2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
25 import jalview.api.AlignViewControllerGuiI;
26 import jalview.api.AlignViewControllerI;
27 import jalview.api.AlignViewportI;
28 import jalview.api.FeatureRenderer;
29 import jalview.api.FeatureSettingsControllerI;
30 import jalview.api.SequenceStructureBinding;
31 import jalview.bin.JalviewLite;
32 import jalview.commands.CommandI;
33 import jalview.commands.EditCommand;
34 import jalview.commands.EditCommand.Action;
35 import jalview.commands.OrderCommand;
36 import jalview.commands.RemoveGapColCommand;
37 import jalview.commands.RemoveGapsCommand;
38 import jalview.commands.SlideSequencesCommand;
39 import jalview.commands.TrimRegionCommand;
40 import jalview.datamodel.Alignment;
41 import jalview.datamodel.AlignmentAnnotation;
42 import jalview.datamodel.AlignmentI;
43 import jalview.datamodel.AlignmentOrder;
44 import jalview.datamodel.ColumnSelection;
45 import jalview.datamodel.PDBEntry;
46 import jalview.datamodel.Sequence;
47 import jalview.datamodel.SequenceGroup;
48 import jalview.datamodel.SequenceI;
49 import jalview.io.AnnotationFile;
50 import jalview.io.AppletFormatAdapter;
51 import jalview.io.FeaturesFile;
52 import jalview.io.TCoffeeScoreFile;
53 import jalview.schemes.Blosum62ColourScheme;
54 import jalview.schemes.BuriedColourScheme;
55 import jalview.schemes.ClustalxColourScheme;
56 import jalview.schemes.ColourSchemeI;
57 import jalview.schemes.HelixColourScheme;
58 import jalview.schemes.HydrophobicColourScheme;
59 import jalview.schemes.NucleotideColourScheme;
60 import jalview.schemes.PIDColourScheme;
61 import jalview.schemes.PurinePyrimidineColourScheme;
62 import jalview.schemes.RNAHelicesColourChooser;
63 import jalview.schemes.RNAInteractionColourScheme;
64 import jalview.schemes.StrandColourScheme;
65 import jalview.schemes.TCoffeeColourScheme;
66 import jalview.schemes.TaylorColourScheme;
67 import jalview.schemes.TurnColourScheme;
68 import jalview.schemes.ZappoColourScheme;
69 import jalview.structure.StructureSelectionManager;
70 import jalview.structures.models.AAStructureBindingModel;
71 import jalview.util.MappingUtils;
72 import jalview.util.MessageManager;
73 import jalview.viewmodel.AlignmentViewport;
75 import java.awt.BorderLayout;
76 import java.awt.Canvas;
77 import java.awt.CheckboxMenuItem;
78 import java.awt.Color;
80 import java.awt.FontMetrics;
81 import java.awt.Frame;
82 import java.awt.Graphics;
83 import java.awt.Label;
85 import java.awt.MenuBar;
86 import java.awt.MenuItem;
87 import java.awt.event.ActionEvent;
88 import java.awt.event.ActionListener;
89 import java.awt.event.FocusEvent;
90 import java.awt.event.FocusListener;
91 import java.awt.event.ItemEvent;
92 import java.awt.event.ItemListener;
93 import java.awt.event.KeyEvent;
94 import java.awt.event.KeyListener;
95 import java.awt.event.WindowAdapter;
96 import java.awt.event.WindowEvent;
97 import java.io.IOException;
99 import java.net.URLEncoder;
100 import java.util.Arrays;
101 import java.util.Deque;
102 import java.util.HashMap;
103 import java.util.Hashtable;
104 import java.util.List;
105 import java.util.Map;
106 import java.util.StringTokenizer;
107 import java.util.Vector;
109 public class AlignFrame extends EmbmenuFrame implements ActionListener,
110 ItemListener, KeyListener, AlignViewControllerGuiI
112 public AlignViewControllerI avc;
114 public AlignmentPanel alignPanel;
116 public AlignViewport viewport;
118 // width and height may be overridden by applet parameters
119 int frameWidth = 700;
121 int frameHeight = 500;
123 String jalviewServletURL;
126 * Flag for showing autocalculated consensus above or below other consensus
129 private boolean showAutoCalculatedAbove;
131 private SequenceAnnotationOrder annotationSortOrder;
134 * Constructor that creates the frame and adds it to the display.
141 public AlignFrame(AlignmentI al, JalviewLite applet,
142 String title, boolean embedded)
144 this(al, applet, title, embedded, true);
148 * Constructor that optionally allows the frame to be displayed or only
155 * @param addToDisplay
157 public AlignFrame(AlignmentI al, JalviewLite applet,
158 String title, boolean embedded, boolean addToDisplay)
160 this(al, null, null, applet, title, embedded, addToDisplay);
163 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
164 ColumnSelection columnSelection, JalviewLite applet,
165 String title, boolean embedded)
167 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
170 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
171 ColumnSelection columnSelection, JalviewLite applet,
172 String title, boolean embedded, boolean addToDisplay)
176 jalviewServletURL = applet.getParameter("APPLICATION_URL");
182 } catch (Exception ex)
184 ex.printStackTrace();
186 // need to get window geometry before we calculate alignment layout
192 param = applet.getParameter("windowWidth");
195 int width = Integer.parseInt(param);
198 param = applet.getParameter("windowHeight");
201 int height = Integer.parseInt(param);
202 frameHeight = height;
204 } catch (Exception ex)
208 viewport = new AlignViewport(al, applet);
210 if (hiddenSeqs != null && hiddenSeqs.length > 0)
212 viewport.hideSequence(hiddenSeqs);
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 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1344 e.getActionCommand(), viewport.getAlignment(),
1345 viewport.getShowJVSuffix()));
1348 public void loadAnnotations()
1350 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1351 cap.setText(MessageManager
1352 .getString("label.paste_features_annotations_Tcoffee_here"));
1353 cap.setAnnotationImport();
1354 Frame frame = new Frame();
1356 jalview.bin.JalviewLite.addFrame(frame,
1357 MessageManager.getString("action.paste_annotations"), 400, 300);
1361 public String outputAnnotations(boolean displayTextbox)
1363 String annotation = new AnnotationFile()
1364 .printAnnotationsForView(viewport);
1368 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1369 Frame frame = new Frame();
1371 jalview.bin.JalviewLite.addFrame(frame,
1372 MessageManager.getString("label.annotations"), 600, 500);
1373 cap.setText(annotation);
1379 private Map<String,Object> getDisplayedFeatureCols()
1381 if (alignPanel.getFeatureRenderer() != null
1382 && viewport.getFeaturesDisplayed()!= null)
1384 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1390 public String outputFeatures(boolean displayTextbox, String format)
1393 if (format.equalsIgnoreCase("Jalview"))
1395 features = new FeaturesFile().printJalviewFormat(viewport
1396 .getAlignment().getSequencesArray(),
1397 getDisplayedFeatureCols());
1401 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1402 .getSequencesArray(), getDisplayedFeatureCols());
1407 boolean frimport = false;
1408 if (features == null || features.equals("No Features Visible"))
1410 features = "# No features visible - paste some and import them here.";
1414 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1417 cap.setAnnotationImport();
1419 Frame frame = new Frame();
1421 jalview.bin.JalviewLite.addFrame(frame,
1422 MessageManager.getString("label.features"), 600, 500);
1423 cap.setText(features);
1427 if (features == null)
1436 void launchFullApplication()
1438 StringBuffer url = new StringBuffer(jalviewServletURL);
1440 // allow servlet parameters to be passed in applet parameter
1441 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1443 url.append(firstSep);
1446 + appendProtocol(viewport.applet.getParameter("file")));
1448 if (viewport.applet.getParameter("features") != null)
1450 url.append("&features=");
1451 url.append(appendProtocol(viewport.applet.getParameter("features")));
1454 if (viewport.applet.getParameter("annotations") != null)
1456 url.append("&annotations=");
1457 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1460 if (viewport.applet.getParameter("jnetfile") != null)
1462 url.append("&annotations=");
1463 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1466 if (viewport.applet.getParameter("defaultColour") != null)
1468 url.append("&colour="
1469 + removeWhiteSpace(viewport.applet
1470 .getParameter("defaultColour")));
1473 if (viewport.applet.getParameter("userDefinedColour") != null)
1475 url.append("&colour="
1476 + removeWhiteSpace(viewport.applet
1477 .getParameter("userDefinedColour")));
1479 if (viewport.applet.getParameter("tree") != null)
1482 + appendProtocol(viewport.applet.getParameter("tree")));
1484 if (viewport.applet.getParameter("treeFile") != null)
1487 + appendProtocol(viewport.applet.getParameter("treeFile")));
1490 showURL(url.toString(), "FULL_APP");
1493 String removeWhiteSpace(String colour)
1495 StringBuffer sb = new StringBuffer();
1496 for (int i = 0; i < colour.length(); i++)
1498 if (Character.isWhitespace(colour.charAt(i)))
1504 sb.append(colour.charAt(i));
1508 return sb.toString();
1511 String appendProtocol(String url)
1516 url = URLEncoder.encode(url);
1519 * When we finally deprecate 1.1 compatibility, we can start to use
1520 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1521 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1522 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1523 * ex.printStackTrace(); }
1525 catch (java.net.MalformedURLException ex)
1527 url = viewport.applet.getCodeBase() + url;
1532 public void closeMenuItem_actionPerformed()
1534 PaintRefresher.RemoveComponent(alignPanel);
1535 if (alignPanel.seqPanel != null
1536 && alignPanel.seqPanel.seqCanvas != null)
1538 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1540 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1542 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1545 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1560 void updateEditMenuBar()
1563 if (viewport.getHistoryList().size() > 0)
1565 undoMenuItem.setEnabled(true);
1566 CommandI command = viewport.getHistoryList().peek();
1567 undoMenuItem.setLabel(MessageManager.formatMessage(
1568 "label.undo_command", new Object[]
1569 { command.getDescription() }));
1573 undoMenuItem.setEnabled(false);
1574 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1577 if (viewport.getRedoList().size() > 0)
1579 redoMenuItem.setEnabled(true);
1581 CommandI command = viewport.getRedoList().peek();
1582 redoMenuItem.setLabel(MessageManager.formatMessage(
1583 "label.redo_command", new Object[]
1584 { command.getDescription() }));
1588 redoMenuItem.setEnabled(false);
1589 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1597 public void addHistoryItem(CommandI command)
1599 if (command.getSize() > 0)
1601 viewport.addToHistoryList(command);
1602 viewport.clearRedoList();
1603 updateEditMenuBar();
1604 viewport.updateHiddenColumns();
1609 * TODO: JAL-1104 DOCUMENT ME!
