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.StrandColourScheme;
64 import jalview.schemes.TCoffeeColourScheme;
65 import jalview.schemes.TaylorColourScheme;
66 import jalview.schemes.TurnColourScheme;
67 import jalview.schemes.ZappoColourScheme;
68 import jalview.structure.StructureSelectionManager;
69 import jalview.structures.models.AAStructureBindingModel;
70 import jalview.util.MappingUtils;
71 import jalview.util.MessageManager;
72 import jalview.viewmodel.AlignmentViewport;
74 import java.awt.BorderLayout;
75 import java.awt.Canvas;
76 import java.awt.CheckboxMenuItem;
77 import java.awt.Color;
79 import java.awt.FontMetrics;
80 import java.awt.Frame;
81 import java.awt.Graphics;
82 import java.awt.Label;
84 import java.awt.MenuBar;
85 import java.awt.MenuItem;
86 import java.awt.event.ActionEvent;
87 import java.awt.event.ActionListener;
88 import java.awt.event.FocusEvent;
89 import java.awt.event.FocusListener;
90 import java.awt.event.ItemEvent;
91 import java.awt.event.ItemListener;
92 import java.awt.event.KeyEvent;
93 import java.awt.event.KeyListener;
94 import java.awt.event.WindowAdapter;
95 import java.awt.event.WindowEvent;
96 import java.io.IOException;
98 import java.net.URLEncoder;
99 import java.util.Arrays;
100 import java.util.Deque;
101 import java.util.HashMap;
102 import java.util.Hashtable;
103 import java.util.List;
104 import java.util.Map;
105 import java.util.StringTokenizer;
106 import java.util.Vector;
108 import org.jmol.viewer.Viewer;
110 public class AlignFrame extends EmbmenuFrame implements ActionListener,
111 ItemListener, KeyListener, AlignViewControllerGuiI
113 public AlignViewControllerI avc;
115 public AlignmentPanel alignPanel;
117 public AlignViewport viewport;
119 // width and height may be overridden by applet parameters
120 int frameWidth = 700;
122 int frameHeight = 500;
124 String jalviewServletURL;
127 * Flag for showing autocalculated consensus above or below other consensus
130 private boolean showAutoCalculatedAbove;
132 private SequenceAnnotationOrder annotationSortOrder;
135 * Constructor that creates the frame and adds it to the display.
142 public AlignFrame(AlignmentI al, JalviewLite applet,
143 String title, boolean embedded)
145 this(al, applet, title, embedded, true);
149 * Constructor that optionally allows the frame to be displayed or only
156 * @param addToDisplay
158 public AlignFrame(AlignmentI al, JalviewLite applet,
159 String title, boolean embedded, boolean addToDisplay)
161 this(al, null, null, applet, title, embedded, addToDisplay);
164 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
165 ColumnSelection columnSelection, JalviewLite applet,
166 String title, boolean embedded)
168 this(al, hiddenSeqs, columnSelection, applet, title, embedded, true);
171 public AlignFrame(AlignmentI al, SequenceI[] hiddenSeqs,
172 ColumnSelection columnSelection, JalviewLite applet,
173 String title, boolean embedded, boolean addToDisplay)
177 jalviewServletURL = applet.getParameter("APPLICATION_URL");
183 } catch (Exception ex)
185 ex.printStackTrace();
187 // need to get window geometry before we calculate alignment layout
193 param = applet.getParameter("windowWidth");
196 int width = Integer.parseInt(param);
199 param = applet.getParameter("windowHeight");
202 int height = Integer.parseInt(param);
203 frameHeight = height;
205 } catch (Exception ex)
209 viewport = new AlignViewport(al, applet);
211 if (hiddenSeqs != null && hiddenSeqs.length > 0)
213 viewport.hideSequence(hiddenSeqs);
215 if (columnSelection != null)
217 viewport.setColumnSelection(columnSelection);
220 alignPanel = new AlignmentPanel(this, viewport);
221 avc = new jalview.controller.AlignViewController(this, viewport,
223 viewport.updateConservation(alignPanel);
224 viewport.updateConsensus(alignPanel);
226 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
227 followMouseOverFlag.setState(viewport.isFollowHighlight());
228 showGroupConsensus.setState(viewport.isShowGroupConsensus());
229 showGroupConservation.setState(viewport.isShowGroupConservation());
230 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
231 showSequenceLogo.setState(viewport.isShowSequenceLogo());
232 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
233 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
234 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
235 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
236 showSequenceAnnotations.setState(viewport.isShowAnnotation());
238 seqLimits.setState(viewport.getShowJVSuffix());
242 String param = applet.getParameter("sortBy");
245 if (param.equalsIgnoreCase("Id"))
247 sortIDMenuItem_actionPerformed();
249 else if (param.equalsIgnoreCase("Pairwise Identity"))
251 sortPairwiseMenuItem_actionPerformed();
253 else if (param.equalsIgnoreCase("Length"))
255 sortLengthMenuItem_actionPerformed();
259 param = applet.getParameter("wrap");
262 if (param.equalsIgnoreCase("true"))
264 wrapMenuItem.setState(true);
265 wrapMenuItem_actionPerformed();
268 param = applet.getParameter("centrecolumnlabels");
271 centreColumnLabelFlag.setState(true);
272 centreColumnLabelFlag_stateChanged();
276 if (viewport.getAlignment().isNucleotide())
278 viewport.updateStrucConsensus(alignPanel);
279 if (viewport.getAlignment().hasRNAStructure())
281 RNAHelixColour.setEnabled(true);
285 RNAHelixColour.setEnabled(false);
290 RNAHelixColour.setEnabled(false);
291 purinePyrimidineColour.setEnabled(false);
293 // Some JVMS send keyevents to Top frame or lowest panel,
294 // Havent worked out why yet. So add to both this frame and seqCanvas for
296 this.addKeyListener(this);
297 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
298 alignPanel.idPanel.idCanvas.addKeyListener(this);
299 alignPanel.scalePanel.addKeyListener(this);
300 alignPanel.annotationPanel.addKeyListener(this);
301 alignPanel.annotationPanelHolder.addKeyListener(this);
302 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
303 alignPanel.alabels.addKeyListener(this);
307 addToDisplay(embedded);
314 public void addToDisplay(boolean embedded)
316 createAlignFrameWindow(embedded);
318 alignPanel.adjustAnnotationHeight();
319 alignPanel.paintAlignment(true);
322 public AlignViewport getAlignViewport()
327 public SeqCanvas getSeqcanvas()
329 return alignPanel.seqPanel.seqCanvas;
333 * Load a features file onto the alignment
336 * file URL, content, or other resolvable path
338 * is protocol for accessing data referred to by file
341 public boolean parseFeaturesFile(String file, String type)
343 return parseFeaturesFile(file, type, true);
347 * Load a features file onto the alignment
350 * file URL, content, or other resolvable path
352 * is protocol for accessing data referred to by file
353 * @param autoenabledisplay
354 * when true, display features flag will be automatically enabled if
355 * features are loaded
356 * @return true if data parsed as a features file
358 public boolean parseFeaturesFile(String file, String type,
359 boolean autoenabledisplay)
361 // TODO: test if importing a features file onto an alignment which already
362 // has features with links overwrites the original links.
364 Hashtable featureLinks = new Hashtable();
365 boolean featuresFile = false;
368 featuresFile = new jalview.io.FeaturesFile(file, type)
369 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
370 .getFeatureRenderer().getFeatureColours(), featureLinks,
371 true, viewport.applet.getDefaultParameter(
372 "relaxedidmatch", false));
373 } catch (Exception ex)
375 ex.printStackTrace();
380 if (featureLinks.size() > 0)
382 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
384 if (autoenabledisplay)
386 viewport.setShowSequenceFeatures(true);
387 sequenceFeatures.setState(true);
389 if (alignPanel.seqPanel.seqCanvas.fr != null)
391 // update the min/max ranges where necessary
392 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
394 if (viewport.featureSettings != null)
396 viewport.featureSettings.refreshTable();
398 alignPanel.paintAlignment(true);
399 statusBar.setText(MessageManager
400 .getString("label.successfully_added_features_alignment"));
406 public void keyPressed(KeyEvent evt)
408 if (viewport.cursorMode
409 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
410 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
411 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
412 && Character.isDigit(evt.getKeyChar()))
414 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
417 switch (evt.getKeyCode())
419 case 27: // escape key
420 deselectAllSequenceMenuItem_actionPerformed();
422 alignPanel.alabels.cancelDrag();
425 if (evt.isControlDown() || evt.isMetaDown())
427 cut_actionPerformed();
431 if (viewport.cursorMode && !evt.isControlDown())
433 alignPanel.seqPanel.setCursorColumn();
435 if (evt.isControlDown() || evt.isMetaDown())
437 copy_actionPerformed();
441 if (evt.isControlDown())
443 paste(evt.isShiftDown());
447 if (evt.isControlDown() || evt.isMetaDown())
449 selectAllSequenceMenuItem_actionPerformed();
452 case KeyEvent.VK_DOWN:
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.moveCursor(0, 1);
459 moveSelectedSequences(false);
464 if (viewport.cursorMode)
466 alignPanel.seqPanel.moveCursor(0, -1);
470 moveSelectedSequences(true);
474 case KeyEvent.VK_LEFT:
475 if (evt.isAltDown() || !viewport.cursorMode)
477 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
481 alignPanel.seqPanel.moveCursor(-1, 0);
485 case KeyEvent.VK_RIGHT:
486 if (evt.isAltDown() || !viewport.cursorMode)
488 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
492 alignPanel.seqPanel.moveCursor(1, 0);
496 case KeyEvent.VK_SPACE:
497 if (viewport.cursorMode)
499 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
500 || evt.isShiftDown() || evt.isAltDown());
504 case KeyEvent.VK_DELETE:
505 case KeyEvent.VK_BACK_SPACE:
506 if (viewport.cursorMode)
508 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
509 || evt.isShiftDown() || evt.isAltDown());
513 cut_actionPerformed();
514 alignPanel.seqPanel.seqCanvas.repaint();
519 if (viewport.cursorMode)
521 alignPanel.seqPanel.setCursorRow();
525 if (viewport.cursorMode)
527 alignPanel.seqPanel.setCursorPosition();
531 case KeyEvent.VK_ENTER:
532 case KeyEvent.VK_COMMA:
533 if (viewport.cursorMode)
535 alignPanel.seqPanel.setCursorRowAndColumn();
540 if (viewport.cursorMode)
542 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
546 if (viewport.cursorMode)
548 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
553 viewport.cursorMode = !viewport.cursorMode;
554 statusBar.setText(MessageManager.formatMessage(
555 "label.keyboard_editing_mode", new String[]
556 { (viewport.cursorMode ? "on" : "off") }));
557 if (viewport.cursorMode)
559 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
560 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
565 if (evt.isControlDown())
567 findMenuItem_actionPerformed();
573 boolean toggleSeqs = !evt.isControlDown();
574 boolean toggleCols = !evt.isShiftDown();
575 toggleHiddenRegions(toggleSeqs, toggleCols);
579 case KeyEvent.VK_PAGE_UP:
580 if (viewport.getWrapAlignment())
582 alignPanel.scrollUp(true);
586 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
587 - viewport.endSeq + viewport.startSeq);
591 case KeyEvent.VK_PAGE_DOWN:
592 if (viewport.getWrapAlignment())
594 alignPanel.scrollUp(false);
598 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
599 + viewport.endSeq - viewport.startSeq);
604 if (evt.isControlDown())
606 undoMenuItem_actionPerformed();
611 if (evt.isControlDown())
613 redoMenuItem_actionPerformed();
618 if (evt.isControlDown())
625 if (evt.isControlDown())
627 trimAlignment(false);
632 if (evt.isControlDown())
634 if (evt.isShiftDown())
636 this.removeAllGapsMenuItem_actionPerformed();
640 removeGappedColumnMenuItem_actionPerformed();
645 if (evt.isControlDown())
649 invertColSel_actionPerformed();
653 invertSequenceMenuItem_actionPerformed();
659 if (evt.isControlDown())
661 if (evt.isShiftDown())
663 this.unGroup_actionPerformed();
667 this.createGroup_actionPerformed();
673 if (evt.isControlDown())
675 this.deleteGroups_actionPerformed();
680 if (evt.isControlDown())
687 alignPanel.paintAlignment(true);
691 * called by key handler and the hide all/show all menu items
696 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
698 boolean hide = false;
699 SequenceGroup sg = viewport.getSelectionGroup();
700 if (!toggleSeqs && !toggleCols)
702 // Hide everything by the current selection - this is a hack - we do the
703 // invert and then hide
704 // first check that there will be visible columns after the invert.
