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.SequenceStructureBinding;
27 import jalview.api.FeatureRenderer;
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.Enumeration;
95 import java.util.Hashtable;
96 import java.util.Iterator;
97 import java.util.List;
99 import java.util.StringTokenizer;
100 import java.util.Vector;
102 public class AlignFrame extends EmbmenuFrame implements ActionListener,
103 ItemListener, KeyListener, AlignViewControllerGuiI
105 public AlignViewControllerI avc;
107 public AlignmentPanel alignPanel;
109 public AlignViewport viewport;
111 int DEFAULT_WIDTH = 700;
113 int DEFAULT_HEIGHT = 500;
115 String jalviewServletURL;
117 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
118 String title, boolean embedded)
122 jalviewServletURL = applet.getParameter("APPLICATION_URL");
128 } catch (Exception ex)
130 ex.printStackTrace();
132 // need to get window geometry before we calculate alignment layout
138 param = applet.getParameter("windowWidth");
141 int width = Integer.parseInt(param);
142 DEFAULT_WIDTH = width;
144 param = applet.getParameter("windowHeight");
147 int height = Integer.parseInt(param);
148 DEFAULT_HEIGHT = height;
150 } catch (Exception ex)
154 viewport = new AlignViewport(al, applet);
155 alignPanel = new AlignmentPanel(this, viewport);
156 avc = new jalview.controller.AlignViewController(this, viewport,
158 viewport.updateConservation(alignPanel);
159 viewport.updateConsensus(alignPanel);
161 annotationPanelMenuItem.setState(viewport.showAnnotation);
162 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
163 followMouseOverFlag.setState(viewport.getFollowHighlight());
164 showGroupConsensus.setState(viewport.isShowGroupConsensus());
165 showGroupConservation.setState(viewport.isShowGroupConservation());
166 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
167 showSequenceLogo.setState(viewport.isShowSequenceLogo());
168 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
169 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
171 seqLimits.setState(viewport.showJVSuffix);
175 String param = applet.getParameter("sortBy");
178 if (param.equalsIgnoreCase("Id"))
180 sortIDMenuItem_actionPerformed();
182 else if (param.equalsIgnoreCase("Pairwise Identity"))
184 sortPairwiseMenuItem_actionPerformed();
186 else if (param.equalsIgnoreCase("Length"))
188 sortLengthMenuItem_actionPerformed();
192 param = applet.getParameter("wrap");
195 if (param.equalsIgnoreCase("true"))
197 wrapMenuItem.setState(true);
198 wrapMenuItem_actionPerformed();
201 param = applet.getParameter("centrecolumnlabels");
204 centreColumnLabelFlag.setState(true);
205 centreColumnLabelFlag_stateChanged();
209 if (viewport.getAlignment().isNucleotide())
211 viewport.updateStrucConsensus(alignPanel);
212 if (viewport.getAlignment().hasRNAStructure())
214 RNAHelixColour.setEnabled(true);
218 RNAHelixColour.setEnabled(false);
223 RNAHelixColour.setEnabled(false);
224 purinePyrimidineColour.setEnabled(false);
226 // Some JVMS send keyevents to Top frame or lowest panel,
227 // Havent worked out why yet. So add to both this frame and seqCanvas for
229 this.addKeyListener(this);
230 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
231 alignPanel.idPanel.idCanvas.addKeyListener(this);
232 alignPanel.scalePanel.addKeyListener(this);
233 alignPanel.annotationPanel.addKeyListener(this);
234 alignPanel.annotationPanelHolder.addKeyListener(this);
235 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
236 alignPanel.alabels.addKeyListener(this);
237 createAlignFrameWindow(embedded, title);
240 alignPanel.adjustAnnotationHeight();
241 alignPanel.paintAlignment(true);
244 public AlignViewport getAlignViewport()
249 public SeqCanvas getSeqcanvas()
251 return alignPanel.seqPanel.seqCanvas;
255 * Load a features file onto the alignment
258 * file URL, content, or other resolvable path
260 * is protocol for accessing data referred to by file
263 public boolean parseFeaturesFile(String file, String type)
265 return parseFeaturesFile(file, type, true);
269 * Load a features file onto the alignment
272 * file URL, content, or other resolvable path
274 * is protocol for accessing data referred to by file
275 * @param autoenabledisplay
276 * when true, display features flag will be automatically enabled if
277 * features are loaded
278 * @return true if data parsed as a features file
280 public boolean parseFeaturesFile(String file, String type,
281 boolean autoenabledisplay)
283 // TODO: test if importing a features file onto an alignment which already
284 // has features with links overwrites the original links.
