2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.FeatureRenderer;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.CommandI;
30 import jalview.commands.EditCommand;
31 import jalview.commands.EditCommand.Action;
32 import jalview.commands.OrderCommand;
33 import jalview.commands.RemoveGapColCommand;
34 import jalview.commands.RemoveGapsCommand;
35 import jalview.commands.SlideSequencesCommand;
36 import jalview.commands.TrimRegionCommand;
37 import jalview.datamodel.Alignment;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.ColumnSelection;
41 import jalview.datamodel.PDBEntry;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceGroup;
44 import jalview.datamodel.SequenceI;
45 import jalview.io.AnnotationFile;
46 import jalview.io.AppletFormatAdapter;
47 import jalview.io.FeaturesFile;
48 import jalview.io.TCoffeeScoreFile;
49 import jalview.schemes.Blosum62ColourScheme;
50 import jalview.schemes.BuriedColourScheme;
51 import jalview.schemes.ClustalxColourScheme;
52 import jalview.schemes.ColourSchemeI;
53 import jalview.schemes.HelixColourScheme;
54 import jalview.schemes.HydrophobicColourScheme;
55 import jalview.schemes.NucleotideColourScheme;
56 import jalview.schemes.PIDColourScheme;
57 import jalview.schemes.PurinePyrimidineColourScheme;
58 import jalview.schemes.RNAHelicesColourChooser;
59 import jalview.schemes.RNAInteractionColourScheme;
60 import jalview.schemes.StrandColourScheme;
61 import jalview.schemes.TCoffeeColourScheme;
62 import jalview.schemes.TaylorColourScheme;
63 import jalview.schemes.TurnColourScheme;
64 import jalview.schemes.ZappoColourScheme;
65 import jalview.structure.StructureSelectionManager;
66 import jalview.util.MessageManager;
68 import java.awt.BorderLayout;
69 import java.awt.Canvas;
70 import java.awt.CheckboxMenuItem;
71 import java.awt.Color;
73 import java.awt.FontMetrics;
74 import java.awt.Frame;
75 import java.awt.Graphics;
76 import java.awt.Label;
78 import java.awt.MenuBar;
79 import java.awt.MenuItem;
80 import java.awt.event.ActionEvent;
81 import java.awt.event.ActionListener;
82 import java.awt.event.FocusEvent;
83 import java.awt.event.FocusListener;
84 import java.awt.event.ItemEvent;
85 import java.awt.event.ItemListener;
86 import java.awt.event.KeyEvent;
87 import java.awt.event.KeyListener;
88 import java.awt.event.WindowAdapter;
89 import java.awt.event.WindowEvent;
90 import java.io.IOException;
92 import java.net.URLEncoder;
93 import java.util.Arrays;
94 import java.util.Hashtable;
95 import java.util.List;
97 import java.util.StringTokenizer;
98 import java.util.Vector;
100 public class AlignFrame extends EmbmenuFrame implements ActionListener,
101 ItemListener, KeyListener, AlignViewControllerGuiI
103 public AlignViewControllerI avc;
105 public AlignmentPanel alignPanel;
107 public AlignViewport viewport;
109 int DEFAULT_WIDTH = 700;
111 int DEFAULT_HEIGHT = 500;
113 String jalviewServletURL;
115 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
116 String title, boolean embedded)
120 jalviewServletURL = applet.getParameter("APPLICATION_URL");
126 } catch (Exception ex)
128 ex.printStackTrace();
130 // need to get window geometry before we calculate alignment layout
136 param = applet.getParameter("windowWidth");
139 int width = Integer.parseInt(param);
140 DEFAULT_WIDTH = width;
142 param = applet.getParameter("windowHeight");
145 int height = Integer.parseInt(param);
146 DEFAULT_HEIGHT = height;
148 } catch (Exception ex)
152 viewport = new AlignViewport(al, applet);
153 alignPanel = new AlignmentPanel(this, viewport);
154 avc = new jalview.controller.AlignViewController(this, viewport,
156 viewport.updateConservation(alignPanel);
157 viewport.updateConsensus(alignPanel);
159 annotationPanelMenuItem.setState(viewport.showAnnotation);
160 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
161 followMouseOverFlag.setState(viewport.getFollowHighlight());
162 showGroupConsensus.setState(viewport.isShowGroupConsensus());
163 showGroupConservation.setState(viewport.isShowGroupConservation());
164 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
165 showSequenceLogo.setState(viewport.isShowSequenceLogo());
166 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
167 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
169 seqLimits.setState(viewport.showJVSuffix);
173 String param = applet.getParameter("sortBy");
176 if (param.equalsIgnoreCase("Id"))
178 sortIDMenuItem_actionPerformed();
180 else if (param.equalsIgnoreCase("Pairwise Identity"))
182 sortPairwiseMenuItem_actionPerformed();
184 else if (param.equalsIgnoreCase("Length"))
186 sortLengthMenuItem_actionPerformed();
190 param = applet.getParameter("wrap");
193 if (param.equalsIgnoreCase("true"))
195 wrapMenuItem.setState(true);
196 wrapMenuItem_actionPerformed();
199 param = applet.getParameter("centrecolumnlabels");
202 centreColumnLabelFlag.setState(true);
203 centreColumnLabelFlag_stateChanged();
207 if (viewport.getAlignment().isNucleotide())
209 viewport.updateStrucConsensus(alignPanel);
210 if (viewport.getAlignment().hasRNAStructure())
212 RNAHelixColour.setEnabled(true);
216 RNAHelixColour.setEnabled(false);
221 RNAHelixColour.setEnabled(false);
222 purinePyrimidineColour.setEnabled(false);
224 // Some JVMS send keyevents to Top frame or lowest panel,
225 // Havent worked out why yet. So add to both this frame and seqCanvas for
227 this.addKeyListener(this);
228 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
229 alignPanel.idPanel.idCanvas.addKeyListener(this);
230 alignPanel.scalePanel.addKeyListener(this);
231 alignPanel.annotationPanel.addKeyListener(this);
232 alignPanel.annotationPanelHolder.addKeyListener(this);
233 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
234 alignPanel.alabels.addKeyListener(this);
235 createAlignFrameWindow(embedded, title);
238 alignPanel.adjustAnnotationHeight();
239 alignPanel.paintAlignment(true);
242 public AlignViewport getAlignViewport()
247 public SeqCanvas getSeqcanvas()
249 return alignPanel.seqPanel.seqCanvas;
253 * Load a features file onto the alignment
256 * file URL, content, or other resolvable path
258 * is protocol for accessing data referred to by file
261 public boolean parseFeaturesFile(String file, String type)
263 return parseFeaturesFile(file, type, true);
267 * Load a features file onto the alignment
270 * file URL, content, or other resolvable path
272 * is protocol for accessing data referred to by file
273 * @param autoenabledisplay
274 * when true, display features flag will be automatically enabled if
275 * features are loaded
276 * @return true if data parsed as a features file
278 public boolean parseFeaturesFile(String file, String type,
279 boolean autoenabledisplay)
281 // TODO: test if importing a features file onto an alignment which already
282 // has features with links overwrites the original links.
284 Hashtable featureLinks = new Hashtable();
285 boolean featuresFile = false;
288 featuresFile = new jalview.io.FeaturesFile(file, type)
289 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
290 .getFeatureRenderer().getFeatureColours(), featureLinks,
291 true, viewport.applet.getDefaultParameter(
292 "relaxedidmatch", false));
293 } catch (Exception ex)
295 ex.printStackTrace();
300 if (featureLinks.size() > 0)
302 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
304 if (autoenabledisplay)
306 viewport.setShowSequenceFeatures(true);
307 sequenceFeatures.setState(true);
309 if (alignPanel.seqPanel.seqCanvas.fr != null)
311 // update the min/max ranges where necessary
312 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
314 if (viewport.featureSettings != null)
316 viewport.featureSettings.refreshTable();
318 alignPanel.paintAlignment(true);
319 statusBar.setText(MessageManager
320 .getString("label.successfully_added_features_alignment"));
326 public void keyPressed(KeyEvent evt)
328 if (viewport.cursorMode
329 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
330 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
331 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
332 && Character.isDigit(evt.getKeyChar()))
334 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
337 switch (evt.getKeyCode())
339 case 27: // escape key
340 deselectAllSequenceMenuItem_actionPerformed();
342 alignPanel.alabels.cancelDrag();
345 if (evt.isControlDown() || evt.isMetaDown())
347 cut_actionPerformed();
351 if (viewport.cursorMode && !evt.isControlDown())
353 alignPanel.seqPanel.setCursorColumn();
355 if (evt.isControlDown() || evt.isMetaDown())
357 copy_actionPerformed();
361 if (evt.isControlDown())
363 paste(evt.isShiftDown());
367 if (evt.isControlDown() || evt.isMetaDown())
369 selectAllSequenceMenuItem_actionPerformed();
372 case KeyEvent.VK_DOWN:
373 if (viewport.cursorMode)
375 alignPanel.seqPanel.moveCursor(0, 1);
379 moveSelectedSequences(false);
384 if (viewport.cursorMode)
386 alignPanel.seqPanel.moveCursor(0, -1);
390 moveSelectedSequences(true);
394 case KeyEvent.VK_LEFT:
395 if (evt.isAltDown() || !viewport.cursorMode)
397 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
401 alignPanel.seqPanel.moveCursor(-1, 0);
405 case KeyEvent.VK_RIGHT:
406 if (evt.isAltDown() || !viewport.cursorMode)
408 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
412 alignPanel.seqPanel.moveCursor(1, 0);
416 case KeyEvent.VK_SPACE:
417 if (viewport.cursorMode)
419 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
420 || evt.isShiftDown() || evt.isAltDown());
424 case KeyEvent.VK_DELETE:
425 case KeyEvent.VK_BACK_SPACE:
426 if (viewport.cursorMode)
428 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
429 || evt.isShiftDown() || evt.isAltDown());
433 cut_actionPerformed();
434 alignPanel.seqPanel.seqCanvas.repaint();
439 if (viewport.cursorMode)
441 alignPanel.seqPanel.setCursorRow();
445 if (viewport.cursorMode)
447 alignPanel.seqPanel.setCursorPosition();
451 case KeyEvent.VK_ENTER:
452 case KeyEvent.VK_COMMA:
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.setCursorRowAndColumn();
460 if (viewport.cursorMode)
462 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
466 if (viewport.cursorMode)
468 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
473 viewport.cursorMode = !viewport.cursorMode;
474 statusBar.setText(MessageManager.formatMessage(
475 "label.keyboard_editing_mode", new String[]
476 { (viewport.cursorMode ? "on" : "off") }));
477 if (viewport.cursorMode)
479 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
480 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
485 if (evt.isControlDown())
487 findMenuItem_actionPerformed();
493 boolean toggleSeqs = !evt.isControlDown();
494 boolean toggleCols = !evt.isShiftDown();
495 toggleHiddenRegions(toggleSeqs, toggleCols);
499 case KeyEvent.VK_PAGE_UP:
500 if (viewport.wrapAlignment)
502 alignPanel.scrollUp(true);
506 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
507 - viewport.endSeq + viewport.startSeq);
511 case KeyEvent.VK_PAGE_DOWN:
512 if (viewport.wrapAlignment)
514 alignPanel.scrollUp(false);
518 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
519 + viewport.endSeq - viewport.startSeq);
524 if (evt.isControlDown())
526 undoMenuItem_actionPerformed();
531 if (evt.isControlDown())
533 redoMenuItem_actionPerformed();
538 if (evt.isControlDown())
545 if (evt.isControlDown())
547 trimAlignment(false);
552 if (evt.isControlDown())
554 if (evt.isShiftDown())
556 this.removeAllGapsMenuItem_actionPerformed();
560 removeGappedColumnMenuItem_actionPerformed();
565 if (evt.isControlDown())
569 invertColSel_actionPerformed();
573 invertSequenceMenuItem_actionPerformed();
579 if (evt.isControlDown())
581 if (evt.isShiftDown())
583 this.unGroup_actionPerformed();
587 this.createGroup_actionPerformed();
593 if (evt.isControlDown())
595 this.deleteGroups_actionPerformed();
600 if (evt.isControlDown())
607 alignPanel.paintAlignment(true);
611 * called by key handler and the hide all/show all menu items
616 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
618 boolean hide = false;
619 SequenceGroup sg = viewport.getSelectionGroup();
620 if (!toggleSeqs && !toggleCols)
622 // Hide everything by the current selection - this is a hack - we do the
623 // invert and then hide
624 // first check that there will be visible columns after the invert.
