2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.AlignViewportI;
27 import jalview.api.FeatureRenderer;
28 import jalview.api.SequenceStructureBinding;
29 import jalview.bin.JalviewLite;
30 import jalview.commands.CommandI;
31 import jalview.commands.EditCommand;
32 import jalview.commands.EditCommand.Action;
33 import jalview.commands.OrderCommand;
34 import jalview.commands.RemoveGapColCommand;
35 import jalview.commands.RemoveGapsCommand;
36 import jalview.commands.SlideSequencesCommand;
37 import jalview.commands.TrimRegionCommand;
38 import jalview.datamodel.Alignment;
39 import jalview.datamodel.AlignmentI;
40 import jalview.datamodel.AlignmentOrder;
41 import jalview.datamodel.ColumnSelection;
42 import jalview.datamodel.PDBEntry;
43 import jalview.datamodel.Sequence;
44 import jalview.datamodel.SequenceGroup;
45 import jalview.datamodel.SequenceI;
46 import jalview.io.AnnotationFile;
47 import jalview.io.AppletFormatAdapter;
48 import jalview.io.FeaturesFile;
49 import jalview.io.TCoffeeScoreFile;
50 import jalview.schemes.Blosum62ColourScheme;
51 import jalview.schemes.BuriedColourScheme;
52 import jalview.schemes.ClustalxColourScheme;
53 import jalview.schemes.ColourSchemeI;
54 import jalview.schemes.HelixColourScheme;
55 import jalview.schemes.HydrophobicColourScheme;
56 import jalview.schemes.NucleotideColourScheme;
57 import jalview.schemes.PIDColourScheme;
58 import jalview.schemes.PurinePyrimidineColourScheme;
59 import jalview.schemes.RNAHelicesColourChooser;
60 import jalview.schemes.RNAInteractionColourScheme;
61 import jalview.schemes.StrandColourScheme;
62 import jalview.schemes.TCoffeeColourScheme;
63 import jalview.schemes.TaylorColourScheme;
64 import jalview.schemes.TurnColourScheme;
65 import jalview.schemes.ZappoColourScheme;
66 import jalview.structure.StructureSelectionManager;
67 import jalview.structures.models.AAStructureBindingModel;
68 import jalview.util.MappingUtils;
69 import jalview.util.MessageManager;
71 import java.awt.BorderLayout;
72 import java.awt.Canvas;
73 import java.awt.CheckboxMenuItem;
74 import java.awt.Color;
76 import java.awt.FontMetrics;
77 import java.awt.Frame;
78 import java.awt.Graphics;
79 import java.awt.Label;
81 import java.awt.MenuBar;
82 import java.awt.MenuItem;
83 import java.awt.event.ActionEvent;
84 import java.awt.event.ActionListener;
85 import java.awt.event.FocusEvent;
86 import java.awt.event.FocusListener;
87 import java.awt.event.ItemEvent;
88 import java.awt.event.ItemListener;
89 import java.awt.event.KeyEvent;
90 import java.awt.event.KeyListener;
91 import java.awt.event.WindowAdapter;
92 import java.awt.event.WindowEvent;
93 import java.io.IOException;
95 import java.net.URLEncoder;
96 import java.util.Arrays;
97 import java.util.Deque;
98 import java.util.Hashtable;
99 import java.util.List;
100 import java.util.Map;
101 import java.util.StringTokenizer;
102 import java.util.Vector;
104 public class AlignFrame extends EmbmenuFrame implements ActionListener,
105 ItemListener, KeyListener, AlignViewControllerGuiI
107 public AlignViewControllerI avc;
109 public AlignmentPanel alignPanel;
111 public AlignViewport viewport;
113 int DEFAULT_WIDTH = 700;
115 int DEFAULT_HEIGHT = 500;
117 String jalviewServletURL;
120 * Constructor that creates the frame and adds it to the display.
127 public AlignFrame(AlignmentI al, JalviewLite applet,
128 String title, boolean embedded)
130 this(al, applet, title, embedded, true);
134 * Constructor that optionally allows the frame to be displayed or only
141 * @param addToDisplay
143 public AlignFrame(AlignmentI al, JalviewLite applet,
144 String title, boolean embedded, boolean addToDisplay)
148 jalviewServletURL = applet.getParameter("APPLICATION_URL");
154 } catch (Exception ex)
156 ex.printStackTrace();
158 // need to get window geometry before we calculate alignment layout
164 param = applet.getParameter("windowWidth");
167 int width = Integer.parseInt(param);
168 DEFAULT_WIDTH = width;
170 param = applet.getParameter("windowHeight");
173 int height = Integer.parseInt(param);
174 DEFAULT_HEIGHT = height;
176 } catch (Exception ex)
180 viewport = new AlignViewport(al, applet);
181 alignPanel = new AlignmentPanel(this, viewport);
182 avc = new jalview.controller.AlignViewController(this, viewport,
184 viewport.updateConservation(alignPanel);
185 viewport.updateConsensus(alignPanel);
187 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
188 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
189 followMouseOverFlag.setState(viewport.getFollowHighlight());
190 showGroupConsensus.setState(viewport.isShowGroupConsensus());
191 showGroupConservation.setState(viewport.isShowGroupConservation());
192 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
193 showSequenceLogo.setState(viewport.isShowSequenceLogo());
194 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
195 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
197 seqLimits.setState(viewport.getShowJVSuffix());
201 String param = applet.getParameter("sortBy");
204 if (param.equalsIgnoreCase("Id"))
206 sortIDMenuItem_actionPerformed();
208 else if (param.equalsIgnoreCase("Pairwise Identity"))
210 sortPairwiseMenuItem_actionPerformed();
212 else if (param.equalsIgnoreCase("Length"))
214 sortLengthMenuItem_actionPerformed();
218 param = applet.getParameter("wrap");
221 if (param.equalsIgnoreCase("true"))
223 wrapMenuItem.setState(true);
224 wrapMenuItem_actionPerformed();
227 param = applet.getParameter("centrecolumnlabels");
230 centreColumnLabelFlag.setState(true);
231 centreColumnLabelFlag_stateChanged();
235 if (viewport.getAlignment().isNucleotide())
237 viewport.updateStrucConsensus(alignPanel);
238 if (viewport.getAlignment().hasRNAStructure())
240 RNAHelixColour.setEnabled(true);
244 RNAHelixColour.setEnabled(false);
249 RNAHelixColour.setEnabled(false);
250 purinePyrimidineColour.setEnabled(false);
252 // Some JVMS send keyevents to Top frame or lowest panel,
253 // Havent worked out why yet. So add to both this frame and seqCanvas for
255 this.addKeyListener(this);
256 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
257 alignPanel.idPanel.idCanvas.addKeyListener(this);
258 alignPanel.scalePanel.addKeyListener(this);
259 alignPanel.annotationPanel.addKeyListener(this);
260 alignPanel.annotationPanelHolder.addKeyListener(this);
261 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
262 alignPanel.alabels.addKeyListener(this);
266 addToDisplay(embedded);
273 public void addToDisplay(boolean embedded)
275 createAlignFrameWindow(embedded);
277 alignPanel.adjustAnnotationHeight();
278 alignPanel.paintAlignment(true);
281 public AlignViewport getAlignViewport()
286 public SeqCanvas getSeqcanvas()
288 return alignPanel.seqPanel.seqCanvas;
292 * Load a features file onto the alignment
295 * file URL, content, or other resolvable path
297 * is protocol for accessing data referred to by file
300 public boolean parseFeaturesFile(String file, String type)
302 return parseFeaturesFile(file, type, true);
306 * Load a features file onto the alignment
309 * file URL, content, or other resolvable path
311 * is protocol for accessing data referred to by file
312 * @param autoenabledisplay
313 * when true, display features flag will be automatically enabled if
314 * features are loaded
315 * @return true if data parsed as a features file
317 public boolean parseFeaturesFile(String file, String type,
318 boolean autoenabledisplay)
320 // TODO: test if importing a features file onto an alignment which already
321 // has features with links overwrites the original links.
323 Hashtable featureLinks = new Hashtable();
324 boolean featuresFile = false;
327 featuresFile = new jalview.io.FeaturesFile(file, type)
328 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
329 .getFeatureRenderer().getFeatureColours(), featureLinks,
330 true, viewport.applet.getDefaultParameter(
331 "relaxedidmatch", false));
332 } catch (Exception ex)
334 ex.printStackTrace();
339 if (featureLinks.size() > 0)
341 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
343 if (autoenabledisplay)
345 viewport.setShowSequenceFeatures(true);
346 sequenceFeatures.setState(true);
348 if (alignPanel.seqPanel.seqCanvas.fr != null)
350 // update the min/max ranges where necessary
351 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
353 if (viewport.featureSettings != null)
355 viewport.featureSettings.refreshTable();
357 alignPanel.paintAlignment(true);
358 statusBar.setText(MessageManager
359 .getString("label.successfully_added_features_alignment"));
365 public void keyPressed(KeyEvent evt)
367 if (viewport.cursorMode
368 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
369 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
370 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
371 && Character.isDigit(evt.getKeyChar()))
373 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
376 switch (evt.getKeyCode())
378 case 27: // escape key
379 deselectAllSequenceMenuItem_actionPerformed();
381 alignPanel.alabels.cancelDrag();
384 if (evt.isControlDown() || evt.isMetaDown())
386 cut_actionPerformed();
390 if (viewport.cursorMode && !evt.isControlDown())
392 alignPanel.seqPanel.setCursorColumn();
394 if (evt.isControlDown() || evt.isMetaDown())
396 copy_actionPerformed();
400 if (evt.isControlDown())
402 paste(evt.isShiftDown());
406 if (evt.isControlDown() || evt.isMetaDown())
408 selectAllSequenceMenuItem_actionPerformed();
411 case KeyEvent.VK_DOWN:
412 if (viewport.cursorMode)
414 alignPanel.seqPanel.moveCursor(0, 1);
418 moveSelectedSequences(false);
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.moveCursor(0, -1);
429 moveSelectedSequences(true);
433 case KeyEvent.VK_LEFT:
434 if (evt.isAltDown() || !viewport.cursorMode)
436 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
440 alignPanel.seqPanel.moveCursor(-1, 0);
444 case KeyEvent.VK_RIGHT:
445 if (evt.isAltDown() || !viewport.cursorMode)
447 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
451 alignPanel.seqPanel.moveCursor(1, 0);
455 case KeyEvent.VK_SPACE:
456 if (viewport.cursorMode)
458 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
459 || evt.isShiftDown() || evt.isAltDown());
463 case KeyEvent.VK_DELETE:
464 case KeyEvent.VK_BACK_SPACE:
465 if (viewport.cursorMode)
467 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
468 || evt.isShiftDown() || evt.isAltDown());
472 cut_actionPerformed();
473 alignPanel.seqPanel.seqCanvas.repaint();
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.setCursorRow();
484 if (viewport.cursorMode)
486 alignPanel.seqPanel.setCursorPosition();
490 case KeyEvent.VK_ENTER:
491 case KeyEvent.VK_COMMA:
492 if (viewport.cursorMode)
494 alignPanel.seqPanel.setCursorRowAndColumn();
499 if (viewport.cursorMode)
501 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
505 if (viewport.cursorMode)
507 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
512 viewport.cursorMode = !viewport.cursorMode;
513 statusBar.setText(MessageManager.formatMessage(
514 "label.keyboard_editing_mode", new String[]
515 { (viewport.cursorMode ? "on" : "off") }));
516 if (viewport.cursorMode)
518 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
519 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
524 if (evt.isControlDown())
526 findMenuItem_actionPerformed();
532 boolean toggleSeqs = !evt.isControlDown();
533 boolean toggleCols = !evt.isShiftDown();
534 toggleHiddenRegions(toggleSeqs, toggleCols);
538 case KeyEvent.VK_PAGE_UP:
539 if (viewport.getWrapAlignment())
541 alignPanel.scrollUp(true);
545 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
546 - viewport.endSeq + viewport.startSeq);
550 case KeyEvent.VK_PAGE_DOWN:
551 if (viewport.getWrapAlignment())
553 alignPanel.scrollUp(false);
557 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
558 + viewport.endSeq - viewport.startSeq);
563 if (evt.isControlDown())
565 undoMenuItem_actionPerformed();
570 if (evt.isControlDown())
572 redoMenuItem_actionPerformed();
577 if (evt.isControlDown())
584 if (evt.isControlDown())
586 trimAlignment(false);
591 if (evt.isControlDown())
593 if (evt.isShiftDown())
595 this.removeAllGapsMenuItem_actionPerformed();
599 removeGappedColumnMenuItem_actionPerformed();
604 if (evt.isControlDown())
608 invertColSel_actionPerformed();
612 invertSequenceMenuItem_actionPerformed();
618 if (evt.isControlDown())
620 if (evt.isShiftDown())
622 this.unGroup_actionPerformed();
626 this.createGroup_actionPerformed();
632 if (evt.isControlDown())
634 this.deleteGroups_actionPerformed();
639 if (evt.isControlDown())
646 alignPanel.paintAlignment(true);
650 * called by key handler and the hide all/show all menu items
655 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
657 boolean hide = false;
658 SequenceGroup sg = viewport.getSelectionGroup();
659 if (!toggleSeqs && !toggleCols)
661 // Hide everything by the current selection - this is a hack - we do the
662 // invert and then hide
663 // first check that there will be visible columns after the invert.
