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.FeatureRenderer;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.CommandI;
30 import jalview.commands.EditCommand;
31 import jalview.commands.EditCommand.Action;
32 import jalview.commands.OrderCommand;
33 import jalview.commands.RemoveGapColCommand;
34 import jalview.commands.RemoveGapsCommand;
35 import jalview.commands.SlideSequencesCommand;
36 import jalview.commands.TrimRegionCommand;
37 import jalview.datamodel.Alignment;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.ColumnSelection;
41 import jalview.datamodel.PDBEntry;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceGroup;
44 import jalview.datamodel.SequenceI;
45 import jalview.io.AnnotationFile;
46 import jalview.io.AppletFormatAdapter;
47 import jalview.io.FeaturesFile;
48 import jalview.io.TCoffeeScoreFile;
49 import jalview.schemes.Blosum62ColourScheme;
50 import jalview.schemes.BuriedColourScheme;
51 import jalview.schemes.ClustalxColourScheme;
52 import jalview.schemes.ColourSchemeI;
53 import jalview.schemes.HelixColourScheme;
54 import jalview.schemes.HydrophobicColourScheme;
55 import jalview.schemes.NucleotideColourScheme;
56 import jalview.schemes.PIDColourScheme;
57 import jalview.schemes.PurinePyrimidineColourScheme;
58 import jalview.schemes.RNAHelicesColourChooser;
59 import jalview.schemes.RNAInteractionColourScheme;
60 import jalview.schemes.StrandColourScheme;
61 import jalview.schemes.TCoffeeColourScheme;
62 import jalview.schemes.TaylorColourScheme;
63 import jalview.schemes.TurnColourScheme;
64 import jalview.schemes.ZappoColourScheme;
65 import jalview.structure.StructureSelectionManager;
66 import jalview.structures.models.AAStructureBindingModel;
67 import jalview.util.MessageManager;
69 import java.awt.BorderLayout;
70 import java.awt.Canvas;
71 import java.awt.CheckboxMenuItem;
72 import java.awt.Color;
74 import java.awt.FontMetrics;
75 import java.awt.Frame;
76 import java.awt.Graphics;
77 import java.awt.Label;
79 import java.awt.MenuBar;
80 import java.awt.MenuItem;
81 import java.awt.event.ActionEvent;
82 import java.awt.event.ActionListener;
83 import java.awt.event.FocusEvent;
84 import java.awt.event.FocusListener;
85 import java.awt.event.ItemEvent;
86 import java.awt.event.ItemListener;
87 import java.awt.event.KeyEvent;
88 import java.awt.event.KeyListener;
89 import java.awt.event.WindowAdapter;
90 import java.awt.event.WindowEvent;
91 import java.io.IOException;
93 import java.net.URLEncoder;
94 import java.util.Arrays;
95 import java.util.Deque;
96 import java.util.Hashtable;
97 import java.util.List;
99 import java.util.StringTokenizer;
100 import java.util.Vector;
102 public class AlignFrame extends EmbmenuFrame implements ActionListener,
103 ItemListener, KeyListener, AlignViewControllerGuiI
105 public AlignViewControllerI avc;
107 public AlignmentPanel alignPanel;
109 public AlignViewport viewport;
111 int DEFAULT_WIDTH = 700;
113 int DEFAULT_HEIGHT = 500;
115 String jalviewServletURL;
118 * Constructor that creates the frame and adds it to the display.
125 public AlignFrame(AlignmentI al, JalviewLite applet,
126 String title, boolean embedded)
128 this(al, applet, title, embedded, true);
132 * Constructor that optionally allows the frame to be displayed or only
139 * @param addToDisplay
141 public AlignFrame(AlignmentI al, JalviewLite applet,
142 String title, boolean embedded, boolean addToDisplay)
146 jalviewServletURL = applet.getParameter("APPLICATION_URL");
152 } catch (Exception ex)
154 ex.printStackTrace();
156 // need to get window geometry before we calculate alignment layout
162 param = applet.getParameter("windowWidth");
165 int width = Integer.parseInt(param);
166 DEFAULT_WIDTH = width;
168 param = applet.getParameter("windowHeight");
171 int height = Integer.parseInt(param);
172 DEFAULT_HEIGHT = height;
174 } catch (Exception ex)
178 viewport = new AlignViewport(al, applet);
179 alignPanel = new AlignmentPanel(this, viewport);
180 avc = new jalview.controller.AlignViewController(this, viewport,
182 viewport.updateConservation(alignPanel);
183 viewport.updateConsensus(alignPanel);
185 annotationPanelMenuItem.setState(viewport.isShowAnnotation());
186 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
187 followMouseOverFlag.setState(viewport.getFollowHighlight());
188 showGroupConsensus.setState(viewport.isShowGroupConsensus());
189 showGroupConservation.setState(viewport.isShowGroupConservation());
190 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
191 showSequenceLogo.setState(viewport.isShowSequenceLogo());
192 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
193 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
195 seqLimits.setState(viewport.getShowJVSuffix());
199 String param = applet.getParameter("sortBy");
202 if (param.equalsIgnoreCase("Id"))
204 sortIDMenuItem_actionPerformed();
206 else if (param.equalsIgnoreCase("Pairwise Identity"))
208 sortPairwiseMenuItem_actionPerformed();
210 else if (param.equalsIgnoreCase("Length"))
212 sortLengthMenuItem_actionPerformed();
216 param = applet.getParameter("wrap");
219 if (param.equalsIgnoreCase("true"))
221 wrapMenuItem.setState(true);
222 wrapMenuItem_actionPerformed();
225 param = applet.getParameter("centrecolumnlabels");
228 centreColumnLabelFlag.setState(true);
229 centreColumnLabelFlag_stateChanged();
233 if (viewport.getAlignment().isNucleotide())
235 viewport.updateStrucConsensus(alignPanel);
236 if (viewport.getAlignment().hasRNAStructure())
238 RNAHelixColour.setEnabled(true);
242 RNAHelixColour.setEnabled(false);
247 RNAHelixColour.setEnabled(false);
248 purinePyrimidineColour.setEnabled(false);
250 // Some JVMS send keyevents to Top frame or lowest panel,
251 // Havent worked out why yet. So add to both this frame and seqCanvas for
253 this.addKeyListener(this);
254 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
255 alignPanel.idPanel.idCanvas.addKeyListener(this);
256 alignPanel.scalePanel.addKeyListener(this);
257 alignPanel.annotationPanel.addKeyListener(this);
258 alignPanel.annotationPanelHolder.addKeyListener(this);
259 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
260 alignPanel.alabels.addKeyListener(this);
264 addToDisplay(embedded);
271 public void addToDisplay(boolean embedded)
273 createAlignFrameWindow(embedded);
275 alignPanel.adjustAnnotationHeight();
276 alignPanel.paintAlignment(true);
279 public AlignViewport getAlignViewport()
284 public SeqCanvas getSeqcanvas()
286 return alignPanel.seqPanel.seqCanvas;
290 * Load a features file onto the alignment
293 * file URL, content, or other resolvable path
295 * is protocol for accessing data referred to by file
298 public boolean parseFeaturesFile(String file, String type)
300 return parseFeaturesFile(file, type, true);
304 * Load a features file onto the alignment
307 * file URL, content, or other resolvable path
309 * is protocol for accessing data referred to by file
310 * @param autoenabledisplay
311 * when true, display features flag will be automatically enabled if
312 * features are loaded
313 * @return true if data parsed as a features file
315 public boolean parseFeaturesFile(String file, String type,
316 boolean autoenabledisplay)
318 // TODO: test if importing a features file onto an alignment which already
319 // has features with links overwrites the original links.
321 Hashtable featureLinks = new Hashtable();
322 boolean featuresFile = false;
325 featuresFile = new jalview.io.FeaturesFile(file, type)
326 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
327 .getFeatureRenderer().getFeatureColours(), featureLinks,
328 true, viewport.applet.getDefaultParameter(
329 "relaxedidmatch", false));
330 } catch (Exception ex)
332 ex.printStackTrace();
337 if (featureLinks.size() > 0)
339 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
341 if (autoenabledisplay)
343 viewport.setShowSequenceFeatures(true);
344 sequenceFeatures.setState(true);
346 if (alignPanel.seqPanel.seqCanvas.fr != null)
348 // update the min/max ranges where necessary
349 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
351 if (viewport.featureSettings != null)
353 viewport.featureSettings.refreshTable();
355 alignPanel.paintAlignment(true);
356 statusBar.setText(MessageManager
357 .getString("label.successfully_added_features_alignment"));
363 public void keyPressed(KeyEvent evt)
365 if (viewport.cursorMode
366 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
367 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
368 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
369 && Character.isDigit(evt.getKeyChar()))
371 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
374 switch (evt.getKeyCode())
376 case 27: // escape key
377 deselectAllSequenceMenuItem_actionPerformed();
379 alignPanel.alabels.cancelDrag();
382 if (evt.isControlDown() || evt.isMetaDown())
384 cut_actionPerformed();
388 if (viewport.cursorMode && !evt.isControlDown())
390 alignPanel.seqPanel.setCursorColumn();
392 if (evt.isControlDown() || evt.isMetaDown())
394 copy_actionPerformed();
398 if (evt.isControlDown())
400 paste(evt.isShiftDown());
404 if (evt.isControlDown() || evt.isMetaDown())
406 selectAllSequenceMenuItem_actionPerformed();
409 case KeyEvent.VK_DOWN:
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.moveCursor(0, 1);
416 moveSelectedSequences(false);
421 if (viewport.cursorMode)
423 alignPanel.seqPanel.moveCursor(0, -1);
427 moveSelectedSequences(true);
431 case KeyEvent.VK_LEFT:
432 if (evt.isAltDown() || !viewport.cursorMode)
434 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
438 alignPanel.seqPanel.moveCursor(-1, 0);
442 case KeyEvent.VK_RIGHT:
443 if (evt.isAltDown() || !viewport.cursorMode)
445 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
449 alignPanel.seqPanel.moveCursor(1, 0);
453 case KeyEvent.VK_SPACE:
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
457 || evt.isShiftDown() || evt.isAltDown());
461 case KeyEvent.VK_DELETE:
462 case KeyEvent.VK_BACK_SPACE:
463 if (viewport.cursorMode)
465 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
466 || evt.isShiftDown() || evt.isAltDown());
470 cut_actionPerformed();
471 alignPanel.seqPanel.seqCanvas.repaint();
476 if (viewport.cursorMode)
478 alignPanel.seqPanel.setCursorRow();
482 if (viewport.cursorMode)
484 alignPanel.seqPanel.setCursorPosition();
488 case KeyEvent.VK_ENTER:
489 case KeyEvent.VK_COMMA:
490 if (viewport.cursorMode)
492 alignPanel.seqPanel.setCursorRowAndColumn();
497 if (viewport.cursorMode)
499 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
503 if (viewport.cursorMode)
505 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
510 viewport.cursorMode = !viewport.cursorMode;
511 statusBar.setText(MessageManager.formatMessage(
512 "label.keyboard_editing_mode", new String[]
513 { (viewport.cursorMode ? "on" : "off") }));
514 if (viewport.cursorMode)
516 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
517 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
522 if (evt.isControlDown())
524 findMenuItem_actionPerformed();
530 boolean toggleSeqs = !evt.isControlDown();
531 boolean toggleCols = !evt.isShiftDown();
532 toggleHiddenRegions(toggleSeqs, toggleCols);
536 case KeyEvent.VK_PAGE_UP:
537 if (viewport.getWrapAlignment())
539 alignPanel.scrollUp(true);
543 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
544 - viewport.endSeq + viewport.startSeq);
548 case KeyEvent.VK_PAGE_DOWN:
549 if (viewport.getWrapAlignment())
551 alignPanel.scrollUp(false);
555 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
556 + viewport.endSeq - viewport.startSeq);
561 if (evt.isControlDown())
563 undoMenuItem_actionPerformed();
568 if (evt.isControlDown())
570 redoMenuItem_actionPerformed();
575 if (evt.isControlDown())
582 if (evt.isControlDown())
584 trimAlignment(false);
589 if (evt.isControlDown())
591 if (evt.isShiftDown())
593 this.removeAllGapsMenuItem_actionPerformed();
597 removeGappedColumnMenuItem_actionPerformed();
602 if (evt.isControlDown())
606 invertColSel_actionPerformed();
610 invertSequenceMenuItem_actionPerformed();
616 if (evt.isControlDown())
618 if (evt.isShiftDown())
620 this.unGroup_actionPerformed();
624 this.createGroup_actionPerformed();
630 if (evt.isControlDown())
632 this.deleteGroups_actionPerformed();
637 if (evt.isControlDown())
644 alignPanel.paintAlignment(true);
648 * called by key handler and the hide all/show all menu items
653 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
655 boolean hide = false;
656 SequenceGroup sg = viewport.getSelectionGroup();
657 if (!toggleSeqs && !toggleCols)
659 // Hide everything by the current selection - this is a hack - we do the
660 // invert and then hide
661 // first check that there will be visible columns after the invert.