1614 protected void undoMenuItem_actionPerformed()
1616 if (viewport.getHistoryList().isEmpty())
1621 CommandI command = viewport.getHistoryList().pop();
1622 viewport.addToRedoList(command);
1623 command.undoCommand(null);
1625 AlignmentViewport originalSource = getOriginatingSource(command);
1627 if (originalSource != viewport)
1630 .println("Warning: Viewport object mismatch whilst undoing");
1632 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1633 // viewport.getColumnSelection().getHiddenColumns()
1635 updateEditMenuBar();
1636 originalSource.firePropertyChange("alignment", null, originalSource
1637 .getAlignment().getSequences());
1641 * TODO: JAL-1104 DOCUMENT ME!
1646 protected void redoMenuItem_actionPerformed()
1648 if (viewport.getRedoList().isEmpty())
1653 CommandI command = viewport.getRedoList().pop();
1654 viewport.addToHistoryList(command);
1655 command.doCommand(null);
1657 AlignmentViewport originalSource = getOriginatingSource(command);
1659 if (originalSource != viewport)
1662 .println("Warning: Viewport object mismatch whilst re-doing");
1664 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1665 // viewport.getColumnSelection().getHiddenColumns()
1668 updateEditMenuBar();
1669 originalSource.firePropertyChange("alignment", null, originalSource
1670 .getAlignment().getSequences());
1673 AlignmentViewport getOriginatingSource(CommandI command)
1675 AlignmentViewport originalSource = null;
1676 // For sequence removal and addition, we need to fire
1677 // the property change event FROM the viewport where the
1678 // original alignment was altered
1679 AlignmentI al = null;
1680 if (command instanceof EditCommand)
1682 EditCommand editCommand = (EditCommand) command;
1683 al = editCommand.getAlignment();
1684 Vector comps = (Vector) PaintRefresher.components.get(viewport
1685 .getSequenceSetId());
1686 for (int i = 0; i < comps.size(); i++)
1688 if (comps.elementAt(i) instanceof AlignmentPanel)
1690 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1692 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1699 if (originalSource == null)
1701 // The original view is closed, we must validate
1702 // the current view against the closed view first
1705 PaintRefresher.validateSequences(al, viewport.getAlignment());
1708 originalSource = viewport;
1711 return originalSource;
1715 * Move the currently selected sequences up or down one position in the
1720 public void moveSelectedSequences(boolean up)
1722 SequenceGroup sg = viewport.getSelectionGroup();
1727 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1728 up ? null : viewport.getHiddenRepSequences(), up);
1729 alignPanel.paintAlignment(true);
1732 * Also move cDNA/protein complement sequences
1734 AlignViewportI complement = viewport.getCodingComplement();
1735 if (complement != null)
1737 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1738 viewport, complement);
1739 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1740 up ? null : complement.getHiddenRepSequences(), up);
1741 // TODO need to trigger a repaint of the complementary panel - how?
1742 // would prefer to handle in SplitFrame but it is not overriding key
1747 synchronized void slideSequences(boolean right, int size)
1749 List<SequenceI> sg = new Vector<SequenceI>();
1750 if (viewport.cursorMode)
1752 sg.add(viewport.getAlignment().getSequenceAt(
1753 alignPanel.seqPanel.seqCanvas.cursorY));
1755 else if (viewport.getSelectionGroup() != null
1756 && viewport.getSelectionGroup().getSize() != viewport
1757 .getAlignment().getHeight())
1759 sg = viewport.getSelectionGroup().getSequences(
1760 viewport.getHiddenRepSequences());
1768 Vector<SequenceI> invertGroup = new Vector();
1770 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1772 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1774 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1778 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1780 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1782 for (int i = 0; i < invertGroup.size(); i++)
1784 seqs2[i] = invertGroup.elementAt(i);
1787 SlideSequencesCommand ssc;
1790 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1791 size, viewport.getGapCharacter());
1795 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1796 size, viewport.getGapCharacter());
1799 int groupAdjustment = 0;
1800 if (ssc.getGapsInsertedBegin() && right)
1802 if (viewport.cursorMode)
1804 alignPanel.seqPanel.moveCursor(size, 0);
1808 groupAdjustment = size;
1811 else if (!ssc.getGapsInsertedBegin() && !right)
1813 if (viewport.cursorMode)
1815 alignPanel.seqPanel.moveCursor(-size, 0);
1819 groupAdjustment = -size;
1823 if (groupAdjustment != 0)
1825 viewport.getSelectionGroup().setStartRes(
1826 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1827 viewport.getSelectionGroup().setEndRes(
1828 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1831 boolean appendHistoryItem = false;
1832 Deque<CommandI> historyList = viewport.getHistoryList();
1833 if (historyList != null && historyList.size() > 0
1834 && historyList.peek() instanceof SlideSequencesCommand)
1836 appendHistoryItem = ssc
1837 .appendSlideCommand((SlideSequencesCommand) historyList
1841 if (!appendHistoryItem)
1843 addHistoryItem(ssc);
1849 static StringBuffer copiedSequences;
1851 static Vector copiedHiddenColumns;
1853 protected void copy_actionPerformed()
1855 if (viewport.getSelectionGroup() == null)
1860 SequenceGroup sg = viewport.getSelectionGroup();
1861 copiedSequences = new StringBuffer();
1862 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1863 for (int i = 0; i < sg.getSize(); i++)
1865 SequenceI seq = sg.getSequenceAt(i);
1866 int index = viewport.getAlignment().findIndex(seq);
1867 orderedSeqs.put(index, seq);
1870 int index = 0, startRes, endRes;
1873 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1875 copiedHiddenColumns = new Vector();
1876 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1877 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1879 copiedHiddenColumns.addElement(new int[]
1880 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1885 copiedHiddenColumns = null;
1888 for (int i = 0; i < sg.getSize(); i++)
1890 SequenceI seq = null;
1894 if (orderedSeqs.containsKey(index))
1896 seq = orderedSeqs.get(index);
1907 // Returns residue following index if gap
1908 startRes = seq.findPosition(sg.getStartRes());
1911 // Need to find the residue preceeding index if gap
1914 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1916 ch = seq.getCharAt(j);
1917 if (!jalview.util.Comparison.isGap((ch)))
1925 endRes += seq.getStart() - 1;
1928 copiedSequences.append(seq.getName()
1934 + seq.getSequenceAsString(sg.getStartRes(),
1935 sg.getEndRes() + 1) + "\n");
1940 protected void pasteNew_actionPerformed()
1945 protected void pasteThis_actionPerformed()
1950 void paste(boolean newAlignment)
1955 if (copiedSequences == null)
1960 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1961 Vector seqs = new Vector();
1962 while (st.hasMoreElements())
1964 String name = st.nextToken();
1965 int start = Integer.parseInt(st.nextToken());
1966 int end = Integer.parseInt(st.nextToken());
1967 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1969 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1970 for (int i = 0; i < seqs.size(); i++)
1972 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1977 String newtitle = MessageManager.getString("label.copied_sequences");
1978 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1980 newtitle = getTitle();
1984 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1986 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1987 viewport.applet, newtitle, false);
1988 if (copiedHiddenColumns != null)
1990 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1992 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1993 af.viewport.hideColumns(region[0], region[1]);
1997 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2002 addSequences(newSeqs);
2005 } catch (Exception ex)
2007 } // could be anything being pasted in here
2011 void addSequences(SequenceI[] seqs)
2013 for (int i = 0; i < seqs.length; i++)
2015 viewport.getAlignment().addSequence(seqs[i]);
2019 addHistoryItem(new EditCommand(
2020 MessageManager.getString("label.add_sequences"), Action.PASTE,
2021 seqs, 0, viewport.getAlignment().getWidth(),
2022 viewport.getAlignment()));
2024 viewport.setEndSeq(viewport.getAlignment().getHeight());
2025 viewport.getAlignment().getWidth();
2026 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2031 protected void cut_actionPerformed()
2033 copy_actionPerformed();
2034 delete_actionPerformed();
2037 protected void delete_actionPerformed()
2040 SequenceGroup sg = viewport.getSelectionGroup();
2046 Vector seqs = new Vector();
2048 for (int i = 0; i < sg.getSize(); i++)
2050 seq = sg.getSequenceAt(i);
2051 seqs.addElement(seq);
2054 // If the cut affects all sequences, remove highlighted columns
2055 if (sg.getSize() == viewport.getAlignment().getHeight())
2057 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2058 sg.getEndRes() + 1);
2061 SequenceI[] cut = new SequenceI[seqs.size()];
2062 for (int i = 0; i < seqs.size(); i++)
2064 cut[i] = (SequenceI) seqs.elementAt(i);
2068 * //ADD HISTORY ITEM
2070 addHistoryItem(new EditCommand(
2071 MessageManager.getString("label.cut_sequences"), Action.CUT,
2072 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2073 viewport.getAlignment()));
2075 viewport.setSelectionGroup(null);
2076 viewport.getAlignment().deleteGroup(sg);
2078 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2081 if (viewport.getAlignment().getHeight() < 1)
2083 this.setVisible(false);
2085 viewport.sendSelection();
2089 * group consensus toggled
2092 protected void showGroupConsensus_actionPerformed()
2094 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2095 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2100 * group conservation toggled.
