservationMenuItem.addItemListener(this);
3464 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3465 noColourmenuItem.addActionListener(this);
3466 abovePIDThreshold.setLabel(MessageManager
3467 .getString("label.above_identity_threshold"));
3468 abovePIDThreshold.addItemListener(this);
3469 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3470 nucleotideColour.addActionListener(this);
3471 modifyPID.setLabel(MessageManager
3472 .getString("label.modify_identity_thereshold"));
3473 modifyPID.addActionListener(this);
3474 modifyConservation.setLabel(MessageManager
3475 .getString("label.modify_conservation_thereshold"));
3476 modifyConservation.addActionListener(this);
3477 annotationColour.setLabel(MessageManager
3478 .getString("action.by_annotation"));
3479 annotationColour.addActionListener(this);
3482 * Configure Calculate menu items and actions
3484 sortPairwiseMenuItem.setLabel(MessageManager
3485 .getString("action.by_pairwise_id"));
3486 sortPairwiseMenuItem.addActionListener(this);
3487 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3488 sortIDMenuItem.addActionListener(this);
3489 sortLengthMenuItem.setLabel(MessageManager
3490 .getString("action.by_length"));
3491 sortLengthMenuItem.addActionListener(this);
3492 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3493 sortGroupMenuItem.addActionListener(this);
3494 pairwiseAlignmentMenuItem.setLabel(MessageManager
3495 .getString("action.pairwise_alignment"));
3496 pairwiseAlignmentMenuItem.addActionListener(this);
3497 PCAMenuItem.setLabel(MessageManager
3498 .getString("label.principal_component_analysis"));
3499 PCAMenuItem.addActionListener(this);
3500 autoCalculate = new CheckboxMenuItem(
3501 MessageManager.getString("label.autocalculate_consensus"), true);
3502 averageDistanceTreeMenuItem.setLabel(MessageManager
3503 .getString("label.average_distance_identity"));
3504 averageDistanceTreeMenuItem.addActionListener(this);
3505 neighbourTreeMenuItem.setLabel(MessageManager
3506 .getString("label.neighbour_joining_identity"));
3507 neighbourTreeMenuItem.addActionListener(this);
3508 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3509 .getString("label.average_distance_bloslum62"));
3510 avDistanceTreeBlosumMenuItem.addActionListener(this);
3511 njTreeBlosumMenuItem.setLabel(MessageManager
3512 .getString("label.neighbour_blosum62"));
3513 njTreeBlosumMenuItem.addActionListener(this);
3514 sortByTreeMenu.setLabel(MessageManager
3515 .getString("action.by_tree_order"));
3516 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3517 Menu calculateTreeMenu = new Menu(
3518 MessageManager.getString("action.calculate_tree"));
3519 autoCalculate.addItemListener(this);
3520 sortByTree.addItemListener(this);
3523 * Configure Help menu items and actions
3525 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3526 documentation.setLabel(MessageManager.getString("label.documentation"));
3527 documentation.addActionListener(this);
3528 about.setLabel(MessageManager.getString("label.about"));
3529 about.addActionListener(this);
3532 * Add top level menus to frame
3534 alignFrameMenuBar.add(fileMenu);
3535 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3536 alignFrameMenuBar.add(editMenu);
3537 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3538 alignFrameMenuBar.add(selectMenu);
3539 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3540 alignFrameMenuBar.add(viewMenu);
3541 Menu annotationsMenu = new Menu(
3542 MessageManager.getString("action.annotations"));
3543 alignFrameMenuBar.add(annotationsMenu);
3544 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3545 alignFrameMenuBar.add(formatMenu);