664 if ((viewport.getColumnSelection() != null
665 && viewport.getColumnSelection().getSelected() != null && viewport
666 .getColumnSelection().getSelected().size() > 0)
667 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
670 // now invert the sequence set, if required - empty selection implies
671 // that no hiding is required.
674 invertSequenceMenuItem_actionPerformed();
675 sg = viewport.getSelectionGroup();
679 viewport.expandColSelection(sg, true);
680 // finally invert the column selection and get the new sequence
681 // selection and indicate it should be hidden.
682 invertColSel_actionPerformed();
689 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
692 viewport.hideAllSelectedSeqs();
694 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
697 viewport.showAllHiddenSeqs();
703 if (viewport.getColumnSelection().getSelected().size() > 0)
705 viewport.hideSelectedColumns();
708 viewport.setSelectionGroup(sg);
713 viewport.showAllHiddenColumns();
719 public void keyReleased(KeyEvent evt)
724 public void keyTyped(KeyEvent evt)
729 public void itemStateChanged(ItemEvent evt)
731 if (evt.getSource() == displayNonconservedMenuItem)
733 displayNonconservedMenuItem_actionPerformed();
735 else if (evt.getSource() == colourTextMenuItem)
737 colourTextMenuItem_actionPerformed();
739 else if (evt.getSource() == wrapMenuItem)
741 wrapMenuItem_actionPerformed();
743 else if (evt.getSource() == scaleAbove)
745 viewport.setScaleAboveWrapped(scaleAbove.getState());
747 else if (evt.getSource() == scaleLeft)
749 viewport.setScaleLeftWrapped(scaleLeft.getState());
751 else if (evt.getSource() == scaleRight)
753 viewport.setScaleRightWrapped(scaleRight.getState());
755 else if (evt.getSource() == seqLimits)
757 seqLimits_itemStateChanged();
759 else if (evt.getSource() == viewBoxesMenuItem)
761 viewport.setShowBoxes(viewBoxesMenuItem.getState());
763 else if (evt.getSource() == viewTextMenuItem)
765 viewport.setShowText(viewTextMenuItem.getState());
767 else if (evt.getSource() == renderGapsMenuItem)
769 viewport.setRenderGaps(renderGapsMenuItem.getState());
771 else if (evt.getSource() == annotationPanelMenuItem)
773 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
774 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
776 else if (evt.getSource() == sequenceFeatures)
778 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
779 alignPanel.seqPanel.seqCanvas.repaint();
781 else if (evt.getSource() == conservationMenuItem)
783 conservationMenuItem_actionPerformed();
785 else if (evt.getSource() == abovePIDThreshold)
787 abovePIDThreshold_actionPerformed();
789 else if (evt.getSource() == applyToAllGroups)
791 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
793 else if (evt.getSource() == autoCalculate)
795 viewport.autoCalculateConsensus = autoCalculate.getState();
797 else if (evt.getSource() == sortByTree)
799 viewport.sortByTree = sortByTree.getState();
801 else if (evt.getSource() == this.centreColumnLabelFlag)
803 centreColumnLabelFlag_stateChanged();
805 else if (evt.getSource() == this.followMouseOverFlag)
807 mouseOverFlag_stateChanged();
809 else if (evt.getSource() == showGroupConsensus)
811 showGroupConsensus_actionPerformed();
813 else if (evt.getSource() == showGroupConservation)
815 showGroupConservation_actionPerformed();
817 else if (evt.getSource() == showSequenceLogo)
819 showSequenceLogo_actionPerformed();
821 else if (evt.getSource() == normSequenceLogo)
823 normSequenceLogo_actionPerformed();
825 else if (evt.getSource() == showConsensusHistogram)
827 showConsensusHistogram_actionPerformed();
829 else if (evt.getSource() == applyAutoAnnotationSettings)
831 applyAutoAnnotationSettings_actionPerformed();
833 alignPanel.paintAlignment(true);
836 private void mouseOverFlag_stateChanged()
838 viewport.followHighlight = followMouseOverFlag.getState();
839 // TODO: could kick the scrollTo mechanism to reset view for current
843 private void centreColumnLabelFlag_stateChanged()
845 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
846 this.alignPanel.annotationPanel.repaint();
850 public void actionPerformed(ActionEvent evt)
852 Object source = evt.getSource();
854 if (source == inputText)
856 inputText_actionPerformed();
858 else if (source == loadTree)
860 loadTree_actionPerformed();
862 else if (source == loadApplication)
864 launchFullApplication();
866 else if (source == loadAnnotations)
870 else if (source == outputAnnotations)
872 outputAnnotations(true);
874 else if (source == outputFeatures)
876 outputFeatures(true, "Jalview");
878 else if (source == closeMenuItem)
880 closeMenuItem_actionPerformed();
882 else if (source == copy)
884 copy_actionPerformed();
886 else if (source == undoMenuItem)
888 undoMenuItem_actionPerformed();
890 else if (source == redoMenuItem)
892 redoMenuItem_actionPerformed();
894 else if (source == inputText)
896 inputText_actionPerformed();
898 else if (source == closeMenuItem)
900 closeMenuItem_actionPerformed();
902 else if (source == undoMenuItem)
904 undoMenuItem_actionPerformed();
906 else if (source == redoMenuItem)
908 redoMenuItem_actionPerformed();
910 else if (source == copy)
912 copy_actionPerformed();
914 else if (source == pasteNew)
916 pasteNew_actionPerformed();
918 else if (source == pasteThis)
920 pasteThis_actionPerformed();
922 else if (source == cut)
924 cut_actionPerformed();
926 else if (source == delete)
928 delete_actionPerformed();
930 else if (source == grpsFromSelection)
932 makeGrpsFromSelection_actionPerformed();
934 else if (source == deleteGroups)
936 deleteGroups_actionPerformed();
938 else if (source == selectAllSequenceMenuItem)
940 selectAllSequenceMenuItem_actionPerformed();
942 else if (source == deselectAllSequenceMenuItem)
944 deselectAllSequenceMenuItem_actionPerformed();
946 else if (source == invertSequenceMenuItem)
948 invertSequenceMenuItem_actionPerformed();
950 else if (source == invertColSel)
952 viewport.invertColumnSelection();
953 alignPanel.paintAlignment(true);
955 else if (source == remove2LeftMenuItem)
959 else if (source == remove2RightMenuItem)
961 trimAlignment(false);
963 else if (source == removeGappedColumnMenuItem)
965 removeGappedColumnMenuItem_actionPerformed();
967 else if (source == removeAllGapsMenuItem)
969 removeAllGapsMenuItem_actionPerformed();
971 else if (source == findMenuItem)
973 findMenuItem_actionPerformed();
975 else if (source == font)
977 new FontChooser(alignPanel);
979 else if (source == newView)
983 else if (source == showColumns)
985 viewport.showAllHiddenColumns();
986 alignPanel.paintAlignment(true);
988 else if (source == showSeqs)
990 viewport.showAllHiddenSeqs();
991 alignPanel.paintAlignment(true);
993 else if (source == hideColumns)
995 viewport.hideSelectedColumns();
996 alignPanel.paintAlignment(true);
998 else if (source == hideSequences
999 && viewport.getSelectionGroup() != null)
1001 viewport.hideAllSelectedSeqs();
1002 alignPanel.paintAlignment(true);
1004 else if (source == hideAllButSelection)
1006 toggleHiddenRegions(false, false);
1007 alignPanel.paintAlignment(true);
1009 else if (source == hideAllSelection)
1011 SequenceGroup sg = viewport.getSelectionGroup();
1012 viewport.expandColSelection(sg, false);
1013 viewport.hideAllSelectedSeqs();
1014 viewport.hideSelectedColumns();
1015 alignPanel.paintAlignment(true);
1017 else if (source == showAllHidden)
1019 viewport.showAllHiddenColumns();
1020 viewport.showAllHiddenSeqs();
1021 alignPanel.paintAlignment(true);
1023 else if (source == showGroupConsensus)
1025 showGroupConsensus_actionPerformed();
1027 else if (source == showGroupConservation)
1029 showGroupConservation_actionPerformed();
1031 else if (source == showSequenceLogo)
1033 showSequenceLogo_actionPerformed();
1035 else if (source == normSequenceLogo)
1037 normSequenceLogo_actionPerformed();
1039 else if (source == showConsensusHistogram)
1041 showConsensusHistogram_actionPerformed();
1043 else if (source == applyAutoAnnotationSettings)
1045 applyAutoAnnotationSettings_actionPerformed();
1047 else if (source == featureSettings)
1049 new FeatureSettings(alignPanel);
1051 else if (source == alProperties)
1053 StringBuffer contents = new jalview.io.AlignmentProperties(
1054 viewport.getAlignment()).formatAsString();
1055 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1056 cap.setText(contents.toString());
1057 Frame frame = new Frame();
1059 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1060 "label.alignment_properties", new String[]
1061 { getTitle() }), 400, 250);
1063 else if (source == overviewMenuItem)
1065 overviewMenuItem_actionPerformed();
1067 else if (source == noColourmenuItem)
1071 else if (source == clustalColour)
1073 abovePIDThreshold.setState(false);
1074 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1076 else if (source == zappoColour)
1078 changeColour(new ZappoColourScheme());
1080 else if (source == taylorColour)
1082 changeColour(new TaylorColourScheme());
1084 else if (source == hydrophobicityColour)
1086 changeColour(new HydrophobicColourScheme());
1088 else if (source == helixColour)
1090 changeColour(new HelixColourScheme());
1092 else if (source == strandColour)
1094 changeColour(new StrandColourScheme());
1096 else if (source == turnColour)
1098 changeColour(new TurnColourScheme());
1100 else if (source == buriedColour)
1102 changeColour(new BuriedColourScheme());
1104 else if (source == nucleotideColour)
1106 changeColour(new NucleotideColourScheme());
1108 else if (source == purinePyrimidineColour)
1110 changeColour(new PurinePyrimidineColourScheme());
1112 else if (source == RNAInteractionColour)
1114 changeColour(new RNAInteractionColourScheme());
1116 else if (source == RNAHelixColour)
1118 new RNAHelicesColourChooser(viewport, alignPanel);
1120 else if (source == modifyPID)
1122 modifyPID_actionPerformed();
1124 else if (source == modifyConservation)
1126 modifyConservation_actionPerformed();
1128 else if (source == userDefinedColour)
1130 new UserDefinedColours(alignPanel, null);
1132 else if (source == PIDColour)
1134 changeColour(new PIDColourScheme());
1136 else if (source == BLOSUM62Colour)
1138 changeColour(new Blosum62ColourScheme());
1140 else if (source == tcoffeeColour)
1142 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1144 else if (source == annotationColour)