2102 protected void showGroupConservation_actionPerformed()
2104 viewport.setShowGroupConservation(showGroupConservation.getState());
2105 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2112 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2113 * .event.ActionEvent)
2115 protected void showConsensusHistogram_actionPerformed()
2117 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2118 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2125 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2126 * .event.ActionEvent)
2128 protected void showSequenceLogo_actionPerformed()
2130 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2131 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2134 protected void normSequenceLogo_actionPerformed()
2136 showSequenceLogo.setState(true);
2137 viewport.setShowSequenceLogo(true);
2138 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2139 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2142 protected void applyAutoAnnotationSettings_actionPerformed()
2144 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2147 protected void makeGrpsFromSelection_actionPerformed()
2149 if (avc.makeGroupsFromSelection())
2151 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2152 alignPanel.updateAnnotation();
2153 alignPanel.paintAlignment(true);
2157 protected void createGroup_actionPerformed()
2162 protected void unGroup_actionPerformed()
2166 alignPanel.alignmentChanged();
2170 protected void deleteGroups_actionPerformed()
2172 if (avc.deleteGroups())
2174 alignPanel.alignmentChanged();
2178 public void selectAllSequenceMenuItem_actionPerformed()
2180 SequenceGroup sg = new SequenceGroup();
2181 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2183 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2185 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2186 viewport.setSelectionGroup(sg);
2187 alignPanel.paintAlignment(true);
2188 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2189 viewport.sendSelection();
2192 public void deselectAllSequenceMenuItem_actionPerformed()
2194 if (viewport.cursorMode)
2196 alignPanel.seqPanel.keyboardNo1 = null;
2197 alignPanel.seqPanel.keyboardNo2 = null;
2199 viewport.setSelectionGroup(null);
2200 viewport.getColumnSelection().clear();
2201 viewport.setSelectionGroup(null);
2202 alignPanel.idPanel.idCanvas.searchResults = null;
2203 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2204 alignPanel.paintAlignment(true);
2205 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2206 viewport.sendSelection();
2209 public void invertSequenceMenuItem_actionPerformed()
2211 SequenceGroup sg = viewport.getSelectionGroup();
2212 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2214 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2217 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2218 viewport.sendSelection();
2221 public void invertColSel_actionPerformed()
2223 viewport.invertColumnSelection();
2224 alignPanel.paintAlignment(true);
2225 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2226 viewport.sendSelection();
2229 void trimAlignment(boolean trimLeft)
2231 ColumnSelection colSel = viewport.getColumnSelection();
2234 if (colSel.size() > 0)
2238 column = colSel.getMin();
2242 column = colSel.getMax();
2246 if (viewport.getSelectionGroup() != null)
2248 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2249 viewport.getHiddenRepSequences());
2253 seqs = viewport.getAlignment().getSequencesArray();
2256 TrimRegionCommand trimRegion;
2259 trimRegion = new TrimRegionCommand("Remove Left",
2260 TrimRegionCommand.TRIM_LEFT, seqs, column,
2261 viewport.getAlignment(), viewport.getColumnSelection(),
2262 viewport.getSelectionGroup());
2263 viewport.setStartRes(0);
2267 trimRegion = new TrimRegionCommand("Remove Right",
2268 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2269 viewport.getAlignment(), viewport.getColumnSelection(),
2270 viewport.getSelectionGroup());
2273 statusBar.setText(MessageManager.formatMessage(
2274 "label.removed_columns", new String[]
2275 { Integer.valueOf(trimRegion.getSize()).toString() }));
2276 addHistoryItem(trimRegion);
2278 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2280 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2281 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2283 viewport.getAlignment().deleteGroup(sg);
2287 viewport.firePropertyChange("alignment", null, viewport
2288 .getAlignment().getSequences());
2292 public void removeGappedColumnMenuItem_actionPerformed()
2294 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2297 if (viewport.getSelectionGroup() != null)
2299 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2300 viewport.getHiddenRepSequences());
2301 start = viewport.getSelectionGroup().getStartRes();
2302 end = viewport.getSelectionGroup().getEndRes();
2306 seqs = viewport.getAlignment().getSequencesArray();
2309 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2310 "Remove Gapped Columns", seqs, start, end,
2311 viewport.getAlignment());
2313 addHistoryItem(removeGapCols);
2315 statusBar.setText(MessageManager.formatMessage(
2316 "label.removed_empty_columns", new String[]
2317 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2319 // This is to maintain viewport position on first residue
2320 // of first sequence
2321 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2322 int startRes = seq.findPosition(viewport.startRes);
2323 // ShiftList shifts;
2324 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2325 // edit.alColumnChanges=shifts.getInverse();
2326 // if (viewport.hasHiddenColumns)
2327 // viewport.getColumnSelection().compensateForEdits(shifts);
2328 viewport.setStartRes(seq.findIndex(startRes) - 1);
2329 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2334 public void removeAllGapsMenuItem_actionPerformed()
2336 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2339 if (viewport.getSelectionGroup() != null)
2341 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2342 viewport.getHiddenRepSequences());
2343 start = viewport.getSelectionGroup().getStartRes();
2344 end = viewport.getSelectionGroup().getEndRes();
2348 seqs = viewport.getAlignment().getSequencesArray();
2351 // This is to maintain viewport position on first residue
2352 // of first sequence
2353 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2354 int startRes = seq.findPosition(viewport.startRes);
2356 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2357 viewport.getAlignment()));
2359 viewport.setStartRes(seq.findIndex(startRes) - 1);
2361 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2366 public void findMenuItem_actionPerformed()
2368 new Finder(alignPanel);
2372 * create a new view derived from the current view
2375 * @return frame for the new view
2377 public AlignFrame newView(String viewtitle)
2380 if (viewport.hasHiddenRows())
2382 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2383 .getFullAlignment().getSequencesArray());
2387 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2390 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2392 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2394 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2396 newal.addAnnotation(viewport.getAlignment()
2397 .getAlignmentAnnotation()[i]);
2402 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2404 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2405 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2406 PaintRefresher.Register(newaf.alignPanel,
2407 newaf.alignPanel.av.getSequenceSetId());
2409 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2410 newaf.alignPanel.av.getSequenceSetId());
2411 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2412 newaf.alignPanel.av.getSequenceSetId());
2414 Vector comps = (Vector) PaintRefresher.components.get(viewport
2415 .getSequenceSetId());
2417 for (int i = 0; i < comps.size(); i++)
2419 if (comps.elementAt(i) instanceof AlignmentPanel)
2425 String title = new String(this.getTitle());
2426 if (viewtitle != null)
2428 title = viewtitle + " ( " + title + ")";
2432 if (title.indexOf("(View") > -1)
2434 title = title.substring(0, title.indexOf("(View"));
2436 title += "(View " + viewSize + ")";
2439 newaf.setTitle(title.toString());
2441 newaf.viewport.setHistoryList(viewport.getHistoryList());
2442 newaf.viewport.setRedoList(viewport.getRedoList());
2448 * @return list of feature groups on the view
2450 public String[] getFeatureGroups()
2452 FeatureRenderer fr = null;
2453 if (alignPanel != null
2454 && (fr = alignPanel.getFeatureRenderer()) != null)
2456 List<String> gps = fr.getFeatureGroups();
2457 String[] _gps = gps.toArray(new String[gps.size()]);
2464 * get sequence feature groups that are hidden or shown
2470 public String[] getFeatureGroupsOfState(boolean visible)
2472 FeatureRenderer fr = null;
2473 if (alignPanel != null
2474 && (fr = alignPanel.getFeatureRenderer()) != null)
2476 List<String> gps = fr.getGroups(visible);
2477 String[] _gps = gps.toArray(new String[gps.size()]);
2484 * Change the display state for the given feature groups
2487 * list of group strings
2489 * visible or invisible
2491 public void setFeatureGroupState(String[] groups, boolean state)
2493 FeatureRenderer fr = null;
2494 this.sequenceFeatures.setState(true);
2495 viewport.setShowSequenceFeatures(true);
2496 if (alignPanel != null
2497 && (fr = alignPanel.getFeatureRenderer()) != null)
2500 fr.setGroupVisibility(Arrays.asList(groups), state);
2501 alignPanel.seqPanel.seqCanvas.repaint();
2502 if (alignPanel.overviewPanel != null)
2504 alignPanel.overviewPanel.updateOverviewImage();
2509 public void seqLimits_itemStateChanged()