3546 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3547 alignFrameMenuBar.add(colourMenu);
3548 Menu calculateMenu = new Menu(
3549 MessageManager.getString("action.calculate"));
3550 alignFrameMenuBar.add(calculateMenu);
3551 alignFrameMenuBar.add(helpMenu);
3556 fileMenu.add(inputText);
3557 fileMenu.add(loadTree);
3558 fileMenu.add(loadAnnotations);
3559 fileMenu.addSeparator();
3560 fileMenu.add(outputTextboxMenu);
3561 fileMenu.add(outputFeatures);
3562 fileMenu.add(outputAnnotations);
3563 if (jalviewServletURL != null)
3565 fileMenu.add(loadApplication);
3567 fileMenu.addSeparator();
3568 fileMenu.add(closeMenuItem);
3573 editMenu.add(undoMenuItem);
3574 editMenu.add(redoMenuItem);
3577 pasteMenu.add(pasteNew);
3578 pasteMenu.add(pasteThis);
3579 editMenu.add(pasteMenu);
3580 editMenu.add(delete);
3581 editMenu.addSeparator();
3582 editMenu.add(remove2LeftMenuItem);
3583 editMenu.add(remove2RightMenuItem);
3584 editMenu.add(removeGappedColumnMenuItem);
3585 editMenu.add(removeAllGapsMenuItem);
3586 editMenu.add(removeRedundancyMenuItem);
3591 selectMenu.add(findMenuItem);
3592 selectMenu.addSeparator();
3593 selectMenu.add(selectAllSequenceMenuItem);
3594 selectMenu.add(deselectAllSequenceMenuItem);
3595 selectMenu.add(invertSequenceMenuItem);
3596 selectMenu.add(invertColSel);
3597 selectMenu.add(createGroup);
3598 selectMenu.add(unGroup);
3599 selectMenu.add(grpsFromSelection);
3600 selectMenu.add(deleteGroups);
3601 selectMenu.add(annotationColumnSelection);
3606 viewMenu.add(newView);
3607 viewMenu.addSeparator();
3608 showMenu.add(showColumns);
3609 showMenu.add(showSeqs);
3610 showMenu.add(showAllHidden);
3611 viewMenu.add(showMenu);
3612 hideMenu.add(hideColumns);
3613 hideMenu.add(hideSequences);
3614 hideMenu.add(hideAllSelection);
3615 hideMenu.add(hideAllButSelection);
3616 viewMenu.add(hideMenu);
3617 viewMenu.addSeparator();
3618 viewMenu.add(followMouseOverFlag);
3619 viewMenu.addSeparator();
3620 viewMenu.add(sequenceFeatures);
3621 viewMenu.add(featureSettings);
3622 viewMenu.addSeparator();
3623 viewMenu.add(alProperties);
3624 viewMenu.addSeparator();
3625 viewMenu.add(overviewMenuItem);
3630 annotationsMenu.add(annotationPanelMenuItem);
3631 annotationsMenu.addSeparator();
3632 annotationsMenu.add(showAlignmentAnnotations);
3633 annotationsMenu.add(showSequenceAnnotations);
3634 annotationsMenu.add(sortAnnBySequence);
3635 annotationsMenu.add(sortAnnByLabel);
3636 annotationsMenu.addSeparator();
3637 autoAnnMenu.add(showAutoFirst);
3638 autoAnnMenu.add(showAutoLast);
3639 autoAnnMenu.addSeparator();
3640 autoAnnMenu.add(applyAutoAnnotationSettings);
3641 autoAnnMenu.add(showConsensusHistogram);
3642 autoAnnMenu.add(showSequenceLogo);
3643 autoAnnMenu.add(normSequenceLogo);
3644 autoAnnMenu.addSeparator();
3645 autoAnnMenu.add(showGroupConservation);
3646 autoAnnMenu.add(showGroupConsensus);
3647 annotationsMenu.add(autoAnnMenu);
3652 formatMenu.add(font);
3653 formatMenu.add(seqLimits);
3654 formatMenu.add(wrapMenuItem);
3655 formatMenu.add(scaleAbove);
3656 formatMenu.add(scaleLeft);
3657 formatMenu.add(scaleRight);
3658 formatMenu.add(viewBoxesMenuItem);
3659 formatMenu.add(viewTextMenuItem);
3660 formatMenu.add(colourTextMenuItem);
3661 formatMenu.add(displayNonconservedMenuItem);
3662 formatMenu.add(renderGapsMenuItem);
3663 formatMenu.add(centreColumnLabelFlag);
3668 colourMenu.add(applyToAllGroups);
3669 colourMenu.addSeparator();
3670 colourMenu.add(noColourmenuItem);
3671 colourMenu.add(clustalColour);
3672 colourMenu.add(BLOSUM62Colour);
3673 colourMenu.add(PIDColour);
3674 colourMenu.add(zappoColour);
