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.SequenceStructureBinding;
24 import jalview.bin.JalviewLite;
25 import jalview.commands.CommandI;
26 import jalview.commands.EditCommand;
27 import jalview.commands.OrderCommand;
28 import jalview.commands.RemoveGapColCommand;
29 import jalview.commands.RemoveGapsCommand;
30 import jalview.commands.SlideSequencesCommand;
31 import jalview.commands.TrimRegionCommand;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.AlignmentOrder;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.AnnotationFile;
41 import jalview.io.AppletFormatAdapter;
42 import jalview.io.FeaturesFile;
43 import jalview.io.TCoffeeScoreFile;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.BuriedColourScheme;
46 import jalview.schemes.ClustalxColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.HelixColourScheme;
49 import jalview.schemes.HydrophobicColourScheme;
50 import jalview.schemes.NucleotideColourScheme;
51 import jalview.schemes.PIDColourScheme;
52 import jalview.schemes.PurinePyrimidineColourScheme;
53 import jalview.schemes.RNAHelicesColourChooser;
54 import jalview.schemes.ResidueProperties;
55 import jalview.schemes.StrandColourScheme;
56 import jalview.schemes.TCoffeeColourScheme;
57 import jalview.schemes.TaylorColourScheme;
58 import jalview.schemes.TurnColourScheme;
59 import jalview.schemes.ZappoColourScheme;
60 import jalview.structure.StructureSelectionManager;
62 import java.awt.BorderLayout;
63 import java.awt.Canvas;
64 import java.awt.CheckboxMenuItem;
65 import java.awt.Color;
67 import java.awt.FontMetrics;
68 import java.awt.Frame;
69 import java.awt.Graphics;
70 import java.awt.Label;
72 import java.awt.MenuBar;
73 import java.awt.MenuItem;
74 import java.awt.event.ActionEvent;
75 import java.awt.event.ActionListener;
76 import java.awt.event.FocusEvent;
77 import java.awt.event.FocusListener;
78 import java.awt.event.ItemEvent;
79 import java.awt.event.ItemListener;
80 import java.awt.event.KeyEvent;
81 import java.awt.event.KeyListener;
82 import java.awt.event.WindowAdapter;
83 import java.awt.event.WindowEvent;
84 import java.io.IOException;
86 import java.net.URLEncoder;
87 import java.util.Enumeration;
88 import java.util.Hashtable;
89 import java.util.List;
90 import java.util.StringTokenizer;
91 import java.util.Vector;
93 public class AlignFrame extends EmbmenuFrame implements ActionListener,
94 ItemListener, KeyListener
96 public AlignmentPanel alignPanel;
98 public AlignViewport viewport;
100 int DEFAULT_WIDTH = 700;
102 int DEFAULT_HEIGHT = 500;
104 String jalviewServletURL;
106 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
107 String title, boolean embedded)
111 jalviewServletURL = applet.getParameter("APPLICATION_URL");
117 } catch (Exception ex)
119 ex.printStackTrace();
122 viewport = new AlignViewport(al, applet);
123 alignPanel = new AlignmentPanel(this, viewport);
125 viewport.updateConservation(alignPanel);
126 viewport.updateConsensus(alignPanel);
128 annotationPanelMenuItem.setState(viewport.showAnnotation);
129 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
130 followMouseOverFlag.setState(viewport.getFollowHighlight());
131 showGroupConsensus.setState(viewport.isShowGroupConsensus());
132 showGroupConservation.setState(viewport.isShowGroupConservation());
133 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
134 showSequenceLogo.setState(viewport.isShowSequenceLogo());
135 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
137 seqLimits.setState(viewport.showJVSuffix);
141 String param = applet.getParameter("sortBy");
144 if (param.equalsIgnoreCase("Id"))
146 sortIDMenuItem_actionPerformed();
148 else if (param.equalsIgnoreCase("Pairwise Identity"))
150 sortPairwiseMenuItem_actionPerformed();
152 else if (param.equalsIgnoreCase("Length"))
154 sortLengthMenuItem_actionPerformed();
158 param = applet.getParameter("wrap");
161 if (param.equalsIgnoreCase("true"))
163 wrapMenuItem.setState(true);
164 wrapMenuItem_actionPerformed();
167 param = applet.getParameter("centrecolumnlabels");
170 centreColumnLabelFlag.setState(true);
171 centreColumnLabelFlag_stateChanged();
175 param = applet.getParameter("windowWidth");
178 int width = Integer.parseInt(param);
179 DEFAULT_WIDTH = width;
181 param = applet.getParameter("windowHeight");
184 int height = Integer.parseInt(param);
185 DEFAULT_HEIGHT = height;
187 } catch (Exception ex)
192 if (viewport.getAlignment().isNucleotide())
194 viewport.updateStrucConsensus(alignPanel);
195 if (viewport.getAlignment().hasRNAStructure())
197 RNAHelixColour.setEnabled(true);
201 RNAHelixColour.setEnabled(false);
206 RNAHelixColour.setEnabled(false);
207 purinePyrimidineColour.setEnabled(false);
209 // Some JVMS send keyevents to Top frame or lowest panel,
210 // Havent worked out why yet. So add to both this frame and seqCanvas for
212 this.addKeyListener(this);
213 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
214 alignPanel.idPanel.idCanvas.addKeyListener(this);
215 alignPanel.scalePanel.addKeyListener(this);
216 alignPanel.annotationPanel.addKeyListener(this);
217 alignPanel.annotationPanelHolder.addKeyListener(this);
218 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
219 alignPanel.alabels.addKeyListener(this);
220 createAlignFrameWindow(embedded, title);
223 alignPanel.adjustAnnotationHeight();
224 alignPanel.paintAlignment(true);
227 public AlignViewport getAlignViewport()
232 public SeqCanvas getSeqcanvas()
234 return alignPanel.seqPanel.seqCanvas;
238 * Load a features file onto the alignment
241 * file URL, content, or other resolvable path
243 * is protocol for accessing data referred to by file
246 public boolean parseFeaturesFile(String file, String type)
248 return parseFeaturesFile(file, type, true);
252 * Load a features file onto the alignment
255 * file URL, content, or other resolvable path
257 * is protocol for accessing data referred to by file
258 * @param autoenabledisplay
259 * when true, display features flag will be automatically enabled if
260 * features are loaded
261 * @return true if data parsed as a features file
263 public boolean parseFeaturesFile(String file, String type,
264 boolean autoenabledisplay)
266 // TODO: test if importing a features file onto an alignment which already
267 // has features with links overwrites the original links.
269 Hashtable featureLinks = new Hashtable();
270 boolean featuresFile = false;
273 featuresFile = new jalview.io.FeaturesFile(file, type)
274 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
275 .getFeatureRenderer().featureColours, featureLinks,
276 true, viewport.applet.getDefaultParameter(
277 "relaxedidmatch", false));
278 } catch (Exception ex)
280 ex.printStackTrace();
285 if (featureLinks.size() > 0)
287 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
289 if (autoenabledisplay)
291 viewport.showSequenceFeatures = true;
292 sequenceFeatures.setState(true);
294 if (viewport.featureSettings != null)
296 viewport.featureSettings.refreshTable();
298 alignPanel.paintAlignment(true);
299 statusBar.setText("Successfully added features to alignment.");
305 public void keyPressed(KeyEvent evt)
307 if (viewport.cursorMode
308 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
309 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
310 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
311 && Character.isDigit(evt.getKeyChar()))
312 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
314 switch (evt.getKeyCode())
316 case 27: // escape key
317 deselectAllSequenceMenuItem_actionPerformed();
319 alignPanel.alabels.cancelDrag();
322 if (evt.isControlDown() || evt.isMetaDown())
324 cut_actionPerformed();
328 if (viewport.cursorMode && !evt.isControlDown())
330 alignPanel.seqPanel.setCursorColumn();
332 if (evt.isControlDown() || evt.isMetaDown())
334 copy_actionPerformed();
338 if (evt.isControlDown())
340 paste(evt.isShiftDown());
344 if (evt.isControlDown() || evt.isMetaDown())
346 selectAllSequenceMenuItem_actionPerformed();
349 case KeyEvent.VK_DOWN:
350 if (viewport.cursorMode)
352 alignPanel.seqPanel.moveCursor(0, 1);
356 moveSelectedSequences(false);
361 if (viewport.cursorMode)
363 alignPanel.seqPanel.moveCursor(0, -1);
367 moveSelectedSequences(true);
371 case KeyEvent.VK_LEFT:
372 if (evt.isAltDown() || !viewport.cursorMode)
373 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
375 alignPanel.seqPanel.moveCursor(-1, 0);
378 case KeyEvent.VK_RIGHT:
379 if (evt.isAltDown() || !viewport.cursorMode)
380 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
382 alignPanel.seqPanel.moveCursor(1, 0);
385 case KeyEvent.VK_SPACE:
386 if (viewport.cursorMode)
388 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
389 || evt.isShiftDown() || evt.isAltDown());
393 case KeyEvent.VK_DELETE:
394 case KeyEvent.VK_BACK_SPACE:
395 if (viewport.cursorMode)
397 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
398 || evt.isShiftDown() || evt.isAltDown());
402 cut_actionPerformed();
403 alignPanel.seqPanel.seqCanvas.repaint();
408 if (viewport.cursorMode)
410 alignPanel.seqPanel.setCursorRow();
414 if (viewport.cursorMode)
416 alignPanel.seqPanel.setCursorPosition();
420 case KeyEvent.VK_ENTER:
421 case KeyEvent.VK_COMMA:
422 if (viewport.cursorMode)
424 alignPanel.seqPanel.setCursorRowAndColumn();
429 if (viewport.cursorMode)
431 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
435 if (viewport.cursorMode)
437 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
442 viewport.cursorMode = !viewport.cursorMode;
443 statusBar.setText("Keyboard editing mode is "
444 + (viewport.cursorMode ? "on" : "off"));
445 if (viewport.cursorMode)
447 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
448 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
453 if (evt.isControlDown())
455 findMenuItem_actionPerformed();
461 boolean toggleSeqs = !evt.isControlDown();
462 boolean toggleCols = !evt.isShiftDown();
463 toggleHiddenRegions(toggleSeqs, toggleCols);
467 case KeyEvent.VK_PAGE_UP:
468 if (viewport.wrapAlignment)
470 alignPanel.scrollUp(true);
474 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
475 - viewport.endSeq + viewport.startSeq);
479 case KeyEvent.VK_PAGE_DOWN:
480 if (viewport.wrapAlignment)
482 alignPanel.scrollUp(false);
486 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
487 + viewport.endSeq - viewport.startSeq);
492 if (evt.isControlDown())
494 undoMenuItem_actionPerformed();
499 if (evt.isControlDown())
501 redoMenuItem_actionPerformed();
506 if (evt.isControlDown())
513 if (evt.isControlDown())
515 trimAlignment(false);
520 if (evt.isControlDown())
522 if (evt.isShiftDown())
524 this.removeAllGapsMenuItem_actionPerformed();
528 removeGappedColumnMenuItem_actionPerformed();
533 if (evt.isControlDown())
537 invertColSel_actionPerformed();
541 invertSequenceMenuItem_actionPerformed();
547 if (evt.isControlDown())
549 this.deleteGroups_actionPerformed();
554 if (evt.isControlDown())
561 alignPanel.paintAlignment(true);
565 * called by key handler and the hide all/show all menu items
570 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
572 boolean hide = false;
573 SequenceGroup sg = viewport.getSelectionGroup();
574 if (!toggleSeqs && !toggleCols)
576 // Hide everything by the current selection - this is a hack - we do the
577 // invert and then hide
578 // first check that there will be visible columns after the invert.