2511 viewport.setShowJVSuffix(seqLimits.getState());
2512 alignPanel.fontChanged();
2513 alignPanel.paintAlignment(true);
2516 protected void colourTextMenuItem_actionPerformed()
2518 viewport.setColourText(colourTextMenuItem.getState());
2519 alignPanel.paintAlignment(true);
2522 protected void displayNonconservedMenuItem_actionPerformed()
2524 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2525 alignPanel.paintAlignment(true);
2528 protected void wrapMenuItem_actionPerformed()
2530 viewport.setWrapAlignment(wrapMenuItem.getState());
2531 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2532 scaleAbove.setEnabled(wrapMenuItem.getState());
2533 scaleLeft.setEnabled(wrapMenuItem.getState());
2534 scaleRight.setEnabled(wrapMenuItem.getState());
2535 alignPanel.paintAlignment(true);
2538 public void overviewMenuItem_actionPerformed()
2540 if (alignPanel.overviewPanel != null)
2545 Frame frame = new Frame();
2546 OverviewPanel overview = new OverviewPanel(alignPanel);
2547 frame.add(overview);
2548 // +50 must allow for applet frame window
2549 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2550 "label.overview_params", new String[]
2551 { this.getTitle() }), overview.getPreferredSize().width,
2552 overview.getPreferredSize().height + 50);
2555 final AlignmentPanel ap = alignPanel;
2556 frame.addWindowListener(new WindowAdapter()
2559 public void windowClosing(WindowEvent e)
2563 ap.setOverviewPanel(null);
2568 alignPanel.setOverviewPanel(overview);
2572 public void changeColour(ColourSchemeI cs)
2578 if (viewport.getAbovePIDThreshold())
2580 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2584 if (viewport.getConservationSelected())
2586 cs.setConservationApplied(true);
2587 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2592 cs.setConservationApplied(false);
2595 viewport.setGlobalColourScheme(cs);
2597 if (alignPanel.getOverviewPanel() != null)
2599 alignPanel.getOverviewPanel().updateOverviewImage();
2602 jalview.structure.StructureSelectionManager
2603 .getStructureSelectionManager(viewport.applet)
2604 .sequenceColoursChanged(alignPanel);
2606 alignPanel.paintAlignment(true);
2609 protected void modifyPID_actionPerformed()
2611 if (viewport.getAbovePIDThreshold()
2612 && viewport.getGlobalColourScheme() != null)
2614 SliderPanel.setPIDSliderSource(alignPanel,
2615 viewport.getGlobalColourScheme(), "Background");
2616 SliderPanel.showPIDSlider();
2620 protected void modifyConservation_actionPerformed()
2622 if (viewport.getConservationSelected()
2623 && viewport.getGlobalColourScheme() != null)
2625 SliderPanel.setConservationSlider(alignPanel,
2626 viewport.getGlobalColourScheme(), "Background");
2627 SliderPanel.showConservationSlider();
2631 protected void conservationMenuItem_actionPerformed()
2633 viewport.setConservationSelected(conservationMenuItem.getState());
2635 viewport.setAbovePIDThreshold(false);
2636 abovePIDThreshold.setState(false);
2638 changeColour(viewport.getGlobalColourScheme());
2640 modifyConservation_actionPerformed();
2643 public void abovePIDThreshold_actionPerformed()
2645 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2647 conservationMenuItem.setState(false);
2648 viewport.setConservationSelected(false);
2650 changeColour(viewport.getGlobalColourScheme());
2652 modifyPID_actionPerformed();
2655 public void sortPairwiseMenuItem_actionPerformed()
2657 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2658 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2659 .getAlignment().getSequenceAt(0), null);
2661 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2662 viewport.getAlignment()));
2663 alignPanel.paintAlignment(true);
2666 public void sortIDMenuItem_actionPerformed()
2668 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2669 AlignmentSorter.sortByID(viewport.getAlignment());
2670 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2671 viewport.getAlignment()));
2672 alignPanel.paintAlignment(true);
2675 public void sortLengthMenuItem_actionPerformed()
2677 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2678 AlignmentSorter.sortByLength(viewport.getAlignment());
2679 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2680 viewport.getAlignment()));
2681 alignPanel.paintAlignment(true);
2684 public void sortGroupMenuItem_actionPerformed()
2686 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2687 AlignmentSorter.sortByGroup(viewport.getAlignment());
2688 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2689 viewport.getAlignment()));
2690 alignPanel.paintAlignment(true);
2694 public void removeRedundancyMenuItem_actionPerformed()
2696 new RedundancyPanel(alignPanel);
2699 public void pairwiseAlignmentMenuItem_actionPerformed()
2701 if (viewport.getSelectionGroup() != null
2702 && viewport.getSelectionGroup().getSize() > 1)
2704 Frame frame = new Frame();
2705 frame.add(new PairwiseAlignPanel(alignPanel));
2706 jalview.bin.JalviewLite.addFrame(frame,
2707 MessageManager.getString("action.pairwise_alignment"), 600,
2712 public void PCAMenuItem_actionPerformed()
2714 // are the sequences aligned?
2715 if (!viewport.getAlignment().isAligned(false))
2718 int Width = viewport.getAlignment().getWidth();
2720 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2722 current = viewport.getAlignment().getSequenceAt(i);
2724 if (current.getLength() < Width)
2726 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2729 alignPanel.paintAlignment(true);
2732 if ((viewport.getSelectionGroup() != null
2733 && viewport.getSelectionGroup().getSize() < 4 && viewport
2734 .getSelectionGroup().getSize() > 0)
2735 || viewport.getAlignment().getHeight() < 4)
2742 new PCAPanel(viewport);
2743 } catch (java.lang.OutOfMemoryError ex)
2749 public void averageDistanceTreeMenuItem_actionPerformed()
2751 NewTreePanel("AV", "PID", "Average distance tree using PID");
2754 public void neighbourTreeMenuItem_actionPerformed()
2756 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2759 protected void njTreeBlosumMenuItem_actionPerformed()
2761 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2764 protected void avTreeBlosumMenuItem_actionPerformed()
2766 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2769 void NewTreePanel(String type, String pwType, String title)
2771 // are the sequences aligned?
2772 if (!viewport.getAlignment().isAligned(false))
2775 int Width = viewport.getAlignment().getWidth();
2777 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2779 current = viewport.getAlignment().getSequenceAt(i);
2781 if (current.getLength() < Width)
2783 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2786 alignPanel.paintAlignment(true);
2790 if ((viewport.getSelectionGroup() != null && viewport
2791 .getSelectionGroup().getSize() > 1)
2792 || (viewport.getAlignment().getHeight() > 1))
2794 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2796 addTreeMenuItem(tp, title);
2798 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2802 void loadTree_actionPerformed()
2804 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2805 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2806 cap.setTreeImport();
2807 Frame frame = new Frame();
2809 jalview.bin.JalviewLite.addFrame(frame,
2810 MessageManager.getString("label.paste_newick_file"), 400, 300);
2813 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2815 TreePanel tp = new TreePanel(alignPanel, treeFile,
2816 MessageManager.getString("label.load_tree_from_file"), tree);
2817 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2818 addTreeMenuItem(tp, treeFile);
2822 * sort the alignment using the given treePanel
2825 * tree used to sort view
2827 * string used for undo event name
2829 public void sortByTree(TreePanel treePanel, String title)
2831 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2833 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2834 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2835 // HistoryItem.SORT));
2836 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2837 "label.order_by_params", new String[]
2838 { title }), oldOrder, viewport.getAlignment()));
2839 alignPanel.paintAlignment(true);
2843 * Do any automatic reordering of the alignment and add the necessary bits to
2844 * the menu structure for the new tree
2849 protected void addTreeMenuItem(final TreePanel treePanel,
2852 final MenuItem item = new MenuItem(title);
2853 sortByTreeMenu.add(item);
2854 item.addActionListener(new java.awt.event.ActionListener()
2857 public void actionPerformed(ActionEvent evt)
2859 sortByTree(treePanel, title); // treePanel.getTitle());
2863 treePanel.addWindowListener(new WindowAdapter()
2866 public void windowOpened(WindowEvent e)
2868 if (viewport.sortByTree)
2870 sortByTree(treePanel, title);
2872 super.windowOpened(e);
2876 public void windowClosing(WindowEvent e)
2878 sortByTreeMenu.remove(item);
2883 public boolean sortBy(AlignmentOrder alorder, String undoname)
2885 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2886 if (viewport.applet.debug)
2888 System.err.println("Sorting " + alorder.getOrder().size()
2889 + " in alignment '" + getTitle() + "'");
2891 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2892 if (undoname != null)
2894 addHistoryItem(new OrderCommand(undoname, oldOrder,
2895 viewport.getAlignment()));
2897 alignPanel.paintAlignment(true);
2901 protected void documentation_actionPerformed()
2903 alignPanel.av.applet.openJalviewHelpUrl();
2906 protected void about_actionPerformed()
2909 class AboutPanel extends Canvas
2915 public AboutPanel(String version, String builddate)
2917 this.version = version;
2918 this.builddate = builddate;
2922 public void paint(Graphics g)
2924 g.setColor(Color.white);
