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.AlignmentSorter;
21 import jalview.analysis.Conservation;
22 import jalview.api.AlignViewControllerI;
23 import jalview.api.SequenceStructureBinding;
24 import jalview.bin.JalviewLite;
25 import jalview.commands.CommandI;
26 import jalview.commands.EditCommand;
27 import jalview.commands.OrderCommand;
28 import jalview.commands.RemoveGapColCommand;
29 import jalview.commands.RemoveGapsCommand;
30 import jalview.commands.SlideSequencesCommand;
31 import jalview.commands.TrimRegionCommand;
32 import jalview.datamodel.Alignment;
33 import jalview.datamodel.AlignmentI;
34 import jalview.datamodel.AlignmentOrder;
35 import jalview.datamodel.ColumnSelection;
36 import jalview.datamodel.PDBEntry;
37 import jalview.datamodel.Sequence;
38 import jalview.datamodel.SequenceGroup;
39 import jalview.datamodel.SequenceI;
40 import jalview.io.AnnotationFile;
41 import jalview.io.AppletFormatAdapter;
42 import jalview.io.FeaturesFile;
43 import jalview.io.TCoffeeScoreFile;
44 import jalview.schemes.Blosum62ColourScheme;
45 import jalview.schemes.BuriedColourScheme;
46 import jalview.schemes.ClustalxColourScheme;
47 import jalview.schemes.ColourSchemeI;
48 import jalview.schemes.HelixColourScheme;
49 import jalview.schemes.HydrophobicColourScheme;
50 import jalview.schemes.NucleotideColourScheme;
51 import jalview.schemes.PIDColourScheme;
52 import jalview.schemes.PurinePyrimidineColourScheme;
53 import jalview.schemes.RNAHelicesColourChooser;
54 import jalview.schemes.ResidueProperties;
55 import jalview.schemes.StrandColourScheme;
56 import jalview.schemes.TCoffeeColourScheme;
57 import jalview.schemes.TaylorColourScheme;
58 import jalview.schemes.TurnColourScheme;
59 import jalview.schemes.ZappoColourScheme;
60 import jalview.structure.StructureSelectionManager;
62 import java.awt.BorderLayout;
63 import java.awt.Canvas;
64 import java.awt.CheckboxMenuItem;
65 import java.awt.Color;
67 import java.awt.FontMetrics;
68 import java.awt.Frame;
69 import java.awt.Graphics;
70 import java.awt.Label;
72 import java.awt.MenuBar;
73 import java.awt.MenuItem;
74 import java.awt.event.ActionEvent;
75 import java.awt.event.ActionListener;
76 import java.awt.event.FocusEvent;
77 import java.awt.event.FocusListener;
78 import java.awt.event.ItemEvent;
79 import java.awt.event.ItemListener;
80 import java.awt.event.KeyEvent;
81 import java.awt.event.KeyListener;
82 import java.awt.event.WindowAdapter;
83 import java.awt.event.WindowEvent;
84 import java.io.IOException;
86 import java.net.URLEncoder;
87 import java.util.Enumeration;
88 import java.util.Hashtable;
89 import java.util.List;
90 import java.util.StringTokenizer;
91 import java.util.Vector;
93 public class AlignFrame extends EmbmenuFrame implements ActionListener,
94 ItemListener, KeyListener
96 public AlignViewControllerI avc;
97 public AlignmentPanel alignPanel;
99 public AlignViewport viewport;
101 int DEFAULT_WIDTH = 700;
103 int DEFAULT_HEIGHT = 500;
105 String jalviewServletURL;
107 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
108 String title, boolean embedded)
112 jalviewServletURL = applet.getParameter("APPLICATION_URL");
118 } catch (Exception ex)
120 ex.printStackTrace();
123 viewport = new AlignViewport(al, applet);
124 alignPanel = new AlignmentPanel(this, viewport);
125 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
126 viewport.updateConservation(alignPanel);
127 viewport.updateConsensus(alignPanel);
129 annotationPanelMenuItem.setState(viewport.showAnnotation);
130 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
131 followMouseOverFlag.setState(viewport.getFollowHighlight());
132 showGroupConsensus.setState(viewport.isShowGroupConsensus());
133 showGroupConservation.setState(viewport.isShowGroupConservation());
134 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
135 showSequenceLogo.setState(viewport.isShowSequenceLogo());
136 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
138 seqLimits.setState(viewport.showJVSuffix);
142 String param = applet.getParameter("sortBy");
145 if (param.equalsIgnoreCase("Id"))
147 sortIDMenuItem_actionPerformed();
149 else if (param.equalsIgnoreCase("Pairwise Identity"))
151 sortPairwiseMenuItem_actionPerformed();
153 else if (param.equalsIgnoreCase("Length"))
155 sortLengthMenuItem_actionPerformed();
159 param = applet.getParameter("wrap");
162 if (param.equalsIgnoreCase("true"))
164 wrapMenuItem.setState(true);
165 wrapMenuItem_actionPerformed();
168 param = applet.getParameter("centrecolumnlabels");
171 centreColumnLabelFlag.setState(true);
172 centreColumnLabelFlag_stateChanged();
176 param = applet.getParameter("windowWidth");
179 int width = Integer.parseInt(param);
180 DEFAULT_WIDTH = width;
182 param = applet.getParameter("windowHeight");
185 int height = Integer.parseInt(param);
186 DEFAULT_HEIGHT = height;
188 } catch (Exception ex)
193 if (viewport.getAlignment().isNucleotide())
195 viewport.updateStrucConsensus(alignPanel);
196 if (viewport.getAlignment().hasRNAStructure())
198 RNAHelixColour.setEnabled(true);
202 RNAHelixColour.setEnabled(false);
207 RNAHelixColour.setEnabled(false);
208 purinePyrimidineColour.setEnabled(false);
210 // Some JVMS send keyevents to Top frame or lowest panel,
211 // Havent worked out why yet. So add to both this frame and seqCanvas for
213 this.addKeyListener(this);
214 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
215 alignPanel.idPanel.idCanvas.addKeyListener(this);
216 alignPanel.scalePanel.addKeyListener(this);
217 alignPanel.annotationPanel.addKeyListener(this);
218 alignPanel.annotationPanelHolder.addKeyListener(this);
219 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
220 alignPanel.alabels.addKeyListener(this);
221 createAlignFrameWindow(embedded, title);
224 alignPanel.adjustAnnotationHeight();
225 alignPanel.paintAlignment(true);
228 public AlignViewport getAlignViewport()
233 public SeqCanvas getSeqcanvas()
235 return alignPanel.seqPanel.seqCanvas;
239 * Load a features file onto the alignment
242 * file URL, content, or other resolvable path
244 * is protocol for accessing data referred to by file
247 public boolean parseFeaturesFile(String file, String type)
249 return parseFeaturesFile(file, type, true);
253 * Load a features file onto the alignment
256 * file URL, content, or other resolvable path
258 * is protocol for accessing data referred to by file
259 * @param autoenabledisplay
260 * when true, display features flag will be automatically enabled if
261 * features are loaded
262 * @return true if data parsed as a features file
264 public boolean parseFeaturesFile(String file, String type,
265 boolean autoenabledisplay)
267 // TODO: test if importing a features file onto an alignment which already
268 // has features with links overwrites the original links.
270 Hashtable featureLinks = new Hashtable();
271 boolean featuresFile = false;
274 featuresFile = new jalview.io.FeaturesFile(file, type)
275 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
276 .getFeatureRenderer().featureColours, featureLinks,
277 true, viewport.applet.getDefaultParameter(
278 "relaxedidmatch", false));
279 } catch (Exception ex)
281 ex.printStackTrace();
286 if (featureLinks.size() > 0)
288 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
290 if (autoenabledisplay)
292 viewport.showSequenceFeatures = true;
293 sequenceFeatures.setState(true);
295 if (viewport.featureSettings != null)
297 viewport.featureSettings.refreshTable();
299 alignPanel.paintAlignment(true);
300 statusBar.setText("Successfully added features to alignment.");
306 public void keyPressed(KeyEvent evt)
308 if (viewport.cursorMode
309 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
310 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
311 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
312 && Character.isDigit(evt.getKeyChar()))
313 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
315 switch (evt.getKeyCode())
317 case 27: // escape key
318 deselectAllSequenceMenuItem_actionPerformed();
320 alignPanel.alabels.cancelDrag();
323 if (evt.isControlDown() || evt.isMetaDown())
325 cut_actionPerformed();
329 if (viewport.cursorMode && !evt.isControlDown())
331 alignPanel.seqPanel.setCursorColumn();
333 if (evt.isControlDown() || evt.isMetaDown())
335 copy_actionPerformed();
339 if (evt.isControlDown())
341 paste(evt.isShiftDown());
345 if (evt.isControlDown() || evt.isMetaDown())
347 selectAllSequenceMenuItem_actionPerformed();
350 case KeyEvent.VK_DOWN:
351 if (viewport.cursorMode)
353 alignPanel.seqPanel.moveCursor(0, 1);
357 moveSelectedSequences(false);
362 if (viewport.cursorMode)
364 alignPanel.seqPanel.moveCursor(0, -1);
368 moveSelectedSequences(true);
372 case KeyEvent.VK_LEFT:
373 if (evt.isAltDown() || !viewport.cursorMode)
374 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
376 alignPanel.seqPanel.moveCursor(-1, 0);
379 case KeyEvent.VK_RIGHT:
380 if (evt.isAltDown() || !viewport.cursorMode)
381 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
383 alignPanel.seqPanel.moveCursor(1, 0);
386 case KeyEvent.VK_SPACE:
387 if (viewport.cursorMode)
389 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
390 || evt.isShiftDown() || evt.isAltDown());
394 case KeyEvent.VK_DELETE:
395 case KeyEvent.VK_BACK_SPACE:
396 if (viewport.cursorMode)
398 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
399 || evt.isShiftDown() || evt.isAltDown());
403 cut_actionPerformed();
404 alignPanel.seqPanel.seqCanvas.repaint();
409 if (viewport.cursorMode)
411 alignPanel.seqPanel.setCursorRow();
415 if (viewport.cursorMode)
417 alignPanel.seqPanel.setCursorPosition();
421 case KeyEvent.VK_ENTER:
422 case KeyEvent.VK_COMMA:
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.setCursorRowAndColumn();
430 if (viewport.cursorMode)
432 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
436 if (viewport.cursorMode)
438 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
443 viewport.cursorMode = !viewport.cursorMode;
444 statusBar.setText("Keyboard editing mode is "
445 + (viewport.cursorMode ? "on" : "off"));
446 if (viewport.cursorMode)
448 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
449 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
454 if (evt.isControlDown())
456 findMenuItem_actionPerformed();
462 boolean toggleSeqs = !evt.isControlDown();
463 boolean toggleCols = !evt.isShiftDown();
464 toggleHiddenRegions(toggleSeqs, toggleCols);
468 case KeyEvent.VK_PAGE_UP:
469 if (viewport.wrapAlignment)
471 alignPanel.scrollUp(true);
475 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
476 - viewport.endSeq + viewport.startSeq);
480 case KeyEvent.VK_PAGE_DOWN:
481 if (viewport.wrapAlignment)
483 alignPanel.scrollUp(false);
487 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
488 + viewport.endSeq - viewport.startSeq);
493 if (evt.isControlDown())
495 undoMenuItem_actionPerformed();
500 if (evt.isControlDown())
502 redoMenuItem_actionPerformed();
507 if (evt.isControlDown())
514 if (evt.isControlDown())
516 trimAlignment(false);
521 if (evt.isControlDown())
523 if (evt.isShiftDown())
525 this.removeAllGapsMenuItem_actionPerformed();
529 removeGappedColumnMenuItem_actionPerformed();
534 if (evt.isControlDown())
538 invertColSel_actionPerformed();
542 invertSequenceMenuItem_actionPerformed();
548 if (evt.isControlDown())
550 this.deleteGroups_actionPerformed();
555 if (evt.isControlDown())
562 alignPanel.paintAlignment(true);
566 * called by key handler and the hide all/show all menu items
571 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
573 boolean hide = false;
574 SequenceGroup sg = viewport.getSelectionGroup();
575 if (!toggleSeqs && !toggleCols)
577 // Hide everything by the current selection - this is a hack - we do the
578 // invert and then hide
579 // first check that there will be visible columns after the invert.
