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);
1317 FeatureRenderer fr = this.alignPanel.cloneFeatureRenderer();
1318 viewport.setFeatureRenderer(fr);
1319 viewport.setIncludeHiddenRegion(false);
1320 cap.setText(new AppletFormatAdapter(viewport).formatSequences(
1321 e.getActionCommand(), viewport.getAlignment(),
1322 viewport.getShowJVSuffix()));
1325 public void loadAnnotations()
1327 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1328 cap.setText(MessageManager
1329 .getString("label.paste_features_annotations_Tcoffee_here"));
1330 cap.setAnnotationImport();
1331 Frame frame = new Frame();
1333 jalview.bin.JalviewLite.addFrame(frame,
1334 MessageManager.getString("action.paste_annotations"), 400, 300);
1338 public String outputAnnotations(boolean displayTextbox)
1340 String annotation = new AnnotationFile()
1341 .printAnnotationsForView(viewport);
1345 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1346 Frame frame = new Frame();
1348 jalview.bin.JalviewLite.addFrame(frame,
1349 MessageManager.getString("label.annotations"), 600, 500);
1350 cap.setText(annotation);
1356 private Map<String,Object> getDisplayedFeatureCols()
1358 if (alignPanel.getFeatureRenderer() != null
1359 && viewport.getFeaturesDisplayed()!= null)
1361 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1367 public String outputFeatures(boolean displayTextbox, String format)
1370 if (format.equalsIgnoreCase("Jalview"))
1372 features = new FeaturesFile().printJalviewFormat(viewport
1373 .getAlignment().getSequencesArray(),
1374 getDisplayedFeatureCols());
1378 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1379 .getSequencesArray(), getDisplayedFeatureCols());
1384 boolean frimport = false;
1385 if (features == null || features.equals("No Features Visible"))
1387 features = "# No features visible - paste some and import them here.";
1391 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1394 cap.setAnnotationImport();
1396 Frame frame = new Frame();
1398 jalview.bin.JalviewLite.addFrame(frame,
1399 MessageManager.getString("label.features"), 600, 500);
1400 cap.setText(features);
1404 if (features == null)
1413 void launchFullApplication()
1415 StringBuffer url = new StringBuffer(jalviewServletURL);
1417 // allow servlet parameters to be passed in applet parameter
1418 String firstSep = url.lastIndexOf("?") > url.lastIndexOf("/") ? "&"
1420 url.append(firstSep);
1423 + appendProtocol(viewport.applet.getParameter("file")));
1425 if (viewport.applet.getParameter("features") != null)
1427 url.append("&features=");
1428 url.append(appendProtocol(viewport.applet.getParameter("features")));
1431 if (viewport.applet.getParameter("annotations") != null)
1433 url.append("&annotations=");
1434 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1437 if (viewport.applet.getParameter("jnetfile") != null)
1439 url.append("&annotations=");
1440 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1443 if (viewport.applet.getParameter("defaultColour") != null)
1445 url.append("&colour="
1446 + removeWhiteSpace(viewport.applet
1447 .getParameter("defaultColour")));
1450 if (viewport.applet.getParameter("userDefinedColour") != null)
1452 url.append("&colour="
1453 + removeWhiteSpace(viewport.applet
1454 .getParameter("userDefinedColour")));
1456 if (viewport.applet.getParameter("tree") != null)
1459 + appendProtocol(viewport.applet.getParameter("tree")));
1461 if (viewport.applet.getParameter("treeFile") != null)
1464 + appendProtocol(viewport.applet.getParameter("treeFile")));
1467 showURL(url.toString(), "FULL_APP");
1470 String removeWhiteSpace(String colour)
1472 StringBuffer sb = new StringBuffer();
1473 for (int i = 0; i < colour.length(); i++)
1475 if (Character.isWhitespace(colour.charAt(i)))
1481 sb.append(colour.charAt(i));
1485 return sb.toString();
1488 String appendProtocol(String url)
1493 url = URLEncoder.encode(url);
1496 * When we finally deprecate 1.1 compatibility, we can start to use
1497 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1498 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1499 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1500 * ex.printStackTrace(); }
1502 catch (java.net.MalformedURLException ex)
1504 url = viewport.applet.getCodeBase() + url;
1509 public void closeMenuItem_actionPerformed()
1511 PaintRefresher.RemoveComponent(alignPanel);
1512 if (alignPanel.seqPanel != null
1513 && alignPanel.seqPanel.seqCanvas != null)
1515 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1517 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1519 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1522 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1537 void updateEditMenuBar()
1540 if (viewport.getHistoryList().size() > 0)
1542 undoMenuItem.setEnabled(true);
1543 CommandI command = viewport.getHistoryList().peek();
1544 undoMenuItem.setLabel(MessageManager.formatMessage(
1545 "label.undo_command", new Object[]
1546 { command.getDescription() }));
1550 undoMenuItem.setEnabled(false);
1551 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1554 if (viewport.getRedoList().size() > 0)
1556 redoMenuItem.setEnabled(true);
1558 CommandI command = viewport.getRedoList().peek();
1559 redoMenuItem.setLabel(MessageManager.formatMessage(
1560 "label.redo_command", new Object[]
1561 { command.getDescription() }));
1565 redoMenuItem.setEnabled(false);
1566 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1574 public void addHistoryItem(CommandI command)
1576 if (command.getSize() > 0)
1578 viewport.addToHistoryList(command);
1579 viewport.clearRedoList();
1580 updateEditMenuBar();
1581 viewport.updateHiddenColumns();
1586 * TODO: JAL-1104 DOCUMENT ME!
1591 protected void undoMenuItem_actionPerformed()
1593 if (viewport.getHistoryList().isEmpty())
1598 CommandI command = viewport.getHistoryList().pop();
1599 viewport.addToRedoList(command);
1600 command.undoCommand(null);
1602 AlignmentViewport originalSource = getOriginatingSource(command);
1604 if (originalSource != viewport)
1607 .println("Warning: Viewport object mismatch whilst undoing");
1609 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1610 // viewport.getColumnSelection().getHiddenColumns()
1612 updateEditMenuBar();
1613 originalSource.firePropertyChange("alignment", null, originalSource
1614 .getAlignment().getSequences());
1618 * TODO: JAL-1104 DOCUMENT ME!
1623 protected void redoMenuItem_actionPerformed()
1625 if (viewport.getRedoList().isEmpty())
1630 CommandI command = viewport.getRedoList().pop();
1631 viewport.addToHistoryList(command);
1632 command.doCommand(null);
1634 AlignmentViewport originalSource = getOriginatingSource(command);
1636 if (originalSource != viewport)
1639 .println("Warning: Viewport object mismatch whilst re-doing");
1641 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1642 // viewport.getColumnSelection().getHiddenColumns()
1645 updateEditMenuBar();
1646 originalSource.firePropertyChange("alignment", null, originalSource
1647 .getAlignment().getSequences());
1650 AlignmentViewport getOriginatingSource(CommandI command)
1652 AlignmentViewport originalSource = null;
1653 // For sequence removal and addition, we need to fire
1654 // the property change event FROM the viewport where the
1655 // original alignment was altered
1656 AlignmentI al = null;
1657 if (command instanceof EditCommand)
1659 EditCommand editCommand = (EditCommand) command;
1660 al = editCommand.getAlignment();
1661 Vector comps = (Vector) PaintRefresher.components.get(viewport
1662 .getSequenceSetId());
1663 for (int i = 0; i < comps.size(); i++)
1665 if (comps.elementAt(i) instanceof AlignmentPanel)
1667 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1669 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1676 if (originalSource == null)
1678 // The original view is closed, we must validate
1679 // the current view against the closed view first
1682 PaintRefresher.validateSequences(al, viewport.getAlignment());
1685 originalSource = viewport;
1688 return originalSource;
1692 * Move the currently selected sequences up or down one position in the
1697 public void moveSelectedSequences(boolean up)
1699 SequenceGroup sg = viewport.getSelectionGroup();
1704 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1705 up ? null : viewport.getHiddenRepSequences(), up);
1706 alignPanel.paintAlignment(true);
1709 * Also move cDNA/protein complement sequences
1711 AlignViewportI complement = viewport.getCodingComplement();
1712 if (complement != null)
1714 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1715 viewport, complement);
1716 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1717 up ? null : complement.getHiddenRepSequences(), up);
1718 // TODO need to trigger a repaint of the complementary panel - how?