662 if ((viewport.getColumnSelection() != null
663 && viewport.getColumnSelection().getSelected() != null && viewport
664 .getColumnSelection().getSelected().size() > 0)
665 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
668 // now invert the sequence set, if required - empty selection implies
669 // that no hiding is required.
672 invertSequenceMenuItem_actionPerformed();
673 sg = viewport.getSelectionGroup();
677 viewport.expandColSelection(sg, true);
678 // finally invert the column selection and get the new sequence
679 // selection and indicate it should be hidden.
680 invertColSel_actionPerformed();
687 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
690 viewport.hideAllSelectedSeqs();
692 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
695 viewport.showAllHiddenSeqs();
701 if (viewport.getColumnSelection().getSelected().size() > 0)
703 viewport.hideSelectedColumns();
706 viewport.setSelectionGroup(sg);
711 viewport.showAllHiddenColumns();
717 public void keyReleased(KeyEvent evt)
722 public void keyTyped(KeyEvent evt)
727 public void itemStateChanged(ItemEvent evt)
729 if (evt.getSource() == displayNonconservedMenuItem)
731 displayNonconservedMenuItem_actionPerformed();
733 else if (evt.getSource() == colourTextMenuItem)
735 colourTextMenuItem_actionPerformed();
737 else if (evt.getSource() == wrapMenuItem)
739 wrapMenuItem_actionPerformed();
741 else if (evt.getSource() == scaleAbove)
743 viewport.setScaleAboveWrapped(scaleAbove.getState());
745 else if (evt.getSource() == scaleLeft)
747 viewport.setScaleLeftWrapped(scaleLeft.getState());
749 else if (evt.getSource() == scaleRight)
751 viewport.setScaleRightWrapped(scaleRight.getState());
753 else if (evt.getSource() == seqLimits)
755 seqLimits_itemStateChanged();
757 else if (evt.getSource() == viewBoxesMenuItem)
759 viewport.setShowBoxes(viewBoxesMenuItem.getState());
761 else if (evt.getSource() == viewTextMenuItem)
763 viewport.setShowText(viewTextMenuItem.getState());
765 else if (evt.getSource() == renderGapsMenuItem)
767 viewport.setRenderGaps(renderGapsMenuItem.getState());
769 else if (evt.getSource() == annotationPanelMenuItem)
771 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
772 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
774 else if (evt.getSource() == sequenceFeatures)
776 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
777 alignPanel.seqPanel.seqCanvas.repaint();
779 else if (evt.getSource() == conservationMenuItem)
781 conservationMenuItem_actionPerformed();
783 else if (evt.getSource() == abovePIDThreshold)
785 abovePIDThreshold_actionPerformed();
787 else if (evt.getSource() == applyToAllGroups)
789 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
791 else if (evt.getSource() == autoCalculate)
793 viewport.autoCalculateConsensus = autoCalculate.getState();
795 else if (evt.getSource() == sortByTree)
797 viewport.sortByTree = sortByTree.getState();
799 else if (evt.getSource() == this.centreColumnLabelFlag)
801 centreColumnLabelFlag_stateChanged();
803 else if (evt.getSource() == this.followMouseOverFlag)
805 mouseOverFlag_stateChanged();
807 else if (evt.getSource() == showGroupConsensus)
809 showGroupConsensus_actionPerformed();
811 else if (evt.getSource() == showGroupConservation)
813 showGroupConservation_actionPerformed();
815 else if (evt.getSource() == showSequenceLogo)
817 showSequenceLogo_actionPerformed();
819 else if (evt.getSource() == normSequenceLogo)
821 normSequenceLogo_actionPerformed();
823 else if (evt.getSource() == showConsensusHistogram)
825 showConsensusHistogram_actionPerformed();
827 else if (evt.getSource() == applyAutoAnnotationSettings)
829 applyAutoAnnotationSettings_actionPerformed();
831 alignPanel.paintAlignment(true);
834 private void mouseOverFlag_stateChanged()
836 viewport.followHighlight = followMouseOverFlag.getState();
837 // TODO: could kick the scrollTo mechanism to reset view for current
841 private void centreColumnLabelFlag_stateChanged()
843 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
844 this.alignPanel.annotationPanel.repaint();
848 public void actionPerformed(ActionEvent evt)
850 Object source = evt.getSource();
852 if (source == inputText)
854 inputText_actionPerformed();
856 else if (source == loadTree)
858 loadTree_actionPerformed();
860 else if (source == loadApplication)
862 launchFullApplication();
864 else if (source == loadAnnotations)
868 else if (source == outputAnnotations)
870 outputAnnotations(true);
872 else if (source == outputFeatures)
874 outputFeatures(true, "Jalview");
876 else if (source == closeMenuItem)
878 closeMenuItem_actionPerformed();
880 else if (source == copy)
882 copy_actionPerformed();
884 else if (source == undoMenuItem)
886 undoMenuItem_actionPerformed();
888 else if (source == redoMenuItem)
890 redoMenuItem_actionPerformed();
892 else if (source == inputText)
894 inputText_actionPerformed();
896 else if (source == closeMenuItem)
898 closeMenuItem_actionPerformed();
900 else if (source == undoMenuItem)
902 undoMenuItem_actionPerformed();
904 else if (source == redoMenuItem)
906 redoMenuItem_actionPerformed();
908 else if (source == copy)
910 copy_actionPerformed();
912 else if (source == pasteNew)
914 pasteNew_actionPerformed();
916 else if (source == pasteThis)
918 pasteThis_actionPerformed();
920 else if (source == cut)
922 cut_actionPerformed();
924 else if (source == delete)
926 delete_actionPerformed();
928 else if (source == grpsFromSelection)
930 makeGrpsFromSelection_actionPerformed();
932 else if (source == deleteGroups)
934 deleteGroups_actionPerformed();
936 else if (source == selectAllSequenceMenuItem)
938 selectAllSequenceMenuItem_actionPerformed();
940 else if (source == deselectAllSequenceMenuItem)
942 deselectAllSequenceMenuItem_actionPerformed();
944 else if (source == invertSequenceMenuItem)
946 invertSequenceMenuItem_actionPerformed();
948 else if (source == invertColSel)
950 viewport.invertColumnSelection();
951 alignPanel.paintAlignment(true);
953 else if (source == remove2LeftMenuItem)
957 else if (source == remove2RightMenuItem)
959 trimAlignment(false);
961 else if (source == removeGappedColumnMenuItem)
963 removeGappedColumnMenuItem_actionPerformed();
965 else if (source == removeAllGapsMenuItem)
967 removeAllGapsMenuItem_actionPerformed();
969 else if (source == findMenuItem)
971 findMenuItem_actionPerformed();
973 else if (source == font)
975 new FontChooser(alignPanel);
977 else if (source == newView)
981 else if (source == showColumns)
983 viewport.showAllHiddenColumns();
984 alignPanel.paintAlignment(true);
986 else if (source == showSeqs)
988 viewport.showAllHiddenSeqs();
989 alignPanel.paintAlignment(true);
991 else if (source == hideColumns)
993 viewport.hideSelectedColumns();
994 alignPanel.paintAlignment(true);
996 else if (source == hideSequences
997 && viewport.getSelectionGroup() != null)
999 viewport.hideAllSelectedSeqs();
1000 alignPanel.paintAlignment(true);
1002 else if (source == hideAllButSelection)
1004 toggleHiddenRegions(false, false);
1005 alignPanel.paintAlignment(true);
1007 else if (source == hideAllSelection)
1009 SequenceGroup sg = viewport.getSelectionGroup();
1010 viewport.expandColSelection(sg, false);
1011 viewport.hideAllSelectedSeqs();
1012 viewport.hideSelectedColumns();
1013 alignPanel.paintAlignment(true);
1015 else if (source == showAllHidden)
1017 viewport.showAllHiddenColumns();
1018 viewport.showAllHiddenSeqs();
1019 alignPanel.paintAlignment(true);
1021 else if (source == showGroupConsensus)
1023 showGroupConsensus_actionPerformed();
1025 else if (source == showGroupConservation)
1027 showGroupConservation_actionPerformed();
1029 else if (source == showSequenceLogo)
1031 showSequenceLogo_actionPerformed();
1033 else if (source == normSequenceLogo)
1035 normSequenceLogo_actionPerformed();
1037 else if (source == showConsensusHistogram)
1039 showConsensusHistogram_actionPerformed();
1041 else if (source == applyAutoAnnotationSettings)
1043 applyAutoAnnotationSettings_actionPerformed();
1045 else if (source == featureSettings)
1047 new FeatureSettings(alignPanel);
1049 else if (source == alProperties)
1051 StringBuffer contents = new jalview.io.AlignmentProperties(
1052 viewport.getAlignment()).formatAsString();
1053 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1054 cap.setText(contents.toString());
1055 Frame frame = new Frame();
1057 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1058 "label.alignment_properties", new String[]
1059 { getTitle() }), 400, 250);
1061 else if (source == overviewMenuItem)
1063 overviewMenuItem_actionPerformed();
1065 else if (source == noColourmenuItem)
1069 else if (source == clustalColour)
1071 abovePIDThreshold.setState(false);
1072 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1074 else if (source == zappoColour)
1076 changeColour(new ZappoColourScheme());
1078 else if (source == taylorColour)
1080 changeColour(new TaylorColourScheme());
1082 else if (source == hydrophobicityColour)
1084 changeColour(new HydrophobicColourScheme());
1086 else if (source == helixColour)
