2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import java.awt.BorderLayout;
24 import java.awt.Canvas;
25 import java.awt.CheckboxMenuItem;
26 import java.awt.Color;
28 import java.awt.FontMetrics;
29 import java.awt.Frame;
30 import java.awt.Graphics;
31 import java.awt.Label;
33 import java.awt.MenuBar;
34 import java.awt.MenuItem;
35 import java.awt.event.ActionEvent;
36 import java.awt.event.ActionListener;
37 import java.awt.event.FocusEvent;
38 import java.awt.event.FocusListener;
39 import java.awt.event.ItemEvent;
40 import java.awt.event.ItemListener;
41 import java.awt.event.KeyEvent;
42 import java.awt.event.KeyListener;
43 import java.awt.event.WindowAdapter;
44 import java.awt.event.WindowEvent;
45 import java.io.IOException;
47 import java.net.URLEncoder;
48 import java.util.Arrays;
49 import java.util.Deque;
50 import java.util.HashMap;
51 import java.util.Hashtable;
52 import java.util.List;
54 import java.util.StringTokenizer;
55 import java.util.Vector;
57 import jalview.analysis.AlignmentSorter;
58 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
59 import jalview.api.AlignViewControllerGuiI;
60 import jalview.api.AlignViewControllerI;
61 import jalview.api.AlignViewportI;
62 import jalview.api.FeatureRenderer;
63 import jalview.api.SequenceStructureBinding;
64 import jalview.bin.JalviewLite;
65 import jalview.commands.CommandI;
66 import jalview.commands.EditCommand;
67 import jalview.commands.EditCommand.Action;
68 import jalview.commands.OrderCommand;
69 import jalview.commands.RemoveGapColCommand;
70 import jalview.commands.RemoveGapsCommand;
71 import jalview.commands.SlideSequencesCommand;
72 import jalview.commands.TrimRegionCommand;
73 import jalview.datamodel.Alignment;
74 import jalview.datamodel.AlignmentAnnotation;
75 import jalview.datamodel.AlignmentI;
76 import jalview.datamodel.AlignmentOrder;
77 import jalview.datamodel.ColumnSelection;
78 import jalview.datamodel.PDBEntry;
79 import jalview.datamodel.Sequence;
80 import jalview.datamodel.SequenceGroup;
81 import jalview.datamodel.SequenceI;
82 import jalview.io.AnnotationFile;
83 import jalview.io.AppletFormatAdapter;
84 import jalview.io.FeaturesFile;
85 import jalview.io.TCoffeeScoreFile;
86 import jalview.schemes.Blosum62ColourScheme;
87 import jalview.schemes.BuriedColourScheme;
88 import jalview.schemes.ClustalxColourScheme;
89 import jalview.schemes.ColourSchemeI;
90 import jalview.schemes.HelixColourScheme;
91 import jalview.schemes.HydrophobicColourScheme;
92 import jalview.schemes.NucleotideColourScheme;
93 import jalview.schemes.PIDColourScheme;
94 import jalview.schemes.PurinePyrimidineColourScheme;
95 import jalview.schemes.RNAHelicesColourChooser;
96 import jalview.schemes.RNAInteractionColourScheme;
97 import jalview.schemes.StrandColourScheme;
98 import jalview.schemes.TCoffeeColourScheme;
99 import jalview.schemes.TaylorColourScheme;
100 import jalview.schemes.TurnColourScheme;
101 import jalview.schemes.ZappoColourScheme;
102 import jalview.structure.StructureSelectionManager;
103 import jalview.structures.models.AAStructureBindingModel;
104 import jalview.util.MappingUtils;
105 import jalview.util.MessageManager;
106 import jalview.viewmodel.AlignmentViewport;
108 public class AlignFrame extends EmbmenuFrame implements ActionListener,
109 ItemListener, KeyListener, AlignViewControllerGuiI
111 public AlignViewControllerI avc;
113 public AlignmentPanel alignPanel;
115 public AlignViewport viewport;
117 // width and height may be overridden by applet parameters
118 int frameWidth = 700;
120 int frameHeight = 500;
122 String jalviewServletURL;
125 * Flag for showing autocalculated consensus above or below other consensus
128 private boolean showAutoCalculatedAbove;
130 private SequenceAnnotationOrder annotationSortOrder;
133 * Constructor that creates the frame and adds it to the display.
140 public AlignFrame(AlignmentI al, JalviewLite applet,
141 String title, boolean embedded)
143 this(al, applet, title, embedded, true);
147 * Constructor that optionally allows the frame to be displayed or only
154 * @param addToDisplay
156 public AlignFrame(AlignmentI al, JalviewLite applet,
157 String title, boolean embedded, boolean addToDisplay)
161 jalviewServletURL = applet.getParameter("APPLICATION_URL");
167 } catch (Exception ex)
169 ex.printStackTrace();
171 // need to get window geometry before we calculate alignment layout
177 param = applet.getParameter("windowWidth");
180 int width = Integer.parseInt(param);
183 param = applet.getParameter("windowHeight");
186 int height = Integer.parseInt(param);
187 frameHeight = height;
189 } catch (Exception ex)
193 viewport = new AlignViewport(al, applet);
194 alignPanel = new AlignmentPanel(this, viewport);
195 avc = new jalview.controller.AlignViewController(this, viewport,
197 viewport.updateConservation(alignPanel);
198 viewport.updateConsensus(alignPanel);
200 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
201 followMouseOverFlag.setState(viewport.isFollowHighlight());
202 showGroupConsensus.setState(viewport.isShowGroupConsensus());
203 showGroupConservation.setState(viewport.isShowGroupConservation());
204 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
205 showSequenceLogo.setState(viewport.isShowSequenceLogo());
206 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
207 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
208 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
209 showAlignmentAnnotations.setState(viewport.isShowAnnotation());
210 showSequenceAnnotations.setState(viewport.isShowAnnotation());
212 seqLimits.setState(viewport.getShowJVSuffix());
216 String param = applet.getParameter("sortBy");
219 if (param.equalsIgnoreCase("Id"))
221 sortIDMenuItem_actionPerformed();
223 else if (param.equalsIgnoreCase("Pairwise Identity"))
225 sortPairwiseMenuItem_actionPerformed();
227 else if (param.equalsIgnoreCase("Length"))
229 sortLengthMenuItem_actionPerformed();
233 param = applet.getParameter("wrap");
236 if (param.equalsIgnoreCase("true"))
238 wrapMenuItem.setState(true);
239 wrapMenuItem_actionPerformed();
242 param = applet.getParameter("centrecolumnlabels");
245 centreColumnLabelFlag.setState(true);
246 centreColumnLabelFlag_stateChanged();
250 if (viewport.getAlignment().isNucleotide())
252 viewport.updateStrucConsensus(alignPanel);
253 if (viewport.getAlignment().hasRNAStructure())
255 RNAHelixColour.setEnabled(true);
259 RNAHelixColour.setEnabled(false);
264 RNAHelixColour.setEnabled(false);
265 purinePyrimidineColour.setEnabled(false);
267 // Some JVMS send keyevents to Top frame or lowest panel,
268 // Havent worked out why yet. So add to both this frame and seqCanvas for
270 this.addKeyListener(this);
271 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
272 alignPanel.idPanel.idCanvas.addKeyListener(this);
273 alignPanel.scalePanel.addKeyListener(this);
274 alignPanel.annotationPanel.addKeyListener(this);
275 alignPanel.annotationPanelHolder.addKeyListener(this);
276 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
277 alignPanel.alabels.addKeyListener(this);
281 addToDisplay(embedded);
288 public void addToDisplay(boolean embedded)
290 createAlignFrameWindow(embedded);
292 alignPanel.adjustAnnotationHeight();
293 alignPanel.paintAlignment(true);
296 public AlignViewport getAlignViewport()
301 public SeqCanvas getSeqcanvas()
303 return alignPanel.seqPanel.seqCanvas;
307 * Load a features file onto the alignment
310 * file URL, content, or other resolvable path
312 * is protocol for accessing data referred to by file
315 public boolean parseFeaturesFile(String file, String type)
317 return parseFeaturesFile(file, type, true);
321 * Load a features file onto the alignment
324 * file URL, content, or other resolvable path
326 * is protocol for accessing data referred to by file
327 * @param autoenabledisplay
328 * when true, display features flag will be automatically enabled if
329 * features are loaded
330 * @return true if data parsed as a features file
332 public boolean parseFeaturesFile(String file, String type,
333 boolean autoenabledisplay)
335 // TODO: test if importing a features file onto an alignment which already
336 // has features with links overwrites the original links.
338 Hashtable featureLinks = new Hashtable();
339 boolean featuresFile = false;
342 featuresFile = new jalview.io.FeaturesFile(file, type)
343 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
344 .getFeatureRenderer().getFeatureColours(), featureLinks,
345 true, viewport.applet.getDefaultParameter(
346 "relaxedidmatch", false));
347 } catch (Exception ex)
349 ex.printStackTrace();
354 if (featureLinks.size() > 0)
356 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
358 if (autoenabledisplay)
360 viewport.setShowSequenceFeatures(true);
361 sequenceFeatures.setState(true);
363 if (alignPanel.seqPanel.seqCanvas.fr != null)
365 // update the min/max ranges where necessary
366 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
368 if (viewport.featureSettings != null)
370 viewport.featureSettings.refreshTable();
372 alignPanel.paintAlignment(true);
373 statusBar.setText(MessageManager
374 .getString("label.successfully_added_features_alignment"));
380 public void keyPressed(KeyEvent evt)
382 if (viewport.cursorMode
383 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
384 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
385 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
386 && Character.isDigit(evt.getKeyChar()))
388 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
391 switch (evt.getKeyCode())
393 case 27: // escape key
394 deselectAllSequenceMenuItem_actionPerformed();
396 alignPanel.alabels.cancelDrag();
399 if (evt.isControlDown() || evt.isMetaDown())
401 cut_actionPerformed();
405 if (viewport.cursorMode && !evt.isControlDown())
407 alignPanel.seqPanel.setCursorColumn();
409 if (evt.isControlDown() || evt.isMetaDown())
411 copy_actionPerformed();
415 if (evt.isControlDown())
417 paste(evt.isShiftDown());
421 if (evt.isControlDown() || evt.isMetaDown())
423 selectAllSequenceMenuItem_actionPerformed();
426 case KeyEvent.VK_DOWN:
427 if (viewport.cursorMode)
429 alignPanel.seqPanel.moveCursor(0, 1);
433 moveSelectedSequences(false);
438 if (viewport.cursorMode)
440 alignPanel.seqPanel.moveCursor(0, -1);
444 moveSelectedSequences(true);
448 case KeyEvent.VK_LEFT:
449 if (evt.isAltDown() || !viewport.cursorMode)
451 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
455 alignPanel.seqPanel.moveCursor(-1, 0);
459 case KeyEvent.VK_RIGHT:
460 if (evt.isAltDown() || !viewport.cursorMode)
462 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
466 alignPanel.seqPanel.moveCursor(1, 0);
470 case KeyEvent.VK_SPACE:
471 if (viewport.cursorMode)
473 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
474 || evt.isShiftDown() || evt.isAltDown());
478 case KeyEvent.VK_DELETE:
479 case KeyEvent.VK_BACK_SPACE:
480 if (viewport.cursorMode)
482 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
483 || evt.isShiftDown() || evt.isAltDown());
487 cut_actionPerformed();
488 alignPanel.seqPanel.seqCanvas.repaint();
493 if (viewport.cursorMode)
495 alignPanel.seqPanel.setCursorRow();
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.setCursorPosition();
505 case KeyEvent.VK_ENTER:
506 case KeyEvent.VK_COMMA:
507 if (viewport.cursorMode)
509 alignPanel.seqPanel.setCursorRowAndColumn();
514 if (viewport.cursorMode)
516 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
520 if (viewport.cursorMode)
522 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
527 viewport.cursorMode = !viewport.cursorMode;
528 statusBar.setText(MessageManager.formatMessage(
529 "label.keyboard_editing_mode", new String[]
530 { (viewport.cursorMode ? "on" : "off") }));
531 if (viewport.cursorMode)
533 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
534 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
539 if (evt.isControlDown())
541 findMenuItem_actionPerformed();
547 boolean toggleSeqs = !evt.isControlDown();
548 boolean toggleCols = !evt.isShiftDown();
549 toggleHiddenRegions(toggleSeqs, toggleCols);
553 case KeyEvent.VK_PAGE_UP:
554 if (viewport.getWrapAlignment())
556 alignPanel.scrollUp(true);
560 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
561 - viewport.endSeq + viewport.startSeq);
565 case KeyEvent.VK_PAGE_DOWN:
566 if (viewport.getWrapAlignment())
568 alignPanel.scrollUp(false);
572 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
573 + viewport.endSeq - viewport.startSeq);
578 if (evt.isControlDown())
580 undoMenuItem_actionPerformed();
585 if (evt.isControlDown())
587 redoMenuItem_actionPerformed();
592 if (evt.isControlDown())
599 if (evt.isControlDown())
601 trimAlignment(false);
606 if (evt.isControlDown())
608 if (evt.isShiftDown())
610 this.removeAllGapsMenuItem_actionPerformed();
614 removeGappedColumnMenuItem_actionPerformed();
619 if (evt.isControlDown())
623 invertColSel_actionPerformed();
627 invertSequenceMenuItem_actionPerformed();
633 if (evt.isControlDown())
635 if (evt.isShiftDown())
637 this.unGroup_actionPerformed();
641 this.createGroup_actionPerformed();
647 if (evt.isControlDown())
649 this.deleteGroups_actionPerformed();
654 if (evt.isControlDown())
661 alignPanel.paintAlignment(true);
665 * called by key handler and the hide all/show all menu items
670 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
672 boolean hide = false;
673 SequenceGroup sg = viewport.getSelectionGroup();
674 if (!toggleSeqs && !toggleCols)
676 // Hide everything by the current selection - this is a hack - we do the
677 // invert and then hide
678 // first check that there will be visible columns after the invert.