580 if ((viewport.getColumnSelection() != null
581 && viewport.getColumnSelection().getSelected() != null && viewport
582 .getColumnSelection().getSelected().size() > 0)
583 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
586 // now invert the sequence set, if required - empty selection implies
587 // that no hiding is required.
590 invertSequenceMenuItem_actionPerformed();
591 sg = viewport.getSelectionGroup();
595 viewport.expandColSelection(sg, true);
596 // finally invert the column selection and get the new sequence
597 // selection and indicate it should be hidden.
598 invertColSel_actionPerformed();
605 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
608 viewport.hideAllSelectedSeqs();
610 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
613 viewport.showAllHiddenSeqs();
619 if (viewport.getColumnSelection().getSelected().size() > 0)
621 viewport.hideSelectedColumns();
624 viewport.setSelectionGroup(sg);
629 viewport.showAllHiddenColumns();
635 public void keyReleased(KeyEvent evt)
640 public void keyTyped(KeyEvent evt)
645 public void itemStateChanged(ItemEvent evt)
647 if (evt.getSource() == displayNonconservedMenuItem)
649 displayNonconservedMenuItem_actionPerformed();
651 else if (evt.getSource() == colourTextMenuItem)
653 colourTextMenuItem_actionPerformed();
655 else if (evt.getSource() == wrapMenuItem)
657 wrapMenuItem_actionPerformed();
659 else if (evt.getSource() == scaleAbove)
661 viewport.setScaleAboveWrapped(scaleAbove.getState());
663 else if (evt.getSource() == scaleLeft)
665 viewport.setScaleLeftWrapped(scaleLeft.getState());
667 else if (evt.getSource() == scaleRight)
669 viewport.setScaleRightWrapped(scaleRight.getState());
671 else if (evt.getSource() == seqLimits)
673 seqLimits_itemStateChanged();
675 else if (evt.getSource() == viewBoxesMenuItem)
677 viewport.setShowBoxes(viewBoxesMenuItem.getState());
679 else if (evt.getSource() == viewTextMenuItem)
681 viewport.setShowText(viewTextMenuItem.getState());
683 else if (evt.getSource() == renderGapsMenuItem)
685 viewport.setRenderGaps(renderGapsMenuItem.getState());
687 else if (evt.getSource() == annotationPanelMenuItem)
689 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
690 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
692 else if (evt.getSource() == sequenceFeatures)
694 viewport.showSequenceFeatures(sequenceFeatures.getState());
695 alignPanel.seqPanel.seqCanvas.repaint();
697 else if (evt.getSource() == conservationMenuItem)
699 conservationMenuItem_actionPerformed();
701 else if (evt.getSource() == abovePIDThreshold)
703 abovePIDThreshold_actionPerformed();
705 else if (evt.getSource() == applyToAllGroups)
707 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
709 else if (evt.getSource() == autoCalculate)
711 viewport.autoCalculateConsensus = autoCalculate.getState();
713 else if (evt.getSource() == sortByTree)
715 viewport.sortByTree = sortByTree.getState();
717 else if (evt.getSource() == this.centreColumnLabelFlag)
719 centreColumnLabelFlag_stateChanged();
721 else if (evt.getSource() == this.followMouseOverFlag)
723 mouseOverFlag_stateChanged();
725 else if (evt.getSource() == showGroupConsensus)
727 showGroupConsensus_actionPerformed();
729 else if (evt.getSource() == showGroupConservation)
731 showGroupConservation_actionPerformed();
733 else if (evt.getSource() == showSequenceLogo)
735 showSequenceLogo_actionPerformed();
737 else if (evt.getSource() == normSequenceLogo)
739 normSequenceLogo_actionPerformed();
741 else if (evt.getSource() == showConsensusHistogram)
743 showConsensusHistogram_actionPerformed();
745 else if (evt.getSource() == applyAutoAnnotationSettings)
747 applyAutoAnnotationSettings_actionPerformed();
749 alignPanel.paintAlignment(true);
752 private void mouseOverFlag_stateChanged()
754 viewport.followHighlight = followMouseOverFlag.getState();
755 // TODO: could kick the scrollTo mechanism to reset view for current
759 private void centreColumnLabelFlag_stateChanged()
761 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
762 this.alignPanel.annotationPanel.repaint();
766 public void actionPerformed(ActionEvent evt)
768 Object source = evt.getSource();
770 if (source == inputText)
772 inputText_actionPerformed();
774 else if (source == loadTree)
776 loadTree_actionPerformed();
778 else if (source == loadApplication)
780 launchFullApplication();
782 else if (source == loadAnnotations)
786 else if (source == outputAnnotations)
788 outputAnnotations(true);
790 else if (source == outputFeatures)
792 outputFeatures(true, "Jalview");
794 else if (source == closeMenuItem)
796 closeMenuItem_actionPerformed();
798 else if (source == copy)
800 copy_actionPerformed();
802 else if (source == undoMenuItem)
804 undoMenuItem_actionPerformed();
806 else if (source == redoMenuItem)
808 redoMenuItem_actionPerformed();
810 else if (source == inputText)
812 inputText_actionPerformed();
814 else if (source == closeMenuItem)
816 closeMenuItem_actionPerformed();
818 else if (source == undoMenuItem)
820 undoMenuItem_actionPerformed();
822 else if (source == redoMenuItem)
824 redoMenuItem_actionPerformed();
826 else if (source == copy)
828 copy_actionPerformed();
830 else if (source == pasteNew)
832 pasteNew_actionPerformed();
834 else if (source == pasteThis)
836 pasteThis_actionPerformed();
838 else if (source == cut)
840 cut_actionPerformed();
842 else if (source == delete)
844 delete_actionPerformed();
846 else if (source == grpsFromSelection)
848 makeGrpsFromSelection_actionPerformed();
850 else if (source == deleteGroups)
852 deleteGroups_actionPerformed();
854 else if (source == selectAllSequenceMenuItem)
856 selectAllSequenceMenuItem_actionPerformed();
858 else if (source == deselectAllSequenceMenuItem)
860 deselectAllSequenceMenuItem_actionPerformed();
862 else if (source == invertSequenceMenuItem)
864 invertSequenceMenuItem_actionPerformed();
866 else if (source == invertColSel)
868 viewport.invertColumnSelection();
869 alignPanel.paintAlignment(true);
871 else if (source == remove2LeftMenuItem)
875 else if (source == remove2RightMenuItem)
877 trimAlignment(false);
879 else if (source == removeGappedColumnMenuItem)
881 removeGappedColumnMenuItem_actionPerformed();
883 else if (source == removeAllGapsMenuItem)
885 removeAllGapsMenuItem_actionPerformed();
887 else if (source == findMenuItem)
889 findMenuItem_actionPerformed();
891 else if (source == font)
893 new FontChooser(alignPanel);
895 else if (source == newView)
899 else if (source == showColumns)
901 viewport.showAllHiddenColumns();
902 alignPanel.paintAlignment(true);
904 else if (source == showSeqs)
906 viewport.showAllHiddenSeqs();
907 alignPanel.paintAlignment(true);
909 else if (source == hideColumns)
911 viewport.hideSelectedColumns();
912 alignPanel.paintAlignment(true);
914 else if (source == hideSequences
915 && viewport.getSelectionGroup() != null)
917 viewport.hideAllSelectedSeqs();
918 alignPanel.paintAlignment(true);
920 else if (source == hideAllButSelection)
922 toggleHiddenRegions(false, false);
923 alignPanel.paintAlignment(true);
925 else if (source == hideAllSelection)
927 SequenceGroup sg = viewport.getSelectionGroup();
928 viewport.expandColSelection(sg, false);
929 viewport.hideAllSelectedSeqs();
930 viewport.hideSelectedColumns();
931 alignPanel.paintAlignment(true);
933 else if (source == showAllHidden)
935 viewport.showAllHiddenColumns();
936 viewport.showAllHiddenSeqs();
937 alignPanel.paintAlignment(true);
939 else if (source == showGroupConsensus)
941 showGroupConsensus_actionPerformed();
943 else if (source == showGroupConservation)
945 showGroupConservation_actionPerformed();
947 else if (source == showSequenceLogo)
949 showSequenceLogo_actionPerformed();
951 else if (source == normSequenceLogo)
953 normSequenceLogo_actionPerformed();
955 else if (source == showConsensusHistogram)
957 showConsensusHistogram_actionPerformed();
959 else if (source == applyAutoAnnotationSettings)
961 applyAutoAnnotationSettings_actionPerformed();
963 else if (source == featureSettings)
965 new FeatureSettings(alignPanel);
967 else if (source == alProperties)
969 StringBuffer contents = new jalview.io.AlignmentProperties(
970 viewport.getAlignment()).formatAsString();
971 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
972 cap.setText(contents.toString());
973 Frame frame = new Frame();
975 jalview.bin.JalviewLite.addFrame(frame, "Alignment Properties: "
976 + getTitle(), 400, 250);
978 else if (source == overviewMenuItem)
980 overviewMenuItem_actionPerformed();
982 else if (source == noColourmenuItem)
986 else if (source == clustalColour)
988 abovePIDThreshold.setState(false);
989 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
991 else if (source == zappoColour)
993 changeColour(new ZappoColourScheme());
995 else if (source == taylorColour)
997 changeColour(new TaylorColourScheme());
999 else if (source == hydrophobicityColour)