1088 changeColour(new HelixColourScheme());
1090 else if (source == strandColour)
1092 changeColour(new StrandColourScheme());
1094 else if (source == turnColour)
1096 changeColour(new TurnColourScheme());
1098 else if (source == buriedColour)
1100 changeColour(new BuriedColourScheme());
1102 else if (source == nucleotideColour)
1104 changeColour(new NucleotideColourScheme());
1106 else if (source == purinePyrimidineColour)
1108 changeColour(new PurinePyrimidineColourScheme());
1110 else if (source == RNAInteractionColour)
1112 changeColour(new RNAInteractionColourScheme());
1114 else if (source == RNAHelixColour)
1116 new RNAHelicesColourChooser(viewport, alignPanel);
1118 else if (source == modifyPID)
1120 modifyPID_actionPerformed();
1122 else if (source == modifyConservation)
1124 modifyConservation_actionPerformed();
1126 else if (source == userDefinedColour)
1128 new UserDefinedColours(alignPanel, null);
1130 else if (source == PIDColour)
1132 changeColour(new PIDColourScheme());
1134 else if (source == BLOSUM62Colour)
1136 changeColour(new Blosum62ColourScheme());
1138 else if (source == tcoffeeColour)
1140 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1142 else if (source == annotationColour)
1144 new AnnotationColourChooser(viewport, alignPanel);
1146 else if (source == annotationColumnSelection)
1148 new AnnotationColumnChooser(viewport, alignPanel);
1150 else if (source == sortPairwiseMenuItem)
1152 sortPairwiseMenuItem_actionPerformed();
1154 else if (source == sortIDMenuItem)
1156 sortIDMenuItem_actionPerformed();
1158 else if (source == sortLengthMenuItem)
1160 sortLengthMenuItem_actionPerformed();
1162 else if (source == sortGroupMenuItem)
1164 sortGroupMenuItem_actionPerformed();
1166 else if (source == removeRedundancyMenuItem)
1168 removeRedundancyMenuItem_actionPerformed();
1170 else if (source == pairwiseAlignmentMenuItem)
1172 pairwiseAlignmentMenuItem_actionPerformed();
1174 else if (source == PCAMenuItem)
1176 PCAMenuItem_actionPerformed();
1178 else if (source == averageDistanceTreeMenuItem)
1180 averageDistanceTreeMenuItem_actionPerformed();
1182 else if (source == neighbourTreeMenuItem)
1184 neighbourTreeMenuItem_actionPerformed();
1186 else if (source == njTreeBlosumMenuItem)
1188 njTreeBlosumMenuItem_actionPerformed();
1190 else if (source == avDistanceTreeBlosumMenuItem)
1192 avTreeBlosumMenuItem_actionPerformed();
1194 else if (source == documentation)
1196 documentation_actionPerformed();
1198 else if (source == about)
1200 about_actionPerformed();
1205 public void inputText_actionPerformed()
1207 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1208 Frame frame = new Frame();
1210 jalview.bin.JalviewLite.addFrame(frame,
1211 MessageManager.getString("label.input_cut_paste"), 500, 500);
1214 protected void outputText_actionPerformed(ActionEvent e)
1216 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1217 Frame frame = new Frame();
1219 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1220 "label.alignment_output_command", new Object[]
1221 { e.getActionCommand() }), 600, 500);
1222 cap.setText(new AppletFormatAdapter().formatSequences(
1223 e.getActionCommand(), viewport.getAlignment(),
1224 viewport.getShowJVSuffix()));
1227 public void loadAnnotations()
1229 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1230 cap.setText(MessageManager
1231 .getString("label.paste_features_annotations_Tcoffee_here"));
1232 cap.setAnnotationImport();
1233 Frame frame = new Frame();
1235 jalview.bin.JalviewLite.addFrame(frame,
1236 MessageManager.getString("action.paste_annotations"), 400, 300);
1240 public String outputAnnotations(boolean displayTextbox)
1242 String annotation = new AnnotationFile()
1243 .printAnnotationsForView(viewport);
1247 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1248 Frame frame = new Frame();
1250 jalview.bin.JalviewLite.addFrame(frame,
1251 MessageManager.getString("label.annotations"), 600, 500);
1252 cap.setText(annotation);
1258 private Map<String,Object> getDisplayedFeatureCols()
1260 if (alignPanel.getFeatureRenderer() != null
1261 && viewport.getFeaturesDisplayed()!= null)
1263 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1269 public String outputFeatures(boolean displayTextbox, String format)
1272 if (format.equalsIgnoreCase("Jalview"))
1274 features = new FeaturesFile().printJalviewFormat(viewport
1275 .getAlignment().getSequencesArray(),
1276 getDisplayedFeatureCols());
1280 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1281 .getSequencesArray(), getDisplayedFeatureCols());
1286 boolean frimport = false;
1287 if (features == null || features.equals("No Features Visible"))
1289 features = "# No features visible - paste some and import them here.";
1293 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1296 cap.setAnnotationImport();
1298 Frame frame = new Frame();
1300 jalview.bin.JalviewLite.addFrame(frame,
1301 MessageManager.getString("label.features"), 600, 500);
1302 cap.setText(features);
1306 if (features == null)
1315 void launchFullApplication()
1317 StringBuffer url = new StringBuffer(jalviewServletURL);
1320 + appendProtocol(viewport.applet.getParameter("file")));
1322 if (viewport.applet.getParameter("features") != null)
1324 url.append("&features=");
1325 url.append(appendProtocol(viewport.applet.getParameter("features")));
1328 if (viewport.applet.getParameter("annotations") != null)
1330 url.append("&annotations=");
1331 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1334 if (viewport.applet.getParameter("jnetfile") != null)
1336 url.append("&annotations=");
1337 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1340 if (viewport.applet.getParameter("defaultColour") != null)
1342 url.append("&colour="
1343 + removeWhiteSpace(viewport.applet
1344 .getParameter("defaultColour")));
1347 if (viewport.applet.getParameter("userDefinedColour") != null)
1349 url.append("&colour="
1350 + removeWhiteSpace(viewport.applet
1351 .getParameter("userDefinedColour")));
1353 if (viewport.applet.getParameter("tree") != null)
1356 + appendProtocol(viewport.applet.getParameter("tree")));
1358 if (viewport.applet.getParameter("treeFile") != null)
1361 + appendProtocol(viewport.applet.getParameter("treeFile")));
1364 showURL(url.toString(), "FULL_APP");
1367 String removeWhiteSpace(String colour)
1369 StringBuffer sb = new StringBuffer();
1370 for (int i = 0; i < colour.length(); i++)
1372 if (Character.isWhitespace(colour.charAt(i)))
1378 sb.append(colour.charAt(i));
1382 return sb.toString();
1385 String appendProtocol(String url)
1390 url = URLEncoder.encode(url);
1393 * When we finally deprecate 1.1 compatibility, we can start to use
1394 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1395 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1396 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1397 * ex.printStackTrace(); }
1399 catch (java.net.MalformedURLException ex)
1401 url = viewport.applet.getCodeBase() + url;
1406 public void closeMenuItem_actionPerformed()
1408 PaintRefresher.RemoveComponent(alignPanel);
1409 if (alignPanel.seqPanel != null
1410 && alignPanel.seqPanel.seqCanvas != null)
1412 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1414 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1416 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1419 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1434 void updateEditMenuBar()
1437 if (viewport.getHistoryList().size() > 0)
1439 undoMenuItem.setEnabled(true);
1440 CommandI command = viewport.getHistoryList().peek();
1441 undoMenuItem.setLabel(MessageManager.formatMessage(
1442 "label.undo_command", new Object[]
1443 { command.getDescription() }));
1447 undoMenuItem.setEnabled(false);
1448 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1451 if (viewport.getRedoList().size() > 0)
1453 redoMenuItem.setEnabled(true);
1455 CommandI command = viewport.getRedoList().peek();
1456 redoMenuItem.setLabel(MessageManager.formatMessage(
1457 "label.redo_command", new Object[]
1458 { command.getDescription() }));
1462 redoMenuItem.setEnabled(false);
1463 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1471 public void addHistoryItem(CommandI command)
1473 if (command.getSize() > 0)
1475 viewport.addToHistoryList(command);
1476 viewport.clearRedoList();
1477 updateEditMenuBar();
1478 viewport.updateHiddenColumns();
1483 * TODO: JAL-1104 DOCUMENT ME!
1488 protected void undoMenuItem_actionPerformed()
1490 if (viewport.getHistoryList().isEmpty())
1495 CommandI command = viewport.getHistoryList().pop();
1496 viewport.addToRedoList(command);
1497 command.undoCommand(null);
1499 AlignViewport originalSource = getOriginatingSource(command);
1501 if (originalSource != viewport)
1504 .println("Warning: Viewport object mismatch whilst undoing");
1506 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1507 // viewport.getColumnSelection().getHiddenColumns()
1509 updateEditMenuBar();
1510 originalSource.firePropertyChange("alignment", null, originalSource
1511 .getAlignment().getSequences());
1515 * TODO: JAL-1104 DOCUMENT ME!