2925 g.fillRect(0, 0, getSize().width, getSize().height);
2926 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2927 FontMetrics fm = g.getFontMetrics();
2928 int fh = fm.getHeight();
2930 g.setColor(Color.black);
2931 // TODO: update this text for each release or centrally store it for
2932 // lite and application
2933 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2934 g.drawString(MessageManager.formatMessage(
2935 "label.jalviewLite_release", new String[]
2936 { version }), x, y += fh);
2937 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2938 g.drawString(MessageManager.formatMessage(
2939 "label.jaview_build_date", new String[]
2940 { builddate }), x, y += fh);
2941 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2942 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2944 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2945 x + 50, y += fh + 8);
2947 MessageManager.getString("label.jalview_dev_managers"), x,
2949 g.drawString(MessageManager
2950 .getString("label.jalview_distribution_lists"), x, y += fh);
2951 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2954 MessageManager.getString("label.jalview_cite_1_authors"),
2957 MessageManager.getString("label.jalview_cite_1_title"), x,
2959 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2964 Frame frame = new Frame();
2965 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2967 jalview.bin.JalviewLite.addFrame(frame,
2968 MessageManager.getString("label.jalview"), 580, 220);
2972 public void showURL(String url, String target)
2974 if (viewport.applet == null)
2976 System.out.println("Not running as applet - no browser available.");
2980 viewport.applet.showURL(url, target);
2984 // ////////////////////////////////////////////////////////////////////////////////
2985 // JBuilder Graphics here
2987 MenuBar alignFrameMenuBar = new MenuBar();
2989 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2991 MenuItem loadApplication = new MenuItem(
2992 MessageManager.getString("label.view_full_application"));
2994 MenuItem loadTree = new MenuItem(
2995 MessageManager.getString("label.load_associated_tree"));
2997 MenuItem loadAnnotations = new MenuItem(
2998 MessageManager.getString("label.load_features_annotations"));
3000 MenuItem outputFeatures = new MenuItem(
3001 MessageManager.getString("label.export_features").concat("..."));
3003 MenuItem outputAnnotations = new MenuItem(
3004 MessageManager.getString("label.export_annotations").concat("..."));
3006 MenuItem closeMenuItem = new MenuItem(
3007 MessageManager.getString("action.close"));
3009 MenuItem selectAllSequenceMenuItem = new MenuItem(
3010 MessageManager.getString("action.select_all"));
3012 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3013 MessageManager.getString("action.deselect_all"));
3015 MenuItem invertSequenceMenuItem = new MenuItem(
3016 MessageManager.getString("action.invert_selection"));
3018 MenuItem remove2LeftMenuItem = new MenuItem();
3020 MenuItem remove2RightMenuItem = new MenuItem();
3022 MenuItem removeGappedColumnMenuItem = new MenuItem();
3024 MenuItem removeAllGapsMenuItem = new MenuItem();
3026 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3028 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3030 MenuItem sortPairwiseMenuItem = new MenuItem();
3032 MenuItem sortIDMenuItem = new MenuItem();
3034 MenuItem sortLengthMenuItem = new MenuItem();
3036 MenuItem sortGroupMenuItem = new MenuItem();
3038 MenuItem removeRedundancyMenuItem = new MenuItem();
3040 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3042 MenuItem PCAMenuItem = new MenuItem();
3044 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3046 MenuItem neighbourTreeMenuItem = new MenuItem();
3048 BorderLayout borderLayout1 = new BorderLayout();
3050 public Label statusBar = new Label();
3052 MenuItem clustalColour = new MenuItem();
3054 MenuItem zappoColour = new MenuItem();
3056 MenuItem taylorColour = new MenuItem();
3058 MenuItem hydrophobicityColour = new MenuItem();
3060 MenuItem helixColour = new MenuItem();
3062 MenuItem strandColour = new MenuItem();
3064 MenuItem turnColour = new MenuItem();
3066 MenuItem buriedColour = new MenuItem();
3068 MenuItem purinePyrimidineColour = new MenuItem();
3070 MenuItem RNAInteractionColour = new MenuItem();
3072 MenuItem RNAHelixColour = new MenuItem();
3074 MenuItem userDefinedColour = new MenuItem();
3076 MenuItem PIDColour = new MenuItem();
3078 MenuItem BLOSUM62Colour = new MenuItem();
3080 MenuItem tcoffeeColour = new MenuItem();
3082 MenuItem njTreeBlosumMenuItem = new MenuItem();
3084 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3086 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3088 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3090 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3092 MenuItem alProperties = new MenuItem(
3093 MessageManager.getString("label.alignment_props"));
3095 MenuItem overviewMenuItem = new MenuItem();
3097 MenuItem undoMenuItem = new MenuItem();
3099 MenuItem redoMenuItem = new MenuItem();
3101 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3103 MenuItem noColourmenuItem = new MenuItem();
3105 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3107 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3109 MenuItem findMenuItem = new MenuItem();
3111 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3113 MenuItem nucleotideColour = new MenuItem();
3115 MenuItem deleteGroups = new MenuItem();
3117 MenuItem grpsFromSelection = new MenuItem();
3119 MenuItem createGroup = new MenuItem();
3121 MenuItem unGroup = new MenuItem();
3123 MenuItem delete = new MenuItem();
3125 MenuItem copy = new MenuItem();
3127 MenuItem cut = new MenuItem();
3129 Menu pasteMenu = new Menu();
3131 MenuItem pasteNew = new MenuItem();
3133 MenuItem pasteThis = new MenuItem();
3135 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3137 MenuItem font = new MenuItem();
3139 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3141 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3143 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3145 MenuItem modifyPID = new MenuItem();
3147 MenuItem modifyConservation = new MenuItem();
3149 CheckboxMenuItem autoCalculate = null;
3151 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3152 "Sort Alignment With New Tree", true);
3154 Menu sortByTreeMenu = new Menu();
3156 MenuItem inputText = new MenuItem();
3158 MenuItem documentation = new MenuItem();
3160 MenuItem about = new MenuItem();
3162 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3164 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3166 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3168 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3170 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3172 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3174 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3176 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3178 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3181 * Initialise menus and other items
3185 private void jbInit() throws Exception
3187 setMenuBar(alignFrameMenuBar);
3190 * Configure File menu items and actions
3193 .setLabel(MessageManager.getString("label.input_from_textbox"));
3194 inputText.addActionListener(this);
3195 Menu outputTextboxMenu = new Menu(
3196 MessageManager.getString("label.out_to_textbox"));
3197 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3200 MenuItem item = new MenuItem(
3201 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3203 item.addActionListener(new java.awt.event.ActionListener()
3206 public void actionPerformed(ActionEvent e)
3208 outputText_actionPerformed(e);
3212 outputTextboxMenu.add(item);
3214 closeMenuItem.addActionListener(this);
3215 loadApplication.addActionListener(this);
3216 loadTree.addActionListener(this);
3217 loadAnnotations.addActionListener(this);
3218 outputFeatures.addActionListener(this);
3219 outputAnnotations.addActionListener(this);
3222 * Configure Edit menu items and actions
3224 undoMenuItem.setEnabled(false);
3225 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3226 undoMenuItem.addActionListener(this);
3227 redoMenuItem.setEnabled(false);
3228 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3229 redoMenuItem.addActionListener(this);
3230 copy.setLabel(MessageManager.getString("action.copy"));
3231 copy.addActionListener(this);
3232 cut.setLabel(MessageManager.getString("action.cut"));
3233 cut.addActionListener(this);
3234 delete.setLabel(MessageManager.getString("action.delete"));
3235 delete.addActionListener(this);
3236 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3237 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3238 pasteNew.addActionListener(this);
3239 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3240 pasteThis.addActionListener(this);
3241 remove2LeftMenuItem.setLabel(MessageManager
3242 .getString("action.remove_left"));
3243 remove2LeftMenuItem.addActionListener(this);
3244 remove2RightMenuItem.setLabel(MessageManager
3245 .getString("action.remove_right"));
3246 remove2RightMenuItem.addActionListener(this);
3247 removeGappedColumnMenuItem.setLabel(MessageManager
3248 .getString("action.remove_empty_columns"));
3249 removeGappedColumnMenuItem.addActionListener(this);
3250 removeAllGapsMenuItem.setLabel(MessageManager
3251 .getString("action.remove_all_gaps"));
3252 removeAllGapsMenuItem.addActionListener(this);
3253 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3254 "action.remove_redundancy").concat("..."));
3255 removeRedundancyMenuItem.addActionListener(this);
3258 * Configure Select menu items and actions
3260 findMenuItem.setLabel(MessageManager.getString("action.find"));