1001 changeColour(new HydrophobicColourScheme());
1003 else if (source == helixColour)
1005 changeColour(new HelixColourScheme());
1007 else if (source == strandColour)
1009 changeColour(new StrandColourScheme());
1011 else if (source == turnColour)
1013 changeColour(new TurnColourScheme());
1015 else if (source == buriedColour)
1017 changeColour(new BuriedColourScheme());
1019 else if (source == nucleotideColour)
1021 changeColour(new NucleotideColourScheme());
1023 else if (source == purinePyrimidineColour)
1025 changeColour(new PurinePyrimidineColourScheme());
1027 else if (source == RNAHelixColour)
1029 new RNAHelicesColourChooser(viewport, alignPanel);
1031 else if (source == modifyPID)
1033 modifyPID_actionPerformed();
1035 else if (source == modifyConservation)
1037 modifyConservation_actionPerformed();
1039 else if (source == userDefinedColour)
1041 new UserDefinedColours(alignPanel, null);
1043 else if (source == PIDColour)
1045 changeColour(new PIDColourScheme());
1047 else if (source == BLOSUM62Colour)
1049 changeColour(new Blosum62ColourScheme());
1051 else if (source == tcoffeeColour)
1053 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1055 else if (source == annotationColour)
1057 new AnnotationColourChooser(viewport, alignPanel);
1059 else if (source == sortPairwiseMenuItem)
1061 sortPairwiseMenuItem_actionPerformed();
1063 else if (source == sortIDMenuItem)
1065 sortIDMenuItem_actionPerformed();
1067 else if (source == sortLengthMenuItem)
1069 sortLengthMenuItem_actionPerformed();
1071 else if (source == sortGroupMenuItem)
1073 sortGroupMenuItem_actionPerformed();
1075 else if (source == removeRedundancyMenuItem)
1077 removeRedundancyMenuItem_actionPerformed();
1079 else if (source == pairwiseAlignmentMenuItem)
1081 pairwiseAlignmentMenuItem_actionPerformed();
1083 else if (source == PCAMenuItem)
1085 PCAMenuItem_actionPerformed();
1087 else if (source == averageDistanceTreeMenuItem)
1089 averageDistanceTreeMenuItem_actionPerformed();
1091 else if (source == neighbourTreeMenuItem)
1093 neighbourTreeMenuItem_actionPerformed();
1095 else if (source == njTreeBlosumMenuItem)
1097 njTreeBlosumMenuItem_actionPerformed();
1099 else if (source == avDistanceTreeBlosumMenuItem)
1101 avTreeBlosumMenuItem_actionPerformed();
1103 else if (source == documentation)
1105 documentation_actionPerformed();
1107 else if (source == about)
1109 about_actionPerformed();
1114 public void inputText_actionPerformed()
1116 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1117 Frame frame = new Frame();
1119 jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);
1122 protected void outputText_actionPerformed(ActionEvent e)
1124 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1125 Frame frame = new Frame();
1127 jalview.bin.JalviewLite.addFrame(frame,
1128 "Alignment output - " + e.getActionCommand(), 600, 500);
1129 cap.setText(new AppletFormatAdapter().formatSequences(
1130 e.getActionCommand(), viewport.getAlignment(),
1131 viewport.showJVSuffix));
1134 public void loadAnnotations()
1136 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1137 cap.setText("Paste your features / annotations / T-coffee score file here.");
1138 cap.setAnnotationImport();
1139 Frame frame = new Frame();
1141 jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);
1145 public String outputAnnotations(boolean displayTextbox)
1147 String annotation = new AnnotationFile().printAnnotations(
1148 viewport.showAnnotation ? viewport.getAlignment()
1149 .getAlignmentAnnotation() : null, viewport
1150 .getAlignment().getGroups(), ((Alignment) viewport
1151 .getAlignment()).alignmentProperties);
1155 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1156 Frame frame = new Frame();
1158 jalview.bin.JalviewLite.addFrame(frame, "Annotations", 600, 500);
1159 cap.setText(annotation);
1165 private Hashtable getDisplayedFeatureCols()
1167 if (alignPanel.getFeatureRenderer() != null
1168 && viewport.featuresDisplayed != null)
1170 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1171 Hashtable fcols = new Hashtable();
1172 Enumeration en = viewport.featuresDisplayed.keys();
1173 while (en.hasMoreElements())
1175 Object col = en.nextElement();
1176 fcols.put(col, fr.featureColours.get(col));
1183 public String outputFeatures(boolean displayTextbox, String format)
1186 if (format.equalsIgnoreCase("Jalview"))
1188 features = new FeaturesFile().printJalviewFormat(viewport
1189 .getAlignment().getSequencesArray(),
1190 getDisplayedFeatureCols());
1194 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1195 .getSequencesArray(), getDisplayedFeatureCols());
1200 boolean frimport = false;
1201 if (features == null || features.equals("No Features Visible"))
1203 features = "# No features visible - paste some and import them here.";
1207 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1210 cap.setAnnotationImport();
1212 Frame frame = new Frame();
1214 jalview.bin.JalviewLite.addFrame(frame, "Features", 600, 500);
1215 cap.setText(features);
1219 if (features == null)
1226 void launchFullApplication()
1228 StringBuffer url = new StringBuffer(jalviewServletURL);
1231 + appendProtocol(viewport.applet.getParameter("file")));
1233 if (viewport.applet.getParameter("features") != null)
1235 url.append("&features=");
1236 url.append(appendProtocol(viewport.applet.getParameter("features")));
1239 if (viewport.applet.getParameter("annotations") != null)
1241 url.append("&annotations=");
1242 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1245 if (viewport.applet.getParameter("jnetfile") != null)
1247 url.append("&annotations=");
1248 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1251 if (viewport.applet.getParameter("defaultColour") != null)
1253 url.append("&colour="
1254 + removeWhiteSpace(viewport.applet
1255 .getParameter("defaultColour")));
1258 if (viewport.applet.getParameter("userDefinedColour") != null)
1260 url.append("&colour="
1261 + removeWhiteSpace(viewport.applet
1262 .getParameter("userDefinedColour")));
1264 if (viewport.applet.getParameter("tree") != null)
1267 + appendProtocol(viewport.applet.getParameter("tree")));
1269 if (viewport.applet.getParameter("treeFile") != null)
1272 + appendProtocol(viewport.applet.getParameter("treeFile")));
1275 showURL(url.toString(), "FULL_APP");
1278 String removeWhiteSpace(String colour)
1280 StringBuffer sb = new StringBuffer();
1281 for (int i = 0; i < colour.length(); i++)
1283 if (Character.isWhitespace(colour.charAt(i)))
1289 sb.append(colour.charAt(i));
1293 return sb.toString();
1296 String appendProtocol(String url)
1301 url = URLEncoder.encode(url);
1304 * When we finally deprecate 1.1 compatibility, we can start to use
1305 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1306 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1307 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1308 * ex.printStackTrace(); }
1310 catch (java.net.MalformedURLException ex)
1312 url = viewport.applet.getCodeBase() + url;
1317 public void closeMenuItem_actionPerformed()
1319 PaintRefresher.RemoveComponent(alignPanel);
1320 if (alignPanel.seqPanel != null
1321 && alignPanel.seqPanel.seqCanvas != null)
1323 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1325 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1327 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1330 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1345 void updateEditMenuBar()
1348 if (viewport.historyList.size() > 0)
1350 undoMenuItem.setEnabled(true);
1351 CommandI command = (CommandI) viewport.historyList.peek();
1352 undoMenuItem.setLabel("Undo " + command.getDescription());
1356 undoMenuItem.setEnabled(false);
1357 undoMenuItem.setLabel("Undo");
1360 if (viewport.redoList.size() > 0)
1362 redoMenuItem.setEnabled(true);
1364 CommandI command = (CommandI) viewport.redoList.peek();
1365 redoMenuItem.setLabel("Redo " + command.getDescription());
1369 redoMenuItem.setEnabled(false);
1370 redoMenuItem.setLabel("Redo");
1377 public void addHistoryItem(CommandI command)
1379 if (command.getSize() > 0)
1381 viewport.historyList.push(command);
1382 viewport.redoList.removeAllElements();
1383 updateEditMenuBar();
1384 viewport.updateHiddenColumns();
1389 * TODO: JAL-1104 DOCUMENT ME!
1394 protected void undoMenuItem_actionPerformed()
1396 if (viewport.historyList.size() < 1)
1401 CommandI command = (CommandI) viewport.historyList.pop();
1402 viewport.redoList.push(command);
1403 command.undoCommand(null);
1405 AlignViewport originalSource = getOriginatingSource(command);
1407 if (originalSource != viewport)
1410 .println("Warning: Viewport object mismatch whilst undoing");
1412 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1413 // viewport.getColumnSelection().getHiddenColumns()
1415 updateEditMenuBar();
1416 originalSource.firePropertyChange("alignment", null, originalSource
1417 .getAlignment().getSequences());
1421 * TODO: JAL-1104 DOCUMENT ME!