579 if ((viewport.getColumnSelection() != null
580 && viewport.getColumnSelection().getSelected() != null && viewport
581 .getColumnSelection().getSelected().size() > 0)
582 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
585 // now invert the sequence set, if required - empty selection implies
586 // that no hiding is required.
589 invertSequenceMenuItem_actionPerformed();
590 sg = viewport.getSelectionGroup();
594 viewport.expandColSelection(sg, true);
595 // finally invert the column selection and get the new sequence
596 // selection and indicate it should be hidden.
597 invertColSel_actionPerformed();
604 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
607 viewport.hideAllSelectedSeqs();
609 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
612 viewport.showAllHiddenSeqs();
618 if (viewport.getColumnSelection().getSelected().size() > 0)
620 viewport.hideSelectedColumns();
623 viewport.setSelectionGroup(sg);
628 viewport.showAllHiddenColumns();
634 public void keyReleased(KeyEvent evt)
639 public void keyTyped(KeyEvent evt)
644 public void itemStateChanged(ItemEvent evt)
646 if (evt.getSource() == displayNonconservedMenuItem)
648 displayNonconservedMenuItem_actionPerformed();
650 else if (evt.getSource() == colourTextMenuItem)
652 colourTextMenuItem_actionPerformed();
654 else if (evt.getSource() == wrapMenuItem)
656 wrapMenuItem_actionPerformed();
658 else if (evt.getSource() == scaleAbove)
660 viewport.setScaleAboveWrapped(scaleAbove.getState());
662 else if (evt.getSource() == scaleLeft)
664 viewport.setScaleLeftWrapped(scaleLeft.getState());
666 else if (evt.getSource() == scaleRight)
668 viewport.setScaleRightWrapped(scaleRight.getState());
670 else if (evt.getSource() == seqLimits)
672 seqLimits_itemStateChanged();
674 else if (evt.getSource() == viewBoxesMenuItem)
676 viewport.setShowBoxes(viewBoxesMenuItem.getState());
678 else if (evt.getSource() == viewTextMenuItem)
680 viewport.setShowText(viewTextMenuItem.getState());
682 else if (evt.getSource() == renderGapsMenuItem)
684 viewport.setRenderGaps(renderGapsMenuItem.getState());
686 else if (evt.getSource() == annotationPanelMenuItem)
688 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
689 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
691 else if (evt.getSource() == sequenceFeatures)
693 viewport.showSequenceFeatures(sequenceFeatures.getState());
694 alignPanel.seqPanel.seqCanvas.repaint();
696 else if (evt.getSource() == conservationMenuItem)
698 conservationMenuItem_actionPerformed();
700 else if (evt.getSource() == abovePIDThreshold)
702 abovePIDThreshold_actionPerformed();
704 else if (evt.getSource() == applyToAllGroups)
706 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
708 else if (evt.getSource() == autoCalculate)
710 viewport.autoCalculateConsensus = autoCalculate.getState();
712 else if (evt.getSource() == sortByTree)
714 viewport.sortByTree = sortByTree.getState();
716 else if (evt.getSource() == this.centreColumnLabelFlag)
718 centreColumnLabelFlag_stateChanged();
720 else if (evt.getSource() == this.followMouseOverFlag)
722 mouseOverFlag_stateChanged();
724 else if (evt.getSource() == showGroupConsensus)
726 showGroupConsensus_actionPerformed();
728 else if (evt.getSource() == showGroupConservation)
730 showGroupConservation_actionPerformed();
732 else if (evt.getSource() == showSequenceLogo)
734 showSequenceLogo_actionPerformed();
736 else if (evt.getSource() == normSequenceLogo)
738 normSequenceLogo_actionPerformed();
740 else if (evt.getSource() == showConsensusHistogram)
742 showConsensusHistogram_actionPerformed();
744 else if (evt.getSource() == applyAutoAnnotationSettings)
746 applyAutoAnnotationSettings_actionPerformed();
748 alignPanel.paintAlignment(true);
751 private void mouseOverFlag_stateChanged()
753 viewport.followHighlight = followMouseOverFlag.getState();
754 // TODO: could kick the scrollTo mechanism to reset view for current
758 private void centreColumnLabelFlag_stateChanged()
760 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
761 this.alignPanel.annotationPanel.repaint();
765 public void actionPerformed(ActionEvent evt)
767 Object source = evt.getSource();
769 if (source == inputText)
771 inputText_actionPerformed();
773 else if (source == loadTree)
775 loadTree_actionPerformed();
777 else if (source == loadApplication)
779 launchFullApplication();
781 else if (source == loadAnnotations)
785 else if (source == outputAnnotations)
787 outputAnnotations(true);
789 else if (source == outputFeatures)
791 outputFeatures(true, "Jalview");
793 else if (source == closeMenuItem)
795 closeMenuItem_actionPerformed();
797 else if (source == copy)
799 copy_actionPerformed();
801 else if (source == undoMenuItem)
803 undoMenuItem_actionPerformed();
805 else if (source == redoMenuItem)
807 redoMenuItem_actionPerformed();
809 else if (source == inputText)
811 inputText_actionPerformed();
813 else if (source == closeMenuItem)
815 closeMenuItem_actionPerformed();
817 else if (source == undoMenuItem)
819 undoMenuItem_actionPerformed();
821 else if (source == redoMenuItem)
823 redoMenuItem_actionPerformed();
825 else if (source == copy)
827 copy_actionPerformed();
829 else if (source == pasteNew)
831 pasteNew_actionPerformed();
833 else if (source == pasteThis)
835 pasteThis_actionPerformed();
837 else if (source == cut)
839 cut_actionPerformed();
841 else if (source == delete)
843 delete_actionPerformed();
845 else if (source == grpsFromSelection)
847 makeGrpsFromSelection_actionPerformed();
849 else if (source == deleteGroups)
851 deleteGroups_actionPerformed();
853 else if (source == selectAllSequenceMenuItem)
855 selectAllSequenceMenuItem_actionPerformed();
857 else if (source == deselectAllSequenceMenuItem)
859 deselectAllSequenceMenuItem_actionPerformed();
861 else if (source == invertSequenceMenuItem)
863 invertSequenceMenuItem_actionPerformed();
865 else if (source == invertColSel)
867 viewport.invertColumnSelection();
868 alignPanel.paintAlignment(true);
870 else if (source == remove2LeftMenuItem)
874 else if (source == remove2RightMenuItem)
876 trimAlignment(false);
878 else if (source == removeGappedColumnMenuItem)
880 removeGappedColumnMenuItem_actionPerformed();
882 else if (source == removeAllGapsMenuItem)
884 removeAllGapsMenuItem_actionPerformed();
886 else if (source == findMenuItem)
888 findMenuItem_actionPerformed();
890 else if (source == font)
892 new FontChooser(alignPanel);
894 else if (source == newView)
898 else if (source == showColumns)
900 viewport.showAllHiddenColumns();
901 alignPanel.paintAlignment(true);
903 else if (source == showSeqs)
905 viewport.showAllHiddenSeqs();
906 alignPanel.paintAlignment(true);
908 else if (source == hideColumns)
910 viewport.hideSelectedColumns();
911 alignPanel.paintAlignment(true);
913 else if (source == hideSequences
914 && viewport.getSelectionGroup() != null)
916 viewport.hideAllSelectedSeqs();
917 alignPanel.paintAlignment(true);
919 else if (source == hideAllButSelection)
921 toggleHiddenRegions(false, false);
922 alignPanel.paintAlignment(true);
924 else if (source == hideAllSelection)
926 SequenceGroup sg = viewport.getSelectionGroup();
927 viewport.expandColSelection(sg, false);
928 viewport.hideAllSelectedSeqs();
929 viewport.hideSelectedColumns();
930 alignPanel.paintAlignment(true);
932 else if (source == showAllHidden)
934 viewport.showAllHiddenColumns();
935 viewport.showAllHiddenSeqs();
936 alignPanel.paintAlignment(true);
938 else if (source == showGroupConsensus)
940 showGroupConsensus_actionPerformed();
942 else if (source == showGroupConservation)
944 showGroupConservation_actionPerformed();
946 else if (source == showSequenceLogo)
948 showSequenceLogo_actionPerformed();
950 else if (source == normSequenceLogo)
952 normSequenceLogo_actionPerformed();
954 else if (source == showConsensusHistogram)
956 showConsensusHistogram_actionPerformed();
958 else if (source == applyAutoAnnotationSettings)
960 applyAutoAnnotationSettings_actionPerformed();
962 else if (source == featureSettings)
964 new FeatureSettings(alignPanel);
966 else if (source == alProperties)
968 StringBuffer contents = new jalview.io.AlignmentProperties(
969 viewport.getAlignment()).formatAsString();
970 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
971 cap.setText(contents.toString());
972 Frame frame = new Frame();
974 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
975 + getTitle(), 400, 250);
977 else if (source == overviewMenuItem)
979 overviewMenuItem_actionPerformed();
981 else if (source == noColourmenuItem)
985 else if (source == clustalColour)
987 abovePIDThreshold.setState(false);
988 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
990 else if (source == zappoColour)
992 changeColour(new ZappoColourScheme());
994 else if (source == taylorColour)
996 changeColour(new TaylorColourScheme());
998 else if (source == hydrophobicityColour)
