2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.api.AlignViewControllerI;
24 import jalview.api.SequenceStructureBinding;
25 import jalview.bin.JalviewLite;
26 import jalview.commands.CommandI;
27 import jalview.commands.EditCommand;
28 import jalview.commands.OrderCommand;
29 import jalview.commands.RemoveGapColCommand;
30 import jalview.commands.RemoveGapsCommand;
31 import jalview.commands.SlideSequencesCommand;
32 import jalview.commands.TrimRegionCommand;
33 import jalview.datamodel.Alignment;
34 import jalview.datamodel.AlignmentI;
35 import jalview.datamodel.AlignmentOrder;
36 import jalview.datamodel.ColumnSelection;
37 import jalview.datamodel.PDBEntry;
38 import jalview.datamodel.Sequence;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.AnnotationFile;
42 import jalview.io.AppletFormatAdapter;
43 import jalview.io.FeaturesFile;
44 import jalview.io.TCoffeeScoreFile;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.BuriedColourScheme;
47 import jalview.schemes.ClustalxColourScheme;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.schemes.HelixColourScheme;
50 import jalview.schemes.HydrophobicColourScheme;
51 import jalview.schemes.NucleotideColourScheme;
52 import jalview.schemes.PIDColourScheme;
53 import jalview.schemes.PurinePyrimidineColourScheme;
54 import jalview.schemes.RNAHelicesColourChooser;
55 import jalview.schemes.ResidueProperties;
56 import jalview.schemes.StrandColourScheme;
57 import jalview.schemes.TCoffeeColourScheme;
58 import jalview.schemes.TaylorColourScheme;
59 import jalview.schemes.TurnColourScheme;
60 import jalview.schemes.ZappoColourScheme;
61 import jalview.structure.StructureSelectionManager;
62 import jalview.util.MessageManager;
64 import java.awt.BorderLayout;
65 import java.awt.Canvas;
66 import java.awt.CheckboxMenuItem;
67 import java.awt.Color;
69 import java.awt.FontMetrics;
70 import java.awt.Frame;
71 import java.awt.Graphics;
72 import java.awt.Label;
74 import java.awt.MenuBar;
75 import java.awt.MenuItem;
76 import java.awt.event.ActionEvent;
77 import java.awt.event.ActionListener;
78 import java.awt.event.FocusEvent;
79 import java.awt.event.FocusListener;
80 import java.awt.event.ItemEvent;
81 import java.awt.event.ItemListener;
82 import java.awt.event.KeyEvent;
83 import java.awt.event.KeyListener;
84 import java.awt.event.WindowAdapter;
85 import java.awt.event.WindowEvent;
86 import java.io.IOException;
88 import java.net.URLEncoder;
89 import java.util.Enumeration;
90 import java.util.Hashtable;
91 import java.util.List;
92 import java.util.StringTokenizer;
93 import java.util.Vector;
95 public class AlignFrame extends EmbmenuFrame implements ActionListener,
96 ItemListener, KeyListener
98 public AlignViewControllerI avc;
99 public AlignmentPanel alignPanel;
101 public AlignViewport viewport;
103 int DEFAULT_WIDTH = 700;
105 int DEFAULT_HEIGHT = 500;
107 String jalviewServletURL;
109 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
110 String title, boolean embedded)
114 jalviewServletURL = applet.getParameter("APPLICATION_URL");
120 } catch (Exception ex)
122 ex.printStackTrace();
125 viewport = new AlignViewport(al, applet);
126 alignPanel = new AlignmentPanel(this, viewport);
127 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
128 viewport.updateConservation(alignPanel);
129 viewport.updateConsensus(alignPanel);
131 annotationPanelMenuItem.setState(viewport.showAnnotation);
132 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
133 followMouseOverFlag.setState(viewport.getFollowHighlight());
134 showGroupConsensus.setState(viewport.isShowGroupConsensus());
135 showGroupConservation.setState(viewport.isShowGroupConservation());
136 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
137 showSequenceLogo.setState(viewport.isShowSequenceLogo());
138 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
140 seqLimits.setState(viewport.showJVSuffix);
144 String param = applet.getParameter("sortBy");
147 if (param.equalsIgnoreCase("Id"))
149 sortIDMenuItem_actionPerformed();
151 else if (param.equalsIgnoreCase("Pairwise Identity"))
153 sortPairwiseMenuItem_actionPerformed();
155 else if (param.equalsIgnoreCase("Length"))
157 sortLengthMenuItem_actionPerformed();
161 param = applet.getParameter("wrap");
164 if (param.equalsIgnoreCase("true"))
166 wrapMenuItem.setState(true);
167 wrapMenuItem_actionPerformed();
170 param = applet.getParameter("centrecolumnlabels");
173 centreColumnLabelFlag.setState(true);
174 centreColumnLabelFlag_stateChanged();
178 param = applet.getParameter("windowWidth");
181 int width = Integer.parseInt(param);
182 DEFAULT_WIDTH = width;
184 param = applet.getParameter("windowHeight");
187 int height = Integer.parseInt(param);
188 DEFAULT_HEIGHT = height;
190 } catch (Exception ex)
195 if (viewport.getAlignment().isNucleotide())
197 viewport.updateStrucConsensus(alignPanel);
198 if (viewport.getAlignment().hasRNAStructure())
200 RNAHelixColour.setEnabled(true);
204 RNAHelixColour.setEnabled(false);
209 RNAHelixColour.setEnabled(false);
210 purinePyrimidineColour.setEnabled(false);
212 // Some JVMS send keyevents to Top frame or lowest panel,
213 // Havent worked out why yet. So add to both this frame and seqCanvas for
215 this.addKeyListener(this);
216 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
217 alignPanel.idPanel.idCanvas.addKeyListener(this);
218 alignPanel.scalePanel.addKeyListener(this);
219 alignPanel.annotationPanel.addKeyListener(this);
220 alignPanel.annotationPanelHolder.addKeyListener(this);
221 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
222 alignPanel.alabels.addKeyListener(this);
223 createAlignFrameWindow(embedded, title);
226 alignPanel.adjustAnnotationHeight();
227 alignPanel.paintAlignment(true);
230 public AlignViewport getAlignViewport()
235 public SeqCanvas getSeqcanvas()
237 return alignPanel.seqPanel.seqCanvas;
241 * Load a features file onto the alignment
244 * file URL, content, or other resolvable path
246 * is protocol for accessing data referred to by file
249 public boolean parseFeaturesFile(String file, String type)
251 return parseFeaturesFile(file, type, true);
255 * Load a features file onto the alignment
258 * file URL, content, or other resolvable path
260 * is protocol for accessing data referred to by file
261 * @param autoenabledisplay
262 * when true, display features flag will be automatically enabled if
263 * features are loaded
264 * @return true if data parsed as a features file
266 public boolean parseFeaturesFile(String file, String type,
267 boolean autoenabledisplay)
269 // TODO: test if importing a features file onto an alignment which already
270 // has features with links overwrites the original links.
272 Hashtable featureLinks = new Hashtable();
273 boolean featuresFile = false;
276 featuresFile = new jalview.io.FeaturesFile(file, type)
277 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
278 .getFeatureRenderer().featureColours, featureLinks,
279 true, viewport.applet.getDefaultParameter(
280 "relaxedidmatch", false));
281 } catch (Exception ex)
283 ex.printStackTrace();
288 if (featureLinks.size() > 0)
290 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
292 if (autoenabledisplay)
294 viewport.showSequenceFeatures = true;
295 sequenceFeatures.setState(true);
297 if (viewport.featureSettings != null)
299 viewport.featureSettings.refreshTable();
301 alignPanel.paintAlignment(true);
302 statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
308 public void keyPressed(KeyEvent evt)
310 if (viewport.cursorMode
311 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
312 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
313 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
314 && Character.isDigit(evt.getKeyChar()))
315 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
317 switch (evt.getKeyCode())
319 case 27: // escape key
320 deselectAllSequenceMenuItem_actionPerformed();
322 alignPanel.alabels.cancelDrag();
325 if (evt.isControlDown() || evt.isMetaDown())
327 cut_actionPerformed();
331 if (viewport.cursorMode && !evt.isControlDown())
333 alignPanel.seqPanel.setCursorColumn();
335 if (evt.isControlDown() || evt.isMetaDown())
337 copy_actionPerformed();
341 if (evt.isControlDown())
343 paste(evt.isShiftDown());
347 if (evt.isControlDown() || evt.isMetaDown())
349 selectAllSequenceMenuItem_actionPerformed();
352 case KeyEvent.VK_DOWN:
353 if (viewport.cursorMode)
355 alignPanel.seqPanel.moveCursor(0, 1);
359 moveSelectedSequences(false);
364 if (viewport.cursorMode)
366 alignPanel.seqPanel.moveCursor(0, -1);
370 moveSelectedSequences(true);
374 case KeyEvent.VK_LEFT:
375 if (evt.isAltDown() || !viewport.cursorMode)
376 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
378 alignPanel.seqPanel.moveCursor(-1, 0);
381 case KeyEvent.VK_RIGHT:
382 if (evt.isAltDown() || !viewport.cursorMode)
383 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
385 alignPanel.seqPanel.moveCursor(1, 0);
388 case KeyEvent.VK_SPACE:
389 if (viewport.cursorMode)
391 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
392 || evt.isShiftDown() || evt.isAltDown());
396 case KeyEvent.VK_DELETE:
397 case KeyEvent.VK_BACK_SPACE:
398 if (viewport.cursorMode)
400 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
401 || evt.isShiftDown() || evt.isAltDown());
405 cut_actionPerformed();
406 alignPanel.seqPanel.seqCanvas.repaint();
411 if (viewport.cursorMode)
413 alignPanel.seqPanel.setCursorRow();
417 if (viewport.cursorMode)
419 alignPanel.seqPanel.setCursorPosition();
423 case KeyEvent.VK_ENTER:
424 case KeyEvent.VK_COMMA:
425 if (viewport.cursorMode)
427 alignPanel.seqPanel.setCursorRowAndColumn();
432 if (viewport.cursorMode)
434 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
438 if (viewport.cursorMode)
440 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
445 viewport.cursorMode = !viewport.cursorMode;
446 statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
447 if (viewport.cursorMode)
449 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
450 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
455 if (evt.isControlDown())
457 findMenuItem_actionPerformed();
463 boolean toggleSeqs = !evt.isControlDown();
464 boolean toggleCols = !evt.isShiftDown();
465 toggleHiddenRegions(toggleSeqs, toggleCols);
469 case KeyEvent.VK_PAGE_UP:
470 if (viewport.wrapAlignment)
472 alignPanel.scrollUp(true);
476 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
477 - viewport.endSeq + viewport.startSeq);
481 case KeyEvent.VK_PAGE_DOWN:
482 if (viewport.wrapAlignment)
484 alignPanel.scrollUp(false);
488 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
489 + viewport.endSeq - viewport.startSeq);
494 if (evt.isControlDown())
496 undoMenuItem_actionPerformed();
501 if (evt.isControlDown())
503 redoMenuItem_actionPerformed();
508 if (evt.isControlDown())
515 if (evt.isControlDown())
517 trimAlignment(false);
522 if (evt.isControlDown())
524 if (evt.isShiftDown())
526 this.removeAllGapsMenuItem_actionPerformed();
530 removeGappedColumnMenuItem_actionPerformed();
535 if (evt.isControlDown())
539 invertColSel_actionPerformed();
543 invertSequenceMenuItem_actionPerformed();
549 if (evt.isControlDown())
551 if (evt.isShiftDown())
553 this.unGroup_actionPerformed();
557 this.createGroup_actionPerformed();
563 if (evt.isControlDown())
565 this.deleteGroups_actionPerformed();
570 if (evt.isControlDown())
577 alignPanel.paintAlignment(true);
581 * called by key handler and the hide all/show all menu items
586 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
588 boolean hide = false;
589 SequenceGroup sg = viewport.getSelectionGroup();
590 if (!toggleSeqs && !toggleCols)
592 // Hide everything by the current selection - this is a hack - we do the
593 // invert and then hide
594 // first check that there will be visible columns after the invert.
