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;
61 import jalview.util.MessageManager;
63 import java.awt.BorderLayout;
64 import java.awt.Canvas;
65 import java.awt.CheckboxMenuItem;
66 import java.awt.Color;
68 import java.awt.FontMetrics;
69 import java.awt.Frame;
70 import java.awt.Graphics;
71 import java.awt.Label;
73 import java.awt.MenuBar;
74 import java.awt.MenuItem;
75 import java.awt.event.ActionEvent;
76 import java.awt.event.ActionListener;
77 import java.awt.event.FocusEvent;
78 import java.awt.event.FocusListener;
79 import java.awt.event.ItemEvent;
80 import java.awt.event.ItemListener;
81 import java.awt.event.KeyEvent;
82 import java.awt.event.KeyListener;
83 import java.awt.event.WindowAdapter;
84 import java.awt.event.WindowEvent;
85 import java.io.IOException;
87 import java.net.URLEncoder;
88 import java.util.Enumeration;
89 import java.util.Hashtable;
90 import java.util.List;
91 import java.util.StringTokenizer;
92 import java.util.Vector;
94 public class AlignFrame extends EmbmenuFrame implements ActionListener,
95 ItemListener, KeyListener
97 public AlignViewControllerI avc;
98 public AlignmentPanel alignPanel;
100 public AlignViewport viewport;
102 int DEFAULT_WIDTH = 700;
104 int DEFAULT_HEIGHT = 500;
106 String jalviewServletURL;
108 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
109 String title, boolean embedded)
113 jalviewServletURL = applet.getParameter("APPLICATION_URL");
119 } catch (Exception ex)
121 ex.printStackTrace();
124 viewport = new AlignViewport(al, applet);
125 alignPanel = new AlignmentPanel(this, viewport);
126 avc = new jalview.controller.AlignViewController(viewport, alignPanel);
127 viewport.updateConservation(alignPanel);
128 viewport.updateConsensus(alignPanel);
130 annotationPanelMenuItem.setState(viewport.showAnnotation);
131 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
132 followMouseOverFlag.setState(viewport.getFollowHighlight());
133 showGroupConsensus.setState(viewport.isShowGroupConsensus());
134 showGroupConservation.setState(viewport.isShowGroupConservation());
135 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
136 showSequenceLogo.setState(viewport.isShowSequenceLogo());
137 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
139 seqLimits.setState(viewport.showJVSuffix);
143 String param = applet.getParameter("sortBy");
146 if (param.equalsIgnoreCase("Id"))
148 sortIDMenuItem_actionPerformed();
150 else if (param.equalsIgnoreCase("Pairwise Identity"))
152 sortPairwiseMenuItem_actionPerformed();
154 else if (param.equalsIgnoreCase("Length"))
156 sortLengthMenuItem_actionPerformed();
160 param = applet.getParameter("wrap");
163 if (param.equalsIgnoreCase("true"))
165 wrapMenuItem.setState(true);
166 wrapMenuItem_actionPerformed();
169 param = applet.getParameter("centrecolumnlabels");
172 centreColumnLabelFlag.setState(true);
173 centreColumnLabelFlag_stateChanged();
177 param = applet.getParameter("windowWidth");
180 int width = Integer.parseInt(param);
181 DEFAULT_WIDTH = width;
183 param = applet.getParameter("windowHeight");
186 int height = Integer.parseInt(param);
187 DEFAULT_HEIGHT = height;
189 } catch (Exception ex)
194 if (viewport.getAlignment().isNucleotide())
196 viewport.updateStrucConsensus(alignPanel);
197 if (viewport.getAlignment().hasRNAStructure())
199 RNAHelixColour.setEnabled(true);
203 RNAHelixColour.setEnabled(false);
208 RNAHelixColour.setEnabled(false);
209 purinePyrimidineColour.setEnabled(false);
211 // Some JVMS send keyevents to Top frame or lowest panel,
212 // Havent worked out why yet. So add to both this frame and seqCanvas for
214 this.addKeyListener(this);
215 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
216 alignPanel.idPanel.idCanvas.addKeyListener(this);
217 alignPanel.scalePanel.addKeyListener(this);
218 alignPanel.annotationPanel.addKeyListener(this);
219 alignPanel.annotationPanelHolder.addKeyListener(this);
220 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
221 alignPanel.alabels.addKeyListener(this);
222 createAlignFrameWindow(embedded, title);
225 alignPanel.adjustAnnotationHeight();
226 alignPanel.paintAlignment(true);
229 public AlignViewport getAlignViewport()
234 public SeqCanvas getSeqcanvas()
236 return alignPanel.seqPanel.seqCanvas;
240 * Load a features file onto the alignment
243 * file URL, content, or other resolvable path
245 * is protocol for accessing data referred to by file
248 public boolean parseFeaturesFile(String file, String type)
250 return parseFeaturesFile(file, type, true);
254 * Load a features file onto the alignment
257 * file URL, content, or other resolvable path
259 * is protocol for accessing data referred to by file
260 * @param autoenabledisplay
261 * when true, display features flag will be automatically enabled if
262 * features are loaded
263 * @return true if data parsed as a features file
265 public boolean parseFeaturesFile(String file, String type,
266 boolean autoenabledisplay)
268 // TODO: test if importing a features file onto an alignment which already
269 // has features with links overwrites the original links.
271 Hashtable featureLinks = new Hashtable();
272 boolean featuresFile = false;
275 featuresFile = new jalview.io.FeaturesFile(file, type)
276 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
277 .getFeatureRenderer().featureColours, featureLinks,
278 true, viewport.applet.getDefaultParameter(
279 "relaxedidmatch", false));
280 } catch (Exception ex)
282 ex.printStackTrace();
287 if (featureLinks.size() > 0)
289 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
291 if (autoenabledisplay)
293 viewport.showSequenceFeatures = true;
294 sequenceFeatures.setState(true);
296 if (viewport.featureSettings != null)
298 viewport.featureSettings.refreshTable();
300 alignPanel.paintAlignment(true);
301 statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
307 public void keyPressed(KeyEvent evt)
309 if (viewport.cursorMode
310 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
311 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
312 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
313 && Character.isDigit(evt.getKeyChar()))
314 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
316 switch (evt.getKeyCode())
318 case 27: // escape key
319 deselectAllSequenceMenuItem_actionPerformed();
321 alignPanel.alabels.cancelDrag();
324 if (evt.isControlDown() || evt.isMetaDown())
326 cut_actionPerformed();
330 if (viewport.cursorMode && !evt.isControlDown())
332 alignPanel.seqPanel.setCursorColumn();
334 if (evt.isControlDown() || evt.isMetaDown())
336 copy_actionPerformed();
340 if (evt.isControlDown())
342 paste(evt.isShiftDown());
346 if (evt.isControlDown() || evt.isMetaDown())
348 selectAllSequenceMenuItem_actionPerformed();
351 case KeyEvent.VK_DOWN:
352 if (viewport.cursorMode)
354 alignPanel.seqPanel.moveCursor(0, 1);
358 moveSelectedSequences(false);
363 if (viewport.cursorMode)
365 alignPanel.seqPanel.moveCursor(0, -1);
369 moveSelectedSequences(true);
373 case KeyEvent.VK_LEFT:
374 if (evt.isAltDown() || !viewport.cursorMode)
375 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
377 alignPanel.seqPanel.moveCursor(-1, 0);
380 case KeyEvent.VK_RIGHT:
381 if (evt.isAltDown() || !viewport.cursorMode)
382 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
384 alignPanel.seqPanel.moveCursor(1, 0);
387 case KeyEvent.VK_SPACE:
388 if (viewport.cursorMode)
390 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
391 || evt.isShiftDown() || evt.isAltDown());
395 case KeyEvent.VK_DELETE:
396 case KeyEvent.VK_BACK_SPACE:
397 if (viewport.cursorMode)
399 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
400 || evt.isShiftDown() || evt.isAltDown());
404 cut_actionPerformed();
405 alignPanel.seqPanel.seqCanvas.repaint();
410 if (viewport.cursorMode)
412 alignPanel.seqPanel.setCursorRow();
416 if (viewport.cursorMode)
418 alignPanel.seqPanel.setCursorPosition();
422 case KeyEvent.VK_ENTER:
423 case KeyEvent.VK_COMMA:
424 if (viewport.cursorMode)
426 alignPanel.seqPanel.setCursorRowAndColumn();
431 if (viewport.cursorMode)
433 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
437 if (viewport.cursorMode)
439 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
444 viewport.cursorMode = !viewport.cursorMode;
445 statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(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 if (evt.isShiftDown())
552 this.unGroup_actionPerformed();
556 this.createGroup_actionPerformed();
562 if (evt.isControlDown())
564 this.deleteGroups_actionPerformed();
569 if (evt.isControlDown())
576 alignPanel.paintAlignment(true);
580 * called by key handler and the hide all/show all menu items
585 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
587 boolean hide = false;
588 SequenceGroup sg = viewport.getSelectionGroup();
589 if (!toggleSeqs && !toggleCols)
591 // Hide everything by the current selection - this is a hack - we do the
592 // invert and then hide
593 // first check that there will be visible columns after the invert.
594 if ((viewport.getColumnSelection() != null
595 && viewport.getColumnSelection().getSelected() != null && viewport
596 .getColumnSelection().getSelected().size() > 0)
597 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
600 // now invert the sequence set, if required - empty selection implies
601 // that no hiding is required.
604 invertSequenceMenuItem_actionPerformed();
605 sg = viewport.getSelectionGroup();
609 viewport.expandColSelection(sg, true);
610 // finally invert the column selection and get the new sequence
611 // selection and indicate it should be hidden.