705 if ((viewport.getColumnSelection() != null
706 && viewport.getColumnSelection().getSelected() != null && viewport
707 .getColumnSelection().getSelected().size() > 0)
708 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
711 // now invert the sequence set, if required - empty selection implies
712 // that no hiding is required.
715 invertSequenceMenuItem_actionPerformed();
716 sg = viewport.getSelectionGroup();
720 viewport.expandColSelection(sg, true);
721 // finally invert the column selection and get the new sequence
722 // selection and indicate it should be hidden.
723 invertColSel_actionPerformed();
730 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
733 viewport.hideAllSelectedSeqs();
735 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
738 viewport.showAllHiddenSeqs();
744 if (viewport.getColumnSelection().getSelected().size() > 0)
746 viewport.hideSelectedColumns();
749 viewport.setSelectionGroup(sg);
754 viewport.showAllHiddenColumns();
760 public void keyReleased(KeyEvent evt)
765 public void keyTyped(KeyEvent evt)
770 public void itemStateChanged(ItemEvent evt)
772 final Object source = evt.getSource();
773 if (source == displayNonconservedMenuItem)
775 displayNonconservedMenuItem_actionPerformed();
777 else if (source == colourTextMenuItem)
779 colourTextMenuItem_actionPerformed();
781 else if (source == wrapMenuItem)
783 wrapMenuItem_actionPerformed();
785 else if (source == scaleAbove)
787 viewport.setScaleAboveWrapped(scaleAbove.getState());
789 else if (source == scaleLeft)
791 viewport.setScaleLeftWrapped(scaleLeft.getState());
793 else if (source == scaleRight)
795 viewport.setScaleRightWrapped(scaleRight.getState());
797 else if (source == seqLimits)
799 seqLimits_itemStateChanged();
801 else if (source == viewBoxesMenuItem)
803 viewport.setShowBoxes(viewBoxesMenuItem.getState());
805 else if (source == viewTextMenuItem)
807 viewport.setShowText(viewTextMenuItem.getState());
809 else if (source == renderGapsMenuItem)
811 viewport.setRenderGaps(renderGapsMenuItem.getState());
813 else if (source == annotationPanelMenuItem)
815 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
816 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
818 else if (source == sequenceFeatures)
820 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
821 alignPanel.seqPanel.seqCanvas.repaint();
823 else if (source == showAlignmentAnnotations)
825 setAnnotationsVisibility();
827 else if (source == showSequenceAnnotations)
829 setAnnotationsVisibility();
831 else if (source == sortAnnBySequence)
833 boolean newState = sortAnnBySequence.getState();
834 sortAnnByLabel.setState(false);
835 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
836 : SequenceAnnotationOrder.NONE);
837 setViewportAnnotationOrder();
839 else if (source == sortAnnByLabel)
841 boolean newState = sortAnnByLabel.getState();
842 sortAnnBySequence.setState(false);
843 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
844 : SequenceAnnotationOrder.NONE);
845 setViewportAnnotationOrder();
847 else if (source == showAutoFirst)
849 showAutoLast.setState(!showAutoFirst.getState());
850 setShowAutoCalculatedAbove(showAutoFirst.getState());
851 setViewportAnnotationOrder();
853 else if (source == showAutoLast)
855 showAutoFirst.setState(!showAutoLast.getState());
856 setShowAutoCalculatedAbove(showAutoFirst.getState());
857 setViewportAnnotationOrder();
859 else if (source == conservationMenuItem)
861 conservationMenuItem_actionPerformed();
863 else if (source == abovePIDThreshold)
865 abovePIDThreshold_actionPerformed();
867 else if (source == applyToAllGroups)
869 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
871 else if (source == autoCalculate)
873 viewport.autoCalculateConsensus = autoCalculate.getState();
875 else if (source == sortByTree)
877 viewport.sortByTree = sortByTree.getState();
879 else if (source == this.centreColumnLabelFlag)
881 centreColumnLabelFlag_stateChanged();
883 else if (source == this.followMouseOverFlag)
885 mouseOverFlag_stateChanged();
887 else if (source == showGroupConsensus)
889 showGroupConsensus_actionPerformed();
891 else if (source == showGroupConservation)
893 showGroupConservation_actionPerformed();
895 else if (source == showSequenceLogo)
897 showSequenceLogo_actionPerformed();
899 else if (source == normSequenceLogo)
901 normSequenceLogo_actionPerformed();
903 else if (source == showConsensusHistogram)
905 showConsensusHistogram_actionPerformed();
907 else if (source == applyAutoAnnotationSettings)
909 applyAutoAnnotationSettings_actionPerformed();
911 alignPanel.paintAlignment(true);
915 * Set the visibility state of sequence-related and/or alignment-related
916 * annotations depending on checkbox selections. Repaint after calling.
920 private void setAnnotationsVisibility()
922 boolean showForAlignment = showAlignmentAnnotations.getState();
923 boolean showForSequences = showSequenceAnnotations.getState();
924 for (AlignmentAnnotation aa : alignPanel.getAlignment()
925 .getAlignmentAnnotation())
927 boolean visible = (aa.sequenceRef == null ? showForAlignment
929 aa.visible = visible;
931 alignPanel.validateAnnotationDimensions(true);
936 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
938 this.annotationSortOrder = order;
942 * Set flags on the viewport that control annotation ordering
944 private void setViewportAnnotationOrder()
946 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
948 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
951 private void setShowAutoCalculatedAbove(boolean showAbove)
953 this.showAutoCalculatedAbove = showAbove;
956 private void mouseOverFlag_stateChanged()
958 viewport.setFollowHighlight(followMouseOverFlag.getState());
959 // TODO: could kick the scrollTo mechanism to reset view for current
963 private void centreColumnLabelFlag_stateChanged()
965 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
966 this.alignPanel.annotationPanel.repaint();
970 public void actionPerformed(ActionEvent evt)
972 Object source = evt.getSource();
974 if (source == inputText)
976 inputText_actionPerformed();
978 else if (source == loadTree)
980 loadTree_actionPerformed();
982 else if (source == loadApplication)
984 launchFullApplication();
986 else if (source == loadAnnotations)
990 else if (source == outputAnnotations)
992 outputAnnotations(true);
994 else if (source == outputFeatures)
996 outputFeatures(true, "Jalview");
998 else if (source == closeMenuItem)
1000 closeMenuItem_actionPerformed();
1002 else if (source == copy)
1004 copy_actionPerformed();
1006 else if (source == undoMenuItem)
1008 undoMenuItem_actionPerformed();
1010 else if (source == redoMenuItem)
1012 redoMenuItem_actionPerformed();
1014 else if (source == inputText)
1016 inputText_actionPerformed();
1018 else if (source == closeMenuItem)
1020 closeMenuItem_actionPerformed();
1022 else if (source == undoMenuItem)
1024 undoMenuItem_actionPerformed();
1026 else if (source == redoMenuItem)
1028 redoMenuItem_actionPerformed();
1030 else if (source == copy)
1032 copy_actionPerformed();
1034 else if (source == pasteNew)
1036 pasteNew_actionPerformed();
1038 else if (source == pasteThis)
1040 pasteThis_actionPerformed();
1042 else if (source == cut)
1044 cut_actionPerformed();
1046 else if (source == delete)
1048 delete_actionPerformed();
1050 else if (source == grpsFromSelection)
1052 makeGrpsFromSelection_actionPerformed();
1054 else if (source == deleteGroups)
1056 deleteGroups_actionPerformed();
1058 else if (source == selectAllSequenceMenuItem)
1060 selectAllSequenceMenuItem_actionPerformed();
1062 else if (source == deselectAllSequenceMenuItem)
1064 deselectAllSequenceMenuItem_actionPerformed();
1066 else if (source == invertSequenceMenuItem)
1068 invertSequenceMenuItem_actionPerformed();
1070 else if (source == invertColSel)
1072 viewport.invertColumnSelection();
1073 alignPanel.paintAlignment(true);
1075 else if (source == remove2LeftMenuItem)
1077 trimAlignment(true);
1079 else if (source == remove2RightMenuItem)
1081 trimAlignment(false);
1083 else if (source == removeGappedColumnMenuItem)
1085 removeGappedColumnMenuItem_actionPerformed();
1087 else if (source == removeAllGapsMenuItem)
1089 removeAllGapsMenuItem_actionPerformed();
1091 else if (source == findMenuItem)
1093 findMenuItem_actionPerformed();
1095 else if (source == font)
1097 new FontChooser(alignPanel);
1099 else if (source == newView)
1103 else if (source == showColumns)
1105 viewport.showAllHiddenColumns();
1106 alignPanel.paintAlignment(true);
1108 else if (source == showSeqs)
1110 viewport.showAllHiddenSeqs();
1111 alignPanel.paintAlignment(true);
1113 else if (source == hideColumns)
1115 viewport.hideSelectedColumns();
1116 alignPanel.paintAlignment(true);
1118 else if (source == hideSequences
1119 && viewport.getSelectionGroup() != null)
1121 viewport.hideAllSelectedSeqs();
1122 alignPanel.paintAlignment(true);
1124 else if (source == hideAllButSelection)
1126 toggleHiddenRegions(false, false);
1127 alignPanel.paintAlignment(true);
1129 else if (source == hideAllSelection)
1131 SequenceGroup sg = viewport.getSelectionGroup();
1132 viewport.expandColSelection(sg, false);
1133 viewport.hideAllSelectedSeqs();
1134 viewport.hideSelectedColumns();
1135 alignPanel.paintAlignment(true);
1137 else if (source == showAllHidden)
1139 viewport.showAllHiddenColumns();
1140 viewport.showAllHiddenSeqs();
1141 alignPanel.paintAlignment(true);
1143 else if (source == showGroupConsensus)
1145 showGroupConsensus_actionPerformed();
1147 else if (source == showGroupConservation)
1149 showGroupConservation_actionPerformed();
1151 else if (source == showSequenceLogo)
1153 showSequenceLogo_actionPerformed();
1155 else if (source == normSequenceLogo)
1157 normSequenceLogo_actionPerformed();
1159 else if (source == showConsensusHistogram)
1161 showConsensusHistogram_actionPerformed();
1163 else if (source == applyAutoAnnotationSettings)
1165 applyAutoAnnotationSettings_actionPerformed();
1167 else if (source == featureSettings)
1169 new FeatureSettings(alignPanel);
1171 else if (source == alProperties)
1173 StringBuffer contents = new jalview.io.AlignmentProperties(
1174 viewport.getAlignment()).formatAsString();
1175 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1176 cap.setText(contents.toString());
1177 Frame frame = new Frame();
1179 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1180 "label.alignment_properties", new String[]
1181 { getTitle() }), 400, 250);
1183 else if (source == overviewMenuItem)
1185 overviewMenuItem_actionPerformed();
1187 else if (source == noColourmenuItem)
1191 else if (source == clustalColour)
1193 abovePIDThreshold.setState(false);
1194 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1196 else if (source == zappoColour)
1198 changeColour(new ZappoColourScheme());
1200 else if (source == taylorColour)
1202 changeColour(new TaylorColourScheme());
1204 else if (source == hydrophobicityColour)
1206 changeColour(new HydrophobicColourScheme());
1208 else if (source == helixColour)
1210 changeColour(new HelixColourScheme());
1212 else if (source == strandColour)
1214 changeColour(new StrandColourScheme());
1216 else if (source == turnColour)
1218 changeColour(new TurnColourScheme());
1220 else if (source == buriedColour)
1222 changeColour(new BuriedColourScheme());
1224 else if (source == nucleotideColour)