3261 findMenuItem.addActionListener(this);
3262 selectAllSequenceMenuItem.addActionListener(this);
3263 deselectAllSequenceMenuItem.addActionListener(this);
3264 invertSequenceMenuItem.setLabel(MessageManager
3265 .getString("action.invert_sequence_selection"));
3266 invertSequenceMenuItem.addActionListener(this);
3267 invertColSel.setLabel(MessageManager
3268 .getString("action.invert_column_selection"));
3269 invertColSel.addActionListener(this);
3270 deleteGroups.setLabel(MessageManager
3271 .getString("action.undefine_groups"));
3272 deleteGroups.addActionListener(this);
3273 grpsFromSelection.setLabel(MessageManager
3274 .getString("action.make_groups_selection"));
3275 grpsFromSelection.addActionListener(this);
3276 createGroup.setLabel(MessageManager.getString("action.create_group"));
3277 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3278 annotationColumnSelection.setLabel("Select by Annotation");
3279 annotationColumnSelection.addActionListener(this);
3282 * Configure View menu items and actions
3284 newView.setLabel(MessageManager.getString("action.new_view"));
3285 newView.addActionListener(this);
3286 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3287 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3288 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3289 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3291 .setLabel(MessageManager.getString("label.selected_columns"));
3292 hideSequences.setLabel(MessageManager
3293 .getString("label.selected_sequences"));
3294 hideAllButSelection.setLabel(MessageManager
3295 .getString("label.all_but_selected_region"));
3296 hideAllSelection.setLabel(MessageManager
3297 .getString("label.selected_region"));
3298 showAllHidden.setLabel(MessageManager
3299 .getString("label.all_sequences_columns"));
3300 showColumns.addActionListener(this);
3301 showSeqs.addActionListener(this);
3302 hideColumns.addActionListener(this);
3303 hideSequences.addActionListener(this);
3304 hideAllButSelection.addActionListener(this);
3305 hideAllSelection.addActionListener(this);
3306 showAllHidden.addActionListener(this);
3307 featureSettings.setLabel(MessageManager
3308 .getString("label.feature_settings"));
3309 featureSettings.addActionListener(this);
3310 sequenceFeatures.setLabel(MessageManager
3311 .getString("label.show_sequence_features"));
3312 sequenceFeatures.addItemListener(this);
3313 sequenceFeatures.setState(false);
3314 followMouseOverFlag.setLabel(MessageManager
3315 .getString("label.automatic_scrolling"));
3316 followMouseOverFlag.addItemListener(this);
3317 alProperties.addActionListener(this);
3318 overviewMenuItem.setLabel(MessageManager
3319 .getString("label.overview_window"));
3320 overviewMenuItem.addActionListener(this);
3323 * Configure Annotations menu items and actions
3325 annotationPanelMenuItem.setLabel(MessageManager
3326 .getString("label.show_annotations"));
3327 annotationPanelMenuItem.addItemListener(this);
3328 showGroupConsensus.setLabel(MessageManager
3329 .getString("label.group_consensus"));
3330 showGroupConservation.setLabel(MessageManager
3331 .getString("label.group_conservation"));
3332 showConsensusHistogram.setLabel(MessageManager
3333 .getString("label.show_consensus_histogram"));
3334 showSequenceLogo.setLabel(MessageManager
3335 .getString("label.show_consensus_logo"));
3336 normSequenceLogo.setLabel(MessageManager
3337 .getString("label.norm_consensus_logo"));
3338 applyAutoAnnotationSettings.setLabel(MessageManager
3339 .getString("label.apply_all_groups"));
3340 applyAutoAnnotationSettings.setState(true);
3341 Menu autoAnnMenu = new Menu(
3342 MessageManager.getString("label.autocalculated_annotation"));
3343 showGroupConsensus.addItemListener(this);
3344 showGroupConservation.addItemListener(this);
3345 showConsensusHistogram.addItemListener(this);
3346 showSequenceLogo.addItemListener(this);
3347 normSequenceLogo.addItemListener(this);
3348 applyAutoAnnotationSettings.addItemListener(this);
3349 showAlignmentAnnotations = new CheckboxMenuItem(
3350 MessageManager.getString("label.show_all_al_annotations"));
3351 showSequenceAnnotations = new CheckboxMenuItem(
3352 MessageManager.getString("label.show_all_seq_annotations"));
3353 sortAnnBySequence = new CheckboxMenuItem(
3354 MessageManager.getString("label.sort_annotations_by_sequence"));
3355 sortAnnByLabel = new CheckboxMenuItem(
3356 MessageManager.getString("label.sort_annotations_by_label"));
3357 showAutoFirst = new CheckboxMenuItem(
3358 MessageManager.getString("label.show_first"));
3359 showAutoLast = new CheckboxMenuItem(
3360 MessageManager.getString("label.show_last"));
3361 showAlignmentAnnotations.addItemListener(this);
3362 showSequenceAnnotations.addItemListener(this);
3363 sortAnnBySequence.addItemListener(this);
3364 sortAnnByLabel.addItemListener(this);
3365 showAutoFirst.addItemListener(this);
3366 showAutoLast.addItemListener(this);
3369 * Configure Format menu items and actions
3371 font.setLabel(MessageManager.getString("action.font"));
3372 font.addActionListener(this);
3373 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3374 scaleAbove.setState(true);
3375 scaleAbove.setEnabled(false);
3376 scaleAbove.addItemListener(this);
3377 scaleLeft.setEnabled(false);
3378 scaleLeft.setState(true);
3379 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3380 scaleLeft.addItemListener(this);
3381 scaleRight.setEnabled(false);
3382 scaleRight.setState(true);
3383 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3384 scaleRight.addItemListener(this);
3385 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3386 viewBoxesMenuItem.setState(true);
3387 viewBoxesMenuItem.addItemListener(this);
3388 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3389 viewTextMenuItem.setState(true);
3390 viewTextMenuItem.addItemListener(this);
3391 colourTextMenuItem.setLabel(MessageManager
3392 .getString("label.colour_text"));
3393 colourTextMenuItem.addItemListener(this);
3394 displayNonconservedMenuItem.setLabel(MessageManager
3395 .getString("label.show_non_conversed"));
3396 displayNonconservedMenuItem.addItemListener(this);
3397 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3398 wrapMenuItem.addItemListener(this);
3399 renderGapsMenuItem.setLabel(MessageManager
3400 .getString("action.show_gaps"));
3401 renderGapsMenuItem.setState(true);
3402 renderGapsMenuItem.addItemListener(this);
3403 centreColumnLabelFlag.setLabel(MessageManager
3404 .getString("label.centre_column_labels"));
3405 centreColumnLabelFlag.addItemListener(this);
3406 seqLimits.setState(true);
3407 seqLimits.setLabel(MessageManager
3408 .getString("label.show_sequence_limits"));
3409 seqLimits.addItemListener(this);
3412 * Configure Colour menu items and actions
3414 applyToAllGroups.setLabel(MessageManager
3415 .getString("label.apply_colour_to_all_groups"));
3416 applyToAllGroups.setState(true);
3417 applyToAllGroups.addItemListener(this);
3418 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3419 clustalColour.addActionListener(this);
3420 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3421 zappoColour.addActionListener(this);
3422 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3423 taylorColour.addActionListener(this);
3424 hydrophobicityColour.setLabel(MessageManager
3425 .getString("label.hydrophobicity"));
3426 hydrophobicityColour.addActionListener(this);
3428 .setLabel(MessageManager.getString("label.helix_propensity"));
3429 helixColour.addActionListener(this);
3430 strandColour.setLabel(MessageManager
3431 .getString("label.strand_propensity"));
3432 strandColour.addActionListener(this);
3433 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3434 turnColour.addActionListener(this);
3435 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3436 buriedColour.addActionListener(this);
3437 purinePyrimidineColour.setLabel(MessageManager
3438 .getString("label.purine_pyrimidine"));
3439 purinePyrimidineColour.addActionListener(this);
3440 RNAInteractionColour.setLabel(MessageManager
3441 .getString("label.rna_interaction"));
3442 RNAInteractionColour.addActionListener(this);
3443 RNAHelixColour.setLabel(MessageManager
3444 .getString("action.by_rna_helixes"));
3445 RNAHelixColour.addActionListener(this);
3446 userDefinedColour.setLabel(MessageManager
3447 .getString("action.user_defined"));
3448 userDefinedColour.addActionListener(this);
3449 PIDColour.setLabel(MessageManager
3450 .getString("label.percentage_identity"));
3451 PIDColour.addActionListener(this);
3452 BLOSUM62Colour.setLabel(MessageManager
3453 .getString("label.blosum62_score"));
3454 BLOSUM62Colour.addActionListener(this);
3456 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3457 // it will be enabled only if a score file is provided
3458 tcoffeeColour.setEnabled(false);
3459 tcoffeeColour.addActionListener(this);
3460 conservationMenuItem.setLabel(MessageManager
3461 .getString("action.by_conservation"));
3462 conservationMenuItem.addItemListener(this);
3463 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3464 noColourmenuItem.addActionListener(this);
3465 abovePIDThreshold.setLabel(MessageManager
3466 .getString("label.above_identity_threshold"));
3467 abovePIDThreshold.addItemListener(this);
3468 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3469 nucleotideColour.addActionListener(this);
3470 modifyPID.setLabel(MessageManager
3471 .getString("label.modify_identity_thereshold"));
3472 modifyPID.addActionListener(this);
3473 modifyConservation.setLabel(MessageManager
3474 .getString("label.modify_conservation_thereshold"));
3475 modifyConservation.addActionListener(this);
3476 annotationColour.setLabel(MessageManager