1000 changeColour(new HydrophobicColourScheme());
1002 else if (source == helixColour)
1004 changeColour(new HelixColourScheme());
1006 else if (source == strandColour)
1008 changeColour(new StrandColourScheme());
1010 else if (source == turnColour)
1012 changeColour(new TurnColourScheme());
1014 else if (source == buriedColour)
1016 changeColour(new BuriedColourScheme());
1018 else if (source == nucleotideColour)
1020 changeColour(new NucleotideColourScheme());
1022 else if (source == purinePyrimidineColour)
1024 changeColour(new PurinePyrimidineColourScheme());
1026 else if (source == RNAHelixColour)
1028 new RNAHelicesColourChooser(viewport, alignPanel);
1030 else if (source == modifyPID)
1032 modifyPID_actionPerformed();
1034 else if (source == modifyConservation)
1036 modifyConservation_actionPerformed();
1038 else if (source == userDefinedColour)
1040 new UserDefinedColours(alignPanel, null);
1042 else if (source == PIDColour)
1044 changeColour(new PIDColourScheme());
1046 else if (source == BLOSUM62Colour)
1048 changeColour(new Blosum62ColourScheme());
1050 else if (source == tcoffeeColour)
1052 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1054 else if (source == annotationColour)
1056 new AnnotationColourChooser(viewport, alignPanel);
1058 else if (source == sortPairwiseMenuItem)
1060 sortPairwiseMenuItem_actionPerformed();
1062 else if (source == sortIDMenuItem)
1064 sortIDMenuItem_actionPerformed();
1066 else if (source == sortLengthMenuItem)
1068 sortLengthMenuItem_actionPerformed();
1070 else if (source == sortGroupMenuItem)
1072 sortGroupMenuItem_actionPerformed();
1074 else if (source == removeRedundancyMenuItem)
1076 removeRedundancyMenuItem_actionPerformed();
1078 else if (source == pairwiseAlignmentMenuItem)
1080 pairwiseAlignmentMenuItem_actionPerformed();
1082 else if (source == PCAMenuItem)
1084 PCAMenuItem_actionPerformed();
1086 else if (source == averageDistanceTreeMenuItem)
1088 averageDistanceTreeMenuItem_actionPerformed();
1090 else if (source == neighbourTreeMenuItem)
1092 neighbourTreeMenuItem_actionPerformed();
1094 else if (source == njTreeBlosumMenuItem)
1096 njTreeBlosumMenuItem_actionPerformed();
1098 else if (source == avDistanceTreeBlosumMenuItem)
1100 avTreeBlosumMenuItem_actionPerformed();
1102 else if (source == documentation)
1104 documentation_actionPerformed();
1106 else if (source == about)
1108 about_actionPerformed();
1113 public void inputText_actionPerformed()
1115 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1116 Frame frame = new Frame();
1118 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
1121 protected void outputText_actionPerformed(ActionEvent e)
1123 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1124 Frame frame = new Frame();
1126 jalview.bin.JalviewLite.addFrame(frame,
1127 "Alignment output - " + e.getActionCommand(), 600, 500);
1128 cap.setText(new AppletFormatAdapter().formatSequences(
1129 e.getActionCommand(), viewport.getAlignment(),
1130 viewport.showJVSuffix));
1133 public void loadAnnotations()
1135 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1136 cap.setText("Paste your features / annotations / T-coffee score file here.");
1137 cap.setAnnotationImport();
1138 Frame frame = new Frame();
1140 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1144 public String outputAnnotations(boolean displayTextbox)
1146 String annotation = new AnnotationFile().printAnnotations(
1147 viewport.showAnnotation ? viewport.getAlignment()
1148 .getAlignmentAnnotation() : null, viewport
1149 .getAlignment().getGroups(), ((Alignment) viewport
1150 .getAlignment()).alignmentProperties);
1154 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1155 Frame frame = new Frame();
1157 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1158 cap.setText(annotation);
1164 private Hashtable getDisplayedFeatureCols()
1166 if (alignPanel.getFeatureRenderer() != null
1167 && viewport.featuresDisplayed != null)
1169 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1170 Hashtable fcols = new Hashtable();
1171 Enumeration en = viewport.featuresDisplayed.keys();
1172 while (en.hasMoreElements())
1174 Object col = en.nextElement();
1175 fcols.put(col, fr.featureColours.get(col));
1182 public String outputFeatures(boolean displayTextbox, String format)
1185 if (format.equalsIgnoreCase("Jalview"))
1187 features = new FeaturesFile().printJalviewFormat(viewport
1188 .getAlignment().getSequencesArray(),
1189 getDisplayedFeatureCols());
1193 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1194 .getSequencesArray(), getDisplayedFeatureCols());
1199 boolean frimport = false;
1200 if (features == null || features.equals("No Features Visible"))
1202 features = "# No features visible - paste some and import them here.";
1206 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1209 cap.setAnnotationImport();
1211 Frame frame = new Frame();
1213 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1214 cap.setText(features);
1218 if (features == null)
1225 void launchFullApplication()
1227 StringBuffer url = new StringBuffer(jalviewServletURL);
1230 + appendProtocol(viewport.applet.getParameter("file")));
1232 if (viewport.applet.getParameter("features") != null)
1234 url.append("&features=");
1235 url.append(appendProtocol(viewport.applet.getParameter("features")));
1238 if (viewport.applet.getParameter("annotations") != null)
1240 url.append("&annotations=");
1241 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1244 if (viewport.applet.getParameter("jnetfile") != null)
1246 url.append("&annotations=");
1247 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1250 if (viewport.applet.getParameter("defaultColour") != null)
1252 url.append("&colour="
1253 + removeWhiteSpace(viewport.applet
1254 .getParameter("defaultColour")));
1257 if (viewport.applet.getParameter("userDefinedColour") != null)
1259 url.append("&colour="
1260 + removeWhiteSpace(viewport.applet
1261 .getParameter("userDefinedColour")));
1263 if (viewport.applet.getParameter("tree") != null)
1266 + appendProtocol(viewport.applet.getParameter("tree")));
1268 if (viewport.applet.getParameter("treeFile") != null)
1271 + appendProtocol(viewport.applet.getParameter("treeFile")));
1274 showURL(url.toString(), "FULL_APP");
1277 String removeWhiteSpace(String colour)
1279 StringBuffer sb = new StringBuffer();
1280 for (int i = 0; i < colour.length(); i++)
1282 if (Character.isWhitespace(colour.charAt(i)))
1288 sb.append(colour.charAt(i));
1292 return sb.toString();
1295 String appendProtocol(String url)
1300 url = URLEncoder.encode(url);
1303 * When we finally deprecate 1.1 compatibility, we can start to use
1304 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1305 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1306 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1307 * ex.printStackTrace(); }
1309 catch (java.net.MalformedURLException ex)
1311 url = viewport.applet.getCodeBase() + url;
1316 public void closeMenuItem_actionPerformed()
1318 PaintRefresher.RemoveComponent(alignPanel);
1319 if (alignPanel.seqPanel != null
1320 && alignPanel.seqPanel.seqCanvas != null)
1322 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1324 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1326 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1329 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1344 void updateEditMenuBar()
1347 if (viewport.historyList.size() > 0)
1349 undoMenuItem.setEnabled(true);
1350 CommandI command = (CommandI) viewport.historyList.peek();
1351 undoMenuItem.setLabel("Undo " + command.getDescription());
1355 undoMenuItem.setEnabled(false);
1356 undoMenuItem.setLabel("Undo");
1359 if (viewport.redoList.size() > 0)
1361 redoMenuItem.setEnabled(true);
1363 CommandI command = (CommandI) viewport.redoList.peek();
1364 redoMenuItem.setLabel("Redo " + command.getDescription());
1368 redoMenuItem.setEnabled(false);
1369 redoMenuItem.setLabel("Redo");
1376 public void addHistoryItem(CommandI command)
1378 if (command.getSize() > 0)
1380 viewport.historyList.push(command);
1381 viewport.redoList.removeAllElements();
1382 updateEditMenuBar();
1383 viewport.updateHiddenColumns();
1388 * TODO: JAL-1104 DOCUMENT ME!
1393 protected void undoMenuItem_actionPerformed()
1395 if (viewport.historyList.size() < 1)
1400 CommandI command = (CommandI) viewport.historyList.pop();
1401 viewport.redoList.push(command);
1402 command.undoCommand(null);
1404 AlignViewport originalSource = getOriginatingSource(command);
1406 if (originalSource != viewport)
1409 .println("Warning: Viewport object mismatch whilst undoing");
1411 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1412 // viewport.getColumnSelection().getHiddenColumns()
1414 updateEditMenuBar();
1415 originalSource.firePropertyChange("alignment", null, originalSource
1416 .getAlignment().getSequences());
1420 * TODO: JAL-1104 DOCUMENT ME!