1719 // would prefer to handle in SplitFrame but it is not overriding key
1724 synchronized void slideSequences(boolean right, int size)
1726 List<SequenceI> sg = new Vector<SequenceI>();
1727 if (viewport.cursorMode)
1729 sg.add(viewport.getAlignment().getSequenceAt(
1730 alignPanel.seqPanel.seqCanvas.cursorY));
1732 else if (viewport.getSelectionGroup() != null
1733 && viewport.getSelectionGroup().getSize() != viewport
1734 .getAlignment().getHeight())
1736 sg = viewport.getSelectionGroup().getSequences(
1737 viewport.getHiddenRepSequences());
1745 Vector<SequenceI> invertGroup = new Vector();
1747 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1749 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1751 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1755 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1757 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1759 for (int i = 0; i < invertGroup.size(); i++)
1761 seqs2[i] = invertGroup.elementAt(i);
1764 SlideSequencesCommand ssc;
1767 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1768 size, viewport.getGapCharacter());
1772 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1773 size, viewport.getGapCharacter());
1776 int groupAdjustment = 0;
1777 if (ssc.getGapsInsertedBegin() && right)
1779 if (viewport.cursorMode)
1781 alignPanel.seqPanel.moveCursor(size, 0);
1785 groupAdjustment = size;
1788 else if (!ssc.getGapsInsertedBegin() && !right)
1790 if (viewport.cursorMode)
1792 alignPanel.seqPanel.moveCursor(-size, 0);
1796 groupAdjustment = -size;
1800 if (groupAdjustment != 0)
1802 viewport.getSelectionGroup().setStartRes(
1803 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1804 viewport.getSelectionGroup().setEndRes(
1805 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1808 boolean appendHistoryItem = false;
1809 Deque<CommandI> historyList = viewport.getHistoryList();
1810 if (historyList != null && historyList.size() > 0
1811 && historyList.peek() instanceof SlideSequencesCommand)
1813 appendHistoryItem = ssc
1814 .appendSlideCommand((SlideSequencesCommand) historyList
1818 if (!appendHistoryItem)
1820 addHistoryItem(ssc);
1826 static StringBuffer copiedSequences;
1828 static Vector copiedHiddenColumns;
1830 protected void copy_actionPerformed()
1832 if (viewport.getSelectionGroup() == null)
1837 SequenceGroup sg = viewport.getSelectionGroup();
1838 copiedSequences = new StringBuffer();
1839 Map<Integer, SequenceI> orderedSeqs = new HashMap<Integer, SequenceI>();
1840 for (int i = 0; i < sg.getSize(); i++)
1842 SequenceI seq = sg.getSequenceAt(i);
1843 int index = viewport.getAlignment().findIndex(seq);
1844 orderedSeqs.put(index, seq);
1847 int index = 0, startRes, endRes;
1850 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1852 copiedHiddenColumns = new Vector();
1853 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1854 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1856 copiedHiddenColumns.addElement(new int[]
1857 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1862 copiedHiddenColumns = null;
1865 for (int i = 0; i < sg.getSize(); i++)
1867 SequenceI seq = null;
1871 if (orderedSeqs.containsKey(index))
1873 seq = orderedSeqs.get(index);
1884 // Returns residue following index if gap
1885 startRes = seq.findPosition(sg.getStartRes());
1888 // Need to find the residue preceeding index if gap
1891 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1893 ch = seq.getCharAt(j);
1894 if (!jalview.util.Comparison.isGap((ch)))
1902 endRes += seq.getStart() - 1;
1905 copiedSequences.append(seq.getName()
1911 + seq.getSequenceAsString(sg.getStartRes(),
1912 sg.getEndRes() + 1) + "\n");
1917 protected void pasteNew_actionPerformed()
1922 protected void pasteThis_actionPerformed()
1927 void paste(boolean newAlignment)
1932 if (copiedSequences == null)
1937 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1938 Vector seqs = new Vector();
1939 while (st.hasMoreElements())
1941 String name = st.nextToken();
1942 int start = Integer.parseInt(st.nextToken());
1943 int end = Integer.parseInt(st.nextToken());
1944 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1946 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1947 for (int i = 0; i < seqs.size(); i++)
1949 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1954 String newtitle = MessageManager.getString("label.copied_sequences");
1955 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1957 newtitle = getTitle();
1961 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1963 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1964 viewport.applet, newtitle, false);
1965 if (copiedHiddenColumns != null)
1967 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1969 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1970 af.viewport.hideColumns(region[0], region[1]);
1974 jalview.bin.JalviewLite.addFrame(af, newtitle, frameWidth,
1979 addSequences(newSeqs);
1982 } catch (Exception ex)
1984 } // could be anything being pasted in here
1988 void addSequences(SequenceI[] seqs)
1990 for (int i = 0; i < seqs.length; i++)
1992 viewport.getAlignment().addSequence(seqs[i]);
1996 addHistoryItem(new EditCommand(
1997 MessageManager.getString("label.add_sequences"), Action.PASTE,
1998 seqs, 0, viewport.getAlignment().getWidth(),
1999 viewport.getAlignment()));
2001 viewport.setEndSeq(viewport.getAlignment().getHeight());
2002 viewport.getAlignment().getWidth();
2003 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2008 protected void cut_actionPerformed()
2010 copy_actionPerformed();
2011 delete_actionPerformed();
2014 protected void delete_actionPerformed()
2017 SequenceGroup sg = viewport.getSelectionGroup();
2023 Vector seqs = new Vector();
2025 for (int i = 0; i < sg.getSize(); i++)
2027 seq = sg.getSequenceAt(i);
2028 seqs.addElement(seq);
2031 // If the cut affects all sequences, remove highlighted columns
2032 if (sg.getSize() == viewport.getAlignment().getHeight())
2034 viewport.getColumnSelection().removeElements(sg.getStartRes(),
2035 sg.getEndRes() + 1);
2038 SequenceI[] cut = new SequenceI[seqs.size()];
2039 for (int i = 0; i < seqs.size(); i++)
2041 cut[i] = (SequenceI) seqs.elementAt(i);
2045 * //ADD HISTORY ITEM
2047 addHistoryItem(new EditCommand(
2048 MessageManager.getString("label.cut_sequences"), Action.CUT,
2049 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
2050 viewport.getAlignment()));
2052 viewport.setSelectionGroup(null);
2053 viewport.getAlignment().deleteGroup(sg);
2055 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2058 if (viewport.getAlignment().getHeight() < 1)
2060 this.setVisible(false);
2062 viewport.sendSelection();
2066 * group consensus toggled
2069 protected void showGroupConsensus_actionPerformed()
2071 viewport.setShowGroupConsensus(showGroupConsensus.getState());
2072 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2077 * group conservation toggled.
2079 protected void showGroupConservation_actionPerformed()
2081 viewport.setShowGroupConservation(showGroupConservation.getState());
2082 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2089 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
2090 * .event.ActionEvent)
2092 protected void showConsensusHistogram_actionPerformed()
2094 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
2095 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2102 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2103 * .event.ActionEvent)
2105 protected void showSequenceLogo_actionPerformed()
2107 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2108 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2111 protected void normSequenceLogo_actionPerformed()
2113 showSequenceLogo.setState(true);
2114 viewport.setShowSequenceLogo(true);
2115 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2116 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2119 protected void applyAutoAnnotationSettings_actionPerformed()
2121 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2124 protected void makeGrpsFromSelection_actionPerformed()
2126 if (avc.makeGroupsFromSelection())
2128 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2129 alignPanel.updateAnnotation();
2130 alignPanel.paintAlignment(true);
2134 protected void createGroup_actionPerformed()
2139 protected void unGroup_actionPerformed()
2143 alignPanel.alignmentChanged();
2147 protected void deleteGroups_actionPerformed()
2149 if (avc.deleteGroups())
2151 alignPanel.alignmentChanged();
2155 public void selectAllSequenceMenuItem_actionPerformed()
2157 SequenceGroup sg = new SequenceGroup();
2158 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2160 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2162 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2163 viewport.setSelectionGroup(sg);
2164 alignPanel.paintAlignment(true);
2165 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2166 viewport.sendSelection();
2169 public void deselectAllSequenceMenuItem_actionPerformed()
2171 if (viewport.cursorMode)
2173 alignPanel.seqPanel.keyboardNo1 = null;
2174 alignPanel.seqPanel.keyboardNo2 = null;
2176 viewport.setSelectionGroup(null);
2177 viewport.getColumnSelection().clear();
2178 viewport.setSelectionGroup(null);
2179 alignPanel.idPanel.idCanvas.searchResults = null;
2180 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2181 alignPanel.paintAlignment(true);
2182 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2183 viewport.sendSelection();
2186 public void invertSequenceMenuItem_actionPerformed()
2188 SequenceGroup sg = viewport.getSelectionGroup();
2189 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2191 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2194 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2195 viewport.sendSelection();
2198 public void invertColSel_actionPerformed()
2200 viewport.invertColumnSelection();
2201 alignPanel.paintAlignment(true);
2202 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2203 viewport.sendSelection();
2206 void trimAlignment(boolean trimLeft)
2208 ColumnSelection colSel = viewport.getColumnSelection();
2211 if (colSel.size() > 0)
2215 column = colSel.getMin();
2219 column = colSel.getMax();
2223 if (viewport.getSelectionGroup() != null)
2225 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2226 viewport.getHiddenRepSequences());
2230 seqs = viewport.getAlignment().getSequencesArray();
2233 TrimRegionCommand trimRegion;
2236 trimRegion = new TrimRegionCommand("Remove Left",
2237 TrimRegionCommand.TRIM_LEFT, seqs, column,
2238 viewport.getAlignment(), viewport.getColumnSelection(),
2239 viewport.getSelectionGroup());
2240 viewport.setStartRes(0);
2244 trimRegion = new TrimRegionCommand("Remove Right",
2245 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2246 viewport.getAlignment(), viewport.getColumnSelection(),
