2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
3 * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
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/>.
18 package jalview.appletgui;
20 import jalview.analysis.AAFrequency;
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.SequenceCollectionI;
39 import jalview.datamodel.SequenceGroup;
40 import jalview.datamodel.SequenceI;
41 import jalview.io.AnnotationFile;
42 import jalview.io.AppletFormatAdapter;
43 import jalview.io.FeaturesFile;
44 import jalview.io.TCoffeeScoreFile;
45 import jalview.schemes.Blosum62ColourScheme;
46 import jalview.schemes.BuriedColourScheme;
47 import jalview.schemes.ClustalxColourScheme;
48 import jalview.schemes.ColourSchemeI;
49 import jalview.schemes.HelixColourScheme;
50 import jalview.schemes.HydrophobicColourScheme;
51 import jalview.schemes.NucleotideColourScheme;
52 import jalview.schemes.PIDColourScheme;
53 import jalview.schemes.PurinePyrimidineColourScheme;
54 import jalview.schemes.RNAHelicesColourChooser;
55 import jalview.schemes.ResidueProperties;
56 import jalview.schemes.StrandColourScheme;
57 import jalview.schemes.TCoffeeColourScheme;
58 import jalview.schemes.TaylorColourScheme;
59 import jalview.schemes.TurnColourScheme;
60 import jalview.schemes.ZappoColourScheme;
61 import jalview.structure.StructureSelectionManager;
63 import java.awt.BorderLayout;
64 import java.awt.Canvas;
65 import java.awt.CheckboxMenuItem;
66 import java.awt.Color;
68 import java.awt.FontMetrics;
69 import java.awt.Frame;
70 import java.awt.Graphics;
71 import java.awt.Label;
73 import java.awt.MenuBar;
74 import java.awt.MenuItem;
75 import java.awt.event.ActionEvent;
76 import java.awt.event.ActionListener;
77 import java.awt.event.FocusEvent;
78 import java.awt.event.FocusListener;
79 import java.awt.event.ItemEvent;
80 import java.awt.event.ItemListener;
81 import java.awt.event.KeyEvent;
82 import java.awt.event.KeyListener;
83 import java.awt.event.WindowAdapter;
84 import java.awt.event.WindowEvent;
85 import java.io.IOException;
86 import java.io.InputStreamReader;
88 import java.net.URLEncoder;
89 import java.util.Enumeration;
90 import java.util.Hashtable;
91 import java.util.List;
92 import java.util.StringTokenizer;
93 import java.util.Vector;
95 public class AlignFrame extends EmbmenuFrame implements ActionListener,
96 ItemListener, KeyListener
98 public AlignmentPanel alignPanel;
100 public AlignViewport viewport;
102 int DEFAULT_WIDTH = 700;
104 int DEFAULT_HEIGHT = 500;
106 String jalviewServletURL;
108 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
109 String title, boolean embedded)
113 jalviewServletURL = applet.getParameter("APPLICATION_URL");
119 } catch (Exception ex)
121 ex.printStackTrace();
124 viewport = new AlignViewport(al, applet);
125 alignPanel = new AlignmentPanel(this, viewport);
127 viewport.updateConservation(alignPanel);
128 viewport.updateConsensus(alignPanel);
130 annotationPanelMenuItem.setState(viewport.showAnnotation);
131 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
132 followMouseOverFlag.setState(viewport.getFollowHighlight());
133 showGroupConsensus.setState(viewport.isShowGroupConsensus());
134 showGroupConservation.setState(viewport.isShowGroupConservation());
135 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
136 showSequenceLogo.setState(viewport.isShowSequenceLogo());
137 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
139 seqLimits.setState(viewport.showJVSuffix);
143 String param = applet.getParameter("sortBy");
146 if (param.equalsIgnoreCase("Id"))
148 sortIDMenuItem_actionPerformed();
150 else if (param.equalsIgnoreCase("Pairwise Identity"))
152 sortPairwiseMenuItem_actionPerformed();
154 else if (param.equalsIgnoreCase("Length"))
156 sortLengthMenuItem_actionPerformed();
160 param = applet.getParameter("wrap");
163 if (param.equalsIgnoreCase("true"))
165 wrapMenuItem.setState(true);
166 wrapMenuItem_actionPerformed();
169 param = applet.getParameter("centrecolumnlabels");
172 centreColumnLabelFlag.setState(true);
173 centreColumnLabelFlag_stateChanged();
177 param = applet.getParameter("windowWidth");
180 int width = Integer.parseInt(param);
181 DEFAULT_WIDTH = width;
183 param = applet.getParameter("windowHeight");
186 int height = Integer.parseInt(param);
187 DEFAULT_HEIGHT = height;
189 } catch (Exception ex)
194 if (viewport.getAlignment().isNucleotide())
196 viewport.updateStrucConsensus(alignPanel);
197 if (viewport.getAlignment().hasRNAStructure())
199 RNAHelixColour.setEnabled(true);
203 RNAHelixColour.setEnabled(false);
208 RNAHelixColour.setEnabled(false);
209 purinePyrimidineColour.setEnabled(false);
211 // Some JVMS send keyevents to Top frame or lowest panel,
212 // Havent worked out why yet. So add to both this frame and seqCanvas for
214 this.addKeyListener(this);
215 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
216 alignPanel.idPanel.idCanvas.addKeyListener(this);
217 alignPanel.scalePanel.addKeyListener(this);
218 alignPanel.annotationPanel.addKeyListener(this);
219 alignPanel.annotationPanelHolder.addKeyListener(this);
220 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
221 alignPanel.alabels.addKeyListener(this);
222 createAlignFrameWindow(embedded, title);
225 alignPanel.adjustAnnotationHeight();
226 alignPanel.paintAlignment(true);
229 public AlignViewport getAlignViewport()
234 public SeqCanvas getSeqcanvas()
236 return alignPanel.seqPanel.seqCanvas;
240 * Load a features file onto the alignment
243 * file URL, content, or other resolvable path
245 * is protocol for accessing data referred to by file
248 public boolean parseFeaturesFile(String file, String type)
250 return parseFeaturesFile(file, type, true);
254 * Load a features file onto the alignment
257 * file URL, content, or other resolvable path
259 * is protocol for accessing data referred to by file
260 * @param autoenabledisplay
261 * when true, display features flag will be automatically enabled if
262 * features are loaded
263 * @return true if data parsed as a features file
265 public boolean parseFeaturesFile(String file, String type,
266 boolean autoenabledisplay)
268 // TODO: test if importing a features file onto an alignment which already
269 // has features with links overwrites the original links.
271 Hashtable featureLinks = new Hashtable();
272 boolean featuresFile = false;
275 featuresFile = new jalview.io.FeaturesFile(file, type)
276 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
277 .getFeatureRenderer().featureColours, featureLinks,
278 true, viewport.applet.getDefaultParameter(
279 "relaxedidmatch", false));
280 } catch (Exception ex)
282 ex.printStackTrace();
287 if (featureLinks.size() > 0)
289 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
291 if (autoenabledisplay)
293 viewport.showSequenceFeatures = true;
294 sequenceFeatures.setState(true);
296 if (viewport.featureSettings != null)
298 viewport.featureSettings.refreshTable();
300 alignPanel.paintAlignment(true);
301 statusBar.setText("Successfully added features to alignment.");
307 public void keyPressed(KeyEvent evt)
309 if (viewport.cursorMode
310 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
311 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
312 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
313 && Character.isDigit(evt.getKeyChar()))
314 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
316 switch (evt.getKeyCode())
318 case 27: // escape key
319 deselectAllSequenceMenuItem_actionPerformed();
321 alignPanel.alabels.cancelDrag();
324 if (evt.isControlDown() || evt.isMetaDown())
326 cut_actionPerformed();
330 if (viewport.cursorMode && !evt.isControlDown())
332 alignPanel.seqPanel.setCursorColumn();
334 if (evt.isControlDown() || evt.isMetaDown())
336 copy_actionPerformed();
340 if (evt.isControlDown())
342 paste(evt.isShiftDown());
346 if (evt.isControlDown() || evt.isMetaDown())
348 selectAllSequenceMenuItem_actionPerformed();
351 case KeyEvent.VK_DOWN:
352 if (viewport.cursorMode)
354 alignPanel.seqPanel.moveCursor(0, 1);
358 moveSelectedSequences(false);
363 if (viewport.cursorMode)
365 alignPanel.seqPanel.moveCursor(0, -1);
369 moveSelectedSequences(true);
373 case KeyEvent.VK_LEFT:
374 if (evt.isAltDown() || !viewport.cursorMode)
375 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
377 alignPanel.seqPanel.moveCursor(-1, 0);
380 case KeyEvent.VK_RIGHT:
381 if (evt.isAltDown() || !viewport.cursorMode)
382 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
384 alignPanel.seqPanel.moveCursor(1, 0);
387 case KeyEvent.VK_SPACE:
388 if (viewport.cursorMode)
390 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
391 || evt.isShiftDown() || evt.isAltDown());
395 case KeyEvent.VK_DELETE:
396 case KeyEvent.VK_BACK_SPACE:
397 if (viewport.cursorMode)
399 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
400 || evt.isShiftDown() || evt.isAltDown());
404 cut_actionPerformed();
405 alignPanel.seqPanel.seqCanvas.repaint();
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.setCursorRow();
416 if (viewport.cursorMode)
418 alignPanel.seqPanel.setCursorPosition();
422 case KeyEvent.VK_ENTER:
423 case KeyEvent.VK_COMMA:
424 if (viewport.cursorMode)
426 alignPanel.seqPanel.setCursorRowAndColumn();
431 if (viewport.cursorMode)
433 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
437 if (viewport.cursorMode)
439 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
444 viewport.cursorMode = !viewport.cursorMode;
445 statusBar.setText("Keyboard editing mode is "
446 + (viewport.cursorMode ? "on" : "off"));
447 if (viewport.cursorMode)
449 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
450 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
455 if (evt.isControlDown())
457 findMenuItem_actionPerformed();
463 boolean toggleSeqs = !evt.isControlDown();
464 boolean toggleCols = !evt.isShiftDown();
465 toggleHiddenRegions(toggleSeqs, toggleCols);
469 case KeyEvent.VK_PAGE_UP:
470 if (viewport.wrapAlignment)
472 alignPanel.scrollUp(true);
476 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
477 - viewport.endSeq + viewport.startSeq);
481 case KeyEvent.VK_PAGE_DOWN:
482 if (viewport.wrapAlignment)
484 alignPanel.scrollUp(false);
488 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
489 + viewport.endSeq - viewport.startSeq);
494 if (evt.isControlDown())
496 undoMenuItem_actionPerformed();
501 if (evt.isControlDown())
503 redoMenuItem_actionPerformed();
508 if (evt.isControlDown())
515 if (evt.isControlDown())
517 trimAlignment(false);
522 if (evt.isControlDown())
524 if (evt.isShiftDown())
526 this.removeAllGapsMenuItem_actionPerformed();
530 removeGappedColumnMenuItem_actionPerformed();
535 if (evt.isControlDown())
539 invertColSel_actionPerformed();
543 invertSequenceMenuItem_actionPerformed();
549 if (evt.isControlDown())
551 this.deleteGroups_actionPerformed();
556 if (evt.isControlDown())
563 alignPanel.paintAlignment(true);
567 * called by key handler and the hide all/show all menu items
572 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
574 boolean hide = false;
575 SequenceGroup sg = viewport.getSelectionGroup();
576 if (!toggleSeqs && !toggleCols)
578 // Hide everything by the current selection - this is a hack - we do the
579 // invert and then hide
580 // first check that there will be visible columns after the invert.