1520 protected void redoMenuItem_actionPerformed()
1522 if (viewport.getRedoList().isEmpty())
1527 CommandI command = viewport.getRedoList().pop();
1528 viewport.addToHistoryList(command);
1529 command.doCommand(null);
1531 AlignViewport originalSource = getOriginatingSource(command);
1533 if (originalSource != viewport)
1536 .println("Warning: Viewport object mismatch whilst re-doing");
1538 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1539 // viewport.getColumnSelection().getHiddenColumns()
1542 updateEditMenuBar();
1543 originalSource.firePropertyChange("alignment", null, originalSource
1544 .getAlignment().getSequences());
1547 AlignViewport getOriginatingSource(CommandI command)
1549 AlignViewport originalSource = null;
1550 // For sequence removal and addition, we need to fire
1551 // the property change event FROM the viewport where the
1552 // original alignment was altered
1553 AlignmentI al = null;
1554 if (command instanceof EditCommand)
1556 EditCommand editCommand = (EditCommand) command;
1557 al = editCommand.getAlignment();
1558 Vector comps = (Vector) PaintRefresher.components.get(viewport
1559 .getSequenceSetId());
1560 for (int i = 0; i < comps.size(); i++)
1562 if (comps.elementAt(i) instanceof AlignmentPanel)
1564 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1566 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1573 if (originalSource == null)
1575 // The original view is closed, we must validate
1576 // the current view against the closed view first
1579 PaintRefresher.validateSequences(al, viewport.getAlignment());
1582 originalSource = viewport;
1585 return originalSource;
1588 public void moveSelectedSequences(boolean up)
1590 SequenceGroup sg = viewport.getSelectionGroup();
1595 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1596 up ? null : viewport.getHiddenRepSequences(), up);
1597 alignPanel.paintAlignment(true);
1600 synchronized void slideSequences(boolean right, int size)
1602 List<SequenceI> sg = new Vector<SequenceI>();
1603 if (viewport.cursorMode)
1605 sg.add(viewport.getAlignment().getSequenceAt(
1606 alignPanel.seqPanel.seqCanvas.cursorY));
1608 else if (viewport.getSelectionGroup() != null
1609 && viewport.getSelectionGroup().getSize() != viewport
1610 .getAlignment().getHeight())
1612 sg = viewport.getSelectionGroup().getSequences(
1613 viewport.getHiddenRepSequences());
1621 Vector<SequenceI> invertGroup = new Vector();
1623 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1625 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1627 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1631 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1633 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1635 for (int i = 0; i < invertGroup.size(); i++)
1637 seqs2[i] = invertGroup.elementAt(i);
1640 SlideSequencesCommand ssc;
1643 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1644 size, viewport.getGapCharacter());
1648 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1649 size, viewport.getGapCharacter());
1652 int groupAdjustment = 0;
1653 if (ssc.getGapsInsertedBegin() && right)
1655 if (viewport.cursorMode)
1657 alignPanel.seqPanel.moveCursor(size, 0);
1661 groupAdjustment = size;
1664 else if (!ssc.getGapsInsertedBegin() && !right)
1666 if (viewport.cursorMode)
1668 alignPanel.seqPanel.moveCursor(-size, 0);
1672 groupAdjustment = -size;
1676 if (groupAdjustment != 0)
1678 viewport.getSelectionGroup().setStartRes(
1679 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1680 viewport.getSelectionGroup().setEndRes(
1681 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1684 boolean appendHistoryItem = false;
1685 Deque<CommandI> historyList = viewport.getHistoryList();
1686 if (historyList != null && historyList.size() > 0
1687 && historyList.peek() instanceof SlideSequencesCommand)
1689 appendHistoryItem = ssc
1690 .appendSlideCommand((SlideSequencesCommand) historyList
1694 if (!appendHistoryItem)
1696 addHistoryItem(ssc);
1702 static StringBuffer copiedSequences;
1704 static Vector copiedHiddenColumns;
1706 protected void copy_actionPerformed()
1708 if (viewport.getSelectionGroup() == null)
1713 SequenceGroup sg = viewport.getSelectionGroup();
1714 copiedSequences = new StringBuffer();
1715 Hashtable orderedSeqs = new Hashtable();
1716 for (int i = 0; i < sg.getSize(); i++)
1718 SequenceI seq = sg.getSequenceAt(i);
1719 int index = viewport.getAlignment().findIndex(seq);
1720 orderedSeqs.put(index + "", seq);
1723 int index = 0, startRes, endRes;
1726 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1728 copiedHiddenColumns = new Vector();
1729 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1730 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1732 copiedHiddenColumns.addElement(new int[]
1733 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1738 copiedHiddenColumns = null;
1741 for (int i = 0; i < sg.getSize(); i++)
1743 SequenceI seq = null;
1747 if (orderedSeqs.containsKey(index + ""))
1749 seq = (SequenceI) orderedSeqs.get(index + "");
1761 // Returns residue following index if gap
1762 startRes = seq.findPosition(sg.getStartRes());
1765 // Need to find the residue preceeding index if gap
1768 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1770 ch = seq.getCharAt(j);
1771 if (!jalview.util.Comparison.isGap((ch)))
1779 endRes += seq.getStart() - 1;
1782 copiedSequences.append(seq.getName()
1788 + seq.getSequenceAsString(sg.getStartRes(),
1789 sg.getEndRes() + 1) + "\n");
1794 protected void pasteNew_actionPerformed()
1799 protected void pasteThis_actionPerformed()
1804 void paste(boolean newAlignment)
1809 if (copiedSequences == null)
1814 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1815 Vector seqs = new Vector();
1816 while (st.hasMoreElements())
1818 String name = st.nextToken();
1819 int start = Integer.parseInt(st.nextToken());
1820 int end = Integer.parseInt(st.nextToken());
1821 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1823 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1824 for (int i = 0; i < seqs.size(); i++)
1826 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1831 String newtitle = MessageManager.getString("label.copied_sequences");
1832 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1834 newtitle = getTitle();
1838 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1840 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1841 viewport.applet, newtitle, false);
1842 if (copiedHiddenColumns != null)
1844 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1846 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1847 af.viewport.hideColumns(region[0], region[1]);
1851 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1856 addSequences(newSeqs);
1859 } catch (Exception ex)
1861 } // could be anything being pasted in here
1865 void addSequences(SequenceI[] seqs)
1867 for (int i = 0; i < seqs.length; i++)
1869 viewport.getAlignment().addSequence(seqs[i]);
1873 addHistoryItem(new EditCommand(
1874 MessageManager.getString("label.add_sequences"), Action.PASTE,
1875 seqs, 0, viewport.getAlignment().getWidth(),
1876 viewport.getAlignment()));
1878 viewport.setEndSeq(viewport.getAlignment().getHeight());
1879 viewport.getAlignment().getWidth();
1880 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1885 protected void cut_actionPerformed()
1887 copy_actionPerformed();
1888 delete_actionPerformed();
1891 protected void delete_actionPerformed()
1894 SequenceGroup sg = viewport.getSelectionGroup();
1900 Vector seqs = new Vector();
1902 for (int i = 0; i < sg.getSize(); i++)
1904 seq = sg.getSequenceAt(i);
1905 seqs.addElement(seq);
1908 // If the cut affects all sequences, remove highlighted columns
1909 if (sg.getSize() == viewport.getAlignment().getHeight())
1911 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1912 sg.getEndRes() + 1);
1915 SequenceI[] cut = new SequenceI[seqs.size()];
1916 for (int i = 0; i < seqs.size(); i++)
1918 cut[i] = (SequenceI) seqs.elementAt(i);
1922 * //ADD HISTORY ITEM
1924 addHistoryItem(new EditCommand(
1925 MessageManager.getString("label.cut_sequences"), Action.CUT,
1926 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1927 viewport.getAlignment()));
1929 viewport.setSelectionGroup(null);
1930 viewport.getAlignment().deleteGroup(sg);
1932 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1935 if (viewport.getAlignment().getHeight() < 1)
1937 this.setVisible(false);
1939 viewport.sendSelection();
1943 * group consensus toggled
1946 protected void showGroupConsensus_actionPerformed()
1948 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1949 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1954 * group conservation toggled.
1956 protected void showGroupConservation_actionPerformed()
1958 viewport.setShowGroupConservation(showGroupConservation.getState());
1959 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1966 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1967 * .event.ActionEvent)
1969 protected void showConsensusHistogram_actionPerformed()
1971 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1972 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1979 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1980 * .event.ActionEvent)
1982 protected void showSequenceLogo_actionPerformed()
1984 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1985 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1988 protected void normSequenceLogo_actionPerformed()
1990 showSequenceLogo.setState(true);
1991 viewport.setShowSequenceLogo(true);
1992 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1993 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1996 protected void applyAutoAnnotationSettings_actionPerformed()
1998 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
2001 protected void makeGrpsFromSelection_actionPerformed()
2003 if (avc.makeGroupsFromSelection())
2005 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
2006 alignPanel.updateAnnotation();
2007 alignPanel.paintAlignment(true);
2011 protected void createGroup_actionPerformed()
2016 protected void unGroup_actionPerformed()
2020 alignPanel.alignmentChanged();
2024 protected void deleteGroups_actionPerformed()
2026 if (avc.deleteGroups())
2028 alignPanel.alignmentChanged();
2032 public void selectAllSequenceMenuItem_actionPerformed()
2034 SequenceGroup sg = new SequenceGroup();
2035 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2037 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2039 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2040 viewport.setSelectionGroup(sg);
2041 alignPanel.paintAlignment(true);
2042 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2043 viewport.sendSelection();
2046 public void deselectAllSequenceMenuItem_actionPerformed()
2048 if (viewport.cursorMode)
2050 alignPanel.seqPanel.keyboardNo1 = null;
2051 alignPanel.seqPanel.keyboardNo2 = null;
2053 viewport.setSelectionGroup(null);
2054 viewport.getColumnSelection().clear();
2055 viewport.setSelectionGroup(null);
2056 alignPanel.idPanel.idCanvas.searchResults = null;
2057 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2058 alignPanel.paintAlignment(true);
2059 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2060 viewport.sendSelection();
2063 public void invertSequenceMenuItem_actionPerformed()
2065 SequenceGroup sg = viewport.getSelectionGroup();
2066 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2068 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2071 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2072 viewport.sendSelection();
2075 public void invertColSel_actionPerformed()
2077 viewport.invertColumnSelection();
2078 alignPanel.paintAlignment(true);
2079 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2080 viewport.sendSelection();
2083 void trimAlignment(boolean trimLeft)
2085 ColumnSelection colSel = viewport.getColumnSelection();
2088 if (colSel.size() > 0)
2092 column = colSel.getMin();
2096 column = colSel.getMax();
2100 if (viewport.getSelectionGroup() != null)
2102 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2103 viewport.getHiddenRepSequences());
2107 seqs = viewport.getAlignment().getSequencesArray();
2110 TrimRegionCommand trimRegion;
2113 trimRegion = new TrimRegionCommand("Remove Left",
2114 TrimRegionCommand.TRIM_LEFT, seqs, column,
2115 viewport.getAlignment(), viewport.getColumnSelection(),
2116 viewport.getSelectionGroup());
2117 viewport.setStartRes(0);
2121 trimRegion = new TrimRegionCommand("Remove Right",
2122 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2123 viewport.getAlignment(), viewport.getColumnSelection(),
2124 viewport.getSelectionGroup());
2127 statusBar.setText(MessageManager.formatMessage(
2128 "label.removed_columns", new String[]
2129 { Integer.valueOf(trimRegion.getSize()).toString() }));
2130 addHistoryItem(trimRegion);
2132 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2134 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2135 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2137 viewport.getAlignment().deleteGroup(sg);
2141 viewport.firePropertyChange("alignment", null, viewport
2142 .getAlignment().getSequences());
2146 public void removeGappedColumnMenuItem_actionPerformed()
2148 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2151 if (viewport.getSelectionGroup() != null)
2153 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2154 viewport.getHiddenRepSequences());
2155 start = viewport.getSelectionGroup().getStartRes();
2156 end = viewport.getSelectionGroup().getEndRes();
2160 seqs = viewport.getAlignment().getSequencesArray();
2163 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2164 "Remove Gapped Columns", seqs, start, end,
2165 viewport.getAlignment());
2167 addHistoryItem(removeGapCols);