1226 changeColour(new NucleotideColourScheme());
1228 else if (source == purinePyrimidineColour)
1230 changeColour(new PurinePyrimidineColourScheme());
1232 // else if (source == RNAInteractionColour)
1234 // changeColour(new RNAInteractionColourScheme());
1236 else if (source == RNAHelixColour)
1238 new RNAHelicesColourChooser(viewport, alignPanel);
1240 else if (source == modifyPID)
1242 modifyPID_actionPerformed();
1244 else if (source == modifyConservation)
1246 modifyConservation_actionPerformed();
1248 else if (source == userDefinedColour)
1250 new UserDefinedColours(alignPanel, null);
1252 else if (source == PIDColour)
1254 changeColour(new PIDColourScheme());
1256 else if (source == BLOSUM62Colour)
1258 changeColour(new Blosum62ColourScheme());
1260 else if (source == tcoffeeColour)
1262 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1264 else if (source == annotationColour)
1266 new AnnotationColourChooser(viewport, alignPanel);
1268 else if (source == annotationColumnSelection)
1270 new AnnotationColumnChooser(viewport, alignPanel);
1272 else if (source == sortPairwiseMenuItem)
1274 sortPairwiseMenuItem_actionPerformed();
1276 else if (source == sortIDMenuItem)
1278 sortIDMenuItem_actionPerformed();
1280 else if (source == sortLengthMenuItem)
1282 sortLengthMenuItem_actionPerformed();
1284 else if (source == sortGroupMenuItem)
1286 sortGroupMenuItem_actionPerformed();
1288 else if (source == removeRedundancyMenuItem)
1290 removeRedundancyMenuItem_actionPerformed();
1292 else if (source == pairwiseAlignmentMenuItem)
1294 pairwiseAlignmentMenuItem_actionPerformed();
1296 else if (source == PCAMenuItem)
1298 PCAMenuItem_actionPerformed();
1300 else if (source == averageDistanceTreeMenuItem)
1302 averageDistanceTreeMenuItem_actionPerformed();
1304 else if (source == neighbourTreeMenuItem)
1306 neighbourTreeMenuItem_actionPerformed();
1308 else if (source == njTreeBlosumMenuItem)
1310 njTreeBlosumMenuItem_actionPerformed();
1312 else if (source == avDistanceTreeBlosumMenuItem)
1314 avTreeBlosumMenuItem_actionPerformed();
1316 else if (source == documentation)
1318 documentation_actionPerformed();
1320 else if (source == about)
1322 about_actionPerformed();
1327 public void inputText_actionPerformed()
1329 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1330 Frame frame = new Frame();
1332 jalview.bin.JalviewLite.addFrame(frame,
1333 MessageManager.getString("label.input_cut_paste"), 500, 500);
1336 protected void outputText_actionPerformed(ActionEvent e)
1338 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1339 Frame frame = new Frame();
1341 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1342 "label.alignment_output_command", new Object[]
1343 { e.getActionCommand() }), 600, 500);
1345 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1346 cap.setText(new AppletFormatAdapter(alignPanel).formatSequences(
1347 e.getActionCommand(), viewport.getAlignment(),
1348 viewport.getShowJVSuffix()));
1351 public void loadAnnotations()
1353 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1354 cap.setText(MessageManager
1355 .getString("label.paste_features_annotations_Tcoffee_here"));
1356 cap.setAnnotationImport();
1357 Frame frame = new Frame();
1359 jalview.bin.JalviewLite.addFrame(frame,
1360 MessageManager.getString("action.paste_annotations"), 400, 300);
1364 public String outputAnnotations(boolean displayTextbox)
1366 String annotation = new AnnotationFile()
1367 .printAnnotationsForView(viewport);
1371 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1372 Frame frame = new Frame();
1374 jalview.bin.JalviewLite.addFrame(frame,
1375 MessageManager.getString("label.annotations"), 600, 500);
1376 cap.setText(annotation);
1382 private Map<String,Object> getDisplayedFeatureCols()
1384 if (alignPanel.getFeatureRenderer() != null
1385 && viewport.getFeaturesDisplayed()!= null)
1387 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1393 public String outputFeatures(boolean displayTextbox, String format)
1396 if (format.equalsIgnoreCase("Jalview"))
1398 features = new FeaturesFile().printJalviewFormat(viewport
1399 .getAlignment().getSequencesArray(),
1400 getDisplayedFeatureCols());
1404 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1405 .getSequencesArray(), getDisplayedFeatureCols());
1410 boolean frimport = false;
1411 if (features == null || features.equals("No Features Visible"))
1413 features = "# No features visible - paste some and import them here.";
1417 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1420 cap.setAnnotationImport();
1422 Frame frame = new Frame();
1424 jalview.bin.JalviewLite.addFrame(frame,
1425 MessageManager.getString("label.features"), 600, 500);
1426 cap.setText(features);
1430 if (features == null)
1439 void launchFullApplication()
1441 StringBuffer url = new StringBuffer(jalviewServletURL);
1443 // allow servlet parameters to be passed in applet parameter
1444 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1446 url.append(firstSep);
1449 + appendProtocol(viewport.applet.getParameter("file")));
1451 if (viewport.applet.getParameter("features") != null)
1453 url.append("&features=");
1454 url.append(appendProtocol(viewport.applet.getParameter("features")));
1457 if (viewport.applet.getParameter("annotations") != null)
1459 url.append("&annotations=");
1460 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1463 if (viewport.applet.getParameter("jnetfile") != null)
1465 url.append("&annotations=");
1466 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1469 if (viewport.applet.getParameter("defaultColour") != null)
1471 url.append("&colour="
1472 + removeWhiteSpace(viewport.applet
1473 .getParameter("defaultColour")));
1476 if (viewport.applet.getParameter("userDefinedColour") != null)
1478 url.append("&colour="
1479 + removeWhiteSpace(viewport.applet
1480 .getParameter("userDefinedColour")));
1482 if (viewport.applet.getParameter("tree") != null)
1485 + appendProtocol(viewport.applet.getParameter("tree")));
1487 if (viewport.applet.getParameter("treeFile") != null)
1490 + appendProtocol(viewport.applet.getParameter("treeFile")));
1493 showURL(url.toString(), "FULL_APP");
1496 String removeWhiteSpace(String colour)
1498 StringBuffer sb = new StringBuffer();
1499 for (int i = 0; i < colour.length(); i++)
1501 if (Character.isWhitespace(colour.charAt(i)))
1507 sb.append(colour.charAt(i));
1511 return sb.toString();
1514 String appendProtocol(String url)
1519 url = URLEncoder.encode(url);
1522 * When we finally deprecate 1.1 compatibility, we can start to use
1523 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1524 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1525 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1526 * ex.printStackTrace(); }
1528 catch (java.net.MalformedURLException ex)
1530 url = viewport.applet.getCodeBase() + url;
1535 public void closeMenuItem_actionPerformed()
1537 PaintRefresher.RemoveComponent(alignPanel);
1538 if (alignPanel.seqPanel != null
1539 && alignPanel.seqPanel.seqCanvas != null)
1541 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1543 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1545 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1548 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1563 void updateEditMenuBar()
1566 if (viewport.getHistoryList().size() > 0)
1568 undoMenuItem.setEnabled(true);
1569 CommandI command = viewport.getHistoryList().peek();
1570 undoMenuItem.setLabel(MessageManager.formatMessage(
1571 "label.undo_command", new Object[]
1572 { command.getDescription() }));
1576 undoMenuItem.setEnabled(false);
1577 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1580 if (viewport.getRedoList().size() > 0)
1582 redoMenuItem.setEnabled(true);
1584 CommandI command = viewport.getRedoList().peek();
1585 redoMenuItem.setLabel(MessageManager.formatMessage(
1586 "label.redo_command", new Object[]
1587 { command.getDescription() }));
1591 redoMenuItem.setEnabled(false);
1592 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1600 public void addHistoryItem(CommandI command)
1602 if (command.getSize() > 0)
1604 viewport.addToHistoryList(command);
1605 viewport.clearRedoList();
1606 updateEditMenuBar();
1607 viewport.updateHiddenColumns();
1612 * TODO: JAL-1104 DOCUMENT ME!
1617 protected void undoMenuItem_actionPerformed()
1619 if (viewport.getHistoryList().isEmpty())
1624 CommandI command = viewport.getHistoryList().pop();
1625 viewport.addToRedoList(command);
1626 command.undoCommand(null);
1628 AlignmentViewport originalSource = getOriginatingSource(command);
1630 if (originalSource != viewport)
1633 .println("Warning: Viewport object mismatch whilst undoing");
1635 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1636 // viewport.getColumnSelection().getHiddenColumns()
1638 updateEditMenuBar();
1639 originalSource.firePropertyChange("alignment", null, originalSource
1640 .getAlignment().getSequences());
1644 * TODO: JAL-1104 DOCUMENT ME!
1649 protected void redoMenuItem_actionPerformed()
1651 if (viewport.getRedoList().isEmpty())
1656 CommandI command = viewport.getRedoList().pop();
1657 viewport.addToHistoryList(command);
1658 command.doCommand(null);
1660 AlignmentViewport originalSource = getOriginatingSource(command);
1662 if (originalSource != viewport)
1665 .println("Warning: Viewport object mismatch whilst re-doing");
1667 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1668 // viewport.getColumnSelection().getHiddenColumns()
1671 updateEditMenuBar();
1672 originalSource.firePropertyChange("alignment", null, originalSource
1673 .getAlignment().getSequences());
1676 AlignmentViewport getOriginatingSource(CommandI command)
1678 AlignmentViewport originalSource = null;
1679 // For sequence removal and addition, we need to fire
1680 // the property change event FROM the viewport where the
1681 // original alignment was altered
1682 AlignmentI al = null;
1683 if (command instanceof EditCommand)
1685 EditCommand editCommand = (EditCommand) command;
1686 al = editCommand.getAlignment();
1687 Vector comps = (Vector) PaintRefresher.components.get(viewport
1688 .getSequenceSetId());
1689 for (int i = 0; i < comps.size(); i++)
1691 if (comps.elementAt(i) instanceof AlignmentPanel)
1693 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1695 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1702 if (originalSource == null)
1704 // The original view is closed, we must validate
1705 // the current view against the closed view first
1708 PaintRefresher.validateSequences(al, viewport.getAlignment());
1711 originalSource = viewport;
1714 return originalSource;
1718 * Move the currently selected sequences up or down one position in the
1723 public void moveSelectedSequences(boolean up)
1725 SequenceGroup sg = viewport.getSelectionGroup();
1730 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1731 up ? null : viewport.getHiddenRepSequences(), up);
1732 alignPanel.paintAlignment(true);
1735 * Also move cDNA/protein complement sequences
1737 AlignViewportI complement = viewport.getCodingComplement();
1738 if (complement != null)
1740 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1741 viewport, complement);
1742 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1743 up ? null : complement.getHiddenRepSequences(), up);
1744 // TODO need to trigger a repaint of the complementary panel - how?