595 if ((viewport.getColumnSelection() != null
596 && viewport.getColumnSelection().getSelected() != null && viewport
597 .getColumnSelection().getSelected().size() > 0)
598 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
601 // now invert the sequence set, if required - empty selection implies
602 // that no hiding is required.
605 invertSequenceMenuItem_actionPerformed();
606 sg = viewport.getSelectionGroup();
610 viewport.expandColSelection(sg, true);
611 // finally invert the column selection and get the new sequence
612 // selection and indicate it should be hidden.
613 invertColSel_actionPerformed();
620 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
623 viewport.hideAllSelectedSeqs();
625 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
628 viewport.showAllHiddenSeqs();
634 if (viewport.getColumnSelection().getSelected().size() > 0)
636 viewport.hideSelectedColumns();
639 viewport.setSelectionGroup(sg);
644 viewport.showAllHiddenColumns();
650 public void keyReleased(KeyEvent evt)
655 public void keyTyped(KeyEvent evt)
660 public void itemStateChanged(ItemEvent evt)
662 if (evt.getSource() == displayNonconservedMenuItem)
664 displayNonconservedMenuItem_actionPerformed();
666 else if (evt.getSource() == colourTextMenuItem)
668 colourTextMenuItem_actionPerformed();
670 else if (evt.getSource() == wrapMenuItem)
672 wrapMenuItem_actionPerformed();
674 else if (evt.getSource() == scaleAbove)
676 viewport.setScaleAboveWrapped(scaleAbove.getState());
678 else if (evt.getSource() == scaleLeft)
680 viewport.setScaleLeftWrapped(scaleLeft.getState());
682 else if (evt.getSource() == scaleRight)
684 viewport.setScaleRightWrapped(scaleRight.getState());
686 else if (evt.getSource() == seqLimits)
688 seqLimits_itemStateChanged();
690 else if (evt.getSource() == viewBoxesMenuItem)
692 viewport.setShowBoxes(viewBoxesMenuItem.getState());
694 else if (evt.getSource() == viewTextMenuItem)
696 viewport.setShowText(viewTextMenuItem.getState());
698 else if (evt.getSource() == renderGapsMenuItem)
700 viewport.setRenderGaps(renderGapsMenuItem.getState());
702 else if (evt.getSource() == annotationPanelMenuItem)
704 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
705 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
707 else if (evt.getSource() == sequenceFeatures)
709 viewport.showSequenceFeatures(sequenceFeatures.getState());
710 alignPanel.seqPanel.seqCanvas.repaint();
712 else if (evt.getSource() == conservationMenuItem)
714 conservationMenuItem_actionPerformed();
716 else if (evt.getSource() == abovePIDThreshold)
718 abovePIDThreshold_actionPerformed();
720 else if (evt.getSource() == applyToAllGroups)
722 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
724 else if (evt.getSource() == autoCalculate)
726 viewport.autoCalculateConsensus = autoCalculate.getState();
728 else if (evt.getSource() == sortByTree)
730 viewport.sortByTree = sortByTree.getState();
732 else if (evt.getSource() == this.centreColumnLabelFlag)
734 centreColumnLabelFlag_stateChanged();
736 else if (evt.getSource() == this.followMouseOverFlag)
738 mouseOverFlag_stateChanged();
740 else if (evt.getSource() == showGroupConsensus)
742 showGroupConsensus_actionPerformed();
744 else if (evt.getSource() == showGroupConservation)
746 showGroupConservation_actionPerformed();
748 else if (evt.getSource() == showSequenceLogo)
750 showSequenceLogo_actionPerformed();
752 else if (evt.getSource() == normSequenceLogo)
754 normSequenceLogo_actionPerformed();
756 else if (evt.getSource() == showConsensusHistogram)
758 showConsensusHistogram_actionPerformed();
760 else if (evt.getSource() == applyAutoAnnotationSettings)
762 applyAutoAnnotationSettings_actionPerformed();
764 alignPanel.paintAlignment(true);
767 private void mouseOverFlag_stateChanged()
769 viewport.followHighlight = followMouseOverFlag.getState();
770 // TODO: could kick the scrollTo mechanism to reset view for current
774 private void centreColumnLabelFlag_stateChanged()
776 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
777 this.alignPanel.annotationPanel.repaint();
781 public void actionPerformed(ActionEvent evt)
783 Object source = evt.getSource();
785 if (source == inputText)
787 inputText_actionPerformed();
789 else if (source == loadTree)
791 loadTree_actionPerformed();
793 else if (source == loadApplication)
795 launchFullApplication();
797 else if (source == loadAnnotations)
801 else if (source == outputAnnotations)
803 outputAnnotations(true);
805 else if (source == outputFeatures)
807 outputFeatures(true, "Jalview");
809 else if (source == closeMenuItem)
811 closeMenuItem_actionPerformed();
813 else if (source == copy)
815 copy_actionPerformed();
817 else if (source == undoMenuItem)
819 undoMenuItem_actionPerformed();
821 else if (source == redoMenuItem)
823 redoMenuItem_actionPerformed();
825 else if (source == inputText)
827 inputText_actionPerformed();
829 else if (source == closeMenuItem)
831 closeMenuItem_actionPerformed();
833 else if (source == undoMenuItem)
835 undoMenuItem_actionPerformed();
837 else if (source == redoMenuItem)
839 redoMenuItem_actionPerformed();
841 else if (source == copy)
843 copy_actionPerformed();
845 else if (source == pasteNew)
847 pasteNew_actionPerformed();
849 else if (source == pasteThis)
851 pasteThis_actionPerformed();
853 else if (source == cut)
855 cut_actionPerformed();
857 else if (source == delete)
859 delete_actionPerformed();
861 else if (source == grpsFromSelection)
863 makeGrpsFromSelection_actionPerformed();
865 else if (source == deleteGroups)
867 deleteGroups_actionPerformed();
869 else if (source == selectAllSequenceMenuItem)
871 selectAllSequenceMenuItem_actionPerformed();
873 else if (source == deselectAllSequenceMenuItem)
875 deselectAllSequenceMenuItem_actionPerformed();
877 else if (source == invertSequenceMenuItem)
879 invertSequenceMenuItem_actionPerformed();
881 else if (source == invertColSel)
883 viewport.invertColumnSelection();
884 alignPanel.paintAlignment(true);
886 else if (source == remove2LeftMenuItem)
890 else if (source == remove2RightMenuItem)
892 trimAlignment(false);
894 else if (source == removeGappedColumnMenuItem)
896 removeGappedColumnMenuItem_actionPerformed();
898 else if (source == removeAllGapsMenuItem)
900 removeAllGapsMenuItem_actionPerformed();
902 else if (source == findMenuItem)
904 findMenuItem_actionPerformed();
906 else if (source == font)
908 new FontChooser(alignPanel);
910 else if (source == newView)
914 else if (source == showColumns)
916 viewport.showAllHiddenColumns();
917 alignPanel.paintAlignment(true);
919 else if (source == showSeqs)
921 viewport.showAllHiddenSeqs();
922 alignPanel.paintAlignment(true);
924 else if (source == hideColumns)
926 viewport.hideSelectedColumns();
927 alignPanel.paintAlignment(true);
929 else if (source == hideSequences
930 && viewport.getSelectionGroup() != null)
932 viewport.hideAllSelectedSeqs();
933 alignPanel.paintAlignment(true);
935 else if (source == hideAllButSelection)
937 toggleHiddenRegions(false, false);
938 alignPanel.paintAlignment(true);
940 else if (source == hideAllSelection)
942 SequenceGroup sg = viewport.getSelectionGroup();
943 viewport.expandColSelection(sg, false);
944 viewport.hideAllSelectedSeqs();
945 viewport.hideSelectedColumns();
946 alignPanel.paintAlignment(true);
948 else if (source == showAllHidden)
950 viewport.showAllHiddenColumns();
951 viewport.showAllHiddenSeqs();
952 alignPanel.paintAlignment(true);
954 else if (source == showGroupConsensus)
956 showGroupConsensus_actionPerformed();
958 else if (source == showGroupConservation)
960 showGroupConservation_actionPerformed();
962 else if (source == showSequenceLogo)
964 showSequenceLogo_actionPerformed();
966 else if (source == normSequenceLogo)
968 normSequenceLogo_actionPerformed();
970 else if (source == showConsensusHistogram)
972 showConsensusHistogram_actionPerformed();
974 else if (source == applyAutoAnnotationSettings)
976 applyAutoAnnotationSettings_actionPerformed();
978 else if (source == featureSettings)
980 new FeatureSettings(alignPanel);
982 else if (source == alProperties)
984 StringBuffer contents = new jalview.io.AlignmentProperties(
985 viewport.getAlignment()).formatAsString();
986 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
987 cap.setText(contents.toString());
988 Frame frame = new Frame();
990 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
993 else if (source == overviewMenuItem)
995 overviewMenuItem_actionPerformed();
997 else if (source == noColourmenuItem)
1001 else if (source == clustalColour)
1003 abovePIDThreshold.setState(false);
1004 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1006 else if (source == zappoColour)
1008 changeColour(new ZappoColourScheme());
1010 else if (source == taylorColour)
1012 changeColour(new TaylorColourScheme());
1014 else if (source == hydrophobicityColour)