1425 protected void redoMenuItem_actionPerformed()
1427 if (viewport.redoList.size() < 1)
1432 CommandI command = (CommandI) viewport.redoList.pop();
1433 viewport.historyList.push(command);
1434 command.doCommand(null);
1436 AlignViewport originalSource = getOriginatingSource(command);
1438 if (originalSource != viewport)
1441 .println("Warning: Viewport object mismatch whilst re-doing");
1443 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1444 // viewport.getColumnSelection().getHiddenColumns()
1447 updateEditMenuBar();
1448 originalSource.firePropertyChange("alignment", null, originalSource
1449 .getAlignment().getSequences());
1452 AlignViewport getOriginatingSource(CommandI command)
1454 AlignViewport originalSource = null;
1455 // For sequence removal and addition, we need to fire
1456 // the property change event FROM the viewport where the
1457 // original alignment was altered
1458 AlignmentI al = null;
1459 if (command instanceof EditCommand)
1461 EditCommand editCommand = (EditCommand) command;
1462 al = editCommand.getAlignment();
1463 Vector comps = (Vector) PaintRefresher.components.get(viewport
1464 .getSequenceSetId());
1465 for (int i = 0; i < comps.size(); i++)
1467 if (comps.elementAt(i) instanceof AlignmentPanel)
1469 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1471 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1478 if (originalSource == null)
1480 // The original view is closed, we must validate
1481 // the current view against the closed view first
1484 PaintRefresher.validateSequences(al, viewport.getAlignment());
1487 originalSource = viewport;
1490 return originalSource;
1493 public void moveSelectedSequences(boolean up)
1495 SequenceGroup sg = viewport.getSelectionGroup();
1500 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1501 up ? null : viewport.getHiddenRepSequences(), up);
1502 alignPanel.paintAlignment(true);
1505 synchronized void slideSequences(boolean right, int size)
1507 List<SequenceI> sg = new Vector<SequenceI>();
1508 if (viewport.cursorMode)
1510 sg.add(viewport.getAlignment().getSequenceAt(
1511 alignPanel.seqPanel.seqCanvas.cursorY));
1513 else if (viewport.getSelectionGroup() != null
1514 && viewport.getSelectionGroup().getSize() != viewport
1515 .getAlignment().getHeight())
1517 sg = viewport.getSelectionGroup().getSequences(
1518 viewport.getHiddenRepSequences());
1526 Vector<SequenceI> invertGroup = new Vector();
1528 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1530 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1531 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1534 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1536 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1538 for (int i = 0; i < invertGroup.size(); i++)
1539 seqs2[i] = invertGroup.elementAt(i);
1541 SlideSequencesCommand ssc;
1543 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1544 size, viewport.getGapCharacter());
1546 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1547 size, viewport.getGapCharacter());
1549 int groupAdjustment = 0;
1550 if (ssc.getGapsInsertedBegin() && right)
1552 if (viewport.cursorMode)
1553 alignPanel.seqPanel.moveCursor(size, 0);
1555 groupAdjustment = size;
1557 else if (!ssc.getGapsInsertedBegin() && !right)
1559 if (viewport.cursorMode)
1560 alignPanel.seqPanel.moveCursor(-size, 0);
1562 groupAdjustment = -size;
1565 if (groupAdjustment != 0)
1567 viewport.getSelectionGroup().setStartRes(
1568 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1569 viewport.getSelectionGroup().setEndRes(
1570 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1573 boolean appendHistoryItem = false;
1574 if (viewport.historyList != null && viewport.historyList.size() > 0
1575 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1577 appendHistoryItem = ssc
1578 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1582 if (!appendHistoryItem)
1583 addHistoryItem(ssc);
1588 static StringBuffer copiedSequences;
1590 static Vector copiedHiddenColumns;
1592 protected void copy_actionPerformed()
1594 if (viewport.getSelectionGroup() == null)
1599 SequenceGroup sg = viewport.getSelectionGroup();
1600 copiedSequences = new StringBuffer();
1601 Hashtable orderedSeqs = new Hashtable();
1602 for (int i = 0; i < sg.getSize(); i++)
1604 SequenceI seq = sg.getSequenceAt(i);
1605 int index = viewport.getAlignment().findIndex(seq);
1606 orderedSeqs.put(index + "", seq);
1609 int index = 0, startRes, endRes;
1612 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1614 copiedHiddenColumns = new Vector();
1615 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1616 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1619 int[] region = (int[]) viewport.getColumnSelection()
1620 .getHiddenColumns().elementAt(i);
1622 copiedHiddenColumns.addElement(new int[]
1623 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1628 copiedHiddenColumns = null;
1631 for (int i = 0; i < sg.getSize(); i++)
1633 SequenceI seq = null;
1637 if (orderedSeqs.containsKey(index + ""))
1639 seq = (SequenceI) orderedSeqs.get(index + "");
1651 // Returns residue following index if gap
1652 startRes = seq.findPosition(sg.getStartRes());
1655 // Need to find the residue preceeding index if gap
1658 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1660 ch = seq.getCharAt(j);
1661 if (!jalview.util.Comparison.isGap((ch)))
1669 endRes += seq.getStart() - 1;
1672 copiedSequences.append(seq.getName()
1678 + seq.getSequenceAsString(sg.getStartRes(),
1679 sg.getEndRes() + 1) + "\n");
1684 protected void pasteNew_actionPerformed()
1689 protected void pasteThis_actionPerformed()
1694 void paste(boolean newAlignment)
1699 if (copiedSequences == null)
1704 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1705 Vector seqs = new Vector();
1706 while (st.hasMoreElements())
1708 String name = st.nextToken();
1709 int start = Integer.parseInt(st.nextToken());
1710 int end = Integer.parseInt(st.nextToken());
1711 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1713 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1714 for (int i = 0; i < seqs.size(); i++)
1716 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1721 String newtitle = new String("Copied sequences");
1722 if (getTitle().startsWith("Copied sequences"))
1724 newtitle = getTitle();
1728 newtitle = newtitle.concat("- from " + getTitle());
1730 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1731 viewport.applet, newtitle, false);
1732 if (copiedHiddenColumns != null)
1734 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1736 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1737 af.viewport.hideColumns(region[0], region[1]);
1741 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1746 addSequences(newSeqs);
1749 } catch (Exception ex)
1751 } // could be anything being pasted in here
1755 void addSequences(SequenceI[] seqs)
1757 for (int i = 0; i < seqs.length; i++)
1759 viewport.getAlignment().addSequence(seqs[i]);
1763 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1764 seqs, 0, viewport.getAlignment().getWidth(),
1765 viewport.getAlignment()));
1767 viewport.setEndSeq(viewport.getAlignment().getHeight());
1768 viewport.getAlignment().getWidth();
1769 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1774 protected void cut_actionPerformed()
1776 copy_actionPerformed();
1777 delete_actionPerformed();
1780 protected void delete_actionPerformed()
1783 SequenceGroup sg = viewport.getSelectionGroup();
1789 Vector seqs = new Vector();
1791 for (int i = 0; i < sg.getSize(); i++)
1793 seq = sg.getSequenceAt(i);
1794 seqs.addElement(seq);
1797 // If the cut affects all sequences, remove highlighted columns
1798 if (sg.getSize() == viewport.getAlignment().getHeight())
1800 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1801 sg.getEndRes() + 1);
1804 SequenceI[] cut = new SequenceI[seqs.size()];
1805 for (int i = 0; i < seqs.size(); i++)
1807 cut[i] = (SequenceI) seqs.elementAt(i);
1811 * //ADD HISTORY ITEM
1813 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1814 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1815 viewport.getAlignment()));
1817 viewport.setSelectionGroup(null);
1818 viewport.getAlignment().deleteGroup(sg);
1820 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1823 if (viewport.getAlignment().getHeight() < 1)
1825 this.setVisible(false);
1827 viewport.sendSelection();
1831 * group consensus toggled
1834 protected void showGroupConsensus_actionPerformed()
1836 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1837 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1842 * group conservation toggled.
1844 protected void showGroupConservation_actionPerformed()
1846 viewport.setShowGroupConservation(showGroupConservation.getState());
1847 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1854 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1855 * .event.ActionEvent)
1857 protected void showConsensusHistogram_actionPerformed()
1859 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1860 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1867 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1868 * .event.ActionEvent)
1870 protected void showSequenceLogo_actionPerformed()
1872 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1873 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1876 protected void normSequenceLogo_actionPerformed()
1878 showSequenceLogo.setState(true);
1879 viewport.setShowSequenceLogo(true);
1880 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1881 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1884 protected void applyAutoAnnotationSettings_actionPerformed()
1886 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1889 protected void makeGrpsFromSelection_actionPerformed()
1891 if (viewport.getSelectionGroup() != null)
1893 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1894 viewport.getSequenceSelection(),
1895 viewport.getAlignmentView(true).getSequenceStrings(
1896 viewport.getGapCharacter()), viewport.getAlignment()
1898 viewport.getAlignment().deleteAllGroups();
1899 viewport.sequenceColours = null;
1900 viewport.setSelectionGroup(null);
1901 // set view properties for each group
1902 for (int g = 0; g < gps.length; g++)
1904 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1905 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1906 viewport.getAlignment().addGroup(gps[g]);
1907 Color col = new Color((int) (Math.random() * 255),
1908 (int) (Math.random() * 255), (int) (Math.random() * 255));
1909 col = col.brighter();
1910 for (SequenceI sq : gps[g].getSequences(null))
1911 viewport.setSequenceColour(sq, col);
1913 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1914 alignPanel.updateAnnotation();
1915 alignPanel.paintAlignment(true);
1919 protected void deleteGroups_actionPerformed()
1921 viewport.getAlignment().deleteAllGroups();
1922 viewport.sequenceColours = null;
1923 viewport.setSelectionGroup(null);
1925 alignPanel.paintAlignment(true);
1928 public void selectAllSequenceMenuItem_actionPerformed()
1930 SequenceGroup sg = new SequenceGroup();
1931 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1933 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1935 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1936 viewport.setSelectionGroup(sg);
1937 alignPanel.paintAlignment(true);
1938 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1939 viewport.sendSelection();
1942 public void deselectAllSequenceMenuItem_actionPerformed()
1944 if (viewport.cursorMode)
1946 alignPanel.seqPanel.keyboardNo1 = null;
1947 alignPanel.seqPanel.keyboardNo2 = null;
1949 viewport.setSelectionGroup(null);
1950 viewport.getColumnSelection().clear();
1951 viewport.setSelectionGroup(null);
1952 alignPanel.idPanel.idCanvas.searchResults = null;
1953 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1954 alignPanel.paintAlignment(true);
1955 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1956 viewport.sendSelection();
1959 public void invertSequenceMenuItem_actionPerformed()
1961 SequenceGroup sg = viewport.getSelectionGroup();
1962 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1964 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1967 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1968 viewport.sendSelection();
1971 public void invertColSel_actionPerformed()
1973 viewport.invertColumnSelection();
1974 alignPanel.paintAlignment(true);
1975 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1976 viewport.sendSelection();
1979 void trimAlignment(boolean trimLeft)
1981 ColumnSelection colSel = viewport.getColumnSelection();
1984 if (colSel.size() > 0)
1988 column = colSel.getMin();