1745 // would prefer to handle in SplitFrame but it is not overriding key
1750 synchronized void slideSequences(boolean right, int size)
1752 List<SequenceI> sg = new Vector<SequenceI>();
1753 if (viewport.cursorMode)
1755 sg.add(viewport.getAlignment().getSequenceAt(
1756 alignPanel.seqPanel.seqCanvas.cursorY));
1758 else if (viewport.getSelectionGroup() != null
1759 && viewport.getSelectionGroup().getSize() != viewport
1760 .getAlignment().getHeight())
1762 sg = viewport.getSelectionGroup().getSequences(
1763 viewport.getHiddenRepSequences());
1771 Vector<SequenceI> invertGroup = new Vector();
1773 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1775 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1777 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1781 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1783 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1785 for (int i = 0; i < invertGroup.size(); i++)
1787 seqs2[i] = invertGroup.elementAt(i);
1790 SlideSequencesCommand ssc;
1793 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1794 size, viewport.getGapCharacter());
1798 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1799 size, viewport.getGapCharacter());
1802 int groupAdjustment = 0;
1803 if (ssc.getGapsInsertedBegin() && right)
1805 if (viewport.cursorMode)
1807 alignPanel.seqPanel.moveCursor(size, 0);
1811 groupAdjustment = size;
1814 else if (!ssc.getGapsInsertedBegin() && !right)
1816 if (viewport.cursorMode)
1818 alignPanel.seqPanel.moveCursor(-size, 0);
1822 groupAdjustment = -size;
1826 if (groupAdjustment != 0)
1828 viewport.getSelectionGroup().setStartRes(
1829 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1830 viewport.getSelectionGroup().setEndRes(
1831 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1834 boolean appendHistoryItem = false;
1835 Deque<CommandI> historyList = viewport.getHistoryList();
1836 if (historyList != null && historyList.size() > 0
1837 && historyList.peek() instanceof SlideSequencesCommand)
1839 appendHistoryItem = ssc
1840 .appendSlideCommand((SlideSequencesCommand) historyList
1844 if (!appendHistoryItem)
1846 addHistoryItem(ssc);
1852 static StringBuffer copiedSequences;
1854 static Vector copiedHiddenColumns;
1856 protected void copy_actionPerformed()
1858 if (viewport.getSelectionGroup() == null)
1863 SequenceGroup sg = viewport.getSelectionGroup();
1864 copiedSequences = new StringBuffer();
1865 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1866 for (int i = 0; i < sg.getSize(); i++)
1868 SequenceI seq = sg.getSequenceAt(i);
1869 int index = viewport.getAlignment().findIndex(seq);
1870 orderedSeqs.put(index, seq);
1873 int index = 0, startRes, endRes;
1876 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1878 copiedHiddenColumns = new Vector();
1879 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1880 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1882 copiedHiddenColumns.addElement(new int[]
1883 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1888 copiedHiddenColumns = null;
1891 for (int i = 0; i < sg.getSize(); i++)
1893 SequenceI seq = null;
1897 if (orderedSeqs.containsKey(index))
1899 seq = orderedSeqs.get(index);
1910 // Returns residue following index if gap
1911 startRes = seq.findPosition(sg.getStartRes());
1914 // Need to find the residue preceeding index if gap
1917 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1919 ch = seq.getCharAt(j);
1920 if (!jalview.util.Comparison.isGap((ch)))
1928 endRes += seq.getStart() - 1;
1931 copiedSequences.append(seq.getName()
1937 + seq.getSequenceAsString(sg.getStartRes(),
1938 sg.getEndRes() + 1) + "\n");
1943 protected void pasteNew_actionPerformed()
1948 protected void pasteThis_actionPerformed()
1953 void paste(boolean newAlignment)
1958 if (copiedSequences == null)
1963 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1964 Vector seqs = new Vector();
1965 while (st.hasMoreElements())
1967 String name = st.nextToken();
1968 int start = Integer.parseInt(st.nextToken());
1969 int end = Integer.parseInt(st.nextToken());
1970 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1972 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1973 for (int i = 0; i < seqs.size(); i++)
1975 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1980 String newtitle = MessageManager.getString("label.copied_sequences");
1981 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1983 newtitle = getTitle();
1987 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1989 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1990 viewport.applet, newtitle, false);
1991 if (copiedHiddenColumns != null)
1993 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1995 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1996 af.viewport.hideColumns(region[0], region[1]);
2000 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
2005 addSequences(newSeqs);
2008 } catch (Exception ex)
2010 } // could be anything being pasted in here
2014 void addSequences(SequenceI[] seqs)
2016 for (int i = 0; i < seqs.length; i++)
2018 viewport.getAlignment().addSequence(seqs[i]);
2022 addHistoryItem(new EditCommand(
2023 MessageManager.getString("label.add_sequences"), Action.PASTE,
2024 seqs, 0, viewport.getAlignment().getWidth(),
2025 viewport.getAlignment()));
2027 viewport.setEndSeq(viewport.getAlignment().getHeight());
2028 viewport.getAlignment().getWidth();
2029 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2034 protected void cut_actionPerformed()
2036 copy_actionPerformed();
2037 delete_actionPerformed();
2040 protected void delete_actionPerformed()
2043 SequenceGroup sg = viewport.getSelectionGroup();
2049 Vector seqs = new Vector();
2051 for (int i = 0; i < sg.getSize(); i++)
2053 seq = sg.getSequenceAt(i);
2054 seqs.addElement(seq);
2057 // If the cut affects all sequences, remove highlighted columns
2058 if (sg.getSize() == viewport.getAlignment().getHeight())
2060 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2061 sg.getEndRes() + 1);
2064 SequenceI[] cut = new SequenceI[seqs.size()];
2065 for (int i = 0; i < seqs.size(); i++)
2067 cut[i] = (SequenceI) seqs.elementAt(i);
2071 * //ADD HISTORY ITEM
2073 addHistoryItem(new EditCommand(
2074 MessageManager.getString("label.cut_sequences"), Action.CUT,
2075 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2076 viewport.getAlignment()));
2078 viewport.setSelectionGroup(null);
2079 viewport.getAlignment().deleteGroup(sg);
2081 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2084 if (viewport.getAlignment().getHeight() < 1)
2086 this.setVisible(false);
2088 viewport.sendSelection();
2092 * group consensus toggled
2095 protected void showGroupConsensus_actionPerformed()
2097 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2098 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2103 * group conservation toggled.
2105 protected void showGroupConservation_actionPerformed()
2107 viewport.setShowGroupConservation(showGroupConservation.getState());
2108 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2115 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2116 * .event.ActionEvent)
2118 protected void showConsensusHistogram_actionPerformed()
2120 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2121 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2128 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2129 * .event.ActionEvent)
2131 protected void showSequenceLogo_actionPerformed()
2133 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2134 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2137 protected void normSequenceLogo_actionPerformed()
2139 showSequenceLogo.setState(true);
2140 viewport.setShowSequenceLogo(true);
2141 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2142 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2145 protected void applyAutoAnnotationSettings_actionPerformed()
2147 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2150 protected void makeGrpsFromSelection_actionPerformed()
2152 if (avc.makeGroupsFromSelection())
2154 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2155 alignPanel.updateAnnotation();
2156 alignPanel.paintAlignment(true);
2160 protected void createGroup_actionPerformed()
2165 protected void unGroup_actionPerformed()
2169 alignPanel.alignmentChanged();
2173 protected void deleteGroups_actionPerformed()
2175 if (avc.deleteGroups())
2177 alignPanel.alignmentChanged();
2181 public void selectAllSequenceMenuItem_actionPerformed()
2183 SequenceGroup sg = new SequenceGroup();
2184 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2186 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2188 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2189 viewport.setSelectionGroup(sg);
2190 alignPanel.paintAlignment(true);
2191 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2192 viewport.sendSelection();
2195 public void deselectAllSequenceMenuItem_actionPerformed()
2197 if (viewport.cursorMode)
2199 alignPanel.seqPanel.keyboardNo1 = null;
2200 alignPanel.seqPanel.keyboardNo2 = null;
2202 viewport.setSelectionGroup(null);
2203 viewport.getColumnSelection().clear();
2204 viewport.setSelectionGroup(null);
2205 alignPanel.idPanel.idCanvas.searchResults = null;
2206 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2207 alignPanel.paintAlignment(true);
2208 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2209 viewport.sendSelection();
2212 public void invertSequenceMenuItem_actionPerformed()
2214 SequenceGroup sg = viewport.getSelectionGroup();
2215 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2217 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2220 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2221 viewport.sendSelection();
2224 public void invertColSel_actionPerformed()
2226 viewport.invertColumnSelection();
2227 alignPanel.paintAlignment(true);
2228 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2229 viewport.sendSelection();
2232 void trimAlignment(boolean trimLeft)
2234 ColumnSelection colSel = viewport.getColumnSelection();
2237 if (colSel.size() > 0)
2241 column = colSel.getMin();
2245 column = colSel.getMax();
2249 if (viewport.getSelectionGroup() != null)
2251 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2252 viewport.getHiddenRepSequences());
2256 seqs = viewport.getAlignment().getSequencesArray();
2259 TrimRegionCommand trimRegion;
2262 trimRegion = new TrimRegionCommand("Remove Left",
2263 TrimRegionCommand.TRIM_LEFT, seqs, column,
2264 viewport.getAlignment(), viewport.getColumnSelection(),
2265 viewport.getSelectionGroup());
2266 viewport.setStartRes(0);
2270 trimRegion = new TrimRegionCommand("Remove Right",
2271 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2272 viewport.getAlignment(), viewport.getColumnSelection(),
2273 viewport.getSelectionGroup());
2276 statusBar.setText(MessageManager.formatMessage(
2277 "label.removed_columns", new String[]
2278 { Integer.valueOf(trimRegion.getSize()).toString() }));
2279 addHistoryItem(trimRegion);
2281 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2283 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2284 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2286 viewport.getAlignment().deleteGroup(sg);
2290 viewport.firePropertyChange("alignment", null, viewport
2291 .getAlignment().getSequences());
2295 public void removeGappedColumnMenuItem_actionPerformed()
2297 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2300 if (viewport.getSelectionGroup() != null)
2302 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2303 viewport.getHiddenRepSequences());
2304 start = viewport.getSelectionGroup().getStartRes();
2305 end = viewport.getSelectionGroup().getEndRes();
2309 seqs = viewport.getAlignment().getSequencesArray();
2312 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2313 "Remove Gapped Columns", seqs, start, end,
2314 viewport.getAlignment());
2316 addHistoryItem(removeGapCols);
2318 statusBar.setText(MessageManager.formatMessage(
2319 "label.removed_empty_columns", new String[]
2320 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2322 // This is to maintain viewport position on first residue
2323 // of first sequence
2324 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2325 int startRes = seq.findPosition(viewport.startRes);
2326 // ShiftList shifts;
2327 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2328 // edit.alColumnChanges=shifts.getInverse();
2329 // if (viewport.hasHiddenColumns)
2330 // viewport.getColumnSelection().compensateForEdits(shifts);
2331 viewport.setStartRes(seq.findIndex(startRes) - 1);
2332 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2337 public void removeAllGapsMenuItem_actionPerformed()
2339 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2342 if (viewport.getSelectionGroup() != null)
2344 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2345 viewport.getHiddenRepSequences());
2346 start = viewport.getSelectionGroup().getStartRes();
2347 end = viewport.getSelectionGroup().getEndRes();
2351 seqs = viewport.getAlignment().getSequencesArray();
2354 // This is to maintain viewport position on first residue
2355 // of first sequence
2356 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2357 int startRes = seq.findPosition(viewport.startRes);
2359 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2360 viewport.getAlignment()));
2362 viewport.setStartRes(seq.findIndex(startRes) - 1);
2364 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2369 public void findMenuItem_actionPerformed()
2371 new Finder(alignPanel);
2375 * create a new view derived from the current view
2378 * @return frame for the new view
2380 public AlignFrame newView(String viewtitle)
2383 if (viewport.hasHiddenRows())