1016 changeColour(new HydrophobicColourScheme());
1018 else if (source == helixColour)
1020 changeColour(new HelixColourScheme());
1022 else if (source == strandColour)
1024 changeColour(new StrandColourScheme());
1026 else if (source == turnColour)
1028 changeColour(new TurnColourScheme());
1030 else if (source == buriedColour)
1032 changeColour(new BuriedColourScheme());
1034 else if (source == nucleotideColour)
1036 changeColour(new NucleotideColourScheme());
1038 else if (source == purinePyrimidineColour)
1040 changeColour(new PurinePyrimidineColourScheme());
1042 else if (source == RNAHelixColour)
1044 new RNAHelicesColourChooser(viewport, alignPanel);
1046 else if (source == modifyPID)
1048 modifyPID_actionPerformed();
1050 else if (source == modifyConservation)
1052 modifyConservation_actionPerformed();
1054 else if (source == userDefinedColour)
1056 new UserDefinedColours(alignPanel, null);
1058 else if (source == PIDColour)
1060 changeColour(new PIDColourScheme());
1062 else if (source == BLOSUM62Colour)
1064 changeColour(new Blosum62ColourScheme());
1066 else if (source == tcoffeeColour)
1068 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1070 else if (source == annotationColour)
1072 new AnnotationColourChooser(viewport, alignPanel);
1074 else if (source == sortPairwiseMenuItem)
1076 sortPairwiseMenuItem_actionPerformed();
1078 else if (source == sortIDMenuItem)
1080 sortIDMenuItem_actionPerformed();
1082 else if (source == sortLengthMenuItem)
1084 sortLengthMenuItem_actionPerformed();
1086 else if (source == sortGroupMenuItem)
1088 sortGroupMenuItem_actionPerformed();
1090 else if (source == removeRedundancyMenuItem)
1092 removeRedundancyMenuItem_actionPerformed();
1094 else if (source == pairwiseAlignmentMenuItem)
1096 pairwiseAlignmentMenuItem_actionPerformed();
1098 else if (source == PCAMenuItem)
1100 PCAMenuItem_actionPerformed();
1102 else if (source == averageDistanceTreeMenuItem)
1104 averageDistanceTreeMenuItem_actionPerformed();
1106 else if (source == neighbourTreeMenuItem)
1108 neighbourTreeMenuItem_actionPerformed();
1110 else if (source == njTreeBlosumMenuItem)
1112 njTreeBlosumMenuItem_actionPerformed();
1114 else if (source == avDistanceTreeBlosumMenuItem)
1116 avTreeBlosumMenuItem_actionPerformed();
1118 else if (source == documentation)
1120 documentation_actionPerformed();
1122 else if (source == about)
1124 about_actionPerformed();
1129 public void inputText_actionPerformed()
1131 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1132 Frame frame = new Frame();
1134 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
1137 protected void outputText_actionPerformed(ActionEvent e)
1139 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1140 Frame frame = new Frame();
1142 jalview.bin.JalviewLite.addFrame(frame,
1143 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
1144 cap.setText(new AppletFormatAdapter().formatSequences(
1145 e.getActionCommand(), viewport.getAlignment(),
1146 viewport.showJVSuffix));
1149 public void loadAnnotations()
1151 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1152 cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
1153 cap.setAnnotationImport();
1154 Frame frame = new Frame();
1156 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
1160 public String outputAnnotations(boolean displayTextbox)
1162 String annotation = new AnnotationFile().printAnnotations(
1163 viewport.showAnnotation ? viewport.getAlignment()
1164 .getAlignmentAnnotation() : null, viewport
1165 .getAlignment().getGroups(), ((Alignment) viewport
1166 .getAlignment()).alignmentProperties);
1170 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1171 Frame frame = new Frame();
1173 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
1174 cap.setText(annotation);
1180 private Hashtable getDisplayedFeatureCols()
1182 if (alignPanel.getFeatureRenderer() != null
1183 && viewport.featuresDisplayed != null)
1185 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1186 Hashtable fcols = new Hashtable();
1187 Enumeration en = viewport.featuresDisplayed.keys();
1188 while (en.hasMoreElements())
1190 Object col = en.nextElement();
1191 fcols.put(col, fr.featureColours.get(col));
1198 public String outputFeatures(boolean displayTextbox, String format)
1201 if (format.equalsIgnoreCase("Jalview"))
1203 features = new FeaturesFile().printJalviewFormat(viewport
1204 .getAlignment().getSequencesArray(),
1205 getDisplayedFeatureCols());
1209 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1210 .getSequencesArray(), getDisplayedFeatureCols());
1215 boolean frimport = false;
1216 if (features == null || features.equals("No Features Visible"))
1218 features = "# No features visible - paste some and import them here.";
1222 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1225 cap.setAnnotationImport();
1227 Frame frame = new Frame();
1229 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
1230 cap.setText(features);
1234 if (features == null)
1241 void launchFullApplication()
1243 StringBuffer url = new StringBuffer(jalviewServletURL);
1246 + appendProtocol(viewport.applet.getParameter("file")));
1248 if (viewport.applet.getParameter("features") != null)
1250 url.append("&features=");
1251 url.append(appendProtocol(viewport.applet.getParameter("features")));
1254 if (viewport.applet.getParameter("annotations") != null)
1256 url.append("&annotations=");
1257 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1260 if (viewport.applet.getParameter("jnetfile") != null)
1262 url.append("&annotations=");
1263 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1266 if (viewport.applet.getParameter("defaultColour") != null)
1268 url.append("&colour="
1269 + removeWhiteSpace(viewport.applet
1270 .getParameter("defaultColour")));
1273 if (viewport.applet.getParameter("userDefinedColour") != null)
1275 url.append("&colour="
1276 + removeWhiteSpace(viewport.applet
1277 .getParameter("userDefinedColour")));
1279 if (viewport.applet.getParameter("tree") != null)
1282 + appendProtocol(viewport.applet.getParameter("tree")));
1284 if (viewport.applet.getParameter("treeFile") != null)
1287 + appendProtocol(viewport.applet.getParameter("treeFile")));
1290 showURL(url.toString(), "FULL_APP");
1293 String removeWhiteSpace(String colour)
1295 StringBuffer sb = new StringBuffer();
1296 for (int i = 0; i < colour.length(); i++)
1298 if (Character.isWhitespace(colour.charAt(i)))
1304 sb.append(colour.charAt(i));
1308 return sb.toString();
1311 String appendProtocol(String url)
1316 url = URLEncoder.encode(url);
1319 * When we finally deprecate 1.1 compatibility, we can start to use
1320 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1321 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1322 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1323 * ex.printStackTrace(); }
1325 catch (java.net.MalformedURLException ex)
1327 url = viewport.applet.getCodeBase() + url;
1332 public void closeMenuItem_actionPerformed()
1334 PaintRefresher.RemoveComponent(alignPanel);
1335 if (alignPanel.seqPanel != null
1336 && alignPanel.seqPanel.seqCanvas != null)
1338 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1340 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1342 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1345 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1360 void updateEditMenuBar()
1363 if (viewport.historyList.size() > 0)
1365 undoMenuItem.setEnabled(true);
1366 CommandI command = (CommandI) viewport.historyList.peek();
1367 undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1371 undoMenuItem.setEnabled(false);
1372 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1375 if (viewport.redoList.size() > 0)
1377 redoMenuItem.setEnabled(true);
1379 CommandI command = (CommandI) viewport.redoList.peek();
1380 redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1384 redoMenuItem.setEnabled(false);
1385 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1392 public void addHistoryItem(CommandI command)
1394 if (command.getSize() > 0)
1396 viewport.historyList.push(command);
1397 viewport.redoList.removeAllElements();
1398 updateEditMenuBar();
1399 viewport.updateHiddenColumns();
1404 * TODO: JAL-1104 DOCUMENT ME!
1409 protected void undoMenuItem_actionPerformed()
1411 if (viewport.historyList.size() < 1)
1416 CommandI command = (CommandI) viewport.historyList.pop();
1417 viewport.redoList.push(command);
1418 command.undoCommand(null);
1420 AlignViewport originalSource = getOriginatingSource(command);
1422 if (originalSource != viewport)
1425 .println("Warning: Viewport object mismatch whilst undoing");
1427 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1428 // viewport.getColumnSelection().getHiddenColumns()
1430 updateEditMenuBar();
1431 originalSource.firePropertyChange("alignment", null, originalSource
1432 .getAlignment().getSequences());
1436 * TODO: JAL-1104 DOCUMENT ME!