2169 statusBar.setText(MessageManager.formatMessage(
2170 "label.removed_empty_columns", new String[]
2171 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2173 // This is to maintain viewport position on first residue
2174 // of first sequence
2175 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2176 int startRes = seq.findPosition(viewport.startRes);
2177 // ShiftList shifts;
2178 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2179 // edit.alColumnChanges=shifts.getInverse();
2180 // if (viewport.hasHiddenColumns)
2181 // viewport.getColumnSelection().compensateForEdits(shifts);
2182 viewport.setStartRes(seq.findIndex(startRes) - 1);
2183 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2188 public void removeAllGapsMenuItem_actionPerformed()
2190 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2193 if (viewport.getSelectionGroup() != null)
2195 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2196 viewport.getHiddenRepSequences());
2197 start = viewport.getSelectionGroup().getStartRes();
2198 end = viewport.getSelectionGroup().getEndRes();
2202 seqs = viewport.getAlignment().getSequencesArray();
2205 // This is to maintain viewport position on first residue
2206 // of first sequence
2207 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2208 int startRes = seq.findPosition(viewport.startRes);
2210 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2211 viewport.getAlignment()));
2213 viewport.setStartRes(seq.findIndex(startRes) - 1);
2215 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2220 public void findMenuItem_actionPerformed()
2222 new Finder(alignPanel);
2226 * create a new view derived from the current view
2229 * @return frame for the new view
2231 public AlignFrame newView(String viewtitle)
2234 if (viewport.hasHiddenRows())
2236 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2237 .getFullAlignment().getSequencesArray());
2241 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2244 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2246 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2248 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2250 newal.addAnnotation(viewport.getAlignment()
2251 .getAlignmentAnnotation()[i]);
2256 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2258 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2259 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2260 PaintRefresher.Register(newaf.alignPanel,
2261 newaf.alignPanel.av.getSequenceSetId());
2263 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2264 newaf.alignPanel.av.getSequenceSetId());
2265 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2266 newaf.alignPanel.av.getSequenceSetId());
2268 Vector comps = (Vector) PaintRefresher.components.get(viewport
2269 .getSequenceSetId());
2271 for (int i = 0; i < comps.size(); i++)
2273 if (comps.elementAt(i) instanceof AlignmentPanel)
2279 String title = new String(this.getTitle());
2280 if (viewtitle != null)
2282 title = viewtitle + " ( " + title + ")";
2286 if (title.indexOf("(View") > -1)
2288 title = title.substring(0, title.indexOf("(View"));
2290 title += "(View " + viewSize + ")";
2293 newaf.setTitle(title.toString());
2295 newaf.viewport.setHistoryList(viewport.getHistoryList());
2296 newaf.viewport.setRedoList(viewport.getRedoList());
2302 * @return list of feature groups on the view
2304 public String[] getFeatureGroups()
2306 FeatureRenderer fr = null;
2307 if (alignPanel != null
2308 && (fr = alignPanel.getFeatureRenderer()) != null)
2310 List gps = fr.getFeatureGroups();
2312 String[] _gps = new String[gps.size()];
2315 _gps[p++] = gp.toString();
2323 * get sequence feature groups that are hidden or shown
2329 public String[] getFeatureGroupsOfState(boolean visible)
2331 FeatureRenderer fr = null;
2332 if (alignPanel != null
2333 && (fr = alignPanel.getFeatureRenderer()) != null)
2335 List gps = fr.getGroups(visible);
2337 String[] _gps = new String[gps.size()];
2340 _gps[p++] = gp.toString();
2348 * Change the display state for the given feature groups
2351 * list of group strings
2353 * visible or invisible
2355 public void setFeatureGroupState(String[] groups, boolean state)
2357 FeatureRenderer fr = null;
2358 this.sequenceFeatures.setState(true);
2359 viewport.setShowSequenceFeatures(true);
2360 if (alignPanel != null
2361 && (fr = alignPanel.getFeatureRenderer()) != null)
2364 fr.setGroupVisibility(Arrays.asList(groups), state);
2365 alignPanel.seqPanel.seqCanvas.repaint();
2366 if (alignPanel.overviewPanel != null)
2368 alignPanel.overviewPanel.updateOverviewImage();
2373 public void seqLimits_itemStateChanged()
2375 viewport.setShowJVSuffix(seqLimits.getState());
2376 alignPanel.fontChanged();
2377 alignPanel.paintAlignment(true);
2380 protected void colourTextMenuItem_actionPerformed()
2382 viewport.setColourText(colourTextMenuItem.getState());
2383 alignPanel.paintAlignment(true);
2386 protected void displayNonconservedMenuItem_actionPerformed()
2388 viewport.setShowUnconserved(displayNonconservedMenuItem.getState());
2389 alignPanel.paintAlignment(true);
2392 protected void wrapMenuItem_actionPerformed()
2394 viewport.setWrapAlignment(wrapMenuItem.getState());
2395 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2396 scaleAbove.setEnabled(wrapMenuItem.getState());
2397 scaleLeft.setEnabled(wrapMenuItem.getState());
2398 scaleRight.setEnabled(wrapMenuItem.getState());
2399 alignPanel.paintAlignment(true);
2402 public void overviewMenuItem_actionPerformed()
2404 if (alignPanel.overviewPanel != null)
2409 Frame frame = new Frame();
2410 OverviewPanel overview = new OverviewPanel(alignPanel);
2411 frame.add(overview);
2412 // +50 must allow for applet frame window
2413 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2414 "label.overview_params", new String[]
2415 { this.getTitle() }), overview.getPreferredSize().width,
2416 overview.getPreferredSize().height + 50);
2419 final AlignmentPanel ap = alignPanel;
2420 frame.addWindowListener(new WindowAdapter()
2423 public void windowClosing(WindowEvent e)
2427 ap.setOverviewPanel(null);
2432 alignPanel.setOverviewPanel(overview);
2436 void changeColour(ColourSchemeI cs)
2442 if (viewport.getAbovePIDThreshold())
2444 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2448 if (viewport.getConservationSelected())
2450 cs.setConservationApplied(true);
2451 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2456 cs.setConservationApplied(false);
2459 viewport.setGlobalColourScheme(cs);
2461 if (alignPanel.getOverviewPanel() != null)
2463 alignPanel.getOverviewPanel().updateOverviewImage();
2466 jalview.structure.StructureSelectionManager
2467 .getStructureSelectionManager(viewport.applet)
2468 .sequenceColoursChanged(alignPanel);
2470 alignPanel.paintAlignment(true);
2473 protected void modifyPID_actionPerformed()
2475 if (viewport.getAbovePIDThreshold()
2476 && viewport.getGlobalColourScheme() != null)
2478 SliderPanel.setPIDSliderSource(alignPanel,
2479 viewport.getGlobalColourScheme(), "Background");
2480 SliderPanel.showPIDSlider();
2484 protected void modifyConservation_actionPerformed()
2486 if (viewport.getConservationSelected()
2487 && viewport.getGlobalColourScheme() != null)
2489 SliderPanel.setConservationSlider(alignPanel,
2490 viewport.getGlobalColourScheme(), "Background");
2491 SliderPanel.showConservationSlider();
2495 protected void conservationMenuItem_actionPerformed()
2497 viewport.setConservationSelected(conservationMenuItem.getState());
2499 viewport.setAbovePIDThreshold(false);
2500 abovePIDThreshold.setState(false);
2502 changeColour(viewport.getGlobalColourScheme());
2504 modifyConservation_actionPerformed();
2507 public void abovePIDThreshold_actionPerformed()
2509 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2511 conservationMenuItem.setState(false);
2512 viewport.setConservationSelected(false);
2514 changeColour(viewport.getGlobalColourScheme());
2516 modifyPID_actionPerformed();
2519 public void sortPairwiseMenuItem_actionPerformed()
2521 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2522 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2523 .getAlignment().getSequenceAt(0), null);
2525 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2526 viewport.getAlignment()));
2527 alignPanel.paintAlignment(true);
2530 public void sortIDMenuItem_actionPerformed()
2532 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2533 AlignmentSorter.sortByID(viewport.getAlignment());
2534 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2535 viewport.getAlignment()));
2536 alignPanel.paintAlignment(true);
2539 public void sortLengthMenuItem_actionPerformed()
2541 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2542 AlignmentSorter.sortByLength(viewport.getAlignment());
2543 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2544 viewport.getAlignment()));
2545 alignPanel.paintAlignment(true);
2548 public void sortGroupMenuItem_actionPerformed()
2550 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2551 AlignmentSorter.sortByGroup(viewport.getAlignment());
2552 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2553 viewport.getAlignment()));
2554 alignPanel.paintAlignment(true);
2558 public void removeRedundancyMenuItem_actionPerformed()
2560 new RedundancyPanel(alignPanel);
2563 public void pairwiseAlignmentMenuItem_actionPerformed()
2565 if (viewport.getSelectionGroup() != null
2566 && viewport.getSelectionGroup().getSize() > 1)
2568 Frame frame = new Frame();
2569 frame.add(new PairwiseAlignPanel(alignPanel));
2570 jalview.bin.JalviewLite.addFrame(frame,
2571 MessageManager.getString("action.pairwise_alignment"), 600,
2576 public void PCAMenuItem_actionPerformed()
2578 // are the sequences aligned?
2579 if (!viewport.getAlignment().isAligned(false))
2582 int Width = viewport.getAlignment().getWidth();
2584 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2586 current = viewport.getAlignment().getSequenceAt(i);
2588 if (current.getLength() < Width)
2590 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2593 alignPanel.paintAlignment(true);
2596 if ((viewport.getSelectionGroup() != null
2597 && viewport.getSelectionGroup().getSize() < 4 && viewport
2598 .getSelectionGroup().getSize() > 0)
2599 || viewport.getAlignment().getHeight() < 4)
2606 new PCAPanel(viewport);
2607 } catch (java.lang.OutOfMemoryError ex)
2613 public void averageDistanceTreeMenuItem_actionPerformed()
2615 NewTreePanel("AV", "PID", "Average distance tree using PID");
2618 public void neighbourTreeMenuItem_actionPerformed()
2620 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2623 protected void njTreeBlosumMenuItem_actionPerformed()
2625 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2628 protected void avTreeBlosumMenuItem_actionPerformed()
2630 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2633 void NewTreePanel(String type, String pwType, String title)
2635 // are the sequences aligned?
2636 if (!viewport.getAlignment().isAligned(false))
2639 int Width = viewport.getAlignment().getWidth();
2641 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2643 current = viewport.getAlignment().getSequenceAt(i);
2645 if (current.getLength() < Width)
2647 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2650 alignPanel.paintAlignment(true);
2654 if ((viewport.getSelectionGroup() != null && viewport
2655 .getSelectionGroup().getSize() > 1)
2656 || (viewport.getAlignment().getHeight() > 1))
2658 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2660 addTreeMenuItem(tp, title);
2662 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2666 void loadTree_actionPerformed()
2668 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2669 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2670 cap.setTreeImport();
2671 Frame frame = new Frame();
2673 jalview.bin.JalviewLite.addFrame(frame,
2674 MessageManager.getString("label.paste_newick_file"), 400, 300);
2677 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2679 TreePanel tp = new TreePanel(alignPanel, treeFile,
2680 MessageManager.getString("label.load_tree_from_file"), tree);
2681 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2682 addTreeMenuItem(tp, treeFile);
2686 * sort the alignment using the given treePanel
2689 * tree used to sort view
2691 * string used for undo event name
2693 public void sortByTree(TreePanel treePanel, String title)
2695 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2697 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2698 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2699 // HistoryItem.SORT));
2700 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2701 "label.order_by_params", new String[]
2702 { title }), oldOrder, viewport.getAlignment()));
2703 alignPanel.paintAlignment(true);
2707 * Do any automatic reordering of the alignment and add the necessary bits to
2708 * the menu structure for the new tree
2713 protected void addTreeMenuItem(final TreePanel treePanel,
2716 final MenuItem item = new MenuItem(title);
2717 sortByTreeMenu.add(item);
2718 item.addActionListener(new java.awt.event.ActionListener()
2721 public void actionPerformed(ActionEvent evt)
2723 sortByTree(treePanel, title); // treePanel.getTitle());
2727 treePanel.addWindowListener(new WindowAdapter()
2730 public void windowOpened(WindowEvent e)
2732 if (viewport.sortByTree)
2734 sortByTree(treePanel, title);
2736 super.windowOpened(e);
2740 public void windowClosing(WindowEvent e)
2742 sortByTreeMenu.remove(item);
2747 public boolean sortBy(AlignmentOrder alorder, String undoname)
2749 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2750 if (viewport.applet.debug)
2752 System.err.println("Sorting " + alorder.getOrder().size()
2753 + " in alignment '" + getTitle() + "'");