3675 colourMenu.add(taylorColour);
3676 colourMenu.add(hydrophobicityColour);
3677 colourMenu.add(helixColour);
3678 colourMenu.add(strandColour);
3679 colourMenu.add(turnColour);
3680 colourMenu.add(buriedColour);
3681 colourMenu.add(nucleotideColour);
3682 colourMenu.add(purinePyrimidineColour);
3683 // colourMenu.add(RNAInteractionColour);
3684 colourMenu.add(tcoffeeColour);
3685 colourMenu.add(userDefinedColour);
3686 colourMenu.addSeparator();
3687 colourMenu.add(conservationMenuItem);
3688 colourMenu.add(modifyConservation);
3689 colourMenu.add(abovePIDThreshold);
3690 colourMenu.add(modifyPID);
3691 colourMenu.add(annotationColour);
3692 colourMenu.add(RNAHelixColour);
3697 sortMenu.add(sortIDMenuItem);
3698 sortMenu.add(sortLengthMenuItem);
3699 sortMenu.add(sortByTreeMenu);
3700 sortMenu.add(sortGroupMenuItem);
3701 sortMenu.add(sortPairwiseMenuItem);
3702 calculateMenu.add(sortMenu);
3703 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3704 calculateTreeMenu.add(neighbourTreeMenuItem);
3705 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3706 calculateTreeMenu.add(njTreeBlosumMenuItem);
3707 calculateMenu.add(calculateTreeMenu);
3708 calculateMenu.addSeparator();
3709 calculateMenu.add(pairwiseAlignmentMenuItem);
3710 calculateMenu.add(PCAMenuItem);
3711 calculateMenu.add(autoCalculate);
3712 calculateMenu.add(sortByTree);
3717 helpMenu.add(documentation);
3718 helpMenu.add(about);
3723 statusBar.setBackground(Color.white);
3724 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3725 statusBar.setText(MessageManager.getString("label.status_bar"));
3726 this.add(statusBar, BorderLayout.SOUTH);
3729 public void setStatus(String string)
3731 statusBar.setText(string);
3734 MenuItem featureSettings = new MenuItem();
3736 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3738 MenuItem annotationColour = new MenuItem();
3740 MenuItem annotationColumnSelection = new MenuItem();
3742 MenuItem invertColSel = new MenuItem();
3744 MenuItem showColumns = new MenuItem();
3746 MenuItem showSeqs = new MenuItem();
3748 MenuItem hideColumns = new MenuItem();
3750 MenuItem hideSequences = new MenuItem();
3752 MenuItem hideAllButSelection = new MenuItem();
3754 MenuItem hideAllSelection = new MenuItem();
3756 MenuItem showAllHidden = new MenuItem();
3758 MenuItem newView = new MenuItem();
3760 private CheckboxMenuItem showAlignmentAnnotations;
3762 private CheckboxMenuItem showSequenceAnnotations;
3764 private CheckboxMenuItem sortAnnBySequence;
3766 private CheckboxMenuItem sortAnnByLabel;
3768 private CheckboxMenuItem showAutoFirst;
3770 private CheckboxMenuItem showAutoLast;
3772 private SplitFrame splitFrame;
3775 * Attach the alignFrame panels after embedding menus, if necessary. This used
3776 * to be called setEmbedded, but is now creates the dropdown menus in a
3777 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3779 * @param reallyEmbedded
3780 * true to attach the view to the applet area on the page rather than
3783 public void createAlignFrameWindow(boolean reallyEmbedded)
3787 embedAlignFrameInApplet(viewport.applet);
3792 // test and embed menu bar if necessary.
3794 if (embedMenuIfNeeded(alignPanel))
3797 * adjust for status bar height too. ? pointless as overridden by layout
3800 alignPanel.setSize(getSize().width,
3801 getSize().height - statusBar.getHeight());
3803 add(statusBar, BorderLayout.SOUTH);
3804 add(alignPanel, BorderLayout.CENTER);
3805 // and register with the applet so it can pass external API calls to us
3806 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3813 * Add the components of this AlignFrame to the applet container.