1992 column = colSel.getMax();
1996 if (viewport.getSelectionGroup() != null)
1998 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1999 viewport.getHiddenRepSequences());
2003 seqs = viewport.getAlignment().getSequencesArray();
2006 TrimRegionCommand trimRegion;
2009 trimRegion = new TrimRegionCommand("Remove Left",
2010 TrimRegionCommand.TRIM_LEFT, seqs, column,
2011 viewport.getAlignment(), viewport.getColumnSelection(),
2012 viewport.getSelectionGroup());
2013 viewport.setStartRes(0);
2017 trimRegion = new TrimRegionCommand("Remove Right",
2018 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2019 viewport.getAlignment(), viewport.getColumnSelection(),
2020 viewport.getSelectionGroup());
2023 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2025 addHistoryItem(trimRegion);
2027 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2029 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2030 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2032 viewport.getAlignment().deleteGroup(sg);
2036 viewport.firePropertyChange("alignment", null, viewport
2037 .getAlignment().getSequences());
2041 public void removeGappedColumnMenuItem_actionPerformed()
2043 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2046 if (viewport.getSelectionGroup() != null)
2048 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2049 viewport.getHiddenRepSequences());
2050 start = viewport.getSelectionGroup().getStartRes();
2051 end = viewport.getSelectionGroup().getEndRes();
2055 seqs = viewport.getAlignment().getSequencesArray();
2058 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2059 "Remove Gapped Columns", seqs, start, end,
2060 viewport.getAlignment());
2062 addHistoryItem(removeGapCols);
2064 statusBar.setText("Removed " + removeGapCols.getSize()
2065 + " empty columns.");
2067 // This is to maintain viewport position on first residue
2068 // of first sequence
2069 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2070 int startRes = seq.findPosition(viewport.startRes);
2071 // ShiftList shifts;
2072 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2073 // edit.alColumnChanges=shifts.getInverse();
2074 // if (viewport.hasHiddenColumns)
2075 // viewport.getColumnSelection().compensateForEdits(shifts);
2076 viewport.setStartRes(seq.findIndex(startRes) - 1);
2077 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2082 public void removeAllGapsMenuItem_actionPerformed()
2084 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2087 if (viewport.getSelectionGroup() != null)
2089 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2090 viewport.getHiddenRepSequences());
2091 start = viewport.getSelectionGroup().getStartRes();
2092 end = viewport.getSelectionGroup().getEndRes();
2096 seqs = viewport.getAlignment().getSequencesArray();
2099 // This is to maintain viewport position on first residue
2100 // of first sequence
2101 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2102 int startRes = seq.findPosition(viewport.startRes);
2104 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2105 viewport.getAlignment()));
2107 viewport.setStartRes(seq.findIndex(startRes) - 1);
2109 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2114 public void findMenuItem_actionPerformed()
2116 new Finder(alignPanel);
2120 * create a new view derived from the current view
2123 * @return frame for the new view
2125 public AlignFrame newView(String viewtitle)
2128 if (viewport.hasHiddenRows())
2130 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2131 .getFullAlignment().getSequencesArray());
2135 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2138 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2140 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2142 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2144 newal.addAnnotation(viewport.getAlignment()
2145 .getAlignmentAnnotation()[i]);
2150 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2152 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2153 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2154 PaintRefresher.Register(newaf.alignPanel,
2155 newaf.alignPanel.av.getSequenceSetId());
2157 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2158 newaf.alignPanel.av.getSequenceSetId());
2159 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2160 newaf.alignPanel.av.getSequenceSetId());
2162 Vector comps = (Vector) PaintRefresher.components.get(viewport
2163 .getSequenceSetId());
2165 for (int i = 0; i < comps.size(); i++)
2167 if (comps.elementAt(i) instanceof AlignmentPanel)
2173 String title = new String(this.getTitle());
2174 if (viewtitle != null)
2176 title = viewtitle + " ( " + title + ")";
2180 if (title.indexOf("(View") > -1)
2182 title = title.substring(0, title.indexOf("(View"));
2184 title += "(View " + viewSize + ")";
2187 newaf.setTitle(title.toString());
2189 newaf.viewport.historyList = viewport.historyList;
2190 newaf.viewport.redoList = viewport.redoList;
2196 * @return list of feature groups on the view
2198 public String[] getFeatureGroups()
2200 FeatureRenderer fr = null;
2201 if (alignPanel != null
2202 && (fr = alignPanel.getFeatureRenderer()) != null)
2204 return fr.getGroups();
2210 * get sequence feature groups that are hidden or shown
2216 public String[] getFeatureGroupsOfState(boolean visible)
2218 FeatureRenderer fr = null;
2219 if (alignPanel != null
2220 && (fr = alignPanel.getFeatureRenderer()) != null)
2222 return fr.getGroups(visible);
2228 * Change the display state for the given feature groups
2231 * list of group strings
2233 * visible or invisible
2235 public void setFeatureGroupState(String[] groups, boolean state)
2237 FeatureRenderer fr = null;
2238 this.sequenceFeatures.setState(true);
2239 viewport.showSequenceFeatures(true);
2240 if (alignPanel != null
2241 && (fr = alignPanel.getFeatureRenderer()) != null)
2243 fr.setGroupState(groups, state);
2244 alignPanel.seqPanel.seqCanvas.repaint();
2245 if (alignPanel.overviewPanel != null)
2247 alignPanel.overviewPanel.updateOverviewImage();
2252 public void seqLimits_itemStateChanged()
2254 viewport.setShowJVSuffix(seqLimits.getState());
2255 alignPanel.fontChanged();
2256 alignPanel.paintAlignment(true);
2259 protected void colourTextMenuItem_actionPerformed()
2261 viewport.setColourText(colourTextMenuItem.getState());
2262 alignPanel.paintAlignment(true);
2265 protected void displayNonconservedMenuItem_actionPerformed()
2267 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2268 alignPanel.paintAlignment(true);
2271 protected void wrapMenuItem_actionPerformed()
2273 viewport.setWrapAlignment(wrapMenuItem.getState());
2274 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2275 scaleAbove.setEnabled(wrapMenuItem.getState());
2276 scaleLeft.setEnabled(wrapMenuItem.getState());
2277 scaleRight.setEnabled(wrapMenuItem.getState());
2278 alignPanel.paintAlignment(true);
2281 public void overviewMenuItem_actionPerformed()
2283 if (alignPanel.overviewPanel != null)
2288 Frame frame = new Frame();
2289 OverviewPanel overview = new OverviewPanel(alignPanel);
2290 frame.add(overview);
2291 // +50 must allow for applet frame window
2292 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2293 overview.getPreferredSize().width,
2294 overview.getPreferredSize().height + 50);
2297 final AlignmentPanel ap = alignPanel;
2298 frame.addWindowListener(new WindowAdapter()
2301 public void windowClosing(WindowEvent e)
2305 ap.setOverviewPanel(null);
2310 alignPanel.setOverviewPanel(overview);
2314 void changeColour(ColourSchemeI cs)
2320 if (viewport.getAbovePIDThreshold())
2322 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2325 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2327 viewport.setGlobalColourScheme(cs);
2331 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2334 if (viewport.getConservationSelected())
2337 Alignment al = (Alignment) viewport.getAlignment();
2338 Conservation c = new Conservation("All",
2339 ResidueProperties.propHash, 3, al.getSequences(), 0,
2343 c.verdict(false, viewport.getConsPercGaps());
2345 cs.setConservation(c);
2347 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2353 cs.setConservation(null);
2356 cs.setConsensus(viewport.getSequenceConsensusHash());
2359 viewport.setGlobalColourScheme(cs);
2361 if (alignPanel.getOverviewPanel() != null)
2363 alignPanel.getOverviewPanel().updateOverviewImage();
2366 jalview.structure.StructureSelectionManager
2367 .getStructureSelectionManager(viewport.applet)
2368 .sequenceColoursChanged(alignPanel);
2370 alignPanel.paintAlignment(true);
2373 protected void modifyPID_actionPerformed()
2375 if (viewport.getAbovePIDThreshold()
2376 && viewport.getGlobalColourScheme() != null)
2378 SliderPanel.setPIDSliderSource(alignPanel,
2379 viewport.getGlobalColourScheme(), "Background");
2380 SliderPanel.showPIDSlider();
2384 protected void modifyConservation_actionPerformed()
2386 if (viewport.getConservationSelected()
2387 && viewport.getGlobalColourScheme() != null)
2389 SliderPanel.setConservationSlider(alignPanel,
2390 viewport.getGlobalColourScheme(), "Background");
2391 SliderPanel.showConservationSlider();
2395 protected void conservationMenuItem_actionPerformed()
2397 viewport.setConservationSelected(conservationMenuItem.getState());
2399 viewport.setAbovePIDThreshold(false);
2400 abovePIDThreshold.setState(false);
2402 changeColour(viewport.getGlobalColourScheme());
2404 modifyConservation_actionPerformed();
2407 public void abovePIDThreshold_actionPerformed()
2409 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2411 conservationMenuItem.setState(false);
2412 viewport.setConservationSelected(false);
2414 changeColour(viewport.getGlobalColourScheme());
2416 modifyPID_actionPerformed();
2419 public void sortPairwiseMenuItem_actionPerformed()
2421 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2422 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2423 .getAlignment().getSequenceAt(0), null);
2425 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2426 viewport.getAlignment()));
2427 alignPanel.paintAlignment(true);
2430 public void sortIDMenuItem_actionPerformed()
2432 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2433 AlignmentSorter.sortByID(viewport.getAlignment());
2434 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2435 viewport.getAlignment()));
2436 alignPanel.paintAlignment(true);
2439 public void sortLengthMenuItem_actionPerformed()
2441 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2442 AlignmentSorter.sortByLength(viewport.getAlignment());
2443 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2444 viewport.getAlignment()));
2445 alignPanel.paintAlignment(true);
2448 public void sortGroupMenuItem_actionPerformed()
2450 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2451 AlignmentSorter.sortByGroup(viewport.getAlignment());
2452 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2453 viewport.getAlignment()));
2454 alignPanel.paintAlignment(true);
2458 public void removeRedundancyMenuItem_actionPerformed()
2460 new RedundancyPanel(alignPanel);
2463 public void pairwiseAlignmentMenuItem_actionPerformed()
2465 if (viewport.getSelectionGroup() != null
2466 && viewport.getSelectionGroup().getSize() > 1)
2468 Frame frame = new Frame();
2469 frame.add(new PairwiseAlignPanel(alignPanel));
2470 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2475 public void PCAMenuItem_actionPerformed()
2477 // are the sequences aligned?
2478 if (!viewport.getAlignment().isAligned(false))
2481 int Width = viewport.getAlignment().getWidth();
2483 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2485 current = viewport.getAlignment().getSequenceAt(i);
2487 if (current.getLength() < Width)
2489 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2492 alignPanel.paintAlignment(true);
2495 if ((viewport.getSelectionGroup() != null
2496 && viewport.getSelectionGroup().getSize() < 4 && viewport
2497 .getSelectionGroup().getSize() > 0)
2498 || viewport.getAlignment().getHeight() < 4)
2505 new PCAPanel(viewport);
2506 } catch (java.lang.OutOfMemoryError ex)
2512 public void averageDistanceTreeMenuItem_actionPerformed()
2514 NewTreePanel("AV", "PID", "Average distance tree using PID");
2517 public void neighbourTreeMenuItem_actionPerformed()
2519 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2522 protected void njTreeBlosumMenuItem_actionPerformed()
2524 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2527 protected void avTreeBlosumMenuItem_actionPerformed()
2529 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2532 void NewTreePanel(String type, String pwType, String title)
2534 // are the sequences aligned?