1426 protected void redoMenuItem_actionPerformed()
1428 if (viewport.redoList.size() < 1)
1433 CommandI command = (CommandI) viewport.redoList.pop();
1434 viewport.historyList.push(command);
1435 command.doCommand(null);
1437 AlignViewport originalSource = getOriginatingSource(command);
1439 if (originalSource != viewport)
1442 .println("Warning: Viewport object mismatch whilst re-doing");
1444 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1445 // viewport.getColumnSelection().getHiddenColumns()
1448 updateEditMenuBar();
1449 originalSource.firePropertyChange("alignment", null, originalSource
1450 .getAlignment().getSequences());
1453 AlignViewport getOriginatingSource(CommandI command)
1455 AlignViewport originalSource = null;
1456 // For sequence removal and addition, we need to fire
1457 // the property change event FROM the viewport where the
1458 // original alignment was altered
1459 AlignmentI al = null;
1460 if (command instanceof EditCommand)
1462 EditCommand editCommand = (EditCommand) command;
1463 al = editCommand.getAlignment();
1464 Vector comps = (Vector) PaintRefresher.components.get(viewport
1465 .getSequenceSetId());
1466 for (int i = 0; i < comps.size(); i++)
1468 if (comps.elementAt(i) instanceof AlignmentPanel)
1470 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1472 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1479 if (originalSource == null)
1481 // The original view is closed, we must validate
1482 // the current view against the closed view first
1485 PaintRefresher.validateSequences(al, viewport.getAlignment());
1488 originalSource = viewport;
1491 return originalSource;
1494 public void moveSelectedSequences(boolean up)
1496 SequenceGroup sg = viewport.getSelectionGroup();
1501 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1502 up ? null : viewport.getHiddenRepSequences(), up);
1503 alignPanel.paintAlignment(true);
1506 synchronized void slideSequences(boolean right, int size)
1508 List<SequenceI> sg = new Vector<SequenceI>();
1509 if (viewport.cursorMode)
1511 sg.add(viewport.getAlignment().getSequenceAt(
1512 alignPanel.seqPanel.seqCanvas.cursorY));
1514 else if (viewport.getSelectionGroup() != null
1515 && viewport.getSelectionGroup().getSize() != viewport
1516 .getAlignment().getHeight())
1518 sg = viewport.getSelectionGroup().getSequences(
1519 viewport.getHiddenRepSequences());
1527 Vector<SequenceI> invertGroup = new Vector();
1529 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1531 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1532 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1535 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1537 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1539 for (int i = 0; i < invertGroup.size(); i++)
1540 seqs2[i] = invertGroup.elementAt(i);
1542 SlideSequencesCommand ssc;
1544 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1545 size, viewport.getGapCharacter());
1547 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1548 size, viewport.getGapCharacter());
1550 int groupAdjustment = 0;
1551 if (ssc.getGapsInsertedBegin() && right)
1553 if (viewport.cursorMode)
1554 alignPanel.seqPanel.moveCursor(size, 0);
1556 groupAdjustment = size;
1558 else if (!ssc.getGapsInsertedBegin() && !right)
1560 if (viewport.cursorMode)
1561 alignPanel.seqPanel.moveCursor(-size, 0);
1563 groupAdjustment = -size;
1566 if (groupAdjustment != 0)
1568 viewport.getSelectionGroup().setStartRes(
1569 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1570 viewport.getSelectionGroup().setEndRes(
1571 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1574 boolean appendHistoryItem = false;
1575 if (viewport.historyList != null && viewport.historyList.size() > 0
1576 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1578 appendHistoryItem = ssc
1579 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1583 if (!appendHistoryItem)
1584 addHistoryItem(ssc);
1589 static StringBuffer copiedSequences;
1591 static Vector copiedHiddenColumns;
1593 protected void copy_actionPerformed()
1595 if (viewport.getSelectionGroup() == null)
1600 SequenceGroup sg = viewport.getSelectionGroup();
1601 copiedSequences = new StringBuffer();
1602 Hashtable orderedSeqs = new Hashtable();
1603 for (int i = 0; i < sg.getSize(); i++)
1605 SequenceI seq = sg.getSequenceAt(i);
1606 int index = viewport.getAlignment().findIndex(seq);
1607 orderedSeqs.put(index + "", seq);
1610 int index = 0, startRes, endRes;
1613 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1615 copiedHiddenColumns = new Vector();
1616 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1617 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1620 int[] region = (int[]) viewport.getColumnSelection()
1621 .getHiddenColumns().elementAt(i);
1623 copiedHiddenColumns.addElement(new int[]
1624 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1629 copiedHiddenColumns = null;
1632 for (int i = 0; i < sg.getSize(); i++)
1634 SequenceI seq = null;
1638 if (orderedSeqs.containsKey(index + ""))
1640 seq = (SequenceI) orderedSeqs.get(index + "");
1652 // Returns residue following index if gap
1653 startRes = seq.findPosition(sg.getStartRes());
1656 // Need to find the residue preceeding index if gap
1659 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1661 ch = seq.getCharAt(j);
1662 if (!jalview.util.Comparison.isGap((ch)))
1670 endRes += seq.getStart() - 1;
1673 copiedSequences.append(seq.getName()
1679 + seq.getSequenceAsString(sg.getStartRes(),
1680 sg.getEndRes() + 1) + "\n");
1685 protected void pasteNew_actionPerformed()
1690 protected void pasteThis_actionPerformed()
1695 void paste(boolean newAlignment)
1700 if (copiedSequences == null)
1705 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1706 Vector seqs = new Vector();
1707 while (st.hasMoreElements())
1709 String name = st.nextToken();
1710 int start = Integer.parseInt(st.nextToken());
1711 int end = Integer.parseInt(st.nextToken());
1712 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1714 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1715 for (int i = 0; i < seqs.size(); i++)
1717 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1722 String newtitle = new String("Copied sequences");
1723 if (getTitle().startsWith("Copied sequences"))
1725 newtitle = getTitle();
1729 newtitle = newtitle.concat("- from " + getTitle());
1731 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1732 viewport.applet, newtitle, false);
1733 if (copiedHiddenColumns != null)
1735 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1737 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1738 af.viewport.hideColumns(region[0], region[1]);
1742 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1747 addSequences(newSeqs);
1750 } catch (Exception ex)
1752 } // could be anything being pasted in here
1756 void addSequences(SequenceI[] seqs)
1758 for (int i = 0; i < seqs.length; i++)
1760 viewport.getAlignment().addSequence(seqs[i]);
1764 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1765 seqs, 0, viewport.getAlignment().getWidth(),
1766 viewport.getAlignment()));
1768 viewport.setEndSeq(viewport.getAlignment().getHeight());
1769 viewport.getAlignment().getWidth();
1770 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1775 protected void cut_actionPerformed()
1777 copy_actionPerformed();
1778 delete_actionPerformed();
1781 protected void delete_actionPerformed()
1784 SequenceGroup sg = viewport.getSelectionGroup();
1790 Vector seqs = new Vector();
1792 for (int i = 0; i < sg.getSize(); i++)
1794 seq = sg.getSequenceAt(i);
1795 seqs.addElement(seq);
1798 // If the cut affects all sequences, remove highlighted columns
1799 if (sg.getSize() == viewport.getAlignment().getHeight())
1801 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1802 sg.getEndRes() + 1);
1805 SequenceI[] cut = new SequenceI[seqs.size()];
1806 for (int i = 0; i < seqs.size(); i++)
1808 cut[i] = (SequenceI) seqs.elementAt(i);
1812 * //ADD HISTORY ITEM
1814 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1815 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1816 viewport.getAlignment()));
1818 viewport.setSelectionGroup(null);
1819 viewport.getAlignment().deleteGroup(sg);
1821 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1824 if (viewport.getAlignment().getHeight() < 1)
1826 this.setVisible(false);
1828 viewport.sendSelection();
1832 * group consensus toggled
1835 protected void showGroupConsensus_actionPerformed()
1837 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1838 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1843 * group conservation toggled.
1845 protected void showGroupConservation_actionPerformed()
1847 viewport.setShowGroupConservation(showGroupConservation.getState());
1848 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1855 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1856 * .event.ActionEvent)
1858 protected void showConsensusHistogram_actionPerformed()
1860 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1861 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1868 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1869 * .event.ActionEvent)
1871 protected void showSequenceLogo_actionPerformed()
1873 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1874 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1877 protected void normSequenceLogo_actionPerformed()
1879 showSequenceLogo.setState(true);
1880 viewport.setShowSequenceLogo(true);
1881 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1882 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1885 protected void applyAutoAnnotationSettings_actionPerformed()
1887 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1890 protected void makeGrpsFromSelection_actionPerformed()
1892 if (avc.makeGroupsFromSelection()) {
1893 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1894 alignPanel.updateAnnotation();
1895 alignPanel.paintAlignment(true);
1899 protected void deleteGroups_actionPerformed()
1901 if (avc.deleteGroups())
1903 alignPanel.alignmentChanged();
1907 public void selectAllSequenceMenuItem_actionPerformed()
1909 SequenceGroup sg = new SequenceGroup();
1910 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1912 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1914 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1915 viewport.setSelectionGroup(sg);
1916 alignPanel.paintAlignment(true);
1917 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1918 viewport.sendSelection();
1921 public void deselectAllSequenceMenuItem_actionPerformed()
1923 if (viewport.cursorMode)
1925 alignPanel.seqPanel.keyboardNo1 = null;
1926 alignPanel.seqPanel.keyboardNo2 = null;
1928 viewport.setSelectionGroup(null);
1929 viewport.getColumnSelection().clear();
1930 viewport.setSelectionGroup(null);
1931 alignPanel.idPanel.idCanvas.searchResults = null;
1932 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1933 alignPanel.paintAlignment(true);
1934 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1935 viewport.sendSelection();
1938 public void invertSequenceMenuItem_actionPerformed()
1940 SequenceGroup sg = viewport.getSelectionGroup();
1941 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1943 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1946 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1947 viewport.sendSelection();
1950 public void invertColSel_actionPerformed()
1952 viewport.invertColumnSelection();
1953 alignPanel.paintAlignment(true);
1954 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1955 viewport.sendSelection();
1958 void trimAlignment(boolean trimLeft)
1960 ColumnSelection colSel = viewport.getColumnSelection();
1963 if (colSel.size() > 0)
1967 column = colSel.getMin();
1971 column = colSel.getMax();
1975 if (viewport.getSelectionGroup() != null)
1977 seqs = viewport.getSelectionGroup().getSequencesAsArray(
1978 viewport.getHiddenRepSequences());
1982 seqs = viewport.getAlignment().getSequencesArray();
1985 TrimRegionCommand trimRegion;
1988 trimRegion = new TrimRegionCommand("Remove Left",
1989 TrimRegionCommand.TRIM_LEFT, seqs, column,
1990 viewport.getAlignment(), viewport.getColumnSelection(),
1991 viewport.getSelectionGroup());