679 if ((viewport.getColumnSelection() != null
680 && viewport.getColumnSelection().getSelected() != null && viewport
681 .getColumnSelection().getSelected().size() > 0)
682 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
685 // now invert the sequence set, if required - empty selection implies
686 // that no hiding is required.
689 invertSequenceMenuItem_actionPerformed();
690 sg = viewport.getSelectionGroup();
694 viewport.expandColSelection(sg, true);
695 // finally invert the column selection and get the new sequence
696 // selection and indicate it should be hidden.
697 invertColSel_actionPerformed();
704 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
707 viewport.hideAllSelectedSeqs();
709 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
712 viewport.showAllHiddenSeqs();
718 if (viewport.getColumnSelection().getSelected().size() > 0)
720 viewport.hideSelectedColumns();
723 viewport.setSelectionGroup(sg);
728 viewport.showAllHiddenColumns();
734 public void keyReleased(KeyEvent evt)
739 public void keyTyped(KeyEvent evt)
744 public void itemStateChanged(ItemEvent evt)
746 final Object source = evt.getSource();
747 if (source == displayNonconservedMenuItem)
749 displayNonconservedMenuItem_actionPerformed();
751 else if (source == colourTextMenuItem)
753 colourTextMenuItem_actionPerformed();
755 else if (source == wrapMenuItem)
757 wrapMenuItem_actionPerformed();
759 else if (source == scaleAbove)
761 viewport.setScaleAboveWrapped(scaleAbove.getState());
763 else if (source == scaleLeft)
765 viewport.setScaleLeftWrapped(scaleLeft.getState());
767 else if (source == scaleRight)
769 viewport.setScaleRightWrapped(scaleRight.getState());
771 else if (source == seqLimits)
773 seqLimits_itemStateChanged();
775 else if (source == viewBoxesMenuItem)
777 viewport.setShowBoxes(viewBoxesMenuItem.getState());
779 else if (source == viewTextMenuItem)
781 viewport.setShowText(viewTextMenuItem.getState());
783 else if (source == renderGapsMenuItem)
785 viewport.setRenderGaps(renderGapsMenuItem.getState());
787 else if (source == annotationPanelMenuItem)
789 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
790 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
792 else if (source == sequenceFeatures)
794 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
795 alignPanel.seqPanel.seqCanvas.repaint();
797 else if (source == showAlignmentAnnotations)
799 setAnnotationsVisibility();
801 else if (source == showSequenceAnnotations)
803 setAnnotationsVisibility();
805 else if (source == sortAnnBySequence)
807 boolean newState = sortAnnBySequence.getState();
808 sortAnnByLabel.setState(false);
809 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.SEQUENCE_AND_LABEL
810 : SequenceAnnotationOrder.NONE);
811 setViewportAnnotationOrder();
813 else if (source == sortAnnByLabel)
815 boolean newState = sortAnnByLabel.getState();
816 sortAnnBySequence.setState(false);
817 setAnnotationSortOrder(newState ? SequenceAnnotationOrder.LABEL_AND_SEQUENCE
818 : SequenceAnnotationOrder.NONE);
819 setViewportAnnotationOrder();
821 else if (source == showAutoFirst)
823 showAutoLast.setState(!showAutoFirst.getState());
824 setShowAutoCalculatedAbove(showAutoFirst.getState());
825 setViewportAnnotationOrder();
827 else if (source == showAutoLast)
829 showAutoFirst.setState(!showAutoLast.getState());
830 setShowAutoCalculatedAbove(showAutoFirst.getState());
831 setViewportAnnotationOrder();
833 else if (source == conservationMenuItem)
835 conservationMenuItem_actionPerformed();
837 else if (source == abovePIDThreshold)
839 abovePIDThreshold_actionPerformed();
841 else if (source == applyToAllGroups)
843 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
845 else if (source == autoCalculate)
847 viewport.autoCalculateConsensus = autoCalculate.getState();
849 else if (source == sortByTree)
851 viewport.sortByTree = sortByTree.getState();
853 else if (source == this.centreColumnLabelFlag)
855 centreColumnLabelFlag_stateChanged();
857 else if (source == this.followMouseOverFlag)
859 mouseOverFlag_stateChanged();
861 else if (source == showGroupConsensus)
863 showGroupConsensus_actionPerformed();
865 else if (source == showGroupConservation)
867 showGroupConservation_actionPerformed();
869 else if (source == showSequenceLogo)
871 showSequenceLogo_actionPerformed();
873 else if (source == normSequenceLogo)
875 normSequenceLogo_actionPerformed();
877 else if (source == showConsensusHistogram)
879 showConsensusHistogram_actionPerformed();
881 else if (source == applyAutoAnnotationSettings)
883 applyAutoAnnotationSettings_actionPerformed();
885 alignPanel.paintAlignment(true);
889 * Set the visibility state of sequence-related and/or alignment-related
890 * annotations depending on checkbox selections. Repaint after calling.
894 private void setAnnotationsVisibility()
896 boolean showForAlignment = showAlignmentAnnotations.getState();
897 boolean showForSequences = showSequenceAnnotations.getState();
898 for (AlignmentAnnotation aa : alignPanel.getAlignment()
899 .getAlignmentAnnotation())
901 boolean visible = (aa.sequenceRef == null ? showForAlignment
903 aa.visible = visible;
905 alignPanel.validateAnnotationDimensions(false);
908 private void setAnnotationSortOrder(SequenceAnnotationOrder order)
910 this.annotationSortOrder = order;
914 * Set flags on the viewport that control annotation ordering
916 private void setViewportAnnotationOrder()
918 this.alignPanel.av.setSortAnnotationsBy(this.annotationSortOrder);
920 .setShowAutocalculatedAbove(this.showAutoCalculatedAbove);
923 private void setShowAutoCalculatedAbove(boolean showAbove)
925 this.showAutoCalculatedAbove = showAbove;
928 private void mouseOverFlag_stateChanged()
930 viewport.setFollowHighlight(followMouseOverFlag.getState());
931 // TODO: could kick the scrollTo mechanism to reset view for current
935 private void centreColumnLabelFlag_stateChanged()
937 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
938 this.alignPanel.annotationPanel.repaint();
942 public void actionPerformed(ActionEvent evt)
944 Object source = evt.getSource();
946 if (source == inputText)
948 inputText_actionPerformed();
950 else if (source == loadTree)
952 loadTree_actionPerformed();
954 else if (source == loadApplication)
956 launchFullApplication();
958 else if (source == loadAnnotations)
962 else if (source == outputAnnotations)
964 outputAnnotations(true);
966 else if (source == outputFeatures)
968 outputFeatures(true, "Jalview");
970 else if (source == closeMenuItem)
972 closeMenuItem_actionPerformed();
974 else if (source == copy)
976 copy_actionPerformed();
978 else if (source == undoMenuItem)
980 undoMenuItem_actionPerformed();
982 else if (source == redoMenuItem)
984 redoMenuItem_actionPerformed();
986 else if (source == inputText)
988 inputText_actionPerformed();
990 else if (source == closeMenuItem)
992 closeMenuItem_actionPerformed();
994 else if (source == undoMenuItem)
996 undoMenuItem_actionPerformed();
998 else if (source == redoMenuItem)
1000 redoMenuItem_actionPerformed();
1002 else if (source == copy)
1004 copy_actionPerformed();
1006 else if (source == pasteNew)
1008 pasteNew_actionPerformed();
1010 else if (source == pasteThis)
1012 pasteThis_actionPerformed();
1014 else if (source == cut)
1016 cut_actionPerformed();
1018 else if (source == delete)
1020 delete_actionPerformed();
1022 else if (source == grpsFromSelection)
1024 makeGrpsFromSelection_actionPerformed();
1026 else if (source == deleteGroups)
1028 deleteGroups_actionPerformed();
1030 else if (source == selectAllSequenceMenuItem)
1032 selectAllSequenceMenuItem_actionPerformed();
1034 else if (source == deselectAllSequenceMenuItem)
1036 deselectAllSequenceMenuItem_actionPerformed();
1038 else if (source == invertSequenceMenuItem)
1040 invertSequenceMenuItem_actionPerformed();
1042 else if (source == invertColSel)
1044 viewport.invertColumnSelection();
1045 alignPanel.paintAlignment(true);
1047 else if (source == remove2LeftMenuItem)
1049 trimAlignment(true);
1051 else if (source == remove2RightMenuItem)
1053 trimAlignment(false);
1055 else if (source == removeGappedColumnMenuItem)
1057 removeGappedColumnMenuItem_actionPerformed();
1059 else if (source == removeAllGapsMenuItem)
1061 removeAllGapsMenuItem_actionPerformed();
1063 else if (source == findMenuItem)
1065 findMenuItem_actionPerformed();
1067 else if (source == font)
1069 new FontChooser(alignPanel);
1071 else if (source == newView)
1075 else if (source == showColumns)
1077 viewport.showAllHiddenColumns();
1078 alignPanel.paintAlignment(true);
1080 else if (source == showSeqs)
1082 viewport.showAllHiddenSeqs();
1083 alignPanel.paintAlignment(true);
1085 else if (source == hideColumns)
1087 viewport.hideSelectedColumns();
1088 alignPanel.paintAlignment(true);
1090 else if (source == hideSequences
1091 && viewport.getSelectionGroup() != null)
1093 viewport.hideAllSelectedSeqs();
1094 alignPanel.paintAlignment(true);
1096 else if (source == hideAllButSelection)
1098 toggleHiddenRegions(false, false);
1099 alignPanel.paintAlignment(true);
1101 else if (source == hideAllSelection)
1103 SequenceGroup sg = viewport.getSelectionGroup();
1104 viewport.expandColSelection(sg, false);
1105 viewport.hideAllSelectedSeqs();
1106 viewport.hideSelectedColumns();
1107 alignPanel.paintAlignment(true);
1109 else if (source == showAllHidden)
1111 viewport.showAllHiddenColumns();
1112 viewport.showAllHiddenSeqs();
1113 alignPanel.paintAlignment(true);
1115 else if (source == showGroupConsensus)
1117 showGroupConsensus_actionPerformed();
1119 else if (source == showGroupConservation)
1121 showGroupConservation_actionPerformed();
1123 else if (source == showSequenceLogo)
1125 showSequenceLogo_actionPerformed();
1127 else if (source == normSequenceLogo)
1129 normSequenceLogo_actionPerformed();
1131 else if (source == showConsensusHistogram)
1133 showConsensusHistogram_actionPerformed();
1135 else if (source == applyAutoAnnotationSettings)
1137 applyAutoAnnotationSettings_actionPerformed();
1139 else if (source == featureSettings)
1141 new FeatureSettings(alignPanel);
1143 else if (source == alProperties)
1145 StringBuffer contents = new jalview.io.AlignmentProperties(
1146 viewport.getAlignment()).formatAsString();
1147 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1148 cap.setText(contents.toString());
1149 Frame frame = new Frame();
1151 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1152 "label.alignment_properties", new String[]
1153 { getTitle() }), 400, 250);
1155 else if (source == overviewMenuItem)
1157 overviewMenuItem_actionPerformed();
1159 else if (source == noColourmenuItem)
1163 else if (source == clustalColour)
1165 abovePIDThreshold.setState(false);
1166 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1168 else if (source == zappoColour)
1170 changeColour(new ZappoColourScheme());
1172 else if (source == taylorColour)
1174 changeColour(new TaylorColourScheme());
1176 else if (source == hydrophobicityColour)
1178 changeColour(new HydrophobicColourScheme());
1180 else if (source == helixColour)
1182 changeColour(new HelixColourScheme());
1184 else if (source == strandColour)
1186 changeColour(new StrandColourScheme());
1188 else if (source == turnColour)
1190 changeColour(new TurnColourScheme());
1192 else if (source == buriedColour)
1194 changeColour(new BuriedColourScheme());