2247 viewport.getSelectionGroup());
2250 statusBar.setText(MessageManager.formatMessage(
2251 "label.removed_columns", new String[]
2252 { Integer.valueOf(trimRegion.getSize()).toString() }));
2253 addHistoryItem(trimRegion);
2255 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2257 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2258 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2260 viewport.getAlignment().deleteGroup(sg);
2264 viewport.firePropertyChange("alignment", null, viewport
2265 .getAlignment().getSequences());
2269 public void removeGappedColumnMenuItem_actionPerformed()
2271 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2274 if (viewport.getSelectionGroup() != null)
2276 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2277 viewport.getHiddenRepSequences());
2278 start = viewport.getSelectionGroup().getStartRes();
2279 end = viewport.getSelectionGroup().getEndRes();
2283 seqs = viewport.getAlignment().getSequencesArray();
2286 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2287 "Remove Gapped Columns", seqs, start, end,
2288 viewport.getAlignment());
2290 addHistoryItem(removeGapCols);
2292 statusBar.setText(MessageManager.formatMessage(
2293 "label.removed_empty_columns", new String[]
2294 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2296 // This is to maintain viewport position on first residue
2297 // of first sequence
2298 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2299 int startRes = seq.findPosition(viewport.startRes);
2300 // ShiftList shifts;
2301 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2302 // edit.alColumnChanges=shifts.getInverse();
2303 // if (viewport.hasHiddenColumns)
2304 // viewport.getColumnSelection().compensateForEdits(shifts);
2305 viewport.setStartRes(seq.findIndex(startRes) - 1);
2306 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2311 public void removeAllGapsMenuItem_actionPerformed()
2313 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2316 if (viewport.getSelectionGroup() != null)
2318 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2319 viewport.getHiddenRepSequences());
2320 start = viewport.getSelectionGroup().getStartRes();
2321 end = viewport.getSelectionGroup().getEndRes();
2325 seqs = viewport.getAlignment().getSequencesArray();
2328 // This is to maintain viewport position on first residue
2329 // of first sequence
2330 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2331 int startRes = seq.findPosition(viewport.startRes);
2333 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2334 viewport.getAlignment()));
2336 viewport.setStartRes(seq.findIndex(startRes) - 1);
2338 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2343 public void findMenuItem_actionPerformed()
2345 new Finder(alignPanel);
2349 * create a new view derived from the current view
2352 * @return frame for the new view
2354 public AlignFrame newView(String viewtitle)
2357 if (viewport.hasHiddenRows())
2359 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2360 .getFullAlignment().getSequencesArray());
2364 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2367 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2369 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2371 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2373 newal.addAnnotation(viewport.getAlignment()
2374 .getAlignmentAnnotation()[i]);
2379 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2381 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2382 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2383 PaintRefresher.Register(newaf.alignPanel,
2384 newaf.alignPanel.av.getSequenceSetId());
2386 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2387 newaf.alignPanel.av.getSequenceSetId());
2388 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2389 newaf.alignPanel.av.getSequenceSetId());
2391 Vector comps = (Vector) PaintRefresher.components.get(viewport
2392 .getSequenceSetId());
2394 for (int i = 0; i < comps.size(); i++)
2396 if (comps.elementAt(i) instanceof AlignmentPanel)
2402 String title = new String(this.getTitle());
2403 if (viewtitle != null)
2405 title = viewtitle + " ( " + title + ")";
2409 if (title.indexOf("(View") > -1)
2411 title = title.substring(0, title.indexOf("(View"));
2413 title += "(View " + viewSize + ")";
2416 newaf.setTitle(title.toString());
2418 newaf.viewport.setHistoryList(viewport.getHistoryList());
2419 newaf.viewport.setRedoList(viewport.getRedoList());
2425 * @return list of feature groups on the view
2427 public String[] getFeatureGroups()
2429 FeatureRenderer fr = null;
2430 if (alignPanel != null
2431 && (fr = alignPanel.getFeatureRenderer()) != null)
2433 List<String> gps = fr.getFeatureGroups();
2434 String[] _gps = gps.toArray(new String[gps.size()]);
2441 * get sequence feature groups that are hidden or shown
2447 public String[] getFeatureGroupsOfState(boolean visible)
2449 FeatureRenderer fr = null;
2450 if (alignPanel != null
2451 && (fr = alignPanel.getFeatureRenderer()) != null)
2453 List<String> gps = fr.getGroups(visible);
2454 String[] _gps = gps.toArray(new String[gps.size()]);
2461 * Change the display state for the given feature groups
2464 * list of group strings
2466 * visible or invisible
2468 public void setFeatureGroupState(String[] groups, boolean state)
2470 FeatureRenderer fr = null;
2471 this.sequenceFeatures.setState(true);
2472 viewport.setShowSequenceFeatures(true);
2473 if (alignPanel != null
2474 && (fr = alignPanel.getFeatureRenderer()) != null)
2477 fr.setGroupVisibility(Arrays.asList(groups), state);
2478 alignPanel.seqPanel.seqCanvas.repaint();
2479 if (alignPanel.overviewPanel != null)
2481 alignPanel.overviewPanel.updateOverviewImage();
2486 public void seqLimits_itemStateChanged()
2488 viewport.setShowJVSuffix(seqLimits.getState());
2489 alignPanel.fontChanged();
2490 alignPanel.paintAlignment(true);
2493 protected void colourTextMenuItem_actionPerformed()
2495 viewport.setColourText(colourTextMenuItem.getState());
2496 alignPanel.paintAlignment(true);
2499 protected void displayNonconservedMenuItem_actionPerformed()
2501 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2502 alignPanel.paintAlignment(true);
2505 protected void wrapMenuItem_actionPerformed()
2507 viewport.setWrapAlignment(wrapMenuItem.getState());
2508 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2509 scaleAbove.setEnabled(wrapMenuItem.getState());
2510 scaleLeft.setEnabled(wrapMenuItem.getState());
2511 scaleRight.setEnabled(wrapMenuItem.getState());
2512 alignPanel.paintAlignment(true);
2515 public void overviewMenuItem_actionPerformed()
2517 if (alignPanel.overviewPanel != null)
2522 Frame frame = new Frame();
2523 OverviewPanel overview = new OverviewPanel(alignPanel);
2524 frame.add(overview);
2525 // +50 must allow for applet frame window
2526 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2527 "label.overview_params", new String[]
2528 { this.getTitle() }), overview.getPreferredSize().width,
2529 overview.getPreferredSize().height + 50);
2532 final AlignmentPanel ap = alignPanel;
2533 frame.addWindowListener(new WindowAdapter()
2536 public void windowClosing(WindowEvent e)
2540 ap.setOverviewPanel(null);
2545 alignPanel.setOverviewPanel(overview);
2549 public void changeColour(ColourSchemeI cs)
2555 if (viewport.getAbovePIDThreshold())
2557 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2561 if (viewport.getConservationSelected())
2563 cs.setConservationApplied(true);
2564 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2569 cs.setConservationApplied(false);
2572 viewport.setGlobalColourScheme(cs);
2574 if (alignPanel.getOverviewPanel() != null)
2576 alignPanel.getOverviewPanel().updateOverviewImage();
2579 jalview.structure.StructureSelectionManager
2580 .getStructureSelectionManager(viewport.applet)
2581 .sequenceColoursChanged(alignPanel);
2583 alignPanel.paintAlignment(true);
2586 protected void modifyPID_actionPerformed()
2588 if (viewport.getAbovePIDThreshold()
2589 && viewport.getGlobalColourScheme() != null)
2591 SliderPanel.setPIDSliderSource(alignPanel,
2592 viewport.getGlobalColourScheme(), "Background");
2593 SliderPanel.showPIDSlider();
2597 protected void modifyConservation_actionPerformed()
2599 if (viewport.getConservationSelected()
2600 && viewport.getGlobalColourScheme() != null)
2602 SliderPanel.setConservationSlider(alignPanel,
2603 viewport.getGlobalColourScheme(), "Background");
2604 SliderPanel.showConservationSlider();
2608 protected void conservationMenuItem_actionPerformed()
2610 viewport.setConservationSelected(conservationMenuItem.getState());
2612 viewport.setAbovePIDThreshold(false);
2613 abovePIDThreshold.setState(false);
2615 changeColour(viewport.getGlobalColourScheme());
2617 modifyConservation_actionPerformed();
2620 public void abovePIDThreshold_actionPerformed()
2622 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2624 conservationMenuItem.setState(false);
2625 viewport.setConservationSelected(false);
2627 changeColour(viewport.getGlobalColourScheme());
2629 modifyPID_actionPerformed();
2632 public void sortPairwiseMenuItem_actionPerformed()
2634 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2635 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2636 .getAlignment().getSequenceAt(0), null);
2638 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2639 viewport.getAlignment()));
2640 alignPanel.paintAlignment(true);
2643 public void sortIDMenuItem_actionPerformed()
2645 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2646 AlignmentSorter.sortByID(viewport.getAlignment());
2647 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2648 viewport.getAlignment()));
2649 alignPanel.paintAlignment(true);
2652 public void sortLengthMenuItem_actionPerformed()
2654 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2655 AlignmentSorter.sortByLength(viewport.getAlignment());
2656 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2657 viewport.getAlignment()));
2658 alignPanel.paintAlignment(true);
2661 public void sortGroupMenuItem_actionPerformed()
2663 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2664 AlignmentSorter.sortByGroup(viewport.getAlignment());
2665 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2666 viewport.getAlignment()));
2667 alignPanel.paintAlignment(true);
2671 public void removeRedundancyMenuItem_actionPerformed()
2673 new RedundancyPanel(alignPanel);
2676 public void pairwiseAlignmentMenuItem_actionPerformed()
2678 if (viewport.getSelectionGroup() != null
2679 && viewport.getSelectionGroup().getSize() > 1)
2681 Frame frame = new Frame();
2682 frame.add(new PairwiseAlignPanel(alignPanel));
2683 jalview.bin.JalviewLite.addFrame(frame,
2684 MessageManager.getString("action.pairwise_alignment"), 600,
2689 public void PCAMenuItem_actionPerformed()
2691 // are the sequences aligned?