3817 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3820 // Explicitly build the embedded menu panel for the on-page applet
3822 // view cannot be closed if its actually on the page
3823 fileMenu.remove(closeMenuItem);
3824 fileMenu.remove(3); // Remove Separator
3825 // construct embedded menu, using default font
3826 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3827 // and actually add the components to the applet area
3828 theApplet.setLayout(new BorderLayout());
3829 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3830 theApplet.add(statusBar, BorderLayout.SOUTH);
3831 // TODO should size be left to the layout manager?
3832 alignPanel.setSize(theApplet.getSize().width,
3833 theApplet.getSize().height - embeddedMenu.getHeight()
3834 - statusBar.getHeight());
3835 theApplet.add(alignPanel, BorderLayout.CENTER);
3836 final AlignFrame me = this;
3837 theApplet.addFocusListener(new FocusListener()
3841 public void focusLost(FocusEvent e)
3843 if (theApplet.currentAlignFrame == me)
3845 theApplet.currentAlignFrame = null;
3850 public void focusGained(FocusEvent e)
3852 theApplet.currentAlignFrame = me;
3855 theApplet.validate();
3859 * create a new binding between structures in an existing jmol viewer instance
3860 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3861 * this does not open a new Jmol window, or modify the display of the
3862 * structures in the original jmol window. Note This method doesn't work
3863 * without an additional javascript library to exchange messages between the
3864 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3867 * JmolViewer instance
3868 * @param sequenceIds
3869 * - sequence Ids to search for associations
3871 public SequenceStructureBinding addStructureViewInstance(
3872 Object jmolviewer, String[] sequenceIds)
3874 org.jmol.api.JmolViewer viewer = null;
3877 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3878 } catch (ClassCastException ex)
3880 System.err.println("Unsupported viewer object :"
3881 + jmolviewer.getClass());
3885 System.err.println("Can't use this object as a structure viewer:"
3886 + jmolviewer.getClass());
3889 SequenceI[] seqs = null;
3890 if (sequenceIds == null || sequenceIds.length == 0)
3892 seqs = viewport.getAlignment().getSequencesArray();
3896 Vector sqi = new Vector();
3897 AlignmentI al = viewport.getAlignment();
3898 for (int sid = 0; sid < sequenceIds.length; sid++)
3900 SequenceI sq = al.findName(sequenceIds[sid]);
3908 seqs = new SequenceI[sqi.size()];
3909 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3911 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3919 AAStructureBindingModel jmv = null;
3920 // TODO: search for a jmv that involves viewer
3922 { // create a new viewer/jalview binding.
3923 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3931 * bind a pdb file to a sequence in the current view
3934 * - sequenceId within the dataset.
3935 * @param pdbEntryString
3936 * - the short name for the PDB file
3938 * - pdb file - either a URL or a valid PDB file.
3939 * @return true if binding was as success TODO: consider making an exception
3940 * structure for indicating when PDB parsing or sequenceId location
3943 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3946 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3947 boolean needtoadd = false;
3948 if (toaddpdb != null)
3950 Vector pdbe = toaddpdb.getPDBId();
3951 PDBEntry pdbentry = null;
3952 if (pdbe != null && pdbe.size() > 0)
3954 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3956 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3957 if (!pdbentry.getId().equals(pdbEntryString)
3958 && !pdbentry.getFile().equals(pdbFile))
3968 if (pdbentry == null)
3970 pdbentry = new PDBEntry();
3971 pdbentry.setId(pdbEntryString);
3972 pdbentry.setFile(pdbFile);
3973 needtoadd = true; // add this new entry to sequence.