1146 new AnnotationColourChooser(viewport, alignPanel);
1148 else if (source == annotationColumnSelection)
1150 new AnnotationColumnChooser(viewport, alignPanel);
1152 else if (source == sortPairwiseMenuItem)
1154 sortPairwiseMenuItem_actionPerformed();
1156 else if (source == sortIDMenuItem)
1158 sortIDMenuItem_actionPerformed();
1160 else if (source == sortLengthMenuItem)
1162 sortLengthMenuItem_actionPerformed();
1164 else if (source == sortGroupMenuItem)
1166 sortGroupMenuItem_actionPerformed();
1168 else if (source == removeRedundancyMenuItem)
1170 removeRedundancyMenuItem_actionPerformed();
1172 else if (source == pairwiseAlignmentMenuItem)
1174 pairwiseAlignmentMenuItem_actionPerformed();
1176 else if (source == PCAMenuItem)
1178 PCAMenuItem_actionPerformed();
1180 else if (source == averageDistanceTreeMenuItem)
1182 averageDistanceTreeMenuItem_actionPerformed();
1184 else if (source == neighbourTreeMenuItem)
1186 neighbourTreeMenuItem_actionPerformed();
1188 else if (source == njTreeBlosumMenuItem)
1190 njTreeBlosumMenuItem_actionPerformed();
1192 else if (source == avDistanceTreeBlosumMenuItem)
1194 avTreeBlosumMenuItem_actionPerformed();
1196 else if (source == documentation)
1198 documentation_actionPerformed();
1200 else if (source == about)
1202 about_actionPerformed();
1207 public void inputText_actionPerformed()
1209 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1210 Frame frame = new Frame();
1212 jalview.bin.JalviewLite.addFrame(frame,
1213 MessageManager.getString("label.input_cut_paste"), 500, 500);
1216 protected void outputText_actionPerformed(ActionEvent e)
1218 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1219 Frame frame = new Frame();
1221 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1222 "label.alignment_output_command", new Object[]
1223 { e.getActionCommand() }), 600, 500);
1224 cap.setText(new AppletFormatAdapter().formatSequences(
1225 e.getActionCommand(), viewport.getAlignment(),
1226 viewport.getShowJVSuffix()));
1229 public void loadAnnotations()
1231 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1232 cap.setText(MessageManager
1233 .getString("label.paste_features_annotations_Tcoffee_here"));
1234 cap.setAnnotationImport();
1235 Frame frame = new Frame();
1237 jalview.bin.JalviewLite.addFrame(frame,
1238 MessageManager.getString("action.paste_annotations"), 400, 300);
1242 public String outputAnnotations(boolean displayTextbox)
1244 String annotation = new AnnotationFile()
1245 .printAnnotationsForView(viewport);
1249 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1250 Frame frame = new Frame();
1252 jalview.bin.JalviewLite.addFrame(frame,
1253 MessageManager.getString("label.annotations"), 600, 500);
1254 cap.setText(annotation);
1260 private Map<String,Object> getDisplayedFeatureCols()
1262 if (alignPanel.getFeatureRenderer() != null
1263 && viewport.getFeaturesDisplayed()!= null)
1265 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1271 public String outputFeatures(boolean displayTextbox, String format)
1274 if (format.equalsIgnoreCase("Jalview"))
1276 features = new FeaturesFile().printJalviewFormat(viewport
1277 .getAlignment().getSequencesArray(),
1278 getDisplayedFeatureCols());
1282 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1283 .getSequencesArray(), getDisplayedFeatureCols());
1288 boolean frimport = false;
1289 if (features == null || features.equals("No Features Visible"))
1291 features = "# No features visible - paste some and import them here.";
1295 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1298 cap.setAnnotationImport();
1300 Frame frame = new Frame();
1302 jalview.bin.JalviewLite.addFrame(frame,
1303 MessageManager.getString("label.features"), 600, 500);
1304 cap.setText(features);
1308 if (features == null)
1317 void launchFullApplication()
1319 StringBuffer url = new StringBuffer(jalviewServletURL);
1322 + appendProtocol(viewport.applet.getParameter("file")));
1324 if (viewport.applet.getParameter("features") != null)
1326 url.append("&features=");
1327 url.append(appendProtocol(viewport.applet.getParameter("features")));
1330 if (viewport.applet.getParameter("annotations") != null)
1332 url.append("&annotations=");
1333 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1336 if (viewport.applet.getParameter("jnetfile") != null)
1338 url.append("&annotations=");
1339 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1342 if (viewport.applet.getParameter("defaultColour") != null)
1344 url.append("&colour="
1345 + removeWhiteSpace(viewport.applet
1346 .getParameter("defaultColour")));
1349 if (viewport.applet.getParameter("userDefinedColour") != null)
1351 url.append("&colour="
1352 + removeWhiteSpace(viewport.applet
1353 .getParameter("userDefinedColour")));
1355 if (viewport.applet.getParameter("tree") != null)
1358 + appendProtocol(viewport.applet.getParameter("tree")));
1360 if (viewport.applet.getParameter("treeFile") != null)
1363 + appendProtocol(viewport.applet.getParameter("treeFile")));
1366 showURL(url.toString(), "FULL_APP");
1369 String removeWhiteSpace(String colour)
1371 StringBuffer sb = new StringBuffer();
1372 for (int i = 0; i < colour.length(); i++)
1374 if (Character.isWhitespace(colour.charAt(i)))
1380 sb.append(colour.charAt(i));
1384 return sb.toString();
1387 String appendProtocol(String url)
1392 url = URLEncoder.encode(url);
1395 * When we finally deprecate 1.1 compatibility, we can start to use
1396 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1397 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1398 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1399 * ex.printStackTrace(); }
1401 catch (java.net.MalformedURLException ex)
1403 url = viewport.applet.getCodeBase() + url;
1408 public void closeMenuItem_actionPerformed()
1410 PaintRefresher.RemoveComponent(alignPanel);
1411 if (alignPanel.seqPanel != null
1412 && alignPanel.seqPanel.seqCanvas != null)
1414 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1416 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1418 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1421 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1436 void updateEditMenuBar()
1439 if (viewport.getHistoryList().size() > 0)
1441 undoMenuItem.setEnabled(true);
1442 CommandI command = viewport.getHistoryList().peek();
1443 undoMenuItem.setLabel(MessageManager.formatMessage(
1444 "label.undo_command", new Object[]
1445 { command.getDescription() }));
1449 undoMenuItem.setEnabled(false);
1450 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1453 if (viewport.getRedoList().size() > 0)
1455 redoMenuItem.setEnabled(true);
1457 CommandI command = viewport.getRedoList().peek();
1458 redoMenuItem.setLabel(MessageManager.formatMessage(
1459 "label.redo_command", new Object[]
1460 { command.getDescription() }));
1464 redoMenuItem.setEnabled(false);
1465 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1473 public void addHistoryItem(CommandI command)
1475 if (command.getSize() > 0)
1477 viewport.addToHistoryList(command);
1478 viewport.clearRedoList();
1479 updateEditMenuBar();
1480 viewport.updateHiddenColumns();
1485 * TODO: JAL-1104 DOCUMENT ME!
1490 protected void undoMenuItem_actionPerformed()
1492 if (viewport.getHistoryList().isEmpty())
1497 CommandI command = viewport.getHistoryList().pop();
1498 viewport.addToRedoList(command);
1499 command.undoCommand(null);
1501 AlignViewport originalSource = getOriginatingSource(command);
1503 if (originalSource != viewport)
1506 .println("Warning: Viewport object mismatch whilst undoing");
1508 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1509 // viewport.getColumnSelection().getHiddenColumns()
1511 updateEditMenuBar();
1512 originalSource.firePropertyChange("alignment", null, originalSource
1513 .getAlignment().getSequences());
1517 * TODO: JAL-1104 DOCUMENT ME!
1522 protected void redoMenuItem_actionPerformed()
1524 if (viewport.getRedoList().isEmpty())
1529 CommandI command = viewport.getRedoList().pop();
1530 viewport.addToHistoryList(command);
1531 command.doCommand(null);
1533 AlignViewport originalSource = getOriginatingSource(command);
1535 if (originalSource != viewport)
1538 .println("Warning: Viewport object mismatch whilst re-doing");
1540 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1541 // viewport.getColumnSelection().getHiddenColumns()
1544 updateEditMenuBar();
1545 originalSource.firePropertyChange("alignment", null, originalSource
1546 .getAlignment().getSequences());
1549 AlignViewport getOriginatingSource(CommandI command)
1551 AlignViewport originalSource = null;
1552 // For sequence removal and addition, we need to fire
1553 // the property change event FROM the viewport where the
1554 // original alignment was altered
1555 AlignmentI al = null;
1556 if (command instanceof EditCommand)
1558 EditCommand editCommand = (EditCommand) command;
1559 al = editCommand.getAlignment();
1560 Vector comps = (Vector) PaintRefresher.components.get(viewport
1561 .getSequenceSetId());
1562 for (int i = 0; i < comps.size(); i++)
1564 if (comps.elementAt(i) instanceof AlignmentPanel)
1566 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1568 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1575 if (originalSource == null)
1577 // The original view is closed, we must validate
1578 // the current view against the closed view first
1581 PaintRefresher.validateSequences(al, viewport.getAlignment());
1584 originalSource = viewport;
1587 return originalSource;
1591 * Move the currently selected sequences up or down one position in the
1596 public void moveSelectedSequences(boolean up)
1598 SequenceGroup sg = viewport.getSelectionGroup();
1603 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1604 up ? null : viewport.getHiddenRepSequences(), up);
1605 alignPanel.paintAlignment(true);
1608 * Also move cDNA/protein complement sequences
1610 AlignViewportI complement = viewport.getCodingComplement();
1611 if (complement != null)
1613 SequenceGroup mappedSelection = MappingUtils.mapSequenceGroup(sg,
1614 viewport, complement);
1615 complement.getAlignment().moveSelectedSequencesByOne(mappedSelection,
1616 up ? null : complement.getHiddenRepSequences(), up);
1617 // TODO need to trigger a repaint of the complementary panel - how?