581 if ((viewport.getColumnSelection() != null
582 && viewport.getColumnSelection().getSelected() != null && viewport
583 .getColumnSelection().getSelected().size() > 0)
584 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
587 // now invert the sequence set, if required - empty selection implies
588 // that no hiding is required.
591 invertSequenceMenuItem_actionPerformed();
592 sg = viewport.getSelectionGroup();
596 viewport.expandColSelection(sg, true);
597 // finally invert the column selection and get the new sequence
598 // selection and indicate it should be hidden.
599 invertColSel_actionPerformed();
606 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
609 viewport.hideAllSelectedSeqs();
611 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
614 viewport.showAllHiddenSeqs();
620 if (viewport.getColumnSelection().getSelected().size() > 0)
622 viewport.hideSelectedColumns();
625 viewport.setSelectionGroup(sg);
630 viewport.showAllHiddenColumns();
636 public void keyReleased(KeyEvent evt)
641 public void keyTyped(KeyEvent evt)
646 public void itemStateChanged(ItemEvent evt)
648 if (evt.getSource() == displayNonconservedMenuItem)
650 displayNonconservedMenuItem_actionPerformed();
652 else if (evt.getSource() == colourTextMenuItem)
654 colourTextMenuItem_actionPerformed();
656 else if (evt.getSource() == wrapMenuItem)
658 wrapMenuItem_actionPerformed();
660 else if (evt.getSource() == scaleAbove)
662 viewport.setScaleAboveWrapped(scaleAbove.getState());
664 else if (evt.getSource() == scaleLeft)
666 viewport.setScaleLeftWrapped(scaleLeft.getState());
668 else if (evt.getSource() == scaleRight)
670 viewport.setScaleRightWrapped(scaleRight.getState());
672 else if (evt.getSource() == seqLimits)
674 seqLimits_itemStateChanged();
676 else if (evt.getSource() == viewBoxesMenuItem)
678 viewport.setShowBoxes(viewBoxesMenuItem.getState());
680 else if (evt.getSource() == viewTextMenuItem)
682 viewport.setShowText(viewTextMenuItem.getState());
684 else if (evt.getSource() == renderGapsMenuItem)
686 viewport.setRenderGaps(renderGapsMenuItem.getState());
688 else if (evt.getSource() == annotationPanelMenuItem)
690 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
691 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
693 else if (evt.getSource() == sequenceFeatures)
695 viewport.showSequenceFeatures(sequenceFeatures.getState());
696 alignPanel.seqPanel.seqCanvas.repaint();
698 else if (evt.getSource() == conservationMenuItem)
700 conservationMenuItem_actionPerformed();
702 else if (evt.getSource() == abovePIDThreshold)
704 abovePIDThreshold_actionPerformed();
706 else if (evt.getSource() == applyToAllGroups)
708 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
710 else if (evt.getSource() == autoCalculate)
712 viewport.autoCalculateConsensus = autoCalculate.getState();
714 else if (evt.getSource() == sortByTree)
716 viewport.sortByTree = sortByTree.getState();
718 else if (evt.getSource() == this.centreColumnLabelFlag)
720 centreColumnLabelFlag_stateChanged();
722 else if (evt.getSource() == this.followMouseOverFlag)
724 mouseOverFlag_stateChanged();
726 else if (evt.getSource() == showGroupConsensus)
728 showGroupConsensus_actionPerformed();
730 else if (evt.getSource() == showGroupConservation)
732 showGroupConservation_actionPerformed();
734 else if (evt.getSource() == showSequenceLogo)
736 showSequenceLogo_actionPerformed();
738 else if (evt.getSource() == normSequenceLogo)
740 normSequenceLogo_actionPerformed();
742 else if (evt.getSource() == showConsensusHistogram)
744 showConsensusHistogram_actionPerformed();
746 else if (evt.getSource() == applyAutoAnnotationSettings)
748 applyAutoAnnotationSettings_actionPerformed();
750 alignPanel.paintAlignment(true);
753 private void mouseOverFlag_stateChanged()
755 viewport.followHighlight = followMouseOverFlag.getState();
756 // TODO: could kick the scrollTo mechanism to reset view for current
760 private void centreColumnLabelFlag_stateChanged()
762 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
763 this.alignPanel.annotationPanel.repaint();
767 public void actionPerformed(ActionEvent evt)
769 Object source = evt.getSource();
771 if (source == inputText)
773 inputText_actionPerformed();
775 else if (source == loadTree)
777 loadTree_actionPerformed();
779 else if (source == loadApplication)
781 launchFullApplication();
783 else if (source == loadAnnotations)
787 else if (source == outputAnnotations)
789 outputAnnotations(true);
791 else if (source == outputFeatures)
793 outputFeatures(true, "Jalview");
795 else if (source == closeMenuItem)
797 closeMenuItem_actionPerformed();
799 else if (source == copy)
801 copy_actionPerformed();
803 else if (source == undoMenuItem)
805 undoMenuItem_actionPerformed();
807 else if (source == redoMenuItem)
809 redoMenuItem_actionPerformed();
811 else if (source == inputText)
813 inputText_actionPerformed();
815 else if (source == closeMenuItem)
817 closeMenuItem_actionPerformed();
819 else if (source == undoMenuItem)
821 undoMenuItem_actionPerformed();
823 else if (source == redoMenuItem)
825 redoMenuItem_actionPerformed();
827 else if (source == copy)
829 copy_actionPerformed();
831 else if (source == pasteNew)
833 pasteNew_actionPerformed();
835 else if (source == pasteThis)
837 pasteThis_actionPerformed();
839 else if (source == cut)
841 cut_actionPerformed();
843 else if (source == delete)
845 delete_actionPerformed();
847 else if (source == grpsFromSelection)
849 makeGrpsFromSelection_actionPerformed();
851 else if (source == deleteGroups)
853 deleteGroups_actionPerformed();
855 else if (source == selectAllSequenceMenuItem)
857 selectAllSequenceMenuItem_actionPerformed();
859 else if (source == deselectAllSequenceMenuItem)
861 deselectAllSequenceMenuItem_actionPerformed();
863 else if (source == invertSequenceMenuItem)
865 invertSequenceMenuItem_actionPerformed();
867 else if (source == invertColSel)
869 viewport.invertColumnSelection();
870 alignPanel.paintAlignment(true);
872 else if (source == remove2LeftMenuItem)
876 else if (source == remove2RightMenuItem)
878 trimAlignment(false);
880 else if (source == removeGappedColumnMenuItem)
882 removeGappedColumnMenuItem_actionPerformed();
884 else if (source == removeAllGapsMenuItem)
886 removeAllGapsMenuItem_actionPerformed();
888 else if (source == findMenuItem)
890 findMenuItem_actionPerformed();
892 else if (source == font)
894 new FontChooser(alignPanel);
896 else if (source == newView)
900 else if (source == showColumns)
902 viewport.showAllHiddenColumns();
903 alignPanel.paintAlignment(true);
905 else if (source == showSeqs)
907 viewport.showAllHiddenSeqs();
908 alignPanel.paintAlignment(true);
910 else if (source == hideColumns)
912 viewport.hideSelectedColumns();
913 alignPanel.paintAlignment(true);
915 else if (source == hideSequences
916 && viewport.getSelectionGroup() != null)
918 viewport.hideAllSelectedSeqs();
919 alignPanel.paintAlignment(true);
921 else if (source == hideAllButSelection)
923 toggleHiddenRegions(false, false);
924 alignPanel.paintAlignment(true);
926 else if (source == hideAllSelection)
928 SequenceGroup sg = viewport.getSelectionGroup();
929 viewport.expandColSelection(sg, false);
930 viewport.hideAllSelectedSeqs();
931 viewport.hideSelectedColumns();
932 alignPanel.paintAlignment(true);
934 else if (source == showAllHidden)
936 viewport.showAllHiddenColumns();
937 viewport.showAllHiddenSeqs();
938 alignPanel.paintAlignment(true);
940 else if (source == showGroupConsensus)
942 showGroupConsensus_actionPerformed();
944 else if (source == showGroupConservation)
946 showGroupConservation_actionPerformed();
948 else if (source == showSequenceLogo)
950 showSequenceLogo_actionPerformed();
952 else if (source == normSequenceLogo)
954 normSequenceLogo_actionPerformed();
956 else if (source == showConsensusHistogram)
958 showConsensusHistogram_actionPerformed();
960 else if (source == applyAutoAnnotationSettings)
962 applyAutoAnnotationSettings_actionPerformed();
964 else if (source == featureSettings)
966 new FeatureSettings(alignPanel);
968 else if (source == alProperties)
970 StringBuffer contents = new jalview.io.AlignmentProperties(
971 viewport.getAlignment()).formatAsString();
972 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
973 cap.setText(contents.toString());
974 Frame frame = new Frame();
976 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
977 + getTitle(), 400, 250);
979 else if (source == overviewMenuItem)
981 overviewMenuItem_actionPerformed();
983 else if (source == noColourmenuItem)
987 else if (source == clustalColour)
989 abovePIDThreshold.setState(false);
990 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
992 else if (source == zappoColour)
994 changeColour(new ZappoColourScheme());
996 else if (source == taylorColour)
998 changeColour(new TaylorColourScheme());
1000 else if (source == hydrophobicityColour)