2692 if (!viewport.getAlignment().isAligned(false))
2695 int Width = viewport.getAlignment().getWidth();
2697 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2699 current = viewport.getAlignment().getSequenceAt(i);
2701 if (current.getLength() < Width)
2703 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2706 alignPanel.paintAlignment(true);
2709 if ((viewport.getSelectionGroup() != null
2710 && viewport.getSelectionGroup().getSize() < 4 && viewport
2711 .getSelectionGroup().getSize() > 0)
2712 || viewport.getAlignment().getHeight() < 4)
2719 new PCAPanel(viewport);
2720 } catch (java.lang.OutOfMemoryError ex)
2726 public void averageDistanceTreeMenuItem_actionPerformed()
2728 NewTreePanel("AV", "PID", "Average distance tree using PID");
2731 public void neighbourTreeMenuItem_actionPerformed()
2733 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2736 protected void njTreeBlosumMenuItem_actionPerformed()
2738 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2741 protected void avTreeBlosumMenuItem_actionPerformed()
2743 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2746 void NewTreePanel(String type, String pwType, String title)
2748 // are the sequences aligned?
2749 if (!viewport.getAlignment().isAligned(false))
2752 int Width = viewport.getAlignment().getWidth();
2754 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2756 current = viewport.getAlignment().getSequenceAt(i);
2758 if (current.getLength() < Width)
2760 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2763 alignPanel.paintAlignment(true);
2767 if ((viewport.getSelectionGroup() != null && viewport
2768 .getSelectionGroup().getSize() > 1)
2769 || (viewport.getAlignment().getHeight() > 1))
2771 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2773 addTreeMenuItem(tp, title);
2775 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2779 void loadTree_actionPerformed()
2781 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2782 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2783 cap.setTreeImport();
2784 Frame frame = new Frame();
2786 jalview.bin.JalviewLite.addFrame(frame,
2787 MessageManager.getString("label.paste_newick_file"), 400, 300);
2790 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2792 TreePanel tp = new TreePanel(alignPanel, treeFile,
2793 MessageManager.getString("label.load_tree_from_file"), tree);
2794 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2795 addTreeMenuItem(tp, treeFile);
2799 * sort the alignment using the given treePanel
2802 * tree used to sort view
2804 * string used for undo event name
2806 public void sortByTree(TreePanel treePanel, String title)
2808 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2810 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2811 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2812 // HistoryItem.SORT));
2813 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2814 "label.order_by_params", new String[]
2815 { title }), oldOrder, viewport.getAlignment()));
2816 alignPanel.paintAlignment(true);
2820 * Do any automatic reordering of the alignment and add the necessary bits to
2821 * the menu structure for the new tree
2826 protected void addTreeMenuItem(final TreePanel treePanel,
2829 final MenuItem item = new MenuItem(title);
2830 sortByTreeMenu.add(item);
2831 item.addActionListener(new java.awt.event.ActionListener()
2834 public void actionPerformed(ActionEvent evt)
2836 sortByTree(treePanel, title); // treePanel.getTitle());
2840 treePanel.addWindowListener(new WindowAdapter()
2843 public void windowOpened(WindowEvent e)
2845 if (viewport.sortByTree)
2847 sortByTree(treePanel, title);
2849 super.windowOpened(e);
2853 public void windowClosing(WindowEvent e)
2855 sortByTreeMenu.remove(item);
2860 public boolean sortBy(AlignmentOrder alorder, String undoname)
2862 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2863 if (viewport.applet.debug)
2865 System.err.println("Sorting " + alorder.getOrder().size()
2866 + " in alignment '" + getTitle() + "'");
2868 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2869 if (undoname != null)
2871 addHistoryItem(new OrderCommand(undoname, oldOrder,
2872 viewport.getAlignment()));
2874 alignPanel.paintAlignment(true);
2878 protected void documentation_actionPerformed()
2880 alignPanel.av.applet.openJalviewHelpUrl();
2883 protected void about_actionPerformed()
2886 class AboutPanel extends Canvas
2892 public AboutPanel(String version, String builddate)
2894 this.version = version;
2895 this.builddate = builddate;
2899 public void paint(Graphics g)
2901 g.setColor(Color.white);
2902 g.fillRect(0, 0, getSize().width, getSize().height);
2903 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2904 FontMetrics fm = g.getFontMetrics();
2905 int fh = fm.getHeight();
2907 g.setColor(Color.black);
2908 // TODO: update this text for each release or centrally store it for
2909 // lite and application
2910 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2911 g.drawString(MessageManager.formatMessage(
2912 "label.jalviewLite_release", new String[]
2913 { version }), x, y += fh);
2914 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2915 g.drawString(MessageManager.formatMessage(
2916 "label.jaview_build_date", new String[]
2917 { builddate }), x, y += fh);
2918 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2919 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2921 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2922 x + 50, y += fh + 8);
2924 MessageManager.getString("label.jalview_dev_managers"), x,
2926 g.drawString(MessageManager
2927 .getString("label.jalview_distribution_lists"), x, y += fh);
2928 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2931 MessageManager.getString("label.jalview_cite_1_authors"),
2934 MessageManager.getString("label.jalview_cite_1_title"), x,
2936 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2941 Frame frame = new Frame();
2942 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2944 jalview.bin.JalviewLite.addFrame(frame,
2945 MessageManager.getString("label.jalview"), 580, 220);
2949 public void showURL(String url, String target)
2951 if (viewport.applet == null)
2953 System.out.println("Not running as applet - no browser available.");
2957 viewport.applet.showURL(url, target);
2961 // ////////////////////////////////////////////////////////////////////////////////
2962 // JBuilder Graphics here
2964 MenuBar alignFrameMenuBar = new MenuBar();
2966 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2968 MenuItem loadApplication = new MenuItem(
2969 MessageManager.getString("label.view_full_application"));
2971 MenuItem loadTree = new MenuItem(
2972 MessageManager.getString("label.load_associated_tree"));
2974 MenuItem loadAnnotations = new MenuItem(
2975 MessageManager.getString("label.load_features_annotations"));
2977 MenuItem outputFeatures = new MenuItem(
2978 MessageManager.getString("label.export_features").concat("..."));
2980 MenuItem outputAnnotations = new MenuItem(
2981 MessageManager.getString("label.export_annotations").concat("..."));
2983 MenuItem closeMenuItem = new MenuItem(
2984 MessageManager.getString("action.close"));
2986 MenuItem selectAllSequenceMenuItem = new MenuItem(
2987 MessageManager.getString("action.select_all"));
2989 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2990 MessageManager.getString("action.deselect_all"));
2992 MenuItem invertSequenceMenuItem = new MenuItem(
2993 MessageManager.getString("action.invert_selection"));
2995 MenuItem remove2LeftMenuItem = new MenuItem();
2997 MenuItem remove2RightMenuItem = new MenuItem();
2999 MenuItem removeGappedColumnMenuItem = new MenuItem();
3001 MenuItem removeAllGapsMenuItem = new MenuItem();
3003 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
3005 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
3007 MenuItem sortPairwiseMenuItem = new MenuItem();
3009 MenuItem sortIDMenuItem = new MenuItem();
3011 MenuItem sortLengthMenuItem = new MenuItem();
3013 MenuItem sortGroupMenuItem = new MenuItem();
3015 MenuItem removeRedundancyMenuItem = new MenuItem();
3017 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
3019 MenuItem PCAMenuItem = new MenuItem();
3021 MenuItem averageDistanceTreeMenuItem = new MenuItem();
3023 MenuItem neighbourTreeMenuItem = new MenuItem();
3025 BorderLayout borderLayout1 = new BorderLayout();
3027 public Label statusBar = new Label();
3029 MenuItem clustalColour = new MenuItem();
3031 MenuItem zappoColour = new MenuItem();
3033 MenuItem taylorColour = new MenuItem();