625 if ((viewport.getColumnSelection() != null
626 && viewport.getColumnSelection().getSelected() != null && viewport
627 .getColumnSelection().getSelected().size() > 0)
628 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
631 // now invert the sequence set, if required - empty selection implies
632 // that no hiding is required.
635 invertSequenceMenuItem_actionPerformed();
636 sg = viewport.getSelectionGroup();
640 viewport.expandColSelection(sg, true);
641 // finally invert the column selection and get the new sequence
642 // selection and indicate it should be hidden.
643 invertColSel_actionPerformed();
650 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
653 viewport.hideAllSelectedSeqs();
655 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
658 viewport.showAllHiddenSeqs();
664 if (viewport.getColumnSelection().getSelected().size() > 0)
666 viewport.hideSelectedColumns();
669 viewport.setSelectionGroup(sg);
674 viewport.showAllHiddenColumns();
680 public void keyReleased(KeyEvent evt)
685 public void keyTyped(KeyEvent evt)
690 public void itemStateChanged(ItemEvent evt)
692 if (evt.getSource() == displayNonconservedMenuItem)
694 displayNonconservedMenuItem_actionPerformed();
696 else if (evt.getSource() == colourTextMenuItem)
698 colourTextMenuItem_actionPerformed();
700 else if (evt.getSource() == wrapMenuItem)
702 wrapMenuItem_actionPerformed();
704 else if (evt.getSource() == scaleAbove)
706 viewport.setScaleAboveWrapped(scaleAbove.getState());
708 else if (evt.getSource() == scaleLeft)
710 viewport.setScaleLeftWrapped(scaleLeft.getState());
712 else if (evt.getSource() == scaleRight)
714 viewport.setScaleRightWrapped(scaleRight.getState());
716 else if (evt.getSource() == seqLimits)
718 seqLimits_itemStateChanged();
720 else if (evt.getSource() == viewBoxesMenuItem)
722 viewport.setShowBoxes(viewBoxesMenuItem.getState());
724 else if (evt.getSource() == viewTextMenuItem)
726 viewport.setShowText(viewTextMenuItem.getState());
728 else if (evt.getSource() == renderGapsMenuItem)
730 viewport.setRenderGaps(renderGapsMenuItem.getState());
732 else if (evt.getSource() == annotationPanelMenuItem)
734 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
735 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
737 else if (evt.getSource() == sequenceFeatures)
739 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
740 alignPanel.seqPanel.seqCanvas.repaint();
742 else if (evt.getSource() == conservationMenuItem)
744 conservationMenuItem_actionPerformed();
746 else if (evt.getSource() == abovePIDThreshold)
748 abovePIDThreshold_actionPerformed();
750 else if (evt.getSource() == applyToAllGroups)
752 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
754 else if (evt.getSource() == autoCalculate)
756 viewport.autoCalculateConsensus = autoCalculate.getState();
758 else if (evt.getSource() == sortByTree)
760 viewport.sortByTree = sortByTree.getState();
762 else if (evt.getSource() == this.centreColumnLabelFlag)
764 centreColumnLabelFlag_stateChanged();
766 else if (evt.getSource() == this.followMouseOverFlag)
768 mouseOverFlag_stateChanged();
770 else if (evt.getSource() == showGroupConsensus)
772 showGroupConsensus_actionPerformed();
774 else if (evt.getSource() == showGroupConservation)
776 showGroupConservation_actionPerformed();
778 else if (evt.getSource() == showSequenceLogo)
780 showSequenceLogo_actionPerformed();
782 else if (evt.getSource() == normSequenceLogo)
784 normSequenceLogo_actionPerformed();
786 else if (evt.getSource() == showConsensusHistogram)
788 showConsensusHistogram_actionPerformed();
790 else if (evt.getSource() == applyAutoAnnotationSettings)
792 applyAutoAnnotationSettings_actionPerformed();
794 alignPanel.paintAlignment(true);
797 private void mouseOverFlag_stateChanged()
799 viewport.followHighlight = followMouseOverFlag.getState();
800 // TODO: could kick the scrollTo mechanism to reset view for current
804 private void centreColumnLabelFlag_stateChanged()
806 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
807 this.alignPanel.annotationPanel.repaint();
811 public void actionPerformed(ActionEvent evt)
813 Object source = evt.getSource();
815 if (source == inputText)
817 inputText_actionPerformed();
819 else if (source == loadTree)
821 loadTree_actionPerformed();
823 else if (source == loadApplication)
825 launchFullApplication();
827 else if (source == loadAnnotations)
831 else if (source == outputAnnotations)
833 outputAnnotations(true);
835 else if (source == outputFeatures)
837 outputFeatures(true, "Jalview");
839 else if (source == closeMenuItem)
841 closeMenuItem_actionPerformed();
843 else if (source == copy)
845 copy_actionPerformed();
847 else if (source == undoMenuItem)
849 undoMenuItem_actionPerformed();
851 else if (source == redoMenuItem)
853 redoMenuItem_actionPerformed();
855 else if (source == inputText)
857 inputText_actionPerformed();
859 else if (source == closeMenuItem)
861 closeMenuItem_actionPerformed();
863 else if (source == undoMenuItem)
865 undoMenuItem_actionPerformed();
867 else if (source == redoMenuItem)
869 redoMenuItem_actionPerformed();
871 else if (source == copy)
873 copy_actionPerformed();
875 else if (source == pasteNew)
877 pasteNew_actionPerformed();
879 else if (source == pasteThis)
881 pasteThis_actionPerformed();
883 else if (source == cut)
885 cut_actionPerformed();
887 else if (source == delete)
889 delete_actionPerformed();
891 else if (source == grpsFromSelection)
893 makeGrpsFromSelection_actionPerformed();
895 else if (source == deleteGroups)
897 deleteGroups_actionPerformed();
899 else if (source == selectAllSequenceMenuItem)
901 selectAllSequenceMenuItem_actionPerformed();
903 else if (source == deselectAllSequenceMenuItem)
905 deselectAllSequenceMenuItem_actionPerformed();
907 else if (source == invertSequenceMenuItem)
909 invertSequenceMenuItem_actionPerformed();
911 else if (source == invertColSel)
913 viewport.invertColumnSelection();
914 alignPanel.paintAlignment(true);
916 else if (source == remove2LeftMenuItem)
920 else if (source == remove2RightMenuItem)
922 trimAlignment(false);
924 else if (source == removeGappedColumnMenuItem)
926 removeGappedColumnMenuItem_actionPerformed();
928 else if (source == removeAllGapsMenuItem)
930 removeAllGapsMenuItem_actionPerformed();
932 else if (source == findMenuItem)
934 findMenuItem_actionPerformed();
936 else if (source == font)
938 new FontChooser(alignPanel);
940 else if (source == newView)
944 else if (source == showColumns)
946 viewport.showAllHiddenColumns();
947 alignPanel.paintAlignment(true);
949 else if (source == showSeqs)
951 viewport.showAllHiddenSeqs();
952 alignPanel.paintAlignment(true);
954 else if (source == hideColumns)
956 viewport.hideSelectedColumns();
957 alignPanel.paintAlignment(true);
959 else if (source == hideSequences
960 && viewport.getSelectionGroup() != null)
962 viewport.hideAllSelectedSeqs();
963 alignPanel.paintAlignment(true);
965 else if (source == hideAllButSelection)
967 toggleHiddenRegions(false, false);
968 alignPanel.paintAlignment(true);
970 else if (source == hideAllSelection)
972 SequenceGroup sg = viewport.getSelectionGroup();
973 viewport.expandColSelection(sg, false);
974 viewport.hideAllSelectedSeqs();
975 viewport.hideSelectedColumns();
976 alignPanel.paintAlignment(true);
978 else if (source == showAllHidden)
980 viewport.showAllHiddenColumns();
981 viewport.showAllHiddenSeqs();
982 alignPanel.paintAlignment(true);
984 else if (source == showGroupConsensus)
986 showGroupConsensus_actionPerformed();
988 else if (source == showGroupConservation)
990 showGroupConservation_actionPerformed();
992 else if (source == showSequenceLogo)
994 showSequenceLogo_actionPerformed();
996 else if (source == normSequenceLogo)
998 normSequenceLogo_actionPerformed();
1000 else if (source == showConsensusHistogram)
1002 showConsensusHistogram_actionPerformed();
1004 else if (source == applyAutoAnnotationSettings)
1006 applyAutoAnnotationSettings_actionPerformed();
1008 else if (source == featureSettings)
1010 new FeatureSettings(alignPanel);
1012 else if (source == alProperties)
1014 StringBuffer contents = new jalview.io.AlignmentProperties(
1015 viewport.getAlignment()).formatAsString();
1016 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1017 cap.setText(contents.toString());
1018 Frame frame = new Frame();
1020 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1021 "label.alignment_properties", new String[]
1022 { getTitle() }), 400, 250);
1024 else if (source == overviewMenuItem)
1026 overviewMenuItem_actionPerformed();
1028 else if (source == noColourmenuItem)
1032 else if (source == clustalColour)
1034 abovePIDThreshold.setState(false);
1035 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1037 else if (source == zappoColour)
1039 changeColour(new ZappoColourScheme());
1041 else if (source == taylorColour)
1043 changeColour(new TaylorColourScheme());
1045 else if (source == hydrophobicityColour)
1047 changeColour(new HydrophobicColourScheme());
1049 else if (source == helixColour)
1051 changeColour(new HelixColourScheme());
1053 else if (source == strandColour)
1055 changeColour(new StrandColourScheme());