1002 changeColour(new HydrophobicColourScheme());
1004 else if (source == helixColour)
1006 changeColour(new HelixColourScheme());
1008 else if (source == strandColour)
1010 changeColour(new StrandColourScheme());
1012 else if (source == turnColour)
1014 changeColour(new TurnColourScheme());
1016 else if (source == buriedColour)
1018 changeColour(new BuriedColourScheme());
1020 else if (source == nucleotideColour)
1022 changeColour(new NucleotideColourScheme());
1024 else if (source == purinePyrimidineColour)
1026 changeColour(new PurinePyrimidineColourScheme());
1028 else if (source == RNAHelixColour)
1030 new RNAHelicesColourChooser(viewport, alignPanel);
1032 else if (source == modifyPID)
1034 modifyPID_actionPerformed();
1036 else if (source == modifyConservation)
1038 modifyConservation_actionPerformed();
1040 else if (source == userDefinedColour)
1042 new UserDefinedColours(alignPanel, null);
1044 else if (source == PIDColour)
1046 changeColour(new PIDColourScheme());
1048 else if (source == BLOSUM62Colour)
1050 changeColour(new Blosum62ColourScheme());
1052 else if (source == tcoffeeColour)
1054 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1056 else if (source == annotationColour)
1058 new AnnotationColourChooser(viewport, alignPanel);
1060 else if (source == sortPairwiseMenuItem)
1062 sortPairwiseMenuItem_actionPerformed();
1064 else if (source == sortIDMenuItem)
1066 sortIDMenuItem_actionPerformed();
1068 else if (source == sortLengthMenuItem)
1070 sortLengthMenuItem_actionPerformed();
1072 else if (source == sortGroupMenuItem)
1074 sortGroupMenuItem_actionPerformed();
1076 else if (source == removeRedundancyMenuItem)
1078 removeRedundancyMenuItem_actionPerformed();
1080 else if (source == pairwiseAlignmentMenuItem)
1082 pairwiseAlignmentMenuItem_actionPerformed();
1084 else if (source == PCAMenuItem)
1086 PCAMenuItem_actionPerformed();
1088 else if (source == averageDistanceTreeMenuItem)
1090 averageDistanceTreeMenuItem_actionPerformed();
1092 else if (source == neighbourTreeMenuItem)
1094 neighbourTreeMenuItem_actionPerformed();
1096 else if (source == njTreeBlosumMenuItem)
1098 njTreeBlosumMenuItem_actionPerformed();
1100 else if (source == avDistanceTreeBlosumMenuItem)
1102 avTreeBlosumMenuItem_actionPerformed();
1104 else if (source == documentation)
1106 documentation_actionPerformed();
1108 else if (source == about)
1110 about_actionPerformed();
1115 public void inputText_actionPerformed()
1117 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1118 Frame frame = new Frame();
1120 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
1123 protected void outputText_actionPerformed(ActionEvent e)
1125 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1126 Frame frame = new Frame();
1128 jalview.bin.JalviewLite.addFrame(frame,
1129 "Alignment output - " + e.getActionCommand(), 600, 500);
1130 cap.setText(new AppletFormatAdapter().formatSequences(
1131 e.getActionCommand(), viewport.getAlignment(),
1132 viewport.showJVSuffix));
1135 public void loadAnnotations()
1137 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1138 cap.setText("Paste your features / annotations / T-coffee score file here.");
1139 cap.setAnnotationImport();
1140 Frame frame = new Frame();
1142 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1146 public String outputAnnotations(boolean displayTextbox)
1148 String annotation = new AnnotationFile().printAnnotations(
1149 viewport.showAnnotation ? viewport.getAlignment()
1150 .getAlignmentAnnotation() : null, viewport
1151 .getAlignment().getGroups(), ((Alignment) viewport
1152 .getAlignment()).alignmentProperties);
1156 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1157 Frame frame = new Frame();
1159 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1160 cap.setText(annotation);
1166 private Hashtable getDisplayedFeatureCols()
1168 if (alignPanel.getFeatureRenderer() != null
1169 && viewport.featuresDisplayed != null)
1171 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1172 Hashtable fcols = new Hashtable();
1173 Enumeration en = viewport.featuresDisplayed.keys();
1174 while (en.hasMoreElements())
1176 Object col = en.nextElement();
1177 fcols.put(col, fr.featureColours.get(col));
1184 public String outputFeatures(boolean displayTextbox, String format)
1187 if (format.equalsIgnoreCase("Jalview"))
1189 features = new FeaturesFile().printJalviewFormat(viewport
1190 .getAlignment().getSequencesArray(),
1191 getDisplayedFeatureCols());
1195 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1196 .getSequencesArray(), getDisplayedFeatureCols());
1201 boolean frimport = false;
1202 if (features == null || features.equals("No Features Visible"))
1204 features = "# No features visible - paste some and import them here.";
1208 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1211 cap.setAnnotationImport();
1213 Frame frame = new Frame();
1215 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1216 cap.setText(features);
1220 if (features == null)
1227 void launchFullApplication()
1229 StringBuffer url = new StringBuffer(jalviewServletURL);
1232 + appendProtocol(viewport.applet.getParameter("file")));
1234 if (viewport.applet.getParameter("features") != null)
1236 url.append("&features=");
1237 url.append(appendProtocol(viewport.applet.getParameter("features")));
1240 if (viewport.applet.getParameter("annotations") != null)
1242 url.append("&annotations=");
1243 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1246 if (viewport.applet.getParameter("jnetfile") != null)
1248 url.append("&annotations=");
1249 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1252 if (viewport.applet.getParameter("defaultColour") != null)
1254 url.append("&colour="
1255 + removeWhiteSpace(viewport.applet
1256 .getParameter("defaultColour")));
1259 if (viewport.applet.getParameter("userDefinedColour") != null)
1261 url.append("&colour="
1262 + removeWhiteSpace(viewport.applet
1263 .getParameter("userDefinedColour")));
1265 if (viewport.applet.getParameter("tree") != null)
1268 + appendProtocol(viewport.applet.getParameter("tree")));
1270 if (viewport.applet.getParameter("treeFile") != null)
1273 + appendProtocol(viewport.applet.getParameter("treeFile")));
1276 showURL(url.toString(), "FULL_APP");
1279 String removeWhiteSpace(String colour)
1281 StringBuffer sb = new StringBuffer();
1282 for (int i = 0; i < colour.length(); i++)
1284 if (Character.isWhitespace(colour.charAt(i)))
1290 sb.append(colour.charAt(i));
1294 return sb.toString();
1297 String appendProtocol(String url)
1302 url = URLEncoder.encode(url);
1305 * When we finally deprecate 1.1 compatibility, we can start to use
1306 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1307 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1308 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1309 * ex.printStackTrace(); }
1311 catch (java.net.MalformedURLException ex)
1313 url = viewport.applet.getCodeBase() + url;
1318 public void closeMenuItem_actionPerformed()
1320 PaintRefresher.RemoveComponent(alignPanel);
1321 if (alignPanel.seqPanel != null
1322 && alignPanel.seqPanel.seqCanvas != null)
1324 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1326 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1328 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1331 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1346 void updateEditMenuBar()
1349 if (viewport.historyList.size() > 0)
1351 undoMenuItem.setEnabled(true);
1352 CommandI command = (CommandI) viewport.historyList.peek();
1353 undoMenuItem.setLabel("Undo " + command.getDescription());
1357 undoMenuItem.setEnabled(false);
1358 undoMenuItem.setLabel("Undo");
1361 if (viewport.redoList.size() > 0)
1363 redoMenuItem.setEnabled(true);
1365 CommandI command = (CommandI) viewport.redoList.peek();
1366 redoMenuItem.setLabel("Redo " + command.getDescription());
1370 redoMenuItem.setEnabled(false);
1371 redoMenuItem.setLabel("Redo");
1378 public void addHistoryItem(CommandI command)
1380 if (command.getSize() > 0)
1382 viewport.historyList.push(command);
1383 viewport.redoList.removeAllElements();
1384 updateEditMenuBar();
1385 viewport.updateHiddenColumns();
1390 * TODO: JAL-1104 DOCUMENT ME!
1395 protected void undoMenuItem_actionPerformed()
1397 if (viewport.historyList.size() < 1)
1402 CommandI command = (CommandI) viewport.historyList.pop();
1403 viewport.redoList.push(command);
1404 command.undoCommand(null);
1406 AlignViewport originalSource = getOriginatingSource(command);
1408 if (originalSource != viewport)
1411 .println("Warning: Viewport object mismatch whilst undoing");
1413 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1414 // viewport.getColumnSelection().getHiddenColumns()
1416 updateEditMenuBar();
1417 originalSource.firePropertyChange("alignment", null, originalSource
1418 .getAlignment().getSequences());
1422 * TODO: JAL-1104 DOCUMENT ME!