3035 MenuItem hydrophobicityColour = new MenuItem();
3037 MenuItem helixColour = new MenuItem();
3039 MenuItem strandColour = new MenuItem();
3041 MenuItem turnColour = new MenuItem();
3043 MenuItem buriedColour = new MenuItem();
3045 MenuItem purinePyrimidineColour = new MenuItem();
3047 MenuItem RNAInteractionColour = new MenuItem();
3049 MenuItem RNAHelixColour = new MenuItem();
3051 MenuItem userDefinedColour = new MenuItem();
3053 MenuItem PIDColour = new MenuItem();
3055 MenuItem BLOSUM62Colour = new MenuItem();
3057 MenuItem tcoffeeColour = new MenuItem();
3059 MenuItem njTreeBlosumMenuItem = new MenuItem();
3061 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
3063 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
3065 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
3067 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
3069 MenuItem alProperties = new MenuItem(
3070 MessageManager.getString("label.alignment_props"));
3072 MenuItem overviewMenuItem = new MenuItem();
3074 MenuItem undoMenuItem = new MenuItem();
3076 MenuItem redoMenuItem = new MenuItem();
3078 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3080 MenuItem noColourmenuItem = new MenuItem();
3082 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3084 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3086 MenuItem findMenuItem = new MenuItem();
3088 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3090 MenuItem nucleotideColour = new MenuItem();
3092 MenuItem deleteGroups = new MenuItem();
3094 MenuItem grpsFromSelection = new MenuItem();
3096 MenuItem createGroup = new MenuItem();
3098 MenuItem unGroup = new MenuItem();
3100 MenuItem delete = new MenuItem();
3102 MenuItem copy = new MenuItem();
3104 MenuItem cut = new MenuItem();
3106 Menu pasteMenu = new Menu();
3108 MenuItem pasteNew = new MenuItem();
3110 MenuItem pasteThis = new MenuItem();
3112 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3114 MenuItem font = new MenuItem();
3116 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3118 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3120 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3122 MenuItem modifyPID = new MenuItem();
3124 MenuItem modifyConservation = new MenuItem();
3126 CheckboxMenuItem autoCalculate = null;
3128 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3129 "Sort Alignment With New Tree", true);
3131 Menu sortByTreeMenu = new Menu();
3133 MenuItem inputText = new MenuItem();
3135 MenuItem documentation = new MenuItem();
3137 MenuItem about = new MenuItem();
3139 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3141 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3143 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3145 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3147 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3149 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3151 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3153 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3155 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3158 * Initialise menus and other items
3162 private void jbInit() throws Exception
3164 setMenuBar(alignFrameMenuBar);
3167 * Configure File menu items and actions
3170 .setLabel(MessageManager.getString("label.input_from_textbox"));
3171 inputText.addActionListener(this);
3172 Menu outputTextboxMenu = new Menu(
3173 MessageManager.getString("label.out_to_textbox"));
3174 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3177 MenuItem item = new MenuItem(
3178 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3180 item.addActionListener(new java.awt.event.ActionListener()
3183 public void actionPerformed(ActionEvent e)
3185 outputText_actionPerformed(e);
3189 outputTextboxMenu.add(item);
3191 closeMenuItem.addActionListener(this);
3192 loadApplication.addActionListener(this);
3193 loadTree.addActionListener(this);
3194 loadAnnotations.addActionListener(this);
3195 outputFeatures.addActionListener(this);
3196 outputAnnotations.addActionListener(this);
3199 * Configure Edit menu items and actions
3201 undoMenuItem.setEnabled(false);
3202 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3203 undoMenuItem.addActionListener(this);
3204 redoMenuItem.setEnabled(false);
3205 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3206 redoMenuItem.addActionListener(this);
3207 copy.setLabel(MessageManager.getString("action.copy"));
3208 copy.addActionListener(this);
3209 cut.setLabel(MessageManager.getString("action.cut"));
3210 cut.addActionListener(this);
3211 delete.setLabel(MessageManager.getString("action.delete"));
3212 delete.addActionListener(this);
3213 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3214 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3215 pasteNew.addActionListener(this);
3216 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3217 pasteThis.addActionListener(this);
3218 remove2LeftMenuItem.setLabel(MessageManager
3219 .getString("action.remove_left"));
3220 remove2LeftMenuItem.addActionListener(this);
3221 remove2RightMenuItem.setLabel(MessageManager
3222 .getString("action.remove_right"));
3223 remove2RightMenuItem.addActionListener(this);
3224 removeGappedColumnMenuItem.setLabel(MessageManager
3225 .getString("action.remove_empty_columns"));
3226 removeGappedColumnMenuItem.addActionListener(this);
3227 removeAllGapsMenuItem.setLabel(MessageManager
3228 .getString("action.remove_all_gaps"));
3229 removeAllGapsMenuItem.addActionListener(this);
3230 removeRedundancyMenuItem.setLabel(MessageManager.getString(
3231 "action.remove_redundancy").concat("..."));
3232 removeRedundancyMenuItem.addActionListener(this);
3235 * Configure Select menu items and actions
3237 findMenuItem.setLabel(MessageManager.getString("action.find"));
3238 findMenuItem.addActionListener(this);
3239 selectAllSequenceMenuItem.addActionListener(this);
3240 deselectAllSequenceMenuItem.addActionListener(this);
3241 invertSequenceMenuItem.setLabel(MessageManager
3242 .getString("action.invert_sequence_selection"));
3243 invertSequenceMenuItem.addActionListener(this);
3244 invertColSel.setLabel(MessageManager
3245 .getString("action.invert_column_selection"));
3246 invertColSel.addActionListener(this);
3247 deleteGroups.setLabel(MessageManager
3248 .getString("action.undefine_groups"));
3249 deleteGroups.addActionListener(this);
3250 grpsFromSelection.setLabel(MessageManager
3251 .getString("action.make_groups_selection"));
3252 grpsFromSelection.addActionListener(this);
3253 createGroup.setLabel(MessageManager.getString("action.create_group"));
3254 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3255 annotationColumnSelection.setLabel("Select by Annotation");
3256 annotationColumnSelection.addActionListener(this);
3259 * Configure View menu items and actions
3261 newView.setLabel(MessageManager.getString("action.new_view"));
3262 newView.addActionListener(this);
3263 Menu showMenu = new Menu(MessageManager.getString("action.show"));
3264 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3265 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3266 Menu hideMenu = new Menu(MessageManager.getString("action.hide"));
3268 .setLabel(MessageManager.getString("label.selected_columns"));
3269 hideSequences.setLabel(MessageManager
3270 .getString("label.selected_sequences"));
3271 hideAllButSelection.setLabel(MessageManager
3272 .getString("label.all_but_selected_region"));
3273 hideAllSelection.setLabel(MessageManager
3274 .getString("label.selected_region"));
3275 showAllHidden.setLabel(MessageManager
3276 .getString("label.all_sequences_columns"));
3277 showColumns.addActionListener(this);
3278 showSeqs.addActionListener(this);
3279 hideColumns.addActionListener(this);
3280 hideSequences.addActionListener(this);
3281 hideAllButSelection.addActionListener(this);
3282 hideAllSelection.addActionListener(this);
3283 showAllHidden.addActionListener(this);
3284 featureSettings.setLabel(MessageManager
3285 .getString("label.feature_settings"));
3286 featureSettings.addActionListener(this);
3287 sequenceFeatures.setLabel(MessageManager
3288 .getString("label.show_sequence_features"));
3289 sequenceFeatures.addItemListener(this);
3290 sequenceFeatures.setState(false);
3291 followMouseOverFlag.setLabel(MessageManager
3292 .getString("label.automatic_scrolling"));
3293 followMouseOverFlag.addItemListener(this);
3294 alProperties.addActionListener(this);
3295 overviewMenuItem.setLabel(MessageManager
3296 .getString("label.overview_window"));
3297 overviewMenuItem.addActionListener(this);