1618 // would prefer to handle in SplitFrame but it is not overriding key
1623 synchronized void slideSequences(boolean right, int size)
1625 List<SequenceI> sg = new Vector<SequenceI>();
1626 if (viewport.cursorMode)
1628 sg.add(viewport.getAlignment().getSequenceAt(
1629 alignPanel.seqPanel.seqCanvas.cursorY));
1631 else if (viewport.getSelectionGroup() != null
1632 && viewport.getSelectionGroup().getSize() != viewport
1633 .getAlignment().getHeight())
1635 sg = viewport.getSelectionGroup().getSequences(
1636 viewport.getHiddenRepSequences());
1644 Vector<SequenceI> invertGroup = new Vector();
1646 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1648 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1650 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1654 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1656 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1658 for (int i = 0; i < invertGroup.size(); i++)
1660 seqs2[i] = invertGroup.elementAt(i);
1663 SlideSequencesCommand ssc;
1666 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1667 size, viewport.getGapCharacter());
1671 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1672 size, viewport.getGapCharacter());
1675 int groupAdjustment = 0;
1676 if (ssc.getGapsInsertedBegin() && right)
1678 if (viewport.cursorMode)
1680 alignPanel.seqPanel.moveCursor(size, 0);
1684 groupAdjustment = size;
1687 else if (!ssc.getGapsInsertedBegin() && !right)
1689 if (viewport.cursorMode)
1691 alignPanel.seqPanel.moveCursor(-size, 0);
1695 groupAdjustment = -size;
1699 if (groupAdjustment != 0)
1701 viewport.getSelectionGroup().setStartRes(
1702 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1703 viewport.getSelectionGroup().setEndRes(
1704 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1707 boolean appendHistoryItem = false;
1708 Deque<CommandI> historyList = viewport.getHistoryList();
1709 if (historyList != null && historyList.size() > 0
1710 && historyList.peek() instanceof SlideSequencesCommand)
1712 appendHistoryItem = ssc
1713 .appendSlideCommand((SlideSequencesCommand) historyList
1717 if (!appendHistoryItem)
1719 addHistoryItem(ssc);
1725 static StringBuffer copiedSequences;
1727 static Vector copiedHiddenColumns;
1729 protected void copy_actionPerformed()
1731 if (viewport.getSelectionGroup() == null)
1736 SequenceGroup sg = viewport.getSelectionGroup();
1737 copiedSequences = new StringBuffer();
1738 Hashtable orderedSeqs = new Hashtable();
1739 for (int i = 0; i < sg.getSize(); i++)
1741 SequenceI seq = sg.getSequenceAt(i);
1742 int index = viewport.getAlignment().findIndex(seq);
1743 orderedSeqs.put(index + "", seq);
1746 int index = 0, startRes, endRes;
1749 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1751 copiedHiddenColumns = new Vector();
1752 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1753 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1755 copiedHiddenColumns.addElement(new int[]
1756 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1761 copiedHiddenColumns = null;
1764 for (int i = 0; i < sg.getSize(); i++)
1766 SequenceI seq = null;
1770 if (orderedSeqs.containsKey(index + ""))
1772 seq = (SequenceI) orderedSeqs.get(index + "");
1784 // Returns residue following index if gap
1785 startRes = seq.findPosition(sg.getStartRes());
1788 // Need to find the residue preceeding index if gap
1791 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1793 ch = seq.getCharAt(j);
1794 if (!jalview.util.Comparison.isGap((ch)))
1802 endRes += seq.getStart() - 1;
1805 copiedSequences.append(seq.getName()
1811 + seq.getSequenceAsString(sg.getStartRes(),
1812 sg.getEndRes() + 1) + "\n");
1817 protected void pasteNew_actionPerformed()
1822 protected void pasteThis_actionPerformed()
1827 void paste(boolean newAlignment)
1832 if (copiedSequences == null)
1837 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1838 Vector seqs = new Vector();
1839 while (st.hasMoreElements())
1841 String name = st.nextToken();
1842 int start = Integer.parseInt(st.nextToken());
1843 int end = Integer.parseInt(st.nextToken());
1844 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1846 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1847 for (int i = 0; i < seqs.size(); i++)
1849 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1854 String newtitle = MessageManager.getString("label.copied_sequences");
1855 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1857 newtitle = getTitle();
1861 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1863 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1864 viewport.applet, newtitle, false);
1865 if (copiedHiddenColumns != null)
1867 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1869 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1870 af.viewport.hideColumns(region[0], region[1]);
1874 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1879 addSequences(newSeqs);
1882 } catch (Exception ex)
1884 } // could be anything being pasted in here
1888 void addSequences(SequenceI[] seqs)
1890 for (int i = 0; i < seqs.length; i++)
1892 viewport.getAlignment().addSequence(seqs[i]);
1896 addHistoryItem(new EditCommand(
1897 MessageManager.getString("label.add_sequences"), Action.PASTE,
1898 seqs, 0, viewport.getAlignment().getWidth(),
1899 viewport.getAlignment()));
1901 viewport.setEndSeq(viewport.getAlignment().getHeight());
1902 viewport.getAlignment().getWidth();
1903 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1908 protected void cut_actionPerformed()
1910 copy_actionPerformed();
1911 delete_actionPerformed();
1914 protected void delete_actionPerformed()
1917 SequenceGroup sg = viewport.getSelectionGroup();
1923 Vector seqs = new Vector();
1925 for (int i = 0; i < sg.getSize(); i++)
1927 seq = sg.getSequenceAt(i);
1928 seqs.addElement(seq);
1931 // If the cut affects all sequences, remove highlighted columns
1932 if (sg.getSize() == viewport.getAlignment().getHeight())
1934 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1935 sg.getEndRes() + 1);
1938 SequenceI[] cut = new SequenceI[seqs.size()];
1939 for (int i = 0; i < seqs.size(); i++)
1941 cut[i] = (SequenceI) seqs.elementAt(i);
1945 * //ADD HISTORY ITEM
1947 addHistoryItem(new EditCommand(
1948 MessageManager.getString("label.cut_sequences"), Action.CUT,
1949 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1950 viewport.getAlignment()));
1952 viewport.setSelectionGroup(null);
1953 viewport.getAlignment().deleteGroup(sg);
1955 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1958 if (viewport.getAlignment().getHeight() < 1)
1960 this.setVisible(false);
1962 viewport.sendSelection();
1966 * group consensus toggled
1969 protected void showGroupConsensus_actionPerformed()
1971 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1972 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1977 * group conservation toggled.
1979 protected void showGroupConservation_actionPerformed()
1981 viewport.setShowGroupConservation(showGroupConservation.getState());
1982 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1989 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1990 * .event.ActionEvent)
1992 protected void showConsensusHistogram_actionPerformed()
1994 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1995 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2002 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
2003 * .event.ActionEvent)
2005 protected void showSequenceLogo_actionPerformed()
2007 viewport.setShowSequenceLogo(showSequenceLogo.getState());
2008 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2011 protected void normSequenceLogo_actionPerformed()
2013 showSequenceLogo.setState(true);
2014 viewport.setShowSequenceLogo(true);
2015 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
2016 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2019 protected void applyAutoAnnotationSettings_actionPerformed()
2021 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2024 protected void makeGrpsFromSelection_actionPerformed()
2026 if (avc.makeGroupsFromSelection())
2028 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2029 alignPanel.updateAnnotation();
2030 alignPanel.paintAlignment(true);
2034 protected void createGroup_actionPerformed()
2039 protected void unGroup_actionPerformed()
2043 alignPanel.alignmentChanged();
2047 protected void deleteGroups_actionPerformed()
2049 if (avc.deleteGroups())
2051 alignPanel.alignmentChanged();
2055 public void selectAllSequenceMenuItem_actionPerformed()
2057 SequenceGroup sg = new SequenceGroup();
2058 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2060 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2062 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2063 viewport.setSelectionGroup(sg);
2064 alignPanel.paintAlignment(true);
2065 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2066 viewport.sendSelection();
2069 public void deselectAllSequenceMenuItem_actionPerformed()
2071 if (viewport.cursorMode)
2073 alignPanel.seqPanel.keyboardNo1 = null;
2074 alignPanel.seqPanel.keyboardNo2 = null;
2076 viewport.setSelectionGroup(null);
2077 viewport.getColumnSelection().clear();
2078 viewport.setSelectionGroup(null);
2079 alignPanel.idPanel.idCanvas.searchResults = null;
2080 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2081 alignPanel.paintAlignment(true);
2082 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2083 viewport.sendSelection();
2086 public void invertSequenceMenuItem_actionPerformed()
2088 SequenceGroup sg = viewport.getSelectionGroup();
2089 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2091 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2094 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2095 viewport.sendSelection();
2098 public void invertColSel_actionPerformed()
2100 viewport.invertColumnSelection();
2101 alignPanel.paintAlignment(true);
2102 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2103 viewport.sendSelection();
2106 void trimAlignment(boolean trimLeft)
2108 ColumnSelection colSel = viewport.getColumnSelection();
2111 if (colSel.size() > 0)
2115 column = colSel.getMin();
2119 column = colSel.getMax();
2123 if (viewport.getSelectionGroup() != null)
2125 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2126 viewport.getHiddenRepSequences());
2130 seqs = viewport.getAlignment().getSequencesArray();
2133 TrimRegionCommand trimRegion;
2136 trimRegion = new TrimRegionCommand("Remove Left",
2137 TrimRegionCommand.TRIM_LEFT, seqs, column,
2138 viewport.getAlignment(), viewport.getColumnSelection(),
2139 viewport.getSelectionGroup());
2140 viewport.setStartRes(0);
2144 trimRegion = new TrimRegionCommand("Remove Right",
2145 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2146 viewport.getAlignment(), viewport.getColumnSelection(),
2147 viewport.getSelectionGroup());
2150 statusBar.setText(MessageManager.formatMessage(
2151 "label.removed_columns", new String[]
2152 { Integer.valueOf(trimRegion.getSize()).toString() }));
2153 addHistoryItem(trimRegion);
2155 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2157 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2158 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2160 viewport.getAlignment().deleteGroup(sg);
2164 viewport.firePropertyChange("alignment", null, viewport
2165 .getAlignment().getSequences());
2169 public void removeGappedColumnMenuItem_actionPerformed()