612 invertColSel_actionPerformed();
619 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
622 viewport.hideAllSelectedSeqs();
624 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
627 viewport.showAllHiddenSeqs();
633 if (viewport.getColumnSelection().getSelected().size() > 0)
635 viewport.hideSelectedColumns();
638 viewport.setSelectionGroup(sg);
643 viewport.showAllHiddenColumns();
649 public void keyReleased(KeyEvent evt)
654 public void keyTyped(KeyEvent evt)
659 public void itemStateChanged(ItemEvent evt)
661 if (evt.getSource() == displayNonconservedMenuItem)
663 displayNonconservedMenuItem_actionPerformed();
665 else if (evt.getSource() == colourTextMenuItem)
667 colourTextMenuItem_actionPerformed();
669 else if (evt.getSource() == wrapMenuItem)
671 wrapMenuItem_actionPerformed();
673 else if (evt.getSource() == scaleAbove)
675 viewport.setScaleAboveWrapped(scaleAbove.getState());
677 else if (evt.getSource() == scaleLeft)
679 viewport.setScaleLeftWrapped(scaleLeft.getState());
681 else if (evt.getSource() == scaleRight)
683 viewport.setScaleRightWrapped(scaleRight.getState());
685 else if (evt.getSource() == seqLimits)
687 seqLimits_itemStateChanged();
689 else if (evt.getSource() == viewBoxesMenuItem)
691 viewport.setShowBoxes(viewBoxesMenuItem.getState());
693 else if (evt.getSource() == viewTextMenuItem)
695 viewport.setShowText(viewTextMenuItem.getState());
697 else if (evt.getSource() == renderGapsMenuItem)
699 viewport.setRenderGaps(renderGapsMenuItem.getState());
701 else if (evt.getSource() == annotationPanelMenuItem)
703 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
704 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
706 else if (evt.getSource() == sequenceFeatures)
708 viewport.showSequenceFeatures(sequenceFeatures.getState());
709 alignPanel.seqPanel.seqCanvas.repaint();
711 else if (evt.getSource() == conservationMenuItem)
713 conservationMenuItem_actionPerformed();
715 else if (evt.getSource() == abovePIDThreshold)
717 abovePIDThreshold_actionPerformed();
719 else if (evt.getSource() == applyToAllGroups)
721 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
723 else if (evt.getSource() == autoCalculate)
725 viewport.autoCalculateConsensus = autoCalculate.getState();
727 else if (evt.getSource() == sortByTree)
729 viewport.sortByTree = sortByTree.getState();
731 else if (evt.getSource() == this.centreColumnLabelFlag)
733 centreColumnLabelFlag_stateChanged();
735 else if (evt.getSource() == this.followMouseOverFlag)
737 mouseOverFlag_stateChanged();
739 else if (evt.getSource() == showGroupConsensus)
741 showGroupConsensus_actionPerformed();
743 else if (evt.getSource() == showGroupConservation)
745 showGroupConservation_actionPerformed();
747 else if (evt.getSource() == showSequenceLogo)
749 showSequenceLogo_actionPerformed();
751 else if (evt.getSource() == normSequenceLogo)
753 normSequenceLogo_actionPerformed();
755 else if (evt.getSource() == showConsensusHistogram)
757 showConsensusHistogram_actionPerformed();
759 else if (evt.getSource() == applyAutoAnnotationSettings)
761 applyAutoAnnotationSettings_actionPerformed();
763 alignPanel.paintAlignment(true);
766 private void mouseOverFlag_stateChanged()
768 viewport.followHighlight = followMouseOverFlag.getState();
769 // TODO: could kick the scrollTo mechanism to reset view for current
773 private void centreColumnLabelFlag_stateChanged()
775 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
776 this.alignPanel.annotationPanel.repaint();
780 public void actionPerformed(ActionEvent evt)
782 Object source = evt.getSource();
784 if (source == inputText)
786 inputText_actionPerformed();
788 else if (source == loadTree)
790 loadTree_actionPerformed();
792 else if (source == loadApplication)
794 launchFullApplication();
796 else if (source == loadAnnotations)
800 else if (source == outputAnnotations)
802 outputAnnotations(true);
804 else if (source == outputFeatures)
806 outputFeatures(true, "Jalview");
808 else if (source == closeMenuItem)
810 closeMenuItem_actionPerformed();
812 else if (source == copy)
814 copy_actionPerformed();
816 else if (source == undoMenuItem)
818 undoMenuItem_actionPerformed();
820 else if (source == redoMenuItem)
822 redoMenuItem_actionPerformed();
824 else if (source == inputText)
826 inputText_actionPerformed();
828 else if (source == closeMenuItem)
830 closeMenuItem_actionPerformed();
832 else if (source == undoMenuItem)
834 undoMenuItem_actionPerformed();
836 else if (source == redoMenuItem)
838 redoMenuItem_actionPerformed();
840 else if (source == copy)
842 copy_actionPerformed();
844 else if (source == pasteNew)
846 pasteNew_actionPerformed();
848 else if (source == pasteThis)
850 pasteThis_actionPerformed();
852 else if (source == cut)
854 cut_actionPerformed();
856 else if (source == delete)
858 delete_actionPerformed();
860 else if (source == grpsFromSelection)
862 makeGrpsFromSelection_actionPerformed();
864 else if (source == deleteGroups)
866 deleteGroups_actionPerformed();
868 else if (source == selectAllSequenceMenuItem)
870 selectAllSequenceMenuItem_actionPerformed();
872 else if (source == deselectAllSequenceMenuItem)
874 deselectAllSequenceMenuItem_actionPerformed();
876 else if (source == invertSequenceMenuItem)
878 invertSequenceMenuItem_actionPerformed();
880 else if (source == invertColSel)
882 viewport.invertColumnSelection();
883 alignPanel.paintAlignment(true);
885 else if (source == remove2LeftMenuItem)
889 else if (source == remove2RightMenuItem)
891 trimAlignment(false);
893 else if (source == removeGappedColumnMenuItem)
895 removeGappedColumnMenuItem_actionPerformed();
897 else if (source == removeAllGapsMenuItem)
899 removeAllGapsMenuItem_actionPerformed();
901 else if (source == findMenuItem)
903 findMenuItem_actionPerformed();
905 else if (source == font)
907 new FontChooser(alignPanel);
909 else if (source == newView)
913 else if (source == showColumns)
915 viewport.showAllHiddenColumns();
916 alignPanel.paintAlignment(true);
918 else if (source == showSeqs)
920 viewport.showAllHiddenSeqs();
921 alignPanel.paintAlignment(true);
923 else if (source == hideColumns)
925 viewport.hideSelectedColumns();
926 alignPanel.paintAlignment(true);
928 else if (source == hideSequences
929 && viewport.getSelectionGroup() != null)
931 viewport.hideAllSelectedSeqs();
932 alignPanel.paintAlignment(true);
934 else if (source == hideAllButSelection)
936 toggleHiddenRegions(false, false);
937 alignPanel.paintAlignment(true);
939 else if (source == hideAllSelection)
941 SequenceGroup sg = viewport.getSelectionGroup();
942 viewport.expandColSelection(sg, false);
943 viewport.hideAllSelectedSeqs();
944 viewport.hideSelectedColumns();
945 alignPanel.paintAlignment(true);
947 else if (source == showAllHidden)
949 viewport.showAllHiddenColumns();
950 viewport.showAllHiddenSeqs();
951 alignPanel.paintAlignment(true);
953 else if (source == showGroupConsensus)
955 showGroupConsensus_actionPerformed();
957 else if (source == showGroupConservation)
959 showGroupConservation_actionPerformed();
961 else if (source == showSequenceLogo)
963 showSequenceLogo_actionPerformed();
965 else if (source == normSequenceLogo)
967 normSequenceLogo_actionPerformed();
969 else if (source == showConsensusHistogram)
971 showConsensusHistogram_actionPerformed();
973 else if (source == applyAutoAnnotationSettings)
975 applyAutoAnnotationSettings_actionPerformed();
977 else if (source == featureSettings)
979 new FeatureSettings(alignPanel);
981 else if (source == alProperties)
983 StringBuffer contents = new jalview.io.AlignmentProperties(
984 viewport.getAlignment()).formatAsString();
985 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
986 cap.setText(contents.toString());
987 Frame frame = new Frame();
989 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
992 else if (source == overviewMenuItem)
994 overviewMenuItem_actionPerformed();
996 else if (source == noColourmenuItem)
1000 else if (source == clustalColour)
1002 abovePIDThreshold.setState(false);
1003 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1005 else if (source == zappoColour)
1007 changeColour(new ZappoColourScheme());
1009 else if (source == taylorColour)
1011 changeColour(new TaylorColourScheme());
1013 else if (source == hydrophobicityColour)
1015 changeColour(new HydrophobicColourScheme());
1017 else if (source == helixColour)
1019 changeColour(new HelixColourScheme());
1021 else if (source == strandColour)
1023 changeColour(new StrandColourScheme());
1025 else if (source == turnColour)
1027 changeColour(new TurnColourScheme());
1029 else if (source == buriedColour)
1031 changeColour(new BuriedColourScheme());
1033 else if (source == nucleotideColour)
1035 changeColour(new NucleotideColourScheme());
1037 else if (source == purinePyrimidineColour)
1039 changeColour(new PurinePyrimidineColourScheme());
1041 else if (source == RNAHelixColour)
1043 new RNAHelicesColourChooser(viewport, alignPanel);
1045 else if (source == modifyPID)
1047 modifyPID_actionPerformed();
1049 else if (source == modifyConservation)
1051 modifyConservation_actionPerformed();
1053 else if (source == userDefinedColour)
1055 new UserDefinedColours(alignPanel, null);
1057 else if (source == PIDColour)
1059 changeColour(new PIDColourScheme());
1061 else if (source == BLOSUM62Colour)
1063 changeColour(new Blosum62ColourScheme());
1065 else if (source == tcoffeeColour)
1067 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1069 else if (source == annotationColour)
1071 new AnnotationColourChooser(viewport, alignPanel);
1073 else if (source == sortPairwiseMenuItem)
1075 sortPairwiseMenuItem_actionPerformed();
1077 else if (source == sortIDMenuItem)
1079 sortIDMenuItem_actionPerformed();
1081 else if (source == sortLengthMenuItem)
1083 sortLengthMenuItem_actionPerformed();
1085 else if (source == sortGroupMenuItem)
1087 sortGroupMenuItem_actionPerformed();
1089 else if (source == removeRedundancyMenuItem)
1091 removeRedundancyMenuItem_actionPerformed();
1093 else if (source == pairwiseAlignmentMenuItem)
1095 pairwiseAlignmentMenuItem_actionPerformed();
1097 else if (source == PCAMenuItem)
1099 PCAMenuItem_actionPerformed();
1101 else if (source == averageDistanceTreeMenuItem)
1103 averageDistanceTreeMenuItem_actionPerformed();
1105 else if (source == neighbourTreeMenuItem)
1107 neighbourTreeMenuItem_actionPerformed();
1109 else if (source == njTreeBlosumMenuItem)