3300 * Configure Annotations menu items and actions
3302 annotationPanelMenuItem.setLabel(MessageManager
3303 .getString("label.show_annotations"));
3304 annotationPanelMenuItem.addItemListener(this);
3305 showGroupConsensus.setLabel(MessageManager
3306 .getString("label.group_consensus"));
3307 showGroupConservation.setLabel(MessageManager
3308 .getString("label.group_conservation"));
3309 showConsensusHistogram.setLabel(MessageManager
3310 .getString("label.show_consensus_histogram"));
3311 showSequenceLogo.setLabel(MessageManager
3312 .getString("label.show_consensus_logo"));
3313 normSequenceLogo.setLabel(MessageManager
3314 .getString("label.norm_consensus_logo"));
3315 applyAutoAnnotationSettings.setLabel(MessageManager
3316 .getString("label.apply_all_groups"));
3317 applyAutoAnnotationSettings.setState(true);
3318 Menu autoAnnMenu = new Menu(
3319 MessageManager.getString("label.autocalculated_annotation"));
3320 showGroupConsensus.addItemListener(this);
3321 showGroupConservation.addItemListener(this);
3322 showConsensusHistogram.addItemListener(this);
3323 showSequenceLogo.addItemListener(this);
3324 normSequenceLogo.addItemListener(this);
3325 applyAutoAnnotationSettings.addItemListener(this);
3326 showAlignmentAnnotations = new CheckboxMenuItem(
3327 MessageManager.getString("label.show_all_al_annotations"));
3328 showSequenceAnnotations = new CheckboxMenuItem(
3329 MessageManager.getString("label.show_all_seq_annotations"));
3330 sortAnnBySequence = new CheckboxMenuItem(
3331 MessageManager.getString("label.sort_annotations_by_sequence"));
3332 sortAnnByLabel = new CheckboxMenuItem(
3333 MessageManager.getString("label.sort_annotations_by_label"));
3334 showAutoFirst = new CheckboxMenuItem(
3335 MessageManager.getString("label.show_first"));
3336 showAutoLast = new CheckboxMenuItem(
3337 MessageManager.getString("label.show_last"));
3338 showAlignmentAnnotations.addItemListener(this);
3339 showSequenceAnnotations.addItemListener(this);
3340 sortAnnBySequence.addItemListener(this);
3341 sortAnnByLabel.addItemListener(this);
3342 showAutoFirst.addItemListener(this);
3343 showAutoLast.addItemListener(this);
3346 * Configure Format menu items and actions
3348 font.setLabel(MessageManager.getString("action.font"));
3349 font.addActionListener(this);
3350 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3351 scaleAbove.setState(true);
3352 scaleAbove.setEnabled(false);
3353 scaleAbove.addItemListener(this);
3354 scaleLeft.setEnabled(false);
3355 scaleLeft.setState(true);
3356 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3357 scaleLeft.addItemListener(this);
3358 scaleRight.setEnabled(false);
3359 scaleRight.setState(true);
3360 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3361 scaleRight.addItemListener(this);
3362 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3363 viewBoxesMenuItem.setState(true);
3364 viewBoxesMenuItem.addItemListener(this);
3365 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3366 viewTextMenuItem.setState(true);
3367 viewTextMenuItem.addItemListener(this);
3368 colourTextMenuItem.setLabel(MessageManager
3369 .getString("label.colour_text"));
3370 colourTextMenuItem.addItemListener(this);
3371 displayNonconservedMenuItem.setLabel(MessageManager
3372 .getString("label.show_non_conversed"));
3373 displayNonconservedMenuItem.addItemListener(this);
3374 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3375 wrapMenuItem.addItemListener(this);
3376 renderGapsMenuItem.setLabel(MessageManager
3377 .getString("action.show_gaps"));
3378 renderGapsMenuItem.setState(true);
3379 renderGapsMenuItem.addItemListener(this);
3380 centreColumnLabelFlag.setLabel(MessageManager
3381 .getString("label.centre_column_labels"));
3382 centreColumnLabelFlag.addItemListener(this);
3383 seqLimits.setState(true);
3384 seqLimits.setLabel(MessageManager
3385 .getString("label.show_sequence_limits"));
3386 seqLimits.addItemListener(this);
3389 * Configure Colour menu items and actions
3391 applyToAllGroups.setLabel(MessageManager
3392 .getString("label.apply_colour_to_all_groups"));
3393 applyToAllGroups.setState(true);
3394 applyToAllGroups.addItemListener(this);
3395 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3396 clustalColour.addActionListener(this);
3397 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3398 zappoColour.addActionListener(this);
3399 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3400 taylorColour.addActionListener(this);
3401 hydrophobicityColour.setLabel(MessageManager
3402 .getString("label.hydrophobicity"));
3403 hydrophobicityColour.addActionListener(this);
3405 .setLabel(MessageManager.getString("label.helix_propensity"));
3406 helixColour.addActionListener(this);
3407 strandColour.setLabel(MessageManager
3408 .getString("label.strand_propensity"));
3409 strandColour.addActionListener(this);
3410 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3411 turnColour.addActionListener(this);
3412 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3413 buriedColour.addActionListener(this);
3414 purinePyrimidineColour.setLabel(MessageManager
3415 .getString("label.purine_pyrimidine"));
3416 purinePyrimidineColour.addActionListener(this);
3417 RNAInteractionColour.setLabel(MessageManager
3418 .getString("label.rna_interaction"));
3419 RNAInteractionColour.addActionListener(this);
3420 RNAHelixColour.setLabel(MessageManager
3421 .getString("action.by_rna_helixes"));
3422 RNAHelixColour.addActionListener(this);
3423 userDefinedColour.setLabel(MessageManager
3424 .getString("action.user_defined"));
3425 userDefinedColour.addActionListener(this);
3426 PIDColour.setLabel(MessageManager
3427 .getString("label.percentage_identity"));
3428 PIDColour.addActionListener(this);
3429 BLOSUM62Colour.setLabel(MessageManager
3430 .getString("label.blosum62_score"));
3431 BLOSUM62Colour.addActionListener(this);
3433 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3434 // it will be enabled only if a score file is provided
3435 tcoffeeColour.setEnabled(false);
3436 tcoffeeColour.addActionListener(this);
3437 conservationMenuItem.setLabel(MessageManager
3438 .getString("action.by_conservation"));
3439 conservationMenuItem.addItemListener(this);
3440 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3441 noColourmenuItem.addActionListener(this);
3442 abovePIDThreshold.setLabel(MessageManager
3443 .getString("label.above_identity_threshold"));
3444 abovePIDThreshold.addItemListener(this);
3445 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3446 nucleotideColour.addActionListener(this);
3447 modifyPID.setLabel(MessageManager
3448 .getString("label.modify_identity_thereshold"));
3449 modifyPID.addActionListener(this);
3450 modifyConservation.setLabel(MessageManager
3451 .getString("label.modify_conservation_thereshold"));
3452 modifyConservation.addActionListener(this);
3453 annotationColour.setLabel(MessageManager
3454 .getString("action.by_annotation"));
3455 annotationColour.addActionListener(this);
3458 * Configure Calculate menu items and actions
3460 sortPairwiseMenuItem.setLabel(MessageManager
3461 .getString("action.by_pairwise_id"));
3462 sortPairwiseMenuItem.addActionListener(this);
3463 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3464 sortIDMenuItem.addActionListener(this);
3465 sortLengthMenuItem.setLabel(MessageManager
3466 .getString("action.by_length"));
3467 sortLengthMenuItem.addActionListener(this);
3468 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3469 sortGroupMenuItem.addActionListener(this);
3470 pairwiseAlignmentMenuItem.setLabel(MessageManager
3471 .getString("action.pairwise_alignment"));
3472 pairwiseAlignmentMenuItem.addActionListener(this);
3473 PCAMenuItem.setLabel(MessageManager
3474 .getString("label.principal_component_analysis"));
3475 PCAMenuItem.addActionListener(this);
3476 autoCalculate = new CheckboxMenuItem(
3477 MessageManager.getString("label.autocalculate_consensus"), true);
3478 averageDistanceTreeMenuItem.setLabel(MessageManager
3479 .getString("label.average_distance_identity"));
3480 averageDistanceTreeMenuItem.addActionListener(this);
3481 neighbourTreeMenuItem.setLabel(MessageManager
3482 .getString("label.neighbour_joining_identity"));
3483 neighbourTreeMenuItem.addActionListener(this);
3484 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3485 .getString("label.average_distance_bloslum62"));
3486 avDistanceTreeBlosumMenuItem.addActionListener(this);
3487 njTreeBlosumMenuItem.setLabel(MessageManager
3488 .getString("label.neighbour_blosum62"));
3489 njTreeBlosumMenuItem.addActionListener(this);