2385 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2386 .getFullAlignment().getSequencesArray());
2390 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2393 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2395 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2397 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2399 newal.addAnnotation(viewport.getAlignment()
2400 .getAlignmentAnnotation()[i]);
2405 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2407 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2408 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2409 PaintRefresher.Register(newaf.alignPanel,
2410 newaf.alignPanel.av.getSequenceSetId());
2412 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2413 newaf.alignPanel.av.getSequenceSetId());
2414 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2415 newaf.alignPanel.av.getSequenceSetId());
2417 Vector comps = (Vector) PaintRefresher.components.get(viewport
2418 .getSequenceSetId());
2420 for (int i = 0; i < comps.size(); i++)
2422 if (comps.elementAt(i) instanceof AlignmentPanel)
2428 String title = new String(this.getTitle());
2429 if (viewtitle != null)
2431 title = viewtitle + " ( " + title + ")";
2435 if (title.indexOf("(View") > -1)
2437 title = title.substring(0, title.indexOf("(View"));
2439 title += "(View " + viewSize + ")";
2442 newaf.setTitle(title.toString());
2444 newaf.viewport.setHistoryList(viewport.getHistoryList());
2445 newaf.viewport.setRedoList(viewport.getRedoList());
2451 * @return list of feature groups on the view
2453 public String[] getFeatureGroups()
2455 FeatureRenderer fr = null;
2456 if (alignPanel != null
2457 && (fr = alignPanel.getFeatureRenderer()) != null)
2459 List<String> gps = fr.getFeatureGroups();
2460 String[] _gps = gps.toArray(new String[gps.size()]);
2467 * get sequence feature groups that are hidden or shown
2473 public String[] getFeatureGroupsOfState(boolean visible)
2475 FeatureRenderer fr = null;
2476 if (alignPanel != null
2477 && (fr = alignPanel.getFeatureRenderer()) != null)
2479 List<String> gps = fr.getGroups(visible);
2480 String[] _gps = gps.toArray(new String[gps.size()]);
2487 * Change the display state for the given feature groups
2490 * list of group strings
2492 * visible or invisible
2494 public void setFeatureGroupState(String[] groups, boolean state)
2496 FeatureRenderer fr = null;
2497 this.sequenceFeatures.setState(true);
2498 viewport.setShowSequenceFeatures(true);
2499 if (alignPanel != null
2500 && (fr = alignPanel.getFeatureRenderer()) != null)
2503 fr.setGroupVisibility(Arrays.asList(groups), state);
2504 alignPanel.seqPanel.seqCanvas.repaint();
2505 if (alignPanel.overviewPanel != null)
2507 alignPanel.overviewPanel.updateOverviewImage();
2512 public void seqLimits_itemStateChanged()
2514 viewport.setShowJVSuffix(seqLimits.getState());
2515 alignPanel.fontChanged();
2516 alignPanel.paintAlignment(true);
2519 protected void colourTextMenuItem_actionPerformed()
2521 viewport.setColourText(colourTextMenuItem.getState());
2522 alignPanel.paintAlignment(true);
2525 protected void displayNonconservedMenuItem_actionPerformed()
2527 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2528 alignPanel.paintAlignment(true);
2531 protected void wrapMenuItem_actionPerformed()
2533 viewport.setWrapAlignment(wrapMenuItem.getState());
2534 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2535 scaleAbove.setEnabled(wrapMenuItem.getState());
2536 scaleLeft.setEnabled(wrapMenuItem.getState());
2537 scaleRight.setEnabled(wrapMenuItem.getState());
2538 alignPanel.paintAlignment(true);
2541 public void overviewMenuItem_actionPerformed()
2543 if (alignPanel.overviewPanel != null)
2548 Frame frame = new Frame();
2549 OverviewPanel overview = new OverviewPanel(alignPanel);
2550 frame.add(overview);
2551 // +50 must allow for applet frame window
2552 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2553 "label.overview_params", new String[]
2554 { this.getTitle() }), overview.getPreferredSize().width,
2555 overview.getPreferredSize().height + 50);
2558 final AlignmentPanel ap = alignPanel;
2559 frame.addWindowListener(new WindowAdapter()
2562 public void windowClosing(WindowEvent e)
2566 ap.setOverviewPanel(null);
2571 alignPanel.setOverviewPanel(overview);
2575 public void changeColour(ColourSchemeI cs)
2580 if (viewport.getAbovePIDThreshold())
2582 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2586 if (viewport.getConservationSelected())
2588 cs.setConservationApplied(true);
2589 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2594 cs.setConservationApplied(false);
2597 viewport.setGlobalColourScheme(cs);
2599 alignPanel.paintAlignment(true);
2602 protected void modifyPID_actionPerformed()
2604 if (viewport.getAbovePIDThreshold()
2605 && viewport.getGlobalColourScheme() != null)
2607 SliderPanel.setPIDSliderSource(alignPanel,
2608 viewport.getGlobalColourScheme(), "Background");
2609 SliderPanel.showPIDSlider();
2613 protected void modifyConservation_actionPerformed()
2615 if (viewport.getConservationSelected()
2616 && viewport.getGlobalColourScheme() != null)
2618 SliderPanel.setConservationSlider(alignPanel,
2619 viewport.getGlobalColourScheme(), "Background");
2620 SliderPanel.showConservationSlider();
2624 protected void conservationMenuItem_actionPerformed()
2626 viewport.setConservationSelected(conservationMenuItem.getState());
2628 viewport.setAbovePIDThreshold(false);
2629 abovePIDThreshold.setState(false);
2631 changeColour(viewport.getGlobalColourScheme());
2633 modifyConservation_actionPerformed();
2636 public void abovePIDThreshold_actionPerformed()
2638 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2640 conservationMenuItem.setState(false);
2641 viewport.setConservationSelected(false);
2643 changeColour(viewport.getGlobalColourScheme());
2645 modifyPID_actionPerformed();
2648 public void sortPairwiseMenuItem_actionPerformed()
2650 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2651 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2652 .getAlignment().getSequenceAt(0), null);
2654 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2655 viewport.getAlignment()));
2656 alignPanel.paintAlignment(true);
2659 public void sortIDMenuItem_actionPerformed()
2661 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2662 AlignmentSorter.sortByID(viewport.getAlignment());
2663 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2664 viewport.getAlignment()));
2665 alignPanel.paintAlignment(true);
2668 public void sortLengthMenuItem_actionPerformed()
2670 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2671 AlignmentSorter.sortByLength(viewport.getAlignment());
2672 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2673 viewport.getAlignment()));
2674 alignPanel.paintAlignment(true);
2677 public void sortGroupMenuItem_actionPerformed()
2679 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2680 AlignmentSorter.sortByGroup(viewport.getAlignment());
2681 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2682 viewport.getAlignment()));
2683 alignPanel.paintAlignment(true);
2687 public void removeRedundancyMenuItem_actionPerformed()
2689 new RedundancyPanel(alignPanel);
2692 public void pairwiseAlignmentMenuItem_actionPerformed()
2694 if (viewport.getSelectionGroup() != null
2695 && viewport.getSelectionGroup().getSize() > 1)
2697 Frame frame = new Frame();
2698 frame.add(new PairwiseAlignPanel(alignPanel));
2699 jalview.bin.JalviewLite.addFrame(frame,
2700 MessageManager.getString("action.pairwise_alignment"), 600,
2705 public void PCAMenuItem_actionPerformed()
2707 // are the sequences aligned?
2708 if (!viewport.getAlignment().isAligned(false))
2711 int Width = viewport.getAlignment().getWidth();
2713 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2715 current = viewport.getAlignment().getSequenceAt(i);
2717 if (current.getLength() < Width)
2719 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2722 alignPanel.paintAlignment(true);
2725 if ((viewport.getSelectionGroup() != null
2726 && viewport.getSelectionGroup().getSize() < 4 && viewport
2727 .getSelectionGroup().getSize() > 0)
2728 || viewport.getAlignment().getHeight() < 4)
2735 new PCAPanel(viewport);
2736 } catch (java.lang.OutOfMemoryError ex)
2742 public void averageDistanceTreeMenuItem_actionPerformed()
2744 NewTreePanel("AV", "PID", "Average distance tree using PID");
2747 public void neighbourTreeMenuItem_actionPerformed()
2749 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2752 protected void njTreeBlosumMenuItem_actionPerformed()
2754 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2757 protected void avTreeBlosumMenuItem_actionPerformed()
2759 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2762 void NewTreePanel(String type, String pwType, String title)
2764 // are the sequences aligned?
2765 if (!viewport.getAlignment().isAligned(false))
2768 int Width = viewport.getAlignment().getWidth();
2770 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2772 current = viewport.getAlignment().getSequenceAt(i);
2774 if (current.getLength() < Width)
2776 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2779 alignPanel.paintAlignment(true);
2783 if ((viewport.getSelectionGroup() != null && viewport
2784 .getSelectionGroup().getSize() > 1)
2785 || (viewport.getAlignment().getHeight() > 1))
2787 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2789 addTreeMenuItem(tp, title);
2791 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2795 void loadTree_actionPerformed()
2797 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2798 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2799 cap.setTreeImport();
2800 Frame frame = new Frame();
2802 jalview.bin.JalviewLite.addFrame(frame,
2803 MessageManager.getString("label.paste_newick_file"), 400, 300);
2806 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2808 TreePanel tp = new TreePanel(alignPanel, treeFile,
2809 MessageManager.getString("label.load_tree_from_file"), tree);
2810 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2811 addTreeMenuItem(tp, treeFile);
2815 * sort the alignment using the given treePanel
2818 * tree used to sort view
2820 * string used for undo event name
2822 public void sortByTree(TreePanel treePanel, String title)
2824 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2826 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2827 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2828 // HistoryItem.SORT));
2829 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2830 "label.order_by_params", new String[]
2831 { title }), oldOrder, viewport.getAlignment()));
2832 alignPanel.paintAlignment(true);
2836 * Do any automatic reordering of the alignment and add the necessary bits to
2837 * the menu structure for the new tree
2842 protected void addTreeMenuItem(final TreePanel treePanel,
2845 final MenuItem item = new MenuItem(title);
2846 sortByTreeMenu.add(item);
2847 item.addActionListener(new java.awt.event.ActionListener()
2850 public void actionPerformed(ActionEvent evt)
2852 sortByTree(treePanel, title); // treePanel.getTitle());
2856 treePanel.addWindowListener(new WindowAdapter()
2859 public void windowOpened(WindowEvent e)
2861 if (viewport.sortByTree)
2863 sortByTree(treePanel, title);
2865 super.windowOpened(e);
2869 public void windowClosing(WindowEvent e)
2871 sortByTreeMenu.remove(item);
2876 public boolean sortBy(AlignmentOrder alorder, String undoname)
2878 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2879 if (viewport.applet.debug)
2881 System.err.println("Sorting " + alorder.getOrder().size()
2882 + " in alignment '" + getTitle() + "'");
2884 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2885 if (undoname != null)
2887 addHistoryItem(new OrderCommand(undoname, oldOrder,
2888 viewport.getAlignment()));
2890 alignPanel.paintAlignment(true);
2894 protected void documentation_actionPerformed()
2896 alignPanel.av.applet.openJalviewHelpUrl();
2899 protected void about_actionPerformed()
2902 class AboutPanel extends Canvas
2908 public AboutPanel(String version, String builddate)
2910 this.version = version;
2911 this.builddate = builddate;
2915 public void paint(Graphics g)
2917 g.setColor(Color.white);
2918 g.fillRect(0, 0, getSize().width, getSize().height);
2919 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2920 FontMetrics fm = g.getFontMetrics();
2921 int fh = fm.getHeight();
2923 g.setColor(Color.black);
2924 // TODO: update this text for each release or centrally store it for
2925 // lite and application
2926 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2927 g.drawString(MessageManager.formatMessage(
2928 "label.jalviewLite_release", new String[]
2929 { version }), x, y += fh);
2930 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2931 g.drawString(MessageManager.formatMessage(
2932 "label.jaview_build_date", new String[]
2933 { builddate }), x, y += fh);
2934 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2935 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2937 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2938 x + 50, y += fh + 8);
2940 MessageManager.getString("label.jalview_dev_managers"), x,
2942 g.drawString(MessageManager
2943 .getString("label.jalview_distribution_lists"), x, y += fh);
2944 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2947 MessageManager.getString("label.jalview_cite_1_authors"),
2950 MessageManager.getString("label.jalview_cite_1_title"), x,
2952 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2957 Frame frame = new Frame();
2958 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2960 jalview.bin.JalviewLite.addFrame(frame,
2961 MessageManager.getString("label.jalview"), 580, 220);
2965 public void showURL(String url, String target)