1441 protected void redoMenuItem_actionPerformed()
1443 if (viewport.redoList.size() < 1)
1448 CommandI command = (CommandI) viewport.redoList.pop();
1449 viewport.historyList.push(command);
1450 command.doCommand(null);
1452 AlignViewport originalSource = getOriginatingSource(command);
1454 if (originalSource != viewport)
1457 .println("Warning: Viewport object mismatch whilst re-doing");
1459 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1460 // viewport.getColumnSelection().getHiddenColumns()
1463 updateEditMenuBar();
1464 originalSource.firePropertyChange("alignment", null, originalSource
1465 .getAlignment().getSequences());
1468 AlignViewport getOriginatingSource(CommandI command)
1470 AlignViewport originalSource = null;
1471 // For sequence removal and addition, we need to fire
1472 // the property change event FROM the viewport where the
1473 // original alignment was altered
1474 AlignmentI al = null;
1475 if (command instanceof EditCommand)
1477 EditCommand editCommand = (EditCommand) command;
1478 al = editCommand.getAlignment();
1479 Vector comps = (Vector) PaintRefresher.components.get(viewport
1480 .getSequenceSetId());
1481 for (int i = 0; i < comps.size(); i++)
1483 if (comps.elementAt(i) instanceof AlignmentPanel)
1485 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1487 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1494 if (originalSource == null)
1496 // The original view is closed, we must validate
1497 // the current view against the closed view first
1500 PaintRefresher.validateSequences(al, viewport.getAlignment());
1503 originalSource = viewport;
1506 return originalSource;
1509 public void moveSelectedSequences(boolean up)
1511 SequenceGroup sg = viewport.getSelectionGroup();
1516 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1517 up ? null : viewport.getHiddenRepSequences(), up);
1518 alignPanel.paintAlignment(true);
1521 synchronized void slideSequences(boolean right, int size)
1523 List<SequenceI> sg = new Vector<SequenceI>();
1524 if (viewport.cursorMode)
1526 sg.add(viewport.getAlignment().getSequenceAt(
1527 alignPanel.seqPanel.seqCanvas.cursorY));
1529 else if (viewport.getSelectionGroup() != null
1530 && viewport.getSelectionGroup().getSize() != viewport
1531 .getAlignment().getHeight())
1533 sg = viewport.getSelectionGroup().getSequences(
1534 viewport.getHiddenRepSequences());
1542 Vector<SequenceI> invertGroup = new Vector();
1544 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1546 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1547 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1550 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1552 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1554 for (int i = 0; i < invertGroup.size(); i++)
1555 seqs2[i] = invertGroup.elementAt(i);
1557 SlideSequencesCommand ssc;
1559 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1560 size, viewport.getGapCharacter());
1562 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1563 size, viewport.getGapCharacter());
1565 int groupAdjustment = 0;
1566 if (ssc.getGapsInsertedBegin() && right)
1568 if (viewport.cursorMode)
1569 alignPanel.seqPanel.moveCursor(size, 0);
1571 groupAdjustment = size;
1573 else if (!ssc.getGapsInsertedBegin() && !right)
1575 if (viewport.cursorMode)
1576 alignPanel.seqPanel.moveCursor(-size, 0);
1578 groupAdjustment = -size;
1581 if (groupAdjustment != 0)
1583 viewport.getSelectionGroup().setStartRes(
1584 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1585 viewport.getSelectionGroup().setEndRes(
1586 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1589 boolean appendHistoryItem = false;
1590 if (viewport.historyList != null && viewport.historyList.size() > 0
1591 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1593 appendHistoryItem = ssc
1594 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1598 if (!appendHistoryItem)
1599 addHistoryItem(ssc);
1604 static StringBuffer copiedSequences;
1606 static Vector copiedHiddenColumns;
1608 protected void copy_actionPerformed()
1610 if (viewport.getSelectionGroup() == null)
1615 SequenceGroup sg = viewport.getSelectionGroup();
1616 copiedSequences = new StringBuffer();
1617 Hashtable orderedSeqs = new Hashtable();
1618 for (int i = 0; i < sg.getSize(); i++)
1620 SequenceI seq = sg.getSequenceAt(i);
1621 int index = viewport.getAlignment().findIndex(seq);
1622 orderedSeqs.put(index + "", seq);
1625 int index = 0, startRes, endRes;
1628 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1630 copiedHiddenColumns = new Vector();
1631 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1632 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1635 int[] region = (int[]) viewport.getColumnSelection()
1636 .getHiddenColumns().elementAt(i);
1638 copiedHiddenColumns.addElement(new int[]
1639 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1644 copiedHiddenColumns = null;
1647 for (int i = 0; i < sg.getSize(); i++)
1649 SequenceI seq = null;
1653 if (orderedSeqs.containsKey(index + ""))
1655 seq = (SequenceI) orderedSeqs.get(index + "");
1667 // Returns residue following index if gap
1668 startRes = seq.findPosition(sg.getStartRes());
1671 // Need to find the residue preceeding index if gap
1674 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1676 ch = seq.getCharAt(j);
1677 if (!jalview.util.Comparison.isGap((ch)))
1685 endRes += seq.getStart() - 1;
1688 copiedSequences.append(seq.getName()
1694 + seq.getSequenceAsString(sg.getStartRes(),
1695 sg.getEndRes() + 1) + "\n");
1700 protected void pasteNew_actionPerformed()
1705 protected void pasteThis_actionPerformed()
1710 void paste(boolean newAlignment)
1715 if (copiedSequences == null)
1720 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1721 Vector seqs = new Vector();
1722 while (st.hasMoreElements())
1724 String name = st.nextToken();
1725 int start = Integer.parseInt(st.nextToken());
1726 int end = Integer.parseInt(st.nextToken());
1727 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1729 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1730 for (int i = 0; i < seqs.size(); i++)
1732 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1737 String newtitle = new String("Copied sequences");
1738 if (getTitle().startsWith("Copied sequences"))
1740 newtitle = getTitle();
1744 newtitle = newtitle.concat("- from " + getTitle());
1746 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1747 viewport.applet, newtitle, false);
1748 if (copiedHiddenColumns != null)
1750 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1752 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1753 af.viewport.hideColumns(region[0], region[1]);
1757 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1762 addSequences(newSeqs);
1765 } catch (Exception ex)
1767 } // could be anything being pasted in here
1771 void addSequences(SequenceI[] seqs)
1773 for (int i = 0; i < seqs.length; i++)
1775 viewport.getAlignment().addSequence(seqs[i]);
1779 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1780 seqs, 0, viewport.getAlignment().getWidth(),
1781 viewport.getAlignment()));
1783 viewport.setEndSeq(viewport.getAlignment().getHeight());
1784 viewport.getAlignment().getWidth();
1785 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1790 protected void cut_actionPerformed()
1792 copy_actionPerformed();
1793 delete_actionPerformed();
1796 protected void delete_actionPerformed()
1799 SequenceGroup sg = viewport.getSelectionGroup();
1805 Vector seqs = new Vector();
1807 for (int i = 0; i < sg.getSize(); i++)
1809 seq = sg.getSequenceAt(i);
1810 seqs.addElement(seq);
1813 // If the cut affects all sequences, remove highlighted columns
1814 if (sg.getSize() == viewport.getAlignment().getHeight())
1816 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1817 sg.getEndRes() + 1);
1820 SequenceI[] cut = new SequenceI[seqs.size()];
1821 for (int i = 0; i < seqs.size(); i++)
1823 cut[i] = (SequenceI) seqs.elementAt(i);
1827 * //ADD HISTORY ITEM
1829 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1830 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1831 viewport.getAlignment()));
1833 viewport.setSelectionGroup(null);
1834 viewport.getAlignment().deleteGroup(sg);
1836 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1839 if (viewport.getAlignment().getHeight() < 1)
1841 this.setVisible(false);
1843 viewport.sendSelection();
1847 * group consensus toggled
1850 protected void showGroupConsensus_actionPerformed()
1852 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1853 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1858 * group conservation toggled.
1860 protected void showGroupConservation_actionPerformed()
1862 viewport.setShowGroupConservation(showGroupConservation.getState());
1863 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1870 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1871 * .event.ActionEvent)
1873 protected void showConsensusHistogram_actionPerformed()
1875 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1876 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1883 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1884 * .event.ActionEvent)
1886 protected void showSequenceLogo_actionPerformed()
1888 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1889 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1892 protected void normSequenceLogo_actionPerformed()
1894 showSequenceLogo.setState(true);
1895 viewport.setShowSequenceLogo(true);
1896 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1897 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1900 protected void applyAutoAnnotationSettings_actionPerformed()
1902 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1905 protected void makeGrpsFromSelection_actionPerformed()
1907 if (avc.makeGroupsFromSelection()) {
1908 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1909 alignPanel.updateAnnotation();
1910 alignPanel.paintAlignment(true);
1914 protected void createGroup_actionPerformed()
1918 protected void unGroup_actionPerformed()
1922 alignPanel.alignmentChanged();
1925 protected void deleteGroups_actionPerformed()
1927 if (avc.deleteGroups())
1929 alignPanel.alignmentChanged();
1933 public void selectAllSequenceMenuItem_actionPerformed()
1935 SequenceGroup sg = new SequenceGroup();
1936 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1938 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1940 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1941 viewport.setSelectionGroup(sg);
1942 alignPanel.paintAlignment(true);
1943 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1944 viewport.sendSelection();
1947 public void deselectAllSequenceMenuItem_actionPerformed()
1949 if (viewport.cursorMode)
1951 alignPanel.seqPanel.keyboardNo1 = null;
1952 alignPanel.seqPanel.keyboardNo2 = null;
1954 viewport.setSelectionGroup(null);
1955 viewport.getColumnSelection().clear();
1956 viewport.setSelectionGroup(null);
1957 alignPanel.idPanel.idCanvas.searchResults = null;
1958 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1959 alignPanel.paintAlignment(true);
1960 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1961 viewport.sendSelection();
1964 public void invertSequenceMenuItem_actionPerformed()
1966 SequenceGroup sg = viewport.getSelectionGroup();
1967 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1969 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1972 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1973 viewport.sendSelection();
1976 public void invertColSel_actionPerformed()
1978 viewport.invertColumnSelection();
1979 alignPanel.paintAlignment(true);
1980 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1981 viewport.sendSelection();
1984 void trimAlignment(boolean trimLeft)
1986 ColumnSelection colSel = viewport.getColumnSelection();
1989 if (colSel.size() > 0)
1993 column = colSel.getMin();
1997 column = colSel.getMax();
2001 if (viewport.getSelectionGroup() != null)
2003 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2004 viewport.getHiddenRepSequences());
2008 seqs = viewport.getAlignment().getSequencesArray();
2011 TrimRegionCommand trimRegion;
2014 trimRegion = new TrimRegionCommand("Remove Left",
2015 TrimRegionCommand.TRIM_LEFT, seqs, column,