2171 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2174 if (viewport.getSelectionGroup() != null)
2176 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2177 viewport.getHiddenRepSequences());
2178 start = viewport.getSelectionGroup().getStartRes();
2179 end = viewport.getSelectionGroup().getEndRes();
2183 seqs = viewport.getAlignment().getSequencesArray();
2186 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2187 "Remove Gapped Columns", seqs, start, end,
2188 viewport.getAlignment());
2190 addHistoryItem(removeGapCols);
2192 statusBar.setText(MessageManager.formatMessage(
2193 "label.removed_empty_columns", new String[]
2194 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2196 // This is to maintain viewport position on first residue
2197 // of first sequence
2198 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2199 int startRes = seq.findPosition(viewport.startRes);
2200 // ShiftList shifts;
2201 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2202 // edit.alColumnChanges=shifts.getInverse();
2203 // if (viewport.hasHiddenColumns)
2204 // viewport.getColumnSelection().compensateForEdits(shifts);
2205 viewport.setStartRes(seq.findIndex(startRes) - 1);
2206 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2211 public void removeAllGapsMenuItem_actionPerformed()
2213 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2216 if (viewport.getSelectionGroup() != null)
2218 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2219 viewport.getHiddenRepSequences());
2220 start = viewport.getSelectionGroup().getStartRes();
2221 end = viewport.getSelectionGroup().getEndRes();
2225 seqs = viewport.getAlignment().getSequencesArray();
2228 // This is to maintain viewport position on first residue
2229 // of first sequence
2230 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2231 int startRes = seq.findPosition(viewport.startRes);
2233 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2234 viewport.getAlignment()));
2236 viewport.setStartRes(seq.findIndex(startRes) - 1);
2238 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2243 public void findMenuItem_actionPerformed()
2245 new Finder(alignPanel);
2249 * create a new view derived from the current view
2252 * @return frame for the new view
2254 public AlignFrame newView(String viewtitle)
2257 if (viewport.hasHiddenRows())
2259 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2260 .getFullAlignment().getSequencesArray());
2264 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2267 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2269 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2271 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2273 newal.addAnnotation(viewport.getAlignment()
2274 .getAlignmentAnnotation()[i]);
2279 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2281 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2282 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2283 PaintRefresher.Register(newaf.alignPanel,
2284 newaf.alignPanel.av.getSequenceSetId());
2286 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2287 newaf.alignPanel.av.getSequenceSetId());
2288 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2289 newaf.alignPanel.av.getSequenceSetId());
2291 Vector comps = (Vector) PaintRefresher.components.get(viewport
2292 .getSequenceSetId());
2294 for (int i = 0; i < comps.size(); i++)
2296 if (comps.elementAt(i) instanceof AlignmentPanel)
2302 String title = new String(this.getTitle());
2303 if (viewtitle != null)
2305 title = viewtitle + " ( " + title + ")";
2309 if (title.indexOf("(View") > -1)
2311 title = title.substring(0, title.indexOf("(View"));
2313 title += "(View " + viewSize + ")";
2316 newaf.setTitle(title.toString());
2318 newaf.viewport.setHistoryList(viewport.getHistoryList());
2319 newaf.viewport.setRedoList(viewport.getRedoList());
2325 * @return list of feature groups on the view
2327 public String[] getFeatureGroups()
2329 FeatureRenderer fr = null;
2330 if (alignPanel != null
2331 && (fr = alignPanel.getFeatureRenderer()) != null)
2333 List gps = fr.getFeatureGroups();
2335 String[] _gps = new String[gps.size()];
2338 _gps[p++] = gp.toString();
2346 * get sequence feature groups that are hidden or shown
2352 public String[] getFeatureGroupsOfState(boolean visible)
2354 FeatureRenderer fr = null;
2355 if (alignPanel != null
2356 && (fr = alignPanel.getFeatureRenderer()) != null)
2358 List gps = fr.getGroups(visible);
2360 String[] _gps = new String[gps.size()];
2363 _gps[p++] = gp.toString();
2371 * Change the display state for the given feature groups
2374 * list of group strings
2376 * visible or invisible
2378 public void setFeatureGroupState(String[] groups, boolean state)
2380 FeatureRenderer fr = null;
2381 this.sequenceFeatures.setState(true);
2382 viewport.setShowSequenceFeatures(true);
2383 if (alignPanel != null
2384 && (fr = alignPanel.getFeatureRenderer()) != null)
2387 fr.setGroupVisibility(Arrays.asList(groups), state);
2388 alignPanel.seqPanel.seqCanvas.repaint();
2389 if (alignPanel.overviewPanel != null)
2391 alignPanel.overviewPanel.updateOverviewImage();
2396 public void seqLimits_itemStateChanged()
2398 viewport.setShowJVSuffix(seqLimits.getState());
2399 alignPanel.fontChanged();
2400 alignPanel.paintAlignment(true);
2403 protected void colourTextMenuItem_actionPerformed()
2405 viewport.setColourText(colourTextMenuItem.getState());
2406 alignPanel.paintAlignment(true);
2409 protected void displayNonconservedMenuItem_actionPerformed()
2411 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2412 alignPanel.paintAlignment(true);
2415 protected void wrapMenuItem_actionPerformed()
2417 viewport.setWrapAlignment(wrapMenuItem.getState());
2418 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2419 scaleAbove.setEnabled(wrapMenuItem.getState());
2420 scaleLeft.setEnabled(wrapMenuItem.getState());
2421 scaleRight.setEnabled(wrapMenuItem.getState());
2422 alignPanel.paintAlignment(true);
2425 public void overviewMenuItem_actionPerformed()
2427 if (alignPanel.overviewPanel != null)
2432 Frame frame = new Frame();
2433 OverviewPanel overview = new OverviewPanel(alignPanel);
2434 frame.add(overview);
2435 // +50 must allow for applet frame window
2436 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2437 "label.overview_params", new String[]
2438 { this.getTitle() }), overview.getPreferredSize().width,
2439 overview.getPreferredSize().height + 50);
2442 final AlignmentPanel ap = alignPanel;
2443 frame.addWindowListener(new WindowAdapter()
2446 public void windowClosing(WindowEvent e)
2450 ap.setOverviewPanel(null);
2455 alignPanel.setOverviewPanel(overview);
2459 void changeColour(ColourSchemeI cs)
2465 if (viewport.getAbovePIDThreshold())
2467 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2471 if (viewport.getConservationSelected())
2473 cs.setConservationApplied(true);
2474 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2479 cs.setConservationApplied(false);
2482 viewport.setGlobalColourScheme(cs);
2484 if (alignPanel.getOverviewPanel() != null)
2486 alignPanel.getOverviewPanel().updateOverviewImage();
2489 jalview.structure.StructureSelectionManager
2490 .getStructureSelectionManager(viewport.applet)
2491 .sequenceColoursChanged(alignPanel);
2493 alignPanel.paintAlignment(true);
2496 protected void modifyPID_actionPerformed()
2498 if (viewport.getAbovePIDThreshold()
2499 && viewport.getGlobalColourScheme() != null)
2501 SliderPanel.setPIDSliderSource(alignPanel,
2502 viewport.getGlobalColourScheme(), "Background");
2503 SliderPanel.showPIDSlider();
2507 protected void modifyConservation_actionPerformed()
2509 if (viewport.getConservationSelected()
2510 && viewport.getGlobalColourScheme() != null)
2512 SliderPanel.setConservationSlider(alignPanel,
2513 viewport.getGlobalColourScheme(), "Background");
2514 SliderPanel.showConservationSlider();
2518 protected void conservationMenuItem_actionPerformed()
2520 viewport.setConservationSelected(conservationMenuItem.getState());
2522 viewport.setAbovePIDThreshold(false);
2523 abovePIDThreshold.setState(false);
2525 changeColour(viewport.getGlobalColourScheme());
2527 modifyConservation_actionPerformed();
2530 public void abovePIDThreshold_actionPerformed()
2532 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2534 conservationMenuItem.setState(false);
2535 viewport.setConservationSelected(false);
2537 changeColour(viewport.getGlobalColourScheme());
2539 modifyPID_actionPerformed();
2542 public void sortPairwiseMenuItem_actionPerformed()
2544 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2545 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2546 .getAlignment().getSequenceAt(0), null);
2548 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2549 viewport.getAlignment()));
2550 alignPanel.paintAlignment(true);
2553 public void sortIDMenuItem_actionPerformed()
2555 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2556 AlignmentSorter.sortByID(viewport.getAlignment());
2557 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2558 viewport.getAlignment()));
2559 alignPanel.paintAlignment(true);
2562 public void sortLengthMenuItem_actionPerformed()
2564 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2565 AlignmentSorter.sortByLength(viewport.getAlignment());
2566 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2567 viewport.getAlignment()));
2568 alignPanel.paintAlignment(true);
2571 public void sortGroupMenuItem_actionPerformed()
2573 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2574 AlignmentSorter.sortByGroup(viewport.getAlignment());
2575 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2576 viewport.getAlignment()));
2577 alignPanel.paintAlignment(true);
2581 public void removeRedundancyMenuItem_actionPerformed()
2583 new RedundancyPanel(alignPanel);
2586 public void pairwiseAlignmentMenuItem_actionPerformed()
2588 if (viewport.getSelectionGroup() != null
2589 && viewport.getSelectionGroup().getSize() > 1)
2591 Frame frame = new Frame();
2592 frame.add(new PairwiseAlignPanel(alignPanel));
2593 jalview.bin.JalviewLite.addFrame(frame,
2594 MessageManager.getString("action.pairwise_alignment"), 600,
2599 public void PCAMenuItem_actionPerformed()
2601 // are the sequences aligned?
2602 if (!viewport.getAlignment().isAligned(false))
2605 int Width = viewport.getAlignment().getWidth();
2607 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2609 current = viewport.getAlignment().getSequenceAt(i);
2611 if (current.getLength() < Width)
2613 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2616 alignPanel.paintAlignment(true);
2619 if ((viewport.getSelectionGroup() != null
2620 && viewport.getSelectionGroup().getSize() < 4 && viewport
2621 .getSelectionGroup().getSize() > 0)
2622 || viewport.getAlignment().getHeight() < 4)
2629 new PCAPanel(viewport);
2630 } catch (java.lang.OutOfMemoryError ex)
2636 public void averageDistanceTreeMenuItem_actionPerformed()
2638 NewTreePanel("AV", "PID", "Average distance tree using PID");
2641 public void neighbourTreeMenuItem_actionPerformed()
2643 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2646 protected void njTreeBlosumMenuItem_actionPerformed()
2648 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2651 protected void avTreeBlosumMenuItem_actionPerformed()
2653 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2656 void NewTreePanel(String type, String pwType, String title)
2658 // are the sequences aligned?