1057 else if (source == turnColour)
1059 changeColour(new TurnColourScheme());
1061 else if (source == buriedColour)
1063 changeColour(new BuriedColourScheme());
1065 else if (source == nucleotideColour)
1067 changeColour(new NucleotideColourScheme());
1069 else if (source == purinePyrimidineColour)
1071 changeColour(new PurinePyrimidineColourScheme());
1073 else if (source == RNAInteractionColour)
1075 changeColour(new RNAInteractionColourScheme());
1077 else if (source == RNAHelixColour)
1079 new RNAHelicesColourChooser(viewport, alignPanel);
1081 else if (source == modifyPID)
1083 modifyPID_actionPerformed();
1085 else if (source == modifyConservation)
1087 modifyConservation_actionPerformed();
1089 else if (source == userDefinedColour)
1091 new UserDefinedColours(alignPanel, null);
1093 else if (source == PIDColour)
1095 changeColour(new PIDColourScheme());
1097 else if (source == BLOSUM62Colour)
1099 changeColour(new Blosum62ColourScheme());
1101 else if (source == tcoffeeColour)
1103 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1105 else if (source == annotationColour)
1107 new AnnotationColourChooser(viewport, alignPanel);
1109 else if (source == annotationColumnSelection)
1111 new AnnotationColumnChooser(viewport, alignPanel);
1113 else if (source == sortPairwiseMenuItem)
1115 sortPairwiseMenuItem_actionPerformed();
1117 else if (source == sortIDMenuItem)
1119 sortIDMenuItem_actionPerformed();
1121 else if (source == sortLengthMenuItem)
1123 sortLengthMenuItem_actionPerformed();
1125 else if (source == sortGroupMenuItem)
1127 sortGroupMenuItem_actionPerformed();
1129 else if (source == removeRedundancyMenuItem)
1131 removeRedundancyMenuItem_actionPerformed();
1133 else if (source == pairwiseAlignmentMenuItem)
1135 pairwiseAlignmentMenuItem_actionPerformed();
1137 else if (source == PCAMenuItem)
1139 PCAMenuItem_actionPerformed();
1141 else if (source == averageDistanceTreeMenuItem)
1143 averageDistanceTreeMenuItem_actionPerformed();
1145 else if (source == neighbourTreeMenuItem)
1147 neighbourTreeMenuItem_actionPerformed();
1149 else if (source == njTreeBlosumMenuItem)
1151 njTreeBlosumMenuItem_actionPerformed();
1153 else if (source == avDistanceTreeBlosumMenuItem)
1155 avTreeBlosumMenuItem_actionPerformed();
1157 else if (source == documentation)
1159 documentation_actionPerformed();
1161 else if (source == about)
1163 about_actionPerformed();
1168 public void inputText_actionPerformed()
1170 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1171 Frame frame = new Frame();
1173 jalview.bin.JalviewLite.addFrame(frame,
1174 MessageManager.getString("label.input_cut_paste"), 500, 500);
1177 protected void outputText_actionPerformed(ActionEvent e)
1179 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1180 Frame frame = new Frame();
1182 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1183 "label.alignment_output_command", new String[]
1184 { e.getActionCommand() }), 600, 500);
1185 cap.setText(new AppletFormatAdapter().formatSequences(
1186 e.getActionCommand(), viewport.getAlignment(),
1187 viewport.showJVSuffix));
1190 public void loadAnnotations()
1192 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1193 cap.setText(MessageManager
1194 .getString("label.paste_features_annotations_Tcoffee_here"));
1195 cap.setAnnotationImport();
1196 Frame frame = new Frame();
1198 jalview.bin.JalviewLite.addFrame(frame,
1199 MessageManager.getString("action.paste_annotations"), 400, 300);
1203 public String outputAnnotations(boolean displayTextbox)
1205 String annotation = new AnnotationFile().printAnnotations(
1206 viewport.showAnnotation ? viewport.getAlignment()
1207 .getAlignmentAnnotation() : null, viewport
1208 .getAlignment().getGroups(), ((Alignment) viewport
1209 .getAlignment()).alignmentProperties);
1213 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1214 Frame frame = new Frame();
1216 jalview.bin.JalviewLite.addFrame(frame,
1217 MessageManager.getString("label.annotations"), 600, 500);
1218 cap.setText(annotation);
1224 private Map<String,Object> getDisplayedFeatureCols()
1226 if (alignPanel.getFeatureRenderer() != null
1227 && viewport.getFeaturesDisplayed()!= null)
1229 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1235 public String outputFeatures(boolean displayTextbox, String format)
1238 if (format.equalsIgnoreCase("Jalview"))
1240 features = new FeaturesFile().printJalviewFormat(viewport
1241 .getAlignment().getSequencesArray(),
1242 getDisplayedFeatureCols());
1246 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1247 .getSequencesArray(), getDisplayedFeatureCols());
1252 boolean frimport = false;
1253 if (features == null || features.equals("No Features Visible"))
1255 features = "# No features visible - paste some and import them here.";
1259 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1262 cap.setAnnotationImport();
1264 Frame frame = new Frame();
1266 jalview.bin.JalviewLite.addFrame(frame,
1267 MessageManager.getString("label.features"), 600, 500);
1268 cap.setText(features);
1272 if (features == null)
1281 void launchFullApplication()
1283 StringBuffer url = new StringBuffer(jalviewServletURL);
1286 + appendProtocol(viewport.applet.getParameter("file")));
1288 if (viewport.applet.getParameter("features") != null)
1290 url.append("&features=");
1291 url.append(appendProtocol(viewport.applet.getParameter("features")));
1294 if (viewport.applet.getParameter("annotations") != null)
1296 url.append("&annotations=");
1297 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1300 if (viewport.applet.getParameter("jnetfile") != null)
1302 url.append("&annotations=");
1303 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1306 if (viewport.applet.getParameter("defaultColour") != null)
1308 url.append("&colour="
1309 + removeWhiteSpace(viewport.applet
1310 .getParameter("defaultColour")));
1313 if (viewport.applet.getParameter("userDefinedColour") != null)
1315 url.append("&colour="
1316 + removeWhiteSpace(viewport.applet
1317 .getParameter("userDefinedColour")));
1319 if (viewport.applet.getParameter("tree") != null)
1322 + appendProtocol(viewport.applet.getParameter("tree")));
1324 if (viewport.applet.getParameter("treeFile") != null)
1327 + appendProtocol(viewport.applet.getParameter("treeFile")));
1330 showURL(url.toString(), "FULL_APP");
1333 String removeWhiteSpace(String colour)
1335 StringBuffer sb = new StringBuffer();
1336 for (int i = 0; i < colour.length(); i++)
1338 if (Character.isWhitespace(colour.charAt(i)))
1344 sb.append(colour.charAt(i));
1348 return sb.toString();
1351 String appendProtocol(String url)
1356 url = URLEncoder.encode(url);
1359 * When we finally deprecate 1.1 compatibility, we can start to use
1360 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1361 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1362 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1363 * ex.printStackTrace(); }
1365 catch (java.net.MalformedURLException ex)
1367 url = viewport.applet.getCodeBase() + url;
1372 public void closeMenuItem_actionPerformed()
1374 PaintRefresher.RemoveComponent(alignPanel);
1375 if (alignPanel.seqPanel != null
1376 && alignPanel.seqPanel.seqCanvas != null)
1378 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1380 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1382 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1385 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1400 void updateEditMenuBar()
1403 if (viewport.historyList.size() > 0)
1405 undoMenuItem.setEnabled(true);
1406 CommandI command = (CommandI) viewport.historyList.peek();
1407 undoMenuItem.setLabel(MessageManager.formatMessage(
1408 "label.undo_command", new String[]
1409 { command.getDescription() }));
1413 undoMenuItem.setEnabled(false);
1414 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1417 if (viewport.redoList.size() > 0)
1419 redoMenuItem.setEnabled(true);
1421 CommandI command = (CommandI) viewport.redoList.peek();
1422 redoMenuItem.setLabel(MessageManager.formatMessage(
1423 "label.redo_command", new String[]
1424 { command.getDescription() }));
1428 redoMenuItem.setEnabled(false);
1429 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1437 public void addHistoryItem(CommandI command)
1439 if (command.getSize() > 0)
1441 viewport.historyList.push(command);
1442 viewport.redoList.removeAllElements();
1443 updateEditMenuBar();
1444 viewport.updateHiddenColumns();
1449 * TODO: JAL-1104 DOCUMENT ME!
1454 protected void undoMenuItem_actionPerformed()
1456 if (viewport.historyList.size() < 1)
1461 CommandI command = (CommandI) viewport.historyList.pop();
1462 viewport.redoList.push(command);
1463 command.undoCommand(null);
1465 AlignViewport originalSource = getOriginatingSource(command);
1467 if (originalSource != viewport)
1470 .println("Warning: Viewport object mismatch whilst undoing");
1472 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1473 // viewport.getColumnSelection().getHiddenColumns()
1475 updateEditMenuBar();
1476 originalSource.firePropertyChange("alignment", null, originalSource
1477 .getAlignment().getSequences());
1481 * TODO: JAL-1104 DOCUMENT ME!