3477 .getString("action.by_annotation"));
3478 annotationColour.addActionListener(this);
3481 * Configure Calculate menu items and actions
3483 sortPairwiseMenuItem.setLabel(MessageManager
3484 .getString("action.by_pairwise_id"));
3485 sortPairwiseMenuItem.addActionListener(this);
3486 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3487 sortIDMenuItem.addActionListener(this);
3488 sortLengthMenuItem.setLabel(MessageManager
3489 .getString("action.by_length"));
3490 sortLengthMenuItem.addActionListener(this);
3491 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3492 sortGroupMenuItem.addActionListener(this);
3493 pairwiseAlignmentMenuItem.setLabel(MessageManager
3494 .getString("action.pairwise_alignment"));
3495 pairwiseAlignmentMenuItem.addActionListener(this);
3496 PCAMenuItem.setLabel(MessageManager
3497 .getString("label.principal_component_analysis"));
3498 PCAMenuItem.addActionListener(this);
3499 autoCalculate = new CheckboxMenuItem(
3500 MessageManager.getString("label.autocalculate_consensus"), true);
3501 averageDistanceTreeMenuItem.setLabel(MessageManager
3502 .getString("label.average_distance_identity"));
3503 averageDistanceTreeMenuItem.addActionListener(this);
3504 neighbourTreeMenuItem.setLabel(MessageManager
3505 .getString("label.neighbour_joining_identity"));
3506 neighbourTreeMenuItem.addActionListener(this);
3507 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3508 .getString("label.average_distance_bloslum62"));
3509 avDistanceTreeBlosumMenuItem.addActionListener(this);
3510 njTreeBlosumMenuItem.setLabel(MessageManager
3511 .getString("label.neighbour_blosum62"));
3512 njTreeBlosumMenuItem.addActionListener(this);
3513 sortByTreeMenu.setLabel(MessageManager
3514 .getString("action.by_tree_order"));
3515 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3516 Menu calculateTreeMenu = new Menu(
3517 MessageManager.getString("action.calculate_tree"));
3518 autoCalculate.addItemListener(this);
3519 sortByTree.addItemListener(this);
3522 * Configure Help menu items and actions
3524 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3525 documentation.setLabel(MessageManager.getString("label.documentation"));
3526 documentation.addActionListener(this);
3527 about.setLabel(MessageManager.getString("label.about"));
3528 about.addActionListener(this);
3531 * Add top level menus to frame
3533 alignFrameMenuBar.add(fileMenu);
3534 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3535 alignFrameMenuBar.add(editMenu);
3536 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3537 alignFrameMenuBar.add(selectMenu);
3538 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3539 alignFrameMenuBar.add(viewMenu);
3540 Menu annotationsMenu = new Menu(
3541 MessageManager.getString("action.annotations"));
3542 alignFrameMenuBar.add(annotationsMenu);
3543 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3544 alignFrameMenuBar.add(formatMenu);
3545 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3546 alignFrameMenuBar.add(colourMenu);
3547 Menu calculateMenu = new Menu(
3548 MessageManager.getString("action.calculate"));
3549 alignFrameMenuBar.add(calculateMenu);
3550 alignFrameMenuBar.add(helpMenu);
3555 fileMenu.add(inputText);
3556 fileMenu.add(loadTree);
3557 fileMenu.add(loadAnnotations);
3558 fileMenu.addSeparator();
3559 fileMenu.add(outputTextboxMenu);
3560 fileMenu.add(outputFeatures);
3561 fileMenu.add(outputAnnotations);
3562 if (jalviewServletURL != null)
3564 fileMenu.add(loadApplication);
3566 fileMenu.addSeparator();
3567 fileMenu.add(closeMenuItem);
3572 editMenu.add(undoMenuItem);
3573 editMenu.add(redoMenuItem);
3576 pasteMenu.add(pasteNew);
3577 pasteMenu.add(pasteThis);
3578 editMenu.add(pasteMenu);
3579 editMenu.add(delete);
3580 editMenu.addSeparator();
3581 editMenu.add(remove2LeftMenuItem);
3582 editMenu.add(remove2RightMenuItem);
3583 editMenu.add(removeGappedColumnMenuItem);
3584 editMenu.add(removeAllGapsMenuItem);
3585 editMenu.add(removeRedundancyMenuItem);
3590 selectMenu.add(findMenuItem);
3591 selectMenu.addSeparator();
3592 selectMenu.add(selectAllSequenceMenuItem);
3593 selectMenu.add(deselectAllSequenceMenuItem);
3594 selectMenu.add(invertSequenceMenuItem);
3595 selectMenu.add(invertColSel);
3596 selectMenu.add(createGroup);
3597 selectMenu.add(unGroup);
3598 selectMenu.add(grpsFromSelection);
3599 selectMenu.add(deleteGroups);
3600 selectMenu.add(annotationColumnSelection);
3605 viewMenu.add(newView);
3606 viewMenu.addSeparator();
3607 showMenu.add(showColumns);
3608 showMenu.add(showSeqs);
3609 showMenu.add(showAllHidden);
3610 viewMenu.add(showMenu);
3611 hideMenu.add(hideColumns);
3612 hideMenu.add(hideSequences);
3613 hideMenu.add(hideAllSelection);
3614 hideMenu.add(hideAllButSelection);
3615 viewMenu.add(hideMenu);
3616 viewMenu.addSeparator();
3617 viewMenu.add(followMouseOverFlag);
3618 viewMenu.addSeparator();
3619 viewMenu.add(sequenceFeatures);
3620 viewMenu.add(featureSettings);
3621 viewMenu.addSeparator();
3622 viewMenu.add(alProperties);
3623 viewMenu.addSeparator();
3624 viewMenu.add(overviewMenuItem);
3629 annotationsMenu.add(annotationPanelMenuItem);
3630 annotationsMenu.addSeparator();
3631 annotationsMenu.add(showAlignmentAnnotations);
3632 annotationsMenu.add(showSequenceAnnotations);
3633 annotationsMenu.add(sortAnnBySequence);
3634 annotationsMenu.add(sortAnnByLabel);
3635 annotationsMenu.addSeparator();
3636 autoAnnMenu.add(showAutoFirst);
3637 autoAnnMenu.add(showAutoLast);
3638 autoAnnMenu.addSeparator();
3639 autoAnnMenu.add(applyAutoAnnotationSettings);
3640 autoAnnMenu.add(showConsensusHistogram);
3641 autoAnnMenu.add(showSequenceLogo);
3642 autoAnnMenu.add(normSequenceLogo);
3643 autoAnnMenu.addSeparator();
3644 autoAnnMenu.add(showGroupConservation);
3645 autoAnnMenu.add(showGroupConsensus);
3646 annotationsMenu.add(autoAnnMenu);
3651 formatMenu.add(font);
3652 formatMenu.add(seqLimits);
3653 formatMenu.add(wrapMenuItem);
3654 formatMenu.add(scaleAbove);
3655 formatMenu.add(scaleLeft);
3656 formatMenu.add(scaleRight);
3657 formatMenu.add(viewBoxesMenuItem);
3658 formatMenu.add(viewTextMenuItem);
3659 formatMenu.add(colourTextMenuItem);
3660 formatMenu.add(displayNonconservedMenuItem);
3661 formatMenu.add(renderGapsMenuItem);
3662 formatMenu.add(centreColumnLabelFlag);
3667 colourMenu.add(applyToAllGroups);
3668 colourMenu.addSeparator();
3669 colourMenu.add(noColourmenuItem);
3670 colourMenu.add(clustalColour);
3671 colourMenu.add(BLOSUM62Colour);
3672 colourMenu.add(PIDColour);
3673 colourMenu.add(zappoColour);
3674 colourMenu.add(taylorColour);
3675 colourMenu.add(hydrophobicityColour);
3676 colourMenu.add(helixColour);
3677 colourMenu.add(strandColour);
3678 colourMenu.add(turnColour);
3679 colourMenu.add(buriedColour);
3680 colourMenu.add(nucleotideColour);
3681 colourMenu.add(purinePyrimidineColour);
3682 // colourMenu.add(RNAInteractionColour);
3683 colourMenu.add(tcoffeeColour);
3684 colourMenu.add(userDefinedColour);
3685 colourMenu.addSeparator();
3686 colourMenu.add(conservationMenuItem);
3687 colourMenu.add(modifyConservation);
3688 colourMenu.add(abovePIDThreshold);
3689 colourMenu.add(modifyPID);
3690 colourMenu.add(annotationColour);
3691 colourMenu.add(RNAHelixColour);
3696 sortMenu.add(sortIDMenuItem);
3697 sortMenu.add(sortLengthMenuItem);
3698 sortMenu.add(sortByTreeMenu);
3699 sortMenu.add(sortGroupMenuItem);
3700 sortMenu.add(sortPairwiseMenuItem);
3701 calculateMenu.add(sortMenu);
3702 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3703 calculateTreeMenu.add(neighbourTreeMenuItem);
3704 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3705 calculateTreeMenu.add(njTreeBlosumMenuItem);
3706 calculateMenu.add(calculateTreeMenu);
3707 calculateMenu.addSeparator();
3708 calculateMenu.add(pairwiseAlignmentMenuItem);
3709 calculateMenu.add(PCAMenuItem);
3710 calculateMenu.add(autoCalculate);
3711 calculateMenu.add(sortByTree);
3716 helpMenu.add(documentation);
3717 helpMenu.add(about);
3722 statusBar.setBackground(Color.white);
3723 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3724 statusBar.setText(MessageManager.getString("label.status_bar"));
3725 this.add(statusBar, BorderLayout.SOUTH);
3728 public void setStatus(String string)
3730 statusBar.setText(string);
3733 MenuItem featureSettings = new MenuItem();
3735 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3737 MenuItem annotationColour = new MenuItem();
3739 MenuItem annotationColumnSelection = new MenuItem();
3741 MenuItem invertColSel = new MenuItem();
3743 MenuItem showColumns = new MenuItem();
3745 MenuItem showSeqs = new MenuItem();
3747 MenuItem hideColumns = new MenuItem();
3749 MenuItem hideSequences = new MenuItem();
3751 MenuItem hideAllButSelection = new MenuItem();
3753 MenuItem hideAllSelection = new MenuItem();
3755 MenuItem showAllHidden = new MenuItem();
3757 MenuItem newView = new MenuItem();
3759 private CheckboxMenuItem showAlignmentAnnotations;
3761 private CheckboxMenuItem showSequenceAnnotations;
3763 private CheckboxMenuItem sortAnnBySequence;
3765 private CheckboxMenuItem sortAnnByLabel;
3767 private CheckboxMenuItem showAutoFirst;
3769 private CheckboxMenuItem showAutoLast;
3771 private SplitFrame splitFrame;
3774 * Attach the alignFrame panels after embedding menus, if necessary. This used
3775 * to be called setEmbedded, but is now creates the dropdown menus in a
3776 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3778 * @param reallyEmbedded
3779 * true to attach the view to the applet area on the page rather than
3782 public void createAlignFrameWindow(boolean reallyEmbedded)
3786 embedAlignFrameInApplet(viewport.applet);
3791 // test and embed menu bar if necessary.