2755 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2756 if (undoname != null)
2758 addHistoryItem(new OrderCommand(undoname, oldOrder,
2759 viewport.getAlignment()));
2761 alignPanel.paintAlignment(true);
2765 protected void documentation_actionPerformed()
2767 alignPanel.av.applet.openJalviewHelpUrl();
2770 protected void about_actionPerformed()
2773 class AboutPanel extends Canvas
2779 public AboutPanel(String version, String builddate)
2781 this.version = version;
2782 this.builddate = builddate;
2786 public void paint(Graphics g)
2788 g.setColor(Color.white);
2789 g.fillRect(0, 0, getSize().width, getSize().height);
2790 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2791 FontMetrics fm = g.getFontMetrics();
2792 int fh = fm.getHeight();
2794 g.setColor(Color.black);
2795 // TODO: update this text for each release or centrally store it for
2796 // lite and application
2797 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2798 g.drawString(MessageManager.formatMessage(
2799 "label.jalviewLite_release", new String[]
2800 { version }), x, y += fh);
2801 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2802 g.drawString(MessageManager.formatMessage(
2803 "label.jaview_build_date", new String[]
2804 { builddate }), x, y += fh);
2805 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2806 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2808 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2809 x + 50, y += fh + 8);
2811 MessageManager.getString("label.jalview_dev_managers"), x,
2813 g.drawString(MessageManager
2814 .getString("label.jalview_distribution_lists"), x, y += fh);
2815 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2818 MessageManager.getString("label.jalview_cite_1_authors"),
2821 MessageManager.getString("label.jalview_cite_1_title"), x,
2823 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2828 Frame frame = new Frame();
2829 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2831 jalview.bin.JalviewLite.addFrame(frame,
2832 MessageManager.getString("label.jalview"), 580, 220);
2836 public void showURL(String url, String target)
2838 if (viewport.applet == null)
2840 System.out.println("Not running as applet - no browser available.");
2844 viewport.applet.showURL(url, target);
2848 // ////////////////////////////////////////////////////////////////////////////////
2849 // JBuilder Graphics here
2851 MenuBar alignFrameMenuBar = new MenuBar();
2853 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2855 MenuItem loadApplication = new MenuItem(
2856 MessageManager.getString("label.view_full_application"));
2858 MenuItem loadTree = new MenuItem(
2859 MessageManager.getString("label.load_associated_tree"));
2861 MenuItem loadAnnotations = new MenuItem(
2862 MessageManager.getString("label.load_features_annotations"));
2864 MenuItem outputFeatures = new MenuItem(
2865 MessageManager.getString("label.export_features").concat("..."));
2867 MenuItem outputAnnotations = new MenuItem(
2868 MessageManager.getString("label.export_annotations").concat("..."));
2870 MenuItem closeMenuItem = new MenuItem(
2871 MessageManager.getString("action.close"));
2873 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2875 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2877 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2879 Menu calculateMenu = new Menu(
2880 MessageManager.getString("action.calculate"));
2882 MenuItem selectAllSequenceMenuItem = new MenuItem(
2883 MessageManager.getString("action.select_all"));
2885 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2886 MessageManager.getString("action.deselect_all"));
2888 MenuItem invertSequenceMenuItem = new MenuItem(
2889 MessageManager.getString("action.invert_selection"));
2891 MenuItem remove2LeftMenuItem = new MenuItem();
2893 MenuItem remove2RightMenuItem = new MenuItem();
2895 MenuItem removeGappedColumnMenuItem = new MenuItem();
2897 MenuItem removeAllGapsMenuItem = new MenuItem();
2899 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2901 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2903 MenuItem sortPairwiseMenuItem = new MenuItem();
2905 MenuItem sortIDMenuItem = new MenuItem();
2907 MenuItem sortLengthMenuItem = new MenuItem();
2909 MenuItem sortGroupMenuItem = new MenuItem();
2911 MenuItem removeRedundancyMenuItem = new MenuItem();
2913 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2915 MenuItem PCAMenuItem = new MenuItem();
2917 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2919 MenuItem neighbourTreeMenuItem = new MenuItem();
2921 BorderLayout borderLayout1 = new BorderLayout();
2923 public Label statusBar = new Label();
2925 Menu outputTextboxMenu = new Menu();
2927 MenuItem clustalColour = new MenuItem();
2929 MenuItem zappoColour = new MenuItem();
2931 MenuItem taylorColour = new MenuItem();
2933 MenuItem hydrophobicityColour = new MenuItem();
2935 MenuItem helixColour = new MenuItem();
2937 MenuItem strandColour = new MenuItem();
2939 MenuItem turnColour = new MenuItem();
2941 MenuItem buriedColour = new MenuItem();
2943 MenuItem purinePyrimidineColour = new MenuItem();
2945 MenuItem RNAInteractionColour = new MenuItem();
2947 MenuItem RNAHelixColour = new MenuItem();
2949 MenuItem userDefinedColour = new MenuItem();
2951 MenuItem PIDColour = new MenuItem();
2953 MenuItem BLOSUM62Colour = new MenuItem();
2955 MenuItem tcoffeeColour = new MenuItem();
2957 MenuItem njTreeBlosumMenuItem = new MenuItem();
2959 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2961 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2963 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2965 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2967 MenuItem alProperties = new MenuItem(
2968 MessageManager.getString("label.alignment_props"));
2970 MenuItem overviewMenuItem = new MenuItem();
2972 MenuItem undoMenuItem = new MenuItem();
2974 MenuItem redoMenuItem = new MenuItem();
2976 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2978 MenuItem noColourmenuItem = new MenuItem();
2980 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2982 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2984 MenuItem findMenuItem = new MenuItem();
2986 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2988 MenuItem nucleotideColour = new MenuItem();
2990 MenuItem deleteGroups = new MenuItem();
2992 MenuItem grpsFromSelection = new MenuItem();
2994 MenuItem createGroup = new MenuItem();
2996 MenuItem unGroup = new MenuItem();
2998 MenuItem delete = new MenuItem();
3000 MenuItem copy = new MenuItem();
3002 MenuItem cut = new MenuItem();
3004 Menu pasteMenu = new Menu();
3006 MenuItem pasteNew = new MenuItem();
3008 MenuItem pasteThis = new MenuItem();
3010 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
3012 MenuItem font = new MenuItem();
3014 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
3016 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
3018 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
3020 MenuItem modifyPID = new MenuItem();
3022 MenuItem modifyConservation = new MenuItem();
3024 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
3025 "Autocalculate Consensus", true);
3027 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
3028 "Sort Alignment With New Tree", true);
3030 Menu sortByTreeMenu = new Menu();
3032 Menu sort = new Menu();
3034 Menu calculate = new Menu();
3036 MenuItem inputText = new MenuItem();
3038 Menu helpMenu = new Menu();
3040 MenuItem documentation = new MenuItem();
3042 MenuItem about = new MenuItem();
3044 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3046 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3048 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3050 Menu autoAnnMenu = new Menu();
3052 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3054 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3056 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3058 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3060 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3062 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3064 private void jbInit() throws Exception
3067 setMenuBar(alignFrameMenuBar);
3071 // dynamically fill save as menu with available formats
3072 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3075 item = new MenuItem(
3076 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3078 item.addActionListener(new java.awt.event.ActionListener()
3081 public void actionPerformed(ActionEvent e)
3083 outputText_actionPerformed(e);
3087 outputTextboxMenu.add(item);
3089 closeMenuItem.addActionListener(this);
3090 loadApplication.addActionListener(this);
3092 loadTree.addActionListener(this);
3093 loadAnnotations.addActionListener(this);
3094 outputFeatures.addActionListener(this);
3095 outputAnnotations.addActionListener(this);
3096 selectAllSequenceMenuItem.addActionListener(this);
3097 deselectAllSequenceMenuItem.addActionListener(this);
3098 invertSequenceMenuItem.addActionListener(this);
3099 remove2LeftMenuItem.setLabel(MessageManager
3100 .getString("action.remove_left"));
3101 remove2LeftMenuItem.addActionListener(this);
3102 remove2RightMenuItem.setLabel(MessageManager
3103 .getString("action.remove_right"));
3104 remove2RightMenuItem.addActionListener(this);
3105 removeGappedColumnMenuItem.setLabel(MessageManager
3106 .getString("action.remove_empty_columns"));
3107 removeGappedColumnMenuItem.addActionListener(this);
3108 removeAllGapsMenuItem.setLabel(MessageManager
3109 .getString("action.remove_all_gaps"));
3110 removeAllGapsMenuItem.addActionListener(this);
3111 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3112 viewBoxesMenuItem.setState(true);
3113 viewBoxesMenuItem.addItemListener(this);
3114 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3115 viewTextMenuItem.setState(true);
3116 viewTextMenuItem.addItemListener(this);
3117 sortPairwiseMenuItem.setLabel(MessageManager
3118 .getString("action.by_pairwise_id"));
3119 sortPairwiseMenuItem.addActionListener(this);
3120 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3121 sortIDMenuItem.addActionListener(this);
3122 sortLengthMenuItem.setLabel(MessageManager
3123 .getString("action.by_length"));
3124 sortLengthMenuItem.addActionListener(this);
3125 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3126 sortGroupMenuItem.addActionListener(this);
3127 removeRedundancyMenuItem.setLabel(MessageManager
3128 .getString("action.remove_redundancy").concat("..."));
3129 removeRedundancyMenuItem.addActionListener(this);
3130 pairwiseAlignmentMenuItem.setLabel(MessageManager
3131 .getString("action.pairwise_alignment"));
3132 pairwiseAlignmentMenuItem.addActionListener(this);
3133 PCAMenuItem.setLabel(MessageManager
3134 .getString("label.principal_component_analysis"));
3135 PCAMenuItem.addActionListener(this);
3136 averageDistanceTreeMenuItem.setLabel(MessageManager
3137 .getString("label.average_distance_identity"));
3138 averageDistanceTreeMenuItem.addActionListener(this);
3139 neighbourTreeMenuItem.setLabel(MessageManager
3140 .getString("label.neighbour_joining_identity"));
3141 neighbourTreeMenuItem.addActionListener(this);
3142 statusBar.setBackground(Color.white);
3143 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3144 statusBar.setText(MessageManager.getString("label.status_bar"));
3145 outputTextboxMenu.setLabel(MessageManager
3146 .getString("label.out_to_textbox"));
3147 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3149 clustalColour.addActionListener(this);
3150 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3151 zappoColour.addActionListener(this);
3152 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3153 taylorColour.addActionListener(this);
3154 hydrophobicityColour.setLabel(MessageManager
3155 .getString("label.hydrophobicity"));
3156 hydrophobicityColour.addActionListener(this);
3158 .setLabel(MessageManager.getString("label.helix_propensity"));
3159 helixColour.addActionListener(this);
3160 strandColour.setLabel(MessageManager
3161 .getString("label.strand_propensity"));
3162 strandColour.addActionListener(this);
3163 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3164 turnColour.addActionListener(this);
3165 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3166 buriedColour.addActionListener(this);
3167 purinePyrimidineColour.setLabel(MessageManager
3168 .getString("label.purine_pyrimidine"));
3169 purinePyrimidineColour.addActionListener(this);
3170 RNAInteractionColour.setLabel(MessageManager
3171 .getString("label.rna_interaction"));
3172 RNAInteractionColour.addActionListener(this);
3173 RNAHelixColour.setLabel(MessageManager
3174 .getString("action.by_rna_helixes"));
3175 RNAHelixColour.addActionListener(this);
3176 userDefinedColour.setLabel(MessageManager
3177 .getString("action.user_defined"));
3178 userDefinedColour.addActionListener(this);
3179 PIDColour.setLabel(MessageManager
3180 .getString("label.percentage_identity"));
3181 PIDColour.addActionListener(this);
3182 BLOSUM62Colour.setLabel(MessageManager
3183 .getString("label.blosum62_score"));
3184 BLOSUM62Colour.addActionListener(this);
3186 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3187 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3189 tcoffeeColour.addActionListener(this);
3190 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3191 .getString("label.average_distance_bloslum62"));
3192 avDistanceTreeBlosumMenuItem.addActionListener(this);
3193 njTreeBlosumMenuItem.setLabel(MessageManager
3194 .getString("label.neighbour_blosum62"));
3195 njTreeBlosumMenuItem.addActionListener(this);
3196 annotationPanelMenuItem.setLabel(MessageManager
3197 .getString("label.show_annotations"));
3198 annotationPanelMenuItem.addItemListener(this);