1486 protected void redoMenuItem_actionPerformed()
1488 if (viewport.redoList.size() < 1)
1493 CommandI command = (CommandI) viewport.redoList.pop();
1494 viewport.historyList.push(command);
1495 command.doCommand(null);
1497 AlignViewport originalSource = getOriginatingSource(command);
1499 if (originalSource != viewport)
1502 .println("Warning: Viewport object mismatch whilst re-doing");
1504 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1505 // viewport.getColumnSelection().getHiddenColumns()
1508 updateEditMenuBar();
1509 originalSource.firePropertyChange("alignment", null, originalSource
1510 .getAlignment().getSequences());
1513 AlignViewport getOriginatingSource(CommandI command)
1515 AlignViewport originalSource = null;
1516 // For sequence removal and addition, we need to fire
1517 // the property change event FROM the viewport where the
1518 // original alignment was altered
1519 AlignmentI al = null;
1520 if (command instanceof EditCommand)
1522 EditCommand editCommand = (EditCommand) command;
1523 al = editCommand.getAlignment();
1524 Vector comps = (Vector) PaintRefresher.components.get(viewport
1525 .getSequenceSetId());
1526 for (int i = 0; i < comps.size(); i++)
1528 if (comps.elementAt(i) instanceof AlignmentPanel)
1530 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1532 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1539 if (originalSource == null)
1541 // The original view is closed, we must validate
1542 // the current view against the closed view first
1545 PaintRefresher.validateSequences(al, viewport.getAlignment());
1548 originalSource = viewport;
1551 return originalSource;
1554 public void moveSelectedSequences(boolean up)
1556 SequenceGroup sg = viewport.getSelectionGroup();
1561 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1562 up ? null : viewport.getHiddenRepSequences(), up);
1563 alignPanel.paintAlignment(true);
1566 synchronized void slideSequences(boolean right, int size)
1568 List<SequenceI> sg = new Vector<SequenceI>();
1569 if (viewport.cursorMode)
1571 sg.add(viewport.getAlignment().getSequenceAt(
1572 alignPanel.seqPanel.seqCanvas.cursorY));
1574 else if (viewport.getSelectionGroup() != null
1575 && viewport.getSelectionGroup().getSize() != viewport
1576 .getAlignment().getHeight())
1578 sg = viewport.getSelectionGroup().getSequences(
1579 viewport.getHiddenRepSequences());
1587 Vector<SequenceI> invertGroup = new Vector();
1589 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1591 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1593 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1597 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1599 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1601 for (int i = 0; i < invertGroup.size(); i++)
1603 seqs2[i] = invertGroup.elementAt(i);
1606 SlideSequencesCommand ssc;
1609 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1610 size, viewport.getGapCharacter());
1614 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1615 size, viewport.getGapCharacter());
1618 int groupAdjustment = 0;
1619 if (ssc.getGapsInsertedBegin() && right)
1621 if (viewport.cursorMode)
1623 alignPanel.seqPanel.moveCursor(size, 0);
1627 groupAdjustment = size;
1630 else if (!ssc.getGapsInsertedBegin() && !right)
1632 if (viewport.cursorMode)
1634 alignPanel.seqPanel.moveCursor(-size, 0);
1638 groupAdjustment = -size;
1642 if (groupAdjustment != 0)
1644 viewport.getSelectionGroup().setStartRes(
1645 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1646 viewport.getSelectionGroup().setEndRes(
1647 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1650 boolean appendHistoryItem = false;
1651 if (viewport.historyList != null && viewport.historyList.size() > 0
1652 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1654 appendHistoryItem = ssc
1655 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1659 if (!appendHistoryItem)
1661 addHistoryItem(ssc);
1667 static StringBuffer copiedSequences;
1669 static Vector copiedHiddenColumns;
1671 protected void copy_actionPerformed()
1673 if (viewport.getSelectionGroup() == null)
1678 SequenceGroup sg = viewport.getSelectionGroup();
1679 copiedSequences = new StringBuffer();
1680 Hashtable orderedSeqs = new Hashtable();
1681 for (int i = 0; i < sg.getSize(); i++)
1683 SequenceI seq = sg.getSequenceAt(i);
1684 int index = viewport.getAlignment().findIndex(seq);
1685 orderedSeqs.put(index + "", seq);
1688 int index = 0, startRes, endRes;
1691 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1693 copiedHiddenColumns = new Vector();
1694 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1695 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1698 int[] region = (int[]) viewport.getColumnSelection()
1699 .getHiddenColumns().elementAt(i);
1701 copiedHiddenColumns.addElement(new int[]
1702 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1707 copiedHiddenColumns = null;
1710 for (int i = 0; i < sg.getSize(); i++)
1712 SequenceI seq = null;
1716 if (orderedSeqs.containsKey(index + ""))
1718 seq = (SequenceI) orderedSeqs.get(index + "");
1730 // Returns residue following index if gap
1731 startRes = seq.findPosition(sg.getStartRes());
1734 // Need to find the residue preceeding index if gap
1737 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1739 ch = seq.getCharAt(j);
1740 if (!jalview.util.Comparison.isGap((ch)))
1748 endRes += seq.getStart() - 1;
1751 copiedSequences.append(seq.getName()
1757 + seq.getSequenceAsString(sg.getStartRes(),
1758 sg.getEndRes() + 1) + "\n");
1763 protected void pasteNew_actionPerformed()
1768 protected void pasteThis_actionPerformed()
1773 void paste(boolean newAlignment)
1778 if (copiedSequences == null)
1783 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1784 Vector seqs = new Vector();
1785 while (st.hasMoreElements())
1787 String name = st.nextToken();
1788 int start = Integer.parseInt(st.nextToken());
1789 int end = Integer.parseInt(st.nextToken());
1790 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1792 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1793 for (int i = 0; i < seqs.size(); i++)
1795 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1800 String newtitle = MessageManager.getString("label.copied_sequences");
1801 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1803 newtitle = getTitle();
1807 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1809 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1810 viewport.applet, newtitle, false);
1811 if (copiedHiddenColumns != null)
1813 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1815 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1816 af.viewport.hideColumns(region[0], region[1]);
1820 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1825 addSequences(newSeqs);
1828 } catch (Exception ex)
1830 } // could be anything being pasted in here
1834 void addSequences(SequenceI[] seqs)
1836 for (int i = 0; i < seqs.length; i++)
1838 viewport.getAlignment().addSequence(seqs[i]);
1842 addHistoryItem(new EditCommand(
1843 MessageManager.getString("label.add_sequences"), Action.PASTE,
1844 seqs, 0, viewport.getAlignment().getWidth(),
1845 viewport.getAlignment()));
1847 viewport.setEndSeq(viewport.getAlignment().getHeight());
1848 viewport.getAlignment().getWidth();
1849 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1854 protected void cut_actionPerformed()
1856 copy_actionPerformed();
1857 delete_actionPerformed();
1860 protected void delete_actionPerformed()
1863 SequenceGroup sg = viewport.getSelectionGroup();
1869 Vector seqs = new Vector();
1871 for (int i = 0; i < sg.getSize(); i++)
1873 seq = sg.getSequenceAt(i);
1874 seqs.addElement(seq);
1877 // If the cut affects all sequences, remove highlighted columns
1878 if (sg.getSize() == viewport.getAlignment().getHeight())
1880 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1881 sg.getEndRes() + 1);
1884 SequenceI[] cut = new SequenceI[seqs.size()];
1885 for (int i = 0; i < seqs.size(); i++)
1887 cut[i] = (SequenceI) seqs.elementAt(i);
1891 * //ADD HISTORY ITEM
1893 addHistoryItem(new EditCommand(
1894 MessageManager.getString("label.cut_sequences"), Action.CUT,
1895 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1896 viewport.getAlignment()));
1898 viewport.setSelectionGroup(null);
1899 viewport.getAlignment().deleteGroup(sg);
1901 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1904 if (viewport.getAlignment().getHeight() < 1)
1906 this.setVisible(false);
1908 viewport.sendSelection();
1912 * group consensus toggled
1915 protected void showGroupConsensus_actionPerformed()
1917 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1918 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1923 * group conservation toggled.
1925 protected void showGroupConservation_actionPerformed()
1927 viewport.setShowGroupConservation(showGroupConservation.getState());
1928 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1935 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1936 * .event.ActionEvent)
1938 protected void showConsensusHistogram_actionPerformed()
1940 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1941 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1948 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1949 * .event.ActionEvent)
1951 protected void showSequenceLogo_actionPerformed()
1953 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1954 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1957 protected void normSequenceLogo_actionPerformed()
1959 showSequenceLogo.setState(true);
1960 viewport.setShowSequenceLogo(true);
1961 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1962 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1965 protected void applyAutoAnnotationSettings_actionPerformed()
1967 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1970 protected void makeGrpsFromSelection_actionPerformed()
1972 if (avc.makeGroupsFromSelection())
1974 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1975 alignPanel.updateAnnotation();
1976 alignPanel.paintAlignment(true);
1980 protected void createGroup_actionPerformed()
1985 protected void unGroup_actionPerformed()
1989 alignPanel.alignmentChanged();
1993 protected void deleteGroups_actionPerformed()
1995 if (avc.deleteGroups())
1997 alignPanel.alignmentChanged();
2001 public void selectAllSequenceMenuItem_actionPerformed()
2003 SequenceGroup sg = new SequenceGroup();
2004 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2006 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2008 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2009 viewport.setSelectionGroup(sg);
2010 alignPanel.paintAlignment(true);
2011 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2012 viewport.sendSelection();
2015 public void deselectAllSequenceMenuItem_actionPerformed()
2017 if (viewport.cursorMode)
2019 alignPanel.seqPanel.keyboardNo1 = null;
2020 alignPanel.seqPanel.keyboardNo2 = null;
2022 viewport.setSelectionGroup(null);
2023 viewport.getColumnSelection().clear();
2024 viewport.setSelectionGroup(null);
2025 alignPanel.idPanel.idCanvas.searchResults = null;
2026 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2027 alignPanel.paintAlignment(true);
2028 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2029 viewport.sendSelection();
2032 public void invertSequenceMenuItem_actionPerformed()
2034 SequenceGroup sg = viewport.getSelectionGroup();
2035 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2037 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2040 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2041 viewport.sendSelection();
2044 public void invertColSel_actionPerformed()
2046 viewport.invertColumnSelection();
2047 alignPanel.paintAlignment(true);
2048 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2049 viewport.sendSelection();
2052 void trimAlignment(boolean trimLeft)
2054 ColumnSelection colSel = viewport.getColumnSelection();
2057 if (colSel.size() > 0)
2061 column = colSel.getMin();
2065 column = colSel.getMax();
2069 if (viewport.getSelectionGroup() != null)
2071 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2072 viewport.getHiddenRepSequences());
2076 seqs = viewport.getAlignment().getSequencesArray();
2079 TrimRegionCommand trimRegion;
2082 trimRegion = new TrimRegionCommand("Remove Left",
2083 TrimRegionCommand.TRIM_LEFT, seqs, column,
2084 viewport.getAlignment(), viewport.getColumnSelection(),
2085 viewport.getSelectionGroup());
2086 viewport.setStartRes(0);
2090 trimRegion = new TrimRegionCommand("Remove Right",
2091 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2092 viewport.getAlignment(), viewport.getColumnSelection(),
2093 viewport.getSelectionGroup());
2096 statusBar.setText(MessageManager.formatMessage(
2097 "label.removed_columns", new String[]
2098 { Integer.valueOf(trimRegion.getSize()).toString() }));