1111 njTreeBlosumMenuItem_actionPerformed();
1113 else if (source == avDistanceTreeBlosumMenuItem)
1115 avTreeBlosumMenuItem_actionPerformed();
1117 else if (source == documentation)
1119 documentation_actionPerformed();
1121 else if (source == about)
1123 about_actionPerformed();
1128 public void inputText_actionPerformed()
1130 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1131 Frame frame = new Frame();
1133 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
1136 protected void outputText_actionPerformed(ActionEvent e)
1138 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1139 Frame frame = new Frame();
1141 jalview.bin.JalviewLite.addFrame(frame,
1142 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
1143 cap.setText(new AppletFormatAdapter().formatSequences(
1144 e.getActionCommand(), viewport.getAlignment(),
1145 viewport.showJVSuffix));
1148 public void loadAnnotations()
1150 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1151 cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
1152 cap.setAnnotationImport();
1153 Frame frame = new Frame();
1155 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
1159 public String outputAnnotations(boolean displayTextbox)
1161 String annotation = new AnnotationFile().printAnnotations(
1162 viewport.showAnnotation ? viewport.getAlignment()
1163 .getAlignmentAnnotation() : null, viewport
1164 .getAlignment().getGroups(), ((Alignment) viewport
1165 .getAlignment()).alignmentProperties);
1169 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1170 Frame frame = new Frame();
1172 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
1173 cap.setText(annotation);
1179 private Hashtable getDisplayedFeatureCols()
1181 if (alignPanel.getFeatureRenderer() != null
1182 && viewport.featuresDisplayed != null)
1184 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1185 Hashtable fcols = new Hashtable();
1186 Enumeration en = viewport.featuresDisplayed.keys();
1187 while (en.hasMoreElements())
1189 Object col = en.nextElement();
1190 fcols.put(col, fr.featureColours.get(col));
1197 public String outputFeatures(boolean displayTextbox, String format)
1200 if (format.equalsIgnoreCase("Jalview"))
1202 features = new FeaturesFile().printJalviewFormat(viewport
1203 .getAlignment().getSequencesArray(),
1204 getDisplayedFeatureCols());
1208 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1209 .getSequencesArray(), getDisplayedFeatureCols());
1214 boolean frimport = false;
1215 if (features == null || features.equals("No Features Visible"))
1217 features = "# No features visible - paste some and import them here.";
1221 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1224 cap.setAnnotationImport();
1226 Frame frame = new Frame();
1228 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
1229 cap.setText(features);
1233 if (features == null)
1240 void launchFullApplication()
1242 StringBuffer url = new StringBuffer(jalviewServletURL);
1245 + appendProtocol(viewport.applet.getParameter("file")));
1247 if (viewport.applet.getParameter("features") != null)
1249 url.append("&features=");
1250 url.append(appendProtocol(viewport.applet.getParameter("features")));
1253 if (viewport.applet.getParameter("annotations") != null)
1255 url.append("&annotations=");
1256 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1259 if (viewport.applet.getParameter("jnetfile") != null)
1261 url.append("&annotations=");
1262 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1265 if (viewport.applet.getParameter("defaultColour") != null)
1267 url.append("&colour="
1268 + removeWhiteSpace(viewport.applet
1269 .getParameter("defaultColour")));
1272 if (viewport.applet.getParameter("userDefinedColour") != null)
1274 url.append("&colour="
1275 + removeWhiteSpace(viewport.applet
1276 .getParameter("userDefinedColour")));
1278 if (viewport.applet.getParameter("tree") != null)
1281 + appendProtocol(viewport.applet.getParameter("tree")));
1283 if (viewport.applet.getParameter("treeFile") != null)
1286 + appendProtocol(viewport.applet.getParameter("treeFile")));
1289 showURL(url.toString(), "FULL_APP");
1292 String removeWhiteSpace(String colour)
1294 StringBuffer sb = new StringBuffer();
1295 for (int i = 0; i < colour.length(); i++)
1297 if (Character.isWhitespace(colour.charAt(i)))
1303 sb.append(colour.charAt(i));
1307 return sb.toString();
1310 String appendProtocol(String url)
1315 url = URLEncoder.encode(url);
1318 * When we finally deprecate 1.1 compatibility, we can start to use
1319 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1320 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1321 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1322 * ex.printStackTrace(); }
1324 catch (java.net.MalformedURLException ex)
1326 url = viewport.applet.getCodeBase() + url;
1331 public void closeMenuItem_actionPerformed()
1333 PaintRefresher.RemoveComponent(alignPanel);
1334 if (alignPanel.seqPanel != null
1335 && alignPanel.seqPanel.seqCanvas != null)
1337 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1339 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1341 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1344 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1359 void updateEditMenuBar()
1362 if (viewport.historyList.size() > 0)
1364 undoMenuItem.setEnabled(true);
1365 CommandI command = (CommandI) viewport.historyList.peek();
1366 undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1370 undoMenuItem.setEnabled(false);
1371 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1374 if (viewport.redoList.size() > 0)
1376 redoMenuItem.setEnabled(true);
1378 CommandI command = (CommandI) viewport.redoList.peek();
1379 redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1383 redoMenuItem.setEnabled(false);
1384 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1391 public void addHistoryItem(CommandI command)
1393 if (command.getSize() > 0)
1395 viewport.historyList.push(command);
1396 viewport.redoList.removeAllElements();
1397 updateEditMenuBar();
1398 viewport.updateHiddenColumns();
1403 * TODO: JAL-1104 DOCUMENT ME!
1408 protected void undoMenuItem_actionPerformed()
1410 if (viewport.historyList.size() < 1)
1415 CommandI command = (CommandI) viewport.historyList.pop();
1416 viewport.redoList.push(command);
1417 command.undoCommand(null);
1419 AlignViewport originalSource = getOriginatingSource(command);
1421 if (originalSource != viewport)
1424 .println("Warning: Viewport object mismatch whilst undoing");
1426 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1427 // viewport.getColumnSelection().getHiddenColumns()
1429 updateEditMenuBar();
1430 originalSource.firePropertyChange("alignment", null, originalSource
1431 .getAlignment().getSequences());
1435 * TODO: JAL-1104 DOCUMENT ME!
1440 protected void redoMenuItem_actionPerformed()
1442 if (viewport.redoList.size() < 1)
1447 CommandI command = (CommandI) viewport.redoList.pop();
1448 viewport.historyList.push(command);
1449 command.doCommand(null);
1451 AlignViewport originalSource = getOriginatingSource(command);
1453 if (originalSource != viewport)
1456 .println("Warning: Viewport object mismatch whilst re-doing");
1458 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1459 // viewport.getColumnSelection().getHiddenColumns()
1462 updateEditMenuBar();
1463 originalSource.firePropertyChange("alignment", null, originalSource
1464 .getAlignment().getSequences());
1467 AlignViewport getOriginatingSource(CommandI command)
1469 AlignViewport originalSource = null;
1470 // For sequence removal and addition, we need to fire
1471 // the property change event FROM the viewport where the
1472 // original alignment was altered
1473 AlignmentI al = null;
1474 if (command instanceof EditCommand)
1476 EditCommand editCommand = (EditCommand) command;
1477 al = editCommand.getAlignment();
1478 Vector comps = (Vector) PaintRefresher.components.get(viewport
1479 .getSequenceSetId());
1480 for (int i = 0; i < comps.size(); i++)
1482 if (comps.elementAt(i) instanceof AlignmentPanel)
1484 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1486 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1493 if (originalSource == null)
1495 // The original view is closed, we must validate
1496 // the current view against the closed view first
1499 PaintRefresher.validateSequences(al, viewport.getAlignment());
1502 originalSource = viewport;
1505 return originalSource;
1508 public void moveSelectedSequences(boolean up)
1510 SequenceGroup sg = viewport.getSelectionGroup();
1515 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1516 up ? null : viewport.getHiddenRepSequences(), up);
1517 alignPanel.paintAlignment(true);
1520 synchronized void slideSequences(boolean right, int size)
1522 List<SequenceI> sg = new Vector<SequenceI>();
1523 if (viewport.cursorMode)
1525 sg.add(viewport.getAlignment().getSequenceAt(
1526 alignPanel.seqPanel.seqCanvas.cursorY));
1528 else if (viewport.getSelectionGroup() != null
1529 && viewport.getSelectionGroup().getSize() != viewport
1530 .getAlignment().getHeight())
1532 sg = viewport.getSelectionGroup().getSequences(
1533 viewport.getHiddenRepSequences());
1541 Vector<SequenceI> invertGroup = new Vector();
1543 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1545 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1546 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1549 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1551 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1553 for (int i = 0; i < invertGroup.size(); i++)
1554 seqs2[i] = invertGroup.elementAt(i);
1556 SlideSequencesCommand ssc;
1558 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1559 size, viewport.getGapCharacter());
1561 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1562 size, viewport.getGapCharacter());
1564 int groupAdjustment = 0;
1565 if (ssc.getGapsInsertedBegin() && right)
1567 if (viewport.cursorMode)
1568 alignPanel.seqPanel.moveCursor(size, 0);
1570 groupAdjustment = size;
1572 else if (!ssc.getGapsInsertedBegin() && !right)
1574 if (viewport.cursorMode)
1575 alignPanel.seqPanel.moveCursor(-size, 0);
1577 groupAdjustment = -size;
1580 if (groupAdjustment != 0)
1582 viewport.getSelectionGroup().setStartRes(
1583 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1584 viewport.getSelectionGroup().setEndRes(
1585 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1588 boolean appendHistoryItem = false;