2967 if (viewport.applet == null)
2969 System.out.println("Not running as applet - no browser available.");
2973 viewport.applet.showURL(url, target);
2977 // ////////////////////////////////////////////////////////////////////////////////
2978 // JBuilder Graphics here
2980 MenuBar alignFrameMenuBar = new MenuBar();
2982 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2984 MenuItem loadApplication = new MenuItem(
2985 MessageManager.getString("label.view_full_application"));
2987 MenuItem loadTree = new MenuItem(
2988 MessageManager.getString("label.load_associated_tree"));
2990 MenuItem loadAnnotations = new MenuItem(
2991 MessageManager.getString("label.load_features_annotations"));
2993 MenuItem outputFeatures = new MenuItem(
2994 MessageManager.getString("label.export_features"));
2996 MenuItem outputAnnotations = new MenuItem(
2997 MessageManager.getString("label.export_annotations"));
2999 MenuItem closeMenuItem = new MenuItem(
3000 MessageManager.getString("action.close"));
3002 MenuItem selectAllSequenceMenuItem = new MenuItem(
3003 MessageManager.getString("action.select_all"));
3005 MenuItem deselectAllSequenceMenuItem = new MenuItem(
3006 MessageManager.getString("action.deselect_all"));
3008 MenuItem invertSequenceMenuItem = new MenuItem(
3009 MessageManager.getString("action.invert_selection"));
3011 MenuItem remove2LeftMenuItem = new MenuItem();
3013 MenuItem remove2RightMenuItem = new MenuItem();
3015 MenuItem removeGappedColumnMenuItem = new MenuItem();
3017 MenuItem removeAllGapsMenuItem = new MenuItem();
3019 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3021 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3023 MenuItem sortPairwiseMenuItem = new MenuItem();
3025 MenuItem sortIDMenuItem = new MenuItem();
3027 MenuItem sortLengthMenuItem = new MenuItem();
3029 MenuItem sortGroupMenuItem = new MenuItem();
3031 MenuItem removeRedundancyMenuItem = new MenuItem();
3033 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3035 MenuItem PCAMenuItem = new MenuItem();
3037 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3039 MenuItem neighbourTreeMenuItem = new MenuItem();
3041 BorderLayout borderLayout1 = new BorderLayout();
3043 public Label statusBar = new Label();
3045 MenuItem clustalColour = new MenuItem();
3047 MenuItem zappoColour = new MenuItem();
3049 MenuItem taylorColour = new MenuItem();
3051 MenuItem hydrophobicityColour = new MenuItem();
3053 MenuItem helixColour = new MenuItem();
3055 MenuItem strandColour = new MenuItem();
3057 MenuItem turnColour = new MenuItem();
3059 MenuItem buriedColour = new MenuItem();
3061 MenuItem purinePyrimidineColour = new MenuItem();
3063 // MenuItem RNAInteractionColour = new MenuItem();
3065 MenuItem RNAHelixColour = new MenuItem();
3067 MenuItem userDefinedColour = new MenuItem();
3069 MenuItem PIDColour = new MenuItem();
3071 MenuItem BLOSUM62Colour = new MenuItem();
3073 MenuItem tcoffeeColour = new MenuItem();
3075 MenuItem njTreeBlosumMenuItem = new MenuItem();
3077 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3079 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3081 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3083 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3085 MenuItem alProperties = new MenuItem(
3086 MessageManager.getString("label.alignment_props"));
3088 MenuItem overviewMenuItem = new MenuItem();
3090 MenuItem undoMenuItem = new MenuItem();
3092 MenuItem redoMenuItem = new MenuItem();
3094 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3096 MenuItem noColourmenuItem = new MenuItem();
3098 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3100 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3102 MenuItem findMenuItem = new MenuItem();
3104 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3106 MenuItem nucleotideColour = new MenuItem();
3108 MenuItem deleteGroups = new MenuItem();
3110 MenuItem grpsFromSelection = new MenuItem();
3112 MenuItem createGroup = new MenuItem();
3114 MenuItem unGroup = new MenuItem();
3116 MenuItem delete = new MenuItem();
3118 MenuItem copy = new MenuItem();
3120 MenuItem cut = new MenuItem();
3122 Menu pasteMenu = new Menu();
3124 MenuItem pasteNew = new MenuItem();
3126 MenuItem pasteThis = new MenuItem();
3128 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3130 MenuItem font = new MenuItem();
3132 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3134 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3136 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3138 MenuItem modifyPID = new MenuItem();
3140 MenuItem modifyConservation = new MenuItem();
3142 CheckboxMenuItem autoCalculate = null;
3144 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3145 "Sort Alignment With New Tree", true);
3147 Menu sortByTreeMenu = new Menu();
3149 MenuItem inputText = new MenuItem();
3151 MenuItem documentation = new MenuItem();
3153 MenuItem about = new MenuItem();
3155 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3157 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3159 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3161 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3163 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3165 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3167 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3169 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3171 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3174 * Initialise menus and other items
3178 private void jbInit() throws Exception
3180 setMenuBar(alignFrameMenuBar);
3183 * Configure File menu items and actions
3186 .setLabel(MessageManager.getString("label.input_from_textbox"));
3187 inputText.addActionListener(this);
3188 Menu outputTextboxMenu = new Menu(
3189 MessageManager.getString("label.out_to_textbox"));
3190 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3193 MenuItem item = new MenuItem(
3194 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3196 item.addActionListener(new java.awt.event.ActionListener()
3199 public void actionPerformed(ActionEvent e)
3201 outputText_actionPerformed(e);
3205 outputTextboxMenu.add(item);
3207 closeMenuItem.addActionListener(this);
3208 loadApplication.addActionListener(this);
3209 loadTree.addActionListener(this);
3210 loadAnnotations.addActionListener(this);
3211 outputFeatures.addActionListener(this);
3212 outputAnnotations.addActionListener(this);
3215 * Configure Edit menu items and actions
3217 undoMenuItem.setEnabled(false);
3218 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3219 undoMenuItem.addActionListener(this);
3220 redoMenuItem.setEnabled(false);
3221 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3222 redoMenuItem.addActionListener(this);
3223 copy.setLabel(MessageManager.getString("action.copy"));
3224 copy.addActionListener(this);
3225 cut.setLabel(MessageManager.getString("action.cut"));
3226 cut.addActionListener(this);
3227 delete.setLabel(MessageManager.getString("action.delete"));
3228 delete.addActionListener(this);
3229 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3230 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3231 pasteNew.addActionListener(this);
3232 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3233 pasteThis.addActionListener(this);
3234 remove2LeftMenuItem.setLabel(MessageManager
3235 .getString("action.remove_left"));
3236 remove2LeftMenuItem.addActionListener(this);
3237 remove2RightMenuItem.setLabel(MessageManager
3238 .getString("action.remove_right"));
3239 remove2RightMenuItem.addActionListener(this);
3240 removeGappedColumnMenuItem.setLabel(MessageManager
3241 .getString("action.remove_empty_columns"));
3242 removeGappedColumnMenuItem.addActionListener(this);
3243 removeAllGapsMenuItem.setLabel(MessageManager
3244 .getString("action.remove_all_gaps"));
3245 removeAllGapsMenuItem.addActionListener(this);
3246 removeRedundancyMenuItem.setLabel(MessageManager
3247 .getString("action.remove_redundancy"));
3248 removeRedundancyMenuItem.addActionListener(this);
3251 * Configure Select menu items and actions
3253 findMenuItem.setLabel(MessageManager.getString("action.find"));
3254 findMenuItem.addActionListener(this);
3255 selectAllSequenceMenuItem.addActionListener(this);
3256 deselectAllSequenceMenuItem.addActionListener(this);
3257 invertSequenceMenuItem.setLabel(MessageManager
3258 .getString("action.invert_sequence_selection"));
3259 invertSequenceMenuItem.addActionListener(this);
3260 invertColSel.setLabel(MessageManager
3261 .getString("action.invert_column_selection"));
3262 invertColSel.addActionListener(this);
3263 deleteGroups.setLabel(MessageManager
3264 .getString("action.undefine_groups"));
3265 deleteGroups.addActionListener(this);
3266 grpsFromSelection.setLabel(MessageManager
3267 .getString("action.make_groups_selection"));
3268 grpsFromSelection.addActionListener(this);
3269 createGroup.setLabel(MessageManager.getString("action.create_group"));
3270 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3271 annotationColumnSelection.setLabel(MessageManager
3272 .getString("action.select_by_annotation"));
3273 annotationColumnSelection.addActionListener(this);
3276 * Configure View menu items and actions
3278 newView.setLabel(MessageManager.getString("action.new_view"));
3279 newView.addActionListener(this);
3280 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3281 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3282 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3283 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3285 .setLabel(MessageManager.getString("label.selected_columns"));
3286 hideSequences.setLabel(MessageManager
3287 .getString("label.selected_sequences"));
3288 hideAllButSelection.setLabel(MessageManager
3289 .getString("label.all_but_selected_region"));
3290 hideAllSelection.setLabel(MessageManager
3291 .getString("label.selected_region"));
3292 showAllHidden.setLabel(MessageManager
3293 .getString("label.all_sequences_columns"));
3294 showColumns.addActionListener(this);
3295 showSeqs.addActionListener(this);
3296 hideColumns.addActionListener(this);
3297 hideSequences.addActionListener(this);
3298 hideAllButSelection.addActionListener(this);
3299 hideAllSelection.addActionListener(this);
3300 showAllHidden.addActionListener(this);
3301 featureSettings.setLabel(MessageManager
3302 .getString("action.feature_settings"));
3303 featureSettings.addActionListener(this);
3304 sequenceFeatures.setLabel(MessageManager
3305 .getString("label.show_sequence_features"));
3306 sequenceFeatures.addItemListener(this);
3307 sequenceFeatures.setState(false);
3308 followMouseOverFlag.setLabel(MessageManager
3309 .getString("label.automatic_scrolling"));
3310 followMouseOverFlag.addItemListener(this);
3311 alProperties.addActionListener(this);
3312 overviewMenuItem.setLabel(MessageManager
3313 .getString("label.overview_window"));
3314 overviewMenuItem.addActionListener(this);
3317 * Configure Annotations menu items and actions
3319 annotationPanelMenuItem.setLabel(MessageManager
3320 .getString("label.show_annotations"));
3321 annotationPanelMenuItem.addItemListener(this);
3322 showGroupConsensus.setLabel(MessageManager
3323 .getString("label.group_consensus"));
3324 showGroupConservation.setLabel(MessageManager
3325 .getString("label.group_conservation"));
3326 showConsensusHistogram.setLabel(MessageManager
3327 .getString("label.show_consensus_histogram"));
3328 showSequenceLogo.setLabel(MessageManager
3329 .getString("label.show_consensus_logo"));
3330 normSequenceLogo.setLabel(MessageManager
3331 .getString("label.norm_consensus_logo"));
3332 applyAutoAnnotationSettings.setLabel(MessageManager
3333 .getString("label.apply_all_groups"));
3334 applyAutoAnnotationSettings.setState(true);
3335 Menu autoAnnMenu = new Menu(
3336 MessageManager.getString("label.autocalculated_annotation"));
3337 showGroupConsensus.addItemListener(this);
3338 showGroupConservation.addItemListener(this);
3339 showConsensusHistogram.addItemListener(this);
3340 showSequenceLogo.addItemListener(this);
3341 normSequenceLogo.addItemListener(this);
3342 applyAutoAnnotationSettings.addItemListener(this);
3343 showAlignmentAnnotations = new CheckboxMenuItem(
3344 MessageManager.getString("label.show_all_al_annotations"));
3345 showSequenceAnnotations = new CheckboxMenuItem(
3346 MessageManager.getString("label.show_all_seq_annotations"));
3347 sortAnnBySequence = new CheckboxMenuItem(
3348 MessageManager.getString("label.sort_annotations_by_sequence"));
3349 sortAnnByLabel = new CheckboxMenuItem(
3350 MessageManager.getString("label.sort_annotations_by_label"));
3351 showAutoFirst = new CheckboxMenuItem(
3352 MessageManager.getString("label.show_first"));
3353 showAutoLast = new CheckboxMenuItem(
3354 MessageManager.getString("label.show_last"));
3355 showAlignmentAnnotations.addItemListener(this);
3356 showSequenceAnnotations.addItemListener(this);
3357 sortAnnBySequence.addItemListener(this);
3358 sortAnnByLabel.addItemListener(this);
3359 showAutoFirst.addItemListener(this);
3360 showAutoLast.addItemListener(this);
3363 * Configure Format menu items and actions
3365 font.setLabel(MessageManager.getString("action.font"));
3366 font.addActionListener(this);
3367 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3368 scaleAbove.setState(true);
3369 scaleAbove.setEnabled(false);
3370 scaleAbove.addItemListener(this);
3371 scaleLeft.setEnabled(false);
3372 scaleLeft.setState(true);
3373 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3374 scaleLeft.addItemListener(this);
3375 scaleRight.setEnabled(false);
3376 scaleRight.setState(true);
3377 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3378 scaleRight.addItemListener(this);