2099 addHistoryItem(trimRegion);
2101 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2103 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2104 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2106 viewport.getAlignment().deleteGroup(sg);
2110 viewport.firePropertyChange("alignment", null, viewport
2111 .getAlignment().getSequences());
2115 public void removeGappedColumnMenuItem_actionPerformed()
2117 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2120 if (viewport.getSelectionGroup() != null)
2122 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2123 viewport.getHiddenRepSequences());
2124 start = viewport.getSelectionGroup().getStartRes();
2125 end = viewport.getSelectionGroup().getEndRes();
2129 seqs = viewport.getAlignment().getSequencesArray();
2132 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2133 "Remove Gapped Columns", seqs, start, end,
2134 viewport.getAlignment());
2136 addHistoryItem(removeGapCols);
2138 statusBar.setText(MessageManager.formatMessage(
2139 "label.removed_empty_columns", new String[]
2140 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2142 // This is to maintain viewport position on first residue
2143 // of first sequence
2144 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2145 int startRes = seq.findPosition(viewport.startRes);
2146 // ShiftList shifts;
2147 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2148 // edit.alColumnChanges=shifts.getInverse();
2149 // if (viewport.hasHiddenColumns)
2150 // viewport.getColumnSelection().compensateForEdits(shifts);
2151 viewport.setStartRes(seq.findIndex(startRes) - 1);
2152 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2157 public void removeAllGapsMenuItem_actionPerformed()
2159 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2162 if (viewport.getSelectionGroup() != null)
2164 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2165 viewport.getHiddenRepSequences());
2166 start = viewport.getSelectionGroup().getStartRes();
2167 end = viewport.getSelectionGroup().getEndRes();
2171 seqs = viewport.getAlignment().getSequencesArray();
2174 // This is to maintain viewport position on first residue
2175 // of first sequence
2176 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2177 int startRes = seq.findPosition(viewport.startRes);
2179 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2180 viewport.getAlignment()));
2182 viewport.setStartRes(seq.findIndex(startRes) - 1);
2184 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2189 public void findMenuItem_actionPerformed()
2191 new Finder(alignPanel);
2195 * create a new view derived from the current view
2198 * @return frame for the new view
2200 public AlignFrame newView(String viewtitle)
2203 if (viewport.hasHiddenRows())
2205 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2206 .getFullAlignment().getSequencesArray());
2210 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2213 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2215 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2217 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2219 newal.addAnnotation(viewport.getAlignment()
2220 .getAlignmentAnnotation()[i]);
2225 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2227 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2228 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2229 PaintRefresher.Register(newaf.alignPanel,
2230 newaf.alignPanel.av.getSequenceSetId());
2232 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2233 newaf.alignPanel.av.getSequenceSetId());
2234 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2235 newaf.alignPanel.av.getSequenceSetId());
2237 Vector comps = (Vector) PaintRefresher.components.get(viewport
2238 .getSequenceSetId());
2240 for (int i = 0; i < comps.size(); i++)
2242 if (comps.elementAt(i) instanceof AlignmentPanel)
2248 String title = new String(this.getTitle());
2249 if (viewtitle != null)
2251 title = viewtitle + " ( " + title + ")";
2255 if (title.indexOf("(View") > -1)
2257 title = title.substring(0, title.indexOf("(View"));
2259 title += "(View " + viewSize + ")";
2262 newaf.setTitle(title.toString());
2264 newaf.viewport.historyList = viewport.historyList;
2265 newaf.viewport.redoList = viewport.redoList;
2271 * @return list of feature groups on the view
2273 public String[] getFeatureGroups()
2275 FeatureRenderer fr = null;
2276 if (alignPanel != null
2277 && (fr = alignPanel.getFeatureRenderer()) != null)
2279 List gps = fr.getFeatureGroups();
2281 String[] _gps = new String[gps.size()];
2284 _gps[p++] = gp.toString();
2292 * get sequence feature groups that are hidden or shown
2298 public String[] getFeatureGroupsOfState(boolean visible)
2300 FeatureRenderer fr = null;
2301 if (alignPanel != null
2302 && (fr = alignPanel.getFeatureRenderer()) != null)
2304 List gps = fr.getGroups(visible);
2306 String[] _gps = new String[gps.size()];
2309 _gps[p++] = gp.toString();
2317 * Change the display state for the given feature groups
2320 * list of group strings
2322 * visible or invisible
2324 public void setFeatureGroupState(String[] groups, boolean state)
2326 FeatureRenderer fr = null;
2327 this.sequenceFeatures.setState(true);
2328 viewport.setShowSequenceFeatures(true);
2329 if (alignPanel != null
2330 && (fr = alignPanel.getFeatureRenderer()) != null)
2333 fr.setGroupVisibility(Arrays.asList(groups), state);
2334 alignPanel.seqPanel.seqCanvas.repaint();
2335 if (alignPanel.overviewPanel != null)
2337 alignPanel.overviewPanel.updateOverviewImage();
2342 public void seqLimits_itemStateChanged()
2344 viewport.setShowJVSuffix(seqLimits.getState());
2345 alignPanel.fontChanged();
2346 alignPanel.paintAlignment(true);
2349 protected void colourTextMenuItem_actionPerformed()
2351 viewport.setColourText(colourTextMenuItem.getState());
2352 alignPanel.paintAlignment(true);
2355 protected void displayNonconservedMenuItem_actionPerformed()
2357 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2358 alignPanel.paintAlignment(true);
2361 protected void wrapMenuItem_actionPerformed()
2363 viewport.setWrapAlignment(wrapMenuItem.getState());
2364 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2365 scaleAbove.setEnabled(wrapMenuItem.getState());
2366 scaleLeft.setEnabled(wrapMenuItem.getState());
2367 scaleRight.setEnabled(wrapMenuItem.getState());
2368 alignPanel.paintAlignment(true);
2371 public void overviewMenuItem_actionPerformed()
2373 if (alignPanel.overviewPanel != null)
2378 Frame frame = new Frame();
2379 OverviewPanel overview = new OverviewPanel(alignPanel);
2380 frame.add(overview);
2381 // +50 must allow for applet frame window
2382 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2383 "label.overview_params", new String[]
2384 { this.getTitle() }), overview.getPreferredSize().width,
2385 overview.getPreferredSize().height + 50);
2388 final AlignmentPanel ap = alignPanel;
2389 frame.addWindowListener(new WindowAdapter()
2392 public void windowClosing(WindowEvent e)
2396 ap.setOverviewPanel(null);
2401 alignPanel.setOverviewPanel(overview);
2405 void changeColour(ColourSchemeI cs)
2411 if (viewport.getAbovePIDThreshold())
2413 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2417 if (viewport.getConservationSelected())
2419 cs.setConservationApplied(true);
2420 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2425 cs.setConservationApplied(false);
2428 viewport.setGlobalColourScheme(cs);
2430 if (alignPanel.getOverviewPanel() != null)
2432 alignPanel.getOverviewPanel().updateOverviewImage();
2435 jalview.structure.StructureSelectionManager
2436 .getStructureSelectionManager(viewport.applet)
2437 .sequenceColoursChanged(alignPanel);
2439 alignPanel.paintAlignment(true);
2442 protected void modifyPID_actionPerformed()
2444 if (viewport.getAbovePIDThreshold()
2445 && viewport.getGlobalColourScheme() != null)
2447 SliderPanel.setPIDSliderSource(alignPanel,
2448 viewport.getGlobalColourScheme(), "Background");
2449 SliderPanel.showPIDSlider();
2453 protected void modifyConservation_actionPerformed()
2455 if (viewport.getConservationSelected()
2456 && viewport.getGlobalColourScheme() != null)
2458 SliderPanel.setConservationSlider(alignPanel,
2459 viewport.getGlobalColourScheme(), "Background");
2460 SliderPanel.showConservationSlider();
2464 protected void conservationMenuItem_actionPerformed()
2466 viewport.setConservationSelected(conservationMenuItem.getState());
2468 viewport.setAbovePIDThreshold(false);
2469 abovePIDThreshold.setState(false);
2471 changeColour(viewport.getGlobalColourScheme());
2473 modifyConservation_actionPerformed();
2476 public void abovePIDThreshold_actionPerformed()
2478 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2480 conservationMenuItem.setState(false);
2481 viewport.setConservationSelected(false);
2483 changeColour(viewport.getGlobalColourScheme());
2485 modifyPID_actionPerformed();
2488 public void sortPairwiseMenuItem_actionPerformed()
2490 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2491 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2492 .getAlignment().getSequenceAt(0), null);
2494 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2495 viewport.getAlignment()));
2496 alignPanel.paintAlignment(true);
2499 public void sortIDMenuItem_actionPerformed()
2501 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2502 AlignmentSorter.sortByID(viewport.getAlignment());
2503 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2504 viewport.getAlignment()));
2505 alignPanel.paintAlignment(true);
2508 public void sortLengthMenuItem_actionPerformed()
2510 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2511 AlignmentSorter.sortByLength(viewport.getAlignment());
2512 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2513 viewport.getAlignment()));
2514 alignPanel.paintAlignment(true);
2517 public void sortGroupMenuItem_actionPerformed()
2519 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2520 AlignmentSorter.sortByGroup(viewport.getAlignment());
2521 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2522 viewport.getAlignment()));
2523 alignPanel.paintAlignment(true);
2527 public void removeRedundancyMenuItem_actionPerformed()
2529 new RedundancyPanel(alignPanel);
2532 public void pairwiseAlignmentMenuItem_actionPerformed()
2534 if (viewport.getSelectionGroup() != null
2535 && viewport.getSelectionGroup().getSize() > 1)
2537 Frame frame = new Frame();
2538 frame.add(new PairwiseAlignPanel(alignPanel));
2539 jalview.bin.JalviewLite.addFrame(frame,
2540 MessageManager.getString("action.pairwise_alignment"), 600,
2545 public void PCAMenuItem_actionPerformed()
2547 // are the sequences aligned?
2548 if (!viewport.getAlignment().isAligned(false))
2551 int Width = viewport.getAlignment().getWidth();
2553 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2555 current = viewport.getAlignment().getSequenceAt(i);
2557 if (current.getLength() < Width)
2559 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2562 alignPanel.paintAlignment(true);
2565 if ((viewport.getSelectionGroup() != null
2566 && viewport.getSelectionGroup().getSize() < 4 && viewport
2567 .getSelectionGroup().getSize() > 0)
2568 || viewport.getAlignment().getHeight() < 4)
2575 new PCAPanel(viewport);
2576 } catch (java.lang.OutOfMemoryError ex)
2582 public void averageDistanceTreeMenuItem_actionPerformed()
2584 NewTreePanel("AV", "PID", "Average distance tree using PID");
2587 public void neighbourTreeMenuItem_actionPerformed()
2589 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2592 protected void njTreeBlosumMenuItem_actionPerformed()
2594 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2597 protected void avTreeBlosumMenuItem_actionPerformed()
2599 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2602 void NewTreePanel(String type, String pwType, String title)
2604 // are the sequences aligned?
2605 if (!viewport.getAlignment().isAligned(false))
2608 int Width = viewport.getAlignment().getWidth();
2610 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2612 current = viewport.getAlignment().getSequenceAt(i);
2614 if (current.getLength() < Width)
2616 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2619 alignPanel.paintAlignment(true);
2623 if ((viewport.getSelectionGroup() != null && viewport
2624 .getSelectionGroup().getSize() > 1)
2625 || (viewport.getAlignment().getHeight() > 1))
2627 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2629 addTreeMenuItem(tp, title);
2631 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2635 void loadTree_actionPerformed()
2637 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2638 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2639 cap.setTreeImport();
2640 Frame frame = new Frame();
2642 jalview.bin.JalviewLite.addFrame(frame,
2643 MessageManager.getString("label.paste_newick_file"), 400, 300);