2016 viewport.getAlignment(), viewport.getColumnSelection(),
2017 viewport.getSelectionGroup());
2018 viewport.setStartRes(0);
2022 trimRegion = new TrimRegionCommand("Remove Right",
2023 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2024 viewport.getAlignment(), viewport.getColumnSelection(),
2025 viewport.getSelectionGroup());
2028 statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2029 addHistoryItem(trimRegion);
2031 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2033 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2034 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2036 viewport.getAlignment().deleteGroup(sg);
2040 viewport.firePropertyChange("alignment", null, viewport
2041 .getAlignment().getSequences());
2045 public void removeGappedColumnMenuItem_actionPerformed()
2047 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2050 if (viewport.getSelectionGroup() != null)
2052 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2053 viewport.getHiddenRepSequences());
2054 start = viewport.getSelectionGroup().getStartRes();
2055 end = viewport.getSelectionGroup().getEndRes();
2059 seqs = viewport.getAlignment().getSequencesArray();
2062 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2063 "Remove Gapped Columns", seqs, start, end,
2064 viewport.getAlignment());
2066 addHistoryItem(removeGapCols);
2068 statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2070 // This is to maintain viewport position on first residue
2071 // of first sequence
2072 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2073 int startRes = seq.findPosition(viewport.startRes);
2074 // ShiftList shifts;
2075 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2076 // edit.alColumnChanges=shifts.getInverse();
2077 // if (viewport.hasHiddenColumns)
2078 // viewport.getColumnSelection().compensateForEdits(shifts);
2079 viewport.setStartRes(seq.findIndex(startRes) - 1);
2080 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2085 public void removeAllGapsMenuItem_actionPerformed()
2087 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2090 if (viewport.getSelectionGroup() != null)
2092 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2093 viewport.getHiddenRepSequences());
2094 start = viewport.getSelectionGroup().getStartRes();
2095 end = viewport.getSelectionGroup().getEndRes();
2099 seqs = viewport.getAlignment().getSequencesArray();
2102 // This is to maintain viewport position on first residue
2103 // of first sequence
2104 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2105 int startRes = seq.findPosition(viewport.startRes);
2107 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2108 viewport.getAlignment()));
2110 viewport.setStartRes(seq.findIndex(startRes) - 1);
2112 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2117 public void findMenuItem_actionPerformed()
2119 new Finder(alignPanel);
2123 * create a new view derived from the current view
2126 * @return frame for the new view
2128 public AlignFrame newView(String viewtitle)
2131 if (viewport.hasHiddenRows())
2133 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2134 .getFullAlignment().getSequencesArray());
2138 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2141 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2143 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2145 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2147 newal.addAnnotation(viewport.getAlignment()
2148 .getAlignmentAnnotation()[i]);
2153 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2155 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2156 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2157 PaintRefresher.Register(newaf.alignPanel,
2158 newaf.alignPanel.av.getSequenceSetId());
2160 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2161 newaf.alignPanel.av.getSequenceSetId());
2162 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2163 newaf.alignPanel.av.getSequenceSetId());
2165 Vector comps = (Vector) PaintRefresher.components.get(viewport
2166 .getSequenceSetId());
2168 for (int i = 0; i < comps.size(); i++)
2170 if (comps.elementAt(i) instanceof AlignmentPanel)
2176 String title = new String(this.getTitle());
2177 if (viewtitle != null)
2179 title = viewtitle + " ( " + title + ")";
2183 if (title.indexOf("(View") > -1)
2185 title = title.substring(0, title.indexOf("(View"));
2187 title += "(View " + viewSize + ")";
2190 newaf.setTitle(title.toString());
2192 newaf.viewport.historyList = viewport.historyList;
2193 newaf.viewport.redoList = viewport.redoList;
2199 * @return list of feature groups on the view
2201 public String[] getFeatureGroups()
2203 FeatureRenderer fr = null;
2204 if (alignPanel != null
2205 && (fr = alignPanel.getFeatureRenderer()) != null)
2207 return fr.getGroups();
2213 * get sequence feature groups that are hidden or shown
2219 public String[] getFeatureGroupsOfState(boolean visible)
2221 FeatureRenderer fr = null;
2222 if (alignPanel != null
2223 && (fr = alignPanel.getFeatureRenderer()) != null)
2225 return fr.getGroups(visible);
2231 * Change the display state for the given feature groups
2234 * list of group strings
2236 * visible or invisible
2238 public void setFeatureGroupState(String[] groups, boolean state)
2240 FeatureRenderer fr = null;
2241 this.sequenceFeatures.setState(true);
2242 viewport.showSequenceFeatures(true);
2243 if (alignPanel != null
2244 && (fr = alignPanel.getFeatureRenderer()) != null)
2246 fr.setGroupState(groups, state);
2247 alignPanel.seqPanel.seqCanvas.repaint();
2248 if (alignPanel.overviewPanel != null)
2250 alignPanel.overviewPanel.updateOverviewImage();
2255 public void seqLimits_itemStateChanged()
2257 viewport.setShowJVSuffix(seqLimits.getState());
2258 alignPanel.fontChanged();
2259 alignPanel.paintAlignment(true);
2262 protected void colourTextMenuItem_actionPerformed()
2264 viewport.setColourText(colourTextMenuItem.getState());
2265 alignPanel.paintAlignment(true);
2268 protected void displayNonconservedMenuItem_actionPerformed()
2270 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2271 alignPanel.paintAlignment(true);
2274 protected void wrapMenuItem_actionPerformed()
2276 viewport.setWrapAlignment(wrapMenuItem.getState());
2277 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2278 scaleAbove.setEnabled(wrapMenuItem.getState());
2279 scaleLeft.setEnabled(wrapMenuItem.getState());
2280 scaleRight.setEnabled(wrapMenuItem.getState());
2281 alignPanel.paintAlignment(true);
2284 public void overviewMenuItem_actionPerformed()
2286 if (alignPanel.overviewPanel != null)
2291 Frame frame = new Frame();
2292 OverviewPanel overview = new OverviewPanel(alignPanel);
2293 frame.add(overview);
2294 // +50 must allow for applet frame window
2295 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
2296 overview.getPreferredSize().width,
2297 overview.getPreferredSize().height + 50);
2300 final AlignmentPanel ap = alignPanel;
2301 frame.addWindowListener(new WindowAdapter()
2304 public void windowClosing(WindowEvent e)
2308 ap.setOverviewPanel(null);
2313 alignPanel.setOverviewPanel(overview);
2317 void changeColour(ColourSchemeI cs)
2323 if (viewport.getAbovePIDThreshold())
2325 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2328 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2330 viewport.setGlobalColourScheme(cs);
2334 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2337 if (viewport.getConservationSelected())
2340 Alignment al = (Alignment) viewport.getAlignment();
2341 Conservation c = new Conservation("All",
2342 ResidueProperties.propHash, 3, al.getSequences(), 0,
2346 c.verdict(false, viewport.getConsPercGaps());
2348 cs.setConservation(c);
2350 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2356 cs.setConservation(null);
2359 cs.setConsensus(viewport.getSequenceConsensusHash());
2362 viewport.setGlobalColourScheme(cs);
2364 if (alignPanel.getOverviewPanel() != null)
2366 alignPanel.getOverviewPanel().updateOverviewImage();
2369 jalview.structure.StructureSelectionManager
2370 .getStructureSelectionManager(viewport.applet)
2371 .sequenceColoursChanged(alignPanel);
2373 alignPanel.paintAlignment(true);
2376 protected void modifyPID_actionPerformed()
2378 if (viewport.getAbovePIDThreshold()
2379 && viewport.getGlobalColourScheme() != null)
2381 SliderPanel.setPIDSliderSource(alignPanel,
2382 viewport.getGlobalColourScheme(), "Background");
2383 SliderPanel.showPIDSlider();
2387 protected void modifyConservation_actionPerformed()
2389 if (viewport.getConservationSelected()
2390 && viewport.getGlobalColourScheme() != null)
2392 SliderPanel.setConservationSlider(alignPanel,
2393 viewport.getGlobalColourScheme(), "Background");
2394 SliderPanel.showConservationSlider();
2398 protected void conservationMenuItem_actionPerformed()
2400 viewport.setConservationSelected(conservationMenuItem.getState());
2402 viewport.setAbovePIDThreshold(false);
2403 abovePIDThreshold.setState(false);
2405 changeColour(viewport.getGlobalColourScheme());
2407 modifyConservation_actionPerformed();
2410 public void abovePIDThreshold_actionPerformed()
2412 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2414 conservationMenuItem.setState(false);
2415 viewport.setConservationSelected(false);
2417 changeColour(viewport.getGlobalColourScheme());
2419 modifyPID_actionPerformed();
2422 public void sortPairwiseMenuItem_actionPerformed()
2424 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2425 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2426 .getAlignment().getSequenceAt(0), null);
2428 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2429 viewport.getAlignment()));
2430 alignPanel.paintAlignment(true);
2433 public void sortIDMenuItem_actionPerformed()
2435 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2436 AlignmentSorter.sortByID(viewport.getAlignment());
2437 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2438 viewport.getAlignment()));
2439 alignPanel.paintAlignment(true);
2442 public void sortLengthMenuItem_actionPerformed()
2444 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2445 AlignmentSorter.sortByLength(viewport.getAlignment());
2446 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2447 viewport.getAlignment()));
2448 alignPanel.paintAlignment(true);
2451 public void sortGroupMenuItem_actionPerformed()
2453 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2454 AlignmentSorter.sortByGroup(viewport.getAlignment());
2455 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2456 viewport.getAlignment()));
2457 alignPanel.paintAlignment(true);
2461 public void removeRedundancyMenuItem_actionPerformed()
2463 new RedundancyPanel(alignPanel);
2466 public void pairwiseAlignmentMenuItem_actionPerformed()
2468 if (viewport.getSelectionGroup() != null
2469 && viewport.getSelectionGroup().getSize() > 1)
2471 Frame frame = new Frame();
2472 frame.add(new PairwiseAlignPanel(alignPanel));
2473 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
2478 public void PCAMenuItem_actionPerformed()
2480 // are the sequences aligned?
2481 if (!viewport.getAlignment().isAligned(false))
2484 int Width = viewport.getAlignment().getWidth();
2486 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2488 current = viewport.getAlignment().getSequenceAt(i);
2490 if (current.getLength() < Width)
2492 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2495 alignPanel.paintAlignment(true);
2498 if ((viewport.getSelectionGroup() != null
2499 && viewport.getSelectionGroup().getSize() < 4 && viewport
2500 .getSelectionGroup().getSize() > 0)
2501 || viewport.getAlignment().getHeight() < 4)
2508 new PCAPanel(viewport);
2509 } catch (java.lang.OutOfMemoryError ex)
2515 public void averageDistanceTreeMenuItem_actionPerformed()
2517 NewTreePanel("AV", "PID", "Average distance tree using PID");
2520 public void neighbourTreeMenuItem_actionPerformed()
2522 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2525 protected void njTreeBlosumMenuItem_actionPerformed()
2527 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2530 protected void avTreeBlosumMenuItem_actionPerformed()
2532 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2535 void NewTreePanel(String type, String pwType, String title)
2537 // are the sequences aligned?