3379 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3380 viewBoxesMenuItem.setState(true);
3381 viewBoxesMenuItem.addItemListener(this);
3382 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3383 viewTextMenuItem.setState(true);
3384 viewTextMenuItem.addItemListener(this);
3385 colourTextMenuItem.setLabel(MessageManager
3386 .getString("label.colour_text"));
3387 colourTextMenuItem.addItemListener(this);
3388 displayNonconservedMenuItem.setLabel(MessageManager
3389 .getString("label.show_non_conversed"));
3390 displayNonconservedMenuItem.addItemListener(this);
3391 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3392 wrapMenuItem.addItemListener(this);
3393 renderGapsMenuItem.setLabel(MessageManager
3394 .getString("action.show_gaps"));
3395 renderGapsMenuItem.setState(true);
3396 renderGapsMenuItem.addItemListener(this);
3397 centreColumnLabelFlag.setLabel(MessageManager
3398 .getString("label.centre_column_labels"));
3399 centreColumnLabelFlag.addItemListener(this);
3400 seqLimits.setState(true);
3401 seqLimits.setLabel(MessageManager
3402 .getString("label.show_sequence_limits"));
3403 seqLimits.addItemListener(this);
3406 * Configure Colour menu items and actions
3408 applyToAllGroups.setLabel(MessageManager
3409 .getString("label.apply_colour_to_all_groups"));
3410 applyToAllGroups.setState(true);
3411 applyToAllGroups.addItemListener(this);
3412 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3413 clustalColour.addActionListener(this);
3414 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3415 zappoColour.addActionListener(this);
3416 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3417 taylorColour.addActionListener(this);
3418 hydrophobicityColour.setLabel(MessageManager
3419 .getString("label.hydrophobicity"));
3420 hydrophobicityColour.addActionListener(this);
3422 .setLabel(MessageManager.getString("label.helix_propensity"));
3423 helixColour.addActionListener(this);
3424 strandColour.setLabel(MessageManager
3425 .getString("label.strand_propensity"));
3426 strandColour.addActionListener(this);
3427 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3428 turnColour.addActionListener(this);
3429 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3430 buriedColour.addActionListener(this);
3431 purinePyrimidineColour.setLabel(MessageManager
3432 .getString("label.purine_pyrimidine"));
3433 purinePyrimidineColour.addActionListener(this);
3434 // RNAInteractionColour.setLabel(MessageManager
3435 // .getString("label.rna_interaction"));
3436 // RNAInteractionColour.addActionListener(this);
3437 RNAHelixColour.setLabel(MessageManager
3438 .getString("action.by_rna_helixes"));
3439 RNAHelixColour.addActionListener(this);
3440 userDefinedColour.setLabel(MessageManager
3441 .getString("action.user_defined"));
3442 userDefinedColour.addActionListener(this);
3443 PIDColour.setLabel(MessageManager
3444 .getString("label.percentage_identity"));
3445 PIDColour.addActionListener(this);
3446 BLOSUM62Colour.setLabel(MessageManager
3447 .getString("label.blosum62_score"));
3448 BLOSUM62Colour.addActionListener(this);
3450 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3451 // it will be enabled only if a score file is provided
3452 tcoffeeColour.setEnabled(false);
3453 tcoffeeColour.addActionListener(this);
3454 conservationMenuItem.setLabel(MessageManager
3455 .getString("action.by_conservation"));
3456 conservationMenuItem.addItemListener(this);
3457 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3458 noColourmenuItem.addActionListener(this);
3459 abovePIDThreshold.setLabel(MessageManager
3460 .getString("label.above_identity_threshold"));
3461 abovePIDThreshold.addItemListener(this);
3462 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3463 nucleotideColour.addActionListener(this);
3464 modifyPID.setLabel(MessageManager
3465 .getString("label.modify_identity_thereshold"));
3466 modifyPID.addActionListener(this);
3467 modifyConservation.setLabel(MessageManager
3468 .getString("label.modify_conservation_thereshold"));
3469 modifyConservation.addActionListener(this);
3470 annotationColour.setLabel(MessageManager
3471 .getString("action.by_annotation"));
3472 annotationColour.addActionListener(this);
3475 * Configure Calculate menu items and actions
3477 sortPairwiseMenuItem.setLabel(MessageManager
3478 .getString("action.by_pairwise_id"));
3479 sortPairwiseMenuItem.addActionListener(this);
3480 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3481 sortIDMenuItem.addActionListener(this);
3482 sortLengthMenuItem.setLabel(MessageManager
3483 .getString("action.by_length"));
3484 sortLengthMenuItem.addActionListener(this);
3485 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3486 sortGroupMenuItem.addActionListener(this);
3487 pairwiseAlignmentMenuItem.setLabel(MessageManager
3488 .getString("action.pairwise_alignment"));
3489 pairwiseAlignmentMenuItem.addActionListener(this);
3490 PCAMenuItem.setLabel(MessageManager
3491 .getString("label.principal_component_analysis"));
3492 PCAMenuItem.addActionListener(this);
3493 autoCalculate = new CheckboxMenuItem(
3494 MessageManager.getString("label.autocalculate_consensus"), true);
3495 averageDistanceTreeMenuItem.setLabel(MessageManager
3496 .getString("label.average_distance_identity"));
3497 averageDistanceTreeMenuItem.addActionListener(this);
3498 neighbourTreeMenuItem.setLabel(MessageManager
3499 .getString("label.neighbour_joining_identity"));
3500 neighbourTreeMenuItem.addActionListener(this);
3501 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3502 .getString("label.average_distance_bloslum62"));
3503 avDistanceTreeBlosumMenuItem.addActionListener(this);
3504 njTreeBlosumMenuItem.setLabel(MessageManager
3505 .getString("label.neighbour_blosum62"));
3506 njTreeBlosumMenuItem.addActionListener(this);
3507 sortByTreeMenu.setLabel(MessageManager
3508 .getString("action.by_tree_order"));
3509 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3510 Menu calculateTreeMenu = new Menu(
3511 MessageManager.getString("action.calculate_tree"));
3512 autoCalculate.addItemListener(this);
3513 sortByTree.addItemListener(this);
3516 * Configure Help menu items and actions
3518 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3519 documentation.setLabel(MessageManager.getString("label.documentation"));
3520 documentation.addActionListener(this);
3521 about.setLabel(MessageManager.getString("label.about"));
3522 about.addActionListener(this);
3525 * Add top level menus to frame
3527 alignFrameMenuBar.add(fileMenu);
3528 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3529 alignFrameMenuBar.add(editMenu);
3530 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3531 alignFrameMenuBar.add(selectMenu);
3532 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3533 alignFrameMenuBar.add(viewMenu);
3534 Menu annotationsMenu = new Menu(
3535 MessageManager.getString("action.annotations"));
3536 alignFrameMenuBar.add(annotationsMenu);
3537 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3538 alignFrameMenuBar.add(formatMenu);
3539 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3540 alignFrameMenuBar.add(colourMenu);
3541 Menu calculateMenu = new Menu(
3542 MessageManager.getString("action.calculate"));
3543 alignFrameMenuBar.add(calculateMenu);
3544 alignFrameMenuBar.add(helpMenu);
3549 fileMenu.add(inputText);
3550 fileMenu.add(loadTree);
3551 fileMenu.add(loadAnnotations);
3552 fileMenu.addSeparator();
3553 fileMenu.add(outputTextboxMenu);
3554 fileMenu.add(outputFeatures);
3555 fileMenu.add(outputAnnotations);
3556 if (jalviewServletURL != null)
3558 fileMenu.add(loadApplication);
3560 fileMenu.addSeparator();
3561 fileMenu.add(closeMenuItem);
3566 editMenu.add(undoMenuItem);
3567 editMenu.add(redoMenuItem);
3570 pasteMenu.add(pasteNew);
3571 pasteMenu.add(pasteThis);
3572 editMenu.add(pasteMenu);
3573 editMenu.add(delete);
3574 editMenu.addSeparator();
3575 editMenu.add(remove2LeftMenuItem);
3576 editMenu.add(remove2RightMenuItem);
3577 editMenu.add(removeGappedColumnMenuItem);
3578 editMenu.add(removeAllGapsMenuItem);
3579 editMenu.add(removeRedundancyMenuItem);
3584 selectMenu.add(findMenuItem);
3585 selectMenu.addSeparator();
3586 selectMenu.add(selectAllSequenceMenuItem);
3587 selectMenu.add(deselectAllSequenceMenuItem);
3588 selectMenu.add(invertSequenceMenuItem);
3589 selectMenu.add(invertColSel);
3590 selectMenu.add(createGroup);
3591 selectMenu.add(unGroup);
3592 selectMenu.add(grpsFromSelection);
3593 selectMenu.add(deleteGroups);
3594 selectMenu.add(annotationColumnSelection);
3599 viewMenu.add(newView);
3600 viewMenu.addSeparator();
3601 showMenu.add(showColumns);
3602 showMenu.add(showSeqs);
3603 showMenu.add(showAllHidden);
3604 viewMenu.add(showMenu);
3605 hideMenu.add(hideColumns);
3606 hideMenu.add(hideSequences);
3607 hideMenu.add(hideAllSelection);
3608 hideMenu.add(hideAllButSelection);
3609 viewMenu.add(hideMenu);
3610 viewMenu.addSeparator();
3611 viewMenu.add(followMouseOverFlag);
3612 viewMenu.addSeparator();
3613 viewMenu.add(sequenceFeatures);
3614 viewMenu.add(featureSettings);
3615 viewMenu.addSeparator();
3616 viewMenu.add(alProperties);
3617 viewMenu.addSeparator();
3618 viewMenu.add(overviewMenuItem);
3623 annotationsMenu.add(annotationPanelMenuItem);
3624 annotationsMenu.addSeparator();
3625 annotationsMenu.add(showAlignmentAnnotations);
3626 annotationsMenu.add(showSequenceAnnotations);
3627 annotationsMenu.add(sortAnnBySequence);
3628 annotationsMenu.add(sortAnnByLabel);
3629 annotationsMenu.addSeparator();
3630 autoAnnMenu.add(showAutoFirst);
3631 autoAnnMenu.add(showAutoLast);
3632 autoAnnMenu.addSeparator();
3633 autoAnnMenu.add(applyAutoAnnotationSettings);
3634 autoAnnMenu.add(showConsensusHistogram);
3635 autoAnnMenu.add(showSequenceLogo);
3636 autoAnnMenu.add(normSequenceLogo);
3637 autoAnnMenu.addSeparator();
3638 autoAnnMenu.add(showGroupConservation);
3639 autoAnnMenu.add(showGroupConsensus);
3640 annotationsMenu.add(autoAnnMenu);
3645 formatMenu.add(font);
3646 formatMenu.add(seqLimits);
3647 formatMenu.add(wrapMenuItem);
3648 formatMenu.add(scaleAbove);
3649 formatMenu.add(scaleLeft);
3650 formatMenu.add(scaleRight);
3651 formatMenu.add(viewBoxesMenuItem);
3652 formatMenu.add(viewTextMenuItem);
3653 formatMenu.add(colourTextMenuItem);
3654 formatMenu.add(displayNonconservedMenuItem);
3655 formatMenu.add(renderGapsMenuItem);
3656 formatMenu.add(centreColumnLabelFlag);
3661 colourMenu.add(applyToAllGroups);
3662 colourMenu.addSeparator();
3663 colourMenu.add(noColourmenuItem);
3664 colourMenu.add(clustalColour);
3665 colourMenu.add(BLOSUM62Colour);
3666 colourMenu.add(PIDColour);
3667 colourMenu.add(zappoColour);
3668 colourMenu.add(taylorColour);
3669 colourMenu.add(hydrophobicityColour);
3670 colourMenu.add(helixColour);
3671 colourMenu.add(strandColour);
3672 colourMenu.add(turnColour);
3673 colourMenu.add(buriedColour);
3674 colourMenu.add(nucleotideColour);
3675 colourMenu.add(purinePyrimidineColour);
3676 // colourMenu.add(RNAInteractionColour);
3677 colourMenu.add(tcoffeeColour);
3678 colourMenu.add(userDefinedColour);
3679 colourMenu.addSeparator();
3680 colourMenu.add(conservationMenuItem);
3681 colourMenu.add(modifyConservation);
3682 colourMenu.add(abovePIDThreshold);
3683 colourMenu.add(modifyPID);
3684 colourMenu.add(annotationColour);
3685 colourMenu.add(RNAHelixColour);
3690 sortMenu.add(sortIDMenuItem);
3691 sortMenu.add(sortLengthMenuItem);
3692 sortMenu.add(sortByTreeMenu);
3693 sortMenu.add(sortGroupMenuItem);
3694 sortMenu.add(sortPairwiseMenuItem);
3695 calculateMenu.add(sortMenu);
3696 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3697 calculateTreeMenu.add(neighbourTreeMenuItem);
3698 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3699 calculateTreeMenu.add(njTreeBlosumMenuItem);
3700 calculateMenu.add(calculateTreeMenu);
3701 calculateMenu.addSeparator();
3702 calculateMenu.add(pairwiseAlignmentMenuItem);
3703 calculateMenu.add(PCAMenuItem);
3704 calculateMenu.add(autoCalculate);
3705 calculateMenu.add(sortByTree);
3710 helpMenu.add(documentation);
3711 helpMenu.add(about);
3716 statusBar.setBackground(Color.white);
3717 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3718 statusBar.setText(MessageManager.getString("label.status_bar"));
3719 this.add(statusBar, BorderLayout.SOUTH);
3722 public void setStatus(String string)
3724 statusBar.setText(string);
3727 MenuItem featureSettings = new MenuItem();
3729 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3731 MenuItem annotationColour = new MenuItem();
3733 MenuItem annotationColumnSelection = new MenuItem();
3735 MenuItem invertColSel = new MenuItem();
3737 MenuItem showColumns = new MenuItem();
3739 MenuItem showSeqs = new MenuItem();
3741 MenuItem hideColumns = new MenuItem();
3743 MenuItem hideSequences = new MenuItem();
3745 MenuItem hideAllButSelection = new MenuItem();
3747 MenuItem hideAllSelection = new MenuItem();
3749 MenuItem showAllHidden = new MenuItem();
3751 MenuItem newView = new MenuItem();
3753 private CheckboxMenuItem showAlignmentAnnotations;
3755 private CheckboxMenuItem showSequenceAnnotations;
3757 private CheckboxMenuItem sortAnnBySequence;
3759 private CheckboxMenuItem sortAnnByLabel;
3761 private CheckboxMenuItem showAutoFirst;
3763 private CheckboxMenuItem showAutoLast;
3765 private SplitFrame splitFrame;
3768 * Attach the alignFrame panels after embedding menus, if necessary. This used
3769 * to be called setEmbedded, but is now creates the dropdown menus in a
3770 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3772 * @param reallyEmbedded
3773 * true to attach the view to the applet area on the page rather than
3776 public void createAlignFrameWindow(boolean reallyEmbedded)
3780 embedAlignFrameInApplet(viewport.applet);
3785 // test and embed menu bar if necessary.