2535 if (!viewport.getAlignment().isAligned(false))
2538 int Width = viewport.getAlignment().getWidth();
2540 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2542 current = viewport.getAlignment().getSequenceAt(i);
2544 if (current.getLength() < Width)
2546 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2549 alignPanel.paintAlignment(true);
2553 if ((viewport.getSelectionGroup() != null && viewport
2554 .getSelectionGroup().getSize() > 1)
2555 || (viewport.getAlignment().getHeight() > 1))
2557 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2559 addTreeMenuItem(tp, title);
2561 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2565 void loadTree_actionPerformed()
2567 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2568 cap.setText("Paste your Newick tree file here.");
2569 cap.setTreeImport();
2570 Frame frame = new Frame();
2572 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2575 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2577 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2578 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2579 addTreeMenuItem(tp, treeFile);
2583 * sort the alignment using the given treePanel
2586 * tree used to sort view
2588 * string used for undo event name
2590 public void sortByTree(TreePanel treePanel, String title)
2592 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2594 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2595 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2596 // HistoryItem.SORT));
2597 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2598 viewport.getAlignment()));
2599 alignPanel.paintAlignment(true);
2603 * Do any automatic reordering of the alignment and add the necessary bits to
2604 * the menu structure for the new tree
2609 protected void addTreeMenuItem(final TreePanel treePanel,
2612 final MenuItem item = new MenuItem(title);
2613 sortByTreeMenu.add(item);
2614 item.addActionListener(new java.awt.event.ActionListener()
2617 public void actionPerformed(ActionEvent evt)
2619 sortByTree(treePanel, title); // treePanel.getTitle());
2623 treePanel.addWindowListener(new WindowAdapter()
2626 public void windowOpened(WindowEvent e)
2628 if (viewport.sortByTree)
2630 sortByTree(treePanel, title);
2632 super.windowOpened(e);
2636 public void windowClosing(WindowEvent e)
2638 sortByTreeMenu.remove(item);
2643 public boolean sortBy(AlignmentOrder alorder, String undoname)
2645 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2646 if (viewport.applet.debug)
2648 System.err.println("Sorting " + alorder.getOrder().size()
2649 + " in alignment '" + getTitle() + "'");
2651 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2652 if (undoname != null)
2654 addHistoryItem(new OrderCommand(undoname, oldOrder,
2655 viewport.getAlignment()));
2657 alignPanel.paintAlignment(true);
2661 protected void documentation_actionPerformed()
2663 alignPanel.av.applet.openJalviewHelpUrl();
2666 protected void about_actionPerformed()
2669 class AboutPanel extends Canvas
2675 public AboutPanel(String version, String builddate)
2677 this.version = version;
2678 this.builddate = builddate;
2682 public void paint(Graphics g)
2684 g.setColor(Color.white);
2685 g.fillRect(0, 0, getSize().width, getSize().height);
2686 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2687 FontMetrics fm = g.getFontMetrics();
2688 int fh = fm.getHeight();
2690 g.setColor(Color.black);
2691 // TODO: update this text for each release or centrally store it for
2692 // lite and application
2693 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2694 g.drawString("JalviewLite - Release " + version, x, y += fh);
2695 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2696 g.drawString("Build date: " + builddate, x, y += fh);
2697 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2699 "Authors: Jim Procter, Andrew Waterhouse, Lauren Lui, Jan Engelhardt, Natasha Sherstnev,",
2701 g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
2703 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2706 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2708 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2710 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2713 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2715 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2720 Frame frame = new Frame();
2721 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2723 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2727 public void showURL(String url, String target)
2729 if (viewport.applet == null)
2731 System.out.println("Not running as applet - no browser available.");
2735 viewport.applet.showURL(url, target);
2739 // ////////////////////////////////////////////////////////////////////////////////
2740 // JBuilder Graphics here
2742 MenuBar alignFrameMenuBar = new MenuBar();
2744 Menu fileMenu = new Menu("File");
2746 MenuItem loadApplication = new MenuItem("View in Full Application");
2748 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2750 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2752 MenuItem outputFeatures = new MenuItem("Export Features ...");
2754 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2756 MenuItem closeMenuItem = new MenuItem("Close");
2758 Menu editMenu = new Menu("Edit");
2760 Menu viewMenu = new Menu("View");
2762 Menu colourMenu = new Menu("Colour");
2764 Menu calculateMenu = new Menu("Calculate");
2766 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2768 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2770 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2772 MenuItem remove2LeftMenuItem = new MenuItem();
2774 MenuItem remove2RightMenuItem = new MenuItem();
2776 MenuItem removeGappedColumnMenuItem = new MenuItem();
2778 MenuItem removeAllGapsMenuItem = new MenuItem();
2780 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2782 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2784 MenuItem sortPairwiseMenuItem = new MenuItem();
2786 MenuItem sortIDMenuItem = new MenuItem();
2788 MenuItem sortLengthMenuItem = new MenuItem();
2790 MenuItem sortGroupMenuItem = new MenuItem();
2792 MenuItem removeRedundancyMenuItem = new MenuItem();
2794 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2796 MenuItem PCAMenuItem = new MenuItem();
2798 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2800 MenuItem neighbourTreeMenuItem = new MenuItem();
2802 BorderLayout borderLayout1 = new BorderLayout();
2804 public Label statusBar = new Label();
2806 Menu outputTextboxMenu = new Menu();
2808 MenuItem clustalColour = new MenuItem();
2810 MenuItem zappoColour = new MenuItem();
2812 MenuItem taylorColour = new MenuItem();
2814 MenuItem hydrophobicityColour = new MenuItem();
2816 MenuItem helixColour = new MenuItem();
2818 MenuItem strandColour = new MenuItem();
2820 MenuItem turnColour = new MenuItem();
2822 MenuItem buriedColour = new MenuItem();
2824 MenuItem purinePyrimidineColour = new MenuItem();
2826 MenuItem RNAHelixColour = new MenuItem();
2828 MenuItem userDefinedColour = new MenuItem();
2830 MenuItem PIDColour = new MenuItem();
2832 MenuItem BLOSUM62Colour = new MenuItem();
2834 MenuItem tcoffeeColour = new MenuItem();
2836 MenuItem njTreeBlosumMenuItem = new MenuItem();
2838 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2840 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2842 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2844 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2846 MenuItem alProperties = new MenuItem("Alignment Properties...");
2848 MenuItem overviewMenuItem = new MenuItem();
2850 MenuItem undoMenuItem = new MenuItem();
2852 MenuItem redoMenuItem = new MenuItem();
2854 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2856 MenuItem noColourmenuItem = new MenuItem();
2858 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2860 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2862 MenuItem findMenuItem = new MenuItem();
2864 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2866 MenuItem nucleotideColour = new MenuItem();
2868 MenuItem deleteGroups = new MenuItem();
2870 MenuItem grpsFromSelection = new MenuItem();
2872 MenuItem delete = new MenuItem();
2874 MenuItem copy = new MenuItem();
2876 MenuItem cut = new MenuItem();
2878 Menu pasteMenu = new Menu();
2880 MenuItem pasteNew = new MenuItem();
2882 MenuItem pasteThis = new MenuItem();
2884 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2886 MenuItem font = new MenuItem();
2888 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2890 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2892 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2894 MenuItem modifyPID = new MenuItem();
2896 MenuItem modifyConservation = new MenuItem();
2898 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2899 "Autocalculate Consensus", true);
2901 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2902 "Sort Alignment With New Tree", true);
2904 Menu sortByTreeMenu = new Menu();
2906 Menu sort = new Menu();
2908 Menu calculate = new Menu();
2910 MenuItem inputText = new MenuItem();
2912 Menu helpMenu = new Menu();
2914 MenuItem documentation = new MenuItem();
2916 MenuItem about = new MenuItem();
2918 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2920 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2922 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2924 Menu autoAnnMenu = new Menu();
2926 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2928 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2930 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2932 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2934 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2936 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2938 private void jbInit() throws Exception
2941 setMenuBar(alignFrameMenuBar);
2945 // dynamically fill save as menu with available formats
2946 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2949 item = new MenuItem(
2950 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2952 item.addActionListener(new java.awt.event.ActionListener()
2955 public void actionPerformed(ActionEvent e)
2957 outputText_actionPerformed(e);
2961 outputTextboxMenu.add(item);
2963 closeMenuItem.addActionListener(this);
2964 loadApplication.addActionListener(this);
2966 loadTree.addActionListener(this);
2967 loadAnnotations.addActionListener(this);
2968 outputFeatures.addActionListener(this);
2969 outputAnnotations.addActionListener(this);
2970 selectAllSequenceMenuItem.addActionListener(this);
2971 deselectAllSequenceMenuItem.addActionListener(this);
2972 invertSequenceMenuItem.addActionListener(this);
2973 remove2LeftMenuItem.setLabel("Remove Left");
2974 remove2LeftMenuItem.addActionListener(this);
2975 remove2RightMenuItem.setLabel("Remove Right");
2976 remove2RightMenuItem.addActionListener(this);
2977 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2978 removeGappedColumnMenuItem.addActionListener(this);
2979 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2980 removeAllGapsMenuItem.addActionListener(this);
2981 viewBoxesMenuItem.setLabel("Boxes");
2982 viewBoxesMenuItem.setState(true);
2983 viewBoxesMenuItem.addItemListener(this);
2984 viewTextMenuItem.setLabel("Text");
2985 viewTextMenuItem.setState(true);
2986 viewTextMenuItem.addItemListener(this);
2987 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2988 sortPairwiseMenuItem.addActionListener(this);
2989 sortIDMenuItem.setLabel("by ID");
2990 sortIDMenuItem.addActionListener(this);
2991 sortLengthMenuItem.setLabel("by Length");
2992 sortLengthMenuItem.addActionListener(this);
2993 sortGroupMenuItem.setLabel("by Group");
2994 sortGroupMenuItem.addActionListener(this);
2995 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2996 removeRedundancyMenuItem.addActionListener(this);
2997 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2998 pairwiseAlignmentMenuItem.addActionListener(this);
2999 PCAMenuItem.setLabel("Principal Component Analysis");
3000 PCAMenuItem.addActionListener(this);
3001 averageDistanceTreeMenuItem
3002 .setLabel("Average Distance Using % Identity");
3003 averageDistanceTreeMenuItem.addActionListener(this);
3004 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
3005 neighbourTreeMenuItem.addActionListener(this);
3006 statusBar.setBackground(Color.white);
3007 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3008 statusBar.setText("Status bar");
3009 outputTextboxMenu.setLabel("Output to Textbox");
3010 clustalColour.setLabel("Clustalx");
3012 clustalColour.addActionListener(this);
3013 zappoColour.setLabel("Zappo");
3014 zappoColour.addActionListener(this);
3015 taylorColour.setLabel("Taylor");
3016 taylorColour.addActionListener(this);
3017 hydrophobicityColour.setLabel("Hydrophobicity");
3018 hydrophobicityColour.addActionListener(this);