3793 if (embedMenuIfNeeded(alignPanel))
3796 * adjust for status bar height too. ? pointless as overridden by layout
3799 alignPanel.setSize(getSize().width,
3800 getSize().height - statusBar.getHeight());
3802 add(statusBar, BorderLayout.SOUTH);
3803 add(alignPanel, BorderLayout.CENTER);
3804 // and register with the applet so it can pass external API calls to us
3805 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3812 * Add the components of this AlignFrame to the applet container.
3816 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3819 // Explicitly build the embedded menu panel for the on-page applet
3821 // view cannot be closed if its actually on the page
3822 fileMenu.remove(closeMenuItem);
3823 fileMenu.remove(3); // Remove Separator
3824 // construct embedded menu, using default font
3825 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3826 // and actually add the components to the applet area
3827 theApplet.setLayout(new BorderLayout());
3828 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3829 theApplet.add(statusBar, BorderLayout.SOUTH);
3830 // TODO should size be left to the layout manager?
3831 alignPanel.setSize(theApplet.getSize().width,
3832 theApplet.getSize().height - embeddedMenu.getHeight()
3833 - statusBar.getHeight());
3834 theApplet.add(alignPanel, BorderLayout.CENTER);
3835 final AlignFrame me = this;
3836 theApplet.addFocusListener(new FocusListener()
3840 public void focusLost(FocusEvent e)
3842 if (theApplet.currentAlignFrame == me)
3844 theApplet.currentAlignFrame = null;
3849 public void focusGained(FocusEvent e)
3851 theApplet.currentAlignFrame = me;
3854 theApplet.validate();
3858 * create a new binding between structures in an existing jmol viewer instance
3859 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3860 * this does not open a new Jmol window, or modify the display of the
3861 * structures in the original jmol window. Note This method doesn't work
3862 * without an additional javascript library to exchange messages between the
3863 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3866 * JmolViewer instance
3867 * @param sequenceIds
3868 * - sequence Ids to search for associations
3870 public SequenceStructureBinding addStructureViewInstance(
3871 Object jmolviewer, String[] sequenceIds)
3873 org.jmol.api.JmolViewer viewer = null;
3876 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3877 } catch (ClassCastException ex)
3879 System.err.println("Unsupported viewer object :"
3880 + jmolviewer.getClass());
3884 System.err.println("Can't use this object as a structure viewer:"
3885 + jmolviewer.getClass());
3888 SequenceI[] seqs = null;
3889 if (sequenceIds == null || sequenceIds.length == 0)
3891 seqs = viewport.getAlignment().getSequencesArray();
3895 Vector sqi = new Vector();
3896 AlignmentI al = viewport.getAlignment();
3897 for (int sid = 0; sid < sequenceIds.length; sid++)
3899 SequenceI sq = al.findName(sequenceIds[sid]);
3907 seqs = new SequenceI[sqi.size()];
3908 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3910 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3918 AAStructureBindingModel jmv = null;
3919 // TODO: search for a jmv that involves viewer
3921 { // create a new viewer/jalview binding.
3922 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3930 * bind a pdb file to a sequence in the current view
3933 * - sequenceId within the dataset.
3934 * @param pdbEntryString
3935 * - the short name for the PDB file
3937 * - pdb file - either a URL or a valid PDB file.
3938 * @return true if binding was as success TODO: consider making an exception
3939 * structure for indicating when PDB parsing or sequenceId location
3942 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3945 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3946 boolean needtoadd = false;
3947 if (toaddpdb != null)
3949 Vector pdbe = toaddpdb.getPDBId();
3950 PDBEntry pdbentry = null;
3951 if (pdbe != null && pdbe.size() > 0)
3953 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3955 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3956 if (!pdbentry.getId().equals(pdbEntryString)
3957 && !pdbentry.getFile().equals(pdbFile))
3967 if (pdbentry == null)
3969 pdbentry = new PDBEntry();
3970 pdbentry.setId(pdbEntryString);
3971 pdbentry.setFile(pdbFile);
3972 needtoadd = true; // add this new entry to sequence.
3974 // resolve data source
3975 // TODO: this code should be a refactored to an io package
3976 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3977 if (protocol == null)
3983 // make a note of the access mode and add
3984 if (pdbentry.getProperty() == null)
3986 pdbentry.setProperty(new Hashtable());
3988 pdbentry.getProperty().put("protocol", protocol);
3989 toaddpdb.addPDBId(pdbentry);
3990 alignPanel.getStructureSelectionManager()
3991 .registerPDBEntry(pdbentry);
3997 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
4001 Vector sequences = new Vector();
4002 for (int i = 0; i < seqs.length; i++)
4004 if (seqs[i] != null)
4006 sequences.addElement(new Object[]
4007 { seqs[i], (chains != null) ? chains[i] : null });
4010 seqs = new SequenceI[sequences.size()];
4011 chains = new String[sequences.size()];
4012 for (int i = 0, isize = sequences.size(); i < isize; i++)
4014 Object[] oj = (Object[]) sequences.elementAt(i);
4016 seqs[i] = (SequenceI) oj[0];
4017 chains[i] = (String) oj[1];
4025 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4026 SequenceI[] seqs, String[] chains, String protocol)
4028 // Scrub any null sequences from the array
4029 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4030 seqs = (SequenceI[]) sqch[0];
4031 chains = (String[]) sqch[1];
4032 if (seqs == null || seqs.length == 0)
4035 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4037 if (protocol == null || protocol.trim().length() == 0
4038 || protocol.equals("null"))
4040 protocol = (String) pdb.getProperty().get("protocol");
4041 if (protocol == null)
4043 System.err.println("Couldn't work out protocol to open structure: "
4048 if (applet.useXtrnalSviewer)
4050 // register the association(s) and quit, don't create any windows.
4051 if (StructureSelectionManager.getStructureSelectionManager(applet)
4052 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4054 System.err.println("Failed to map " + pdb.getFile() + " ("
4055 + protocol + ") to any sequences");
4059 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4061 // can only do alignments with Jmol
4062 // find the last jmol window assigned to this alignment
4063 jalview.appletgui.AppletJmol ajm = null, tajm;
4064 Vector jmols = applet
4065 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4066 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4068 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4069 if (tajm.ap.alignFrame == this)
4078 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4079 // try and add the pdb structure
4084 // otherwise, create a new window
4085 if (applet.jmolAvailable)
4087 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4089 applet.lastFrameX += 40;
4090 applet.lastFrameY += 40;
4094 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4099 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4100 SequenceI[][] seqs, String[][] chains, String[] protocols)
4102 // TODO Auto-generated method stub
4103 System.err.println("Aligned Structure View: Not yet implemented.");
4107 * modify the current selection, providing the user has not made a selection
4111 * - sequences from this alignment
4113 * - columns to be selected on the alignment
4115 public void select(SequenceGroup sel, ColumnSelection csel)
4117 alignPanel.seqPanel.selection(sel, csel, null);
4120 public void scrollTo(int row, int column)
4122 alignPanel.seqPanel.scrollTo(row, column);
4125 public void scrollToRow(int row)
4127 alignPanel.seqPanel.scrollToRow(row);
4130 public void scrollToColumn(int column)
4132 alignPanel.seqPanel.scrollToColumn(column);
4136 * @return the alignments unique ID.
4138 public String getSequenceSetId()
4140 return viewport.getSequenceSetId();
4144 * Load the (T-Coffee) score file from the specified url
4147 * File/URL/T-COFFEE score file contents
4148 * @throws IOException
4149 * @return true if alignment was annotated with data from source
4151 public boolean loadScoreFile(String source) throws IOException
4154 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4155 AppletFormatAdapter.checkProtocol(source));
4156 if (!file.isValid())
4158 // TODO: raise dialog for gui
4159 System.err.println("Problems parsing T-Coffee scores: "
4160 + file.getWarningMessage());
4161 System.err.println("Origin was:\n" + source);
4166 * check that the score matrix matches the alignment dimensions
4169 if ((aln = viewport.getAlignment()) != null
4170 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4173 // TODO: raise a dialog box here rather than bomb out.
4175 .println("The scores matrix does not match the alignment dimensions");
4179 // TODO add parameter to indicate if matching should be done
4180 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4182 alignPanel.fontChanged();
4183 tcoffeeColour.setEnabled(true);
4184 // switch to this color
4185 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4190 System.err.println("Problems resolving T-Coffee scores:");
4191 if (file.getWarningMessage() != null)
4193 System.err.println(file.getWarningMessage());
4199 public SplitFrame getSplitFrame()
4201 return this.splitFrame;
4204 public void setSplitFrame(SplitFrame sf)
4206 this.splitFrame = sf;
4209 // may not need this
4211 public void setShowSeqFeatures(boolean b)
4213 // showSeqFeatures.setSelected(b);
4214 viewport.setShowSequenceFeatures(b);
4219 public void setMenusForViewport()
4221 // setMenusFromViewport(viewport);
4225 public void refreshFeatureUI(boolean enableIfNecessary)
4227 if (enableIfNecessary)
4229 sequenceFeatures.setState(true);
4230 alignPanel.av.setShowSequenceFeatures(true);
4235 public FeatureSettingsControllerI getFeatureSettingsUI()
4237 return alignPanel.av.featureSettings;