3199 colourTextMenuItem.setLabel(MessageManager
3200 .getString("label.colour_text"));
3201 colourTextMenuItem.addItemListener(this);
3202 displayNonconservedMenuItem.setLabel(MessageManager
3203 .getString("label.show_non_conversed"));
3204 displayNonconservedMenuItem.addItemListener(this);
3205 alProperties.addActionListener(this);
3206 overviewMenuItem.setLabel(MessageManager
3207 .getString("label.overview_window"));
3208 overviewMenuItem.addActionListener(this);
3209 undoMenuItem.setEnabled(false);
3210 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3211 undoMenuItem.addActionListener(this);
3212 redoMenuItem.setEnabled(false);
3213 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3214 redoMenuItem.addActionListener(this);
3215 conservationMenuItem.setLabel(MessageManager
3216 .getString("action.by_conservation"));
3217 conservationMenuItem.addItemListener(this);
3218 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3219 noColourmenuItem.addActionListener(this);
3220 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3221 wrapMenuItem.addItemListener(this);
3222 renderGapsMenuItem.setLabel(MessageManager
3223 .getString("action.show_gaps"));
3224 renderGapsMenuItem.setState(true);
3225 renderGapsMenuItem.addItemListener(this);
3226 findMenuItem.setLabel(MessageManager.getString("action.find"));
3227 findMenuItem.addActionListener(this);
3228 abovePIDThreshold.setLabel(MessageManager
3229 .getString("label.above_identity_threshold"));
3230 abovePIDThreshold.addItemListener(this);
3231 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3232 nucleotideColour.addActionListener(this);
3233 deleteGroups.setLabel(MessageManager
3234 .getString("action.undefine_groups"));
3235 deleteGroups.addActionListener(this);
3236 grpsFromSelection.setLabel(MessageManager
3237 .getString("action.make_groups_selection"));
3238 grpsFromSelection.addActionListener(this);
3239 createGroup.setLabel(MessageManager.getString("action.create_group"));
3240 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3241 copy.setLabel(MessageManager.getString("action.copy"));
3242 copy.addActionListener(this);
3243 cut.setLabel(MessageManager.getString("action.cut"));
3244 cut.addActionListener(this);
3245 delete.setLabel(MessageManager.getString("action.delete"));
3246 delete.addActionListener(this);
3247 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3248 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3249 pasteNew.addActionListener(this);
3250 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3251 pasteThis.addActionListener(this);
3252 applyToAllGroups.setLabel(MessageManager
3253 .getString("label.apply_colour_to_all_groups"));
3254 applyToAllGroups.setState(true);
3255 applyToAllGroups.addItemListener(this);
3256 font.setLabel(MessageManager.getString("action.font"));
3257 font.addActionListener(this);
3258 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3259 scaleAbove.setState(true);
3260 scaleAbove.setEnabled(false);
3261 scaleAbove.addItemListener(this);
3262 scaleLeft.setEnabled(false);
3263 scaleLeft.setState(true);
3264 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3265 scaleLeft.addItemListener(this);
3266 scaleRight.setEnabled(false);
3267 scaleRight.setState(true);
3268 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3269 scaleRight.addItemListener(this);
3270 modifyPID.setLabel(MessageManager
3271 .getString("label.modify_identity_thereshold"));
3272 modifyPID.addActionListener(this);
3273 modifyConservation.setLabel(MessageManager
3274 .getString("label.modify_conservation_thereshold"));
3275 modifyConservation.addActionListener(this);
3276 sortByTreeMenu.setLabel(MessageManager
3277 .getString("action.by_tree_order"));
3278 sort.setLabel(MessageManager.getString("action.sort"));
3279 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3280 autoCalculate.addItemListener(this);
3281 sortByTree.addItemListener(this);
3283 .setLabel(MessageManager.getString("label.input_from_textbox"));
3284 inputText.addActionListener(this);
3285 centreColumnLabelFlag.setLabel(MessageManager
3286 .getString("label.centre_column_labels"));
3287 centreColumnLabelFlag.addItemListener(this);
3288 followMouseOverFlag.setLabel(MessageManager
3289 .getString("label.automatic_scrolling"));
3290 followMouseOverFlag.addItemListener(this);
3291 helpMenu.setLabel(MessageManager.getString("action.help"));
3292 documentation.setLabel(MessageManager.getString("label.documentation"));
3293 documentation.addActionListener(this);
3295 about.setLabel(MessageManager.getString("label.about"));
3296 about.addActionListener(this);
3297 seqLimits.setState(true);
3298 seqLimits.setLabel(MessageManager
3299 .getString("label.show_sequence_limits"));
3300 seqLimits.addItemListener(this);
3301 featureSettings.setLabel(MessageManager
3302 .getString("label.feature_settings"));
3303 featureSettings.addActionListener(this);
3304 sequenceFeatures.setLabel(MessageManager
3305 .getString("label.sequence_features"));
3306 sequenceFeatures.addItemListener(this);
3307 sequenceFeatures.setState(false);
3308 annotationColour.setLabel(MessageManager
3309 .getString("action.by_annotation"));
3310 annotationColour.addActionListener(this);
3312 annotationColumnSelection.setLabel("Select by Annotation");
3313 annotationColumnSelection.addActionListener(this);
3315 invertSequenceMenuItem.setLabel(MessageManager
3316 .getString("action.invert_sequence_selection"));
3317 invertColSel.setLabel(MessageManager
3318 .getString("action.invert_column_selection"));
3319 menu1.setLabel(MessageManager.getString("action.show"));
3320 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3321 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3322 menu2.setLabel(MessageManager.getString("action.hide"));
3324 .setLabel(MessageManager.getString("label.selected_columns"));
3325 hideSequences.setLabel(MessageManager
3326 .getString("label.selected_sequences"));
3327 hideAllButSelection.setLabel(MessageManager
3328 .getString("label.all_but_selected_region"));
3329 hideAllSelection.setLabel(MessageManager
3330 .getString("label.selected_region"));
3331 showAllHidden.setLabel(MessageManager
3332 .getString("label.all_sequences_columns"));
3333 showGroupConsensus.setLabel(MessageManager
3334 .getString("label.group_consensus"));
3335 showGroupConservation.setLabel(MessageManager
3336 .getString("label.group_conservation"));
3337 showConsensusHistogram.setLabel(MessageManager
3338 .getString("label.show_consensus_histogram"));
3339 showSequenceLogo.setLabel(MessageManager
3340 .getString("label.show_consensus_logo"));
3341 normSequenceLogo.setLabel(MessageManager
3342 .getString("label.norm_consensus_logo"));
3343 applyAutoAnnotationSettings.setLabel(MessageManager
3344 .getString("label.apply_all_groups"));
3345 applyAutoAnnotationSettings.setState(true);
3346 autoAnnMenu.setLabel(MessageManager
3347 .getString("label.autocalculated_annotation"));
3349 invertColSel.addActionListener(this);
3350 showColumns.addActionListener(this);
3351 showSeqs.addActionListener(this);
3352 hideColumns.addActionListener(this);
3353 hideSequences.addActionListener(this);
3354 hideAllButSelection.addActionListener(this);
3355 hideAllSelection.addActionListener(this);
3356 showAllHidden.addActionListener(this);
3357 showGroupConsensus.addItemListener(this);
3358 showGroupConservation.addItemListener(this);
3359 showConsensusHistogram.addItemListener(this);
3360 showSequenceLogo.addItemListener(this);
3361 normSequenceLogo.addItemListener(this);
3363 applyAutoAnnotationSettings.addItemListener(this);
3364 formatMenu.setLabel(MessageManager.getString("action.format"));
3365 selectMenu.setLabel(MessageManager.getString("action.select"));
3366 newView.setLabel(MessageManager.getString("action.new_view"));
3367 newView.addActionListener(this);
3368 alignFrameMenuBar.add(fileMenu);
3369 alignFrameMenuBar.add(editMenu);
3370 alignFrameMenuBar.add(selectMenu);
3371 alignFrameMenuBar.add(viewMenu);
3372 alignFrameMenuBar.add(formatMenu);
3373 alignFrameMenuBar.add(colourMenu);
3374 alignFrameMenuBar.add(calculateMenu);
3375 alignFrameMenuBar.add(helpMenu);
3377 fileMenu.add(inputText);
3378 fileMenu.add(loadTree);
3379 fileMenu.add(loadAnnotations);
3381 fileMenu.addSeparator();
3382 fileMenu.add(outputTextboxMenu);
3383 fileMenu.add(outputFeatures);
3384 fileMenu.add(outputAnnotations);
3386 if (jalviewServletURL != null)
3388 fileMenu.add(loadApplication);
3391 fileMenu.addSeparator();
3392 fileMenu.add(closeMenuItem);
3394 editMenu.add(undoMenuItem);
3395 editMenu.add(redoMenuItem);
3398 editMenu.add(pasteMenu);
3399 editMenu.add(delete);
3400 editMenu.addSeparator();
3401 editMenu.add(remove2LeftMenuItem);
3402 editMenu.add(remove2RightMenuItem);
3403 editMenu.add(removeGappedColumnMenuItem);
3404 editMenu.add(removeAllGapsMenuItem);
3405 editMenu.add(removeRedundancyMenuItem);
3406 viewMenu.add(newView);
3407 viewMenu.addSeparator();
3408 viewMenu.add(menu1);
3409 viewMenu.add(menu2);
3410 viewMenu.addSeparator();
3411 viewMenu.add(followMouseOverFlag);
3412 viewMenu.add(annotationPanelMenuItem);
3413 autoAnnMenu.add(applyAutoAnnotationSettings);
3414 autoAnnMenu.add(showConsensusHistogram);
3415 autoAnnMenu.add(showSequenceLogo);
3416 autoAnnMenu.add(normSequenceLogo);
3417 autoAnnMenu.addSeparator();
3418 autoAnnMenu.add(showGroupConservation);
3419 autoAnnMenu.add(showGroupConsensus);
3420 viewMenu.add(autoAnnMenu);
3421 viewMenu.addSeparator();
3422 viewMenu.add(sequenceFeatures);
3423 viewMenu.add(featureSettings);
3424 viewMenu.addSeparator();
3425 viewMenu.add(alProperties);
3426 viewMenu.addSeparator();
3427 viewMenu.add(overviewMenuItem);
3428 colourMenu.add(applyToAllGroups);
3429 colourMenu.addSeparator();
3430 colourMenu.add(noColourmenuItem);
3431 colourMenu.add(clustalColour);
3432 colourMenu.add(BLOSUM62Colour);
3433 colourMenu.add(PIDColour);
3434 colourMenu.add(zappoColour);
3435 colourMenu.add(taylorColour);
3436 colourMenu.add(hydrophobicityColour);
3437 colourMenu.add(helixColour);
3438 colourMenu.add(strandColour);
3439 colourMenu.add(turnColour);
3440 colourMenu.add(buriedColour);
3441 colourMenu.add(nucleotideColour);
3442 colourMenu.add(purinePyrimidineColour);
3443 // colourMenu.add(RNAInteractionColour);
3444 colourMenu.add(tcoffeeColour);
3445 colourMenu.add(userDefinedColour);
3446 colourMenu.addSeparator();
3447 colourMenu.add(conservationMenuItem);
3448 colourMenu.add(modifyConservation);
3449 colourMenu.add(abovePIDThreshold);
3450 colourMenu.add(modifyPID);
3451 colourMenu.add(annotationColour);
3452 colourMenu.add(RNAHelixColour);
3453 calculateMenu.add(sort);
3454 calculateMenu.add(calculate);
3455 calculateMenu.addSeparator();
3456 calculateMenu.add(pairwiseAlignmentMenuItem);
3457 calculateMenu.add(PCAMenuItem);
3458 calculateMenu.add(autoCalculate);
3459 calculateMenu.add(sortByTree);
3460 this.add(statusBar, BorderLayout.SOUTH);
3461 pasteMenu.add(pasteNew);
3462 pasteMenu.add(pasteThis);
3463 sort.add(sortIDMenuItem);
3464 sort.add(sortLengthMenuItem);
3465 sort.add(sortByTreeMenu);
3466 sort.add(sortGroupMenuItem);
3467 sort.add(sortPairwiseMenuItem);
3468 calculate.add(averageDistanceTreeMenuItem);
3469 calculate.add(neighbourTreeMenuItem);
3470 calculate.add(avDistanceTreeBlosumMenuItem);
3471 calculate.add(njTreeBlosumMenuItem);
3472 helpMenu.add(documentation);
3473 helpMenu.add(about);
3474 menu1.add(showColumns);
3475 menu1.add(showSeqs);
3476 menu1.add(showAllHidden);
3477 menu2.add(hideColumns);
3478 menu2.add(hideSequences);
3479 menu2.add(hideAllSelection);
3480 menu2.add(hideAllButSelection);
3481 formatMenu.add(font);
3482 formatMenu.add(seqLimits);
3483 formatMenu.add(wrapMenuItem);
3484 formatMenu.add(scaleAbove);
3485 formatMenu.add(scaleLeft);
3486 formatMenu.add(scaleRight);
3487 formatMenu.add(viewBoxesMenuItem);
3488 formatMenu.add(viewTextMenuItem);
3489 formatMenu.add(colourTextMenuItem);
3490 formatMenu.add(displayNonconservedMenuItem);
3491 formatMenu.add(renderGapsMenuItem);
3492 formatMenu.add(centreColumnLabelFlag);
3493 selectMenu.add(findMenuItem);
3494 selectMenu.addSeparator();
3495 selectMenu.add(selectAllSequenceMenuItem);
3496 selectMenu.add(deselectAllSequenceMenuItem);
3497 selectMenu.add(invertSequenceMenuItem);
3498 selectMenu.add(invertColSel);
3499 selectMenu.add(createGroup);
3500 selectMenu.add(unGroup);
3501 selectMenu.add(grpsFromSelection);
3502 selectMenu.add(deleteGroups);
3503 selectMenu.add(annotationColumnSelection);
3507 public void setStatus(String string)
3509 statusBar.setText(string);
3512 MenuItem featureSettings = new MenuItem();
3514 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3516 MenuItem annotationColour = new MenuItem();
3518 MenuItem annotationColumnSelection = new MenuItem();
3520 MenuItem invertColSel = new MenuItem();
3522 Menu menu1 = new Menu();
3524 MenuItem showColumns = new MenuItem();
3526 MenuItem showSeqs = new MenuItem();
3528 Menu menu2 = new Menu();
3530 MenuItem hideColumns = new MenuItem();
3532 MenuItem hideSequences = new MenuItem();
3534 MenuItem hideAllButSelection = new MenuItem();
3536 MenuItem hideAllSelection = new MenuItem();
3538 MenuItem showAllHidden = new MenuItem();
3540 Menu formatMenu = new Menu();
3542 Menu selectMenu = new Menu();
3544 MenuItem newView = new MenuItem();
3547 * Attach the alignFrame panels after embedding menus, if necessary. This used
3548 * to be called setEmbedded, but is now creates the dropdown menus in a
3549 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3551 * @param reallyEmbedded
3552 * true to attach the view to the applet area on the page rather than
3555 public void createAlignFrameWindow(boolean reallyEmbedded)
3559 embedAlignFrameInApplet(viewport.applet);
3564 // test and embed menu bar if necessary.