2538 if (!viewport.getAlignment().isAligned(false))
2541 int Width = viewport.getAlignment().getWidth();
2543 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2545 current = viewport.getAlignment().getSequenceAt(i);
2547 if (current.getLength() < Width)
2549 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2552 alignPanel.paintAlignment(true);
2556 if ((viewport.getSelectionGroup() != null && viewport
2557 .getSelectionGroup().getSize() > 1)
2558 || (viewport.getAlignment().getHeight() > 1))
2560 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2562 addTreeMenuItem(tp, title);
2564 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2568 void loadTree_actionPerformed()
2570 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2571 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2572 cap.setTreeImport();
2573 Frame frame = new Frame();
2575 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
2578 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2580 TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
2581 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2582 addTreeMenuItem(tp, treeFile);
2586 * sort the alignment using the given treePanel
2589 * tree used to sort view
2591 * string used for undo event name
2593 public void sortByTree(TreePanel treePanel, String title)
2595 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2597 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2598 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2599 // HistoryItem.SORT));
2600 addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
2601 viewport.getAlignment()));
2602 alignPanel.paintAlignment(true);
2606 * Do any automatic reordering of the alignment and add the necessary bits to
2607 * the menu structure for the new tree
2612 protected void addTreeMenuItem(final TreePanel treePanel,
2615 final MenuItem item = new MenuItem(title);
2616 sortByTreeMenu.add(item);
2617 item.addActionListener(new java.awt.event.ActionListener()
2620 public void actionPerformed(ActionEvent evt)
2622 sortByTree(treePanel, title); // treePanel.getTitle());
2626 treePanel.addWindowListener(new WindowAdapter()
2629 public void windowOpened(WindowEvent e)
2631 if (viewport.sortByTree)
2633 sortByTree(treePanel, title);
2635 super.windowOpened(e);
2639 public void windowClosing(WindowEvent e)
2641 sortByTreeMenu.remove(item);
2646 public boolean sortBy(AlignmentOrder alorder, String undoname)
2648 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2649 if (viewport.applet.debug)
2651 System.err.println("Sorting " + alorder.getOrder().size()
2652 + " in alignment '" + getTitle() + "'");
2654 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2655 if (undoname != null)
2657 addHistoryItem(new OrderCommand(undoname, oldOrder,
2658 viewport.getAlignment()));
2660 alignPanel.paintAlignment(true);
2664 protected void documentation_actionPerformed()
2666 alignPanel.av.applet.openJalviewHelpUrl();
2669 protected void about_actionPerformed()
2672 class AboutPanel extends Canvas
2678 public AboutPanel(String version, String builddate)
2680 this.version = version;
2681 this.builddate = builddate;
2685 public void paint(Graphics g)
2687 g.setColor(Color.white);
2688 g.fillRect(0, 0, getSize().width, getSize().height);
2689 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2690 FontMetrics fm = g.getFontMetrics();
2691 int fh = fm.getHeight();
2693 g.setColor(Color.black);
2694 // TODO: update this text for each release or centrally store it for
2695 // lite and application
2696 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2697 g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
2698 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2699 g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
2700 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2702 MessageManager.getString("label.jalview_authors_1"),
2704 g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
2706 MessageManager.getString("label.jalview_dev_managers"),
2709 MessageManager.getString("label.jalview_distribution_lists"),
2711 g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
2713 MessageManager.getString("label.jalview_cite_1_authors"),
2716 MessageManager.getString("label.jalview_cite_1_title"),
2718 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2723 Frame frame = new Frame();
2724 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2726 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
2730 public void showURL(String url, String target)
2732 if (viewport.applet == null)
2734 System.out.println("Not running as applet - no browser available.");
2738 viewport.applet.showURL(url, target);
2742 // ////////////////////////////////////////////////////////////////////////////////
2743 // JBuilder Graphics here
2745 MenuBar alignFrameMenuBar = new MenuBar();
2747 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2749 MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
2751 MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
2753 MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
2755 MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
2757 MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
2759 MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
2761 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2763 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2765 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2767 Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
2769 MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
2771 MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
2773 MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
2775 MenuItem remove2LeftMenuItem = new MenuItem();
2777 MenuItem remove2RightMenuItem = new MenuItem();
2779 MenuItem removeGappedColumnMenuItem = new MenuItem();
2781 MenuItem removeAllGapsMenuItem = new MenuItem();
2783 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2785 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2787 MenuItem sortPairwiseMenuItem = new MenuItem();
2789 MenuItem sortIDMenuItem = new MenuItem();
2791 MenuItem sortLengthMenuItem = new MenuItem();
2793 MenuItem sortGroupMenuItem = new MenuItem();
2795 MenuItem removeRedundancyMenuItem = new MenuItem();
2797 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2799 MenuItem PCAMenuItem = new MenuItem();
2801 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2803 MenuItem neighbourTreeMenuItem = new MenuItem();
2805 BorderLayout borderLayout1 = new BorderLayout();
2807 public Label statusBar = new Label();
2809 Menu outputTextboxMenu = new Menu();
2811 MenuItem clustalColour = new MenuItem();
2813 MenuItem zappoColour = new MenuItem();
2815 MenuItem taylorColour = new MenuItem();
2817 MenuItem hydrophobicityColour = new MenuItem();
2819 MenuItem helixColour = new MenuItem();
2821 MenuItem strandColour = new MenuItem();
2823 MenuItem turnColour = new MenuItem();
2825 MenuItem buriedColour = new MenuItem();
2827 MenuItem purinePyrimidineColour = new MenuItem();
2829 MenuItem RNAHelixColour = new MenuItem();
2831 MenuItem userDefinedColour = new MenuItem();
2833 MenuItem PIDColour = new MenuItem();
2835 MenuItem BLOSUM62Colour = new MenuItem();
2837 MenuItem tcoffeeColour = new MenuItem();
2839 MenuItem njTreeBlosumMenuItem = new MenuItem();
2841 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2843 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2845 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2847 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2849 MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
2851 MenuItem overviewMenuItem = new MenuItem();
2853 MenuItem undoMenuItem = new MenuItem();
2855 MenuItem redoMenuItem = new MenuItem();
2857 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2859 MenuItem noColourmenuItem = new MenuItem();
2861 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2863 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2865 MenuItem findMenuItem = new MenuItem();
2867 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2869 MenuItem nucleotideColour = new MenuItem();
2871 MenuItem deleteGroups = new MenuItem();
2873 MenuItem grpsFromSelection = new MenuItem();
2875 MenuItem createGroup = new MenuItem();
2877 MenuItem unGroup = new MenuItem();
2879 MenuItem delete = new MenuItem();
2881 MenuItem copy = new MenuItem();
2883 MenuItem cut = new MenuItem();
2885 Menu pasteMenu = new Menu();
2887 MenuItem pasteNew = new MenuItem();
2889 MenuItem pasteThis = new MenuItem();
2891 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2893 MenuItem font = new MenuItem();
2895 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2897 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2899 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2901 MenuItem modifyPID = new MenuItem();
2903 MenuItem modifyConservation = new MenuItem();
2905 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2906 "Autocalculate Consensus", true);
2908 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2909 "Sort Alignment With New Tree", true);
2911 Menu sortByTreeMenu = new Menu();
2913 Menu sort = new Menu();
2915 Menu calculate = new Menu();
2917 MenuItem inputText = new MenuItem();
2919 Menu helpMenu = new Menu();
2921 MenuItem documentation = new MenuItem();
2923 MenuItem about = new MenuItem();
2925 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2927 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2929 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2931 Menu autoAnnMenu = new Menu();
2933 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2935 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2937 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2939 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2941 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2943 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2945 private void jbInit() throws Exception
2948 setMenuBar(alignFrameMenuBar);
2952 // dynamically fill save as menu with available formats
2953 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2956 item = new MenuItem(
2957 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2959 item.addActionListener(new java.awt.event.ActionListener()
2962 public void actionPerformed(ActionEvent e)
2964 outputText_actionPerformed(e);
2968 outputTextboxMenu.add(item);
2970 closeMenuItem.addActionListener(this);
2971 loadApplication.addActionListener(this);
2973 loadTree.addActionListener(this);
2974 loadAnnotations.addActionListener(this);
2975 outputFeatures.addActionListener(this);
2976 outputAnnotations.addActionListener(this);
2977 selectAllSequenceMenuItem.addActionListener(this);
2978 deselectAllSequenceMenuItem.addActionListener(this);
2979 invertSequenceMenuItem.addActionListener(this);
2980 remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
2981 remove2LeftMenuItem.addActionListener(this);
2982 remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
2983 remove2RightMenuItem.addActionListener(this);
2984 removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
2985 removeGappedColumnMenuItem.addActionListener(this);
2986 removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
2987 removeAllGapsMenuItem.addActionListener(this);
2988 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
2989 viewBoxesMenuItem.setState(true);
2990 viewBoxesMenuItem.addItemListener(this);
2991 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
2992 viewTextMenuItem.setState(true);
2993 viewTextMenuItem.addItemListener(this);
2994 sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
2995 sortPairwiseMenuItem.addActionListener(this);
2996 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
2997 sortIDMenuItem.addActionListener(this);
2998 sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
2999 sortLengthMenuItem.addActionListener(this);
3000 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3001 sortGroupMenuItem.addActionListener(this);
3002 removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
3003 removeRedundancyMenuItem.addActionListener(this);
3004 pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
3005 pairwiseAlignmentMenuItem.addActionListener(this);
3006 PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
3007 PCAMenuItem.addActionListener(this);
3008 averageDistanceTreeMenuItem
3009 .setLabel(MessageManager.getString("label.average_distance_identity"));
3010 averageDistanceTreeMenuItem.addActionListener(this);
3011 neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
3012 neighbourTreeMenuItem.addActionListener(this);
3013 statusBar.setBackground(Color.white);
3014 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3015 statusBar.setText(MessageManager.getString("label.status_bar"));
3016 outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
3017 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3019 clustalColour.addActionListener(this);
3020 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3021 zappoColour.addActionListener(this);
3022 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3023 taylorColour.addActionListener(this);
3024 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
3025 hydrophobicityColour.addActionListener(this);
3026 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
3027 helixColour.addActionListener(this);
3028 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
3029 strandColour.addActionListener(this);
3030 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3031 turnColour.addActionListener(this);
3032 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3033 buriedColour.addActionListener(this);