1589 if (viewport.historyList != null && viewport.historyList.size() > 0
1590 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1592 appendHistoryItem = ssc
1593 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1597 if (!appendHistoryItem)
1598 addHistoryItem(ssc);
1603 static StringBuffer copiedSequences;
1605 static Vector copiedHiddenColumns;
1607 protected void copy_actionPerformed()
1609 if (viewport.getSelectionGroup() == null)
1614 SequenceGroup sg = viewport.getSelectionGroup();
1615 copiedSequences = new StringBuffer();
1616 Hashtable orderedSeqs = new Hashtable();
1617 for (int i = 0; i < sg.getSize(); i++)
1619 SequenceI seq = sg.getSequenceAt(i);
1620 int index = viewport.getAlignment().findIndex(seq);
1621 orderedSeqs.put(index + "", seq);
1624 int index = 0, startRes, endRes;
1627 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1629 copiedHiddenColumns = new Vector();
1630 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1631 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1634 int[] region = (int[]) viewport.getColumnSelection()
1635 .getHiddenColumns().elementAt(i);
1637 copiedHiddenColumns.addElement(new int[]
1638 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1643 copiedHiddenColumns = null;
1646 for (int i = 0; i < sg.getSize(); i++)
1648 SequenceI seq = null;
1652 if (orderedSeqs.containsKey(index + ""))
1654 seq = (SequenceI) orderedSeqs.get(index + "");
1666 // Returns residue following index if gap
1667 startRes = seq.findPosition(sg.getStartRes());
1670 // Need to find the residue preceeding index if gap
1673 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1675 ch = seq.getCharAt(j);
1676 if (!jalview.util.Comparison.isGap((ch)))
1684 endRes += seq.getStart() - 1;
1687 copiedSequences.append(seq.getName()
1693 + seq.getSequenceAsString(sg.getStartRes(),
1694 sg.getEndRes() + 1) + "\n");
1699 protected void pasteNew_actionPerformed()
1704 protected void pasteThis_actionPerformed()
1709 void paste(boolean newAlignment)
1714 if (copiedSequences == null)
1719 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1720 Vector seqs = new Vector();
1721 while (st.hasMoreElements())
1723 String name = st.nextToken();
1724 int start = Integer.parseInt(st.nextToken());
1725 int end = Integer.parseInt(st.nextToken());
1726 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1728 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1729 for (int i = 0; i < seqs.size(); i++)
1731 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1736 String newtitle = new String("Copied sequences");
1737 if (getTitle().startsWith("Copied sequences"))
1739 newtitle = getTitle();
1743 newtitle = newtitle.concat("- from " + getTitle());
1745 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1746 viewport.applet, newtitle, false);
1747 if (copiedHiddenColumns != null)
1749 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1751 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1752 af.viewport.hideColumns(region[0], region[1]);
1756 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1761 addSequences(newSeqs);
1764 } catch (Exception ex)
1766 } // could be anything being pasted in here
1770 void addSequences(SequenceI[] seqs)
1772 for (int i = 0; i < seqs.length; i++)
1774 viewport.getAlignment().addSequence(seqs[i]);
1778 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1779 seqs, 0, viewport.getAlignment().getWidth(),
1780 viewport.getAlignment()));
1782 viewport.setEndSeq(viewport.getAlignment().getHeight());
1783 viewport.getAlignment().getWidth();
1784 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1789 protected void cut_actionPerformed()
1791 copy_actionPerformed();
1792 delete_actionPerformed();
1795 protected void delete_actionPerformed()
1798 SequenceGroup sg = viewport.getSelectionGroup();
1804 Vector seqs = new Vector();
1806 for (int i = 0; i < sg.getSize(); i++)
1808 seq = sg.getSequenceAt(i);
1809 seqs.addElement(seq);
1812 // If the cut affects all sequences, remove highlighted columns
1813 if (sg.getSize() == viewport.getAlignment().getHeight())
1815 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1816 sg.getEndRes() + 1);
1819 SequenceI[] cut = new SequenceI[seqs.size()];
1820 for (int i = 0; i < seqs.size(); i++)
1822 cut[i] = (SequenceI) seqs.elementAt(i);
1826 * //ADD HISTORY ITEM
1828 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1829 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1830 viewport.getAlignment()));
1832 viewport.setSelectionGroup(null);
1833 viewport.getAlignment().deleteGroup(sg);
1835 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1838 if (viewport.getAlignment().getHeight() < 1)
1840 this.setVisible(false);
1842 viewport.sendSelection();
1846 * group consensus toggled
1849 protected void showGroupConsensus_actionPerformed()
1851 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1852 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1857 * group conservation toggled.
1859 protected void showGroupConservation_actionPerformed()
1861 viewport.setShowGroupConservation(showGroupConservation.getState());
1862 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1869 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1870 * .event.ActionEvent)
1872 protected void showConsensusHistogram_actionPerformed()
1874 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1875 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1882 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1883 * .event.ActionEvent)
1885 protected void showSequenceLogo_actionPerformed()
1887 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1888 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1891 protected void normSequenceLogo_actionPerformed()
1893 showSequenceLogo.setState(true);
1894 viewport.setShowSequenceLogo(true);
1895 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1896 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1899 protected void applyAutoAnnotationSettings_actionPerformed()
1901 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1904 protected void makeGrpsFromSelection_actionPerformed()
1906 if (avc.makeGroupsFromSelection()) {
1907 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1908 alignPanel.updateAnnotation();
1909 alignPanel.paintAlignment(true);
1913 protected void createGroup_actionPerformed()
1917 protected void unGroup_actionPerformed()
1921 alignPanel.alignmentChanged();
1924 protected void deleteGroups_actionPerformed()
1926 if (avc.deleteGroups())
1928 alignPanel.alignmentChanged();
1932 public void selectAllSequenceMenuItem_actionPerformed()
1934 SequenceGroup sg = new SequenceGroup();
1935 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1937 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1939 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1940 viewport.setSelectionGroup(sg);
1941 alignPanel.paintAlignment(true);
1942 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1943 viewport.sendSelection();
1946 public void deselectAllSequenceMenuItem_actionPerformed()
1948 if (viewport.cursorMode)
1950 alignPanel.seqPanel.keyboardNo1 = null;
1951 alignPanel.seqPanel.keyboardNo2 = null;
1953 viewport.setSelectionGroup(null);
1954 viewport.getColumnSelection().clear();
1955 viewport.setSelectionGroup(null);
1956 alignPanel.idPanel.idCanvas.searchResults = null;
1957 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1958 alignPanel.paintAlignment(true);
1959 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1960 viewport.sendSelection();
1963 public void invertSequenceMenuItem_actionPerformed()
1965 SequenceGroup sg = viewport.getSelectionGroup();
1966 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1968 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1971 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1972 viewport.sendSelection();
1975 public void invertColSel_actionPerformed()
1977 viewport.invertColumnSelection();
1978 alignPanel.paintAlignment(true);
1979 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1980 viewport.sendSelection();
1983 void trimAlignment(boolean trimLeft)
1985 ColumnSelection colSel = viewport.getColumnSelection();
1988 if (colSel.size() > 0)
1992 column = colSel.getMin();
1996 column = colSel.getMax();
2000 if (viewport.getSelectionGroup() != null)
2002 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2003 viewport.getHiddenRepSequences());
2007 seqs = viewport.getAlignment().getSequencesArray();
2010 TrimRegionCommand trimRegion;
2013 trimRegion = new TrimRegionCommand("Remove Left",
2014 TrimRegionCommand.TRIM_LEFT, seqs, column,
2015 viewport.getAlignment(), viewport.getColumnSelection(),
2016 viewport.getSelectionGroup());
2017 viewport.setStartRes(0);
2021 trimRegion = new TrimRegionCommand("Remove Right",
2022 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2023 viewport.getAlignment(), viewport.getColumnSelection(),
2024 viewport.getSelectionGroup());
2027 statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2028 addHistoryItem(trimRegion);
2030 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2032 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2033 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2035 viewport.getAlignment().deleteGroup(sg);
2039 viewport.firePropertyChange("alignment", null, viewport
2040 .getAlignment().getSequences());
2044 public void removeGappedColumnMenuItem_actionPerformed()
2046 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2049 if (viewport.getSelectionGroup() != null)
2051 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2052 viewport.getHiddenRepSequences());
2053 start = viewport.getSelectionGroup().getStartRes();
2054 end = viewport.getSelectionGroup().getEndRes();
2058 seqs = viewport.getAlignment().getSequencesArray();
2061 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2062 "Remove Gapped Columns", seqs, start, end,
2063 viewport.getAlignment());
2065 addHistoryItem(removeGapCols);
2067 statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2069 // This is to maintain viewport position on first residue
2070 // of first sequence
2071 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2072 int startRes = seq.findPosition(viewport.startRes);
2073 // ShiftList shifts;
2074 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2075 // edit.alColumnChanges=shifts.getInverse();
2076 // if (viewport.hasHiddenColumns)
2077 // viewport.getColumnSelection().compensateForEdits(shifts);