2659 if (!viewport.getAlignment().isAligned(false))
2662 int Width = viewport.getAlignment().getWidth();
2664 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2666 current = viewport.getAlignment().getSequenceAt(i);
2668 if (current.getLength() < Width)
2670 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2673 alignPanel.paintAlignment(true);
2677 if ((viewport.getSelectionGroup() != null && viewport
2678 .getSelectionGroup().getSize() > 1)
2679 || (viewport.getAlignment().getHeight() > 1))
2681 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2683 addTreeMenuItem(tp, title);
2685 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2689 void loadTree_actionPerformed()
2691 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2692 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2693 cap.setTreeImport();
2694 Frame frame = new Frame();
2696 jalview.bin.JalviewLite.addFrame(frame,
2697 MessageManager.getString("label.paste_newick_file"), 400, 300);
2700 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2702 TreePanel tp = new TreePanel(alignPanel, treeFile,
2703 MessageManager.getString("label.load_tree_from_file"), tree);
2704 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2705 addTreeMenuItem(tp, treeFile);
2709 * sort the alignment using the given treePanel
2712 * tree used to sort view
2714 * string used for undo event name
2716 public void sortByTree(TreePanel treePanel, String title)
2718 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2720 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2721 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2722 // HistoryItem.SORT));
2723 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2724 "label.order_by_params", new String[]
2725 { title }), oldOrder, viewport.getAlignment()));
2726 alignPanel.paintAlignment(true);
2730 * Do any automatic reordering of the alignment and add the necessary bits to
2731 * the menu structure for the new tree
2736 protected void addTreeMenuItem(final TreePanel treePanel,
2739 final MenuItem item = new MenuItem(title);
2740 sortByTreeMenu.add(item);
2741 item.addActionListener(new java.awt.event.ActionListener()
2744 public void actionPerformed(ActionEvent evt)
2746 sortByTree(treePanel, title); // treePanel.getTitle());
2750 treePanel.addWindowListener(new WindowAdapter()
2753 public void windowOpened(WindowEvent e)
2755 if (viewport.sortByTree)
2757 sortByTree(treePanel, title);
2759 super.windowOpened(e);
2763 public void windowClosing(WindowEvent e)
2765 sortByTreeMenu.remove(item);
2770 public boolean sortBy(AlignmentOrder alorder, String undoname)
2772 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2773 if (viewport.applet.debug)
2775 System.err.println("Sorting " + alorder.getOrder().size()
2776 + " in alignment '" + getTitle() + "'");
2778 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2779 if (undoname != null)
2781 addHistoryItem(new OrderCommand(undoname, oldOrder,
2782 viewport.getAlignment()));
2784 alignPanel.paintAlignment(true);
2788 protected void documentation_actionPerformed()
2790 alignPanel.av.applet.openJalviewHelpUrl();
2793 protected void about_actionPerformed()
2796 class AboutPanel extends Canvas
2802 public AboutPanel(String version, String builddate)
2804 this.version = version;
2805 this.builddate = builddate;
2809 public void paint(Graphics g)
2811 g.setColor(Color.white);
2812 g.fillRect(0, 0, getSize().width, getSize().height);
2813 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2814 FontMetrics fm = g.getFontMetrics();
2815 int fh = fm.getHeight();
2817 g.setColor(Color.black);
2818 // TODO: update this text for each release or centrally store it for
2819 // lite and application
2820 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2821 g.drawString(MessageManager.formatMessage(
2822 "label.jalviewLite_release", new String[]
2823 { version }), x, y += fh);
2824 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2825 g.drawString(MessageManager.formatMessage(
2826 "label.jaview_build_date", new String[]
2827 { builddate }), x, y += fh);
2828 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2829 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2831 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2832 x + 50, y += fh + 8);
2834 MessageManager.getString("label.jalview_dev_managers"), x,
2836 g.drawString(MessageManager
2837 .getString("label.jalview_distribution_lists"), x, y += fh);
2838 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2841 MessageManager.getString("label.jalview_cite_1_authors"),
2844 MessageManager.getString("label.jalview_cite_1_title"), x,
2846 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2851 Frame frame = new Frame();
2852 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2854 jalview.bin.JalviewLite.addFrame(frame,
2855 MessageManager.getString("label.jalview"), 580, 220);
2859 public void showURL(String url, String target)
2861 if (viewport.applet == null)
2863 System.out.println("Not running as applet - no browser available.");
2867 viewport.applet.showURL(url, target);
2871 // ////////////////////////////////////////////////////////////////////////////////
2872 // JBuilder Graphics here
2874 MenuBar alignFrameMenuBar = new MenuBar();
2876 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2878 MenuItem loadApplication = new MenuItem(
2879 MessageManager.getString("label.view_full_application"));
2881 MenuItem loadTree = new MenuItem(
2882 MessageManager.getString("label.load_associated_tree"));
2884 MenuItem loadAnnotations = new MenuItem(
2885 MessageManager.getString("label.load_features_annotations"));
2887 MenuItem outputFeatures = new MenuItem(
2888 MessageManager.getString("label.export_features").concat("..."));
2890 MenuItem outputAnnotations = new MenuItem(
2891 MessageManager.getString("label.export_annotations").concat("..."));
2893 MenuItem closeMenuItem = new MenuItem(
2894 MessageManager.getString("action.close"));
2896 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2898 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2900 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2902 Menu calculateMenu = new Menu(
2903 MessageManager.getString("action.calculate"));
2905 MenuItem selectAllSequenceMenuItem = new MenuItem(
2906 MessageManager.getString("action.select_all"));
2908 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2909 MessageManager.getString("action.deselect_all"));
2911 MenuItem invertSequenceMenuItem = new MenuItem(
2912 MessageManager.getString("action.invert_selection"));
2914 MenuItem remove2LeftMenuItem = new MenuItem();
2916 MenuItem remove2RightMenuItem = new MenuItem();
2918 MenuItem removeGappedColumnMenuItem = new MenuItem();
2920 MenuItem removeAllGapsMenuItem = new MenuItem();
2922 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2924 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2926 MenuItem sortPairwiseMenuItem = new MenuItem();
2928 MenuItem sortIDMenuItem = new MenuItem();
2930 MenuItem sortLengthMenuItem = new MenuItem();
2932 MenuItem sortGroupMenuItem = new MenuItem();
2934 MenuItem removeRedundancyMenuItem = new MenuItem();
2936 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2938 MenuItem PCAMenuItem = new MenuItem();
2940 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2942 MenuItem neighbourTreeMenuItem = new MenuItem();
2944 BorderLayout borderLayout1 = new BorderLayout();
2946 public Label statusBar = new Label();
2948 Menu outputTextboxMenu = new Menu();
2950 MenuItem clustalColour = new MenuItem();
2952 MenuItem zappoColour = new MenuItem();
2954 MenuItem taylorColour = new MenuItem();
2956 MenuItem hydrophobicityColour = new MenuItem();
2958 MenuItem helixColour = new MenuItem();
2960 MenuItem strandColour = new MenuItem();
2962 MenuItem turnColour = new MenuItem();
2964 MenuItem buriedColour = new MenuItem();
2966 MenuItem purinePyrimidineColour = new MenuItem();
2968 MenuItem RNAInteractionColour = new MenuItem();
2970 MenuItem RNAHelixColour = new MenuItem();
2972 MenuItem userDefinedColour = new MenuItem();
2974 MenuItem PIDColour = new MenuItem();
2976 MenuItem BLOSUM62Colour = new MenuItem();
2978 MenuItem tcoffeeColour = new MenuItem();
2980 MenuItem njTreeBlosumMenuItem = new MenuItem();
2982 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2984 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2986 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2988 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2990 MenuItem alProperties = new MenuItem(
2991 MessageManager.getString("label.alignment_props"));
2993 MenuItem overviewMenuItem = new MenuItem();
2995 MenuItem undoMenuItem = new MenuItem();
2997 MenuItem redoMenuItem = new MenuItem();
2999 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
3001 MenuItem noColourmenuItem = new MenuItem();
3003 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
3005 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
3007 MenuItem findMenuItem = new MenuItem();
3009 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
3011 MenuItem nucleotideColour = new MenuItem();
3013 MenuItem deleteGroups = new MenuItem();
3015 MenuItem grpsFromSelection = new MenuItem();
3017 MenuItem createGroup = new MenuItem();
3019 MenuItem unGroup = new MenuItem();
3021 MenuItem delete = new MenuItem();
3023 MenuItem copy = new MenuItem();
3025 MenuItem cut = new MenuItem();
3027 Menu pasteMenu = new Menu();
3029 MenuItem pasteNew = new MenuItem();
3031 MenuItem pasteThis = new MenuItem();
3033 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3035 MenuItem font = new MenuItem();
3037 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3039 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3041 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3043 MenuItem modifyPID = new MenuItem();
3045 MenuItem modifyConservation = new MenuItem();
3047 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
3048 "Autocalculate Consensus", true);
3050 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3051 "Sort Alignment With New Tree", true);
3053 Menu sortByTreeMenu = new Menu();
3055 Menu sort = new Menu();
3057 Menu calculate = new Menu();
3059 MenuItem inputText = new MenuItem();
3061 Menu helpMenu = new Menu();
3063 MenuItem documentation = new MenuItem();
3065 MenuItem about = new MenuItem();
3067 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3069 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3071 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3073 Menu autoAnnMenu = new Menu();
3075 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3077 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3079 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3081 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3083 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3085 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3087 private void jbInit() throws Exception
3090 setMenuBar(alignFrameMenuBar);
3094 // dynamically fill save as menu with available formats
3095 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3098 item = new MenuItem(
3099 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3101 item.addActionListener(new java.awt.event.ActionListener()
3104 public void actionPerformed(ActionEvent e)
3106 outputText_actionPerformed(e);
3110 outputTextboxMenu.add(item);
3112 closeMenuItem.addActionListener(this);
3113 loadApplication.addActionListener(this);
3115 loadTree.addActionListener(this);
3116 loadAnnotations.addActionListener(this);
3117 outputFeatures.addActionListener(this);
3118 outputAnnotations.addActionListener(this);
3119 selectAllSequenceMenuItem.addActionListener(this);
3120 deselectAllSequenceMenuItem.addActionListener(this);
3121 invertSequenceMenuItem.addActionListener(this);
3122 remove2LeftMenuItem.setLabel(MessageManager
3123 .getString("action.remove_left"));
3124 remove2LeftMenuItem.addActionListener(this);
3125 remove2RightMenuItem.setLabel(MessageManager
3126 .getString("action.remove_right"));
3127 remove2RightMenuItem.addActionListener(this);
3128 removeGappedColumnMenuItem.setLabel(MessageManager
3129 .getString("action.remove_empty_columns"));
3130 removeGappedColumnMenuItem.addActionListener(this);
3131 removeAllGapsMenuItem.setLabel(MessageManager
3132 .getString("action.remove_all_gaps"));
3133 removeAllGapsMenuItem.addActionListener(this);
3134 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3135 viewBoxesMenuItem.setState(true);
3136 viewBoxesMenuItem.addItemListener(this);
3137 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3138 viewTextMenuItem.setState(true);
3139 viewTextMenuItem.addItemListener(this);
3140 sortPairwiseMenuItem.setLabel(MessageManager
3141 .getString("action.by_pairwise_id"));
3142 sortPairwiseMenuItem.addActionListener(this);
3143 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3144 sortIDMenuItem.addActionListener(this);
3145 sortLengthMenuItem.setLabel(MessageManager
3146 .getString("action.by_length"));
3147 sortLengthMenuItem.addActionListener(this);
3148 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3149 sortGroupMenuItem.addActionListener(this);
3150 removeRedundancyMenuItem.setLabel(MessageManager
3151 .getString("action.remove_redundancy").concat("..."));
3152 removeRedundancyMenuItem.addActionListener(this);
3153 pairwiseAlignmentMenuItem.setLabel(MessageManager
3154 .getString("action.pairwise_alignment"));
3155 pairwiseAlignmentMenuItem.addActionListener(this);
3156 PCAMenuItem.setLabel(MessageManager
3157 .getString("label.principal_component_analysis"));
3158 PCAMenuItem.addActionListener(this);
3159 averageDistanceTreeMenuItem.setLabel(MessageManager
3160 .getString("label.average_distance_identity"));
3161 averageDistanceTreeMenuItem.addActionListener(this);
3162 neighbourTreeMenuItem.setLabel(MessageManager
3163 .getString("label.neighbour_joining_identity"));
3164 neighbourTreeMenuItem.addActionListener(this);
3165 statusBar.setBackground(Color.white);
3166 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3167 statusBar.setText(MessageManager.getString("label.status_bar"));
3168 outputTextboxMenu.setLabel(MessageManager
3169 .getString("label.out_to_textbox"));
3170 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3172 clustalColour.addActionListener(this);
3173 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3174 zappoColour.addActionListener(this);
3175 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3176 taylorColour.addActionListener(this);
3177 hydrophobicityColour.setLabel(MessageManager
3178 .getString("label.hydrophobicity"));
3179 hydrophobicityColour.addActionListener(this);
3181 .setLabel(MessageManager.getString("label.helix_propensity"));
3182 helixColour.addActionListener(this);
3183 strandColour.setLabel(MessageManager
3184 .getString("label.strand_propensity"));
3185 strandColour.addActionListener(this);
3186 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3187 turnColour.addActionListener(this);
3188 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3189 buriedColour.addActionListener(this);
3190 purinePyrimidineColour.setLabel(MessageManager