1196 else if (source == nucleotideColour)
1198 changeColour(new NucleotideColourScheme());
1200 else if (source == purinePyrimidineColour)
1202 changeColour(new PurinePyrimidineColourScheme());
1204 else if (source == RNAInteractionColour)
1206 changeColour(new RNAInteractionColourScheme());
1208 else if (source == RNAHelixColour)
1210 new RNAHelicesColourChooser(viewport, alignPanel);
1212 else if (source == modifyPID)
1214 modifyPID_actionPerformed();
1216 else if (source == modifyConservation)
1218 modifyConservation_actionPerformed();
1220 else if (source == userDefinedColour)
1222 new UserDefinedColours(alignPanel, null);
1224 else if (source == PIDColour)
1226 changeColour(new PIDColourScheme());
1228 else if (source == BLOSUM62Colour)
1230 changeColour(new Blosum62ColourScheme());
1232 else if (source == tcoffeeColour)
1234 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1236 else if (source == annotationColour)
1238 new AnnotationColourChooser(viewport, alignPanel);
1240 else if (source == annotationColumnSelection)
1242 new AnnotationColumnChooser(viewport, alignPanel);
1244 else if (source == sortPairwiseMenuItem)
1246 sortPairwiseMenuItem_actionPerformed();
1248 else if (source == sortIDMenuItem)
1250 sortIDMenuItem_actionPerformed();
1252 else if (source == sortLengthMenuItem)
1254 sortLengthMenuItem_actionPerformed();
1256 else if (source == sortGroupMenuItem)
1258 sortGroupMenuItem_actionPerformed();
1260 else if (source == removeRedundancyMenuItem)
1262 removeRedundancyMenuItem_actionPerformed();
1264 else if (source == pairwiseAlignmentMenuItem)
1266 pairwiseAlignmentMenuItem_actionPerformed();
1268 else if (source == PCAMenuItem)
1270 PCAMenuItem_actionPerformed();
1272 else if (source == averageDistanceTreeMenuItem)
1274 averageDistanceTreeMenuItem_actionPerformed();
1276 else if (source == neighbourTreeMenuItem)
1278 neighbourTreeMenuItem_actionPerformed();
1280 else if (source == njTreeBlosumMenuItem)
1282 njTreeBlosumMenuItem_actionPerformed();
1284 else if (source == avDistanceTreeBlosumMenuItem)
1286 avTreeBlosumMenuItem_actionPerformed();
1288 else if (source == documentation)
1290 documentation_actionPerformed();
1292 else if (source == about)
1294 about_actionPerformed();
1299 public void inputText_actionPerformed()
1301 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1302 Frame frame = new Frame();
1304 jalview.bin.JalviewLite.addFrame(frame,
1305 MessageManager.getString("label.input_cut_paste"), 500, 500);
1308 protected void outputText_actionPerformed(ActionEvent e)
1310 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1311 Frame frame = new Frame();
1313 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1314 "label.alignment_output_command", new Object[]
1315 { e.getActionCommand() }), 600, 500);
1316 cap.setText(new AppletFormatAdapter().formatSequences(
1317 e.getActionCommand(), viewport.getAlignment(),
1318 viewport.getShowJVSuffix()));
1321 public void loadAnnotations()
1323 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1324 cap.setText(MessageManager
1325 .getString("label.paste_features_annotations_Tcoffee_here"));
1326 cap.setAnnotationImport();
1327 Frame frame = new Frame();
1329 jalview.bin.JalviewLite.addFrame(frame,
1330 MessageManager.getString("action.paste_annotations"), 400, 300);
1334 public String outputAnnotations(boolean displayTextbox)
1336 String annotation = new AnnotationFile()
1337 .printAnnotationsForView(viewport);
1341 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1342 Frame frame = new Frame();
1344 jalview.bin.JalviewLite.addFrame(frame,
1345 MessageManager.getString("label.annotations"), 600, 500);
1346 cap.setText(annotation);
1352 private Map<String,Object> getDisplayedFeatureCols()
1354 if (alignPanel.getFeatureRenderer() != null
1355 && viewport.getFeaturesDisplayed()!= null)
1357 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1363 public String outputFeatures(boolean displayTextbox, String format)
1366 if (format.equalsIgnoreCase("Jalview"))
1368 features = new FeaturesFile().printJalviewFormat(viewport
1369 .getAlignment().getSequencesArray(),
1370 getDisplayedFeatureCols());
1374 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1375 .getSequencesArray(), getDisplayedFeatureCols());
1380 boolean frimport = false;
1381 if (features == null || features.equals("No Features Visible"))
1383 features = "# No features visible - paste some and import them here.";
1387 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1390 cap.setAnnotationImport();
1392 Frame frame = new Frame();
1394 jalview.bin.JalviewLite.addFrame(frame,
1395 MessageManager.getString("label.features"), 600, 500);
1396 cap.setText(features);
1400 if (features == null)
1409 void launchFullApplication()
1411 StringBuffer url = new StringBuffer(jalviewServletURL);
1413 // allow servlet parameters to be passed in applet parameter
1414 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1416 url.append(firstSep);
1419 + appendProtocol(viewport.applet.getParameter("file")));
1421 if (viewport.applet.getParameter("features") != null)
1423 url.append("&features=");
1424 url.append(appendProtocol(viewport.applet.getParameter("features")));
1427 if (viewport.applet.getParameter("annotations") != null)
1429 url.append("&annotations=");
1430 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1433 if (viewport.applet.getParameter("jnetfile") != null)
1435 url.append("&annotations=");
1436 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1439 if (viewport.applet.getParameter("defaultColour") != null)
1441 url.append("&colour="
1442 + removeWhiteSpace(viewport.applet
1443 .getParameter("defaultColour")));
1446 if (viewport.applet.getParameter("userDefinedColour") != null)
1448 url.append("&colour="
1449 + removeWhiteSpace(viewport.applet
1450 .getParameter("userDefinedColour")));
1452 if (viewport.applet.getParameter("tree") != null)
1455 + appendProtocol(viewport.applet.getParameter("tree")));
1457 if (viewport.applet.getParameter("treeFile") != null)
1460 + appendProtocol(viewport.applet.getParameter("treeFile")));
1463 showURL(url.toString(), "FULL_APP");
1466 String removeWhiteSpace(String colour)
1468 StringBuffer sb = new StringBuffer();
1469 for (int i = 0; i < colour.length(); i++)
1471 if (Character.isWhitespace(colour.charAt(i)))
1477 sb.append(colour.charAt(i));
1481 return sb.toString();
1484 String appendProtocol(String url)
1489 url = URLEncoder.encode(url);
1492 * When we finally deprecate 1.1 compatibility, we can start to use
1493 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1494 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1495 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1496 * ex.printStackTrace(); }
1498 catch (java.net.MalformedURLException ex)
1500 url = viewport.applet.getCodeBase() + url;
1505 public void closeMenuItem_actionPerformed()
1507 PaintRefresher.RemoveComponent(alignPanel);
1508 if (alignPanel.seqPanel != null
1509 && alignPanel.seqPanel.seqCanvas != null)
1511 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1513 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1515 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1518 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1533 void updateEditMenuBar()
1536 if (viewport.getHistoryList().size() > 0)
1538 undoMenuItem.setEnabled(true);
1539 CommandI command = viewport.getHistoryList().peek();
1540 undoMenuItem.setLabel(MessageManager.formatMessage(
1541 "label.undo_command", new Object[]
1542 { command.getDescription() }));
1546 undoMenuItem.setEnabled(false);
1547 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1550 if (viewport.getRedoList().size() > 0)
1552 redoMenuItem.setEnabled(true);
1554 CommandI command = viewport.getRedoList().peek();
1555 redoMenuItem.setLabel(MessageManager.formatMessage(
1556 "label.redo_command", new Object[]
1557 { command.getDescription() }));
1561 redoMenuItem.setEnabled(false);
1562 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1570 public void addHistoryItem(CommandI command)
1572 if (command.getSize() > 0)
1574 viewport.addToHistoryList(command);
1575 viewport.clearRedoList();
1576 updateEditMenuBar();
1577 viewport.updateHiddenColumns();
1582 * TODO: JAL-1104 DOCUMENT ME!
1587 protected void undoMenuItem_actionPerformed()
1589 if (viewport.getHistoryList().isEmpty())
1594 CommandI command = viewport.getHistoryList().pop();
1595 viewport.addToRedoList(command);
1596 command.undoCommand(null);
1598 AlignmentViewport originalSource = getOriginatingSource(command);
1600 if (originalSource != viewport)
1603 .println("Warning: Viewport object mismatch whilst undoing");
1605 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1606 // viewport.getColumnSelection().getHiddenColumns()
1608 updateEditMenuBar();
1609 originalSource.firePropertyChange("alignment", null, originalSource
1610 .getAlignment().getSequences());
1614 * TODO: JAL-1104 DOCUMENT ME!
1619 protected void redoMenuItem_actionPerformed()
1621 if (viewport.getRedoList().isEmpty())
1626 CommandI command = viewport.getRedoList().pop();
1627 viewport.addToHistoryList(command);
1628 command.doCommand(null);
1630 AlignmentViewport originalSource = getOriginatingSource(command);
1632 if (originalSource != viewport)
1635 .println("Warning: Viewport object mismatch whilst re-doing");
1637 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1638 // viewport.getColumnSelection().getHiddenColumns()
1641 updateEditMenuBar();
1642 originalSource.firePropertyChange("alignment", null, originalSource
1643 .getAlignment().getSequences());
1646 AlignmentViewport getOriginatingSource(CommandI command)
1648 AlignmentViewport originalSource = null;
1649 // For sequence removal and addition, we need to fire
1650 // the property change event FROM the viewport where the
1651 // original alignment was altered
1652 AlignmentI al = null;
1653 if (command instanceof EditCommand)
1655 EditCommand editCommand = (EditCommand) command;
1656 al = editCommand.getAlignment();
1657 Vector comps = (Vector) PaintRefresher.components.get(viewport
1658 .getSequenceSetId());
1659 for (int i = 0; i < comps.size(); i++)
1661 if (comps.elementAt(i) instanceof AlignmentPanel)
1663 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1665 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1672 if (originalSource == null)
1674 // The original view is closed, we must validate
1675 // the current view against the closed view first
1678 PaintRefresher.validateSequences(al, viewport.getAlignment());
1681 originalSource = viewport;
1684 return originalSource;
1688 * Move the currently selected sequences up or down one position in the
1693 public void moveSelectedSequences(boolean up)
1695 SequenceGroup sg = viewport.getSelectionGroup();
1700 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1701 up ? null : viewport.getHiddenRepSequences(), up);
1702 alignPanel.paintAlignment(true);
1705 * Also move cDNA/protein complement sequences
1707 AlignViewportI complement = viewport.getCodingComplement();
1708 if (complement != null)
1710 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1711 viewport, complement);
1712 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1713 up ? null : complement.getHiddenRepSequences(), up);
1714 // TODO need to trigger a repaint of the complementary panel - how?