3034 purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
3035 purinePyrimidineColour.addActionListener(this);
3036 RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
3037 RNAHelixColour.addActionListener(this);
3038 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
3039 userDefinedColour.addActionListener(this);
3040 PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
3041 PIDColour.addActionListener(this);
3042 BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
3043 BLOSUM62Colour.addActionListener(this);
3044 tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
3045 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3047 tcoffeeColour.addActionListener(this);
3048 avDistanceTreeBlosumMenuItem
3049 .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
3050 avDistanceTreeBlosumMenuItem.addActionListener(this);
3051 njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
3052 njTreeBlosumMenuItem.addActionListener(this);
3053 annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
3054 annotationPanelMenuItem.addItemListener(this);
3055 colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
3056 colourTextMenuItem.addItemListener(this);
3057 displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
3058 displayNonconservedMenuItem.addItemListener(this);
3059 alProperties.addActionListener(this);
3060 overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
3061 overviewMenuItem.addActionListener(this);
3062 undoMenuItem.setEnabled(false);
3063 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3064 undoMenuItem.addActionListener(this);
3065 redoMenuItem.setEnabled(false);
3066 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3067 redoMenuItem.addActionListener(this);
3068 conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
3069 conservationMenuItem.addItemListener(this);
3070 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3071 noColourmenuItem.addActionListener(this);
3072 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3073 wrapMenuItem.addItemListener(this);
3074 renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
3075 renderGapsMenuItem.setState(true);
3076 renderGapsMenuItem.addItemListener(this);
3077 findMenuItem.setLabel(MessageManager.getString("action.find"));
3078 findMenuItem.addActionListener(this);
3079 abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
3080 abovePIDThreshold.addItemListener(this);
3081 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3082 nucleotideColour.addActionListener(this);
3083 deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
3084 deleteGroups.addActionListener(this);
3085 grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
3086 grpsFromSelection.addActionListener(this);
3087 createGroup.setLabel(MessageManager.getString("action.create_group"));
3088 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3089 copy.setLabel(MessageManager.getString("action.copy"));
3090 copy.addActionListener(this);
3091 cut.setLabel(MessageManager.getString("action.cut"));
3092 cut.addActionListener(this);
3093 delete.setLabel(MessageManager.getString("action.delete"));
3094 delete.addActionListener(this);
3095 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3096 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3097 pasteNew.addActionListener(this);
3098 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3099 pasteThis.addActionListener(this);
3100 applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
3101 applyToAllGroups.setState(true);
3102 applyToAllGroups.addItemListener(this);
3103 font.setLabel(MessageManager.getString("action.font"));
3104 font.addActionListener(this);
3105 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3106 scaleAbove.setState(true);
3107 scaleAbove.setEnabled(false);
3108 scaleAbove.addItemListener(this);
3109 scaleLeft.setEnabled(false);
3110 scaleLeft.setState(true);
3111 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3112 scaleLeft.addItemListener(this);
3113 scaleRight.setEnabled(false);
3114 scaleRight.setState(true);
3115 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3116 scaleRight.addItemListener(this);
3117 modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
3118 modifyPID.addActionListener(this);
3119 modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
3120 modifyConservation.addActionListener(this);
3121 sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
3122 sort.setLabel(MessageManager.getString("action.sort"));
3123 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3124 autoCalculate.addItemListener(this);
3125 sortByTree.addItemListener(this);
3126 inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
3127 inputText.addActionListener(this);
3128 centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
3129 centreColumnLabelFlag.addItemListener(this);
3130 followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
3131 followMouseOverFlag.addItemListener(this);
3132 helpMenu.setLabel(MessageManager.getString("action.help"));
3133 documentation.setLabel(MessageManager.getString("label.documentation"));
3134 documentation.addActionListener(this);
3136 about.setLabel(MessageManager.getString("label.about"));
3137 about.addActionListener(this);
3138 seqLimits.setState(true);
3139 seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
3140 seqLimits.addItemListener(this);
3141 featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
3142 featureSettings.addActionListener(this);
3143 sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
3144 sequenceFeatures.addItemListener(this);
3145 sequenceFeatures.setState(false);
3146 annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
3147 annotationColour.addActionListener(this);
3148 invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
3149 invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
3150 menu1.setLabel(MessageManager.getString("action.show"));
3151 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3152 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3153 menu2.setLabel(MessageManager.getString("aciton.hide"));
3154 hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
3155 hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
3156 hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
3157 hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
3158 showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
3159 showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
3160 showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
3161 showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
3162 showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
3163 normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
3164 applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
3165 applyAutoAnnotationSettings.setState(true);
3166 autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
3168 invertColSel.addActionListener(this);
3169 showColumns.addActionListener(this);
3170 showSeqs.addActionListener(this);
3171 hideColumns.addActionListener(this);
3172 hideSequences.addActionListener(this);
3173 hideAllButSelection.addActionListener(this);
3174 hideAllSelection.addActionListener(this);
3175 showAllHidden.addActionListener(this);
3176 showGroupConsensus.addItemListener(this);
3177 showGroupConservation.addItemListener(this);
3178 showConsensusHistogram.addItemListener(this);
3179 showSequenceLogo.addItemListener(this);
3180 normSequenceLogo.addItemListener(this);
3182 applyAutoAnnotationSettings.addItemListener(this);
3183 formatMenu.setLabel(MessageManager.getString("action.format"));
3184 selectMenu.setLabel(MessageManager.getString("action.select"));
3185 newView.setLabel(MessageManager.getString("action.new_view"));
3186 newView.addActionListener(this);
3187 alignFrameMenuBar.add(fileMenu);
3188 alignFrameMenuBar.add(editMenu);
3189 alignFrameMenuBar.add(selectMenu);
3190 alignFrameMenuBar.add(viewMenu);
3191 alignFrameMenuBar.add(formatMenu);
3192 alignFrameMenuBar.add(colourMenu);
3193 alignFrameMenuBar.add(calculateMenu);
3194 alignFrameMenuBar.add(helpMenu);
3196 fileMenu.add(inputText);
3197 fileMenu.add(loadTree);
3198 fileMenu.add(loadAnnotations);
3200 fileMenu.addSeparator();
3201 fileMenu.add(outputTextboxMenu);
3202 fileMenu.add(outputFeatures);
3203 fileMenu.add(outputAnnotations);
3205 if (jalviewServletURL != null)
3207 fileMenu.add(loadApplication);
3210 fileMenu.addSeparator();
3211 fileMenu.add(closeMenuItem);
3213 editMenu.add(undoMenuItem);
3214 editMenu.add(redoMenuItem);
3217 editMenu.add(pasteMenu);
3218 editMenu.add(delete);
3219 editMenu.addSeparator();
3220 editMenu.add(remove2LeftMenuItem);
3221 editMenu.add(remove2RightMenuItem);
3222 editMenu.add(removeGappedColumnMenuItem);
3223 editMenu.add(removeAllGapsMenuItem);
3224 editMenu.add(removeRedundancyMenuItem);
3225 viewMenu.add(newView);
3226 viewMenu.addSeparator();
3227 viewMenu.add(menu1);
3228 viewMenu.add(menu2);
3229 viewMenu.addSeparator();
3230 viewMenu.add(followMouseOverFlag);
3231 viewMenu.add(annotationPanelMenuItem);
3232 autoAnnMenu.add(applyAutoAnnotationSettings);
3233 autoAnnMenu.add(showConsensusHistogram);
3234 autoAnnMenu.add(showSequenceLogo);
3235 autoAnnMenu.add(normSequenceLogo);
3236 autoAnnMenu.addSeparator();
3237 autoAnnMenu.add(showGroupConservation);
3238 autoAnnMenu.add(showGroupConsensus);
3239 viewMenu.add(autoAnnMenu);
3240 viewMenu.addSeparator();
3241 viewMenu.add(sequenceFeatures);
3242 viewMenu.add(featureSettings);
3243 viewMenu.addSeparator();
3244 viewMenu.add(alProperties);
3245 viewMenu.addSeparator();
3246 viewMenu.add(overviewMenuItem);
3247 colourMenu.add(applyToAllGroups);
3248 colourMenu.addSeparator();
3249 colourMenu.add(noColourmenuItem);
3250 colourMenu.add(clustalColour);
3251 colourMenu.add(BLOSUM62Colour);
3252 colourMenu.add(PIDColour);
3253 colourMenu.add(zappoColour);
3254 colourMenu.add(taylorColour);
3255 colourMenu.add(hydrophobicityColour);
3256 colourMenu.add(helixColour);
3257 colourMenu.add(strandColour);
3258 colourMenu.add(turnColour);
3259 colourMenu.add(buriedColour);
3260 colourMenu.add(nucleotideColour);
3261 colourMenu.add(purinePyrimidineColour);
3262 colourMenu.add(tcoffeeColour);
3263 colourMenu.add(userDefinedColour);
3264 colourMenu.addSeparator();
3265 colourMenu.add(conservationMenuItem);
3266 colourMenu.add(modifyConservation);
3267 colourMenu.add(abovePIDThreshold);
3268 colourMenu.add(modifyPID);
3269 colourMenu.add(annotationColour);
3270 colourMenu.add(RNAHelixColour);
3271 calculateMenu.add(sort);
3272 calculateMenu.add(calculate);
3273 calculateMenu.addSeparator();
3274 calculateMenu.add(pairwiseAlignmentMenuItem);
3275 calculateMenu.add(PCAMenuItem);
3276 calculateMenu.add(autoCalculate);
3277 calculateMenu.add(sortByTree);
3278 this.add(statusBar, BorderLayout.SOUTH);
3279 pasteMenu.add(pasteNew);
3280 pasteMenu.add(pasteThis);
3281 sort.add(sortIDMenuItem);
3282 sort.add(sortLengthMenuItem);
3283 sort.add(sortByTreeMenu);
3284 sort.add(sortGroupMenuItem);
3285 sort.add(sortPairwiseMenuItem);
3286 calculate.add(averageDistanceTreeMenuItem);
3287 calculate.add(neighbourTreeMenuItem);
3288 calculate.add(avDistanceTreeBlosumMenuItem);
3289 calculate.add(njTreeBlosumMenuItem);
3290 helpMenu.add(documentation);
3291 helpMenu.add(about);
3292 menu1.add(showColumns);
3293 menu1.add(showSeqs);
3294 menu1.add(showAllHidden);
3295 menu2.add(hideColumns);
3296 menu2.add(hideSequences);
3297 menu2.add(hideAllSelection);
3298 menu2.add(hideAllButSelection);
3299 formatMenu.add(font);
3300 formatMenu.add(seqLimits);
3301 formatMenu.add(wrapMenuItem);
3302 formatMenu.add(scaleAbove);
3303 formatMenu.add(scaleLeft);
3304 formatMenu.add(scaleRight);
3305 formatMenu.add(viewBoxesMenuItem);
3306 formatMenu.add(viewTextMenuItem);
3307 formatMenu.add(colourTextMenuItem);
3308 formatMenu.add(displayNonconservedMenuItem);
3309 formatMenu.add(renderGapsMenuItem);
3310 formatMenu.add(centreColumnLabelFlag);
3311 selectMenu.add(findMenuItem);
3312 selectMenu.addSeparator();
3313 selectMenu.add(selectAllSequenceMenuItem);
3314 selectMenu.add(deselectAllSequenceMenuItem);
3315 selectMenu.add(invertSequenceMenuItem);
3316 selectMenu.add(invertColSel);
3317 selectMenu.add(createGroup);
3318 selectMenu.add(unGroup);
3319 selectMenu.add(grpsFromSelection);
3320 selectMenu.add(deleteGroups);
3324 MenuItem featureSettings = new MenuItem();
3326 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3328 MenuItem annotationColour = new MenuItem();
3330 MenuItem invertColSel = new MenuItem();
3332 Menu menu1 = new Menu();
3334 MenuItem showColumns = new MenuItem();
3336 MenuItem showSeqs = new MenuItem();
3338 Menu menu2 = new Menu();
3340 MenuItem hideColumns = new MenuItem();
3342 MenuItem hideSequences = new MenuItem();
3344 MenuItem hideAllButSelection = new MenuItem();
3346 MenuItem hideAllSelection = new MenuItem();
3348 MenuItem showAllHidden = new MenuItem();
3350 Menu formatMenu = new Menu();
3352 Menu selectMenu = new Menu();
3354 MenuItem newView = new MenuItem();
3357 * Attach the alignFrame panels after embedding menus, if necessary. This used
3358 * to be called setEmbedded, but is now creates the dropdown menus in a
3359 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3361 * @param reallyEmbedded
3362 * true to attach the view to the applet area on the page rather than
3365 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3370 // Explicly build the embedded menu panel for the on-page applet
3372 // view cannot be closed if its actually on the page
3373 fileMenu.remove(closeMenuItem);
3374 fileMenu.remove(3); // Remove Seperator
3375 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3376 Font.PLAIN, 10, false); // use our own fonts.