286 Hashtable featureLinks = new Hashtable();
287 boolean featuresFile = false;
290 featuresFile = new jalview.io.FeaturesFile(file, type)
291 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
292 .getFeatureRenderer().getFeatureColours(), featureLinks,
293 true, viewport.applet.getDefaultParameter(
294 "relaxedidmatch", false));
295 } catch (Exception ex)
297 ex.printStackTrace();
302 if (featureLinks.size() > 0)
304 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
306 if (autoenabledisplay)
308 viewport.setShowSequenceFeatures(true);
309 sequenceFeatures.setState(true);
311 if (alignPanel.seqPanel.seqCanvas.fr != null)
313 // update the min/max ranges where necessary
314 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
316 if (viewport.featureSettings != null)
318 viewport.featureSettings.refreshTable();
320 alignPanel.paintAlignment(true);
321 statusBar.setText(MessageManager
322 .getString("label.successfully_added_features_alignment"));
328 public void keyPressed(KeyEvent evt)
330 if (viewport.cursorMode
331 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
332 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
333 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
334 && Character.isDigit(evt.getKeyChar()))
336 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
339 switch (evt.getKeyCode())
341 case 27: // escape key
342 deselectAllSequenceMenuItem_actionPerformed();
344 alignPanel.alabels.cancelDrag();
347 if (evt.isControlDown() || evt.isMetaDown())
349 cut_actionPerformed();
353 if (viewport.cursorMode && !evt.isControlDown())
355 alignPanel.seqPanel.setCursorColumn();
357 if (evt.isControlDown() || evt.isMetaDown())
359 copy_actionPerformed();
363 if (evt.isControlDown())
365 paste(evt.isShiftDown());
369 if (evt.isControlDown() || evt.isMetaDown())
371 selectAllSequenceMenuItem_actionPerformed();
374 case KeyEvent.VK_DOWN:
375 if (viewport.cursorMode)
377 alignPanel.seqPanel.moveCursor(0, 1);
381 moveSelectedSequences(false);
386 if (viewport.cursorMode)
388 alignPanel.seqPanel.moveCursor(0, -1);
392 moveSelectedSequences(true);
396 case KeyEvent.VK_LEFT:
397 if (evt.isAltDown() || !viewport.cursorMode)
399 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
403 alignPanel.seqPanel.moveCursor(-1, 0);
407 case KeyEvent.VK_RIGHT:
408 if (evt.isAltDown() || !viewport.cursorMode)
410 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
414 alignPanel.seqPanel.moveCursor(1, 0);
418 case KeyEvent.VK_SPACE:
419 if (viewport.cursorMode)
421 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
422 || evt.isShiftDown() || evt.isAltDown());
426 case KeyEvent.VK_DELETE:
427 case KeyEvent.VK_BACK_SPACE:
428 if (viewport.cursorMode)
430 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
431 || evt.isShiftDown() || evt.isAltDown());
435 cut_actionPerformed();
436 alignPanel.seqPanel.seqCanvas.repaint();
441 if (viewport.cursorMode)
443 alignPanel.seqPanel.setCursorRow();
447 if (viewport.cursorMode)
449 alignPanel.seqPanel.setCursorPosition();
453 case KeyEvent.VK_ENTER:
454 case KeyEvent.VK_COMMA:
455 if (viewport.cursorMode)
457 alignPanel.seqPanel.setCursorRowAndColumn();
462 if (viewport.cursorMode)
464 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
468 if (viewport.cursorMode)
470 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
475 viewport.cursorMode = !viewport.cursorMode;
476 statusBar.setText(MessageManager.formatMessage(
477 "label.keyboard_editing_mode", new String[]
478 { (viewport.cursorMode ? "on" : "off") }));
479 if (viewport.cursorMode)
481 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
482 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
487 if (evt.isControlDown())
489 findMenuItem_actionPerformed();
495 boolean toggleSeqs = !evt.isControlDown();
496 boolean toggleCols = !evt.isShiftDown();
497 toggleHiddenRegions(toggleSeqs, toggleCols);
501 case KeyEvent.VK_PAGE_UP:
502 if (viewport.wrapAlignment)
504 alignPanel.scrollUp(true);
508 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
509 - viewport.endSeq + viewport.startSeq);
513 case KeyEvent.VK_PAGE_DOWN:
514 if (viewport.wrapAlignment)
516 alignPanel.scrollUp(false);
520 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
521 + viewport.endSeq - viewport.startSeq);
526 if (evt.isControlDown())
528 undoMenuItem_actionPerformed();
533 if (evt.isControlDown())
535 redoMenuItem_actionPerformed();
540 if (evt.isControlDown())
547 if (evt.isControlDown())
549 trimAlignment(false);
554 if (evt.isControlDown())
556 if (evt.isShiftDown())
558 this.removeAllGapsMenuItem_actionPerformed();
562 removeGappedColumnMenuItem_actionPerformed();
567 if (evt.isControlDown())
571 invertColSel_actionPerformed();
575 invertSequenceMenuItem_actionPerformed();
581 if (evt.isControlDown())
583 if (evt.isShiftDown())
585 this.unGroup_actionPerformed();
589 this.createGroup_actionPerformed();
595 if (evt.isControlDown())
597 this.deleteGroups_actionPerformed();
602 if (evt.isControlDown())
609 alignPanel.paintAlignment(true);
613 * called by key handler and the hide all/show all menu items
618 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
620 boolean hide = false;
621 SequenceGroup sg = viewport.getSelectionGroup();
622 if (!toggleSeqs && !toggleCols)
624 // Hide everything by the current selection - this is a hack - we do the
625 // invert and then hide
626 // first check that there will be visible columns after the invert.