1427 protected void redoMenuItem_actionPerformed()
1429 if (viewport.redoList.size() < 1)
1434 CommandI command = (CommandI) viewport.redoList.pop();
1435 viewport.historyList.push(command);
1436 command.doCommand(null);
1438 AlignViewport originalSource = getOriginatingSource(command);
1440 if (originalSource != viewport)
1443 .println("Warning: Viewport object mismatch whilst re-doing");
1445 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1446 // viewport.getColumnSelection().getHiddenColumns()
1449 updateEditMenuBar();
1450 originalSource.firePropertyChange("alignment", null, originalSource
1451 .getAlignment().getSequences());
1454 AlignViewport getOriginatingSource(CommandI command)
1456 AlignViewport originalSource = null;
1457 // For sequence removal and addition, we need to fire
1458 // the property change event FROM the viewport where the
1459 // original alignment was altered
1460 AlignmentI al = null;
1461 if (command instanceof EditCommand)
1463 EditCommand editCommand = (EditCommand) command;
1464 al = editCommand.getAlignment();
1465 Vector comps = (Vector) PaintRefresher.components.get(viewport
1466 .getSequenceSetId());
1467 for (int i = 0; i < comps.size(); i++)
1469 if (comps.elementAt(i) instanceof AlignmentPanel)
1471 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1473 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1480 if (originalSource == null)
1482 // The original view is closed, we must validate
1483 // the current view against the closed view first
1486 PaintRefresher.validateSequences(al, viewport.getAlignment());
1489 originalSource = viewport;
1492 return originalSource;
1495 public void moveSelectedSequences(boolean up)
1497 SequenceGroup sg = viewport.getSelectionGroup();
1502 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1503 up ? null : viewport.getHiddenRepSequences(), up);
1504 alignPanel.paintAlignment(true);
1507 synchronized void slideSequences(boolean right, int size)
1509 List<SequenceI> sg = new Vector<SequenceI>();
1510 if (viewport.cursorMode)
1512 sg.add(viewport.getAlignment().getSequenceAt(
1513 alignPanel.seqPanel.seqCanvas.cursorY));
1515 else if (viewport.getSelectionGroup() != null
1516 && viewport.getSelectionGroup().getSize() != viewport
1517 .getAlignment().getHeight())
1519 sg = viewport.getSelectionGroup().getSequences(
1520 viewport.getHiddenRepSequences());
1528 Vector<SequenceI> invertGroup = new Vector();
1530 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1532 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1533 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1536 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1538 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1540 for (int i = 0; i < invertGroup.size(); i++)
1541 seqs2[i] = invertGroup.elementAt(i);
1543 SlideSequencesCommand ssc;
1545 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1546 size, viewport.getGapCharacter());
1548 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1549 size, viewport.getGapCharacter());
1551 int groupAdjustment = 0;
1552 if (ssc.getGapsInsertedBegin() && right)
1554 if (viewport.cursorMode)
1555 alignPanel.seqPanel.moveCursor(size, 0);
1557 groupAdjustment = size;
1559 else if (!ssc.getGapsInsertedBegin() && !right)
1561 if (viewport.cursorMode)
1562 alignPanel.seqPanel.moveCursor(-size, 0);
1564 groupAdjustment = -size;
1567 if (groupAdjustment != 0)
1569 viewport.getSelectionGroup().setStartRes(
1570 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1571 viewport.getSelectionGroup().setEndRes(
1572 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1575 boolean appendHistoryItem = false;
1576 if (viewport.historyList != null && viewport.historyList.size() > 0
1577 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1579 appendHistoryItem = ssc
1580 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1584 if (!appendHistoryItem)
1585 addHistoryItem(ssc);
1590 static StringBuffer copiedSequences;
1592 static Vector copiedHiddenColumns;
1594 protected void copy_actionPerformed()
1596 if (viewport.getSelectionGroup() == null)
1601 SequenceGroup sg = viewport.getSelectionGroup();
1602 copiedSequences = new StringBuffer();
1603 Hashtable orderedSeqs = new Hashtable();
1604 for (int i = 0; i < sg.getSize(); i++)
1606 SequenceI seq = sg.getSequenceAt(i);
1607 int index = viewport.getAlignment().findIndex(seq);
1608 orderedSeqs.put(index + "", seq);
1611 int index = 0, startRes, endRes;
1614 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1616 copiedHiddenColumns = new Vector();
1617 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1618 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1621 int[] region = (int[]) viewport.getColumnSelection()
1622 .getHiddenColumns().elementAt(i);
1624 copiedHiddenColumns.addElement(new int[]
1625 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1630 copiedHiddenColumns = null;
1633 for (int i = 0; i < sg.getSize(); i++)
1635 SequenceI seq = null;
1639 if (orderedSeqs.containsKey(index + ""))
1641 seq = (SequenceI) orderedSeqs.get(index + "");
1653 // Returns residue following index if gap
1654 startRes = seq.findPosition(sg.getStartRes());
1657 // Need to find the residue preceeding index if gap
1660 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1662 ch = seq.getCharAt(j);
1663 if (!jalview.util.Comparison.isGap((ch)))
1671 endRes += seq.getStart() - 1;
1674 copiedSequences.append(seq.getName()
1680 + seq.getSequenceAsString(sg.getStartRes(),
1681 sg.getEndRes() + 1) + "\n");
1686 protected void pasteNew_actionPerformed()
1691 protected void pasteThis_actionPerformed()
1696 void paste(boolean newAlignment)
1701 if (copiedSequences == null)
1706 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1707 Vector seqs = new Vector();
1708 while (st.hasMoreElements())
1710 String name = st.nextToken();
1711 int start = Integer.parseInt(st.nextToken());
1712 int end = Integer.parseInt(st.nextToken());
1713 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1715 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1716 for (int i = 0; i < seqs.size(); i++)
1718 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1723 String newtitle = new String("Copied sequences");
1724 if (getTitle().startsWith("Copied sequences"))
1726 newtitle = getTitle();
1730 newtitle = newtitle.concat("- from " + getTitle());
1732 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1733 viewport.applet, newtitle, false);
1734 if (copiedHiddenColumns != null)
1736 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1738 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1739 af.viewport.hideColumns(region[0], region[1]);
1743 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1748 addSequences(newSeqs);
1751 } catch (Exception ex)
1753 } // could be anything being pasted in here
1757 void addSequences(SequenceI[] seqs)
1759 for (int i = 0; i < seqs.length; i++)
1761 viewport.getAlignment().addSequence(seqs[i]);
1765 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1766 seqs, 0, viewport.getAlignment().getWidth(),
1767 viewport.getAlignment()));
1769 viewport.setEndSeq(viewport.getAlignment().getHeight());
1770 viewport.getAlignment().getWidth();
1771 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1776 protected void cut_actionPerformed()
1778 copy_actionPerformed();
1779 delete_actionPerformed();
1782 protected void delete_actionPerformed()
1785 SequenceGroup sg = viewport.getSelectionGroup();
1791 Vector seqs = new Vector();
1793 for (int i = 0; i < sg.getSize(); i++)
1795 seq = sg.getSequenceAt(i);
1796 seqs.addElement(seq);
1799 // If the cut affects all sequences, remove highlighted columns
1800 if (sg.getSize() == viewport.getAlignment().getHeight())
1802 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1803 sg.getEndRes() + 1);
1806 SequenceI[] cut = new SequenceI[seqs.size()];
1807 for (int i = 0; i < seqs.size(); i++)
1809 cut[i] = (SequenceI) seqs.elementAt(i);
1813 * //ADD HISTORY ITEM
1815 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1816 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1817 viewport.getAlignment()));
1819 viewport.setSelectionGroup(null);
1820 viewport.getAlignment().deleteGroup(sg);
1822 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1825 if (viewport.getAlignment().getHeight() < 1)
1827 this.setVisible(false);
1829 viewport.sendSelection();
1833 * group consensus toggled
1836 protected void showGroupConsensus_actionPerformed()
1838 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1839 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1844 * group conservation toggled.
1846 protected void showGroupConservation_actionPerformed()
1848 viewport.setShowGroupConservation(showGroupConservation.getState());
1849 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1856 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1857 * .event.ActionEvent)
1859 protected void showConsensusHistogram_actionPerformed()
1861 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1869 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1870 * .event.ActionEvent)
1872 protected void showSequenceLogo_actionPerformed()
1874 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1878 protected void normSequenceLogo_actionPerformed()
1880 showSequenceLogo.setState(true);
1881 viewport.setShowSequenceLogo(true);
1882 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1883 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1886 protected void applyAutoAnnotationSettings_actionPerformed()
1888 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1891 protected void makeGrpsFromSelection_actionPerformed()
1893 if (viewport.getSelectionGroup() != null)
1895 SequenceGroup[] gps = jalview.analysis.Grouping.makeGroupsFrom(
1896 viewport.getSequenceSelection(),
1897 viewport.getAlignmentView(true).getSequenceStrings(
1898 viewport.getGapCharacter()), viewport.getAlignment()
1900 viewport.getAlignment().deleteAllGroups();
1901 viewport.sequenceColours = null;
1902 viewport.setSelectionGroup(null);
1903 // set view properties for each group
1904 for (int g = 0; g < gps.length; g++)
1906 // gps[g].setShowunconserved(viewport.getShowUnconserved());
1907 gps[g].setshowSequenceLogo(viewport.isShowSequenceLogo());
1908 viewport.getAlignment().addGroup(gps[g]);
1909 Color col = new Color((int) (Math.random() * 255),
1910 (int) (Math.random() * 255), (int) (Math.random() * 255));
1911 col = col.brighter();
1912 for (SequenceI sq : gps[g].getSequences(null))
1913 viewport.setSequenceColour(sq, col);
1915 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1916 alignPanel.updateAnnotation();
1917 alignPanel.paintAlignment(true);
1921 protected void deleteGroups_actionPerformed()
1923 viewport.getAlignment().deleteAllGroups();
1924 viewport.sequenceColours = null;
1925 viewport.setSelectionGroup(null);
1927 alignPanel.paintAlignment(true);
1930 public void selectAllSequenceMenuItem_actionPerformed()
1932 SequenceGroup sg = new SequenceGroup();
1933 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1935 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1937 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1938 viewport.setSelectionGroup(sg);
1939 alignPanel.paintAlignment(true);
1940 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1941 viewport.sendSelection();
1944 public void deselectAllSequenceMenuItem_actionPerformed()
1946 if (viewport.cursorMode)
1948 alignPanel.seqPanel.keyboardNo1 = null;
1949 alignPanel.seqPanel.keyboardNo2 = null;
1951 viewport.setSelectionGroup(null);
1952 viewport.getColumnSelection().clear();
1953 viewport.setSelectionGroup(null);
1954 alignPanel.idPanel.idCanvas.searchResults = null;
1955 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1956 alignPanel.paintAlignment(true);
1957 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1958 viewport.sendSelection();
1961 public void invertSequenceMenuItem_actionPerformed()
1963 SequenceGroup sg = viewport.getSelectionGroup();
1964 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1966 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1969 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1970 viewport.sendSelection();
1973 public void invertColSel_actionPerformed()
1975 viewport.invertColumnSelection();
1976 alignPanel.paintAlignment(true);
1977 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1978 viewport.sendSelection();
1981 void trimAlignment(boolean trimLeft)
1983 ColumnSelection colSel = viewport.getColumnSelection();
1986 if (colSel.size() > 0)
1990 column = colSel.getMin();
1994 column = colSel.getMax();