3377 // and actually add the components to the applet area
3378 viewport.applet.setLayout(new BorderLayout());
3379 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3380 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3381 alignPanel.setSize(viewport.applet.getSize().width,
3382 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3383 - statusBar.HEIGHT);
3384 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3385 final AlignFrame me = this;
3386 viewport.applet.addFocusListener(new FocusListener()
3390 public void focusLost(FocusEvent e)
3392 if (me.viewport.applet.currentAlignFrame == me)
3394 me.viewport.applet.currentAlignFrame = null;
3399 public void focusGained(FocusEvent e)
3401 me.viewport.applet.currentAlignFrame = me;
3404 viewport.applet.validate();
3409 // test and embed menu bar if necessary.
3411 if (embedMenuIfNeeded(alignPanel))
3413 // adjust for status bar height too
3414 alignPanel.setSize(getSize().width, getSize().height
3415 - statusBar.HEIGHT);
3417 add(statusBar, BorderLayout.SOUTH);
3418 add(alignPanel, BorderLayout.CENTER);
3419 // and register with the applet so it can pass external API calls to us
3420 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3426 * create a new binding between structures in an existing jmol viewer instance
3427 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3428 * this does not open a new Jmol window, or modify the display of the
3429 * structures in the original jmol window. Note This method doesn't work
3430 * without an additional javascript library to exchange messages between the
3431 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3434 * JmolViewer instance
3435 * @param sequenceIds
3436 * - sequence Ids to search for associations
3438 public SequenceStructureBinding addStructureViewInstance(
3439 Object jmolviewer, String[] sequenceIds)
3441 org.jmol.api.JmolViewer viewer = null;
3444 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3445 } catch (ClassCastException ex)
3447 System.err.println("Unsupported viewer object :"
3448 + jmolviewer.getClass());
3452 System.err.println("Can't use this object as a structure viewer:"
3453 + jmolviewer.getClass());
3456 SequenceI[] seqs = null;
3457 if (sequenceIds == null || sequenceIds.length == 0)
3459 seqs = viewport.getAlignment().getSequencesArray();
3463 Vector sqi = new Vector();
3464 AlignmentI al = viewport.getAlignment();
3465 for (int sid = 0; sid < sequenceIds.length; sid++)
3467 SequenceI sq = al.findName(sequenceIds[sid]);
3475 seqs = new SequenceI[sqi.size()];
3476 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3478 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3487 // TODO: search for a jmv that involves viewer
3489 { // create a new viewer/jalview binding.
3490 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3498 * bind a pdb file to a sequence in the current view
3501 * - sequenceId within the dataset.
3502 * @param pdbEntryString
3503 * - the short name for the PDB file
3505 * - pdb file - either a URL or a valid PDB file.
3506 * @return true if binding was as success TODO: consider making an exception
3507 * structure for indicating when PDB parsing or sequenceId location
3510 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3513 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3514 boolean needtoadd = false;
3515 if (toaddpdb != null)
3517 Vector pdbe = toaddpdb.getPDBId();
3518 PDBEntry pdbentry = null;
3519 if (pdbe != null && pdbe.size() > 0)
3521 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3523 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3524 if (!pdbentry.getId().equals(pdbEntryString)
3525 && !pdbentry.getFile().equals(pdbFile))
3535 if (pdbentry == null)
3537 pdbentry = new PDBEntry();
3538 pdbentry.setId(pdbEntryString);
3539 pdbentry.setFile(pdbFile);
3540 needtoadd = true; // add this new entry to sequence.
3542 // resolve data source
3543 // TODO: this code should be a refactored to an io package
3544 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3545 if (protocol == null)
3551 // make a note of the access mode and add
3552 if (pdbentry.getProperty() == null)
3554 pdbentry.setProperty(new Hashtable());
3556 pdbentry.getProperty().put("protocol", protocol);
3557 toaddpdb.addPDBId(pdbentry);
3563 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3567 Vector sequences = new Vector();
3568 for (int i = 0; i < seqs.length; i++)
3570 if (seqs[i] != null)
3572 sequences.addElement(new Object[]
3573 { seqs[i], (chains != null) ? chains[i] : null });
3576 seqs = new SequenceI[sequences.size()];
3577 chains = new String[sequences.size()];
3578 for (int i = 0, isize = sequences.size(); i < isize; i++)
3580 Object[] oj = (Object[]) sequences.elementAt(i);
3582 seqs[i] = (SequenceI) oj[0];
3583 chains[i] = (String) oj[1];
3591 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3592 SequenceI[] seqs, String[] chains, String protocol)
3594 // Scrub any null sequences from the array
3595 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3596 seqs = (SequenceI[]) sqch[0];
3597 chains = (String[]) sqch[1];
3598 if (seqs == null || seqs.length == 0)
3601 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3603 if (protocol == null || protocol.trim().length() == 0
3604 || protocol.equals("null"))
3606 protocol = (String) pdb.getProperty().get("protocol");
3607 if (protocol == null)
3609 System.err.println("Couldn't work out protocol to open structure: "
3614 if (applet.useXtrnalSviewer)
3616 // register the association(s) and quit, don't create any windows.
3617 if (StructureSelectionManager.getStructureSelectionManager(applet)
3618 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3620 System.err.println("Failed to map " + pdb.getFile() + " ("
3621 + protocol + ") to any sequences");
3625 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3627 // can only do alignments with Jmol
3628 // find the last jmol window assigned to this alignment
3629 jalview.appletgui.AppletJmol ajm = null, tajm;
3630 Vector jmols = applet
3631 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3632 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3634 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3635 if (tajm.ap.alignFrame == this)
3644 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3645 // try and add the pdb structure
3650 // otherwise, create a new window
3651 if (applet.jmolAvailable)
3653 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3655 applet.lastFrameX += 40;
3656 applet.lastFrameY += 40;
3660 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3665 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3666 SequenceI[][] seqs, String[][] chains, String[] protocols)
3668 // TODO Auto-generated method stub
3669 System.err.println("Aligned Structure View: Not yet implemented.");
3673 * modify the current selection, providing the user has not made a selection
3677 * - sequences from this alignment
3679 * - columns to be selected on the alignment
3681 public void select(SequenceGroup sel, ColumnSelection csel)
3683 alignPanel.seqPanel.selection(sel, csel, null);
3686 public void scrollTo(int row, int column)
3688 alignPanel.seqPanel.scrollTo(row, column);
3691 public void scrollToRow(int row)
3693 alignPanel.seqPanel.scrollToRow(row);
3696 public void scrollToColumn(int column)
3698 alignPanel.seqPanel.scrollToColumn(column);
3702 * @return the alignments unique ID.
3704 public String getSequenceSetId()
3706 return viewport.getSequenceSetId();
3710 * Load the (T-Coffee) score file from the specified url
3713 * File/URL/T-COFFEE score file contents
3714 * @throws IOException
3715 * @return true if alignment was annotated with data from source
3717 public boolean loadScoreFile(String source) throws IOException
3720 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3721 AppletFormatAdapter.checkProtocol(source));
3722 if (!file.isValid())
3724 // TODO: raise dialog for gui
3725 System.err.println("Problems parsing T-Coffee scores: "
3726 + file.getWarningMessage());
3727 System.err.println("Origin was:\n" + source);
3732 * check that the score matrix matches the alignment dimensions
3735 if ((aln = viewport.getAlignment()) != null
3736 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3739 // TODO: raise a dialog box here rather than bomb out.
3741 .println("The scores matrix does not match the alignment dimensions");
3745 // TODO add parameter to indicate if matching should be done
3746 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3748 alignPanel.fontChanged();
3749 tcoffeeColour.setEnabled(true);
3750 // switch to this color
3751 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3756 System.err.println("Problems resolving T-Coffee scores:");
3757 if (file.getWarningMessage() != null)
3759 System.err.println(file.getWarningMessage());