2078 viewport.setStartRes(seq.findIndex(startRes) - 1);
2079 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2084 public void removeAllGapsMenuItem_actionPerformed()
2086 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2089 if (viewport.getSelectionGroup() != null)
2091 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2092 viewport.getHiddenRepSequences());
2093 start = viewport.getSelectionGroup().getStartRes();
2094 end = viewport.getSelectionGroup().getEndRes();
2098 seqs = viewport.getAlignment().getSequencesArray();
2101 // This is to maintain viewport position on first residue
2102 // of first sequence
2103 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2104 int startRes = seq.findPosition(viewport.startRes);
2106 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2107 viewport.getAlignment()));
2109 viewport.setStartRes(seq.findIndex(startRes) - 1);
2111 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2116 public void findMenuItem_actionPerformed()
2118 new Finder(alignPanel);
2122 * create a new view derived from the current view
2125 * @return frame for the new view
2127 public AlignFrame newView(String viewtitle)
2130 if (viewport.hasHiddenRows())
2132 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2133 .getFullAlignment().getSequencesArray());
2137 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2140 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2142 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2144 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2146 newal.addAnnotation(viewport.getAlignment()
2147 .getAlignmentAnnotation()[i]);
2152 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2154 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2155 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2156 PaintRefresher.Register(newaf.alignPanel,
2157 newaf.alignPanel.av.getSequenceSetId());
2159 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2160 newaf.alignPanel.av.getSequenceSetId());
2161 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2162 newaf.alignPanel.av.getSequenceSetId());
2164 Vector comps = (Vector) PaintRefresher.components.get(viewport
2165 .getSequenceSetId());
2167 for (int i = 0; i < comps.size(); i++)
2169 if (comps.elementAt(i) instanceof AlignmentPanel)
2175 String title = new String(this.getTitle());
2176 if (viewtitle != null)
2178 title = viewtitle + " ( " + title + ")";
2182 if (title.indexOf("(View") > -1)
2184 title = title.substring(0, title.indexOf("(View"));
2186 title += "(View " + viewSize + ")";
2189 newaf.setTitle(title.toString());
2191 newaf.viewport.historyList = viewport.historyList;
2192 newaf.viewport.redoList = viewport.redoList;
2198 * @return list of feature groups on the view
2200 public String[] getFeatureGroups()
2202 FeatureRenderer fr = null;
2203 if (alignPanel != null
2204 && (fr = alignPanel.getFeatureRenderer()) != null)
2206 return fr.getGroups();
2212 * get sequence feature groups that are hidden or shown
2218 public String[] getFeatureGroupsOfState(boolean visible)
2220 FeatureRenderer fr = null;
2221 if (alignPanel != null
2222 && (fr = alignPanel.getFeatureRenderer()) != null)
2224 return fr.getGroups(visible);
2230 * Change the display state for the given feature groups
2233 * list of group strings
2235 * visible or invisible
2237 public void setFeatureGroupState(String[] groups, boolean state)
2239 FeatureRenderer fr = null;
2240 this.sequenceFeatures.setState(true);
2241 viewport.showSequenceFeatures(true);
2242 if (alignPanel != null
2243 && (fr = alignPanel.getFeatureRenderer()) != null)
2245 fr.setGroupState(groups, state);
2246 alignPanel.seqPanel.seqCanvas.repaint();
2247 if (alignPanel.overviewPanel != null)
2249 alignPanel.overviewPanel.updateOverviewImage();
2254 public void seqLimits_itemStateChanged()
2256 viewport.setShowJVSuffix(seqLimits.getState());
2257 alignPanel.fontChanged();
2258 alignPanel.paintAlignment(true);
2261 protected void colourTextMenuItem_actionPerformed()
2263 viewport.setColourText(colourTextMenuItem.getState());
2264 alignPanel.paintAlignment(true);
2267 protected void displayNonconservedMenuItem_actionPerformed()
2269 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2270 alignPanel.paintAlignment(true);
2273 protected void wrapMenuItem_actionPerformed()
2275 viewport.setWrapAlignment(wrapMenuItem.getState());
2276 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2277 scaleAbove.setEnabled(wrapMenuItem.getState());
2278 scaleLeft.setEnabled(wrapMenuItem.getState());
2279 scaleRight.setEnabled(wrapMenuItem.getState());
2280 alignPanel.paintAlignment(true);
2283 public void overviewMenuItem_actionPerformed()
2285 if (alignPanel.overviewPanel != null)
2290 Frame frame = new Frame();
2291 OverviewPanel overview = new OverviewPanel(alignPanel);
2292 frame.add(overview);
2293 // +50 must allow for applet frame window
2294 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
2295 overview.getPreferredSize().width,
2296 overview.getPreferredSize().height + 50);
2299 final AlignmentPanel ap = alignPanel;
2300 frame.addWindowListener(new WindowAdapter()
2303 public void windowClosing(WindowEvent e)
2307 ap.setOverviewPanel(null);
2312 alignPanel.setOverviewPanel(overview);
2316 void changeColour(ColourSchemeI cs)
2322 if (viewport.getAbovePIDThreshold())
2324 threshold = SliderPanel.setPIDSliderSource(alignPanel, cs,
2327 cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());
2329 viewport.setGlobalColourScheme(cs);
2333 cs.setThreshold(0, viewport.getIgnoreGapsConsensus());
2336 if (viewport.getConservationSelected())
2339 Alignment al = (Alignment) viewport.getAlignment();
2340 Conservation c = new Conservation("All",
2341 ResidueProperties.propHash, 3, al.getSequences(), 0,
2345 c.verdict(false, viewport.getConsPercGaps());
2347 cs.setConservation(c);
2349 cs.setConservationInc(SliderPanel.setConservationSlider(alignPanel,
2355 cs.setConservation(null);
2358 cs.setConsensus(viewport.getSequenceConsensusHash());
2361 viewport.setGlobalColourScheme(cs);
2363 if (alignPanel.getOverviewPanel() != null)
2365 alignPanel.getOverviewPanel().updateOverviewImage();
2368 jalview.structure.StructureSelectionManager
2369 .getStructureSelectionManager(viewport.applet)
2370 .sequenceColoursChanged(alignPanel);
2372 alignPanel.paintAlignment(true);
2375 protected void modifyPID_actionPerformed()
2377 if (viewport.getAbovePIDThreshold()
2378 && viewport.getGlobalColourScheme() != null)
2380 SliderPanel.setPIDSliderSource(alignPanel,
2381 viewport.getGlobalColourScheme(), "Background");
2382 SliderPanel.showPIDSlider();
2386 protected void modifyConservation_actionPerformed()
2388 if (viewport.getConservationSelected()
2389 && viewport.getGlobalColourScheme() != null)
2391 SliderPanel.setConservationSlider(alignPanel,
2392 viewport.getGlobalColourScheme(), "Background");
2393 SliderPanel.showConservationSlider();
2397 protected void conservationMenuItem_actionPerformed()
2399 viewport.setConservationSelected(conservationMenuItem.getState());
2401 viewport.setAbovePIDThreshold(false);
2402 abovePIDThreshold.setState(false);
2404 changeColour(viewport.getGlobalColourScheme());
2406 modifyConservation_actionPerformed();
2409 public void abovePIDThreshold_actionPerformed()
2411 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2413 conservationMenuItem.setState(false);
2414 viewport.setConservationSelected(false);
2416 changeColour(viewport.getGlobalColourScheme());
2418 modifyPID_actionPerformed();
2421 public void sortPairwiseMenuItem_actionPerformed()
2423 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2424 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2425 .getAlignment().getSequenceAt(0), null);
2427 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2428 viewport.getAlignment()));
2429 alignPanel.paintAlignment(true);
2432 public void sortIDMenuItem_actionPerformed()
2434 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2435 AlignmentSorter.sortByID(viewport.getAlignment());
2436 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2437 viewport.getAlignment()));
2438 alignPanel.paintAlignment(true);
2441 public void sortLengthMenuItem_actionPerformed()
2443 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2444 AlignmentSorter.sortByLength(viewport.getAlignment());
2445 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2446 viewport.getAlignment()));
2447 alignPanel.paintAlignment(true);
2450 public void sortGroupMenuItem_actionPerformed()
2452 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2453 AlignmentSorter.sortByGroup(viewport.getAlignment());
2454 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2455 viewport.getAlignment()));
2456 alignPanel.paintAlignment(true);
2460 public void removeRedundancyMenuItem_actionPerformed()
2462 new RedundancyPanel(alignPanel);
2465 public void pairwiseAlignmentMenuItem_actionPerformed()
2467 if (viewport.getSelectionGroup() != null
2468 && viewport.getSelectionGroup().getSize() > 1)
2470 Frame frame = new Frame();
2471 frame.add(new PairwiseAlignPanel(alignPanel));
2472 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
2477 public void PCAMenuItem_actionPerformed()
2479 // are the sequences aligned?
2480 if (!viewport.getAlignment().isAligned(false))
2483 int Width = viewport.getAlignment().getWidth();
2485 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2487 current = viewport.getAlignment().getSequenceAt(i);
2489 if (current.getLength() < Width)
2491 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2494 alignPanel.paintAlignment(true);
2497 if ((viewport.getSelectionGroup() != null
2498 && viewport.getSelectionGroup().getSize() < 4 && viewport
2499 .getSelectionGroup().getSize() > 0)
2500 || viewport.getAlignment().getHeight() < 4)
2507 new PCAPanel(viewport);
2508 } catch (java.lang.OutOfMemoryError ex)
2514 public void averageDistanceTreeMenuItem_actionPerformed()
2516 NewTreePanel("AV", "PID", "Average distance tree using PID");
2519 public void neighbourTreeMenuItem_actionPerformed()
2521 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2524 protected void njTreeBlosumMenuItem_actionPerformed()
2526 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2529 protected void avTreeBlosumMenuItem_actionPerformed()
2531 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2534 void NewTreePanel(String type, String pwType, String title)
2536 // are the sequences aligned?