1992 viewport.setStartRes(0);
1996 trimRegion = new TrimRegionCommand("Remove Right",
1997 TrimRegionCommand.TRIM_RIGHT, seqs, column,
1998 viewport.getAlignment(), viewport.getColumnSelection(),
1999 viewport.getSelectionGroup());
2002 statusBar.setText("Removed " + trimRegion.getSize() + " columns.");
2004 addHistoryItem(trimRegion);
2006 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2008 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2009 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2011 viewport.getAlignment().deleteGroup(sg);
2015 viewport.firePropertyChange("alignment", null, viewport
2016 .getAlignment().getSequences());
2020 public void removeGappedColumnMenuItem_actionPerformed()
2022 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2025 if (viewport.getSelectionGroup() != null)
2027 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2028 viewport.getHiddenRepSequences());
2029 start = viewport.getSelectionGroup().getStartRes();
2030 end = viewport.getSelectionGroup().getEndRes();
2034 seqs = viewport.getAlignment().getSequencesArray();
2037 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2038 "Remove Gapped Columns", seqs, start, end,
2039 viewport.getAlignment());
2041 addHistoryItem(removeGapCols);
2043 statusBar.setText("Removed " + removeGapCols.getSize()
2044 + " empty columns.");
2046 // This is to maintain viewport position on first residue
2047 // of first sequence
2048 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2049 int startRes = seq.findPosition(viewport.startRes);
2050 // ShiftList shifts;
2051 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2052 // edit.alColumnChanges=shifts.getInverse();
2053 // if (viewport.hasHiddenColumns)
2054 // viewport.getColumnSelection().compensateForEdits(shifts);
2055 viewport.setStartRes(seq.findIndex(startRes) - 1);
2056 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2061 public void removeAllGapsMenuItem_actionPerformed()
2063 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2066 if (viewport.getSelectionGroup() != null)
2068 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2069 viewport.getHiddenRepSequences());
2070 start = viewport.getSelectionGroup().getStartRes();
2071 end = viewport.getSelectionGroup().getEndRes();
2075 seqs = viewport.getAlignment().getSequencesArray();
2078 // This is to maintain viewport position on first residue
2079 // of first sequence
2080 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2081 int startRes = seq.findPosition(viewport.startRes);
2083 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2084 viewport.getAlignment()));
2086 viewport.setStartRes(seq.findIndex(startRes) - 1);
2088 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2093 public void findMenuItem_actionPerformed()
2095 new Finder(alignPanel);
2099 * create a new view derived from the current view
2102 * @return frame for the new view
2104 public AlignFrame newView(String viewtitle)
2107 if (viewport.hasHiddenRows())
2109 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2110 .getFullAlignment().getSequencesArray());
2114 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2117 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2119 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2121 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2123 newal.addAnnotation(viewport.getAlignment()
2124 .getAlignmentAnnotation()[i]);
2129 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2131 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2132 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2133 PaintRefresher.Register(newaf.alignPanel,
2134 newaf.alignPanel.av.getSequenceSetId());
2136 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2137 newaf.alignPanel.av.getSequenceSetId());
2138 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2139 newaf.alignPanel.av.getSequenceSetId());
2141 Vector comps = (Vector) PaintRefresher.components.get(viewport
2142 .getSequenceSetId());
2144 for (int i = 0; i < comps.size(); i++)
2146 if (comps.elementAt(i) instanceof AlignmentPanel)
2152 String title = new String(this.getTitle());
2153 if (viewtitle != null)
2155 title = viewtitle + " ( " + title + ")";
2159 if (title.indexOf("(View") > -1)
2161 title = title.substring(0, title.indexOf("(View"));
2163 title += "(View " + viewSize + ")";
2166 newaf.setTitle(title.toString());
2168 newaf.viewport.historyList = viewport.historyList;
2169 newaf.viewport.redoList = viewport.redoList;
2175 * @return list of feature groups on the view
2177 public String[] getFeatureGroups()
2179 FeatureRenderer fr = null;
2180 if (alignPanel != null
2181 && (fr = alignPanel.getFeatureRenderer()) != null)
2183 return fr.getGroups();
2189 * get sequence feature groups that are hidden or shown
2195 public String[] getFeatureGroupsOfState(boolean visible)
2197 FeatureRenderer fr = null;
2198 if (alignPanel != null
2199 && (fr = alignPanel.getFeatureRenderer()) != null)
2201 return fr.getGroups(visible);
2207 * Change the display state for the given feature groups
2210 * list of group strings
2212 * visible or invisible
2214 public void setFeatureGroupState(String[] groups, boolean state)
2216 FeatureRenderer fr = null;
2217 this.sequenceFeatures.setState(true);
2218 viewport.showSequenceFeatures(true);
2219 if (alignPanel != null
2220 && (fr = alignPanel.getFeatureRenderer()) != null)
2222 fr.setGroupState(groups, state);
2223 alignPanel.seqPanel.seqCanvas.repaint();
2224 if (alignPanel.overviewPanel != null)
2226 alignPanel.overviewPanel.updateOverviewImage();
2231 public void seqLimits_itemStateChanged()
2233 viewport.setShowJVSuffix(seqLimits.getState());
2234 alignPanel.fontChanged();
2235 alignPanel.paintAlignment(true);
2238 protected void colourTextMenuItem_actionPerformed()
2240 viewport.setColourText(colourTextMenuItem.getState());
2241 alignPanel.paintAlignment(true);
2244 protected void displayNonconservedMenuItem_actionPerformed()
2246 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2247 alignPanel.paintAlignment(true);
2250 protected void wrapMenuItem_actionPerformed()
2252 viewport.setWrapAlignment(wrapMenuItem.getState());
2253 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2254 scaleAbove.setEnabled(wrapMenuItem.getState());
2255 scaleLeft.setEnabled(wrapMenuItem.getState());
2256 scaleRight.setEnabled(wrapMenuItem.getState());
2257 alignPanel.paintAlignment(true);
2260 public void overviewMenuItem_actionPerformed()
2262 if (alignPanel.overviewPanel != null)
2267 Frame frame = new Frame();
2268 OverviewPanel overview = new OverviewPanel(alignPanel);
2269 frame.add(overview);
2270 // +50 must allow for applet frame window
2271 jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),
2272 overview.getPreferredSize().width,
2273 overview.getPreferredSize().height + 50);
2276 final AlignmentPanel ap = alignPanel;
2277 frame.addWindowListener(new WindowAdapter()
2280 public void windowClosing(WindowEvent e)
2284 ap.setOverviewPanel(null);
2289 alignPanel.setOverviewPanel(overview);
2293 void changeColour(ColourSchemeI cs)
2299 if (viewport.getAbovePIDThreshold())
2301 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2304 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2306 viewport.setGlobalColourScheme(cs);
2310 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2313 if (viewport.getConservationSelected())
2316 Alignment al = (Alignment) viewport.getAlignment();
2317 Conservation c = new Conservation("All",
2318 ResidueProperties.propHash, 3, al.getSequences(), 0,
2322 c.verdict(false, viewport.getConsPercGaps());
2324 cs.setConservation(c);
2326 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2332 cs.setConservation(null);
2335 cs.setConsensus(viewport.getSequenceConsensusHash());
2338 viewport.setGlobalColourScheme(cs);
2340 if (alignPanel.getOverviewPanel() != null)
2342 alignPanel.getOverviewPanel().updateOverviewImage();
2345 jalview.structure.StructureSelectionManager
2346 .getStructureSelectionManager(viewport.applet)
2347 .sequenceColoursChanged(alignPanel);
2349 alignPanel.paintAlignment(true);
2352 protected void modifyPID_actionPerformed()
2354 if (viewport.getAbovePIDThreshold()
2355 && viewport.getGlobalColourScheme() != null)
2357 SliderPanel.setPIDSliderSource(alignPanel,
2358 viewport.getGlobalColourScheme(), "Background");
2359 SliderPanel.showPIDSlider();
2363 protected void modifyConservation_actionPerformed()
2365 if (viewport.getConservationSelected()
2366 && viewport.getGlobalColourScheme() != null)
2368 SliderPanel.setConservationSlider(alignPanel,
2369 viewport.getGlobalColourScheme(), "Background");
2370 SliderPanel.showConservationSlider();
2374 protected void conservationMenuItem_actionPerformed()
2376 viewport.setConservationSelected(conservationMenuItem.getState());
2378 viewport.setAbovePIDThreshold(false);
2379 abovePIDThreshold.setState(false);
2381 changeColour(viewport.getGlobalColourScheme());
2383 modifyConservation_actionPerformed();
2386 public void abovePIDThreshold_actionPerformed()
2388 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2390 conservationMenuItem.setState(false);
2391 viewport.setConservationSelected(false);
2393 changeColour(viewport.getGlobalColourScheme());
2395 modifyPID_actionPerformed();
2398 public void sortPairwiseMenuItem_actionPerformed()
2400 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2401 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2402 .getAlignment().getSequenceAt(0), null);
2404 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2405 viewport.getAlignment()));
2406 alignPanel.paintAlignment(true);
2409 public void sortIDMenuItem_actionPerformed()
2411 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2412 AlignmentSorter.sortByID(viewport.getAlignment());
2413 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2414 viewport.getAlignment()));
2415 alignPanel.paintAlignment(true);
2418 public void sortLengthMenuItem_actionPerformed()
2420 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2421 AlignmentSorter.sortByLength(viewport.getAlignment());
2422 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2423 viewport.getAlignment()));
2424 alignPanel.paintAlignment(true);
2427 public void sortGroupMenuItem_actionPerformed()
2429 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2430 AlignmentSorter.sortByGroup(viewport.getAlignment());
2431 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2432 viewport.getAlignment()));
2433 alignPanel.paintAlignment(true);
2437 public void removeRedundancyMenuItem_actionPerformed()
2439 new RedundancyPanel(alignPanel);
2442 public void pairwiseAlignmentMenuItem_actionPerformed()
2444 if (viewport.getSelectionGroup() != null
2445 && viewport.getSelectionGroup().getSize() > 1)
2447 Frame frame = new Frame();
2448 frame.add(new PairwiseAlignPanel(alignPanel));
2449 jalview.bin.JalviewLite.addFrame(frame, "Pairwise Alignment", 600,
2454 public void PCAMenuItem_actionPerformed()
2456 // are the sequences aligned?
2457 if (!viewport.getAlignment().isAligned(false))
2460 int Width = viewport.getAlignment().getWidth();
2462 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2464 current = viewport.getAlignment().getSequenceAt(i);
2466 if (current.getLength() < Width)
2468 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2471 alignPanel.paintAlignment(true);
2474 if ((viewport.getSelectionGroup() != null
2475 && viewport.getSelectionGroup().getSize() < 4 && viewport
2476 .getSelectionGroup().getSize() > 0)
2477 || viewport.getAlignment().getHeight() < 4)
2484 new PCAPanel(viewport);
2485 } catch (java.lang.OutOfMemoryError ex)
2491 public void averageDistanceTreeMenuItem_actionPerformed()
2493 NewTreePanel("AV", "PID", "Average distance tree using PID");
2496 public void neighbourTreeMenuItem_actionPerformed()
2498 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2501 protected void njTreeBlosumMenuItem_actionPerformed()
2503 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2506 protected void avTreeBlosumMenuItem_actionPerformed()
2508 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2511 void NewTreePanel(String type, String pwType, String title)
2513 // are the sequences aligned?