1998 if (viewport.getSelectionGroup() != null)
2000 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2001 viewport.getHiddenRepSequences());
2005 seqs = viewport.getAlignment().getSequencesArray();
2008 TrimRegionCommand trimRegion;
2011 trimRegion = new TrimRegionCommand("Remove Left",
2012 TrimRegionCommand.TRIM_LEFT, seqs, column,
2013 viewport.getAlignment(), viewport.getColumnSelection(),
2014 viewport.getSelectionGroup());
2015 viewport.setStartRes(0);
2019 trimRegion = new TrimRegionCommand("Remove Right",
2020 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2021 viewport.getAlignment(), viewport.getColumnSelection(),
2022 viewport.getSelectionGroup());
2025 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2027 addHistoryItem(trimRegion);
2029 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2031 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2032 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2034 viewport.getAlignment().deleteGroup(sg);
2038 viewport.firePropertyChange("alignment", null, viewport
2039 .getAlignment().getSequences());
2043 public void removeGappedColumnMenuItem_actionPerformed()
2045 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2048 if (viewport.getSelectionGroup() != null)
2050 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2051 viewport.getHiddenRepSequences());
2052 start = viewport.getSelectionGroup().getStartRes();
2053 end = viewport.getSelectionGroup().getEndRes();
2057 seqs = viewport.getAlignment().getSequencesArray();
2060 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2061 "Remove Gapped Columns", seqs, start, end,
2062 viewport.getAlignment());
2064 addHistoryItem(removeGapCols);
2066 statusBar.setText("Removed " + removeGapCols.getSize()
2067 + " empty columns.");
2069 // This is to maintain viewport position on first residue
2070 // of first sequence
2071 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2072 int startRes = seq.findPosition(viewport.startRes);
2073 // ShiftList shifts;
2074 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2075 // edit.alColumnChanges=shifts.getInverse();
2076 // if (viewport.hasHiddenColumns)
2077 // viewport.getColumnSelection().compensateForEdits(shifts);
2078 viewport.setStartRes(seq.findIndex(startRes) - 1);
2079 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2084 public void removeAllGapsMenuItem_actionPerformed()
2086 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2089 if (viewport.getSelectionGroup() != null)
2091 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2092 viewport.getHiddenRepSequences());
2093 start = viewport.getSelectionGroup().getStartRes();
2094 end = viewport.getSelectionGroup().getEndRes();
2098 seqs = viewport.getAlignment().getSequencesArray();
2101 // This is to maintain viewport position on first residue
2102 // of first sequence
2103 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2104 int startRes = seq.findPosition(viewport.startRes);
2106 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2107 viewport.getAlignment()));
2109 viewport.setStartRes(seq.findIndex(startRes) - 1);
2111 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2116 public void findMenuItem_actionPerformed()
2118 new Finder(alignPanel);
2122 * create a new view derived from the current view
2125 * @return frame for the new view
2127 public AlignFrame newView(String viewtitle)
2130 if (viewport.hasHiddenRows())
2132 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2133 .getFullAlignment().getSequencesArray());
2137 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2140 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2142 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2144 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2146 newal.addAnnotation(viewport.getAlignment()
2147 .getAlignmentAnnotation()[i]);
2152 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2154 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2155 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2156 PaintRefresher.Register(newaf.alignPanel,
2157 newaf.alignPanel.av.getSequenceSetId());
2159 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2160 newaf.alignPanel.av.getSequenceSetId());
2161 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2162 newaf.alignPanel.av.getSequenceSetId());
2164 Vector comps = (Vector) PaintRefresher.components.get(viewport
2165 .getSequenceSetId());
2167 for (int i = 0; i < comps.size(); i++)
2169 if (comps.elementAt(i) instanceof AlignmentPanel)
2175 String title = new String(this.getTitle());
2176 if (viewtitle != null)
2178 title = viewtitle + " ( " + title + ")";
2182 if (title.indexOf("(View") > -1)
2184 title = title.substring(0, title.indexOf("(View"));
2186 title += "(View " + viewSize + ")";
2189 newaf.setTitle(title.toString());
2191 newaf.viewport.historyList = viewport.historyList;
2192 newaf.viewport.redoList = viewport.redoList;
2198 * @return list of feature groups on the view
2200 public String[] getFeatureGroups()
2202 FeatureRenderer fr = null;
2203 if (alignPanel != null
2204 && (fr = alignPanel.getFeatureRenderer()) != null)
2206 return fr.getGroups();
2212 * get sequence feature groups that are hidden or shown
2218 public String[] getFeatureGroupsOfState(boolean visible)
2220 FeatureRenderer fr = null;
2221 if (alignPanel != null
2222 && (fr = alignPanel.getFeatureRenderer()) != null)
2224 return fr.getGroups(visible);
2230 * Change the display state for the given feature groups
2233 * list of group strings
2235 * visible or invisible
2237 public void setFeatureGroupState(String[] groups, boolean state)
2239 FeatureRenderer fr = null;
2240 this.sequenceFeatures.setState(true);
2241 viewport.showSequenceFeatures(true);
2242 if (alignPanel != null
2243 && (fr = alignPanel.getFeatureRenderer()) != null)
2245 fr.setGroupState(groups, state);
2246 alignPanel.seqPanel.seqCanvas.repaint();
2247 if (alignPanel.overviewPanel != null)
2249 alignPanel.overviewPanel.updateOverviewImage();
2254 public void seqLimits_itemStateChanged()
2256 viewport.setShowJVSuffix(seqLimits.getState());
2257 alignPanel.fontChanged();
2258 alignPanel.paintAlignment(true);
2261 protected void colourTextMenuItem_actionPerformed()
2263 viewport.setColourText(colourTextMenuItem.getState());
2264 alignPanel.paintAlignment(true);
2267 protected void displayNonconservedMenuItem_actionPerformed()
2269 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2270 alignPanel.paintAlignment(true);
2273 protected void wrapMenuItem_actionPerformed()
2275 viewport.setWrapAlignment(wrapMenuItem.getState());
2276 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2277 scaleAbove.setEnabled(wrapMenuItem.getState());
2278 scaleLeft.setEnabled(wrapMenuItem.getState());
2279 scaleRight.setEnabled(wrapMenuItem.getState());
2280 alignPanel.paintAlignment(true);
2283 public void overviewMenuItem_actionPerformed()
2285 if (alignPanel.overviewPanel != null)
2290 Frame frame = new Frame();
2291 OverviewPanel overview = new OverviewPanel(alignPanel);
2292 frame.add(overview);
2293 // +50 must allow for applet frame window
2294 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2295 overview.getPreferredSize().width,
2296 overview.getPreferredSize().height + 50);
2299 final AlignmentPanel ap = alignPanel;
2300 frame.addWindowListener(new WindowAdapter()
2303 public void windowClosing(WindowEvent e)
2307 ap.setOverviewPanel(null);
2312 alignPanel.setOverviewPanel(overview);
2316 void changeColour(ColourSchemeI cs)
2322 if (viewport.getAbovePIDThreshold())
2324 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2327 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2329 viewport.setGlobalColourScheme(cs);
2333 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2336 if (viewport.getConservationSelected())
2339 Alignment al = (Alignment) viewport.getAlignment();
2340 Conservation c = new Conservation("All",
2341 ResidueProperties.propHash, 3, al.getSequences(), 0,
2345 c.verdict(false, viewport.getConsPercGaps());
2347 cs.setConservation(c);
2349 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2355 cs.setConservation(null);
2358 cs.setConsensus(viewport.getSequenceConsensusHash());
2361 viewport.setGlobalColourScheme(cs);
2363 if (alignPanel.getOverviewPanel() != null)
2365 alignPanel.getOverviewPanel().updateOverviewImage();
2368 jalview.structure.StructureSelectionManager
2369 .getStructureSelectionManager(viewport.applet)
2370 .sequenceColoursChanged(alignPanel);
2372 alignPanel.paintAlignment(true);
2375 protected void modifyPID_actionPerformed()
2377 if (viewport.getAbovePIDThreshold()
2378 && viewport.getGlobalColourScheme() != null)
2380 SliderPanel.setPIDSliderSource(alignPanel,
2381 viewport.getGlobalColourScheme(), "Background");
2382 SliderPanel.showPIDSlider();
2386 protected void modifyConservation_actionPerformed()
2388 if (viewport.getConservationSelected()
2389 && viewport.getGlobalColourScheme() != null)
2391 SliderPanel.setConservationSlider(alignPanel,
2392 viewport.getGlobalColourScheme(), "Background");
2393 SliderPanel.showConservationSlider();
2397 protected void conservationMenuItem_actionPerformed()
2399 viewport.setConservationSelected(conservationMenuItem.getState());
2401 viewport.setAbovePIDThreshold(false);
2402 abovePIDThreshold.setState(false);
2404 changeColour(viewport.getGlobalColourScheme());
2406 modifyConservation_actionPerformed();
2409 public void abovePIDThreshold_actionPerformed()
2411 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2413 conservationMenuItem.setState(false);
2414 viewport.setConservationSelected(false);
2416 changeColour(viewport.getGlobalColourScheme());
2418 modifyPID_actionPerformed();
2421 public void sortPairwiseMenuItem_actionPerformed()
2423 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2424 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2425 .getAlignment().getSequenceAt(0), null);
2427 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2428 viewport.getAlignment()));
2429 alignPanel.paintAlignment(true);
2432 public void sortIDMenuItem_actionPerformed()
2434 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2435 AlignmentSorter.sortByID(viewport.getAlignment());
2436 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2437 viewport.getAlignment()));
2438 alignPanel.paintAlignment(true);
2441 public void sortLengthMenuItem_actionPerformed()
2443 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2444 AlignmentSorter.sortByLength(viewport.getAlignment());
2445 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2446 viewport.getAlignment()));
2447 alignPanel.paintAlignment(true);
2450 public void sortGroupMenuItem_actionPerformed()
2452 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2453 AlignmentSorter.sortByGroup(viewport.getAlignment());
2454 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2455 viewport.getAlignment()));
2456 alignPanel.paintAlignment(true);
2460 public void removeRedundancyMenuItem_actionPerformed()
2462 new RedundancyPanel(alignPanel);
2465 public void pairwiseAlignmentMenuItem_actionPerformed()
2467 if (viewport.getSelectionGroup() != null
2468 && viewport.getSelectionGroup().getSize() > 1)
2470 Frame frame = new Frame();
2471 frame.add(new PairwiseAlignPanel(alignPanel));
2472 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2477 public void PCAMenuItem_actionPerformed()
2479 // are the sequences aligned?
2480 if (!viewport.getAlignment().isAligned(false))
2483 int Width = viewport.getAlignment().getWidth();
2485 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487 current = viewport.getAlignment().getSequenceAt(i);
2489 if (current.getLength() < Width)
2491 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2494 alignPanel.paintAlignment(true);
2497 if ((viewport.getSelectionGroup() != null
2498 && viewport.getSelectionGroup().getSize() < 4 && viewport
2499 .getSelectionGroup().getSize() > 0)
2500 || viewport.getAlignment().getHeight() < 4)
2507 new PCAPanel(viewport);
2508 } catch (java.lang.OutOfMemoryError ex)
2514 public void averageDistanceTreeMenuItem_actionPerformed()
2516 NewTreePanel("AV", "PID", "Average distance tree using PID");
2519 public void neighbourTreeMenuItem_actionPerformed()
2521 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2524 protected void njTreeBlosumMenuItem_actionPerformed()
2526 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2529 protected void avTreeBlosumMenuItem_actionPerformed()
2531 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2534 void NewTreePanel(String type, String pwType, String title)
2536 // are the sequences aligned?