2537 if (!viewport.getAlignment().isAligned(false))
2540 int Width = viewport.getAlignment().getWidth();
2542 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2544 current = viewport.getAlignment().getSequenceAt(i);
2546 if (current.getLength() < Width)
2548 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2551 alignPanel.paintAlignment(true);
2555 if ((viewport.getSelectionGroup() != null && viewport
2556 .getSelectionGroup().getSize() > 1)
2557 || (viewport.getAlignment().getHeight() > 1))
2559 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2561 addTreeMenuItem(tp, title);
2563 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2567 void loadTree_actionPerformed()
2569 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2570 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2571 cap.setTreeImport();
2572 Frame frame = new Frame();
2574 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
2577 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2579 TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
2580 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2581 addTreeMenuItem(tp, treeFile);
2585 * sort the alignment using the given treePanel
2588 * tree used to sort view
2590 * string used for undo event name
2592 public void sortByTree(TreePanel treePanel, String title)
2594 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2596 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2597 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2598 // HistoryItem.SORT));
2599 addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
2600 viewport.getAlignment()));
2601 alignPanel.paintAlignment(true);
2605 * Do any automatic reordering of the alignment and add the necessary bits to
2606 * the menu structure for the new tree
2611 protected void addTreeMenuItem(final TreePanel treePanel,
2614 final MenuItem item = new MenuItem(title);
2615 sortByTreeMenu.add(item);
2616 item.addActionListener(new java.awt.event.ActionListener()
2619 public void actionPerformed(ActionEvent evt)
2621 sortByTree(treePanel, title); // treePanel.getTitle());
2625 treePanel.addWindowListener(new WindowAdapter()
2628 public void windowOpened(WindowEvent e)
2630 if (viewport.sortByTree)
2632 sortByTree(treePanel, title);
2634 super.windowOpened(e);
2638 public void windowClosing(WindowEvent e)
2640 sortByTreeMenu.remove(item);
2645 public boolean sortBy(AlignmentOrder alorder, String undoname)
2647 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2648 if (viewport.applet.debug)
2650 System.err.println("Sorting " + alorder.getOrder().size()
2651 + " in alignment '" + getTitle() + "'");
2653 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2654 if (undoname != null)
2656 addHistoryItem(new OrderCommand(undoname, oldOrder,
2657 viewport.getAlignment()));
2659 alignPanel.paintAlignment(true);
2663 protected void documentation_actionPerformed()
2665 alignPanel.av.applet.openJalviewHelpUrl();
2668 protected void about_actionPerformed()
2671 class AboutPanel extends Canvas
2677 public AboutPanel(String version, String builddate)
2679 this.version = version;
2680 this.builddate = builddate;
2684 public void paint(Graphics g)
2686 g.setColor(Color.white);
2687 g.fillRect(0, 0, getSize().width, getSize().height);
2688 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2689 FontMetrics fm = g.getFontMetrics();
2690 int fh = fm.getHeight();
2692 g.setColor(Color.black);
2693 // TODO: update this text for each release or centrally store it for
2694 // lite and application
2695 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2696 g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
2697 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2698 g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
2699 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2701 MessageManager.getString("label.jalview_authors_1"),
2703 g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
2705 MessageManager.getString("label.jalview_dev_managers"),
2708 MessageManager.getString("label.jalview_distribution_lists"),
2710 g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
2712 MessageManager.getString("label.jalview_cite_1_authors"),
2715 MessageManager.getString("label.jalview_cite_1_title"),
2717 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2722 Frame frame = new Frame();
2723 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2725 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
2729 public void showURL(String url, String target)
2731 if (viewport.applet == null)
2733 System.out.println("Not running as applet - no browser available.");
2737 viewport.applet.showURL(url, target);
2741 // ////////////////////////////////////////////////////////////////////////////////
2742 // JBuilder Graphics here
2744 MenuBar alignFrameMenuBar = new MenuBar();
2746 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2748 MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
2750 MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
2752 MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
2754 MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
2756 MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
2758 MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
2760 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2762 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2764 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2766 Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
2768 MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
2770 MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
2772 MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
2774 MenuItem remove2LeftMenuItem = new MenuItem();
2776 MenuItem remove2RightMenuItem = new MenuItem();
2778 MenuItem removeGappedColumnMenuItem = new MenuItem();
2780 MenuItem removeAllGapsMenuItem = new MenuItem();
2782 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2784 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2786 MenuItem sortPairwiseMenuItem = new MenuItem();
2788 MenuItem sortIDMenuItem = new MenuItem();
2790 MenuItem sortLengthMenuItem = new MenuItem();
2792 MenuItem sortGroupMenuItem = new MenuItem();
2794 MenuItem removeRedundancyMenuItem = new MenuItem();
2796 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2798 MenuItem PCAMenuItem = new MenuItem();
2800 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2802 MenuItem neighbourTreeMenuItem = new MenuItem();
2804 BorderLayout borderLayout1 = new BorderLayout();
2806 public Label statusBar = new Label();
2808 Menu outputTextboxMenu = new Menu();
2810 MenuItem clustalColour = new MenuItem();
2812 MenuItem zappoColour = new MenuItem();
2814 MenuItem taylorColour = new MenuItem();
2816 MenuItem hydrophobicityColour = new MenuItem();
2818 MenuItem helixColour = new MenuItem();
2820 MenuItem strandColour = new MenuItem();
2822 MenuItem turnColour = new MenuItem();
2824 MenuItem buriedColour = new MenuItem();
2826 MenuItem purinePyrimidineColour = new MenuItem();
2828 MenuItem RNAHelixColour = new MenuItem();
2830 MenuItem userDefinedColour = new MenuItem();
2832 MenuItem PIDColour = new MenuItem();
2834 MenuItem BLOSUM62Colour = new MenuItem();
2836 MenuItem tcoffeeColour = new MenuItem();
2838 MenuItem njTreeBlosumMenuItem = new MenuItem();
2840 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2842 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2844 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2846 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2848 MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
2850 MenuItem overviewMenuItem = new MenuItem();
2852 MenuItem undoMenuItem = new MenuItem();
2854 MenuItem redoMenuItem = new MenuItem();
2856 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2858 MenuItem noColourmenuItem = new MenuItem();
2860 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2862 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2864 MenuItem findMenuItem = new MenuItem();
2866 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2868 MenuItem nucleotideColour = new MenuItem();
2870 MenuItem deleteGroups = new MenuItem();
2872 MenuItem grpsFromSelection = new MenuItem();
2874 MenuItem createGroup = new MenuItem();
2876 MenuItem unGroup = new MenuItem();
2878 MenuItem delete = new MenuItem();
2880 MenuItem copy = new MenuItem();
2882 MenuItem cut = new MenuItem();
2884 Menu pasteMenu = new Menu();
2886 MenuItem pasteNew = new MenuItem();
2888 MenuItem pasteThis = new MenuItem();
2890 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2892 MenuItem font = new MenuItem();
2894 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2896 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2898 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2900 MenuItem modifyPID = new MenuItem();
2902 MenuItem modifyConservation = new MenuItem();
2904 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2905 "Autocalculate Consensus", true);
2907 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2908 "Sort Alignment With New Tree", true);
2910 Menu sortByTreeMenu = new Menu();
2912 Menu sort = new Menu();
2914 Menu calculate = new Menu();
2916 MenuItem inputText = new MenuItem();
2918 Menu helpMenu = new Menu();
2920 MenuItem documentation = new MenuItem();
2922 MenuItem about = new MenuItem();
2924 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2926 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2928 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2930 Menu autoAnnMenu = new Menu();
2932 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2934 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2936 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2938 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2940 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2942 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2944 private void jbInit() throws Exception
2947 setMenuBar(alignFrameMenuBar);
2951 // dynamically fill save as menu with available formats
2952 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2955 item = new MenuItem(
2956 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2958 item.addActionListener(new java.awt.event.ActionListener()
2961 public void actionPerformed(ActionEvent e)
2963 outputText_actionPerformed(e);
2967 outputTextboxMenu.add(item);
2969 closeMenuItem.addActionListener(this);
2970 loadApplication.addActionListener(this);
2972 loadTree.addActionListener(this);
2973 loadAnnotations.addActionListener(this);
2974 outputFeatures.addActionListener(this);
2975 outputAnnotations.addActionListener(this);
2976 selectAllSequenceMenuItem.addActionListener(this);
2977 deselectAllSequenceMenuItem.addActionListener(this);
2978 invertSequenceMenuItem.addActionListener(this);
2979 remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
2980 remove2LeftMenuItem.addActionListener(this);
2981 remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
2982 remove2RightMenuItem.addActionListener(this);
2983 removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
2984 removeGappedColumnMenuItem.addActionListener(this);
2985 removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
2986 removeAllGapsMenuItem.addActionListener(this);
2987 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
2988 viewBoxesMenuItem.setState(true);
2989 viewBoxesMenuItem.addItemListener(this);
2990 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
2991 viewTextMenuItem.setState(true);
2992 viewTextMenuItem.addItemListener(this);
2993 sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
2994 sortPairwiseMenuItem.addActionListener(this);
2995 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
2996 sortIDMenuItem.addActionListener(this);
2997 sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
2998 sortLengthMenuItem.addActionListener(this);
2999 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3000 sortGroupMenuItem.addActionListener(this);
3001 removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
3002 removeRedundancyMenuItem.addActionListener(this);
3003 pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
3004 pairwiseAlignmentMenuItem.addActionListener(this);
3005 PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
3006 PCAMenuItem.addActionListener(this);
3007 averageDistanceTreeMenuItem
3008 .setLabel(MessageManager.getString("label.average_distance_identity"));
3009 averageDistanceTreeMenuItem.addActionListener(this);
3010 neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
3011 neighbourTreeMenuItem.addActionListener(this);
3012 statusBar.setBackground(Color.white);
3013 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3014 statusBar.setText(MessageManager.getString("label.status_bar"));
3015 outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
3016 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3018 clustalColour.addActionListener(this);
3019 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3020 zappoColour.addActionListener(this);
3021 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3022 taylorColour.addActionListener(this);
3023 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
3024 hydrophobicityColour.addActionListener(this);
3025 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
3026 helixColour.addActionListener(this);
3027 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
3028 strandColour.addActionListener(this);
3029 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3030 turnColour.addActionListener(this);
3031 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3032 buriedColour.addActionListener(this);