2646 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2648 TreePanel tp = new TreePanel(alignPanel, treeFile,
2649 MessageManager.getString("label.load_tree_from_file"), tree);
2650 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2651 addTreeMenuItem(tp, treeFile);
2655 * sort the alignment using the given treePanel
2658 * tree used to sort view
2660 * string used for undo event name
2662 public void sortByTree(TreePanel treePanel, String title)
2664 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2666 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2667 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2668 // HistoryItem.SORT));
2669 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2670 "label.order_by_params", new String[]
2671 { title }), oldOrder, viewport.getAlignment()));
2672 alignPanel.paintAlignment(true);
2676 * Do any automatic reordering of the alignment and add the necessary bits to
2677 * the menu structure for the new tree
2682 protected void addTreeMenuItem(final TreePanel treePanel,
2685 final MenuItem item = new MenuItem(title);
2686 sortByTreeMenu.add(item);
2687 item.addActionListener(new java.awt.event.ActionListener()
2690 public void actionPerformed(ActionEvent evt)
2692 sortByTree(treePanel, title); // treePanel.getTitle());
2696 treePanel.addWindowListener(new WindowAdapter()
2699 public void windowOpened(WindowEvent e)
2701 if (viewport.sortByTree)
2703 sortByTree(treePanel, title);
2705 super.windowOpened(e);
2709 public void windowClosing(WindowEvent e)
2711 sortByTreeMenu.remove(item);
2716 public boolean sortBy(AlignmentOrder alorder, String undoname)
2718 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2719 if (viewport.applet.debug)
2721 System.err.println("Sorting " + alorder.getOrder().size()
2722 + " in alignment '" + getTitle() + "'");
2724 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2725 if (undoname != null)
2727 addHistoryItem(new OrderCommand(undoname, oldOrder,
2728 viewport.getAlignment()));
2730 alignPanel.paintAlignment(true);
2734 protected void documentation_actionPerformed()
2736 alignPanel.av.applet.openJalviewHelpUrl();
2739 protected void about_actionPerformed()
2742 class AboutPanel extends Canvas
2748 public AboutPanel(String version, String builddate)
2750 this.version = version;
2751 this.builddate = builddate;
2755 public void paint(Graphics g)
2757 g.setColor(Color.white);
2758 g.fillRect(0, 0, getSize().width, getSize().height);
2759 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2760 FontMetrics fm = g.getFontMetrics();
2761 int fh = fm.getHeight();
2763 g.setColor(Color.black);
2764 // TODO: update this text for each release or centrally store it for
2765 // lite and application
2766 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2767 g.drawString(MessageManager.formatMessage(
2768 "label.jalviewLite_release", new String[]
2769 { version }), x, y += fh);
2770 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2771 g.drawString(MessageManager.formatMessage(
2772 "label.jaview_build_date", new String[]
2773 { builddate }), x, y += fh);
2774 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2775 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2777 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2778 x + 50, y += fh + 8);
2780 MessageManager.getString("label.jalview_dev_managers"), x,
2782 g.drawString(MessageManager
2783 .getString("label.jalview_distribution_lists"), x, y += fh);
2784 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2787 MessageManager.getString("label.jalview_cite_1_authors"),
2790 MessageManager.getString("label.jalview_cite_1_title"), x,
2792 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2797 Frame frame = new Frame();
2798 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2800 jalview.bin.JalviewLite.addFrame(frame,
2801 MessageManager.getString("label.jalview"), 580, 220);
2805 public void showURL(String url, String target)
2807 if (viewport.applet == null)
2809 System.out.println("Not running as applet - no browser available.");
2813 viewport.applet.showURL(url, target);
2817 // ////////////////////////////////////////////////////////////////////////////////
2818 // JBuilder Graphics here
2820 MenuBar alignFrameMenuBar = new MenuBar();
2822 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2824 MenuItem loadApplication = new MenuItem(
2825 MessageManager.getString("label.view_full_application"));
2827 MenuItem loadTree = new MenuItem(
2828 MessageManager.getString("label.load_associated_tree"));
2830 MenuItem loadAnnotations = new MenuItem(
2831 MessageManager.getString("label.load_features_annotations"));
2833 MenuItem outputFeatures = new MenuItem(
2834 MessageManager.getString("label.export_features").concat("..."));
2836 MenuItem outputAnnotations = new MenuItem(
2837 MessageManager.getString("label.export_annotations").concat("..."));
2839 MenuItem closeMenuItem = new MenuItem(
2840 MessageManager.getString("action.close"));
2842 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2844 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2846 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2848 Menu calculateMenu = new Menu(
2849 MessageManager.getString("action.calculate"));
2851 MenuItem selectAllSequenceMenuItem = new MenuItem(
2852 MessageManager.getString("action.select_all"));
2854 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2855 MessageManager.getString("action.deselect_all"));
2857 MenuItem invertSequenceMenuItem = new MenuItem(
2858 MessageManager.getString("action.invert_selection"));
2860 MenuItem remove2LeftMenuItem = new MenuItem();
2862 MenuItem remove2RightMenuItem = new MenuItem();
2864 MenuItem removeGappedColumnMenuItem = new MenuItem();
2866 MenuItem removeAllGapsMenuItem = new MenuItem();
2868 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2870 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2872 MenuItem sortPairwiseMenuItem = new MenuItem();
2874 MenuItem sortIDMenuItem = new MenuItem();
2876 MenuItem sortLengthMenuItem = new MenuItem();
2878 MenuItem sortGroupMenuItem = new MenuItem();
2880 MenuItem removeRedundancyMenuItem = new MenuItem();
2882 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2884 MenuItem PCAMenuItem = new MenuItem();
2886 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2888 MenuItem neighbourTreeMenuItem = new MenuItem();
2890 BorderLayout borderLayout1 = new BorderLayout();
2892 public Label statusBar = new Label();
2894 Menu outputTextboxMenu = new Menu();
2896 MenuItem clustalColour = new MenuItem();
2898 MenuItem zappoColour = new MenuItem();
2900 MenuItem taylorColour = new MenuItem();
2902 MenuItem hydrophobicityColour = new MenuItem();
2904 MenuItem helixColour = new MenuItem();
2906 MenuItem strandColour = new MenuItem();
2908 MenuItem turnColour = new MenuItem();
2910 MenuItem buriedColour = new MenuItem();
2912 MenuItem purinePyrimidineColour = new MenuItem();
2914 MenuItem RNAInteractionColour = new MenuItem();
2916 MenuItem RNAHelixColour = new MenuItem();
2918 MenuItem userDefinedColour = new MenuItem();
2920 MenuItem PIDColour = new MenuItem();
2922 MenuItem BLOSUM62Colour = new MenuItem();
2924 MenuItem tcoffeeColour = new MenuItem();
2926 MenuItem njTreeBlosumMenuItem = new MenuItem();
2928 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2930 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2932 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2934 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2936 MenuItem alProperties = new MenuItem(
2937 MessageManager.getString("label.alignment_props"));
2939 MenuItem overviewMenuItem = new MenuItem();
2941 MenuItem undoMenuItem = new MenuItem();
2943 MenuItem redoMenuItem = new MenuItem();
2945 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2947 MenuItem noColourmenuItem = new MenuItem();
2949 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2951 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2953 MenuItem findMenuItem = new MenuItem();
2955 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2957 MenuItem nucleotideColour = new MenuItem();
2959 MenuItem deleteGroups = new MenuItem();
2961 MenuItem grpsFromSelection = new MenuItem();
2963 MenuItem createGroup = new MenuItem();
2965 MenuItem unGroup = new MenuItem();
2967 MenuItem delete = new MenuItem();
2969 MenuItem copy = new MenuItem();
2971 MenuItem cut = new MenuItem();
2973 Menu pasteMenu = new Menu();
2975 MenuItem pasteNew = new MenuItem();
2977 MenuItem pasteThis = new MenuItem();
2979 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2981 MenuItem font = new MenuItem();
2983 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2985 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2987 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2989 MenuItem modifyPID = new MenuItem();
2991 MenuItem modifyConservation = new MenuItem();
2993 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2994 "Autocalculate Consensus", true);
2996 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2997 "Sort Alignment With New Tree", true);
2999 Menu sortByTreeMenu = new Menu();
3001 Menu sort = new Menu();
3003 Menu calculate = new Menu();
3005 MenuItem inputText = new MenuItem();
3007 Menu helpMenu = new Menu();
3009 MenuItem documentation = new MenuItem();
3011 MenuItem about = new MenuItem();
3013 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3015 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3017 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3019 Menu autoAnnMenu = new Menu();
3021 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3023 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3025 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3027 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3029 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3031 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3033 private void jbInit() throws Exception
3036 setMenuBar(alignFrameMenuBar);
3040 // dynamically fill save as menu with available formats
3041 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3044 item = new MenuItem(
3045 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3047 item.addActionListener(new java.awt.event.ActionListener()
3050 public void actionPerformed(ActionEvent e)
3052 outputText_actionPerformed(e);
3056 outputTextboxMenu.add(item);
3058 closeMenuItem.addActionListener(this);
3059 loadApplication.addActionListener(this);
3061 loadTree.addActionListener(this);
3062 loadAnnotations.addActionListener(this);
3063 outputFeatures.addActionListener(this);
3064 outputAnnotations.addActionListener(this);
3065 selectAllSequenceMenuItem.addActionListener(this);
3066 deselectAllSequenceMenuItem.addActionListener(this);
3067 invertSequenceMenuItem.addActionListener(this);
3068 remove2LeftMenuItem.setLabel(MessageManager
3069 .getString("action.remove_left"));
3070 remove2LeftMenuItem.addActionListener(this);
3071 remove2RightMenuItem.setLabel(MessageManager
3072 .getString("action.remove_right"));
3073 remove2RightMenuItem.addActionListener(this);
3074 removeGappedColumnMenuItem.setLabel(MessageManager
3075 .getString("action.remove_empty_columns"));
3076 removeGappedColumnMenuItem.addActionListener(this);
3077 removeAllGapsMenuItem.setLabel(MessageManager
3078 .getString("action.remove_all_gaps"));
3079 removeAllGapsMenuItem.addActionListener(this);
3080 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3081 viewBoxesMenuItem.setState(true);
3082 viewBoxesMenuItem.addItemListener(this);
3083 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3084 viewTextMenuItem.setState(true);
3085 viewTextMenuItem.addItemListener(this);
3086 sortPairwiseMenuItem.setLabel(MessageManager
3087 .getString("action.by_pairwise_id"));
3088 sortPairwiseMenuItem.addActionListener(this);
3089 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3090 sortIDMenuItem.addActionListener(this);
3091 sortLengthMenuItem.setLabel(MessageManager
3092 .getString("action.by_length"));
3093 sortLengthMenuItem.addActionListener(this);
3094 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3095 sortGroupMenuItem.addActionListener(this);
3096 removeRedundancyMenuItem.setLabel(MessageManager
3097 .getString("action.remove_redundancy").concat("..."));
3098 removeRedundancyMenuItem.addActionListener(this);
3099 pairwiseAlignmentMenuItem.setLabel(MessageManager
3100 .getString("action.pairwise_alignment"));
3101 pairwiseAlignmentMenuItem.addActionListener(this);
3102 PCAMenuItem.setLabel(MessageManager
3103 .getString("label.principal_component_analysis"));
3104 PCAMenuItem.addActionListener(this);
3105 averageDistanceTreeMenuItem.setLabel(MessageManager
3106 .getString("label.average_distance_identity"));
3107 averageDistanceTreeMenuItem.addActionListener(this);