2514 if (!viewport.getAlignment().isAligned(false))
2517 int Width = viewport.getAlignment().getWidth();
2519 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2521 current = viewport.getAlignment().getSequenceAt(i);
2523 if (current.getLength() < Width)
2525 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2528 alignPanel.paintAlignment(true);
2532 if ((viewport.getSelectionGroup() != null && viewport
2533 .getSelectionGroup().getSize() > 1)
2534 || (viewport.getAlignment().getHeight() > 1))
2536 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2538 addTreeMenuItem(tp, title);
2540 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2544 void loadTree_actionPerformed()
2546 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2547 cap.setText("Paste your Newick tree file here.");
2548 cap.setTreeImport();
2549 Frame frame = new Frame();
2551 jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);
2554 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2556 TreePanel tp = new TreePanel(alignPanel, treeFile, "From File - ", tree);
2557 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2558 addTreeMenuItem(tp, treeFile);
2562 * sort the alignment using the given treePanel
2565 * tree used to sort view
2567 * string used for undo event name
2569 public void sortByTree(TreePanel treePanel, String title)
2571 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2573 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2574 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2575 // HistoryItem.SORT));
2576 addHistoryItem(new OrderCommand("Order by " + title, oldOrder,
2577 viewport.getAlignment()));
2578 alignPanel.paintAlignment(true);
2582 * Do any automatic reordering of the alignment and add the necessary bits to
2583 * the menu structure for the new tree
2588 protected void addTreeMenuItem(final TreePanel treePanel,
2591 final MenuItem item = new MenuItem(title);
2592 sortByTreeMenu.add(item);
2593 item.addActionListener(new java.awt.event.ActionListener()
2596 public void actionPerformed(ActionEvent evt)
2598 sortByTree(treePanel, title); // treePanel.getTitle());
2602 treePanel.addWindowListener(new WindowAdapter()
2605 public void windowOpened(WindowEvent e)
2607 if (viewport.sortByTree)
2609 sortByTree(treePanel, title);
2611 super.windowOpened(e);
2615 public void windowClosing(WindowEvent e)
2617 sortByTreeMenu.remove(item);
2622 public boolean sortBy(AlignmentOrder alorder, String undoname)
2624 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2625 if (viewport.applet.debug)
2627 System.err.println("Sorting " + alorder.getOrder().size()
2628 + " in alignment '" + getTitle() + "'");
2630 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2631 if (undoname != null)
2633 addHistoryItem(new OrderCommand(undoname, oldOrder,
2634 viewport.getAlignment()));
2636 alignPanel.paintAlignment(true);
2640 protected void documentation_actionPerformed()
2642 alignPanel.av.applet.openJalviewHelpUrl();
2645 protected void about_actionPerformed()
2648 class AboutPanel extends Canvas
2654 public AboutPanel(String version, String builddate)
2656 this.version = version;
2657 this.builddate = builddate;
2661 public void paint(Graphics g)
2663 g.setColor(Color.white);
2664 g.fillRect(0, 0, getSize().width, getSize().height);
2665 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2666 FontMetrics fm = g.getFontMetrics();
2667 int fh = fm.getHeight();
2669 g.setColor(Color.black);
2670 // TODO: update this text for each release or centrally store it for
2671 // lite and application
2672 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2673 g.drawString("JalviewLite - Release " + version, x, y += fh);
2674 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2675 g.drawString("Build date: " + builddate, x, y += fh);
2676 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2678 "Authors: Jim Procter, Andrew Waterhouse, Jan Engelhardt, Lauren Lui,",
2680 g.drawString("Michele Clamp, James Cuff, Steve Searle, David Martin & Geoff Barton.", x + 50, y += fh+8);
2682 "Development managed by The Barton Group, University of Dundee, Scotland, UK.",
2685 "For help, see the FAQ at www.jalview.org and/or join the jalview-discuss@jalview.org mailing list",
2687 g.drawString("If you use Jalview, please cite:", x, y += fh + 8);
2689 "Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)",
2692 "Jalview Version 2 - a multiple sequence alignment editor and analysis workbench",
2694 g.drawString("Bioinformatics doi: 10.1093/bioinformatics/btp033",
2699 Frame frame = new Frame();
2700 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2702 jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 220);
2706 public void showURL(String url, String target)
2708 if (viewport.applet == null)
2710 System.out.println("Not running as applet - no browser available.");
2714 viewport.applet.showURL(url, target);
2718 // ////////////////////////////////////////////////////////////////////////////////
2719 // JBuilder Graphics here
2721 MenuBar alignFrameMenuBar = new MenuBar();
2723 Menu fileMenu = new Menu("File");
2725 MenuItem loadApplication = new MenuItem("View in Full Application");
2727 MenuItem loadTree = new MenuItem("Load Associated Tree ...");
2729 MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");
2731 MenuItem outputFeatures = new MenuItem("Export Features ...");
2733 MenuItem outputAnnotations = new MenuItem("Export Annotations ...");
2735 MenuItem closeMenuItem = new MenuItem("Close");
2737 Menu editMenu = new Menu("Edit");
2739 Menu viewMenu = new Menu("View");
2741 Menu colourMenu = new Menu("Colour");
2743 Menu calculateMenu = new Menu("Calculate");
2745 MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");
2747 MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");
2749 MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");
2751 MenuItem remove2LeftMenuItem = new MenuItem();
2753 MenuItem remove2RightMenuItem = new MenuItem();
2755 MenuItem removeGappedColumnMenuItem = new MenuItem();
2757 MenuItem removeAllGapsMenuItem = new MenuItem();
2759 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2761 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2763 MenuItem sortPairwiseMenuItem = new MenuItem();
2765 MenuItem sortIDMenuItem = new MenuItem();
2767 MenuItem sortLengthMenuItem = new MenuItem();
2769 MenuItem sortGroupMenuItem = new MenuItem();
2771 MenuItem removeRedundancyMenuItem = new MenuItem();
2773 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2775 MenuItem PCAMenuItem = new MenuItem();
2777 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2779 MenuItem neighbourTreeMenuItem = new MenuItem();
2781 BorderLayout borderLayout1 = new BorderLayout();
2783 public Label statusBar = new Label();
2785 Menu outputTextboxMenu = new Menu();
2787 MenuItem clustalColour = new MenuItem();
2789 MenuItem zappoColour = new MenuItem();
2791 MenuItem taylorColour = new MenuItem();
2793 MenuItem hydrophobicityColour = new MenuItem();
2795 MenuItem helixColour = new MenuItem();
2797 MenuItem strandColour = new MenuItem();
2799 MenuItem turnColour = new MenuItem();
2801 MenuItem buriedColour = new MenuItem();
2803 MenuItem purinePyrimidineColour = new MenuItem();
2805 MenuItem RNAHelixColour = new MenuItem();
2807 MenuItem userDefinedColour = new MenuItem();
2809 MenuItem PIDColour = new MenuItem();
2811 MenuItem BLOSUM62Colour = new MenuItem();
2813 MenuItem tcoffeeColour = new MenuItem();
2815 MenuItem njTreeBlosumMenuItem = new MenuItem();
2817 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2819 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2821 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2823 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2825 MenuItem alProperties = new MenuItem("Alignment Properties...");
2827 MenuItem overviewMenuItem = new MenuItem();
2829 MenuItem undoMenuItem = new MenuItem();
2831 MenuItem redoMenuItem = new MenuItem();
2833 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2835 MenuItem noColourmenuItem = new MenuItem();
2837 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2839 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2841 MenuItem findMenuItem = new MenuItem();
2843 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2845 MenuItem nucleotideColour = new MenuItem();
2847 MenuItem deleteGroups = new MenuItem();
2849 MenuItem grpsFromSelection = new MenuItem();
2851 MenuItem delete = new MenuItem();
2853 MenuItem copy = new MenuItem();
2855 MenuItem cut = new MenuItem();
2857 Menu pasteMenu = new Menu();
2859 MenuItem pasteNew = new MenuItem();
2861 MenuItem pasteThis = new MenuItem();
2863 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2865 MenuItem font = new MenuItem();
2867 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2869 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2871 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2873 MenuItem modifyPID = new MenuItem();
2875 MenuItem modifyConservation = new MenuItem();
2877 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2878 "Autocalculate Consensus", true);
2880 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2881 "Sort Alignment With New Tree", true);
2883 Menu sortByTreeMenu = new Menu();
2885 Menu sort = new Menu();
2887 Menu calculate = new Menu();
2889 MenuItem inputText = new MenuItem();
2891 Menu helpMenu = new Menu();
2893 MenuItem documentation = new MenuItem();
2895 MenuItem about = new MenuItem();
2897 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2899 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2901 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2903 Menu autoAnnMenu = new Menu();
2905 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2907 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2909 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2911 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2913 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2915 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2917 private void jbInit() throws Exception
2920 setMenuBar(alignFrameMenuBar);
2924 // dynamically fill save as menu with available formats
2925 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2928 item = new MenuItem(
2929 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2931 item.addActionListener(new java.awt.event.ActionListener()
2934 public void actionPerformed(ActionEvent e)
2936 outputText_actionPerformed(e);
2940 outputTextboxMenu.add(item);
2942 closeMenuItem.addActionListener(this);
2943 loadApplication.addActionListener(this);
2945 loadTree.addActionListener(this);
2946 loadAnnotations.addActionListener(this);
2947 outputFeatures.addActionListener(this);
2948 outputAnnotations.addActionListener(this);
2949 selectAllSequenceMenuItem.addActionListener(this);
2950 deselectAllSequenceMenuItem.addActionListener(this);
2951 invertSequenceMenuItem.addActionListener(this);
2952 remove2LeftMenuItem.setLabel("Remove Left");
2953 remove2LeftMenuItem.addActionListener(this);
2954 remove2RightMenuItem.setLabel("Remove Right");
2955 remove2RightMenuItem.addActionListener(this);
2956 removeGappedColumnMenuItem.setLabel("Remove Empty Columns");
2957 removeGappedColumnMenuItem.addActionListener(this);
2958 removeAllGapsMenuItem.setLabel("Remove All Gaps");
2959 removeAllGapsMenuItem.addActionListener(this);
2960 viewBoxesMenuItem.setLabel("Boxes");
2961 viewBoxesMenuItem.setState(true);
2962 viewBoxesMenuItem.addItemListener(this);
2963 viewTextMenuItem.setLabel("Text");
2964 viewTextMenuItem.setState(true);
2965 viewTextMenuItem.addItemListener(this);
2966 sortPairwiseMenuItem.setLabel("by Pairwise Identity");
2967 sortPairwiseMenuItem.addActionListener(this);
2968 sortIDMenuItem.setLabel("by ID");
2969 sortIDMenuItem.addActionListener(this);
2970 sortLengthMenuItem.setLabel("by Length");
2971 sortLengthMenuItem.addActionListener(this);
2972 sortGroupMenuItem.setLabel("by Group");
2973 sortGroupMenuItem.addActionListener(this);
2974 removeRedundancyMenuItem.setLabel("Remove Redundancy...");
2975 removeRedundancyMenuItem.addActionListener(this);
2976 pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");
2977 pairwiseAlignmentMenuItem.addActionListener(this);
2978 PCAMenuItem.setLabel("Principal Component Analysis");
2979 PCAMenuItem.addActionListener(this);
2980 averageDistanceTreeMenuItem
2981 .setLabel("Average Distance Using % Identity");
2982 averageDistanceTreeMenuItem.addActionListener(this);
2983 neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");
2984 neighbourTreeMenuItem.addActionListener(this);
2985 statusBar.setBackground(Color.white);
2986 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2987 statusBar.setText("Status bar");
2988 outputTextboxMenu.setLabel("Output to Textbox");
2989 clustalColour.setLabel("Clustalx");
2991 clustalColour.addActionListener(this);
2992 zappoColour.setLabel("Zappo");
2993 zappoColour.addActionListener(this);
2994 taylorColour.setLabel("Taylor");
2995 taylorColour.addActionListener(this);