1715 // would prefer to handle in SplitFrame but it is not overriding key
1720 synchronized void slideSequences(boolean right, int size)
1722 List<SequenceI> sg = new Vector<SequenceI>();
1723 if (viewport.cursorMode)
1725 sg.add(viewport.getAlignment().getSequenceAt(
1726 alignPanel.seqPanel.seqCanvas.cursorY));
1728 else if (viewport.getSelectionGroup() != null
1729 && viewport.getSelectionGroup().getSize() != viewport
1730 .getAlignment().getHeight())
1732 sg = viewport.getSelectionGroup().getSequences(
1733 viewport.getHiddenRepSequences());
1741 Vector<SequenceI> invertGroup = new Vector();
1743 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1745 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1747 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1751 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1753 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1755 for (int i = 0; i < invertGroup.size(); i++)
1757 seqs2[i] = invertGroup.elementAt(i);
1760 SlideSequencesCommand ssc;
1763 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1764 size, viewport.getGapCharacter());
1768 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1769 size, viewport.getGapCharacter());
1772 int groupAdjustment = 0;
1773 if (ssc.getGapsInsertedBegin() && right)
1775 if (viewport.cursorMode)
1777 alignPanel.seqPanel.moveCursor(size, 0);
1781 groupAdjustment = size;
1784 else if (!ssc.getGapsInsertedBegin() && !right)
1786 if (viewport.cursorMode)
1788 alignPanel.seqPanel.moveCursor(-size, 0);
1792 groupAdjustment = -size;
1796 if (groupAdjustment != 0)
1798 viewport.getSelectionGroup().setStartRes(
1799 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1800 viewport.getSelectionGroup().setEndRes(
1801 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1804 boolean appendHistoryItem = false;
1805 Deque<CommandI> historyList = viewport.getHistoryList();
1806 if (historyList != null && historyList.size() > 0
1807 && historyList.peek() instanceof SlideSequencesCommand)
1809 appendHistoryItem = ssc
1810 .appendSlideCommand((SlideSequencesCommand) historyList
1814 if (!appendHistoryItem)
1816 addHistoryItem(ssc);
1822 static StringBuffer copiedSequences;
1824 static Vector copiedHiddenColumns;
1826 protected void copy_actionPerformed()
1828 if (viewport.getSelectionGroup() == null)
1833 SequenceGroup sg = viewport.getSelectionGroup();
1834 copiedSequences = new StringBuffer();
1835 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1836 for (int i = 0; i < sg.getSize(); i++)
1838 SequenceI seq = sg.getSequenceAt(i);
1839 int index = viewport.getAlignment().findIndex(seq);
1840 orderedSeqs.put(index, seq);
1843 int index = 0, startRes, endRes;
1846 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1848 copiedHiddenColumns = new Vector();
1849 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1850 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1852 copiedHiddenColumns.addElement(new int[]
1853 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1858 copiedHiddenColumns = null;
1861 for (int i = 0; i < sg.getSize(); i++)
1863 SequenceI seq = null;
1867 if (orderedSeqs.containsKey(index))
1869 seq = orderedSeqs.get(index);
1880 // Returns residue following index if gap
1881 startRes = seq.findPosition(sg.getStartRes());
1884 // Need to find the residue preceeding index if gap
1887 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1889 ch = seq.getCharAt(j);
1890 if (!jalview.util.Comparison.isGap((ch)))
1898 endRes += seq.getStart() - 1;
1901 copiedSequences.append(seq.getName()
1907 + seq.getSequenceAsString(sg.getStartRes(),
1908 sg.getEndRes() + 1) + "\n");
1913 protected void pasteNew_actionPerformed()
1918 protected void pasteThis_actionPerformed()
1923 void paste(boolean newAlignment)
1928 if (copiedSequences == null)
1933 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1934 Vector seqs = new Vector();
1935 while (st.hasMoreElements())
1937 String name = st.nextToken();
1938 int start = Integer.parseInt(st.nextToken());
1939 int end = Integer.parseInt(st.nextToken());
1940 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1942 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1943 for (int i = 0; i < seqs.size(); i++)
1945 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1950 String newtitle = MessageManager.getString("label.copied_sequences");
1951 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1953 newtitle = getTitle();
1957 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1959 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1960 viewport.applet, newtitle, false);
1961 if (copiedHiddenColumns != null)
1963 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1965 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1966 af.viewport.hideColumns(region[0], region[1]);
1970 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
1975 addSequences(newSeqs);
1978 } catch (Exception ex)
1980 } // could be anything being pasted in here
1984 void addSequences(SequenceI[] seqs)
1986 for (int i = 0; i < seqs.length; i++)
1988 viewport.getAlignment().addSequence(seqs[i]);
1992 addHistoryItem(new EditCommand(
1993 MessageManager.getString("label.add_sequences"), Action.PASTE,
1994 seqs, 0, viewport.getAlignment().getWidth(),
1995 viewport.getAlignment()));
1997 viewport.setEndSeq(viewport.getAlignment().getHeight());
1998 viewport.getAlignment().getWidth();
1999 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2004 protected void cut_actionPerformed()
2006 copy_actionPerformed();
2007 delete_actionPerformed();
2010 protected void delete_actionPerformed()
2013 SequenceGroup sg = viewport.getSelectionGroup();
2019 Vector seqs = new Vector();
2021 for (int i = 0; i < sg.getSize(); i++)
2023 seq = sg.getSequenceAt(i);
2024 seqs.addElement(seq);
2027 // If the cut affects all sequences, remove highlighted columns
2028 if (sg.getSize() == viewport.getAlignment().getHeight())
2030 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2031 sg.getEndRes() + 1);
2034 SequenceI[] cut = new SequenceI[seqs.size()];
2035 for (int i = 0; i < seqs.size(); i++)
2037 cut[i] = (SequenceI) seqs.elementAt(i);
2041 * //ADD HISTORY ITEM
2043 addHistoryItem(new EditCommand(
2044 MessageManager.getString("label.cut_sequences"), Action.CUT,
2045 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2046 viewport.getAlignment()));
2048 viewport.setSelectionGroup(null);
2049 viewport.getAlignment().deleteGroup(sg);
2051 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2054 if (viewport.getAlignment().getHeight() < 1)
2056 this.setVisible(false);
2058 viewport.sendSelection();
2062 * group consensus toggled
2065 protected void showGroupConsensus_actionPerformed()
2067 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2068 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2073 * group conservation toggled.
2075 protected void showGroupConservation_actionPerformed()
2077 viewport.setShowGroupConservation(showGroupConservation.getState());
2078 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2085 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2086 * .event.ActionEvent)
2088 protected void showConsensusHistogram_actionPerformed()
2090 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2091 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2098 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2099 * .event.ActionEvent)
2101 protected void showSequenceLogo_actionPerformed()
2103 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2104 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2107 protected void normSequenceLogo_actionPerformed()
2109 showSequenceLogo.setState(true);
2110 viewport.setShowSequenceLogo(true);
2111 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2112 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2115 protected void applyAutoAnnotationSettings_actionPerformed()
2117 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2120 protected void makeGrpsFromSelection_actionPerformed()
2122 if (avc.makeGroupsFromSelection())
2124 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2125 alignPanel.updateAnnotation();
2126 alignPanel.paintAlignment(true);
2130 protected void createGroup_actionPerformed()
2135 protected void unGroup_actionPerformed()
2139 alignPanel.alignmentChanged();
2143 protected void deleteGroups_actionPerformed()
2145 if (avc.deleteGroups())
2147 alignPanel.alignmentChanged();
2151 public void selectAllSequenceMenuItem_actionPerformed()
2153 SequenceGroup sg = new SequenceGroup();
2154 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2156 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2158 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2159 viewport.setSelectionGroup(sg);
2160 alignPanel.paintAlignment(true);
2161 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2162 viewport.sendSelection();
2165 public void deselectAllSequenceMenuItem_actionPerformed()
2167 if (viewport.cursorMode)
2169 alignPanel.seqPanel.keyboardNo1 = null;
2170 alignPanel.seqPanel.keyboardNo2 = null;
2172 viewport.setSelectionGroup(null);
2173 viewport.getColumnSelection().clear();
2174 viewport.setSelectionGroup(null);
2175 alignPanel.idPanel.idCanvas.searchResults = null;
2176 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2177 alignPanel.paintAlignment(true);
2178 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2179 viewport.sendSelection();
2182 public void invertSequenceMenuItem_actionPerformed()
2184 SequenceGroup sg = viewport.getSelectionGroup();
2185 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2187 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2190 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2191 viewport.sendSelection();
2194 public void invertColSel_actionPerformed()
2196 viewport.invertColumnSelection();
2197 alignPanel.paintAlignment(true);
2198 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2199 viewport.sendSelection();
2202 void trimAlignment(boolean trimLeft)
2204 ColumnSelection colSel = viewport.getColumnSelection();
2207 if (colSel.size() > 0)
2211 column = colSel.getMin();
2215 column = colSel.getMax();
2219 if (viewport.getSelectionGroup() != null)
2221 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2222 viewport.getHiddenRepSequences());
2226 seqs = viewport.getAlignment().getSequencesArray();
2229 TrimRegionCommand trimRegion;
2232 trimRegion = new TrimRegionCommand("Remove Left",
2233 TrimRegionCommand.TRIM_LEFT, seqs, column,
2234 viewport.getAlignment(), viewport.getColumnSelection(),
2235 viewport.getSelectionGroup());
2236 viewport.setStartRes(0);
2240 trimRegion = new TrimRegionCommand("Remove Right",
2241 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2242 viewport.getAlignment(), viewport.getColumnSelection(),
2243 viewport.getSelectionGroup());
2246 statusBar.setText(MessageManager.formatMessage(
2247 "label.removed_columns", new String[]
2248 { Integer.valueOf(trimRegion.getSize()).toString() }));
2249 addHistoryItem(trimRegion);
2251 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2253 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2254 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2256 viewport.getAlignment().deleteGroup(sg);
2260 viewport.firePropertyChange("alignment", null, viewport
2261 .getAlignment().getSequences());
2265 public void removeGappedColumnMenuItem_actionPerformed()
2267 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2270 if (viewport.getSelectionGroup() != null)
2272 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2273 viewport.getHiddenRepSequences());
2274 start = viewport.getSelectionGroup().getStartRes();
2275 end = viewport.getSelectionGroup().getEndRes();
2279 seqs = viewport.getAlignment().getSequencesArray();
2282 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2283 "Remove Gapped Columns", seqs, start, end,
2284 viewport.getAlignment());
2286 addHistoryItem(removeGapCols);
2288 statusBar.setText(MessageManager.formatMessage(
2289 "label.removed_empty_columns", new String[]
2290 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2292 // This is to maintain viewport position on first residue
2293 // of first sequence
2294 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2295 int startRes = seq.findPosition(viewport.startRes);
2296 // ShiftList shifts;
2297 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2298 // edit.alColumnChanges=shifts.getInverse();
2299 // if (viewport.hasHiddenColumns)
2300 // viewport.getColumnSelection().compensateForEdits(shifts);
2301 viewport.setStartRes(seq.findIndex(startRes) - 1);
2302 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2307 public void removeAllGapsMenuItem_actionPerformed()
2309 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2312 if (viewport.getSelectionGroup() != null)
2314 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2315 viewport.getHiddenRepSequences());
2316 start = viewport.getSelectionGroup().getStartRes();