3033 purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
3034 purinePyrimidineColour.addActionListener(this);
3035 RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
3036 RNAHelixColour.addActionListener(this);
3037 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
3038 userDefinedColour.addActionListener(this);
3039 PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
3040 PIDColour.addActionListener(this);
3041 BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
3042 BLOSUM62Colour.addActionListener(this);
3043 tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
3044 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3046 tcoffeeColour.addActionListener(this);
3047 avDistanceTreeBlosumMenuItem
3048 .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
3049 avDistanceTreeBlosumMenuItem.addActionListener(this);
3050 njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
3051 njTreeBlosumMenuItem.addActionListener(this);
3052 annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
3053 annotationPanelMenuItem.addItemListener(this);
3054 colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
3055 colourTextMenuItem.addItemListener(this);
3056 displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
3057 displayNonconservedMenuItem.addItemListener(this);
3058 alProperties.addActionListener(this);
3059 overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
3060 overviewMenuItem.addActionListener(this);
3061 undoMenuItem.setEnabled(false);
3062 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3063 undoMenuItem.addActionListener(this);
3064 redoMenuItem.setEnabled(false);
3065 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3066 redoMenuItem.addActionListener(this);
3067 conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
3068 conservationMenuItem.addItemListener(this);
3069 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3070 noColourmenuItem.addActionListener(this);
3071 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3072 wrapMenuItem.addItemListener(this);
3073 renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
3074 renderGapsMenuItem.setState(true);
3075 renderGapsMenuItem.addItemListener(this);
3076 findMenuItem.setLabel(MessageManager.getString("action.find"));
3077 findMenuItem.addActionListener(this);
3078 abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
3079 abovePIDThreshold.addItemListener(this);
3080 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3081 nucleotideColour.addActionListener(this);
3082 deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
3083 deleteGroups.addActionListener(this);
3084 grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
3085 grpsFromSelection.addActionListener(this);
3086 createGroup.setLabel(MessageManager.getString("action.create_group"));
3087 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3088 copy.setLabel(MessageManager.getString("action.copy"));
3089 copy.addActionListener(this);
3090 cut.setLabel(MessageManager.getString("action.cut"));
3091 cut.addActionListener(this);
3092 delete.setLabel(MessageManager.getString("action.delete"));
3093 delete.addActionListener(this);
3094 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3095 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3096 pasteNew.addActionListener(this);
3097 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3098 pasteThis.addActionListener(this);
3099 applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
3100 applyToAllGroups.setState(true);
3101 applyToAllGroups.addItemListener(this);
3102 font.setLabel(MessageManager.getString("action.font"));
3103 font.addActionListener(this);
3104 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3105 scaleAbove.setState(true);
3106 scaleAbove.setEnabled(false);
3107 scaleAbove.addItemListener(this);
3108 scaleLeft.setEnabled(false);
3109 scaleLeft.setState(true);
3110 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3111 scaleLeft.addItemListener(this);
3112 scaleRight.setEnabled(false);
3113 scaleRight.setState(true);
3114 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3115 scaleRight.addItemListener(this);
3116 modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
3117 modifyPID.addActionListener(this);
3118 modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
3119 modifyConservation.addActionListener(this);
3120 sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
3121 sort.setLabel(MessageManager.getString("action.sort"));
3122 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3123 autoCalculate.addItemListener(this);
3124 sortByTree.addItemListener(this);
3125 inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
3126 inputText.addActionListener(this);
3127 centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
3128 centreColumnLabelFlag.addItemListener(this);
3129 followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
3130 followMouseOverFlag.addItemListener(this);
3131 helpMenu.setLabel(MessageManager.getString("action.help"));
3132 documentation.setLabel(MessageManager.getString("label.documentation"));
3133 documentation.addActionListener(this);
3135 about.setLabel(MessageManager.getString("label.about"));
3136 about.addActionListener(this);
3137 seqLimits.setState(true);
3138 seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
3139 seqLimits.addItemListener(this);
3140 featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
3141 featureSettings.addActionListener(this);
3142 sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
3143 sequenceFeatures.addItemListener(this);
3144 sequenceFeatures.setState(false);
3145 annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
3146 annotationColour.addActionListener(this);
3147 invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
3148 invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
3149 menu1.setLabel(MessageManager.getString("action.show"));
3150 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3151 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3152 menu2.setLabel(MessageManager.getString("aciton.hide"));
3153 hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
3154 hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
3155 hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
3156 hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
3157 showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
3158 showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
3159 showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
3160 showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
3161 showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
3162 normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
3163 applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
3164 applyAutoAnnotationSettings.setState(true);
3165 autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
3167 invertColSel.addActionListener(this);
3168 showColumns.addActionListener(this);
3169 showSeqs.addActionListener(this);
3170 hideColumns.addActionListener(this);
3171 hideSequences.addActionListener(this);
3172 hideAllButSelection.addActionListener(this);
3173 hideAllSelection.addActionListener(this);
3174 showAllHidden.addActionListener(this);
3175 showGroupConsensus.addItemListener(this);
3176 showGroupConservation.addItemListener(this);
3177 showConsensusHistogram.addItemListener(this);
3178 showSequenceLogo.addItemListener(this);
3179 normSequenceLogo.addItemListener(this);
3181 applyAutoAnnotationSettings.addItemListener(this);
3182 formatMenu.setLabel(MessageManager.getString("action.format"));
3183 selectMenu.setLabel(MessageManager.getString("action.select"));
3184 newView.setLabel(MessageManager.getString("action.new_view"));
3185 newView.addActionListener(this);
3186 alignFrameMenuBar.add(fileMenu);
3187 alignFrameMenuBar.add(editMenu);
3188 alignFrameMenuBar.add(selectMenu);
3189 alignFrameMenuBar.add(viewMenu);
3190 alignFrameMenuBar.add(formatMenu);
3191 alignFrameMenuBar.add(colourMenu);
3192 alignFrameMenuBar.add(calculateMenu);
3193 alignFrameMenuBar.add(helpMenu);
3195 fileMenu.add(inputText);
3196 fileMenu.add(loadTree);
3197 fileMenu.add(loadAnnotations);
3199 fileMenu.addSeparator();
3200 fileMenu.add(outputTextboxMenu);
3201 fileMenu.add(outputFeatures);
3202 fileMenu.add(outputAnnotations);
3204 if (jalviewServletURL != null)
3206 fileMenu.add(loadApplication);
3209 fileMenu.addSeparator();
3210 fileMenu.add(closeMenuItem);
3212 editMenu.add(undoMenuItem);
3213 editMenu.add(redoMenuItem);
3216 editMenu.add(pasteMenu);
3217 editMenu.add(delete);
3218 editMenu.addSeparator();
3219 editMenu.add(remove2LeftMenuItem);
3220 editMenu.add(remove2RightMenuItem);
3221 editMenu.add(removeGappedColumnMenuItem);
3222 editMenu.add(removeAllGapsMenuItem);
3223 editMenu.add(removeRedundancyMenuItem);
3224 viewMenu.add(newView);
3225 viewMenu.addSeparator();
3226 viewMenu.add(menu1);
3227 viewMenu.add(menu2);
3228 viewMenu.addSeparator();
3229 viewMenu.add(followMouseOverFlag);
3230 viewMenu.add(annotationPanelMenuItem);
3231 autoAnnMenu.add(applyAutoAnnotationSettings);
3232 autoAnnMenu.add(showConsensusHistogram);
3233 autoAnnMenu.add(showSequenceLogo);
3234 autoAnnMenu.add(normSequenceLogo);
3235 autoAnnMenu.addSeparator();
3236 autoAnnMenu.add(showGroupConservation);
3237 autoAnnMenu.add(showGroupConsensus);
3238 viewMenu.add(autoAnnMenu);
3239 viewMenu.addSeparator();
3240 viewMenu.add(sequenceFeatures);
3241 viewMenu.add(featureSettings);
3242 viewMenu.addSeparator();
3243 viewMenu.add(alProperties);
3244 viewMenu.addSeparator();
3245 viewMenu.add(overviewMenuItem);
3246 colourMenu.add(applyToAllGroups);
3247 colourMenu.addSeparator();
3248 colourMenu.add(noColourmenuItem);
3249 colourMenu.add(clustalColour);
3250 colourMenu.add(BLOSUM62Colour);
3251 colourMenu.add(PIDColour);
3252 colourMenu.add(zappoColour);
3253 colourMenu.add(taylorColour);
3254 colourMenu.add(hydrophobicityColour);
3255 colourMenu.add(helixColour);
3256 colourMenu.add(strandColour);
3257 colourMenu.add(turnColour);
3258 colourMenu.add(buriedColour);
3259 colourMenu.add(nucleotideColour);
3260 colourMenu.add(purinePyrimidineColour);
3261 colourMenu.add(tcoffeeColour);
3262 colourMenu.add(userDefinedColour);
3263 colourMenu.addSeparator();
3264 colourMenu.add(conservationMenuItem);
3265 colourMenu.add(modifyConservation);
3266 colourMenu.add(abovePIDThreshold);
3267 colourMenu.add(modifyPID);
3268 colourMenu.add(annotationColour);
3269 colourMenu.add(RNAHelixColour);
3270 calculateMenu.add(sort);
3271 calculateMenu.add(calculate);
3272 calculateMenu.addSeparator();
3273 calculateMenu.add(pairwiseAlignmentMenuItem);
3274 calculateMenu.add(PCAMenuItem);
3275 calculateMenu.add(autoCalculate);
3276 calculateMenu.add(sortByTree);
3277 this.add(statusBar, BorderLayout.SOUTH);
3278 pasteMenu.add(pasteNew);
3279 pasteMenu.add(pasteThis);
3280 sort.add(sortIDMenuItem);
3281 sort.add(sortLengthMenuItem);
3282 sort.add(sortByTreeMenu);
3283 sort.add(sortGroupMenuItem);
3284 sort.add(sortPairwiseMenuItem);
3285 calculate.add(averageDistanceTreeMenuItem);
3286 calculate.add(neighbourTreeMenuItem);
3287 calculate.add(avDistanceTreeBlosumMenuItem);
3288 calculate.add(njTreeBlosumMenuItem);
3289 helpMenu.add(documentation);
3290 helpMenu.add(about);
3291 menu1.add(showColumns);
3292 menu1.add(showSeqs);
3293 menu1.add(showAllHidden);
3294 menu2.add(hideColumns);
3295 menu2.add(hideSequences);
3296 menu2.add(hideAllSelection);
3297 menu2.add(hideAllButSelection);
3298 formatMenu.add(font);
3299 formatMenu.add(seqLimits);
3300 formatMenu.add(wrapMenuItem);
3301 formatMenu.add(scaleAbove);
3302 formatMenu.add(scaleLeft);
3303 formatMenu.add(scaleRight);
3304 formatMenu.add(viewBoxesMenuItem);
3305 formatMenu.add(viewTextMenuItem);
3306 formatMenu.add(colourTextMenuItem);
3307 formatMenu.add(displayNonconservedMenuItem);
3308 formatMenu.add(renderGapsMenuItem);
3309 formatMenu.add(centreColumnLabelFlag);
3310 selectMenu.add(findMenuItem);
3311 selectMenu.addSeparator();
3312 selectMenu.add(selectAllSequenceMenuItem);
3313 selectMenu.add(deselectAllSequenceMenuItem);
3314 selectMenu.add(invertSequenceMenuItem);
3315 selectMenu.add(invertColSel);
3316 selectMenu.add(createGroup);
3317 selectMenu.add(unGroup);
3318 selectMenu.add(grpsFromSelection);
3319 selectMenu.add(deleteGroups);
3323 MenuItem featureSettings = new MenuItem();
3325 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3327 MenuItem annotationColour = new MenuItem();
3329 MenuItem invertColSel = new MenuItem();
3331 Menu menu1 = new Menu();
3333 MenuItem showColumns = new MenuItem();
3335 MenuItem showSeqs = new MenuItem();
3337 Menu menu2 = new Menu();
3339 MenuItem hideColumns = new MenuItem();
3341 MenuItem hideSequences = new MenuItem();
3343 MenuItem hideAllButSelection = new MenuItem();
3345 MenuItem hideAllSelection = new MenuItem();
3347 MenuItem showAllHidden = new MenuItem();
3349 Menu formatMenu = new Menu();
3351 Menu selectMenu = new Menu();
3353 MenuItem newView = new MenuItem();
3356 * Attach the alignFrame panels after embedding menus, if necessary. This used
3357 * to be called setEmbedded, but is now creates the dropdown menus in a
3358 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3360 * @param reallyEmbedded
3361 * true to attach the view to the applet area on the page rather than
3364 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3369 // Explicly build the embedded menu panel for the on-page applet
3371 // view cannot be closed if its actually on the page
3372 fileMenu.remove(closeMenuItem);
3373 fileMenu.remove(3); // Remove Seperator
3374 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3375 Font.PLAIN, 10, false); // use our own fonts.