2996 hydrophobicityColour.setLabel("Hydrophobicity");
2997 hydrophobicityColour.addActionListener(this);
2998 helixColour.setLabel("Helix Propensity");
2999 helixColour.addActionListener(this);
3000 strandColour.setLabel("Strand Propensity");
3001 strandColour.addActionListener(this);
3002 turnColour.setLabel("Turn Propensity");
3003 turnColour.addActionListener(this);
3004 buriedColour.setLabel("Buried Index");
3005 buriedColour.addActionListener(this);
3006 purinePyrimidineColour.setLabel("Purine/Pyrimidine");
3007 purinePyrimidineColour.addActionListener(this);
3008 RNAHelixColour.setLabel("by RNA Helices");
3009 RNAHelixColour.addActionListener(this);
3010 userDefinedColour.setLabel("User Defined...");
3011 userDefinedColour.addActionListener(this);
3012 PIDColour.setLabel("Percentage Identity");
3013 PIDColour.addActionListener(this);
3014 BLOSUM62Colour.setLabel("BLOSUM62 Score");
3015 BLOSUM62Colour.addActionListener(this);
3016 tcoffeeColour.setLabel("T-Coffee Scores");
3017 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3019 tcoffeeColour.addActionListener(this);
3020 avDistanceTreeBlosumMenuItem
3021 .setLabel("Average Distance Using BLOSUM62");
3022 avDistanceTreeBlosumMenuItem.addActionListener(this);
3023 njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");
3024 njTreeBlosumMenuItem.addActionListener(this);
3025 annotationPanelMenuItem.setLabel("Show Annotations");
3026 annotationPanelMenuItem.addItemListener(this);
3027 colourTextMenuItem.setLabel("Colour Text");
3028 colourTextMenuItem.addItemListener(this);
3029 displayNonconservedMenuItem.setLabel("Show nonconserved");
3030 displayNonconservedMenuItem.addItemListener(this);
3031 alProperties.addActionListener(this);
3032 overviewMenuItem.setLabel("Overview Window");
3033 overviewMenuItem.addActionListener(this);
3034 undoMenuItem.setEnabled(false);
3035 undoMenuItem.setLabel("Undo");
3036 undoMenuItem.addActionListener(this);
3037 redoMenuItem.setEnabled(false);
3038 redoMenuItem.setLabel("Redo");
3039 redoMenuItem.addActionListener(this);
3040 conservationMenuItem.setLabel("by Conservation");
3041 conservationMenuItem.addItemListener(this);
3042 noColourmenuItem.setLabel("None");
3043 noColourmenuItem.addActionListener(this);
3044 wrapMenuItem.setLabel("Wrap");
3045 wrapMenuItem.addItemListener(this);
3046 renderGapsMenuItem.setLabel("Show Gaps");
3047 renderGapsMenuItem.setState(true);
3048 renderGapsMenuItem.addItemListener(this);
3049 findMenuItem.setLabel("Find...");
3050 findMenuItem.addActionListener(this);
3051 abovePIDThreshold.setLabel("Above Identity Threshold");
3052 abovePIDThreshold.addItemListener(this);
3053 nucleotideColour.setLabel("Nucleotide");
3054 nucleotideColour.addActionListener(this);
3055 deleteGroups.setLabel("Undefine Groups");
3056 deleteGroups.addActionListener(this);
3057 grpsFromSelection.setLabel("Make Groups for selection");
3058 grpsFromSelection.addActionListener(this);
3059 copy.setLabel("Copy");
3060 copy.addActionListener(this);
3061 cut.setLabel("Cut");
3062 cut.addActionListener(this);
3063 delete.setLabel("Delete");
3064 delete.addActionListener(this);
3065 pasteMenu.setLabel("Paste");
3066 pasteNew.setLabel("To New Alignment");
3067 pasteNew.addActionListener(this);
3068 pasteThis.setLabel("Add To This Alignment");
3069 pasteThis.addActionListener(this);
3070 applyToAllGroups.setLabel("Apply Colour To All Groups");
3071 applyToAllGroups.setState(true);
3072 applyToAllGroups.addItemListener(this);
3073 font.setLabel("Font...");
3074 font.addActionListener(this);
3075 scaleAbove.setLabel("Scale Above");
3076 scaleAbove.setState(true);
3077 scaleAbove.setEnabled(false);
3078 scaleAbove.addItemListener(this);
3079 scaleLeft.setEnabled(false);
3080 scaleLeft.setState(true);
3081 scaleLeft.setLabel("Scale Left");
3082 scaleLeft.addItemListener(this);
3083 scaleRight.setEnabled(false);
3084 scaleRight.setState(true);
3085 scaleRight.setLabel("Scale Right");
3086 scaleRight.addItemListener(this);
3087 modifyPID.setLabel("Modify Identity Threshold...");
3088 modifyPID.addActionListener(this);
3089 modifyConservation.setLabel("Modify Conservation Threshold...");
3090 modifyConservation.addActionListener(this);
3091 sortByTreeMenu.setLabel("By Tree Order");
3092 sort.setLabel("Sort");
3093 calculate.setLabel("Calculate Tree");
3094 autoCalculate.addItemListener(this);
3095 sortByTree.addItemListener(this);
3096 inputText.setLabel("Input from textbox");
3097 inputText.addActionListener(this);
3098 centreColumnLabelFlag.setLabel("Centre column labels");
3099 centreColumnLabelFlag.addItemListener(this);
3100 followMouseOverFlag.setLabel("Automatic Scrolling");
3101 followMouseOverFlag.addItemListener(this);
3102 helpMenu.setLabel("Help");
3103 documentation.setLabel("Documentation");
3104 documentation.addActionListener(this);
3106 about.setLabel("About...");
3107 about.addActionListener(this);
3108 seqLimits.setState(true);
3109 seqLimits.setLabel("Show Sequence Limits");
3110 seqLimits.addItemListener(this);
3111 featureSettings.setLabel("Feature Settings...");
3112 featureSettings.addActionListener(this);
3113 sequenceFeatures.setLabel("Sequence Features");
3114 sequenceFeatures.addItemListener(this);
3115 sequenceFeatures.setState(false);
3116 annotationColour.setLabel("by Annotation...");
3117 annotationColour.addActionListener(this);
3118 invertSequenceMenuItem.setLabel("Invert Sequence Selection");
3119 invertColSel.setLabel("Invert Column Selection");
3120 menu1.setLabel("Show");
3121 showColumns.setLabel("All Columns ");
3122 showSeqs.setLabel("All Sequences");
3123 menu2.setLabel("Hide");
3124 hideColumns.setLabel("Selected Columns");
3125 hideSequences.setLabel("Selected Sequences");
3126 hideAllButSelection.setLabel("All but Selected Region (Shift+Ctrl+H)");
3127 hideAllSelection.setLabel("Selected Region");
3128 showAllHidden.setLabel("All Sequences and Columns");
3129 showGroupConsensus.setLabel("Group Consensus");
3130 showGroupConservation.setLabel("Group Conservation");
3131 showConsensusHistogram.setLabel("Show Consensus Histogram");
3132 showSequenceLogo.setLabel("Show Consensus Logo");
3133 normSequenceLogo.setLabel("Normalise Consensus Logo");
3134 applyAutoAnnotationSettings.setLabel("Apply to all groups");
3135 applyAutoAnnotationSettings.setState(true);
3136 autoAnnMenu.setLabel("Autocalculated Annotation");
3138 invertColSel.addActionListener(this);
3139 showColumns.addActionListener(this);
3140 showSeqs.addActionListener(this);
3141 hideColumns.addActionListener(this);
3142 hideSequences.addActionListener(this);
3143 hideAllButSelection.addActionListener(this);
3144 hideAllSelection.addActionListener(this);
3145 showAllHidden.addActionListener(this);
3146 showGroupConsensus.addItemListener(this);
3147 showGroupConservation.addItemListener(this);
3148 showConsensusHistogram.addItemListener(this);
3149 showSequenceLogo.addItemListener(this);
3150 normSequenceLogo.addItemListener(this);
3152 applyAutoAnnotationSettings.addItemListener(this);
3153 formatMenu.setLabel("Format");
3154 selectMenu.setLabel("Select");
3155 newView.setLabel("New View");
3156 newView.addActionListener(this);
3157 alignFrameMenuBar.add(fileMenu);
3158 alignFrameMenuBar.add(editMenu);
3159 alignFrameMenuBar.add(selectMenu);
3160 alignFrameMenuBar.add(viewMenu);
3161 alignFrameMenuBar.add(formatMenu);
3162 alignFrameMenuBar.add(colourMenu);
3163 alignFrameMenuBar.add(calculateMenu);
3164 alignFrameMenuBar.add(helpMenu);
3166 fileMenu.add(inputText);
3167 fileMenu.add(loadTree);
3168 fileMenu.add(loadAnnotations);
3170 fileMenu.addSeparator();
3171 fileMenu.add(outputTextboxMenu);
3172 fileMenu.add(outputFeatures);
3173 fileMenu.add(outputAnnotations);
3175 if (jalviewServletURL != null)
3177 fileMenu.add(loadApplication);
3180 fileMenu.addSeparator();
3181 fileMenu.add(closeMenuItem);
3183 editMenu.add(undoMenuItem);
3184 editMenu.add(redoMenuItem);
3187 editMenu.add(pasteMenu);
3188 editMenu.add(delete);
3189 editMenu.addSeparator();
3190 editMenu.add(remove2LeftMenuItem);
3191 editMenu.add(remove2RightMenuItem);
3192 editMenu.add(removeGappedColumnMenuItem);
3193 editMenu.add(removeAllGapsMenuItem);
3194 editMenu.add(removeRedundancyMenuItem);
3195 viewMenu.add(newView);
3196 viewMenu.addSeparator();
3197 viewMenu.add(menu1);
3198 viewMenu.add(menu2);
3199 viewMenu.addSeparator();
3200 viewMenu.add(followMouseOverFlag);
3201 viewMenu.add(annotationPanelMenuItem);
3202 autoAnnMenu.add(applyAutoAnnotationSettings);
3203 autoAnnMenu.add(showConsensusHistogram);
3204 autoAnnMenu.add(showSequenceLogo);
3205 autoAnnMenu.add(normSequenceLogo);
3206 autoAnnMenu.addSeparator();
3207 autoAnnMenu.add(showGroupConservation);
3208 autoAnnMenu.add(showGroupConsensus);
3209 viewMenu.add(autoAnnMenu);
3210 viewMenu.addSeparator();
3211 viewMenu.add(sequenceFeatures);
3212 viewMenu.add(featureSettings);
3213 viewMenu.addSeparator();
3214 viewMenu.add(alProperties);
3215 viewMenu.addSeparator();
3216 viewMenu.add(overviewMenuItem);
3217 colourMenu.add(applyToAllGroups);
3218 colourMenu.addSeparator();
3219 colourMenu.add(noColourmenuItem);
3220 colourMenu.add(clustalColour);
3221 colourMenu.add(BLOSUM62Colour);
3222 colourMenu.add(PIDColour);
3223 colourMenu.add(zappoColour);
3224 colourMenu.add(taylorColour);
3225 colourMenu.add(hydrophobicityColour);
3226 colourMenu.add(helixColour);
3227 colourMenu.add(strandColour);
3228 colourMenu.add(turnColour);
3229 colourMenu.add(buriedColour);
3230 colourMenu.add(nucleotideColour);
3231 colourMenu.add(purinePyrimidineColour);
3232 colourMenu.add(tcoffeeColour);
3233 colourMenu.add(userDefinedColour);
3234 colourMenu.addSeparator();
3235 colourMenu.add(conservationMenuItem);
3236 colourMenu.add(modifyConservation);
3237 colourMenu.add(abovePIDThreshold);
3238 colourMenu.add(modifyPID);
3239 colourMenu.add(annotationColour);
3240 colourMenu.add(RNAHelixColour);
3241 calculateMenu.add(sort);
3242 calculateMenu.add(calculate);
3243 calculateMenu.addSeparator();
3244 calculateMenu.add(pairwiseAlignmentMenuItem);
3245 calculateMenu.add(PCAMenuItem);
3246 calculateMenu.add(autoCalculate);
3247 calculateMenu.add(sortByTree);
3248 this.add(statusBar, BorderLayout.SOUTH);
3249 pasteMenu.add(pasteNew);
3250 pasteMenu.add(pasteThis);
3251 sort.add(sortIDMenuItem);
3252 sort.add(sortLengthMenuItem);
3253 sort.add(sortByTreeMenu);
3254 sort.add(sortGroupMenuItem);
3255 sort.add(sortPairwiseMenuItem);
3256 calculate.add(averageDistanceTreeMenuItem);
3257 calculate.add(neighbourTreeMenuItem);
3258 calculate.add(avDistanceTreeBlosumMenuItem);
3259 calculate.add(njTreeBlosumMenuItem);
3260 helpMenu.add(documentation);
3261 helpMenu.add(about);
3262 menu1.add(showColumns);
3263 menu1.add(showSeqs);
3264 menu1.add(showAllHidden);
3265 menu2.add(hideColumns);
3266 menu2.add(hideSequences);
3267 menu2.add(hideAllSelection);
3268 menu2.add(hideAllButSelection);
3269 formatMenu.add(font);
3270 formatMenu.add(seqLimits);
3271 formatMenu.add(wrapMenuItem);
3272 formatMenu.add(scaleAbove);
3273 formatMenu.add(scaleLeft);
3274 formatMenu.add(scaleRight);
3275 formatMenu.add(viewBoxesMenuItem);
3276 formatMenu.add(viewTextMenuItem);
3277 formatMenu.add(colourTextMenuItem);
3278 formatMenu.add(displayNonconservedMenuItem);
3279 formatMenu.add(renderGapsMenuItem);
3280 formatMenu.add(centreColumnLabelFlag);
3281 selectMenu.add(findMenuItem);
3282 selectMenu.addSeparator();
3283 selectMenu.add(selectAllSequenceMenuItem);
3284 selectMenu.add(deselectAllSequenceMenuItem);
3285 selectMenu.add(invertSequenceMenuItem);
3286 selectMenu.add(invertColSel);
3287 selectMenu.add(grpsFromSelection);
3288 selectMenu.add(deleteGroups);
3292 MenuItem featureSettings = new MenuItem();
3294 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3296 MenuItem annotationColour = new MenuItem();
3298 MenuItem invertColSel = new MenuItem();
3300 Menu menu1 = new Menu();
3302 MenuItem showColumns = new MenuItem();
3304 MenuItem showSeqs = new MenuItem();
3306 Menu menu2 = new Menu();
3308 MenuItem hideColumns = new MenuItem();
3310 MenuItem hideSequences = new MenuItem();
3312 MenuItem hideAllButSelection = new MenuItem();
3314 MenuItem hideAllSelection = new MenuItem();
3316 MenuItem showAllHidden = new MenuItem();
3318 Menu formatMenu = new Menu();
3320 Menu selectMenu = new Menu();
3322 MenuItem newView = new MenuItem();
3325 * Attach the alignFrame panels after embedding menus, if necessary. This used
3326 * to be called setEmbedded, but is now creates the dropdown menus in a
3327 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3329 * @param reallyEmbedded
3330 * true to attach the view to the applet area on the page rather than
3333 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3338 // Explicly build the embedded menu panel for the on-page applet
3340 // view cannot be closed if its actually on the page
3341 fileMenu.remove(closeMenuItem);
3342 fileMenu.remove(3); // Remove Seperator
3343 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3344 Font.PLAIN, 10, false); // use our own fonts.