2537 if (!viewport.getAlignment().isAligned(false))
2540 int Width = viewport.getAlignment().getWidth();
2542 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2544 current = viewport.getAlignment().getSequenceAt(i);
2546 if (current.getLength() < Width)
2548 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2551 alignPanel.paintAlignment(true);
2555 if ((viewport.getSelectionGroup() != null && viewport
2556 .getSelectionGroup().getSize() > 1)
2557 || (viewport.getAlignment().getHeight() > 1))
2559 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2561 addTreeMenuItem(tp, title);
2563 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2567 void loadTree_actionPerformed()
2569 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2570 cap.setText("Paste your Newick tree file here.");
2571 cap.setTreeImport();
2572 Frame frame = new Frame();
2574 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2577 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2579 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2580 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2581 addTreeMenuItem(tp, treeFile);
2585 * sort the alignment using the given treePanel
2588 * tree used to sort view
2590 * string used for undo event name
2592 public void sortByTree(TreePanel treePanel, String title)
2594 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2596 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2597 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2598 // HistoryItem.SORT));
2599 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2600 viewport.getAlignment()));
2601 alignPanel.paintAlignment(true);
2605 * Do any automatic reordering of the alignment and add the necessary bits to
2606 * the menu structure for the new tree
2611 protected void addTreeMenuItem(final TreePanel treePanel,
2614 final MenuItem item = new MenuItem(title);
2615 sortByTreeMenu.add(item);
2616 item.addActionListener(new java.awt.event.ActionListener()
2619 public void actionPerformed(ActionEvent evt)
2621 sortByTree(treePanel, title); // treePanel.getTitle());
2625 treePanel.addWindowListener(new WindowAdapter()
2628 public void windowOpened(WindowEvent e)
2630 if (viewport.sortByTree)
2632 sortByTree(treePanel, title);
2634 super.windowOpened(e);
2638 public void windowClosing(WindowEvent e)
2640 sortByTreeMenu.remove(item);
2645 public boolean sortBy(AlignmentOrder alorder, String undoname)
2647 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2648 if (viewport.applet.debug)
2650 System.err.println("Sorting " + alorder.getOrder().size()
2651 + " in alignment '" + getTitle() + "'");
2653 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2654 if (undoname != null)
2656 addHistoryItem(new OrderCommand(undoname, oldOrder,
2657 viewport.getAlignment()));
2659 alignPanel.paintAlignment(true);
2663 protected void documentation_actionPerformed()
2665 alignPanel.av.applet.openJalviewHelpUrl();
2668 protected void about_actionPerformed()
2671 class AboutPanel extends Canvas
2677 public AboutPanel(String version, String builddate)
2679 this.version = version;
2680 this.builddate = builddate;
2684 public void paint(Graphics g)
2686 g.setColor(Color.white);
2687 g.fillRect(0, 0, getSize().width, getSize().height);
2688 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2689 FontMetrics fm = g.getFontMetrics();
2690 int fh = fm.getHeight();
2692 g.setColor(Color.black);
2693 // TODO: update this text for each release or centrally store it for
2694 // lite and application
2695 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2696 g.drawString("JalviewLite - Release " + version, x, y += fh);
2697 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2698 g.drawString("Build date: " + builddate, x, y += fh);
2699 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2701 "Authors: Jim Procter, Andrew Waterhouse, Michele Clamp, James Cuff, Steve Searle,",
2703 g.drawString("David Martin & Geoff Barton.", x + 50, y += fh);
2705 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2708 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2710 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2712 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2715 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2717 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2722 Frame frame = new Frame();
2723 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2725 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2729 public void showURL(String url, String target)
2731 if (viewport.applet == null)
2733 System.out.println("Not running as applet - no browser available.");
2737 viewport.applet.showURL(url, target);
2741 // ////////////////////////////////////////////////////////////////////////////////
2742 // JBuilder Graphics here
2744 MenuBar alignFrameMenuBar = new MenuBar();
2746 Menu fileMenu = new Menu("File");
2748 MenuItem loadApplication = new MenuItem("View in Full Application");
2750 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2752 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2754 MenuItem outputFeatures = new MenuItem("Export Features ...");
2756 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2758 MenuItem closeMenuItem = new MenuItem("Close");
2760 Menu editMenu = new Menu("Edit");
2762 Menu viewMenu = new Menu("View");
2764 Menu colourMenu = new Menu("Colour");
2766 Menu calculateMenu = new Menu("Calculate");
2768 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2770 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2772 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2774 MenuItem remove2LeftMenuItem = new MenuItem();
2776 MenuItem remove2RightMenuItem = new MenuItem();
2778 MenuItem removeGappedColumnMenuItem = new MenuItem();
2780 MenuItem removeAllGapsMenuItem = new MenuItem();
2782 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2784 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2786 MenuItem sortPairwiseMenuItem = new MenuItem();
2788 MenuItem sortIDMenuItem = new MenuItem();
2790 MenuItem sortLengthMenuItem = new MenuItem();
2792 MenuItem sortGroupMenuItem = new MenuItem();
2794 MenuItem removeRedundancyMenuItem = new MenuItem();
2796 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2798 MenuItem PCAMenuItem = new MenuItem();
2800 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2802 MenuItem neighbourTreeMenuItem = new MenuItem();
2804 BorderLayout borderLayout1 = new BorderLayout();
2806 public Label statusBar = new Label();
2808 Menu outputTextboxMenu = new Menu();
2810 MenuItem clustalColour = new MenuItem();
2812 MenuItem zappoColour = new MenuItem();
2814 MenuItem taylorColour = new MenuItem();
2816 MenuItem hydrophobicityColour = new MenuItem();
2818 MenuItem helixColour = new MenuItem();
2820 MenuItem strandColour = new MenuItem();
2822 MenuItem turnColour = new MenuItem();
2824 MenuItem buriedColour = new MenuItem();
2826 MenuItem purinePyrimidineColour = new MenuItem();
2828 MenuItem RNAHelixColour = new MenuItem();
2830 MenuItem userDefinedColour = new MenuItem();
2832 MenuItem PIDColour = new MenuItem();
2834 MenuItem BLOSUM62Colour = new MenuItem();
2836 MenuItem tcoffeeColour = new MenuItem();
2838 MenuItem njTreeBlosumMenuItem = new MenuItem();
2840 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2842 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2844 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2846 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2848 MenuItem alProperties = new MenuItem("Alignment Properties...");
2850 MenuItem overviewMenuItem = new MenuItem();
2852 MenuItem undoMenuItem = new MenuItem();
2854 MenuItem redoMenuItem = new MenuItem();
2856 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2858 MenuItem noColourmenuItem = new MenuItem();
2860 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2862 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2864 MenuItem findMenuItem = new MenuItem();
2866 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2868 MenuItem nucleotideColour = new MenuItem();
2870 MenuItem deleteGroups = new MenuItem();
2872 MenuItem grpsFromSelection = new MenuItem();
2874 MenuItem delete = new MenuItem();
2876 MenuItem copy = new MenuItem();
2878 MenuItem cut = new MenuItem();
2880 Menu pasteMenu = new Menu();
2882 MenuItem pasteNew = new MenuItem();
2884 MenuItem pasteThis = new MenuItem();
2886 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2888 MenuItem font = new MenuItem();
2890 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2892 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2894 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2896 MenuItem modifyPID = new MenuItem();
2898 MenuItem modifyConservation = new MenuItem();
2900 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2901 "Autocalculate Consensus", true);
2903 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2904 "Sort Alignment With New Tree", true);
2906 Menu sortByTreeMenu = new Menu();
2908 Menu sort = new Menu();
2910 Menu calculate = new Menu();
2912 MenuItem inputText = new MenuItem();
2914 Menu helpMenu = new Menu();
2916 MenuItem documentation = new MenuItem();
2918 MenuItem about = new MenuItem();
2920 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2922 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2924 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2926 Menu autoAnnMenu = new Menu();
2928 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2930 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2932 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2934 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2936 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2938 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2940 private void jbInit() throws Exception
2943 setMenuBar(alignFrameMenuBar);
2947 // dynamically fill save as menu with available formats
2948 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2951 item = new MenuItem(
2952 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2954 item.addActionListener(new java.awt.event.ActionListener()
2957 public void actionPerformed(ActionEvent e)
2959 outputText_actionPerformed(e);
2963 outputTextboxMenu.add(item);
2965 closeMenuItem.addActionListener(this);
2966 loadApplication.addActionListener(this);
2968 loadTree.addActionListener(this);
2969 loadAnnotations.addActionListener(this);
2970 outputFeatures.addActionListener(this);
2971 outputAnnotations.addActionListener(this);
2972 selectAllSequenceMenuItem.addActionListener(this);
2973 deselectAllSequenceMenuItem.addActionListener(this);
2974 invertSequenceMenuItem.addActionListener(this);
2975 remove2LeftMenuItem.setLabel("Remove Left");
2976 remove2LeftMenuItem.addActionListener(this);
2977 remove2RightMenuItem.setLabel("Remove Right");
2978 remove2RightMenuItem.addActionListener(this);
2979 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2980 removeGappedColumnMenuItem.addActionListener(this);
2981 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2982 removeAllGapsMenuItem.addActionListener(this);
2983 viewBoxesMenuItem.setLabel("Boxes");
2984 viewBoxesMenuItem.setState(true);
2985 viewBoxesMenuItem.addItemListener(this);
2986 viewTextMenuItem.setLabel("Text");
2987 viewTextMenuItem.setState(true);
2988 viewTextMenuItem.addItemListener(this);
2989 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2990 sortPairwiseMenuItem.addActionListener(this);
2991 sortIDMenuItem.setLabel("by ID");
2992 sortIDMenuItem.addActionListener(this);
2993 sortLengthMenuItem.setLabel("by Length");
2994 sortLengthMenuItem.addActionListener(this);
2995 sortGroupMenuItem.setLabel("by Group");
2996 sortGroupMenuItem.addActionListener(this);
2997 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2998 removeRedundancyMenuItem.addActionListener(this);
2999 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
3000 pairwiseAlignmentMenuItem.addActionListener(this);
3001 PCAMenuItem.setLabel("Principal Component Analysis");
3002 PCAMenuItem.addActionListener(this);
3003 averageDistanceTreeMenuItem
3004 .setLabel("Average Distance Using % Identity");
3005 averageDistanceTreeMenuItem.addActionListener(this);
3006 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
3007 neighbourTreeMenuItem.addActionListener(this);
3008 statusBar.setBackground(Color.white);
3009 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3010 statusBar.setText("Status bar");
3011 outputTextboxMenu.setLabel("Output to Textbox");
3012 clustalColour.setLabel("Clustalx");
3014 clustalColour.addActionListener(this);
3015 zappoColour.setLabel("Zappo");
3016 zappoColour.addActionListener(this);
3017 taylorColour.setLabel("Taylor");
3018 taylorColour.addActionListener(this);
3019 hydrophobicityColour.setLabel("Hydrophobicity");
3020 hydrophobicityColour.addActionListener(this);