2317 end = viewport.getSelectionGroup().getEndRes();
2321 seqs = viewport.getAlignment().getSequencesArray();
2324 // This is to maintain viewport position on first residue
2325 // of first sequence
2326 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2327 int startRes = seq.findPosition(viewport.startRes);
2329 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2330 viewport.getAlignment()));
2332 viewport.setStartRes(seq.findIndex(startRes) - 1);
2334 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2339 public void findMenuItem_actionPerformed()
2341 new Finder(alignPanel);
2345 * create a new view derived from the current view
2348 * @return frame for the new view
2350 public AlignFrame newView(String viewtitle)
2353 if (viewport.hasHiddenRows())
2355 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2356 .getFullAlignment().getSequencesArray());
2360 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2363 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2365 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2367 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2369 newal.addAnnotation(viewport.getAlignment()
2370 .getAlignmentAnnotation()[i]);
2375 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2377 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2378 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2379 PaintRefresher.Register(newaf.alignPanel,
2380 newaf.alignPanel.av.getSequenceSetId());
2382 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2383 newaf.alignPanel.av.getSequenceSetId());
2384 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2385 newaf.alignPanel.av.getSequenceSetId());
2387 Vector comps = (Vector) PaintRefresher.components.get(viewport
2388 .getSequenceSetId());
2390 for (int i = 0; i < comps.size(); i++)
2392 if (comps.elementAt(i) instanceof AlignmentPanel)
2398 String title = new String(this.getTitle());
2399 if (viewtitle != null)
2401 title = viewtitle + " ( " + title + ")";
2405 if (title.indexOf("(View") > -1)
2407 title = title.substring(0, title.indexOf("(View"));
2409 title += "(View " + viewSize + ")";
2412 newaf.setTitle(title.toString());
2414 newaf.viewport.setHistoryList(viewport.getHistoryList());
2415 newaf.viewport.setRedoList(viewport.getRedoList());
2421 * @return list of feature groups on the view
2423 public String[] getFeatureGroups()
2425 FeatureRenderer fr = null;
2426 if (alignPanel != null
2427 && (fr = alignPanel.getFeatureRenderer()) != null)
2429 List<String> gps = fr.getFeatureGroups();
2430 String[] _gps = gps.toArray(new String[gps.size()]);
2437 * get sequence feature groups that are hidden or shown
2443 public String[] getFeatureGroupsOfState(boolean visible)
2445 FeatureRenderer fr = null;
2446 if (alignPanel != null
2447 && (fr = alignPanel.getFeatureRenderer()) != null)
2449 List<String> gps = fr.getGroups(visible);
2450 String[] _gps = gps.toArray(new String[gps.size()]);
2457 * Change the display state for the given feature groups
2460 * list of group strings
2462 * visible or invisible
2464 public void setFeatureGroupState(String[] groups, boolean state)
2466 FeatureRenderer fr = null;
2467 this.sequenceFeatures.setState(true);
2468 viewport.setShowSequenceFeatures(true);
2469 if (alignPanel != null
2470 && (fr = alignPanel.getFeatureRenderer()) != null)
2473 fr.setGroupVisibility(Arrays.asList(groups), state);
2474 alignPanel.seqPanel.seqCanvas.repaint();
2475 if (alignPanel.overviewPanel != null)
2477 alignPanel.overviewPanel.updateOverviewImage();
2482 public void seqLimits_itemStateChanged()
2484 viewport.setShowJVSuffix(seqLimits.getState());
2485 alignPanel.fontChanged();
2486 alignPanel.paintAlignment(true);
2489 protected void colourTextMenuItem_actionPerformed()
2491 viewport.setColourText(colourTextMenuItem.getState());
2492 alignPanel.paintAlignment(true);
2495 protected void displayNonconservedMenuItem_actionPerformed()
2497 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2498 alignPanel.paintAlignment(true);
2501 protected void wrapMenuItem_actionPerformed()
2503 viewport.setWrapAlignment(wrapMenuItem.getState());
2504 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2505 scaleAbove.setEnabled(wrapMenuItem.getState());
2506 scaleLeft.setEnabled(wrapMenuItem.getState());
2507 scaleRight.setEnabled(wrapMenuItem.getState());
2508 alignPanel.paintAlignment(true);
2511 public void overviewMenuItem_actionPerformed()
2513 if (alignPanel.overviewPanel != null)
2518 Frame frame = new Frame();
2519 OverviewPanel overview = new OverviewPanel(alignPanel);
2520 frame.add(overview);
2521 // +50 must allow for applet frame window
2522 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2523 "label.overview_params", new String[]
2524 { this.getTitle() }), overview.getPreferredSize().width,
2525 overview.getPreferredSize().height + 50);
2528 final AlignmentPanel ap = alignPanel;
2529 frame.addWindowListener(new WindowAdapter()
2532 public void windowClosing(WindowEvent e)
2536 ap.setOverviewPanel(null);
2541 alignPanel.setOverviewPanel(overview);
2545 void changeColour(ColourSchemeI cs)
2551 if (viewport.getAbovePIDThreshold())
2553 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2557 if (viewport.getConservationSelected())
2559 cs.setConservationApplied(true);
2560 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2565 cs.setConservationApplied(false);
2568 viewport.setGlobalColourScheme(cs);
2570 if (alignPanel.getOverviewPanel() != null)
2572 alignPanel.getOverviewPanel().updateOverviewImage();
2575 jalview.structure.StructureSelectionManager
2576 .getStructureSelectionManager(viewport.applet)
2577 .sequenceColoursChanged(alignPanel);
2579 alignPanel.paintAlignment(true);
2582 protected void modifyPID_actionPerformed()
2584 if (viewport.getAbovePIDThreshold()
2585 && viewport.getGlobalColourScheme() != null)
2587 SliderPanel.setPIDSliderSource(alignPanel,
2588 viewport.getGlobalColourScheme(), "Background");
2589 SliderPanel.showPIDSlider();
2593 protected void modifyConservation_actionPerformed()
2595 if (viewport.getConservationSelected()
2596 && viewport.getGlobalColourScheme() != null)
2598 SliderPanel.setConservationSlider(alignPanel,
2599 viewport.getGlobalColourScheme(), "Background");
2600 SliderPanel.showConservationSlider();
2604 protected void conservationMenuItem_actionPerformed()
2606 viewport.setConservationSelected(conservationMenuItem.getState());
2608 viewport.setAbovePIDThreshold(false);
2609 abovePIDThreshold.setState(false);
2611 changeColour(viewport.getGlobalColourScheme());
2613 modifyConservation_actionPerformed();
2616 public void abovePIDThreshold_actionPerformed()
2618 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2620 conservationMenuItem.setState(false);
2621 viewport.setConservationSelected(false);
2623 changeColour(viewport.getGlobalColourScheme());
2625 modifyPID_actionPerformed();
2628 public void sortPairwiseMenuItem_actionPerformed()
2630 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2631 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2632 .getAlignment().getSequenceAt(0), null);
2634 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2635 viewport.getAlignment()));
2636 alignPanel.paintAlignment(true);
2639 public void sortIDMenuItem_actionPerformed()
2641 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2642 AlignmentSorter.sortByID(viewport.getAlignment());
2643 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2644 viewport.getAlignment()));
2645 alignPanel.paintAlignment(true);
2648 public void sortLengthMenuItem_actionPerformed()
2650 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2651 AlignmentSorter.sortByLength(viewport.getAlignment());
2652 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2653 viewport.getAlignment()));
2654 alignPanel.paintAlignment(true);
2657 public void sortGroupMenuItem_actionPerformed()
2659 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2660 AlignmentSorter.sortByGroup(viewport.getAlignment());
2661 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2662 viewport.getAlignment()));
2663 alignPanel.paintAlignment(true);
2667 public void removeRedundancyMenuItem_actionPerformed()
2669 new RedundancyPanel(alignPanel);
2672 public void pairwiseAlignmentMenuItem_actionPerformed()
2674 if (viewport.getSelectionGroup() != null
2675 && viewport.getSelectionGroup().getSize() > 1)
2677 Frame frame = new Frame();
2678 frame.add(new PairwiseAlignPanel(alignPanel));
2679 jalview.bin.JalviewLite.addFrame(frame,
2680 MessageManager.getString("action.pairwise_alignment"), 600,
2685 public void PCAMenuItem_actionPerformed()
2687 // are the sequences aligned?
2688 if (!viewport.getAlignment().isAligned(false))
2691 int Width = viewport.getAlignment().getWidth();
2693 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2695 current = viewport.getAlignment().getSequenceAt(i);
2697 if (current.getLength() < Width)
2699 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2702 alignPanel.paintAlignment(true);
2705 if ((viewport.getSelectionGroup() != null
2706 && viewport.getSelectionGroup().getSize() < 4 && viewport
2707 .getSelectionGroup().getSize() > 0)
2708 || viewport.getAlignment().getHeight() < 4)
2715 new PCAPanel(viewport);
2716 } catch (java.lang.OutOfMemoryError ex)
2722 public void averageDistanceTreeMenuItem_actionPerformed()
2724 NewTreePanel("AV", "PID", "Average distance tree using PID");
2727 public void neighbourTreeMenuItem_actionPerformed()
2729 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2732 protected void njTreeBlosumMenuItem_actionPerformed()
2734 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2737 protected void avTreeBlosumMenuItem_actionPerformed()
2739 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2742 void NewTreePanel(String type, String pwType, String title)
2744 // are the sequences aligned?
2745 if (!viewport.getAlignment().isAligned(false))
2748 int Width = viewport.getAlignment().getWidth();
2750 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2752 current = viewport.getAlignment().getSequenceAt(i);
2754 if (current.getLength() < Width)
2756 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2759 alignPanel.paintAlignment(true);
2763 if ((viewport.getSelectionGroup() != null && viewport
2764 .getSelectionGroup().getSize() > 1)
2765 || (viewport.getAlignment().getHeight() > 1))
2767 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2769 addTreeMenuItem(tp, title);
2771 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2775 void loadTree_actionPerformed()
2777 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2778 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2779 cap.setTreeImport();
2780 Frame frame = new Frame();
2782 jalview.bin.JalviewLite.addFrame(frame,
2783 MessageManager.getString("label.paste_newick_file"), 400, 300);
2786 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2788 TreePanel tp = new TreePanel(alignPanel, treeFile,
2789 MessageManager.getString("label.load_tree_from_file"), tree);
2790 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2791 addTreeMenuItem(tp, treeFile);
2795 * sort the alignment using the given treePanel
2798 * tree used to sort view
2800 * string used for undo event name
2802 public void sortByTree(TreePanel treePanel, String title)
2804 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2806 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2807 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2808 // HistoryItem.SORT));
2809 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2810 "label.order_by_params", new String[]
2811 { title }), oldOrder, viewport.getAlignment()));
2812 alignPanel.paintAlignment(true);
2816 * Do any automatic reordering of the alignment and add the necessary bits to
2817 * the menu structure for the new tree
2822 protected void addTreeMenuItem(final TreePanel treePanel,
2825 final MenuItem item = new MenuItem(title);
2826 sortByTreeMenu.add(item);
2827 item.addActionListener(new java.awt.event.ActionListener()
2830 public void actionPerformed(ActionEvent evt)
2832 sortByTree(treePanel, title); // treePanel.getTitle());
2836 treePanel.addWindowListener(new WindowAdapter()
2839 public void windowOpened(WindowEvent e)
2841 if (viewport.sortByTree)
2843 sortByTree(treePanel, title);
2845 super.windowOpened(e);
2849 public void windowClosing(WindowEvent e)
2851 sortByTreeMenu.remove(item);
2856 public boolean sortBy(AlignmentOrder alorder, String undoname)
2858 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2859 if (viewport.applet.debug)
2861 System.err.println("Sorting " + alorder.getOrder().size()
2862 + " in alignment '" + getTitle() + "'");
2864 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2865 if (undoname != null)
2867 addHistoryItem(new OrderCommand(undoname, oldOrder,
2868 viewport.getAlignment()));
2870 alignPanel.paintAlignment(true);
2874 protected void documentation_actionPerformed()
2876 alignPanel.av.applet.openJalviewHelpUrl();