3345 // and actually add the components to the applet area
3346 viewport.applet.setLayout(new BorderLayout());
3347 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3348 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3349 alignPanel.setSize(viewport.applet.getSize().width,
3350 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3351 - statusBar.HEIGHT);
3352 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3353 final AlignFrame me = this;
3354 viewport.applet.addFocusListener(new FocusListener()
3358 public void focusLost(FocusEvent e)
3360 if (me.viewport.applet.currentAlignFrame == me)
3362 me.viewport.applet.currentAlignFrame = null;
3367 public void focusGained(FocusEvent e)
3369 me.viewport.applet.currentAlignFrame = me;
3372 viewport.applet.validate();
3377 // test and embed menu bar if necessary.
3379 if (embedMenuIfNeeded(alignPanel))
3381 // adjust for status bar height too
3382 alignPanel.setSize(getSize().width, getSize().height
3383 - statusBar.HEIGHT);
3385 add(statusBar, BorderLayout.SOUTH);
3386 add(alignPanel, BorderLayout.CENTER);
3387 // and register with the applet so it can pass external API calls to us
3388 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3394 * create a new binding between structures in an existing jmol viewer instance
3395 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3396 * this does not open a new Jmol window, or modify the display of the
3397 * structures in the original jmol window. Note This method doesn't work
3398 * without an additional javascript library to exchange messages between the
3399 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3402 * JmolViewer instance
3403 * @param sequenceIds
3404 * - sequence Ids to search for associations
3406 public SequenceStructureBinding addStructureViewInstance(
3407 Object jmolviewer, String[] sequenceIds)
3409 org.jmol.api.JmolViewer viewer = null;
3412 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3413 } catch (ClassCastException ex)
3415 System.err.println("Unsupported viewer object :"
3416 + jmolviewer.getClass());
3420 System.err.println("Can't use this object as a structure viewer:"
3421 + jmolviewer.getClass());
3424 SequenceI[] seqs = null;
3425 if (sequenceIds == null || sequenceIds.length == 0)
3427 seqs = viewport.getAlignment().getSequencesArray();
3431 Vector sqi = new Vector();
3432 AlignmentI al = viewport.getAlignment();
3433 for (int sid = 0; sid < sequenceIds.length; sid++)
3435 SequenceI sq = al.findName(sequenceIds[sid]);
3443 seqs = new SequenceI[sqi.size()];
3444 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3446 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3455 // TODO: search for a jmv that involves viewer
3457 { // create a new viewer/jalview binding.
3458 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3466 * bind a pdb file to a sequence in the current view
3469 * - sequenceId within the dataset.
3470 * @param pdbEntryString
3471 * - the short name for the PDB file
3473 * - pdb file - either a URL or a valid PDB file.
3474 * @return true if binding was as success TODO: consider making an exception
3475 * structure for indicating when PDB parsing or sequenceId location
3478 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3481 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3482 boolean needtoadd = false;
3483 if (toaddpdb != null)
3485 Vector pdbe = toaddpdb.getPDBId();
3486 PDBEntry pdbentry = null;
3487 if (pdbe != null && pdbe.size() > 0)
3489 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3491 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3492 if (!pdbentry.getId().equals(pdbEntryString)
3493 && !pdbentry.getFile().equals(pdbFile))
3503 if (pdbentry == null)
3505 pdbentry = new PDBEntry();
3506 pdbentry.setId(pdbEntryString);
3507 pdbentry.setFile(pdbFile);
3508 needtoadd = true; // add this new entry to sequence.
3510 // resolve data source
3511 // TODO: this code should be a refactored to an io package
3512 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3513 if (protocol == null)
3519 // make a note of the access mode and add
3520 if (pdbentry.getProperty() == null)
3522 pdbentry.setProperty(new Hashtable());
3524 pdbentry.getProperty().put("protocol", protocol);
3525 toaddpdb.addPDBId(pdbentry);
3531 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3535 Vector sequences = new Vector();
3536 for (int i = 0; i < seqs.length; i++)
3538 if (seqs[i] != null)
3540 sequences.addElement(new Object[]
3541 { seqs[i], (chains != null) ? chains[i] : null });
3544 seqs = new SequenceI[sequences.size()];
3545 chains = new String[sequences.size()];
3546 for (int i = 0, isize = sequences.size(); i < isize; i++)
3548 Object[] oj = (Object[]) sequences.elementAt(i);
3550 seqs[i] = (SequenceI) oj[0];
3551 chains[i] = (String) oj[1];
3559 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3560 SequenceI[] seqs, String[] chains, String protocol)
3562 // Scrub any null sequences from the array
3563 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3564 seqs = (SequenceI[]) sqch[0];
3565 chains = (String[]) sqch[1];
3566 if (seqs == null || seqs.length == 0)
3569 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3571 if (protocol == null || protocol.trim().length() == 0
3572 || protocol.equals("null"))
3574 protocol = (String) pdb.getProperty().get("protocol");
3575 if (protocol == null)
3577 System.err.println("Couldn't work out protocol to open structure: "
3582 if (applet.useXtrnalSviewer)
3584 // register the association(s) and quit, don't create any windows.
3585 if (StructureSelectionManager.getStructureSelectionManager(applet)
3586 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3588 System.err.println("Failed to map " + pdb.getFile() + " ("
3589 + protocol + ") to any sequences");
3593 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3595 // can only do alignments with Jmol
3596 // find the last jmol window assigned to this alignment
3597 jalview.appletgui.AppletJmol ajm = null, tajm;
3598 Vector jmols = applet
3599 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3600 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3602 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3603 if (tajm.ap.alignFrame == this)
3612 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3613 // try and add the pdb structure
3618 // otherwise, create a new window
3619 if (applet.jmolAvailable)
3621 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3623 applet.lastFrameX += 40;
3624 applet.lastFrameY += 40;
3628 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3633 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3634 SequenceI[][] seqs, String[][] chains, String[] protocols)
3636 // TODO Auto-generated method stub
3637 System.err.println("Aligned Structure View: Not yet implemented.");
3641 * modify the current selection, providing the user has not made a selection
3645 * - sequences from this alignment
3647 * - columns to be selected on the alignment
3649 public void select(SequenceGroup sel, ColumnSelection csel)
3651 alignPanel.seqPanel.selection(sel, csel, null);
3654 public void scrollTo(int row, int column)
3656 alignPanel.seqPanel.scrollTo(row, column);
3659 public void scrollToRow(int row)
3661 alignPanel.seqPanel.scrollToRow(row);
3664 public void scrollToColumn(int column)
3666 alignPanel.seqPanel.scrollToColumn(column);
3670 * @return the alignments unique ID.
3672 public String getSequenceSetId()
3674 return viewport.getSequenceSetId();
3678 * Load the (T-Coffee) score file from the specified url
3681 * File/URL/T-COFFEE score file contents
3682 * @throws IOException
3683 * @return true if alignment was annotated with data from source
3685 public boolean loadScoreFile(String source) throws IOException
3688 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3689 AppletFormatAdapter.checkProtocol(source));
3690 if (!file.isValid())
3692 // TODO: raise dialog for gui
3693 System.err.println("Problems parsing T-Coffee scores: "
3694 + file.getWarningMessage());
3695 System.err.println("Origin was:\n" + source);
3700 * check that the score matrix matches the alignment dimensions
3703 if ((aln = viewport.getAlignment()) != null
3704 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3707 // TODO: raise a dialog box here rather than bomb out.
3709 .println("The scores matrix does not match the alignment dimensions");
3713 // TODO add parameter to indicate if matching should be done
3714 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3716 alignPanel.fontChanged();
3717 tcoffeeColour.setEnabled(true);
3718 // switch to this color
3719 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3724 System.err.println("Problems resolving T-Coffee scores:");
3725 if (file.getWarningMessage() != null)
3727 System.err.println(file.getWarningMessage());