3108 neighbourTreeMenuItem.setLabel(MessageManager
3109 .getString("label.neighbour_joining_identity"));
3110 neighbourTreeMenuItem.addActionListener(this);
3111 statusBar.setBackground(Color.white);
3112 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3113 statusBar.setText(MessageManager.getString("label.status_bar"));
3114 outputTextboxMenu.setLabel(MessageManager
3115 .getString("label.out_to_textbox"));
3116 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3118 clustalColour.addActionListener(this);
3119 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3120 zappoColour.addActionListener(this);
3121 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3122 taylorColour.addActionListener(this);
3123 hydrophobicityColour.setLabel(MessageManager
3124 .getString("label.hydrophobicity"));
3125 hydrophobicityColour.addActionListener(this);
3127 .setLabel(MessageManager.getString("label.helix_propensity"));
3128 helixColour.addActionListener(this);
3129 strandColour.setLabel(MessageManager
3130 .getString("label.strand_propensity"));
3131 strandColour.addActionListener(this);
3132 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3133 turnColour.addActionListener(this);
3134 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3135 buriedColour.addActionListener(this);
3136 purinePyrimidineColour.setLabel(MessageManager
3137 .getString("label.purine_pyrimidine"));
3138 purinePyrimidineColour.addActionListener(this);
3139 RNAInteractionColour.setLabel(MessageManager
3140 .getString("label.rna_interaction"));
3141 RNAInteractionColour.addActionListener(this);
3142 RNAHelixColour.setLabel(MessageManager
3143 .getString("action.by_rna_helixes"));
3144 RNAHelixColour.addActionListener(this);
3145 userDefinedColour.setLabel(MessageManager
3146 .getString("action.user_defined"));
3147 userDefinedColour.addActionListener(this);
3148 PIDColour.setLabel(MessageManager
3149 .getString("label.percentage_identity"));
3150 PIDColour.addActionListener(this);
3151 BLOSUM62Colour.setLabel(MessageManager
3152 .getString("label.blosum62_score"));
3153 BLOSUM62Colour.addActionListener(this);
3155 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3156 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3158 tcoffeeColour.addActionListener(this);
3159 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3160 .getString("label.average_distance_bloslum62"));
3161 avDistanceTreeBlosumMenuItem.addActionListener(this);
3162 njTreeBlosumMenuItem.setLabel(MessageManager
3163 .getString("label.neighbour_blosum62"));
3164 njTreeBlosumMenuItem.addActionListener(this);
3165 annotationPanelMenuItem.setLabel(MessageManager
3166 .getString("label.show_annotations"));
3167 annotationPanelMenuItem.addItemListener(this);
3168 colourTextMenuItem.setLabel(MessageManager
3169 .getString("label.colour_text"));
3170 colourTextMenuItem.addItemListener(this);
3171 displayNonconservedMenuItem.setLabel(MessageManager
3172 .getString("label.show_non_conversed"));
3173 displayNonconservedMenuItem.addItemListener(this);
3174 alProperties.addActionListener(this);
3175 overviewMenuItem.setLabel(MessageManager
3176 .getString("label.overview_window"));
3177 overviewMenuItem.addActionListener(this);
3178 undoMenuItem.setEnabled(false);
3179 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3180 undoMenuItem.addActionListener(this);
3181 redoMenuItem.setEnabled(false);
3182 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3183 redoMenuItem.addActionListener(this);
3184 conservationMenuItem.setLabel(MessageManager
3185 .getString("action.by_conservation"));
3186 conservationMenuItem.addItemListener(this);
3187 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3188 noColourmenuItem.addActionListener(this);
3189 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3190 wrapMenuItem.addItemListener(this);
3191 renderGapsMenuItem.setLabel(MessageManager
3192 .getString("action.show_gaps"));
3193 renderGapsMenuItem.setState(true);
3194 renderGapsMenuItem.addItemListener(this);
3195 findMenuItem.setLabel(MessageManager.getString("action.find"));
3196 findMenuItem.addActionListener(this);
3197 abovePIDThreshold.setLabel(MessageManager
3198 .getString("label.above_identity_threshold"));
3199 abovePIDThreshold.addItemListener(this);
3200 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3201 nucleotideColour.addActionListener(this);
3202 deleteGroups.setLabel(MessageManager
3203 .getString("action.undefine_groups"));
3204 deleteGroups.addActionListener(this);
3205 grpsFromSelection.setLabel(MessageManager
3206 .getString("action.make_groups_selection"));
3207 grpsFromSelection.addActionListener(this);
3208 createGroup.setLabel(MessageManager.getString("action.create_group"));
3209 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3210 copy.setLabel(MessageManager.getString("action.copy"));
3211 copy.addActionListener(this);
3212 cut.setLabel(MessageManager.getString("action.cut"));
3213 cut.addActionListener(this);
3214 delete.setLabel(MessageManager.getString("action.delete"));
3215 delete.addActionListener(this);
3216 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3217 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3218 pasteNew.addActionListener(this);
3219 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3220 pasteThis.addActionListener(this);
3221 applyToAllGroups.setLabel(MessageManager
3222 .getString("label.apply_colour_to_all_groups"));
3223 applyToAllGroups.setState(true);
3224 applyToAllGroups.addItemListener(this);
3225 font.setLabel(MessageManager.getString("action.font"));
3226 font.addActionListener(this);
3227 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3228 scaleAbove.setState(true);
3229 scaleAbove.setEnabled(false);
3230 scaleAbove.addItemListener(this);
3231 scaleLeft.setEnabled(false);
3232 scaleLeft.setState(true);
3233 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3234 scaleLeft.addItemListener(this);
3235 scaleRight.setEnabled(false);
3236 scaleRight.setState(true);
3237 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3238 scaleRight.addItemListener(this);
3239 modifyPID.setLabel(MessageManager
3240 .getString("label.modify_identity_thereshold"));
3241 modifyPID.addActionListener(this);
3242 modifyConservation.setLabel(MessageManager
3243 .getString("label.modify_conservation_thereshold"));
3244 modifyConservation.addActionListener(this);
3245 sortByTreeMenu.setLabel(MessageManager
3246 .getString("action.by_tree_order"));
3247 sort.setLabel(MessageManager.getString("action.sort"));
3248 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3249 autoCalculate.addItemListener(this);
3250 sortByTree.addItemListener(this);
3252 .setLabel(MessageManager.getString("label.input_from_textbox"));
3253 inputText.addActionListener(this);
3254 centreColumnLabelFlag.setLabel(MessageManager
3255 .getString("label.centre_column_labels"));
3256 centreColumnLabelFlag.addItemListener(this);
3257 followMouseOverFlag.setLabel(MessageManager
3258 .getString("label.automatic_scrolling"));
3259 followMouseOverFlag.addItemListener(this);
3260 helpMenu.setLabel(MessageManager.getString("action.help"));
3261 documentation.setLabel(MessageManager.getString("label.documentation"));
3262 documentation.addActionListener(this);
3264 about.setLabel(MessageManager.getString("label.about"));
3265 about.addActionListener(this);
3266 seqLimits.setState(true);
3267 seqLimits.setLabel(MessageManager
3268 .getString("label.show_sequence_limits"));
3269 seqLimits.addItemListener(this);
3270 featureSettings.setLabel(MessageManager
3271 .getString("label.feature_settings"));
3272 featureSettings.addActionListener(this);
3273 sequenceFeatures.setLabel(MessageManager
3274 .getString("label.sequence_features"));
3275 sequenceFeatures.addItemListener(this);
3276 sequenceFeatures.setState(false);
3277 annotationColour.setLabel(MessageManager
3278 .getString("action.by_annotation"));
3279 annotationColour.addActionListener(this);
3281 annotationColumnSelection.setLabel("Select by Annotation");
3282 annotationColumnSelection.addActionListener(this);
3284 invertSequenceMenuItem.setLabel(MessageManager
3285 .getString("action.invert_sequence_selection"));
3286 invertColSel.setLabel(MessageManager
3287 .getString("action.invert_column_selection"));
3288 menu1.setLabel(MessageManager.getString("action.show"));
3289 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3290 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3291 menu2.setLabel(MessageManager.getString("action.hide"));
3293 .setLabel(MessageManager.getString("label.selected_columns"));
3294 hideSequences.setLabel(MessageManager
3295 .getString("label.selected_sequences"));
3296 hideAllButSelection.setLabel(MessageManager
3297 .getString("label.all_but_selected_region"));
3298 hideAllSelection.setLabel(MessageManager
3299 .getString("label.selected_region"));
3300 showAllHidden.setLabel(MessageManager
3301 .getString("label.all_sequences_columns"));
3302 showGroupConsensus.setLabel(MessageManager
3303 .getString("label.group_consensus"));
3304 showGroupConservation.setLabel(MessageManager
3305 .getString("label.group_conservation"));
3306 showConsensusHistogram.setLabel(MessageManager
3307 .getString("label.show_consensus_histogram"));
3308 showSequenceLogo.setLabel(MessageManager
3309 .getString("label.show_consensus_logo"));
3310 normSequenceLogo.setLabel(MessageManager
3311 .getString("label.norm_consensus_logo"));
3312 applyAutoAnnotationSettings.setLabel(MessageManager
3313 .getString("label.apply_all_groups"));
3314 applyAutoAnnotationSettings.setState(true);
3315 autoAnnMenu.setLabel(MessageManager
3316 .getString("label.autocalculated_annotation"));
3318 invertColSel.addActionListener(this);
3319 showColumns.addActionListener(this);
3320 showSeqs.addActionListener(this);
3321 hideColumns.addActionListener(this);
3322 hideSequences.addActionListener(this);
3323 hideAllButSelection.addActionListener(this);
3324 hideAllSelection.addActionListener(this);
3325 showAllHidden.addActionListener(this);
3326 showGroupConsensus.addItemListener(this);
3327 showGroupConservation.addItemListener(this);
3328 showConsensusHistogram.addItemListener(this);
3329 showSequenceLogo.addItemListener(this);
3330 normSequenceLogo.addItemListener(this);
3332 applyAutoAnnotationSettings.addItemListener(this);
3333 formatMenu.setLabel(MessageManager.getString("action.format"));
3334 selectMenu.setLabel(MessageManager.getString("action.select"));
3335 newView.setLabel(MessageManager.getString("action.new_view"));
3336 newView.addActionListener(this);
3337 alignFrameMenuBar.add(fileMenu);
3338 alignFrameMenuBar.add(editMenu);
3339 alignFrameMenuBar.add(selectMenu);
3340 alignFrameMenuBar.add(viewMenu);
3341 alignFrameMenuBar.add(formatMenu);
3342 alignFrameMenuBar.add(colourMenu);
3343 alignFrameMenuBar.add(calculateMenu);
3344 alignFrameMenuBar.add(helpMenu);
3346 fileMenu.add(inputText);
3347 fileMenu.add(loadTree);
3348 fileMenu.add(loadAnnotations);
3350 fileMenu.addSeparator();
3351 fileMenu.add(outputTextboxMenu);
3352 fileMenu.add(outputFeatures);
3353 fileMenu.add(outputAnnotations);
3355 if (jalviewServletURL != null)
3357 fileMenu.add(loadApplication);
3360 fileMenu.addSeparator();
3361 fileMenu.add(closeMenuItem);
3363 editMenu.add(undoMenuItem);
3364 editMenu.add(redoMenuItem);
3367 editMenu.add(pasteMenu);
3368 editMenu.add(delete);
3369 editMenu.addSeparator();
3370 editMenu.add(remove2LeftMenuItem);
3371 editMenu.add(remove2RightMenuItem);
3372 editMenu.add(removeGappedColumnMenuItem);
3373 editMenu.add(removeAllGapsMenuItem);
3374 editMenu.add(removeRedundancyMenuItem);
3375 viewMenu.add(newView);
3376 viewMenu.addSeparator();
3377 viewMenu.add(menu1);
3378 viewMenu.add(menu2);
3379 viewMenu.addSeparator();
3380 viewMenu.add(followMouseOverFlag);
3381 viewMenu.add(annotationPanelMenuItem);
3382 autoAnnMenu.add(applyAutoAnnotationSettings);
3383 autoAnnMenu.add(showConsensusHistogram);
3384 autoAnnMenu.add(showSequenceLogo);
3385 autoAnnMenu.add(normSequenceLogo);
3386 autoAnnMenu.addSeparator();
3387 autoAnnMenu.add(showGroupConservation);
3388 autoAnnMenu.add(showGroupConsensus);
3389 viewMenu.add(autoAnnMenu);
3390 viewMenu.addSeparator();
3391 viewMenu.add(sequenceFeatures);
3392 viewMenu.add(featureSettings);
3393 viewMenu.addSeparator();
3394 viewMenu.add(alProperties);
3395 viewMenu.addSeparator();
3396 viewMenu.add(overviewMenuItem);
3397 colourMenu.add(applyToAllGroups);
3398 colourMenu.addSeparator();
3399 colourMenu.add(noColourmenuItem);
3400 colourMenu.add(clustalColour);
3401 colourMenu.add(BLOSUM62Colour);
3402 colourMenu.add(PIDColour);
3403 colourMenu.add(zappoColour);
3404 colourMenu.add(taylorColour);
3405 colourMenu.add(hydrophobicityColour);
3406 colourMenu.add(helixColour);
3407 colourMenu.add(strandColour);