3191 .getString("label.purine_pyrimidine"));
3192 purinePyrimidineColour.addActionListener(this);
3193 RNAInteractionColour.setLabel(MessageManager
3194 .getString("label.rna_interaction"));
3195 RNAInteractionColour.addActionListener(this);
3196 RNAHelixColour.setLabel(MessageManager
3197 .getString("action.by_rna_helixes"));
3198 RNAHelixColour.addActionListener(this);
3199 userDefinedColour.setLabel(MessageManager
3200 .getString("action.user_defined"));
3201 userDefinedColour.addActionListener(this);
3202 PIDColour.setLabel(MessageManager
3203 .getString("label.percentage_identity"));
3204 PIDColour.addActionListener(this);
3205 BLOSUM62Colour.setLabel(MessageManager
3206 .getString("label.blosum62_score"));
3207 BLOSUM62Colour.addActionListener(this);
3209 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3210 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3212 tcoffeeColour.addActionListener(this);
3213 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3214 .getString("label.average_distance_bloslum62"));
3215 avDistanceTreeBlosumMenuItem.addActionListener(this);
3216 njTreeBlosumMenuItem.setLabel(MessageManager
3217 .getString("label.neighbour_blosum62"));
3218 njTreeBlosumMenuItem.addActionListener(this);
3219 annotationPanelMenuItem.setLabel(MessageManager
3220 .getString("label.show_annotations"));
3221 annotationPanelMenuItem.addItemListener(this);
3222 colourTextMenuItem.setLabel(MessageManager
3223 .getString("label.colour_text"));
3224 colourTextMenuItem.addItemListener(this);
3225 displayNonconservedMenuItem.setLabel(MessageManager
3226 .getString("label.show_non_conversed"));
3227 displayNonconservedMenuItem.addItemListener(this);
3228 alProperties.addActionListener(this);
3229 overviewMenuItem.setLabel(MessageManager
3230 .getString("label.overview_window"));
3231 overviewMenuItem.addActionListener(this);
3232 undoMenuItem.setEnabled(false);
3233 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3234 undoMenuItem.addActionListener(this);
3235 redoMenuItem.setEnabled(false);
3236 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3237 redoMenuItem.addActionListener(this);
3238 conservationMenuItem.setLabel(MessageManager
3239 .getString("action.by_conservation"));
3240 conservationMenuItem.addItemListener(this);
3241 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3242 noColourmenuItem.addActionListener(this);
3243 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3244 wrapMenuItem.addItemListener(this);
3245 renderGapsMenuItem.setLabel(MessageManager
3246 .getString("action.show_gaps"));
3247 renderGapsMenuItem.setState(true);
3248 renderGapsMenuItem.addItemListener(this);
3249 findMenuItem.setLabel(MessageManager.getString("action.find"));
3250 findMenuItem.addActionListener(this);
3251 abovePIDThreshold.setLabel(MessageManager
3252 .getString("label.above_identity_threshold"));
3253 abovePIDThreshold.addItemListener(this);
3254 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3255 nucleotideColour.addActionListener(this);
3256 deleteGroups.setLabel(MessageManager
3257 .getString("action.undefine_groups"));
3258 deleteGroups.addActionListener(this);
3259 grpsFromSelection.setLabel(MessageManager
3260 .getString("action.make_groups_selection"));
3261 grpsFromSelection.addActionListener(this);
3262 createGroup.setLabel(MessageManager.getString("action.create_group"));
3263 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3264 copy.setLabel(MessageManager.getString("action.copy"));
3265 copy.addActionListener(this);
3266 cut.setLabel(MessageManager.getString("action.cut"));
3267 cut.addActionListener(this);
3268 delete.setLabel(MessageManager.getString("action.delete"));
3269 delete.addActionListener(this);
3270 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3271 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3272 pasteNew.addActionListener(this);
3273 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3274 pasteThis.addActionListener(this);
3275 applyToAllGroups.setLabel(MessageManager
3276 .getString("label.apply_colour_to_all_groups"));
3277 applyToAllGroups.setState(true);
3278 applyToAllGroups.addItemListener(this);
3279 font.setLabel(MessageManager.getString("action.font"));
3280 font.addActionListener(this);
3281 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3282 scaleAbove.setState(true);
3283 scaleAbove.setEnabled(false);
3284 scaleAbove.addItemListener(this);
3285 scaleLeft.setEnabled(false);
3286 scaleLeft.setState(true);
3287 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3288 scaleLeft.addItemListener(this);
3289 scaleRight.setEnabled(false);
3290 scaleRight.setState(true);
3291 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3292 scaleRight.addItemListener(this);
3293 modifyPID.setLabel(MessageManager
3294 .getString("label.modify_identity_thereshold"));
3295 modifyPID.addActionListener(this);
3296 modifyConservation.setLabel(MessageManager
3297 .getString("label.modify_conservation_thereshold"));
3298 modifyConservation.addActionListener(this);
3299 sortByTreeMenu.setLabel(MessageManager
3300 .getString("action.by_tree_order"));
3301 sort.setLabel(MessageManager.getString("action.sort"));
3302 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3303 autoCalculate.addItemListener(this);
3304 sortByTree.addItemListener(this);
3306 .setLabel(MessageManager.getString("label.input_from_textbox"));
3307 inputText.addActionListener(this);
3308 centreColumnLabelFlag.setLabel(MessageManager
3309 .getString("label.centre_column_labels"));
3310 centreColumnLabelFlag.addItemListener(this);
3311 followMouseOverFlag.setLabel(MessageManager
3312 .getString("label.automatic_scrolling"));
3313 followMouseOverFlag.addItemListener(this);
3314 helpMenu.setLabel(MessageManager.getString("action.help"));
3315 documentation.setLabel(MessageManager.getString("label.documentation"));
3316 documentation.addActionListener(this);
3318 about.setLabel(MessageManager.getString("label.about"));
3319 about.addActionListener(this);
3320 seqLimits.setState(true);
3321 seqLimits.setLabel(MessageManager
3322 .getString("label.show_sequence_limits"));
3323 seqLimits.addItemListener(this);
3324 featureSettings.setLabel(MessageManager
3325 .getString("label.feature_settings"));
3326 featureSettings.addActionListener(this);
3327 sequenceFeatures.setLabel(MessageManager
3328 .getString("label.sequence_features"));
3329 sequenceFeatures.addItemListener(this);
3330 sequenceFeatures.setState(false);
3331 annotationColour.setLabel(MessageManager
3332 .getString("action.by_annotation"));
3333 annotationColour.addActionListener(this);
3335 annotationColumnSelection.setLabel("Select by Annotation");
3336 annotationColumnSelection.addActionListener(this);
3338 invertSequenceMenuItem.setLabel(MessageManager
3339 .getString("action.invert_sequence_selection"));
3340 invertColSel.setLabel(MessageManager
3341 .getString("action.invert_column_selection"));
3342 menu1.setLabel(MessageManager.getString("action.show"));
3343 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3344 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3345 menu2.setLabel(MessageManager.getString("action.hide"));
3347 .setLabel(MessageManager.getString("label.selected_columns"));
3348 hideSequences.setLabel(MessageManager
3349 .getString("label.selected_sequences"));
3350 hideAllButSelection.setLabel(MessageManager
3351 .getString("label.all_but_selected_region"));
3352 hideAllSelection.setLabel(MessageManager
3353 .getString("label.selected_region"));
3354 showAllHidden.setLabel(MessageManager
3355 .getString("label.all_sequences_columns"));
3356 showGroupConsensus.setLabel(MessageManager
3357 .getString("label.group_consensus"));
3358 showGroupConservation.setLabel(MessageManager
3359 .getString("label.group_conservation"));
3360 showConsensusHistogram.setLabel(MessageManager
3361 .getString("label.show_consensus_histogram"));
3362 showSequenceLogo.setLabel(MessageManager
3363 .getString("label.show_consensus_logo"));
3364 normSequenceLogo.setLabel(MessageManager
3365 .getString("label.norm_consensus_logo"));
3366 applyAutoAnnotationSettings.setLabel(MessageManager
3367 .getString("label.apply_all_groups"));
3368 applyAutoAnnotationSettings.setState(true);
3369 autoAnnMenu.setLabel(MessageManager
3370 .getString("label.autocalculated_annotation"));
3372 invertColSel.addActionListener(this);
3373 showColumns.addActionListener(this);
3374 showSeqs.addActionListener(this);
3375 hideColumns.addActionListener(this);
3376 hideSequences.addActionListener(this);
3377 hideAllButSelection.addActionListener(this);
3378 hideAllSelection.addActionListener(this);
3379 showAllHidden.addActionListener(this);
3380 showGroupConsensus.addItemListener(this);
3381 showGroupConservation.addItemListener(this);
3382 showConsensusHistogram.addItemListener(this);
3383 showSequenceLogo.addItemListener(this);
3384 normSequenceLogo.addItemListener(this);
3386 applyAutoAnnotationSettings.addItemListener(this);
3387 formatMenu.setLabel(MessageManager.getString("action.format"));
3388 selectMenu.setLabel(MessageManager.getString("action.select"));
3389 newView.setLabel(MessageManager.getString("action.new_view"));
3390 newView.addActionListener(this);
3391 alignFrameMenuBar.add(fileMenu);
3392 alignFrameMenuBar.add(editMenu);
3393 alignFrameMenuBar.add(selectMenu);
3394 alignFrameMenuBar.add(viewMenu);
3395 alignFrameMenuBar.add(formatMenu);
3396 alignFrameMenuBar.add(colourMenu);
3397 alignFrameMenuBar.add(calculateMenu);
3398 alignFrameMenuBar.add(helpMenu);
3400 fileMenu.add(inputText);
3401 fileMenu.add(loadTree);
3402 fileMenu.add(loadAnnotations);
3404 fileMenu.addSeparator();
3405 fileMenu.add(outputTextboxMenu);
3406 fileMenu.add(outputFeatures);
3407 fileMenu.add(outputAnnotations);
3409 if (jalviewServletURL != null)
3411 fileMenu.add(loadApplication);
3414 fileMenu.addSeparator();
3415 fileMenu.add(closeMenuItem);
3417 editMenu.add(undoMenuItem);
3418 editMenu.add(redoMenuItem);
3421 editMenu.add(pasteMenu);
3422 editMenu.add(delete);
3423 editMenu.addSeparator();
3424 editMenu.add(remove2LeftMenuItem);
3425 editMenu.add(remove2RightMenuItem);
3426 editMenu.add(removeGappedColumnMenuItem);
3427 editMenu.add(removeAllGapsMenuItem);
3428 editMenu.add(removeRedundancyMenuItem);
3429 viewMenu.add(newView);
3430 viewMenu.addSeparator();
3431 viewMenu.add(menu1);
3432 viewMenu.add(menu2);
3433 viewMenu.addSeparator();
3434 viewMenu.add(followMouseOverFlag);
3435 viewMenu.add(annotationPanelMenuItem);
3436 autoAnnMenu.add(applyAutoAnnotationSettings);
3437 autoAnnMenu.add(showConsensusHistogram);
3438 autoAnnMenu.add(showSequenceLogo);
3439 autoAnnMenu.add(normSequenceLogo);
3440 autoAnnMenu.addSeparator();
3441 autoAnnMenu.add(showGroupConservation);
3442 autoAnnMenu.add(showGroupConsensus);
3443 viewMenu.add(autoAnnMenu);
3444 viewMenu.addSeparator();
3445 viewMenu.add(sequenceFeatures);
3446 viewMenu.add(featureSettings);
3447 viewMenu.addSeparator();
3448 viewMenu.add(alProperties);
3449 viewMenu.addSeparator();
3450 viewMenu.add(overviewMenuItem);
3451 colourMenu.add(applyToAllGroups);
3452 colourMenu.addSeparator();
3453 colourMenu.add(noColourmenuItem);
3454 colourMenu.add(clustalColour);
3455 colourMenu.add(BLOSUM62Colour);
3456 colourMenu.add(PIDColour);
3457 colourMenu.add(zappoColour);
3458 colourMenu.add(taylorColour);
3459 colourMenu.add(hydrophobicityColour);
3460 colourMenu.add(helixColour);
3461 colourMenu.add(strandColour);
3462 colourMenu.add(turnColour);
3463 colourMenu.add(buriedColour);
3464 colourMenu.add(nucleotideColour);
3465 colourMenu.add(purinePyrimidineColour);
3466 // colourMenu.add(RNAInteractionColour);
3467 colourMenu.add(tcoffeeColour);
3468 colourMenu.add(userDefinedColour);
3469 colourMenu.addSeparator();
3470 colourMenu.add(conservationMenuItem);
3471 colourMenu.add(modifyConservation);
3472 colourMenu.add(abovePIDThreshold);
3473 colourMenu.add(modifyPID);
3474 colourMenu.add(annotationColour);
3475 colourMenu.add(RNAHelixColour);
3476 calculateMenu.add(sort);
3477 calculateMenu.add(calculate);
3478 calculateMenu.addSeparator();
3479 calculateMenu.add(pairwiseAlignmentMenuItem);
3480 calculateMenu.add(PCAMenuItem);
3481 calculateMenu.add(autoCalculate);
3482 calculateMenu.add(sortByTree);
3483 this.add(statusBar, BorderLayout.SOUTH);
3484 pasteMenu.add(pasteNew);
3485 pasteMenu.add(pasteThis);
3486 sort.add(sortIDMenuItem);
3487 sort.add(sortLengthMenuItem);
3488 sort.add(sortByTreeMenu);
3489 sort.add(sortGroupMenuItem);
3490 sort.add(sortPairwiseMenuItem);
3491 calculate.add(averageDistanceTreeMenuItem);
3492 calculate.add(neighbourTreeMenuItem);
3493 calculate.add(avDistanceTreeBlosumMenuItem);
3494 calculate.add(njTreeBlosumMenuItem);
3495 helpMenu.add(documentation);
3496 helpMenu.add(about);
3497 menu1.add(showColumns);
3498 menu1.add(showSeqs);
3499 menu1.add(showAllHidden);
3500 menu2.add(hideColumns);
3501 menu2.add(hideSequences);
3502 menu2.add(hideAllSelection);
3503 menu2.add(hideAllButSelection);
3504 formatMenu.add(font);
3505 formatMenu.add(seqLimits);
3506 formatMenu.add(wrapMenuItem);
3507 formatMenu.add(scaleAbove);
3508 formatMenu.add(scaleLeft);
3509 formatMenu.add(scaleRight);
3510 formatMenu.add(viewBoxesMenuItem);
3511 formatMenu.add(viewTextMenuItem);
3512 formatMenu.add(colourTextMenuItem);
3513 formatMenu.add(displayNonconservedMenuItem);
3514 formatMenu.add(renderGapsMenuItem);
3515 formatMenu.add(centreColumnLabelFlag);
3516 selectMenu.add(findMenuItem);
3517 selectMenu.addSeparator();
3518 selectMenu.add(selectAllSequenceMenuItem);
3519 selectMenu.add(deselectAllSequenceMenuItem);
3520 selectMenu.add(invertSequenceMenuItem);
3521 selectMenu.add(invertColSel);
3522 selectMenu.add(createGroup);
3523 selectMenu.add(unGroup);
3524 selectMenu.add(grpsFromSelection);
3525 selectMenu.add(deleteGroups);
3526 selectMenu.add(annotationColumnSelection);
3530 public void setStatus(String string)
3532 statusBar.setText(string);
3535 MenuItem featureSettings = new MenuItem();
3537 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3539 MenuItem annotationColour = new MenuItem();
3541 MenuItem annotationColumnSelection = new MenuItem();
3543 MenuItem invertColSel = new MenuItem();
3545 Menu menu1 = new Menu();
3547 MenuItem showColumns = new MenuItem();
3549 MenuItem showSeqs = new MenuItem();
3551 Menu menu2 = new Menu();
3553 MenuItem hideColumns = new MenuItem();
3555 MenuItem hideSequences = new MenuItem();
3557 MenuItem hideAllButSelection = new MenuItem();
3559 MenuItem hideAllSelection = new MenuItem();
3561 MenuItem showAllHidden = new MenuItem();
3563 Menu formatMenu = new Menu();
3565 Menu selectMenu = new Menu();
3567 MenuItem newView = new MenuItem();
3570 * Attach the alignFrame panels after embedding menus, if necessary. This used
3571 * to be called setEmbedded, but is now creates the dropdown menus in a
3572 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3574 * @param reallyEmbedded
3575 * true to attach the view to the applet area on the page rather than
3578 public void createAlignFrameWindow(boolean reallyEmbedded)
3582 embedAlignFrameInApplet(viewport.applet);
3587 // test and embed menu bar if necessary.