2879 protected void about_actionPerformed()
2882 class AboutPanel extends Canvas
2888 public AboutPanel(String version, String builddate)
2890 this.version = version;
2891 this.builddate = builddate;
2895 public void paint(Graphics g)
2897 g.setColor(Color.white);
2898 g.fillRect(0, 0, getSize().width, getSize().height);
2899 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2900 FontMetrics fm = g.getFontMetrics();
2901 int fh = fm.getHeight();
2903 g.setColor(Color.black);
2904 // TODO: update this text for each release or centrally store it for
2905 // lite and application
2906 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2907 g.drawString(MessageManager.formatMessage(
2908 "label.jalviewLite_release", new String[]
2909 { version }), x, y += fh);
2910 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2911 g.drawString(MessageManager.formatMessage(
2912 "label.jaview_build_date", new String[]
2913 { builddate }), x, y += fh);
2914 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2915 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2917 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2918 x + 50, y += fh + 8);
2920 MessageManager.getString("label.jalview_dev_managers"), x,
2922 g.drawString(MessageManager
2923 .getString("label.jalview_distribution_lists"), x, y += fh);
2924 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2927 MessageManager.getString("label.jalview_cite_1_authors"),
2930 MessageManager.getString("label.jalview_cite_1_title"), x,
2932 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2937 Frame frame = new Frame();
2938 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2940 jalview.bin.JalviewLite.addFrame(frame,
2941 MessageManager.getString("label.jalview"), 580, 220);
2945 public void showURL(String url, String target)
2947 if (viewport.applet == null)
2949 System.out.println("Not running as applet - no browser available.");
2953 viewport.applet.showURL(url, target);
2957 // ////////////////////////////////////////////////////////////////////////////////
2958 // JBuilder Graphics here
2960 MenuBar alignFrameMenuBar = new MenuBar();
2962 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2964 MenuItem loadApplication = new MenuItem(
2965 MessageManager.getString("label.view_full_application"));
2967 MenuItem loadTree = new MenuItem(
2968 MessageManager.getString("label.load_associated_tree"));
2970 MenuItem loadAnnotations = new MenuItem(
2971 MessageManager.getString("label.load_features_annotations"));
2973 MenuItem outputFeatures = new MenuItem(
2974 MessageManager.getString("label.export_features").concat("..."));
2976 MenuItem outputAnnotations = new MenuItem(
2977 MessageManager.getString("label.export_annotations").concat("..."));
2979 MenuItem closeMenuItem = new MenuItem(
2980 MessageManager.getString("action.close"));
2982 MenuItem selectAllSequenceMenuItem = new MenuItem(
2983 MessageManager.getString("action.select_all"));
2985 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2986 MessageManager.getString("action.deselect_all"));
2988 MenuItem invertSequenceMenuItem = new MenuItem(
2989 MessageManager.getString("action.invert_selection"));
2991 MenuItem remove2LeftMenuItem = new MenuItem();
2993 MenuItem remove2RightMenuItem = new MenuItem();
2995 MenuItem removeGappedColumnMenuItem = new MenuItem();
2997 MenuItem removeAllGapsMenuItem = new MenuItem();
2999 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3001 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3003 MenuItem sortPairwiseMenuItem = new MenuItem();
3005 MenuItem sortIDMenuItem = new MenuItem();
3007 MenuItem sortLengthMenuItem = new MenuItem();
3009 MenuItem sortGroupMenuItem = new MenuItem();
3011 MenuItem removeRedundancyMenuItem = new MenuItem();
3013 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3015 MenuItem PCAMenuItem = new MenuItem();
3017 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3019 MenuItem neighbourTreeMenuItem = new MenuItem();
3021 BorderLayout borderLayout1 = new BorderLayout();
3023 public Label statusBar = new Label();
3025 MenuItem clustalColour = new MenuItem();
3027 MenuItem zappoColour = new MenuItem();
3029 MenuItem taylorColour = new MenuItem();
3031 MenuItem hydrophobicityColour = new MenuItem();
3033 MenuItem helixColour = new MenuItem();
3035 MenuItem strandColour = new MenuItem();
3037 MenuItem turnColour = new MenuItem();
3039 MenuItem buriedColour = new MenuItem();
3041 MenuItem purinePyrimidineColour = new MenuItem();
3043 MenuItem RNAInteractionColour = new MenuItem();
3045 MenuItem RNAHelixColour = new MenuItem();
3047 MenuItem userDefinedColour = new MenuItem();
3049 MenuItem PIDColour = new MenuItem();
3051 MenuItem BLOSUM62Colour = new MenuItem();
3053 MenuItem tcoffeeColour = new MenuItem();
3055 MenuItem njTreeBlosumMenuItem = new MenuItem();
3057 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3059 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3061 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3063 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3065 MenuItem alProperties = new MenuItem(
3066 MessageManager.getString("label.alignment_props"));
3068 MenuItem overviewMenuItem = new MenuItem();
3070 MenuItem undoMenuItem = new MenuItem();
3072 MenuItem redoMenuItem = new MenuItem();
3074 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3076 MenuItem noColourmenuItem = new MenuItem();
3078 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3080 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3082 MenuItem findMenuItem = new MenuItem();
3084 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3086 MenuItem nucleotideColour = new MenuItem();
3088 MenuItem deleteGroups = new MenuItem();
3090 MenuItem grpsFromSelection = new MenuItem();
3092 MenuItem createGroup = new MenuItem();
3094 MenuItem unGroup = new MenuItem();
3096 MenuItem delete = new MenuItem();
3098 MenuItem copy = new MenuItem();
3100 MenuItem cut = new MenuItem();
3102 Menu pasteMenu = new Menu();
3104 MenuItem pasteNew = new MenuItem();
3106 MenuItem pasteThis = new MenuItem();
3108 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3110 MenuItem font = new MenuItem();
3112 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3114 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3116 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3118 MenuItem modifyPID = new MenuItem();
3120 MenuItem modifyConservation = new MenuItem();
3122 CheckboxMenuItem autoCalculate = null;
3124 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3125 "Sort Alignment With New Tree", true);
3127 Menu sortByTreeMenu = new Menu();
3129 MenuItem inputText = new MenuItem();
3131 MenuItem documentation = new MenuItem();
3133 MenuItem about = new MenuItem();
3135 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3137 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3139 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3141 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3143 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3145 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3147 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3149 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3151 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3154 * Initialise menus and other items
3158 private void jbInit() throws Exception
3160 setMenuBar(alignFrameMenuBar);
3163 * Configure File menu items and actions
3166 .setLabel(MessageManager.getString("label.input_from_textbox"));
3167 inputText.addActionListener(this);
3168 Menu outputTextboxMenu = new Menu(
3169 MessageManager.getString("label.out_to_textbox"));
3170 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3173 MenuItem item = new MenuItem(
3174 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3176 item.addActionListener(new java.awt.event.ActionListener()
3179 public void actionPerformed(ActionEvent e)
3181 outputText_actionPerformed(e);
3185 outputTextboxMenu.add(item);
3187 closeMenuItem.addActionListener(this);
3188 loadApplication.addActionListener(this);
3189 loadTree.addActionListener(this);
3190 loadAnnotations.addActionListener(this);
3191 outputFeatures.addActionListener(this);
3192 outputAnnotations.addActionListener(this);
3195 * Configure Edit menu items and actions
3197 undoMenuItem.setEnabled(false);
3198 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3199 undoMenuItem.addActionListener(this);
3200 redoMenuItem.setEnabled(false);
3201 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3202 redoMenuItem.addActionListener(this);
3203 copy.setLabel(MessageManager.getString("action.copy"));
3204 copy.addActionListener(this);
3205 cut.setLabel(MessageManager.getString("action.cut"));
3206 cut.addActionListener(this);
3207 delete.setLabel(MessageManager.getString("action.delete"));
3208 delete.addActionListener(this);
3209 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3210 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3211 pasteNew.addActionListener(this);
3212 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3213 pasteThis.addActionListener(this);
3214 remove2LeftMenuItem.setLabel(MessageManager
3215 .getString("action.remove_left"));
3216 remove2LeftMenuItem.addActionListener(this);
3217 remove2RightMenuItem.setLabel(MessageManager
3218 .getString("action.remove_right"));
3219 remove2RightMenuItem.addActionListener(this);
3220 removeGappedColumnMenuItem.setLabel(MessageManager
3221 .getString("action.remove_empty_columns"));
3222 removeGappedColumnMenuItem.addActionListener(this);
3223 removeAllGapsMenuItem.setLabel(MessageManager
3224 .getString("action.remove_all_gaps"));
3225 removeAllGapsMenuItem.addActionListener(this);
3226 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3227 "action.remove_redundancy").concat("..."));
3228 removeRedundancyMenuItem.addActionListener(this);
3231 * Configure Select menu items and actions
3233 findMenuItem.setLabel(MessageManager.getString("action.find"));
3234 findMenuItem.addActionListener(this);
3235 selectAllSequenceMenuItem.addActionListener(this);
3236 deselectAllSequenceMenuItem.addActionListener(this);
3237 invertSequenceMenuItem.setLabel(MessageManager
3238 .getString("action.invert_sequence_selection"));
3239 invertSequenceMenuItem.addActionListener(this);
3240 invertColSel.setLabel(MessageManager
3241 .getString("action.invert_column_selection"));
3242 invertColSel.addActionListener(this);
3243 deleteGroups.setLabel(MessageManager
3244 .getString("action.undefine_groups"));
3245 deleteGroups.addActionListener(this);
3246 grpsFromSelection.setLabel(MessageManager
3247 .getString("action.make_groups_selection"));
3248 grpsFromSelection.addActionListener(this);
3249 createGroup.setLabel(MessageManager.getString("action.create_group"));
3250 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3251 annotationColumnSelection.setLabel("Select by Annotation");
3252 annotationColumnSelection.addActionListener(this);
3255 * Configure View menu items and actions
3257 newView.setLabel(MessageManager.getString("action.new_view"));
3258 newView.addActionListener(this);
3259 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3260 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3261 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3262 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3264 .setLabel(MessageManager.getString("label.selected_columns"));
3265 hideSequences.setLabel(MessageManager
3266 .getString("label.selected_sequences"));
3267 hideAllButSelection.setLabel(MessageManager
3268 .getString("label.all_but_selected_region"));
3269 hideAllSelection.setLabel(MessageManager
3270 .getString("label.selected_region"));
3271 showAllHidden.setLabel(MessageManager
3272 .getString("label.all_sequences_columns"));
3273 showColumns.addActionListener(this);
3274 showSeqs.addActionListener(this);
3275 hideColumns.addActionListener(this);
3276 hideSequences.addActionListener(this);
3277 hideAllButSelection.addActionListener(this);
3278 hideAllSelection.addActionListener(this);
3279 showAllHidden.addActionListener(this);
3280 featureSettings.setLabel(MessageManager
3281 .getString("label.feature_settings"));
3282 featureSettings.addActionListener(this);
3283 sequenceFeatures.setLabel(MessageManager
3284 .getString("label.show_sequence_features"));
3285 sequenceFeatures.addItemListener(this);
3286 sequenceFeatures.setState(false);
3287 followMouseOverFlag.setLabel(MessageManager
3288 .getString("label.automatic_scrolling"));
3289 followMouseOverFlag.addItemListener(this);
3290 alProperties.addActionListener(this);
3291 overviewMenuItem.setLabel(MessageManager
3292 .getString("label.overview_window"));
3293 overviewMenuItem.addActionListener(this);
3296 * Configure Annotations menu items and actions
3298 annotationPanelMenuItem.setLabel(MessageManager
3299 .getString("label.show_annotations"));
3300 annotationPanelMenuItem.addItemListener(this);