3408 colourMenu.add(turnColour);
3409 colourMenu.add(buriedColour);
3410 colourMenu.add(nucleotideColour);
3411 colourMenu.add(purinePyrimidineColour);
3412 // colourMenu.add(RNAInteractionColour);
3413 colourMenu.add(tcoffeeColour);
3414 colourMenu.add(userDefinedColour);
3415 colourMenu.addSeparator();
3416 colourMenu.add(conservationMenuItem);
3417 colourMenu.add(modifyConservation);
3418 colourMenu.add(abovePIDThreshold);
3419 colourMenu.add(modifyPID);
3420 colourMenu.add(annotationColour);
3421 colourMenu.add(RNAHelixColour);
3422 calculateMenu.add(sort);
3423 calculateMenu.add(calculate);
3424 calculateMenu.addSeparator();
3425 calculateMenu.add(pairwiseAlignmentMenuItem);
3426 calculateMenu.add(PCAMenuItem);
3427 calculateMenu.add(autoCalculate);
3428 calculateMenu.add(sortByTree);
3429 this.add(statusBar, BorderLayout.SOUTH);
3430 pasteMenu.add(pasteNew);
3431 pasteMenu.add(pasteThis);
3432 sort.add(sortIDMenuItem);
3433 sort.add(sortLengthMenuItem);
3434 sort.add(sortByTreeMenu);
3435 sort.add(sortGroupMenuItem);
3436 sort.add(sortPairwiseMenuItem);
3437 calculate.add(averageDistanceTreeMenuItem);
3438 calculate.add(neighbourTreeMenuItem);
3439 calculate.add(avDistanceTreeBlosumMenuItem);
3440 calculate.add(njTreeBlosumMenuItem);
3441 helpMenu.add(documentation);
3442 helpMenu.add(about);
3443 menu1.add(showColumns);
3444 menu1.add(showSeqs);
3445 menu1.add(showAllHidden);
3446 menu2.add(hideColumns);
3447 menu2.add(hideSequences);
3448 menu2.add(hideAllSelection);
3449 menu2.add(hideAllButSelection);
3450 formatMenu.add(font);
3451 formatMenu.add(seqLimits);
3452 formatMenu.add(wrapMenuItem);
3453 formatMenu.add(scaleAbove);
3454 formatMenu.add(scaleLeft);
3455 formatMenu.add(scaleRight);
3456 formatMenu.add(viewBoxesMenuItem);
3457 formatMenu.add(viewTextMenuItem);
3458 formatMenu.add(colourTextMenuItem);
3459 formatMenu.add(displayNonconservedMenuItem);
3460 formatMenu.add(renderGapsMenuItem);
3461 formatMenu.add(centreColumnLabelFlag);
3462 selectMenu.add(findMenuItem);
3463 selectMenu.addSeparator();
3464 selectMenu.add(selectAllSequenceMenuItem);
3465 selectMenu.add(deselectAllSequenceMenuItem);
3466 selectMenu.add(invertSequenceMenuItem);
3467 selectMenu.add(invertColSel);
3468 selectMenu.add(createGroup);
3469 selectMenu.add(unGroup);
3470 selectMenu.add(grpsFromSelection);
3471 selectMenu.add(deleteGroups);
3472 selectMenu.add(annotationColumnSelection);
3476 public void setStatus(String string)
3478 statusBar.setText(string);
3481 MenuItem featureSettings = new MenuItem();
3483 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3485 MenuItem annotationColour = new MenuItem();
3487 MenuItem annotationColumnSelection = new MenuItem();
3489 MenuItem invertColSel = new MenuItem();
3491 Menu menu1 = new Menu();
3493 MenuItem showColumns = new MenuItem();
3495 MenuItem showSeqs = new MenuItem();
3497 Menu menu2 = new Menu();
3499 MenuItem hideColumns = new MenuItem();
3501 MenuItem hideSequences = new MenuItem();
3503 MenuItem hideAllButSelection = new MenuItem();
3505 MenuItem hideAllSelection = new MenuItem();
3507 MenuItem showAllHidden = new MenuItem();
3509 Menu formatMenu = new Menu();
3511 Menu selectMenu = new Menu();
3513 MenuItem newView = new MenuItem();
3516 * Attach the alignFrame panels after embedding menus, if necessary. This used
3517 * to be called setEmbedded, but is now creates the dropdown menus in a
3518 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3520 * @param reallyEmbedded
3521 * true to attach the view to the applet area on the page rather than
3524 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3529 // Explicly build the embedded menu panel for the on-page applet
3531 // view cannot be closed if its actually on the page
3532 fileMenu.remove(closeMenuItem);
3533 fileMenu.remove(3); // Remove Seperator
3534 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3535 Font.PLAIN, 11, false); // use our own fonts.
3536 // and actually add the components to the applet area
3537 viewport.applet.setLayout(new BorderLayout());
3538 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3539 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3540 alignPanel.setSize(viewport.applet.getSize().width,
3541 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3542 - statusBar.HEIGHT);
3543 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3544 final AlignFrame me = this;
3545 viewport.applet.addFocusListener(new FocusListener()
3549 public void focusLost(FocusEvent e)
3551 if (me.viewport.applet.currentAlignFrame == me)
3553 me.viewport.applet.currentAlignFrame = null;
3558 public void focusGained(FocusEvent e)
3560 me.viewport.applet.currentAlignFrame = me;
3563 viewport.applet.validate();
3568 // test and embed menu bar if necessary.
3570 if (embedMenuIfNeeded(alignPanel))
3572 // adjust for status bar height too
3573 alignPanel.setSize(getSize().width, getSize().height
3574 - statusBar.HEIGHT);
3576 add(statusBar, BorderLayout.SOUTH);
3577 add(alignPanel, BorderLayout.CENTER);
3578 // and register with the applet so it can pass external API calls to us
3579 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3585 * create a new binding between structures in an existing jmol viewer instance
3586 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3587 * this does not open a new Jmol window, or modify the display of the
3588 * structures in the original jmol window. Note This method doesn't work
3589 * without an additional javascript library to exchange messages between the
3590 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3593 * JmolViewer instance
3594 * @param sequenceIds
3595 * - sequence Ids to search for associations
3597 public SequenceStructureBinding addStructureViewInstance(
3598 Object jmolviewer, String[] sequenceIds)
3600 org.jmol.api.JmolViewer viewer = null;
3603 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3604 } catch (ClassCastException ex)
3606 System.err.println("Unsupported viewer object :"
3607 + jmolviewer.getClass());
3611 System.err.println("Can't use this object as a structure viewer:"
3612 + jmolviewer.getClass());
3615 SequenceI[] seqs = null;
3616 if (sequenceIds == null || sequenceIds.length == 0)
3618 seqs = viewport.getAlignment().getSequencesArray();
3622 Vector sqi = new Vector();
3623 AlignmentI al = viewport.getAlignment();
3624 for (int sid = 0; sid < sequenceIds.length; sid++)
3626 SequenceI sq = al.findName(sequenceIds[sid]);
3634 seqs = new SequenceI[sqi.size()];
3635 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3637 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3646 // TODO: search for a jmv that involves viewer
3648 { // create a new viewer/jalview binding.
3649 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3657 * bind a pdb file to a sequence in the current view
3660 * - sequenceId within the dataset.
3661 * @param pdbEntryString
3662 * - the short name for the PDB file
3664 * - pdb file - either a URL or a valid PDB file.
3665 * @return true if binding was as success TODO: consider making an exception
3666 * structure for indicating when PDB parsing or sequenceId location
3669 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3672 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3673 boolean needtoadd = false;
3674 if (toaddpdb != null)
3676 Vector pdbe = toaddpdb.getPDBId();
3677 PDBEntry pdbentry = null;
3678 if (pdbe != null && pdbe.size() > 0)
3680 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3682 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3683 if (!pdbentry.getId().equals(pdbEntryString)
3684 && !pdbentry.getFile().equals(pdbFile))
3694 if (pdbentry == null)
3696 pdbentry = new PDBEntry();
3697 pdbentry.setId(pdbEntryString);
3698 pdbentry.setFile(pdbFile);
3699 needtoadd = true; // add this new entry to sequence.
3701 // resolve data source
3702 // TODO: this code should be a refactored to an io package
3703 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3704 if (protocol == null)
3710 // make a note of the access mode and add
3711 if (pdbentry.getProperty() == null)
3713 pdbentry.setProperty(new Hashtable());
3715 pdbentry.getProperty().put("protocol", protocol);
3716 toaddpdb.addPDBId(pdbentry);
3717 alignPanel.getStructureSelectionManager()
3718 .registerPDBEntry(pdbentry);
3724 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3728 Vector sequences = new Vector();
3729 for (int i = 0; i < seqs.length; i++)
3731 if (seqs[i] != null)
3733 sequences.addElement(new Object[]
3734 { seqs[i], (chains != null) ? chains[i] : null });
3737 seqs = new SequenceI[sequences.size()];
3738 chains = new String[sequences.size()];
3739 for (int i = 0, isize = sequences.size(); i < isize; i++)
3741 Object[] oj = (Object[]) sequences.elementAt(i);
3743 seqs[i] = (SequenceI) oj[0];
3744 chains[i] = (String) oj[1];
3752 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3753 SequenceI[] seqs, String[] chains, String protocol)
3755 // Scrub any null sequences from the array
3756 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3757 seqs = (SequenceI[]) sqch[0];
3758 chains = (String[]) sqch[1];
3759 if (seqs == null || seqs.length == 0)
3762 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3764 if (protocol == null || protocol.trim().length() == 0
3765 || protocol.equals("null"))
3767 protocol = (String) pdb.getProperty().get("protocol");
3768 if (protocol == null)
3770 System.err.println("Couldn't work out protocol to open structure: "
3775 if (applet.useXtrnalSviewer)
3777 // register the association(s) and quit, don't create any windows.
3778 if (StructureSelectionManager.getStructureSelectionManager(applet)
3779 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3781 System.err.println("Failed to map " + pdb.getFile() + " ("
3782 + protocol + ") to any sequences");
3786 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3788 // can only do alignments with Jmol
3789 // find the last jmol window assigned to this alignment
3790 jalview.appletgui.AppletJmol ajm = null, tajm;
3791 Vector jmols = applet
3792 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3793 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3795 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3796 if (tajm.ap.alignFrame == this)
3805 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3806 // try and add the pdb structure
3811 // otherwise, create a new window
3812 if (applet.jmolAvailable)
3814 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3816 applet.lastFrameX += 40;
3817 applet.lastFrameY += 40;
3821 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3826 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3827 SequenceI[][] seqs, String[][] chains, String[] protocols)
3829 // TODO Auto-generated method stub
3830 System.err.println("Aligned Structure View: Not yet implemented.");
3834 * modify the current selection, providing the user has not made a selection
3838 * - sequences from this alignment
3840 * - columns to be selected on the alignment
3842 public void select(SequenceGroup sel, ColumnSelection csel)
3844 alignPanel.seqPanel.selection(sel, csel, null);
3847 public void scrollTo(int row, int column)
3849 alignPanel.seqPanel.scrollTo(row, column);
3852 public void scrollToRow(int row)
3854 alignPanel.seqPanel.scrollToRow(row);
3857 public void scrollToColumn(int column)
3859 alignPanel.seqPanel.scrollToColumn(column);
3863 * @return the alignments unique ID.
3865 public String getSequenceSetId()
3867 return viewport.getSequenceSetId();
3871 * Load the (T-Coffee) score file from the specified url
3874 * File/URL/T-COFFEE score file contents
3875 * @throws IOException
3876 * @return true if alignment was annotated with data from source
3878 public boolean loadScoreFile(String source) throws IOException
3881 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3882 AppletFormatAdapter.checkProtocol(source));
3883 if (!file.isValid())
3885 // TODO: raise dialog for gui
3886 System.err.println("Problems parsing T-Coffee scores: "
3887 + file.getWarningMessage());
3888 System.err.println("Origin was:\n" + source);
3893 * check that the score matrix matches the alignment dimensions
3896 if ((aln = viewport.getAlignment()) != null
3897 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3900 // TODO: raise a dialog box here rather than bomb out.
3902 .println("The scores matrix does not match the alignment dimensions");
3906 // TODO add parameter to indicate if matching should be done
3907 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3909 alignPanel.fontChanged();
3910 tcoffeeColour.setEnabled(true);
3911 // switch to this color
3912 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3917 System.err.println("Problems resolving T-Coffee scores:");
3918 if (file.getWarningMessage() != null)
3920 System.err.println(file.getWarningMessage());