3490 sortByTreeMenu.setLabel(MessageManager
3491 .getString("action.by_tree_order"));
3492 Menu sortMenu = new Menu(MessageManager.getString("action.sort"));
3493 Menu calculateTreeMenu = new Menu(
3494 MessageManager.getString("action.calculate_tree"));
3495 autoCalculate.addItemListener(this);
3496 sortByTree.addItemListener(this);
3499 * Configure Help menu items and actions
3501 Menu helpMenu = new Menu(MessageManager.getString("action.help"));
3502 documentation.setLabel(MessageManager.getString("label.documentation"));
3503 documentation.addActionListener(this);
3504 about.setLabel(MessageManager.getString("label.about"));
3505 about.addActionListener(this);
3508 * Add top level menus to frame
3510 alignFrameMenuBar.add(fileMenu);
3511 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
3512 alignFrameMenuBar.add(editMenu);
3513 Menu selectMenu = new Menu(MessageManager.getString("action.select"));
3514 alignFrameMenuBar.add(selectMenu);
3515 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
3516 alignFrameMenuBar.add(viewMenu);
3517 Menu annotationsMenu = new Menu(
3518 MessageManager.getString("action.annotations"));
3519 alignFrameMenuBar.add(annotationsMenu);
3520 Menu formatMenu = new Menu(MessageManager.getString("action.format"));
3521 alignFrameMenuBar.add(formatMenu);
3522 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
3523 alignFrameMenuBar.add(colourMenu);
3524 Menu calculateMenu = new Menu(
3525 MessageManager.getString("action.calculate"));
3526 alignFrameMenuBar.add(calculateMenu);
3527 alignFrameMenuBar.add(helpMenu);
3532 fileMenu.add(inputText);
3533 fileMenu.add(loadTree);
3534 fileMenu.add(loadAnnotations);
3535 fileMenu.addSeparator();
3536 fileMenu.add(outputTextboxMenu);
3537 fileMenu.add(outputFeatures);
3538 fileMenu.add(outputAnnotations);
3539 if (jalviewServletURL != null)
3541 fileMenu.add(loadApplication);
3543 fileMenu.addSeparator();
3544 fileMenu.add(closeMenuItem);
3549 editMenu.add(undoMenuItem);
3550 editMenu.add(redoMenuItem);
3553 pasteMenu.add(pasteNew);
3554 pasteMenu.add(pasteThis);
3555 editMenu.add(pasteMenu);
3556 editMenu.add(delete);
3557 editMenu.addSeparator();
3558 editMenu.add(remove2LeftMenuItem);
3559 editMenu.add(remove2RightMenuItem);
3560 editMenu.add(removeGappedColumnMenuItem);
3561 editMenu.add(removeAllGapsMenuItem);
3562 editMenu.add(removeRedundancyMenuItem);
3567 selectMenu.add(findMenuItem);
3568 selectMenu.addSeparator();
3569 selectMenu.add(selectAllSequenceMenuItem);
3570 selectMenu.add(deselectAllSequenceMenuItem);
3571 selectMenu.add(invertSequenceMenuItem);
3572 selectMenu.add(invertColSel);
3573 selectMenu.add(createGroup);
3574 selectMenu.add(unGroup);
3575 selectMenu.add(grpsFromSelection);
3576 selectMenu.add(deleteGroups);
3577 selectMenu.add(annotationColumnSelection);
3582 viewMenu.add(newView);
3583 viewMenu.addSeparator();
3584 showMenu.add(showColumns);
3585 showMenu.add(showSeqs);
3586 showMenu.add(showAllHidden);
3587 viewMenu.add(showMenu);
3588 hideMenu.add(hideColumns);
3589 hideMenu.add(hideSequences);
3590 hideMenu.add(hideAllSelection);
3591 hideMenu.add(hideAllButSelection);
3592 viewMenu.add(hideMenu);
3593 viewMenu.addSeparator();
3594 viewMenu.add(followMouseOverFlag);
3595 viewMenu.addSeparator();
3596 viewMenu.add(sequenceFeatures);
3597 viewMenu.add(featureSettings);
3598 viewMenu.addSeparator();
3599 viewMenu.add(alProperties);
3600 viewMenu.addSeparator();
3601 viewMenu.add(overviewMenuItem);
3606 annotationsMenu.add(annotationPanelMenuItem);
3607 annotationsMenu.addSeparator();
3608 annotationsMenu.add(showAlignmentAnnotations);
3609 annotationsMenu.add(showSequenceAnnotations);
3610 annotationsMenu.add(sortAnnBySequence);
3611 annotationsMenu.add(sortAnnByLabel);
3612 annotationsMenu.addSeparator();
3613 autoAnnMenu.add(showAutoFirst);
3614 autoAnnMenu.add(showAutoLast);
3615 autoAnnMenu.addSeparator();
3616 autoAnnMenu.add(applyAutoAnnotationSettings);
3617 autoAnnMenu.add(showConsensusHistogram);
3618 autoAnnMenu.add(showSequenceLogo);
3619 autoAnnMenu.add(normSequenceLogo);
3620 autoAnnMenu.addSeparator();
3621 autoAnnMenu.add(showGroupConservation);
3622 autoAnnMenu.add(showGroupConsensus);
3623 annotationsMenu.add(autoAnnMenu);
3628 formatMenu.add(font);
3629 formatMenu.add(seqLimits);
3630 formatMenu.add(wrapMenuItem);
3631 formatMenu.add(scaleAbove);
3632 formatMenu.add(scaleLeft);
3633 formatMenu.add(scaleRight);
3634 formatMenu.add(viewBoxesMenuItem);
3635 formatMenu.add(viewTextMenuItem);
3636 formatMenu.add(colourTextMenuItem);
3637 formatMenu.add(displayNonconservedMenuItem);
3638 formatMenu.add(renderGapsMenuItem);
3639 formatMenu.add(centreColumnLabelFlag);
3644 colourMenu.add(applyToAllGroups);
3645 colourMenu.addSeparator();
3646 colourMenu.add(noColourmenuItem);
3647 colourMenu.add(clustalColour);
3648 colourMenu.add(BLOSUM62Colour);
3649 colourMenu.add(PIDColour);
3650 colourMenu.add(zappoColour);
3651 colourMenu.add(taylorColour);
3652 colourMenu.add(hydrophobicityColour);
3653 colourMenu.add(helixColour);
3654 colourMenu.add(strandColour);
3655 colourMenu.add(turnColour);
3656 colourMenu.add(buriedColour);
3657 colourMenu.add(nucleotideColour);
3658 colourMenu.add(purinePyrimidineColour);
3659 // colourMenu.add(RNAInteractionColour);
3660 colourMenu.add(tcoffeeColour);
3661 colourMenu.add(userDefinedColour);
3662 colourMenu.addSeparator();
3663 colourMenu.add(conservationMenuItem);
3664 colourMenu.add(modifyConservation);
3665 colourMenu.add(abovePIDThreshold);
3666 colourMenu.add(modifyPID);
3667 colourMenu.add(annotationColour);
3668 colourMenu.add(RNAHelixColour);
3673 sortMenu.add(sortIDMenuItem);
3674 sortMenu.add(sortLengthMenuItem);
3675 sortMenu.add(sortByTreeMenu);
3676 sortMenu.add(sortGroupMenuItem);
3677 sortMenu.add(sortPairwiseMenuItem);
3678 calculateMenu.add(sortMenu);
3679 calculateTreeMenu.add(averageDistanceTreeMenuItem);
3680 calculateTreeMenu.add(neighbourTreeMenuItem);
3681 calculateTreeMenu.add(avDistanceTreeBlosumMenuItem);
3682 calculateTreeMenu.add(njTreeBlosumMenuItem);
3683 calculateMenu.add(calculateTreeMenu);
3684 calculateMenu.addSeparator();
3685 calculateMenu.add(pairwiseAlignmentMenuItem);
3686 calculateMenu.add(PCAMenuItem);
3687 calculateMenu.add(autoCalculate);
3688 calculateMenu.add(sortByTree);
3693 helpMenu.add(documentation);
3694 helpMenu.add(about);
3699 statusBar.setBackground(Color.white);
3700 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3701 statusBar.setText(MessageManager.getString("label.status_bar"));
3702 this.add(statusBar, BorderLayout.SOUTH);
3705 public void setStatus(String string)
3707 statusBar.setText(string);
3710 MenuItem featureSettings = new MenuItem();
3712 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3714 MenuItem annotationColour = new MenuItem();
3716 MenuItem annotationColumnSelection = new MenuItem();
3718 MenuItem invertColSel = new MenuItem();
3720 MenuItem showColumns = new MenuItem();
3722 MenuItem showSeqs = new MenuItem();
3724 MenuItem hideColumns = new MenuItem();
3726 MenuItem hideSequences = new MenuItem();
3728 MenuItem hideAllButSelection = new MenuItem();
3730 MenuItem hideAllSelection = new MenuItem();
3732 MenuItem showAllHidden = new MenuItem();
3734 MenuItem newView = new MenuItem();
3736 private CheckboxMenuItem showAlignmentAnnotations;
3738 private CheckboxMenuItem showSequenceAnnotations;
3740 private CheckboxMenuItem sortAnnBySequence;
3742 private CheckboxMenuItem sortAnnByLabel;
3744 private CheckboxMenuItem showAutoFirst;
3746 private CheckboxMenuItem showAutoLast;
3748 private SplitFrame splitFrame;
3751 * Attach the alignFrame panels after embedding menus, if necessary. This used
3752 * to be called setEmbedded, but is now creates the dropdown menus in a
3753 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3755 * @param reallyEmbedded
3756 * true to attach the view to the applet area on the page rather than
3759 public void createAlignFrameWindow(boolean reallyEmbedded)
3763 embedAlignFrameInApplet(viewport.applet);
3768 // test and embed menu bar if necessary.
3770 if (embedMenuIfNeeded(alignPanel))
3773 * adjust for status bar height too. ? pointless as overridden by layout
3776 alignPanel.setSize(getSize().width,
3777 getSize().height - statusBar.getHeight());
3779 add(statusBar, BorderLayout.SOUTH);
3780 add(alignPanel, BorderLayout.CENTER);
3781 // and register with the applet so it can pass external API calls to us
3782 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3789 * Add the components of this AlignFrame to the applet container.