3019 helixColour.setLabel("Helix Propensity");
3020 helixColour.addActionListener(this);
3021 strandColour.setLabel("Strand Propensity");
3022 strandColour.addActionListener(this);
3023 turnColour.setLabel("Turn Propensity");
3024 turnColour.addActionListener(this);
3025 buriedColour.setLabel("Buried Index");
3026 buriedColour.addActionListener(this);
3027 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
3028 purinePyrimidineColour.addActionListener(this);
3029 RNAHelixColour.setLabel("by RNA Helices");
3030 RNAHelixColour.addActionListener(this);
3031 userDefinedColour.setLabel("User Defined...");
3032 userDefinedColour.addActionListener(this);
3033 PIDColour.setLabel("Percentage Identity");
3034 PIDColour.addActionListener(this);
3035 BLOSUM62Colour.setLabel("BLOSUM62 Score");
3036 BLOSUM62Colour.addActionListener(this);
3037 tcoffeeColour.setLabel("T-Coffee Scores");
3038 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3040 tcoffeeColour.addActionListener(this);
3041 avDistanceTreeBlosumMenuItem
3042 .setLabel("Average Distance Using BLOSUM62");
3043 avDistanceTreeBlosumMenuItem.addActionListener(this);
3044 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
3045 njTreeBlosumMenuItem.addActionListener(this);
3046 annotationPanelMenuItem.setLabel("Show Annotations");
3047 annotationPanelMenuItem.addItemListener(this);
3048 colourTextMenuItem.setLabel("Colour Text");
3049 colourTextMenuItem.addItemListener(this);
3050 displayNonconservedMenuItem.setLabel("Show nonconserved");
3051 displayNonconservedMenuItem.addItemListener(this);
3052 alProperties.addActionListener(this);
3053 overviewMenuItem.setLabel("Overview Window");
3054 overviewMenuItem.addActionListener(this);
3055 undoMenuItem.setEnabled(false);
3056 undoMenuItem.setLabel("Undo");
3057 undoMenuItem.addActionListener(this);
3058 redoMenuItem.setEnabled(false);
3059 redoMenuItem.setLabel("Redo");
3060 redoMenuItem.addActionListener(this);
3061 conservationMenuItem.setLabel("by Conservation");
3062 conservationMenuItem.addItemListener(this);
3063 noColourmenuItem.setLabel("None");
3064 noColourmenuItem.addActionListener(this);
3065 wrapMenuItem.setLabel("Wrap");
3066 wrapMenuItem.addItemListener(this);
3067 renderGapsMenuItem.setLabel("Show Gaps");
3068 renderGapsMenuItem.setState(true);
3069 renderGapsMenuItem.addItemListener(this);
3070 findMenuItem.setLabel("Find...");
3071 findMenuItem.addActionListener(this);
3072 abovePIDThreshold.setLabel("Above Identity Threshold");
3073 abovePIDThreshold.addItemListener(this);
3074 nucleotideColour.setLabel("Nucleotide");
3075 nucleotideColour.addActionListener(this);
3076 deleteGroups.setLabel("Undefine Groups");
3077 deleteGroups.addActionListener(this);
3078 grpsFromSelection.setLabel("Make Groups for selection");
3079 grpsFromSelection.addActionListener(this);
3080 copy.setLabel("Copy");
3081 copy.addActionListener(this);
3082 cut.setLabel("Cut");
3083 cut.addActionListener(this);
3084 delete.setLabel("Delete");
3085 delete.addActionListener(this);
3086 pasteMenu.setLabel("Paste");
3087 pasteNew.setLabel("To New Alignment");
3088 pasteNew.addActionListener(this);
3089 pasteThis.setLabel("Add To This Alignment");
3090 pasteThis.addActionListener(this);
3091 applyToAllGroups.setLabel("Apply Colour To All Groups");
3092 applyToAllGroups.setState(true);
3093 applyToAllGroups.addItemListener(this);
3094 font.setLabel("Font...");
3095 font.addActionListener(this);
3096 scaleAbove.setLabel("Scale Above");
3097 scaleAbove.setState(true);
3098 scaleAbove.setEnabled(false);
3099 scaleAbove.addItemListener(this);
3100 scaleLeft.setEnabled(false);
3101 scaleLeft.setState(true);
3102 scaleLeft.setLabel("Scale Left");
3103 scaleLeft.addItemListener(this);
3104 scaleRight.setEnabled(false);
3105 scaleRight.setState(true);
3106 scaleRight.setLabel("Scale Right");
3107 scaleRight.addItemListener(this);
3108 modifyPID.setLabel("Modify Identity Threshold...");
3109 modifyPID.addActionListener(this);
3110 modifyConservation.setLabel("Modify Conservation Threshold...");
3111 modifyConservation.addActionListener(this);
3112 sortByTreeMenu.setLabel("By Tree Order");
3113 sort.setLabel("Sort");
3114 calculate.setLabel("Calculate Tree");
3115 autoCalculate.addItemListener(this);
3116 sortByTree.addItemListener(this);
3117 inputText.setLabel("Input from textbox");
3118 inputText.addActionListener(this);
3119 centreColumnLabelFlag.setLabel("Centre column labels");
3120 centreColumnLabelFlag.addItemListener(this);
3121 followMouseOverFlag.setLabel("Automatic Scrolling");
3122 followMouseOverFlag.addItemListener(this);
3123 helpMenu.setLabel("Help");
3124 documentation.setLabel("Documentation");
3125 documentation.addActionListener(this);
3127 about.setLabel("About...");
3128 about.addActionListener(this);
3129 seqLimits.setState(true);
3130 seqLimits.setLabel("Show Sequence Limits");
3131 seqLimits.addItemListener(this);
3132 featureSettings.setLabel("Feature Settings...");
3133 featureSettings.addActionListener(this);
3134 sequenceFeatures.setLabel("Sequence Features");
3135 sequenceFeatures.addItemListener(this);
3136 sequenceFeatures.setState(false);
3137 annotationColour.setLabel("by Annotation...");
3138 annotationColour.addActionListener(this);
3139 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3140 invertColSel.setLabel("Invert Column Selection");
3141 menu1.setLabel("Show");
3142 showColumns.setLabel("All Columns ");
3143 showSeqs.setLabel("All Sequences");
3144 menu2.setLabel("Hide");
3145 hideColumns.setLabel("Selected Columns");
3146 hideSequences.setLabel("Selected Sequences");
3147 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3148 hideAllSelection.setLabel("Selected Region");
3149 showAllHidden.setLabel("All Sequences and Columns");
3150 showGroupConsensus.setLabel("Group Consensus");
3151 showGroupConservation.setLabel("Group Conservation");
3152 showConsensusHistogram.setLabel("Show Consensus Histogram");
3153 showSequenceLogo.setLabel("Show Consensus Logo");
3154 normSequenceLogo.setLabel("Normalise Consensus Logo");
3155 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3156 applyAutoAnnotationSettings.setState(true);
3157 autoAnnMenu.setLabel("Autocalculated Annotation");
3159 invertColSel.addActionListener(this);
3160 showColumns.addActionListener(this);
3161 showSeqs.addActionListener(this);
3162 hideColumns.addActionListener(this);
3163 hideSequences.addActionListener(this);
3164 hideAllButSelection.addActionListener(this);
3165 hideAllSelection.addActionListener(this);
3166 showAllHidden.addActionListener(this);
3167 showGroupConsensus.addItemListener(this);
3168 showGroupConservation.addItemListener(this);
3169 showConsensusHistogram.addItemListener(this);
3170 showSequenceLogo.addItemListener(this);
3171 normSequenceLogo.addItemListener(this);
3173 applyAutoAnnotationSettings.addItemListener(this);
3174 formatMenu.setLabel("Format");
3175 selectMenu.setLabel("Select");
3176 newView.setLabel("New View");
3177 newView.addActionListener(this);
3178 alignFrameMenuBar.add(fileMenu);
3179 alignFrameMenuBar.add(editMenu);
3180 alignFrameMenuBar.add(selectMenu);
3181 alignFrameMenuBar.add(viewMenu);
3182 alignFrameMenuBar.add(formatMenu);
3183 alignFrameMenuBar.add(colourMenu);
3184 alignFrameMenuBar.add(calculateMenu);
3185 alignFrameMenuBar.add(helpMenu);
3187 fileMenu.add(inputText);
3188 fileMenu.add(loadTree);
3189 fileMenu.add(loadAnnotations);
3191 fileMenu.addSeparator();
3192 fileMenu.add(outputTextboxMenu);
3193 fileMenu.add(outputFeatures);
3194 fileMenu.add(outputAnnotations);
3196 if (jalviewServletURL != null)
3198 fileMenu.add(loadApplication);
3201 fileMenu.addSeparator();
3202 fileMenu.add(closeMenuItem);
3204 editMenu.add(undoMenuItem);
3205 editMenu.add(redoMenuItem);
3208 editMenu.add(pasteMenu);
3209 editMenu.add(delete);
3210 editMenu.addSeparator();
3211 editMenu.add(remove2LeftMenuItem);
3212 editMenu.add(remove2RightMenuItem);
3213 editMenu.add(removeGappedColumnMenuItem);
3214 editMenu.add(removeAllGapsMenuItem);
3215 editMenu.add(removeRedundancyMenuItem);
3216 viewMenu.add(newView);
3217 viewMenu.addSeparator();
3218 viewMenu.add(menu1);
3219 viewMenu.add(menu2);
3220 viewMenu.addSeparator();
3221 viewMenu.add(followMouseOverFlag);
3222 viewMenu.add(annotationPanelMenuItem);
3223 autoAnnMenu.add(applyAutoAnnotationSettings);
3224 autoAnnMenu.add(showConsensusHistogram);
3225 autoAnnMenu.add(showSequenceLogo);
3226 autoAnnMenu.add(normSequenceLogo);
3227 autoAnnMenu.addSeparator();
3228 autoAnnMenu.add(showGroupConservation);
3229 autoAnnMenu.add(showGroupConsensus);
3230 viewMenu.add(autoAnnMenu);
3231 viewMenu.addSeparator();
3232 viewMenu.add(sequenceFeatures);
3233 viewMenu.add(featureSettings);
3234 viewMenu.addSeparator();
3235 viewMenu.add(alProperties);
3236 viewMenu.addSeparator();
3237 viewMenu.add(overviewMenuItem);
3238 colourMenu.add(applyToAllGroups);
3239 colourMenu.addSeparator();
3240 colourMenu.add(noColourmenuItem);
3241 colourMenu.add(clustalColour);
3242 colourMenu.add(BLOSUM62Colour);
3243 colourMenu.add(PIDColour);
3244 colourMenu.add(zappoColour);
3245 colourMenu.add(taylorColour);
3246 colourMenu.add(hydrophobicityColour);
3247 colourMenu.add(helixColour);
3248 colourMenu.add(strandColour);
3249 colourMenu.add(turnColour);
3250 colourMenu.add(buriedColour);
3251 colourMenu.add(nucleotideColour);
3252 colourMenu.add(purinePyrimidineColour);
3253 colourMenu.add(tcoffeeColour);
3254 colourMenu.add(userDefinedColour);
3255 colourMenu.addSeparator();
3256 colourMenu.add(conservationMenuItem);
3257 colourMenu.add(modifyConservation);
3258 colourMenu.add(abovePIDThreshold);
3259 colourMenu.add(modifyPID);
3260 colourMenu.add(annotationColour);
3261 colourMenu.add(RNAHelixColour);
3262 calculateMenu.add(sort);
3263 calculateMenu.add(calculate);
3264 calculateMenu.addSeparator();
3265 calculateMenu.add(pairwiseAlignmentMenuItem);
3266 calculateMenu.add(PCAMenuItem);
3267 calculateMenu.add(autoCalculate);
3268 calculateMenu.add(sortByTree);
3269 this.add(statusBar, BorderLayout.SOUTH);
3270 pasteMenu.add(pasteNew);
3271 pasteMenu.add(pasteThis);
3272 sort.add(sortIDMenuItem);
3273 sort.add(sortLengthMenuItem);
3274 sort.add(sortByTreeMenu);
3275 sort.add(sortGroupMenuItem);
3276 sort.add(sortPairwiseMenuItem);
3277 calculate.add(averageDistanceTreeMenuItem);
3278 calculate.add(neighbourTreeMenuItem);
3279 calculate.add(avDistanceTreeBlosumMenuItem);
3280 calculate.add(njTreeBlosumMenuItem);
3281 helpMenu.add(documentation);
3282 helpMenu.add(about);
3283 menu1.add(showColumns);
3284 menu1.add(showSeqs);
3285 menu1.add(showAllHidden);
3286 menu2.add(hideColumns);
3287 menu2.add(hideSequences);
3288 menu2.add(hideAllSelection);
3289 menu2.add(hideAllButSelection);
3290 formatMenu.add(font);
3291 formatMenu.add(seqLimits);
3292 formatMenu.add(wrapMenuItem);
3293 formatMenu.add(scaleAbove);
3294 formatMenu.add(scaleLeft);
3295 formatMenu.add(scaleRight);
3296 formatMenu.add(viewBoxesMenuItem);
3297 formatMenu.add(viewTextMenuItem);
3298 formatMenu.add(colourTextMenuItem);
3299 formatMenu.add(displayNonconservedMenuItem);
3300 formatMenu.add(renderGapsMenuItem);
3301 formatMenu.add(centreColumnLabelFlag);
3302 selectMenu.add(findMenuItem);
3303 selectMenu.addSeparator();
3304 selectMenu.add(selectAllSequenceMenuItem);
3305 selectMenu.add(deselectAllSequenceMenuItem);
3306 selectMenu.add(invertSequenceMenuItem);
3307 selectMenu.add(invertColSel);
3308 selectMenu.add(grpsFromSelection);
3309 selectMenu.add(deleteGroups);
3313 MenuItem featureSettings = new MenuItem();
3315 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3317 MenuItem annotationColour = new MenuItem();
3319 MenuItem invertColSel = new MenuItem();
3321 Menu menu1 = new Menu();
3323 MenuItem showColumns = new MenuItem();
3325 MenuItem showSeqs = new MenuItem();
3327 Menu menu2 = new Menu();
3329 MenuItem hideColumns = new MenuItem();
3331 MenuItem hideSequences = new MenuItem();
3333 MenuItem hideAllButSelection = new MenuItem();
3335 MenuItem hideAllSelection = new MenuItem();
3337 MenuItem showAllHidden = new MenuItem();
3339 Menu formatMenu = new Menu();
3341 Menu selectMenu = new Menu();
3343 MenuItem newView = new MenuItem();
3346 * Attach the alignFrame panels after embedding menus, if necessary. This used
3347 * to be called setEmbedded, but is now creates the dropdown menus in a
3348 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3350 * @param reallyEmbedded
3351 * true to attach the view to the applet area on the page rather than
3354 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3359 // Explicly build the embedded menu panel for the on-page applet
3361 // view cannot be closed if its actually on the page
3362 fileMenu.remove(closeMenuItem);
3363 fileMenu.remove(3); // Remove Seperator
3364 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3365 Font.PLAIN, 10, false); // use our own fonts.