3021 helixColour.setLabel("Helix Propensity");
3022 helixColour.addActionListener(this);
3023 strandColour.setLabel("Strand Propensity");
3024 strandColour.addActionListener(this);
3025 turnColour.setLabel("Turn Propensity");
3026 turnColour.addActionListener(this);
3027 buriedColour.setLabel("Buried Index");
3028 buriedColour.addActionListener(this);
3029 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
3030 purinePyrimidineColour.addActionListener(this);
3031 RNAHelixColour.setLabel("by RNA Helices");
3032 RNAHelixColour.addActionListener(this);
3033 userDefinedColour.setLabel("User Defined...");
3034 userDefinedColour.addActionListener(this);
3035 PIDColour.setLabel("Percentage Identity");
3036 PIDColour.addActionListener(this);
3037 BLOSUM62Colour.setLabel("BLOSUM62 Score");
3038 BLOSUM62Colour.addActionListener(this);
3039 tcoffeeColour.setLabel("T-Coffee Scores");
3040 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3042 tcoffeeColour.addActionListener(this);
3043 avDistanceTreeBlosumMenuItem
3044 .setLabel("Average Distance Using BLOSUM62");
3045 avDistanceTreeBlosumMenuItem.addActionListener(this);
3046 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
3047 njTreeBlosumMenuItem.addActionListener(this);
3048 annotationPanelMenuItem.setLabel("Show Annotations");
3049 annotationPanelMenuItem.addItemListener(this);
3050 colourTextMenuItem.setLabel("Colour Text");
3051 colourTextMenuItem.addItemListener(this);
3052 displayNonconservedMenuItem.setLabel("Show nonconserved");
3053 displayNonconservedMenuItem.addItemListener(this);
3054 alProperties.addActionListener(this);
3055 overviewMenuItem.setLabel("Overview Window");
3056 overviewMenuItem.addActionListener(this);
3057 undoMenuItem.setEnabled(false);
3058 undoMenuItem.setLabel("Undo");
3059 undoMenuItem.addActionListener(this);
3060 redoMenuItem.setEnabled(false);
3061 redoMenuItem.setLabel("Redo");
3062 redoMenuItem.addActionListener(this);
3063 conservationMenuItem.setLabel("by Conservation");
3064 conservationMenuItem.addItemListener(this);
3065 noColourmenuItem.setLabel("None");
3066 noColourmenuItem.addActionListener(this);
3067 wrapMenuItem.setLabel("Wrap");
3068 wrapMenuItem.addItemListener(this);
3069 renderGapsMenuItem.setLabel("Show Gaps");
3070 renderGapsMenuItem.setState(true);
3071 renderGapsMenuItem.addItemListener(this);
3072 findMenuItem.setLabel("Find...");
3073 findMenuItem.addActionListener(this);
3074 abovePIDThreshold.setLabel("Above Identity Threshold");
3075 abovePIDThreshold.addItemListener(this);
3076 nucleotideColour.setLabel("Nucleotide");
3077 nucleotideColour.addActionListener(this);
3078 deleteGroups.setLabel("Undefine Groups");
3079 deleteGroups.addActionListener(this);
3080 grpsFromSelection.setLabel("Make Groups for selection");
3081 grpsFromSelection.addActionListener(this);
3082 copy.setLabel("Copy");
3083 copy.addActionListener(this);
3084 cut.setLabel("Cut");
3085 cut.addActionListener(this);
3086 delete.setLabel("Delete");
3087 delete.addActionListener(this);
3088 pasteMenu.setLabel("Paste");
3089 pasteNew.setLabel("To New Alignment");
3090 pasteNew.addActionListener(this);
3091 pasteThis.setLabel("Add To This Alignment");
3092 pasteThis.addActionListener(this);
3093 applyToAllGroups.setLabel("Apply Colour To All Groups");
3094 applyToAllGroups.setState(true);
3095 applyToAllGroups.addItemListener(this);
3096 font.setLabel("Font...");
3097 font.addActionListener(this);
3098 scaleAbove.setLabel("Scale Above");
3099 scaleAbove.setState(true);
3100 scaleAbove.setEnabled(false);
3101 scaleAbove.addItemListener(this);
3102 scaleLeft.setEnabled(false);
3103 scaleLeft.setState(true);
3104 scaleLeft.setLabel("Scale Left");
3105 scaleLeft.addItemListener(this);
3106 scaleRight.setEnabled(false);
3107 scaleRight.setState(true);
3108 scaleRight.setLabel("Scale Right");
3109 scaleRight.addItemListener(this);
3110 modifyPID.setLabel("Modify Identity Threshold...");
3111 modifyPID.addActionListener(this);
3112 modifyConservation.setLabel("Modify Conservation Threshold...");
3113 modifyConservation.addActionListener(this);
3114 sortByTreeMenu.setLabel("By Tree Order");
3115 sort.setLabel("Sort");
3116 calculate.setLabel("Calculate Tree");
3117 autoCalculate.addItemListener(this);
3118 sortByTree.addItemListener(this);
3119 inputText.setLabel("Input from textbox");
3120 inputText.addActionListener(this);
3121 centreColumnLabelFlag.setLabel("Centre column labels");
3122 centreColumnLabelFlag.addItemListener(this);
3123 followMouseOverFlag.setLabel("Automatic Scrolling");
3124 followMouseOverFlag.addItemListener(this);
3125 helpMenu.setLabel("Help");
3126 documentation.setLabel("Documentation");
3127 documentation.addActionListener(this);
3129 about.setLabel("About...");
3130 about.addActionListener(this);
3131 seqLimits.setState(true);
3132 seqLimits.setLabel("Show Sequence Limits");
3133 seqLimits.addItemListener(this);
3134 featureSettings.setLabel("Feature Settings...");
3135 featureSettings.addActionListener(this);
3136 sequenceFeatures.setLabel("Sequence Features");
3137 sequenceFeatures.addItemListener(this);
3138 sequenceFeatures.setState(false);
3139 annotationColour.setLabel("by Annotation...");
3140 annotationColour.addActionListener(this);
3141 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3142 invertColSel.setLabel("Invert Column Selection");
3143 menu1.setLabel("Show");
3144 showColumns.setLabel("All Columns ");
3145 showSeqs.setLabel("All Sequences");
3146 menu2.setLabel("Hide");
3147 hideColumns.setLabel("Selected Columns");
3148 hideSequences.setLabel("Selected Sequences");
3149 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3150 hideAllSelection.setLabel("Selected Region");
3151 showAllHidden.setLabel("All Sequences and Columns");
3152 showGroupConsensus.setLabel("Group Consensus");
3153 showGroupConservation.setLabel("Group Conservation");
3154 showConsensusHistogram.setLabel("Show Consensus Histogram");
3155 showSequenceLogo.setLabel("Show Consensus Logo");
3156 normSequenceLogo.setLabel("Normalise Consensus Logo");
3157 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3158 applyAutoAnnotationSettings.setState(true);
3159 autoAnnMenu.setLabel("Autocalculated Annotation");
3161 invertColSel.addActionListener(this);
3162 showColumns.addActionListener(this);
3163 showSeqs.addActionListener(this);
3164 hideColumns.addActionListener(this);
3165 hideSequences.addActionListener(this);
3166 hideAllButSelection.addActionListener(this);
3167 hideAllSelection.addActionListener(this);
3168 showAllHidden.addActionListener(this);
3169 showGroupConsensus.addItemListener(this);
3170 showGroupConservation.addItemListener(this);
3171 showConsensusHistogram.addItemListener(this);
3172 showSequenceLogo.addItemListener(this);
3173 normSequenceLogo.addItemListener(this);
3175 applyAutoAnnotationSettings.addItemListener(this);
3176 formatMenu.setLabel("Format");
3177 selectMenu.setLabel("Select");
3178 newView.setLabel("New View");
3179 newView.addActionListener(this);
3180 alignFrameMenuBar.add(fileMenu);
3181 alignFrameMenuBar.add(editMenu);
3182 alignFrameMenuBar.add(selectMenu);
3183 alignFrameMenuBar.add(viewMenu);
3184 alignFrameMenuBar.add(formatMenu);
3185 alignFrameMenuBar.add(colourMenu);
3186 alignFrameMenuBar.add(calculateMenu);
3187 alignFrameMenuBar.add(helpMenu);
3189 fileMenu.add(inputText);
3190 fileMenu.add(loadTree);
3191 fileMenu.add(loadAnnotations);
3193 fileMenu.addSeparator();
3194 fileMenu.add(outputTextboxMenu);
3195 fileMenu.add(outputFeatures);
3196 fileMenu.add(outputAnnotations);
3198 if (jalviewServletURL != null)
3200 fileMenu.add(loadApplication);
3203 fileMenu.addSeparator();
3204 fileMenu.add(closeMenuItem);
3206 editMenu.add(undoMenuItem);
3207 editMenu.add(redoMenuItem);
3210 editMenu.add(pasteMenu);
3211 editMenu.add(delete);
3212 editMenu.addSeparator();
3213 editMenu.add(remove2LeftMenuItem);
3214 editMenu.add(remove2RightMenuItem);
3215 editMenu.add(removeGappedColumnMenuItem);
3216 editMenu.add(removeAllGapsMenuItem);
3217 editMenu.add(removeRedundancyMenuItem);
3218 viewMenu.add(newView);
3219 viewMenu.addSeparator();
3220 viewMenu.add(menu1);
3221 viewMenu.add(menu2);
3222 viewMenu.addSeparator();
3223 viewMenu.add(followMouseOverFlag);
3224 viewMenu.add(annotationPanelMenuItem);
3225 autoAnnMenu.add(applyAutoAnnotationSettings);
3226 autoAnnMenu.add(showConsensusHistogram);
3227 autoAnnMenu.add(showSequenceLogo);
3228 autoAnnMenu.add(normSequenceLogo);
3229 autoAnnMenu.addSeparator();
3230 autoAnnMenu.add(showGroupConservation);
3231 autoAnnMenu.add(showGroupConsensus);
3232 viewMenu.add(autoAnnMenu);
3233 viewMenu.addSeparator();
3234 viewMenu.add(sequenceFeatures);
3235 viewMenu.add(featureSettings);
3236 viewMenu.addSeparator();
3237 viewMenu.add(alProperties);
3238 viewMenu.addSeparator();
3239 viewMenu.add(overviewMenuItem);
3240 colourMenu.add(applyToAllGroups);
3241 colourMenu.addSeparator();
3242 colourMenu.add(noColourmenuItem);
3243 colourMenu.add(clustalColour);
3244 colourMenu.add(BLOSUM62Colour);
3245 colourMenu.add(PIDColour);
3246 colourMenu.add(zappoColour);
3247 colourMenu.add(taylorColour);
3248 colourMenu.add(hydrophobicityColour);
3249 colourMenu.add(helixColour);
3250 colourMenu.add(strandColour);
3251 colourMenu.add(turnColour);
3252 colourMenu.add(buriedColour);
3253 colourMenu.add(nucleotideColour);
3254 colourMenu.add(purinePyrimidineColour);
3255 colourMenu.add(tcoffeeColour);
3256 colourMenu.add(userDefinedColour);
3257 colourMenu.addSeparator();
3258 colourMenu.add(conservationMenuItem);
3259 colourMenu.add(modifyConservation);
3260 colourMenu.add(abovePIDThreshold);
3261 colourMenu.add(modifyPID);
3262 colourMenu.add(annotationColour);
3263 colourMenu.add(RNAHelixColour);
3264 calculateMenu.add(sort);
3265 calculateMenu.add(calculate);
3266 calculateMenu.addSeparator();
3267 calculateMenu.add(pairwiseAlignmentMenuItem);
3268 calculateMenu.add(PCAMenuItem);
3269 calculateMenu.add(autoCalculate);
3270 calculateMenu.add(sortByTree);
3271 this.add(statusBar, BorderLayout.SOUTH);
3272 pasteMenu.add(pasteNew);
3273 pasteMenu.add(pasteThis);
3274 sort.add(sortIDMenuItem);
3275 sort.add(sortLengthMenuItem);
3276 sort.add(sortByTreeMenu);
3277 sort.add(sortGroupMenuItem);
3278 sort.add(sortPairwiseMenuItem);
3279 calculate.add(averageDistanceTreeMenuItem);
3280 calculate.add(neighbourTreeMenuItem);
3281 calculate.add(avDistanceTreeBlosumMenuItem);
3282 calculate.add(njTreeBlosumMenuItem);
3283 helpMenu.add(documentation);
3284 helpMenu.add(about);
3285 menu1.add(showColumns);
3286 menu1.add(showSeqs);
3287 menu1.add(showAllHidden);
3288 menu2.add(hideColumns);
3289 menu2.add(hideSequences);
3290 menu2.add(hideAllSelection);
3291 menu2.add(hideAllButSelection);
3292 formatMenu.add(font);
3293 formatMenu.add(seqLimits);
3294 formatMenu.add(wrapMenuItem);
3295 formatMenu.add(scaleAbove);
3296 formatMenu.add(scaleLeft);
3297 formatMenu.add(scaleRight);
3298 formatMenu.add(viewBoxesMenuItem);
3299 formatMenu.add(viewTextMenuItem);
3300 formatMenu.add(colourTextMenuItem);
3301 formatMenu.add(displayNonconservedMenuItem);
3302 formatMenu.add(renderGapsMenuItem);
3303 formatMenu.add(centreColumnLabelFlag);
3304 selectMenu.add(findMenuItem);
3305 selectMenu.addSeparator();
3306 selectMenu.add(selectAllSequenceMenuItem);
3307 selectMenu.add(deselectAllSequenceMenuItem);
3308 selectMenu.add(invertSequenceMenuItem);
3309 selectMenu.add(invertColSel);
3310 selectMenu.add(grpsFromSelection);
3311 selectMenu.add(deleteGroups);
3315 MenuItem featureSettings = new MenuItem();
3317 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3319 MenuItem annotationColour = new MenuItem();
3321 MenuItem invertColSel = new MenuItem();
3323 Menu menu1 = new Menu();
3325 MenuItem showColumns = new MenuItem();
3327 MenuItem showSeqs = new MenuItem();
3329 Menu menu2 = new Menu();
3331 MenuItem hideColumns = new MenuItem();
3333 MenuItem hideSequences = new MenuItem();
3335 MenuItem hideAllButSelection = new MenuItem();
3337 MenuItem hideAllSelection = new MenuItem();
3339 MenuItem showAllHidden = new MenuItem();
3341 Menu formatMenu = new Menu();
3343 Menu selectMenu = new Menu();
3345 MenuItem newView = new MenuItem();
3348 * Attach the alignFrame panels after embedding menus, if necessary. This used
3349 * to be called setEmbedded, but is now creates the dropdown menus in a
3350 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3352 * @param reallyEmbedded
3353 * true to attach the view to the applet area on the page rather than
3356 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3361 // Explicly build the embedded menu panel for the on-page applet
3363 // view cannot be closed if its actually on the page
3364 fileMenu.remove(closeMenuItem);
3365 fileMenu.remove(3); // Remove Seperator
3366 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3367 Font.PLAIN, 10, false); // use our own fonts.