3793 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3796 // Explicitly build the embedded menu panel for the on-page applet
3798 // view cannot be closed if its actually on the page
3799 fileMenu.remove(closeMenuItem);
3800 fileMenu.remove(3); // Remove Separator
3801 // construct embedded menu, using default font
3802 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3803 // and actually add the components to the applet area
3804 theApplet.setLayout(new BorderLayout());
3805 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3806 theApplet.add(statusBar, BorderLayout.SOUTH);
3807 // TODO should size be left to the layout manager?
3808 alignPanel.setSize(theApplet.getSize().width,
3809 theApplet.getSize().height - embeddedMenu.getHeight()
3810 - statusBar.getHeight());
3811 theApplet.add(alignPanel, BorderLayout.CENTER);
3812 final AlignFrame me = this;
3813 theApplet.addFocusListener(new FocusListener()
3817 public void focusLost(FocusEvent e)
3819 if (theApplet.currentAlignFrame == me)
3821 theApplet.currentAlignFrame = null;
3826 public void focusGained(FocusEvent e)
3828 theApplet.currentAlignFrame = me;
3831 theApplet.validate();
3835 * create a new binding between structures in an existing jmol viewer instance
3836 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3837 * this does not open a new Jmol window, or modify the display of the
3838 * structures in the original jmol window. Note This method doesn't work
3839 * without an additional javascript library to exchange messages between the
3840 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3843 * JmolViewer instance
3844 * @param sequenceIds
3845 * - sequence Ids to search for associations
3847 public SequenceStructureBinding addStructureViewInstance(
3848 Object jmolviewer, String[] sequenceIds)
3850 org.jmol.api.JmolViewer viewer = null;
3853 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3854 } catch (ClassCastException ex)
3856 System.err.println("Unsupported viewer object :"
3857 + jmolviewer.getClass());
3861 System.err.println("Can't use this object as a structure viewer:"
3862 + jmolviewer.getClass());
3865 SequenceI[] seqs = null;
3866 if (sequenceIds == null || sequenceIds.length == 0)
3868 seqs = viewport.getAlignment().getSequencesArray();
3872 Vector sqi = new Vector();
3873 AlignmentI al = viewport.getAlignment();
3874 for (int sid = 0; sid < sequenceIds.length; sid++)
3876 SequenceI sq = al.findName(sequenceIds[sid]);
3884 seqs = new SequenceI[sqi.size()];
3885 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3887 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3895 AAStructureBindingModel jmv = null;
3896 // TODO: search for a jmv that involves viewer
3898 { // create a new viewer/jalview binding.
3899 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3907 * bind a pdb file to a sequence in the current view
3910 * - sequenceId within the dataset.
3911 * @param pdbEntryString
3912 * - the short name for the PDB file
3914 * - pdb file - either a URL or a valid PDB file.
3915 * @return true if binding was as success TODO: consider making an exception
3916 * structure for indicating when PDB parsing or sequenceId location
3919 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3922 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3923 boolean needtoadd = false;
3924 if (toaddpdb != null)
3926 Vector pdbe = toaddpdb.getPDBId();
3927 PDBEntry pdbentry = null;
3928 if (pdbe != null && pdbe.size() > 0)
3930 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3932 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3933 if (!pdbentry.getId().equals(pdbEntryString)
3934 && !pdbentry.getFile().equals(pdbFile))
3944 if (pdbentry == null)
3946 pdbentry = new PDBEntry();
3947 pdbentry.setId(pdbEntryString);
3948 pdbentry.setFile(pdbFile);
3949 needtoadd = true; // add this new entry to sequence.
3951 // resolve data source
3952 // TODO: this code should be a refactored to an io package
3953 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3954 if (protocol == null)
3960 // make a note of the access mode and add
3961 if (pdbentry.getProperty() == null)
3963 pdbentry.setProperty(new Hashtable());
3965 pdbentry.getProperty().put("protocol", protocol);
3966 toaddpdb.addPDBId(pdbentry);
3967 alignPanel.getStructureSelectionManager()
3968 .registerPDBEntry(pdbentry);
3974 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3978 Vector sequences = new Vector();
3979 for (int i = 0; i < seqs.length; i++)
3981 if (seqs[i] != null)
3983 sequences.addElement(new Object[]
3984 { seqs[i], (chains != null) ? chains[i] : null });
3987 seqs = new SequenceI[sequences.size()];
3988 chains = new String[sequences.size()];
3989 for (int i = 0, isize = sequences.size(); i < isize; i++)
3991 Object[] oj = (Object[]) sequences.elementAt(i);
3993 seqs[i] = (SequenceI) oj[0];
3994 chains[i] = (String) oj[1];
4002 public void newStructureView(JalviewLite applet, PDBEntry pdb,
4003 SequenceI[] seqs, String[] chains, String protocol)
4005 // Scrub any null sequences from the array
4006 Object[] sqch = cleanSeqChainArrays(seqs, chains);
4007 seqs = (SequenceI[]) sqch[0];
4008 chains = (String[]) sqch[1];
4009 if (seqs == null || seqs.length == 0)
4012 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
4014 if (protocol == null || protocol.trim().length() == 0
4015 || protocol.equals("null"))
4017 protocol = (String) pdb.getProperty().get("protocol");
4018 if (protocol == null)
4020 System.err.println("Couldn't work out protocol to open structure: "
4025 if (applet.useXtrnalSviewer)
4027 // register the association(s) and quit, don't create any windows.
4028 if (StructureSelectionManager.getStructureSelectionManager(applet)
4029 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
4031 System.err.println("Failed to map " + pdb.getFile() + " ("
4032 + protocol + ") to any sequences");
4036 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
4038 // can only do alignments with Jmol
4039 // find the last jmol window assigned to this alignment
4040 jalview.appletgui.AppletJmol ajm = null, tajm;
4041 Vector jmols = applet
4042 .getAppletWindow(jalview.appletgui.AppletJmol.class);
4043 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
4045 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
4046 if (tajm.ap.alignFrame == this)
4055 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
4056 // try and add the pdb structure
4061 // otherwise, create a new window
4062 if (applet.jmolAvailable)
4064 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
4066 applet.lastFrameX += 40;
4067 applet.lastFrameY += 40;
4071 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
4076 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
4077 SequenceI[][] seqs, String[][] chains, String[] protocols)
4079 // TODO Auto-generated method stub
4080 System.err.println("Aligned Structure View: Not yet implemented.");
4084 * modify the current selection, providing the user has not made a selection
4088 * - sequences from this alignment
4090 * - columns to be selected on the alignment
4092 public void select(SequenceGroup sel, ColumnSelection csel)
4094 alignPanel.seqPanel.selection(sel, csel, null);
4097 public void scrollTo(int row, int column)
4099 alignPanel.seqPanel.scrollTo(row, column);
4102 public void scrollToRow(int row)
4104 alignPanel.seqPanel.scrollToRow(row);
4107 public void scrollToColumn(int column)
4109 alignPanel.seqPanel.scrollToColumn(column);
4113 * @return the alignments unique ID.
4115 public String getSequenceSetId()
4117 return viewport.getSequenceSetId();
4121 * Load the (T-Coffee) score file from the specified url
4124 * File/URL/T-COFFEE score file contents
4125 * @throws IOException
4126 * @return true if alignment was annotated with data from source
4128 public boolean loadScoreFile(String source) throws IOException
4131 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
4132 AppletFormatAdapter.checkProtocol(source));
4133 if (!file.isValid())
4135 // TODO: raise dialog for gui
4136 System.err.println("Problems parsing T-Coffee scores: "
4137 + file.getWarningMessage());
4138 System.err.println("Origin was:\n" + source);
4143 * check that the score matrix matches the alignment dimensions
4146 if ((aln = viewport.getAlignment()) != null
4147 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
4150 // TODO: raise a dialog box here rather than bomb out.
4152 .println("The scores matrix does not match the alignment dimensions");
4156 // TODO add parameter to indicate if matching should be done
4157 if (file.annotateAlignment(alignPanel.getAlignment(), false))
4159 alignPanel.fontChanged();
4160 tcoffeeColour.setEnabled(true);
4161 // switch to this color
4162 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
4167 System.err.println("Problems resolving T-Coffee scores:");
4168 if (file.getWarningMessage() != null)
4170 System.err.println(file.getWarningMessage());
4176 public SplitFrame getSplitFrame()
4178 return this.splitFrame;
4181 public void setSplitFrame(SplitFrame sf)
4183 this.splitFrame = sf;
4187 public void setShowSeqFeatures(boolean b)
4189 this.sequenceFeatures.setState(b);
4190 viewport.setShowSequenceFeatures(b);
4194 public void setMenusForViewport()
4196 // setMenusFromViewport(viewport);
4201 public void hideColumns(List<int[]> colsToHide)
4203 // TODO Auto-generated method stub
4208 public void syncHiddenSequences()
4210 // TODO Auto-generated method stub