3301 showGroupConsensus.setLabel(MessageManager
3302 .getString("label.group_consensus"));
3303 showGroupConservation.setLabel(MessageManager
3304 .getString("label.group_conservation"));
3305 showConsensusHistogram.setLabel(MessageManager
3306 .getString("label.show_consensus_histogram"));
3307 showSequenceLogo.setLabel(MessageManager
3308 .getString("label.show_consensus_logo"));
3309 normSequenceLogo.setLabel(MessageManager
3310 .getString("label.norm_consensus_logo"));
3311 applyAutoAnnotationSettings.setLabel(MessageManager
3312 .getString("label.apply_all_groups"));
3313 applyAutoAnnotationSettings.setState(true);
3314 Menu autoAnnMenu = new Menu(
3315 MessageManager.getString("label.autocalculated_annotation"));
3316 showGroupConsensus.addItemListener(this);
3317 showGroupConservation.addItemListener(this);
3318 showConsensusHistogram.addItemListener(this);
3319 showSequenceLogo.addItemListener(this);
3320 normSequenceLogo.addItemListener(this);
3321 applyAutoAnnotationSettings.addItemListener(this);
3322 showAlignmentAnnotations = new CheckboxMenuItem(
3323 MessageManager.getString("label.show_all_al_annotations"));
3324 showSequenceAnnotations = new CheckboxMenuItem(
3325 MessageManager.getString("label.show_all_seq_annotations"));
3326 sortAnnBySequence = new CheckboxMenuItem(
3327 MessageManager.getString("label.sort_annotations_by_sequence"));
3328 sortAnnByLabel = new CheckboxMenuItem(
3329 MessageManager.getString("label.sort_annotations_by_label"));
3330 showAutoFirst = new CheckboxMenuItem(
3331 MessageManager.getString("label.show_first"));
3332 showAutoLast = new CheckboxMenuItem(
3333 MessageManager.getString("label.show_last"));
3334 showAlignmentAnnotations.addItemListener(this);
3335 showSequenceAnnotations.addItemListener(this);
3336 sortAnnBySequence.addItemListener(this);
3337 sortAnnByLabel.addItemListener(this);
3338 showAutoFirst.addItemListener(this);
3339 showAutoLast.addItemListener(this);
3342 * Configure Format menu items and actions
3344 font.setLabel(MessageManager.getString("action.font"));
3345 font.addActionListener(this);
3346 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3347 scaleAbove.setState(true);
3348 scaleAbove.setEnabled(false);
3349 scaleAbove.addItemListener(this);
3350 scaleLeft.setEnabled(false);
3351 scaleLeft.setState(true);
3352 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3353 scaleLeft.addItemListener(this);
3354 scaleRight.setEnabled(false);
3355 scaleRight.setState(true);
3356 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3357 scaleRight.addItemListener(this);
3358 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3359 viewBoxesMenuItem.setState(true);
3360 viewBoxesMenuItem.addItemListener(this);
3361 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3362 viewTextMenuItem.setState(true);
3363 viewTextMenuItem.addItemListener(this);
3364 colourTextMenuItem.setLabel(MessageManager
3365 .getString("label.colour_text"));
3366 colourTextMenuItem.addItemListener(this);
3367 displayNonconservedMenuItem.setLabel(MessageManager
3368 .getString("label.show_non_conversed"));
3369 displayNonconservedMenuItem.addItemListener(this);
3370 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3371 wrapMenuItem.addItemListener(this);
3372 renderGapsMenuItem.setLabel(MessageManager
3373 .getString("action.show_gaps"));
3374 renderGapsMenuItem.setState(true);
3375 renderGapsMenuItem.addItemListener(this);
3376 centreColumnLabelFlag.setLabel(MessageManager
3377 .getString("label.centre_column_labels"));
3378 centreColumnLabelFlag.addItemListener(this);
3379 seqLimits.setState(true);
3380 seqLimits.setLabel(MessageManager
3381 .getString("label.show_sequence_limits"));
3382 seqLimits.addItemListener(this);
3385 * Configure Colour menu items and actions
3387 applyToAllGroups.setLabel(MessageManager
3388 .getString("label.apply_colour_to_all_groups"));
3389 applyToAllGroups.setState(true);
3390 applyToAllGroups.addItemListener(this);
3391 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3392 clustalColour.addActionListener(this);
3393 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3394 zappoColour.addActionListener(this);
3395 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3396 taylorColour.addActionListener(this);
3397 hydrophobicityColour.setLabel(MessageManager
3398 .getString("label.hydrophobicity"));
3399 hydrophobicityColour.addActionListener(this);
3401 .setLabel(MessageManager.getString("label.helix_propensity"));
3402 helixColour.addActionListener(this);
3403 strandColour.setLabel(MessageManager
3404 .getString("label.strand_propensity"));
3405 strandColour.addActionListener(this);
3406 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3407 turnColour.addActionListener(this);
3408 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3409 buriedColour.addActionListener(this);
3410 purinePyrimidineColour.setLabel(MessageManager
3411 .getString("label.purine_pyrimidine"));
3412 purinePyrimidineColour.addActionListener(this);
3413 RNAInteractionColour.setLabel(MessageManager
3414 .getString("label.rna_interaction"));
3415 RNAInteractionColour.addActionListener(this);
3416 RNAHelixColour.setLabel(MessageManager
3417 .getString("action.by_rna_helixes"));
3418 RNAHelixColour.addActionListener(this);
3419 userDefinedColour.setLabel(MessageManager
3420 .getString("action.user_defined"));
3421 userDefinedColour.addActionListener(this);
3422 PIDColour.setLabel(MessageManager
3423 .getString("label.percentage_identity"));
3424 PIDColour.addActionListener(this);
3425 BLOSUM62Colour.setLabel(MessageManager
3426 .getString("label.blosum62_score"));
3427 BLOSUM62Colour.addActionListener(this);
3429 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3430 // it will be enabled only if a score file is provided
3431 tcoffeeColour.setEnabled(false);
3432 tcoffeeColour.addActionListener(this);
3433 conservationMenuItem.setLabel(MessageManager
3434 .getString("action.by_conservation"));
3435 conservationMenuItem.addItemListener(this);
3436 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3437 noColourmenuItem.addActionListener(this);
3438 abovePIDThreshold.setLabel(MessageManager
3439 .getString("label.above_identity_threshold"));
3440 abovePIDThreshold.addItemListener(this);
3441 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3442 nucleotideColour.addActionListener(this);
3443 modifyPID.setLabel(MessageManager
3444 .getString("label.modify_identity_thereshold"));
3445 modifyPID.addActionListener(this);
3446 modifyConservation.setLabel(MessageManager
3447 .getString("label.modify_conservation_thereshold"));
3448 modifyConservation.addActionListener(this);
3449 annotationColour.setLabel(MessageManager
3450 .getString("action.by_annotation"));
3451 annotationColour.addActionListener(this);
3454 * Configure Calculate menu items and actions
3456 sortPairwiseMenuItem.setLabel(MessageManager
3457 .getString("action.by_pairwise_id"));
3458 sortPairwiseMenuItem.addActionListener(this);
3459 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3460 sortIDMenuItem.addActionListener(this);
3461 sortLengthMenuItem.setLabel(MessageManager
3462 .getString("action.by_length"));
3463 sortLengthMenuItem.addActionListener(this);
3464 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3465 sortGroupMenuItem.addActionListener(this);
3466 pairwiseAlignmentMenuItem.setLabel(MessageManager
3467 .getString("action.pairwise_alignment"));
3468 pairwiseAlignmentMenuItem.addActionListener(this);
3469 PCAMenuItem.setLabel(MessageManager
3470 .getString("label.principal_component_analysis"));
3471 PCAMenuItem.addActionListener(this);
3472 autoCalculate = new CheckboxMenuItem(
3473 MessageManager.getString("label.autocalculate_consensus"), true);
3474 averageDistanceTreeMenuItem.setLabel(MessageManager
3475 .getString("label.average_distance_identity"));
3476 averageDistanceTreeMenuItem.addActionListener(this);
3477 neighbourTreeMenuItem.setLabel(MessageManager
3478 .getString("label.neighbour_joining_identity"));
3479 neighbourTreeMenuItem.addActionListener(this);
3480 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3481 .getString("label.average_distance_bloslum62"));
3482 avDistanceTreeBlosumMenuItem.addActionListener(this);
3483 njTreeBlosumMenuItem.setLabel(MessageManager
3484 .getString("label.neighbour_blosum62"));
3485 njTreeBlosumMenuItem.addActionListener(this);
3486 sortByTreeMenu.setLabel(MessageManager
3487 .getString("action.by_tree_order"));
3488 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3489 Menu calculateTreeMenu = new Menu(
3490 MessageManager.getString("action.calculate_tree"));
3491 autoCalculate.addItemListener(this);
3492 sortByTree.addItemListener(this);
3495 * Configure Help menu items and actions
3497 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3498 documentation.setLabel(MessageManager.getString("label.documentation"));
3499 documentation.addActionListener(this);
3500 about.setLabel(MessageManager.getString("label.about"));
3501 about.addActionListener(this);
3504 * Add top level menus to frame
3506 alignFrameMenuBar.add(fileMenu);
3507 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3508 alignFrameMenuBar.add(editMenu);
3509 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3510 alignFrameMenuBar.add(selectMenu);
3511 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3512 alignFrameMenuBar.add(viewMenu);
3513 Menu annotationsMenu = new Menu(
3514 MessageManager.getString("action.annotations"));
3515 alignFrameMenuBar.add(annotationsMenu);
3516 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3517 alignFrameMenuBar.add(formatMenu);
3518 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3519 alignFrameMenuBar.add(colourMenu);
3520 Menu calculateMenu = new Menu(
3521 MessageManager.getString("action.calculate"));
3522 alignFrameMenuBar.add(calculateMenu);
3523 alignFrameMenuBar.add(helpMenu);
3528 fileMenu.add(inputText);
3529 fileMenu.add(loadTree);
3530 fileMenu.add(loadAnnotations);
3531 fileMenu.addSeparator();
3532 fileMenu.add(outputTextboxMenu);
3533 fileMenu.add(outputFeatures);
3534 fileMenu.add(outputAnnotations);
3535 if (jalviewServletURL != null)
3537 fileMenu.add(loadApplication);
3539 fileMenu.addSeparator();
3540 fileMenu.add(closeMenuItem);
3545 editMenu.add(undoMenuItem);
3546 editMenu.add(redoMenuItem);
3549 pasteMenu.add(pasteNew);
3550 pasteMenu.add(pasteThis);
3551 editMenu.add(pasteMenu);
3552 editMenu.add(delete);
3553 editMenu.addSeparator();
3554 editMenu.add(remove2LeftMenuItem);
3555 editMenu.add(remove2RightMenuItem);
3556 editMenu.add(removeGappedColumnMenuItem);
3557 editMenu.add(removeAllGapsMenuItem);
3558 editMenu.add(removeRedundancyMenuItem);
3563 selectMenu.add(findMenuItem);
3564 selectMenu.addSeparator();
3565 selectMenu.add(selectAllSequenceMenuItem);
3566 selectMenu.add(deselectAllSequenceMenuItem);
3567 selectMenu.add(invertSequenceMenuItem);
3568 selectMenu.add(invertColSel);
3569 selectMenu.add(createGroup);
3570 selectMenu.add(unGroup);
3571 selectMenu.add(grpsFromSelection);
3572 selectMenu.add(deleteGroups);
3573 selectMenu.add(annotationColumnSelection);
3578 viewMenu.add(newView);
3579 viewMenu.addSeparator();
3580 showMenu.add(showColumns);
3581 showMenu.add(showSeqs);
3582 showMenu.add(showAllHidden);
3583 viewMenu.add(showMenu);
3584 hideMenu.add(hideColumns);
3585 hideMenu.add(hideSequences);
3586 hideMenu.add(hideAllSelection);
3587 hideMenu.add(hideAllButSelection);
3588 viewMenu.add(hideMenu);
3589 viewMenu.addSeparator();
3590 viewMenu.add(followMouseOverFlag);
3591 viewMenu.addSeparator();
3592 viewMenu.add(sequenceFeatures);
3593 viewMenu.add(featureSettings);
3594 viewMenu.addSeparator();
3595 viewMenu.add(alProperties);
3596 viewMenu.addSeparator();
3597 viewMenu.add(overviewMenuItem);
3602 annotationsMenu.add(annotationPanelMenuItem);
3603 annotationsMenu.addSeparator();
3604 annotationsMenu.add(showAlignmentAnnotations);
3605 annotationsMenu.add(showSequenceAnnotations);
3606 annotationsMenu.add(sortAnnBySequence);
3607 annotationsMenu.add(sortAnnByLabel);
3608 annotationsMenu.addSeparator();
3609 autoAnnMenu.add(showAutoFirst);
3610 autoAnnMenu.add(showAutoLast);
3611 autoAnnMenu.addSeparator();
3612 autoAnnMenu.add(applyAutoAnnotationSettings);
3613 autoAnnMenu.add(showConsensusHistogram);
3614 autoAnnMenu.add(showSequenceLogo);
3615 autoAnnMenu.add(normSequenceLogo);
3616 autoAnnMenu.addSeparator();
3617 autoAnnMenu.add(showGroupConservation);
3618 autoAnnMenu.add(showGroupConsensus);
3619 annotationsMenu.add(autoAnnMenu);
3624 formatMenu.add(font);
3625 formatMenu.add(seqLimits);
3626 formatMenu.add(wrapMenuItem);
3627 formatMenu.add(scaleAbove);
3628 formatMenu.add(scaleLeft);
3629 formatMenu.add(scaleRight);
3630 formatMenu.add(viewBoxesMenuItem);
3631 formatMenu.add(viewTextMenuItem);
3632 formatMenu.add(colourTextMenuItem);
3633 formatMenu.add(displayNonconservedMenuItem);
3634 formatMenu.add(renderGapsMenuItem);