3566 if (embedMenuIfNeeded(alignPanel))
3569 * adjust for status bar height too. ? pointless as overridden by layout
3572 alignPanel.setSize(getSize().width,
3573 getSize().height - statusBar.getHeight());
3575 add(statusBar, BorderLayout.SOUTH);
3576 add(alignPanel, BorderLayout.CENTER);
3577 // and register with the applet so it can pass external API calls to us
3578 jalview.bin.JalviewLite.addFrame(this, this.getTitle(),
3585 * Add the components of this AlignFrame to the applet container.
3589 public void embedAlignFrameInApplet(final JalviewLite theApplet)
3592 // Explicitly build the embedded menu panel for the on-page applet
3594 // view cannot be closed if its actually on the page
3595 fileMenu.remove(closeMenuItem);
3596 fileMenu.remove(3); // Remove Separator
3597 // construct embedded menu, using default font
3598 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, false, false);
3599 // and actually add the components to the applet area
3600 theApplet.setLayout(new BorderLayout());
3601 theApplet.add(embeddedMenu, BorderLayout.NORTH);
3602 theApplet.add(statusBar, BorderLayout.SOUTH);
3603 // TODO should size be left to the layout manager?
3604 alignPanel.setSize(theApplet.getSize().width,
3605 theApplet.getSize().height - embeddedMenu.getHeight()
3606 - statusBar.getHeight());
3607 theApplet.add(alignPanel, BorderLayout.CENTER);
3608 final AlignFrame me = this;
3609 theApplet.addFocusListener(new FocusListener()
3613 public void focusLost(FocusEvent e)
3615 if (theApplet.currentAlignFrame == me)
3617 theApplet.currentAlignFrame = null;
3622 public void focusGained(FocusEvent e)
3624 theApplet.currentAlignFrame = me;
3627 theApplet.validate();
3631 * create a new binding between structures in an existing jmol viewer instance
3632 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3633 * this does not open a new Jmol window, or modify the display of the
3634 * structures in the original jmol window. Note This method doesn't work
3635 * without an additional javascript library to exchange messages between the
3636 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3639 * JmolViewer instance
3640 * @param sequenceIds
3641 * - sequence Ids to search for associations
3643 public SequenceStructureBinding addStructureViewInstance(
3644 Object jmolviewer, String[] sequenceIds)
3646 org.jmol.api.JmolViewer viewer = null;
3649 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3650 } catch (ClassCastException ex)
3652 System.err.println("Unsupported viewer object :"
3653 + jmolviewer.getClass());
3657 System.err.println("Can't use this object as a structure viewer:"
3658 + jmolviewer.getClass());
3661 SequenceI[] seqs = null;
3662 if (sequenceIds == null || sequenceIds.length == 0)
3664 seqs = viewport.getAlignment().getSequencesArray();
3668 Vector sqi = new Vector();
3669 AlignmentI al = viewport.getAlignment();
3670 for (int sid = 0; sid < sequenceIds.length; sid++)
3672 SequenceI sq = al.findName(sequenceIds[sid]);
3680 seqs = new SequenceI[sqi.size()];
3681 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3683 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3691 AAStructureBindingModel jmv = null;
3692 // TODO: search for a jmv that involves viewer
3694 { // create a new viewer/jalview binding.
3695 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3703 * bind a pdb file to a sequence in the current view
3706 * - sequenceId within the dataset.
3707 * @param pdbEntryString
3708 * - the short name for the PDB file
3710 * - pdb file - either a URL or a valid PDB file.
3711 * @return true if binding was as success TODO: consider making an exception
3712 * structure for indicating when PDB parsing or sequenceId location
3715 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3718 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3719 boolean needtoadd = false;
3720 if (toaddpdb != null)
3722 Vector pdbe = toaddpdb.getPDBId();
3723 PDBEntry pdbentry = null;
3724 if (pdbe != null && pdbe.size() > 0)
3726 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3728 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3729 if (!pdbentry.getId().equals(pdbEntryString)
3730 && !pdbentry.getFile().equals(pdbFile))
3740 if (pdbentry == null)
3742 pdbentry = new PDBEntry();
3743 pdbentry.setId(pdbEntryString);
3744 pdbentry.setFile(pdbFile);
3745 needtoadd = true; // add this new entry to sequence.
3747 // resolve data source
3748 // TODO: this code should be a refactored to an io package
3749 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3750 if (protocol == null)
3756 // make a note of the access mode and add
3757 if (pdbentry.getProperty() == null)
3759 pdbentry.setProperty(new Hashtable());
3761 pdbentry.getProperty().put("protocol", protocol);
3762 toaddpdb.addPDBId(pdbentry);
3763 alignPanel.getStructureSelectionManager()
3764 .registerPDBEntry(pdbentry);
3770 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3774 Vector sequences = new Vector();
3775 for (int i = 0; i < seqs.length; i++)
3777 if (seqs[i] != null)
3779 sequences.addElement(new Object[]
3780 { seqs[i], (chains != null) ? chains[i] : null });
3783 seqs = new SequenceI[sequences.size()];
3784 chains = new String[sequences.size()];
3785 for (int i = 0, isize = sequences.size(); i < isize; i++)
3787 Object[] oj = (Object[]) sequences.elementAt(i);
3789 seqs[i] = (SequenceI) oj[0];
3790 chains[i] = (String) oj[1];
3798 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3799 SequenceI[] seqs, String[] chains, String protocol)
3801 // Scrub any null sequences from the array
3802 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3803 seqs = (SequenceI[]) sqch[0];
3804 chains = (String[]) sqch[1];
3805 if (seqs == null || seqs.length == 0)
3808 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3810 if (protocol == null || protocol.trim().length() == 0
3811 || protocol.equals("null"))
3813 protocol = (String) pdb.getProperty().get("protocol");
3814 if (protocol == null)
3816 System.err.println("Couldn't work out protocol to open structure: "
3821 if (applet.useXtrnalSviewer)
3823 // register the association(s) and quit, don't create any windows.
3824 if (StructureSelectionManager.getStructureSelectionManager(applet)
3825 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3827 System.err.println("Failed to map " + pdb.getFile() + " ("
3828 + protocol + ") to any sequences");
3832 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3834 // can only do alignments with Jmol
3835 // find the last jmol window assigned to this alignment
3836 jalview.appletgui.AppletJmol ajm = null, tajm;
3837 Vector jmols = applet
3838 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3839 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3841 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3842 if (tajm.ap.alignFrame == this)
3851 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3852 // try and add the pdb structure
3857 // otherwise, create a new window
3858 if (applet.jmolAvailable)
3860 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3862 applet.lastFrameX += 40;
3863 applet.lastFrameY += 40;
3867 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3872 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3873 SequenceI[][] seqs, String[][] chains, String[] protocols)
3875 // TODO Auto-generated method stub
3876 System.err.println("Aligned Structure View: Not yet implemented.");
3880 * modify the current selection, providing the user has not made a selection
3884 * - sequences from this alignment
3886 * - columns to be selected on the alignment
3888 public void select(SequenceGroup sel, ColumnSelection csel)
3890 alignPanel.seqPanel.selection(sel, csel, null);
3893 public void scrollTo(int row, int column)
3895 alignPanel.seqPanel.scrollTo(row, column);
3898 public void scrollToRow(int row)
3900 alignPanel.seqPanel.scrollToRow(row);
3903 public void scrollToColumn(int column)
3905 alignPanel.seqPanel.scrollToColumn(column);
3909 * @return the alignments unique ID.
3911 public String getSequenceSetId()
3913 return viewport.getSequenceSetId();
3917 * Load the (T-Coffee) score file from the specified url
3920 * File/URL/T-COFFEE score file contents
3921 * @throws IOException
3922 * @return true if alignment was annotated with data from source
3924 public boolean loadScoreFile(String source) throws IOException
3927 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3928 AppletFormatAdapter.checkProtocol(source));
3929 if (!file.isValid())
3931 // TODO: raise dialog for gui
3932 System.err.println("Problems parsing T-Coffee scores: "
3933 + file.getWarningMessage());
3934 System.err.println("Origin was:\n" + source);
3939 * check that the score matrix matches the alignment dimensions
3942 if ((aln = viewport.getAlignment()) != null
3943 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3946 // TODO: raise a dialog box here rather than bomb out.
3948 .println("The scores matrix does not match the alignment dimensions");
3952 // TODO add parameter to indicate if matching should be done
3953 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3955 alignPanel.fontChanged();
3956 tcoffeeColour.setEnabled(true);
3957 // switch to this color
3958 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3963 System.err.println("Problems resolving T-Coffee scores:");
3964 if (file.getWarningMessage() != null)
3966 System.err.println(file.getWarningMessage());