3589 if (embedMenuIfNeeded(alignPanel))
3592 * adjust for status bar height too. ? pointless as overridden by layout
3595 alignPanel.setSize(getSize().width,
3596 getSize().height - statusBar.getHeight());
3598 add(statusBar, BorderLayout.SOUTH);
3599 add(alignPanel, BorderLayout.CENTER);
3600 // and register with the applet so it can pass external API calls to us
3601 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3608 * Add the components of this AlignFrame to the applet container.
3612 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3615 // Explicitly build the embedded menu panel for the on-page applet
3617 // view cannot be closed if its actually on the page
3618 fileMenu.remove(closeMenuItem);
3619 fileMenu.remove(3); // Remove Separator
3620 // construct embedded menu, using default font
3621 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3622 // and actually add the components to the applet area
3623 theApplet.setLayout(new BorderLayout());
3624 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3625 theApplet.add(statusBar, BorderLayout.SOUTH);
3626 // TODO should size be left to the layout manager?
3627 alignPanel.setSize(theApplet.getSize().width,
3628 theApplet.getSize().height - embeddedMenu.getHeight()
3629 - statusBar.getHeight());
3630 theApplet.add(alignPanel, BorderLayout.CENTER);
3631 final AlignFrame me = this;
3632 theApplet.addFocusListener(new FocusListener()
3636 public void focusLost(FocusEvent e)
3638 if (theApplet.currentAlignFrame == me)
3640 theApplet.currentAlignFrame = null;
3645 public void focusGained(FocusEvent e)
3647 theApplet.currentAlignFrame = me;
3650 theApplet.validate();
3654 * create a new binding between structures in an existing jmol viewer instance
3655 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3656 * this does not open a new Jmol window, or modify the display of the
3657 * structures in the original jmol window. Note This method doesn't work
3658 * without an additional javascript library to exchange messages between the
3659 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3662 * JmolViewer instance
3663 * @param sequenceIds
3664 * - sequence Ids to search for associations
3666 public SequenceStructureBinding addStructureViewInstance(
3667 Object jmolviewer, String[] sequenceIds)
3669 org.jmol.api.JmolViewer viewer = null;
3672 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3673 } catch (ClassCastException ex)
3675 System.err.println("Unsupported viewer object :"
3676 + jmolviewer.getClass());
3680 System.err.println("Can't use this object as a structure viewer:"
3681 + jmolviewer.getClass());
3684 SequenceI[] seqs = null;
3685 if (sequenceIds == null || sequenceIds.length == 0)
3687 seqs = viewport.getAlignment().getSequencesArray();
3691 Vector sqi = new Vector();
3692 AlignmentI al = viewport.getAlignment();
3693 for (int sid = 0; sid < sequenceIds.length; sid++)
3695 SequenceI sq = al.findName(sequenceIds[sid]);
3703 seqs = new SequenceI[sqi.size()];
3704 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3706 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3714 AAStructureBindingModel jmv = null;
3715 // TODO: search for a jmv that involves viewer
3717 { // create a new viewer/jalview binding.
3718 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3726 * bind a pdb file to a sequence in the current view
3729 * - sequenceId within the dataset.
3730 * @param pdbEntryString
3731 * - the short name for the PDB file
3733 * - pdb file - either a URL or a valid PDB file.
3734 * @return true if binding was as success TODO: consider making an exception
3735 * structure for indicating when PDB parsing or sequenceId location
3738 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3741 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3742 boolean needtoadd = false;
3743 if (toaddpdb != null)
3745 Vector pdbe = toaddpdb.getPDBId();
3746 PDBEntry pdbentry = null;
3747 if (pdbe != null && pdbe.size() > 0)
3749 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3751 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3752 if (!pdbentry.getId().equals(pdbEntryString)
3753 && !pdbentry.getFile().equals(pdbFile))
3763 if (pdbentry == null)
3765 pdbentry = new PDBEntry();
3766 pdbentry.setId(pdbEntryString);
3767 pdbentry.setFile(pdbFile);
3768 needtoadd = true; // add this new entry to sequence.
3770 // resolve data source
3771 // TODO: this code should be a refactored to an io package
3772 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3773 if (protocol == null)
3779 // make a note of the access mode and add
3780 if (pdbentry.getProperty() == null)
3782 pdbentry.setProperty(new Hashtable());
3784 pdbentry.getProperty().put("protocol", protocol);
3785 toaddpdb.addPDBId(pdbentry);
3786 alignPanel.getStructureSelectionManager()
3787 .registerPDBEntry(pdbentry);
3793 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3797 Vector sequences = new Vector();
3798 for (int i = 0; i < seqs.length; i++)
3800 if (seqs[i] != null)
3802 sequences.addElement(new Object[]
3803 { seqs[i], (chains != null) ? chains[i] : null });
3806 seqs = new SequenceI[sequences.size()];
3807 chains = new String[sequences.size()];
3808 for (int i = 0, isize = sequences.size(); i < isize; i++)
3810 Object[] oj = (Object[]) sequences.elementAt(i);
3812 seqs[i] = (SequenceI) oj[0];
3813 chains[i] = (String) oj[1];
3821 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3822 SequenceI[] seqs, String[] chains, String protocol)
3824 // Scrub any null sequences from the array
3825 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3826 seqs = (SequenceI[]) sqch[0];
3827 chains = (String[]) sqch[1];
3828 if (seqs == null || seqs.length == 0)
3831 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3833 if (protocol == null || protocol.trim().length() == 0
3834 || protocol.equals("null"))
3836 protocol = (String) pdb.getProperty().get("protocol");
3837 if (protocol == null)
3839 System.err.println("Couldn't work out protocol to open structure: "
3844 if (applet.useXtrnalSviewer)
3846 // register the association(s) and quit, don't create any windows.
3847 if (StructureSelectionManager.getStructureSelectionManager(applet)
3848 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3850 System.err.println("Failed to map " + pdb.getFile() + " ("
3851 + protocol + ") to any sequences");
3855 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3857 // can only do alignments with Jmol
3858 // find the last jmol window assigned to this alignment
3859 jalview.appletgui.AppletJmol ajm = null, tajm;
3860 Vector jmols = applet
3861 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3862 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3864 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3865 if (tajm.ap.alignFrame == this)
3874 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3875 // try and add the pdb structure
3880 // otherwise, create a new window
3881 if (applet.jmolAvailable)
3883 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3885 applet.lastFrameX += 40;
3886 applet.lastFrameY += 40;
3890 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3895 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3896 SequenceI[][] seqs, String[][] chains, String[] protocols)
3898 // TODO Auto-generated method stub
3899 System.err.println("Aligned Structure View: Not yet implemented.");
3903 * modify the current selection, providing the user has not made a selection
3907 * - sequences from this alignment
3909 * - columns to be selected on the alignment
3911 public void select(SequenceGroup sel, ColumnSelection csel)
3913 alignPanel.seqPanel.selection(sel, csel, null);
3916 public void scrollTo(int row, int column)
3918 alignPanel.seqPanel.scrollTo(row, column);
3921 public void scrollToRow(int row)
3923 alignPanel.seqPanel.scrollToRow(row);
3926 public void scrollToColumn(int column)
3928 alignPanel.seqPanel.scrollToColumn(column);
3932 * @return the alignments unique ID.
3934 public String getSequenceSetId()
3936 return viewport.getSequenceSetId();
3940 * Load the (T-Coffee) score file from the specified url
3943 * File/URL/T-COFFEE score file contents
3944 * @throws IOException
3945 * @return true if alignment was annotated with data from source
3947 public boolean loadScoreFile(String source) throws IOException
3950 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3951 AppletFormatAdapter.checkProtocol(source));
3952 if (!file.isValid())
3954 // TODO: raise dialog for gui
3955 System.err.println("Problems parsing T-Coffee scores: "
3956 + file.getWarningMessage());
3957 System.err.println("Origin was:\n" + source);
3962 * check that the score matrix matches the alignment dimensions
3965 if ((aln = viewport.getAlignment()) != null
3966 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3969 // TODO: raise a dialog box here rather than bomb out.
3971 .println("The scores matrix does not match the alignment dimensions");
3975 // TODO add parameter to indicate if matching should be done
3976 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3978 alignPanel.fontChanged();
3979 tcoffeeColour.setEnabled(true);
3980 // switch to this color
3981 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3986 System.err.println("Problems resolving T-Coffee scores:");
3987 if (file.getWarningMessage() != null)
3989 System.err.println(file.getWarningMessage());