3635 formatMenu.add(centreColumnLabelFlag);
3640 colourMenu.add(applyToAllGroups);
3641 colourMenu.addSeparator();
3642 colourMenu.add(noColourmenuItem);
3643 colourMenu.add(clustalColour);
3644 colourMenu.add(BLOSUM62Colour);
3645 colourMenu.add(PIDColour);
3646 colourMenu.add(zappoColour);
3647 colourMenu.add(taylorColour);
3648 colourMenu.add(hydrophobicityColour);
3649 colourMenu.add(helixColour);
3650 colourMenu.add(strandColour);
3651 colourMenu.add(turnColour);
3652 colourMenu.add(buriedColour);
3653 colourMenu.add(nucleotideColour);
3654 colourMenu.add(purinePyrimidineColour);
3655 // colourMenu.add(RNAInteractionColour);
3656 colourMenu.add(tcoffeeColour);
3657 colourMenu.add(userDefinedColour);
3658 colourMenu.addSeparator();
3659 colourMenu.add(conservationMenuItem);
3660 colourMenu.add(modifyConservation);
3661 colourMenu.add(abovePIDThreshold);
3662 colourMenu.add(modifyPID);
3663 colourMenu.add(annotationColour);
3664 colourMenu.add(RNAHelixColour);
3669 sortMenu.add(sortIDMenuItem);
3670 sortMenu.add(sortLengthMenuItem);
3671 sortMenu.add(sortByTreeMenu);
3672 sortMenu.add(sortGroupMenuItem);
3673 sortMenu.add(sortPairwiseMenuItem);
3674 calculateMenu.add(sortMenu);
3675 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3676 calculateTreeMenu.add(neighbourTreeMenuItem);
3677 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3678 calculateTreeMenu.add(njTreeBlosumMenuItem);
3679 calculateMenu.add(calculateTreeMenu);
3680 calculateMenu.addSeparator();
3681 calculateMenu.add(pairwiseAlignmentMenuItem);
3682 calculateMenu.add(PCAMenuItem);
3683 calculateMenu.add(autoCalculate);
3684 calculateMenu.add(sortByTree);
3689 helpMenu.add(documentation);
3690 helpMenu.add(about);
3695 statusBar.setBackground(Color.white);
3696 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3697 statusBar.setText(MessageManager.getString("label.status_bar"));
3698 this.add(statusBar, BorderLayout.SOUTH);
3701 public void setStatus(String string)
3703 statusBar.setText(string);
3706 MenuItem featureSettings = new MenuItem();
3708 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3710 MenuItem annotationColour = new MenuItem();
3712 MenuItem annotationColumnSelection = new MenuItem();
3714 MenuItem invertColSel = new MenuItem();
3716 MenuItem showColumns = new MenuItem();
3718 MenuItem showSeqs = new MenuItem();
3720 MenuItem hideColumns = new MenuItem();
3722 MenuItem hideSequences = new MenuItem();
3724 MenuItem hideAllButSelection = new MenuItem();
3726 MenuItem hideAllSelection = new MenuItem();
3728 MenuItem showAllHidden = new MenuItem();
3730 MenuItem newView = new MenuItem();
3732 private CheckboxMenuItem showAlignmentAnnotations;
3734 private CheckboxMenuItem showSequenceAnnotations;
3736 private CheckboxMenuItem sortAnnBySequence;
3738 private CheckboxMenuItem sortAnnByLabel;
3740 private CheckboxMenuItem showAutoFirst;
3742 private CheckboxMenuItem showAutoLast;
3744 private SplitFrame splitFrame;
3747 * Attach the alignFrame panels after embedding menus, if necessary. This used
3748 * to be called setEmbedded, but is now creates the dropdown menus in a
3749 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3751 * @param reallyEmbedded
3752 * true to attach the view to the applet area on the page rather than
3755 public void createAlignFrameWindow(boolean reallyEmbedded)
3759 embedAlignFrameInApplet(viewport.applet);
3764 // test and embed menu bar if necessary.
3766 if (embedMenuIfNeeded(alignPanel))
3769 * adjust for status bar height too. ? pointless as overridden by layout
3772 alignPanel.setSize(getSize().width,
3773 getSize().height - statusBar.getHeight());
3775 add(statusBar, BorderLayout.SOUTH);
3776 add(alignPanel, BorderLayout.CENTER);
3777 // and register with the applet so it can pass external API calls to us
3778 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3785 * Add the components of this AlignFrame to the applet container.
3789 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3792 // Explicitly build the embedded menu panel for the on-page applet
3794 // view cannot be closed if its actually on the page
3795 fileMenu.remove(closeMenuItem);
3796 fileMenu.remove(3); // Remove Separator
3797 // construct embedded menu, using default font
3798 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3799 // and actually add the components to the applet area
3800 theApplet.setLayout(new BorderLayout());
3801 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3802 theApplet.add(statusBar, BorderLayout.SOUTH);
3803 // TODO should size be left to the layout manager?
3804 alignPanel.setSize(theApplet.getSize().width,
3805 theApplet.getSize().height - embeddedMenu.getHeight()
3806 - statusBar.getHeight());
3807 theApplet.add(alignPanel, BorderLayout.CENTER);
3808 final AlignFrame me = this;
3809 theApplet.addFocusListener(new FocusListener()
3813 public void focusLost(FocusEvent e)
3815 if (theApplet.currentAlignFrame == me)
3817 theApplet.currentAlignFrame = null;
3822 public void focusGained(FocusEvent e)
3824 theApplet.currentAlignFrame = me;
3827 theApplet.validate();
3831 * create a new binding between structures in an existing jmol viewer instance
3832 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3833 * this does not open a new Jmol window, or modify the display of the
3834 * structures in the original jmol window. Note This method doesn't work
3835 * without an additional javascript library to exchange messages between the
3836 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3839 * JmolViewer instance
3840 * @param sequenceIds
3841 * - sequence Ids to search for associations
3843 public SequenceStructureBinding addStructureViewInstance(
3844 Object jmolviewer, String[] sequenceIds)
3846 org.jmol.api.JmolViewer viewer = null;
3849 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3850 } catch (ClassCastException ex)
3852 System.err.println("Unsupported viewer object :"
3853 + jmolviewer.getClass());
3857 System.err.println("Can't use this object as a structure viewer:"
3858 + jmolviewer.getClass());
3861 SequenceI[] seqs = null;
3862 if (sequenceIds == null || sequenceIds.length == 0)
3864 seqs = viewport.getAlignment().getSequencesArray();
3868 Vector sqi = new Vector();
3869 AlignmentI al = viewport.getAlignment();
3870 for (int sid = 0; sid < sequenceIds.length; sid++)
3872 SequenceI sq = al.findName(sequenceIds[sid]);
3880 seqs = new SequenceI[sqi.size()];
3881 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3883 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3891 AAStructureBindingModel jmv = null;
3892 // TODO: search for a jmv that involves viewer
3894 { // create a new viewer/jalview binding.
3895 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3903 * bind a pdb file to a sequence in the current view
3906 * - sequenceId within the dataset.
3907 * @param pdbEntryString
3908 * - the short name for the PDB file
3910 * - pdb file - either a URL or a valid PDB file.
3911 * @return true if binding was as success TODO: consider making an exception
3912 * structure for indicating when PDB parsing or sequenceId location
3915 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3918 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3919 boolean needtoadd = false;
3920 if (toaddpdb != null)
3922 Vector pdbe = toaddpdb.getPDBId();
3923 PDBEntry pdbentry = null;
3924 if (pdbe != null && pdbe.size() > 0)
3926 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3928 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3929 if (!pdbentry.getId().equals(pdbEntryString)
3930 && !pdbentry.getFile().equals(pdbFile))
3940 if (pdbentry == null)
3942 pdbentry = new PDBEntry();
3943 pdbentry.setId(pdbEntryString);
3944 pdbentry.setFile(pdbFile);
3945 needtoadd = true; // add this new entry to sequence.
3947 // resolve data source
3948 // TODO: this code should be a refactored to an io package
3949 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3950 if (protocol == null)
3956 // make a note of the access mode and add
3957 if (pdbentry.getProperty() == null)
3959 pdbentry.setProperty(new Hashtable());
3961 pdbentry.getProperty().put("protocol", protocol);
3962 toaddpdb.addPDBId(pdbentry);
3963 alignPanel.getStructureSelectionManager()
3964 .registerPDBEntry(pdbentry);
3970 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3974 Vector sequences = new Vector();
3975 for (int i = 0; i < seqs.length; i++)
3977 if (seqs[i] != null)
3979 sequences.addElement(new Object[]
3980 { seqs[i], (chains != null) ? chains[i] : null });
3983 seqs = new SequenceI[sequences.size()];
3984 chains = new String[sequences.size()];
3985 for (int i = 0, isize = sequences.size(); i < isize; i++)
3987 Object[] oj = (Object[]) sequences.elementAt(i);
3989 seqs[i] = (SequenceI) oj[0];
3990 chains[i] = (String) oj[1];
3998 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3999 SequenceI[] seqs, String[] chains, String protocol)
4001 // Scrub any null sequences from the array
4002 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4003 seqs = (SequenceI[]) sqch[0];
4004 chains = (String[]) sqch[1];
4005 if (seqs == null || seqs.length == 0)
4008 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4010 if (protocol == null || protocol.trim().length() == 0
4011 || protocol.equals("null"))
4013 protocol = (String) pdb.getProperty().get("protocol");
4014 if (protocol == null)
4016 System.err.println("Couldn't work out protocol to open structure: "
4021 if (applet.useXtrnalSviewer)
4023 // register the association(s) and quit, don't create any windows.
4024 if (StructureSelectionManager.getStructureSelectionManager(applet)
4025 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4027 System.err.println("Failed to map " + pdb.getFile() + " ("
4028 + protocol + ") to any sequences");
4032 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4034 // can only do alignments with Jmol
4035 // find the last jmol window assigned to this alignment
4036 jalview.appletgui.AppletJmol ajm = null, tajm;
4037 Vector jmols = applet
4038 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4039 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4041 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4042 if (tajm.ap.alignFrame == this)
4051 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4052 // try and add the pdb structure
4057 // otherwise, create a new window
4058 if (applet.jmolAvailable)
4060 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4062 applet.lastFrameX += 40;
4063 applet.lastFrameY += 40;
4067 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4072 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4073 SequenceI[][] seqs, String[][] chains, String[] protocols)
4075 // TODO Auto-generated method stub
4076 System.err.println("Aligned Structure View: Not yet implemented.");
4080 * modify the current selection, providing the user has not made a selection
4084 * - sequences from this alignment
4086 * - columns to be selected on the alignment
4088 public void select(SequenceGroup sel, ColumnSelection csel)
4090 alignPanel.seqPanel.selection(sel, csel, null);
4093 public void scrollTo(int row, int column)
4095 alignPanel.seqPanel.scrollTo(row, column);
4098 public void scrollToRow(int row)
4100 alignPanel.seqPanel.scrollToRow(row);
4103 public void scrollToColumn(int column)
4105 alignPanel.seqPanel.scrollToColumn(column);
4109 * @return the alignments unique ID.
4111 public String getSequenceSetId()
4113 return viewport.getSequenceSetId();
4117 * Load the (T-Coffee) score file from the specified url
4120 * File/URL/T-COFFEE score file contents
4121 * @throws IOException
4122 * @return true if alignment was annotated with data from source
4124 public boolean loadScoreFile(String source) throws IOException
4127 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4128 AppletFormatAdapter.checkProtocol(source));
4129 if (!file.isValid())
4131 // TODO: raise dialog for gui
4132 System.err.println("Problems parsing T-Coffee scores: "
4133 + file.getWarningMessage());
4134 System.err.println("Origin was:\n" + source);
4139 * check that the score matrix matches the alignment dimensions
4142 if ((aln = viewport.getAlignment()) != null
4143 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4146 // TODO: raise a dialog box here rather than bomb out.
4148 .println("The scores matrix does not match the alignment dimensions");
4152 // TODO add parameter to indicate if matching should be done
4153 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4155 alignPanel.fontChanged();
4156 tcoffeeColour.setEnabled(true);
4157 // switch to this color
4158 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4163 System.err.println("Problems resolving T-Coffee scores:");
4164 if (file.getWarningMessage() != null)
4166 System.err.println(file.getWarningMessage());
4172 public SplitFrame getSplitFrame()
4174 return this.splitFrame;
4177 public void setSplitFrame(SplitFrame sf)
4179 this.splitFrame = sf;