3975 // resolve data source
3976 // TODO: this code should be a refactored to an io package
3977 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3978 if (protocol == null)
3984 // make a note of the access mode and add
3985 if (pdbentry.getProperty() == null)
3987 pdbentry.setProperty(new Hashtable());
3989 pdbentry.getProperty().put("protocol", protocol);
3990 toaddpdb.addPDBId(pdbentry);
3991 alignPanel.getStructureSelectionManager()
3992 .registerPDBEntry(pdbentry);
3998 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4002 Vector sequences = new Vector();
4003 for (int i = 0; i < seqs.length; i++)
4005 if (seqs[i] != null)
4007 sequences.addElement(new Object[]
4008 { seqs[i], (chains != null) ? chains[i] : null });
4011 seqs = new SequenceI[sequences.size()];
4012 chains = new String[sequences.size()];
4013 for (int i = 0, isize = sequences.size(); i < isize; i++)
4015 Object[] oj = (Object[]) sequences.elementAt(i);
4017 seqs[i] = (SequenceI) oj[0];
4018 chains[i] = (String) oj[1];
4026 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4027 SequenceI[] seqs, String[] chains, String protocol)
4029 // Scrub any null sequences from the array
4030 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4031 seqs = (SequenceI[]) sqch[0];
4032 chains = (String[]) sqch[1];
4033 if (seqs == null || seqs.length == 0)
4036 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4038 if (protocol == null || protocol.trim().length() == 0
4039 || protocol.equals("null"))
4041 protocol = (String) pdb.getProperty().get("protocol");
4042 if (protocol == null)
4044 System.err.println("Couldn't work out protocol to open structure: "
4049 if (applet.useXtrnalSviewer)
4051 // register the association(s) and quit, don't create any windows.
4052 if (StructureSelectionManager.getStructureSelectionManager(applet)
4053 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4055 System.err.println("Failed to map " + pdb.getFile() + " ("
4056 + protocol + ") to any sequences");
4060 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4062 // can only do alignments with Jmol
4063 // find the last jmol window assigned to this alignment
4064 jalview.appletgui.AppletJmol ajm = null, tajm;
4065 Vector jmols = applet
4066 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4067 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4069 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4070 if (tajm.ap.alignFrame == this)
4079 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4080 // try and add the pdb structure
4085 // otherwise, create a new window
4086 if (applet.jmolAvailable)
4088 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4090 applet.lastFrameX += 40;
4091 applet.lastFrameY += 40;
4095 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4100 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4101 SequenceI[][] seqs, String[][] chains, String[] protocols)
4103 // TODO Auto-generated method stub
4104 System.err.println("Aligned Structure View: Not yet implemented.");
4108 * modify the current selection, providing the user has not made a selection
4112 * - sequences from this alignment
4114 * - columns to be selected on the alignment
4116 public void select(SequenceGroup sel, ColumnSelection csel)
4118 alignPanel.seqPanel.selection(sel, csel, null);
4121 public void scrollTo(int row, int column)
4123 alignPanel.seqPanel.scrollTo(row, column);
4126 public void scrollToRow(int row)
4128 alignPanel.seqPanel.scrollToRow(row);
4131 public void scrollToColumn(int column)
4133 alignPanel.seqPanel.scrollToColumn(column);
4137 * @return the alignments unique ID.
4139 public String getSequenceSetId()
4141 return viewport.getSequenceSetId();
4145 * Load the (T-Coffee) score file from the specified url
4148 * File/URL/T-COFFEE score file contents
4149 * @throws IOException
4150 * @return true if alignment was annotated with data from source
4152 public boolean loadScoreFile(String source) throws IOException
4155 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4156 AppletFormatAdapter.checkProtocol(source));
4157 if (!file.isValid())
4159 // TODO: raise dialog for gui
4160 System.err.println("Problems parsing T-Coffee scores: "
4161 + file.getWarningMessage());
4162 System.err.println("Origin was:\n" + source);
4167 * check that the score matrix matches the alignment dimensions
4170 if ((aln = viewport.getAlignment()) != null
4171 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4174 // TODO: raise a dialog box here rather than bomb out.
4176 .println("The scores matrix does not match the alignment dimensions");
4180 // TODO add parameter to indicate if matching should be done
4181 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4183 alignPanel.fontChanged();
4184 tcoffeeColour.setEnabled(true);
4185 // switch to this color
4186 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4191 System.err.println("Problems resolving T-Coffee scores:");
4192 if (file.getWarningMessage() != null)
4194 System.err.println(file.getWarningMessage());
4200 public SplitFrame getSplitFrame()
4202 return this.splitFrame;
4205 public void setSplitFrame(SplitFrame sf)
4207 this.splitFrame = sf;