3368 // and actually add the components to the applet area
3369 viewport.applet.setLayout(new BorderLayout());
3370 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3371 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3372 alignPanel.setSize(viewport.applet.getSize().width,
3373 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3374 - statusBar.HEIGHT);
3375 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3376 final AlignFrame me = this;
3377 viewport.applet.addFocusListener(new FocusListener()
3381 public void focusLost(FocusEvent e)
3383 if (me.viewport.applet.currentAlignFrame == me)
3385 me.viewport.applet.currentAlignFrame = null;
3390 public void focusGained(FocusEvent e)
3392 me.viewport.applet.currentAlignFrame = me;
3395 viewport.applet.validate();
3400 // test and embed menu bar if necessary.
3402 if (embedMenuIfNeeded(alignPanel))
3404 // adjust for status bar height too
3405 alignPanel.setSize(getSize().width, getSize().height
3406 - statusBar.HEIGHT);
3408 add(statusBar, BorderLayout.SOUTH);
3409 add(alignPanel, BorderLayout.CENTER);
3410 // and register with the applet so it can pass external API calls to us
3411 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3417 * create a new binding between structures in an existing jmol viewer instance
3418 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3419 * this does not open a new Jmol window, or modify the display of the
3420 * structures in the original jmol window. Note This method doesn't work
3421 * without an additional javascript library to exchange messages between the
3422 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3425 * JmolViewer instance
3426 * @param sequenceIds
3427 * - sequence Ids to search for associations
3429 public SequenceStructureBinding addStructureViewInstance(
3430 Object jmolviewer, String[] sequenceIds)
3432 org.jmol.api.JmolViewer viewer = null;
3435 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3436 } catch (ClassCastException ex)
3438 System.err.println("Unsupported viewer object :"
3439 + jmolviewer.getClass());
3443 System.err.println("Can't use this object as a structure viewer:"
3444 + jmolviewer.getClass());
3447 SequenceI[] seqs = null;
3448 if (sequenceIds == null || sequenceIds.length == 0)
3450 seqs = viewport.getAlignment().getSequencesArray();
3454 Vector sqi = new Vector();
3455 AlignmentI al = viewport.getAlignment();
3456 for (int sid = 0; sid < sequenceIds.length; sid++)
3458 SequenceI sq = al.findName(sequenceIds[sid]);
3466 seqs = new SequenceI[sqi.size()];
3467 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3469 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3478 // TODO: search for a jmv that involves viewer
3480 { // create a new viewer/jalview binding.
3481 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3489 * bind a pdb file to a sequence in the current view
3492 * - sequenceId within the dataset.
3493 * @param pdbEntryString
3494 * - the short name for the PDB file
3496 * - pdb file - either a URL or a valid PDB file.
3497 * @return true if binding was as success TODO: consider making an exception
3498 * structure for indicating when PDB parsing or sequenceId location
3501 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3504 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3505 boolean needtoadd = false;
3506 if (toaddpdb != null)
3508 Vector pdbe = toaddpdb.getPDBId();
3509 PDBEntry pdbentry = null;
3510 if (pdbe != null && pdbe.size() > 0)
3512 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3514 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3515 if (!pdbentry.getId().equals(pdbEntryString)
3516 && !pdbentry.getFile().equals(pdbFile))
3526 if (pdbentry == null)
3528 pdbentry = new PDBEntry();
3529 pdbentry.setId(pdbEntryString);
3530 pdbentry.setFile(pdbFile);
3531 needtoadd = true; // add this new entry to sequence.
3533 // resolve data source
3534 // TODO: this code should be a refactored to an io package
3535 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3536 if (protocol == null)
3542 // make a note of the access mode and add
3543 if (pdbentry.getProperty() == null)
3545 pdbentry.setProperty(new Hashtable());
3547 pdbentry.getProperty().put("protocol", protocol);
3548 toaddpdb.addPDBId(pdbentry);
3554 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3558 Vector sequences = new Vector();
3559 for (int i = 0; i < seqs.length; i++)
3561 if (seqs[i] != null)
3563 sequences.addElement(new Object[]
3564 { seqs[i], (chains != null) ? chains[i] : null });
3567 seqs = new SequenceI[sequences.size()];
3568 chains = new String[sequences.size()];
3569 for (int i = 0, isize = sequences.size(); i < isize; i++)
3571 Object[] oj = (Object[]) sequences.elementAt(i);
3573 seqs[i] = (SequenceI) oj[0];
3574 chains[i] = (String) oj[1];
3582 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3583 SequenceI[] seqs, String[] chains, String protocol)
3585 // Scrub any null sequences from the array
3586 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3587 seqs = (SequenceI[]) sqch[0];
3588 chains = (String[]) sqch[1];
3589 if (seqs == null || seqs.length == 0)
3592 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3594 if (protocol == null || protocol.trim().length() == 0
3595 || protocol.equals("null"))
3597 protocol = (String) pdb.getProperty().get("protocol");
3598 if (protocol == null)
3600 System.err.println("Couldn't work out protocol to open structure: "
3605 if (applet.useXtrnalSviewer)
3607 // register the association(s) and quit, don't create any windows.
3608 if (StructureSelectionManager.getStructureSelectionManager(applet)
3609 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3611 System.err.println("Failed to map " + pdb.getFile() + " ("
3612 + protocol + ") to any sequences");
3616 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3618 // can only do alignments with Jmol
3619 // find the last jmol window assigned to this alignment
3620 jalview.appletgui.AppletJmol ajm = null, tajm;
3621 Vector jmols = applet
3622 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3623 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3625 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3626 if (tajm.ap.alignFrame == this)
3635 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3636 // try and add the pdb structure
3641 // otherwise, create a new window
3642 if (applet.jmolAvailable)
3644 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3646 applet.lastFrameX += 40;
3647 applet.lastFrameY += 40;
3651 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3656 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3657 SequenceI[][] seqs, String[][] chains, String[] protocols)
3659 // TODO Auto-generated method stub
3660 System.err.println("Aligned Structure View: Not yet implemented.");
3664 * modify the current selection, providing the user has not made a selection
3668 * - sequences from this alignment
3670 * - columns to be selected on the alignment
3672 public void select(SequenceGroup sel, ColumnSelection csel)
3674 alignPanel.seqPanel.selection(sel, csel, null);
3677 public void scrollTo(int row, int column)
3679 alignPanel.seqPanel.scrollTo(row, column);
3682 public void scrollToRow(int row)
3684 alignPanel.seqPanel.scrollToRow(row);
3687 public void scrollToColumn(int column)
3689 alignPanel.seqPanel.scrollToColumn(column);
3693 * @return the alignments unique ID.
3695 public String getSequenceSetId()
3697 return viewport.getSequenceSetId();
3701 * Load the (T-Coffee) score file from the specified url
3704 * File/URL/T-COFFEE score file contents
3705 * @throws IOException
3706 * @return true if alignment was annotated with data from source
3708 public boolean loadScoreFile(String source) throws IOException
3711 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3712 AppletFormatAdapter.checkProtocol(source));
3713 if (!file.isValid())
3715 // TODO: raise dialog for gui
3716 System.err.println("Problems parsing T-Coffee scores: "
3717 + file.getWarningMessage());
3718 System.err.println("Origin was:\n" + source);
3723 * check that the score matrix matches the alignment dimensions
3726 if ((aln = viewport.getAlignment()) != null
3727 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3730 // TODO: raise a dialog box here rather than bomb out.
3732 .println("The scores matrix does not match the alignment dimensions");
3736 // TODO add parameter to indicate if matching should be done
3737 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3739 alignPanel.fontChanged();
3740 tcoffeeColour.setEnabled(true);
3741 // switch to this color
3742 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3747 System.err.println("Problems resolving T-Coffee scores:");
3748 if (file.getWarningMessage() != null)
3750 System.err.println(file.getWarningMessage());