3787 if (embedMenuIfNeeded(alignPanel))
3790 * adjust for status bar height too. ? pointless as overridden by layout
3793 alignPanel.setSize(getSize().width,
3794 getSize().height - statusBar.getHeight());
3796 add(statusBar, BorderLayout.SOUTH);
3797 add(alignPanel, BorderLayout.CENTER);
3798 // and register with the applet so it can pass external API calls to us
3799 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3806 * Add the components of this AlignFrame to the applet container.
3810 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3813 // Explicitly build the embedded menu panel for the on-page applet
3815 // view cannot be closed if its actually on the page
3816 fileMenu.remove(closeMenuItem);
3817 fileMenu.remove(3); // Remove Separator
3818 // construct embedded menu, using default font
3819 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3820 // and actually add the components to the applet area
3821 theApplet.setLayout(new BorderLayout());
3822 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3823 theApplet.add(statusBar, BorderLayout.SOUTH);
3824 // TODO should size be left to the layout manager?
3825 alignPanel.setSize(theApplet.getSize().width,
3826 theApplet.getSize().height - embeddedMenu.getHeight()
3827 - statusBar.getHeight());
3828 theApplet.add(alignPanel, BorderLayout.CENTER);
3829 final AlignFrame me = this;
3830 theApplet.addFocusListener(new FocusListener()
3834 public void focusLost(FocusEvent e)
3836 if (theApplet.currentAlignFrame == me)
3838 theApplet.currentAlignFrame = null;
3843 public void focusGained(FocusEvent e)
3845 theApplet.currentAlignFrame = me;
3848 theApplet.validate();
3852 * create a new binding between structures in an existing jmol viewer instance
3853 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3854 * this does not open a new Jmol window, or modify the display of the
3855 * structures in the original jmol window. Note This method doesn't work
3856 * without an additional javascript library to exchange messages between the
3857 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3860 * JmolViewer instance
3861 * @param sequenceIds
3862 * - sequence Ids to search for associations
3864 public SequenceStructureBinding addStructureViewInstance(
3865 Object jmolviewer, String[] sequenceIds)
3867 Viewer viewer = null;
3870 viewer = (Viewer) jmolviewer;
3871 } catch (ClassCastException ex)
3873 System.err.println("Unsupported viewer object :"
3874 + jmolviewer.getClass());
3878 System.err.println("Can't use this object as a structure viewer:"
3879 + jmolviewer.getClass());
3882 SequenceI[] seqs = null;
3883 if (sequenceIds == null || sequenceIds.length == 0)
3885 seqs = viewport.getAlignment().getSequencesArray();
3889 Vector sqi = new Vector();
3890 AlignmentI al = viewport.getAlignment();
3891 for (int sid = 0; sid < sequenceIds.length; sid++)
3893 SequenceI sq = al.findName(sequenceIds[sid]);
3901 seqs = new SequenceI[sqi.size()];
3902 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3904 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3912 AAStructureBindingModel jmv = null;
3913 // TODO: search for a jmv that involves viewer
3915 { // create a new viewer/jalview binding.
3916 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3924 * bind a pdb file to a sequence in the current view
3927 * - sequenceId within the dataset.
3928 * @param pdbEntryString
3929 * - the short name for the PDB file
3931 * - pdb file - either a URL or a valid PDB file.
3932 * @return true if binding was as success TODO: consider making an exception
3933 * structure for indicating when PDB parsing or sequenceId location
3936 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3939 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3940 boolean needtoadd = false;
3941 if (toaddpdb != null)
3943 Vector pdbe = toaddpdb.getAllPDBEntries();
3944 PDBEntry pdbentry = null;
3945 if (pdbe != null && pdbe.size() > 0)
3947 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3949 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3950 if (!pdbentry.getId().equals(pdbEntryString)
3951 && !pdbentry.getFile().equals(pdbFile))
3961 if (pdbentry == null)
3963 pdbentry = new PDBEntry();
3964 pdbentry.setId(pdbEntryString);
3965 pdbentry.setFile(pdbFile);
3966 needtoadd = true; // add this new entry to sequence.
3968 // resolve data source
3969 // TODO: this code should be a refactored to an io package
3970 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3971 if (protocol == null)
3977 // make a note of the access mode and add
3978 if (pdbentry.getProperty() == null)
3980 pdbentry.setProperty(new Hashtable());
3982 pdbentry.getProperty().put("protocol", protocol);
3983 toaddpdb.addPDBId(pdbentry);
3984 alignPanel.getStructureSelectionManager()
3985 .registerPDBEntry(pdbentry);
3991 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3995 Vector sequences = new Vector();
3996 for (int i = 0; i < seqs.length; i++)
3998 if (seqs[i] != null)
4000 sequences.addElement(new Object[]
4001 { seqs[i], (chains != null) ? chains[i] : null });
4004 seqs = new SequenceI[sequences.size()];
4005 chains = new String[sequences.size()];
4006 for (int i = 0, isize = sequences.size(); i < isize; i++)
4008 Object[] oj = (Object[]) sequences.elementAt(i);
4010 seqs[i] = (SequenceI) oj[0];
4011 chains[i] = (String) oj[1];
4019 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4020 SequenceI[] seqs, String[] chains, String protocol)
4022 // Scrub any null sequences from the array
4023 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4024 seqs = (SequenceI[]) sqch[0];
4025 chains = (String[]) sqch[1];
4026 if (seqs == null || seqs.length == 0)
4029 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4031 if (protocol == null || protocol.trim().length() == 0
4032 || protocol.equals("null"))
4034 protocol = (String) pdb.getProperty().get("protocol");
4035 if (protocol == null)
4037 System.err.println("Couldn't work out protocol to open structure: "
4042 if (applet.useXtrnalSviewer)
4044 // register the association(s) and quit, don't create any windows.
4045 if (StructureSelectionManager.getStructureSelectionManager(applet)
4046 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4048 System.err.println("Failed to map " + pdb.getFile() + " ("
4049 + protocol + ") to any sequences");
4053 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4055 // can only do alignments with Jmol
4056 // find the last jmol window assigned to this alignment
4057 jalview.appletgui.AppletJmol ajm = null, tajm;
4058 Vector jmols = applet
4059 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4060 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4062 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4063 if (tajm.ap.alignFrame == this)
4072 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4073 // try and add the pdb structure
4078 // otherwise, create a new window
4079 if (applet.jmolAvailable)
4081 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4083 applet.lastFrameX += 40;
4084 applet.lastFrameY += 40;
4088 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4093 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4094 SequenceI[][] seqs, String[][] chains, String[] protocols)
4096 // TODO Auto-generated method stub
4097 System.err.println("Aligned Structure View: Not yet implemented.");
4101 * modify the current selection, providing the user has not made a selection
4105 * - sequences from this alignment
4107 * - columns to be selected on the alignment
4109 public void select(SequenceGroup sel, ColumnSelection csel)
4111 alignPanel.seqPanel.selection(sel, csel, null);
4114 public void scrollTo(int row, int column)
4116 alignPanel.seqPanel.scrollTo(row, column);
4119 public void scrollToRow(int row)
4121 alignPanel.seqPanel.scrollToRow(row);
4124 public void scrollToColumn(int column)
4126 alignPanel.seqPanel.scrollToColumn(column);
4130 * @return the alignments unique ID.
4132 public String getSequenceSetId()
4134 return viewport.getSequenceSetId();
4138 * Load the (T-Coffee) score file from the specified url
4141 * File/URL/T-COFFEE score file contents
4142 * @throws IOException
4143 * @return true if alignment was annotated with data from source
4145 public boolean loadScoreFile(String source) throws IOException
4148 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4149 AppletFormatAdapter.checkProtocol(source));
4150 if (!file.isValid())
4152 // TODO: raise dialog for gui
4153 System.err.println("Problems parsing T-Coffee scores: "
4154 + file.getWarningMessage());
4155 System.err.println("Origin was:\n" + source);
4160 * check that the score matrix matches the alignment dimensions
4163 if ((aln = viewport.getAlignment()) != null
4164 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4167 // TODO: raise a dialog box here rather than bomb out.
4169 .println("The scores matrix does not match the alignment dimensions");
4173 // TODO add parameter to indicate if matching should be done
4174 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4176 alignPanel.fontChanged();
4177 tcoffeeColour.setEnabled(true);
4178 // switch to this color
4179 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4184 System.err.println("Problems resolving T-Coffee scores:");
4185 if (file.getWarningMessage() != null)
4187 System.err.println(file.getWarningMessage());
4193 public SplitFrame getSplitFrame()
4195 return this.splitFrame;
4198 public void setSplitFrame(SplitFrame sf)
4200 this.splitFrame = sf;
4203 // may not need this
4205 public void setShowSeqFeatures(boolean b)
4207 // showSeqFeatures.setSelected(b);
4208 viewport.setShowSequenceFeatures(b);
4213 public void setMenusForViewport()
4215 // setMenusFromViewport(viewport);
4219 public void refreshFeatureUI(boolean enableIfNecessary)
4221 if (enableIfNecessary)
4223 sequenceFeatures.setState(true);
4224 alignPanel.av.setShowSequenceFeatures(true);
4229 public FeatureSettingsControllerI getFeatureSettingsUI()
4231 return alignPanel.av.featureSettings;