3366 // and actually add the components to the applet area
3367 viewport.applet.setLayout(new BorderLayout());
3368 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3369 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3370 alignPanel.setSize(viewport.applet.getSize().width,
3371 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3372 - statusBar.HEIGHT);
3373 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3374 final AlignFrame me = this;
3375 viewport.applet.addFocusListener(new FocusListener()
3379 public void focusLost(FocusEvent e)
3381 if (me.viewport.applet.currentAlignFrame == me)
3383 me.viewport.applet.currentAlignFrame = null;
3388 public void focusGained(FocusEvent e)
3390 me.viewport.applet.currentAlignFrame = me;
3393 viewport.applet.validate();
3398 // test and embed menu bar if necessary.
3400 if (embedMenuIfNeeded(alignPanel))
3402 // adjust for status bar height too
3403 alignPanel.setSize(getSize().width, getSize().height
3404 - statusBar.HEIGHT);
3406 add(statusBar, BorderLayout.SOUTH);
3407 add(alignPanel, BorderLayout.CENTER);
3408 // and register with the applet so it can pass external API calls to us
3409 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3415 * create a new binding between structures in an existing jmol viewer instance
3416 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3417 * this does not open a new Jmol window, or modify the display of the
3418 * structures in the original jmol window. Note This method doesn't work
3419 * without an additional javascript library to exchange messages between the
3420 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3423 * JmolViewer instance
3424 * @param sequenceIds
3425 * - sequence Ids to search for associations
3427 public SequenceStructureBinding addStructureViewInstance(
3428 Object jmolviewer, String[] sequenceIds)
3430 org.jmol.api.JmolViewer viewer = null;
3433 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3434 } catch (ClassCastException ex)
3436 System.err.println("Unsupported viewer object :"
3437 + jmolviewer.getClass());
3441 System.err.println("Can't use this object as a structure viewer:"
3442 + jmolviewer.getClass());
3445 SequenceI[] seqs = null;
3446 if (sequenceIds == null || sequenceIds.length == 0)
3448 seqs = viewport.getAlignment().getSequencesArray();
3452 Vector sqi = new Vector();
3453 AlignmentI al = viewport.getAlignment();
3454 for (int sid = 0; sid < sequenceIds.length; sid++)
3456 SequenceI sq = al.findName(sequenceIds[sid]);
3464 seqs = new SequenceI[sqi.size()];
3465 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3467 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3476 // TODO: search for a jmv that involves viewer
3478 { // create a new viewer/jalview binding.
3479 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3487 * bind a pdb file to a sequence in the current view
3490 * - sequenceId within the dataset.
3491 * @param pdbEntryString
3492 * - the short name for the PDB file
3494 * - pdb file - either a URL or a valid PDB file.
3495 * @return true if binding was as success TODO: consider making an exception
3496 * structure for indicating when PDB parsing or sequenceId location
3499 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3502 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3503 boolean needtoadd = false;
3504 if (toaddpdb != null)
3506 Vector pdbe = toaddpdb.getPDBId();
3507 PDBEntry pdbentry = null;
3508 if (pdbe != null && pdbe.size() > 0)
3510 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3512 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3513 if (!pdbentry.getId().equals(pdbEntryString)
3514 && !pdbentry.getFile().equals(pdbFile))
3524 if (pdbentry == null)
3526 pdbentry = new PDBEntry();
3527 pdbentry.setId(pdbEntryString);
3528 pdbentry.setFile(pdbFile);
3529 needtoadd = true; // add this new entry to sequence.
3531 // resolve data source
3532 // TODO: this code should be a refactored to an io package
3533 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3534 if (protocol == null)
3540 // make a note of the access mode and add
3541 if (pdbentry.getProperty() == null)
3543 pdbentry.setProperty(new Hashtable());
3545 pdbentry.getProperty().put("protocol", protocol);
3546 toaddpdb.addPDBId(pdbentry);
3552 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3556 Vector sequences = new Vector();
3557 for (int i = 0; i < seqs.length; i++)
3559 if (seqs[i] != null)
3561 sequences.addElement(new Object[]
3562 { seqs[i], (chains != null) ? chains[i] : null });
3565 seqs = new SequenceI[sequences.size()];
3566 chains = new String[sequences.size()];
3567 for (int i = 0, isize = sequences.size(); i < isize; i++)
3569 Object[] oj = (Object[]) sequences.elementAt(i);
3571 seqs[i] = (SequenceI) oj[0];
3572 chains[i] = (String) oj[1];
3580 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3581 SequenceI[] seqs, String[] chains, String protocol)
3583 // Scrub any null sequences from the array
3584 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3585 seqs = (SequenceI[]) sqch[0];
3586 chains = (String[]) sqch[1];
3587 if (seqs == null || seqs.length == 0)
3590 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3592 if (protocol == null || protocol.trim().length() == 0
3593 || protocol.equals("null"))
3595 protocol = (String) pdb.getProperty().get("protocol");
3596 if (protocol == null)
3598 System.err.println("Couldn't work out protocol to open structure: "
3603 if (applet.useXtrnalSviewer)
3605 // register the association(s) and quit, don't create any windows.
3606 if (StructureSelectionManager.getStructureSelectionManager(applet)
3607 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3609 System.err.println("Failed to map " + pdb.getFile() + " ("
3610 + protocol + ") to any sequences");
3614 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3616 // can only do alignments with Jmol
3617 // find the last jmol window assigned to this alignment
3618 jalview.appletgui.AppletJmol ajm = null, tajm;
3619 Vector jmols = applet
3620 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3621 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3623 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3624 if (tajm.ap.alignFrame == this)
3633 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3634 // try and add the pdb structure
3639 // otherwise, create a new window
3640 if (applet.jmolAvailable)
3642 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3644 applet.lastFrameX += 40;
3645 applet.lastFrameY += 40;
3649 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3654 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3655 SequenceI[][] seqs, String[][] chains, String[] protocols)
3657 // TODO Auto-generated method stub
3658 System.err.println("Aligned Structure View: Not yet implemented.");
3662 * modify the current selection, providing the user has not made a selection
3666 * - sequences from this alignment
3668 * - columns to be selected on the alignment
3670 public void select(SequenceGroup sel, ColumnSelection csel)
3672 alignPanel.seqPanel.selection(sel, csel, null);
3675 public void scrollTo(int row, int column)
3677 alignPanel.seqPanel.scrollTo(row, column);
3680 public void scrollToRow(int row)
3682 alignPanel.seqPanel.scrollToRow(row);
3685 public void scrollToColumn(int column)
3687 alignPanel.seqPanel.scrollToColumn(column);
3691 * @return the alignments unique ID.
3693 public String getSequenceSetId()
3695 return viewport.getSequenceSetId();
3699 * Load the (T-Coffee) score file from the specified url
3702 * File/URL/T-COFFEE score file contents
3703 * @throws IOException
3704 * @return true if alignment was annotated with data from source
3706 public boolean loadScoreFile(String source) throws IOException
3709 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3710 AppletFormatAdapter.checkProtocol(source));
3711 if (!file.isValid())
3713 // TODO: raise dialog for gui
3714 System.err.println("Problems parsing T-Coffee scores: "
3715 + file.getWarningMessage());
3716 System.err.println("Origin was:\n" + source);
3721 * check that the score matrix matches the alignment dimensions
3724 if ((aln = viewport.getAlignment()) != null
3725 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3728 // TODO: raise a dialog box here rather than bomb out.
3730 .println("The scores matrix does not match the alignment dimensions");
3734 // TODO add parameter to indicate if matching should be done
3735 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3737 alignPanel.fontChanged();
3738 tcoffeeColour.setEnabled(true);
3739 // switch to this color
3740 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3745 System.err.println("Problems resolving T-Coffee scores:");
3746 if (file.getWarningMessage() != null)
3748 System.err.println(file.getWarningMessage());