3376 // and actually add the components to the applet area
3377 viewport.applet.setLayout(new BorderLayout());
3378 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3379 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3380 alignPanel.setSize(viewport.applet.getSize().width,
3381 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3382 - statusBar.HEIGHT);
3383 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3384 final AlignFrame me = this;
3385 viewport.applet.addFocusListener(new FocusListener()
3389 public void focusLost(FocusEvent e)
3391 if (me.viewport.applet.currentAlignFrame == me)
3393 me.viewport.applet.currentAlignFrame = null;
3398 public void focusGained(FocusEvent e)
3400 me.viewport.applet.currentAlignFrame = me;
3403 viewport.applet.validate();
3408 // test and embed menu bar if necessary.
3410 if (embedMenuIfNeeded(alignPanel))
3412 // adjust for status bar height too
3413 alignPanel.setSize(getSize().width, getSize().height
3414 - statusBar.HEIGHT);
3416 add(statusBar, BorderLayout.SOUTH);
3417 add(alignPanel, BorderLayout.CENTER);
3418 // and register with the applet so it can pass external API calls to us
3419 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3425 * create a new binding between structures in an existing jmol viewer instance
3426 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3427 * this does not open a new Jmol window, or modify the display of the
3428 * structures in the original jmol window. Note This method doesn't work
3429 * without an additional javascript library to exchange messages between the
3430 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3433 * JmolViewer instance
3434 * @param sequenceIds
3435 * - sequence Ids to search for associations
3437 public SequenceStructureBinding addStructureViewInstance(
3438 Object jmolviewer, String[] sequenceIds)
3440 org.jmol.api.JmolViewer viewer = null;
3443 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3444 } catch (ClassCastException ex)
3446 System.err.println("Unsupported viewer object :"
3447 + jmolviewer.getClass());
3451 System.err.println("Can't use this object as a structure viewer:"
3452 + jmolviewer.getClass());
3455 SequenceI[] seqs = null;
3456 if (sequenceIds == null || sequenceIds.length == 0)
3458 seqs = viewport.getAlignment().getSequencesArray();
3462 Vector sqi = new Vector();
3463 AlignmentI al = viewport.getAlignment();
3464 for (int sid = 0; sid < sequenceIds.length; sid++)
3466 SequenceI sq = al.findName(sequenceIds[sid]);
3474 seqs = new SequenceI[sqi.size()];
3475 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3477 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3486 // TODO: search for a jmv that involves viewer
3488 { // create a new viewer/jalview binding.
3489 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3497 * bind a pdb file to a sequence in the current view
3500 * - sequenceId within the dataset.
3501 * @param pdbEntryString
3502 * - the short name for the PDB file
3504 * - pdb file - either a URL or a valid PDB file.
3505 * @return true if binding was as success TODO: consider making an exception
3506 * structure for indicating when PDB parsing or sequenceId location
3509 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3512 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3513 boolean needtoadd = false;
3514 if (toaddpdb != null)
3516 Vector pdbe = toaddpdb.getPDBId();
3517 PDBEntry pdbentry = null;
3518 if (pdbe != null && pdbe.size() > 0)
3520 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3522 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3523 if (!pdbentry.getId().equals(pdbEntryString)
3524 && !pdbentry.getFile().equals(pdbFile))
3534 if (pdbentry == null)
3536 pdbentry = new PDBEntry();
3537 pdbentry.setId(pdbEntryString);
3538 pdbentry.setFile(pdbFile);
3539 needtoadd = true; // add this new entry to sequence.
3541 // resolve data source
3542 // TODO: this code should be a refactored to an io package
3543 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3544 if (protocol == null)
3550 // make a note of the access mode and add
3551 if (pdbentry.getProperty() == null)
3553 pdbentry.setProperty(new Hashtable());
3555 pdbentry.getProperty().put("protocol", protocol);
3556 toaddpdb.addPDBId(pdbentry);
3562 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3566 Vector sequences = new Vector();
3567 for (int i = 0; i < seqs.length; i++)
3569 if (seqs[i] != null)
3571 sequences.addElement(new Object[]
3572 { seqs[i], (chains != null) ? chains[i] : null });
3575 seqs = new SequenceI[sequences.size()];
3576 chains = new String[sequences.size()];
3577 for (int i = 0, isize = sequences.size(); i < isize; i++)
3579 Object[] oj = (Object[]) sequences.elementAt(i);
3581 seqs[i] = (SequenceI) oj[0];
3582 chains[i] = (String) oj[1];
3590 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3591 SequenceI[] seqs, String[] chains, String protocol)
3593 // Scrub any null sequences from the array
3594 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3595 seqs = (SequenceI[]) sqch[0];
3596 chains = (String[]) sqch[1];
3597 if (seqs == null || seqs.length == 0)
3600 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3602 if (protocol == null || protocol.trim().length() == 0
3603 || protocol.equals("null"))
3605 protocol = (String) pdb.getProperty().get("protocol");
3606 if (protocol == null)
3608 System.err.println("Couldn't work out protocol to open structure: "
3613 if (applet.useXtrnalSviewer)
3615 // register the association(s) and quit, don't create any windows.
3616 if (StructureSelectionManager.getStructureSelectionManager(applet)
3617 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3619 System.err.println("Failed to map " + pdb.getFile() + " ("
3620 + protocol + ") to any sequences");
3624 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3626 // can only do alignments with Jmol
3627 // find the last jmol window assigned to this alignment
3628 jalview.appletgui.AppletJmol ajm = null, tajm;
3629 Vector jmols = applet
3630 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3631 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3633 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3634 if (tajm.ap.alignFrame == this)
3643 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3644 // try and add the pdb structure
3649 // otherwise, create a new window
3650 if (applet.jmolAvailable)
3652 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3654 applet.lastFrameX += 40;
3655 applet.lastFrameY += 40;
3659 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3664 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3665 SequenceI[][] seqs, String[][] chains, String[] protocols)
3667 // TODO Auto-generated method stub
3668 System.err.println("Aligned Structure View: Not yet implemented.");
3672 * modify the current selection, providing the user has not made a selection
3676 * - sequences from this alignment
3678 * - columns to be selected on the alignment
3680 public void select(SequenceGroup sel, ColumnSelection csel)
3682 alignPanel.seqPanel.selection(sel, csel, null);
3685 public void scrollTo(int row, int column)
3687 alignPanel.seqPanel.scrollTo(row, column);
3690 public void scrollToRow(int row)
3692 alignPanel.seqPanel.scrollToRow(row);
3695 public void scrollToColumn(int column)
3697 alignPanel.seqPanel.scrollToColumn(column);
3701 * @return the alignments unique ID.
3703 public String getSequenceSetId()
3705 return viewport.getSequenceSetId();
3709 * Load the (T-Coffee) score file from the specified url
3712 * File/URL/T-COFFEE score file contents
3713 * @throws IOException
3714 * @return true if alignment was annotated with data from source
3716 public boolean loadScoreFile(String source) throws IOException
3719 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3720 AppletFormatAdapter.checkProtocol(source));
3721 if (!file.isValid())
3723 // TODO: raise dialog for gui
3724 System.err.println("Problems parsing T-Coffee scores: "
3725 + file.getWarningMessage());
3726 System.err.println("Origin was:\n" + source);
3731 * check that the score matrix matches the alignment dimensions
3734 if ((aln = viewport.getAlignment()) != null
3735 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3738 // TODO: raise a dialog box here rather than bomb out.
3740 .println("The scores matrix does not match the alignment dimensions");
3744 // TODO add parameter to indicate if matching should be done
3745 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3747 alignPanel.fontChanged();
3748 tcoffeeColour.setEnabled(true);
3749 // switch to this color
3750 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3755 System.err.println("Problems resolving T-Coffee scores:");
3756 if (file.getWarningMessage() != null)
3758 System.err.println(file.getWarningMessage());