627 if ((viewport.getColumnSelection() != null
628 && viewport.getColumnSelection().getSelected() != null && viewport
629 .getColumnSelection().getSelected().size() > 0)
630 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
633 // now invert the sequence set, if required - empty selection implies
634 // that no hiding is required.
637 invertSequenceMenuItem_actionPerformed();
638 sg = viewport.getSelectionGroup();
642 viewport.expandColSelection(sg, true);
643 // finally invert the column selection and get the new sequence
644 // selection and indicate it should be hidden.
645 invertColSel_actionPerformed();
652 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
655 viewport.hideAllSelectedSeqs();
657 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
660 viewport.showAllHiddenSeqs();
666 if (viewport.getColumnSelection().getSelected().size() > 0)
668 viewport.hideSelectedColumns();
671 viewport.setSelectionGroup(sg);
676 viewport.showAllHiddenColumns();
682 public void keyReleased(KeyEvent evt)
687 public void keyTyped(KeyEvent evt)
692 public void itemStateChanged(ItemEvent evt)
694 if (evt.getSource() == displayNonconservedMenuItem)
696 displayNonconservedMenuItem_actionPerformed();
698 else if (evt.getSource() == colourTextMenuItem)
700 colourTextMenuItem_actionPerformed();
702 else if (evt.getSource() == wrapMenuItem)
704 wrapMenuItem_actionPerformed();
706 else if (evt.getSource() == scaleAbove)
708 viewport.setScaleAboveWrapped(scaleAbove.getState());
710 else if (evt.getSource() == scaleLeft)
712 viewport.setScaleLeftWrapped(scaleLeft.getState());
714 else if (evt.getSource() == scaleRight)
716 viewport.setScaleRightWrapped(scaleRight.getState());
718 else if (evt.getSource() == seqLimits)
720 seqLimits_itemStateChanged();
722 else if (evt.getSource() == viewBoxesMenuItem)
724 viewport.setShowBoxes(viewBoxesMenuItem.getState());
726 else if (evt.getSource() == viewTextMenuItem)
728 viewport.setShowText(viewTextMenuItem.getState());
730 else if (evt.getSource() == renderGapsMenuItem)
732 viewport.setRenderGaps(renderGapsMenuItem.getState());
734 else if (evt.getSource() == annotationPanelMenuItem)
736 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
737 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
739 else if (evt.getSource() == sequenceFeatures)
741 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
742 alignPanel.seqPanel.seqCanvas.repaint();
744 else if (evt.getSource() == conservationMenuItem)
746 conservationMenuItem_actionPerformed();
748 else if (evt.getSource() == abovePIDThreshold)
750 abovePIDThreshold_actionPerformed();
752 else if (evt.getSource() == applyToAllGroups)
754 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
756 else if (evt.getSource() == autoCalculate)
758 viewport.autoCalculateConsensus = autoCalculate.getState();
760 else if (evt.getSource() == sortByTree)
762 viewport.sortByTree = sortByTree.getState();
764 else if (evt.getSource() == this.centreColumnLabelFlag)
766 centreColumnLabelFlag_stateChanged();
768 else if (evt.getSource() == this.followMouseOverFlag)
770 mouseOverFlag_stateChanged();
772 else if (evt.getSource() == showGroupConsensus)
774 showGroupConsensus_actionPerformed();
776 else if (evt.getSource() == showGroupConservation)
778 showGroupConservation_actionPerformed();
780 else if (evt.getSource() == showSequenceLogo)
782 showSequenceLogo_actionPerformed();
784 else if (evt.getSource() == normSequenceLogo)
786 normSequenceLogo_actionPerformed();
788 else if (evt.getSource() == showConsensusHistogram)
790 showConsensusHistogram_actionPerformed();
792 else if (evt.getSource() == applyAutoAnnotationSettings)
794 applyAutoAnnotationSettings_actionPerformed();
796 alignPanel.paintAlignment(true);
799 private void mouseOverFlag_stateChanged()
801 viewport.followHighlight = followMouseOverFlag.getState();
802 // TODO: could kick the scrollTo mechanism to reset view for current
806 private void centreColumnLabelFlag_stateChanged()
808 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
809 this.alignPanel.annotationPanel.repaint();
813 public void actionPerformed(ActionEvent evt)
815 Object source = evt.getSource();
817 if (source == inputText)
819 inputText_actionPerformed();
821 else if (source == loadTree)
823 loadTree_actionPerformed();
825 else if (source == loadApplication)
827 launchFullApplication();
829 else if (source == loadAnnotations)
833 else if (source == outputAnnotations)
835 outputAnnotations(true);
837 else if (source == outputFeatures)
839 outputFeatures(true, "Jalview");
841 else if (source == closeMenuItem)
843 closeMenuItem_actionPerformed();
845 else if (source == copy)
847 copy_actionPerformed();
849 else if (source == undoMenuItem)
851 undoMenuItem_actionPerformed();
853 else if (source == redoMenuItem)
855 redoMenuItem_actionPerformed();
857 else if (source == inputText)
859 inputText_actionPerformed();
861 else if (source == closeMenuItem)
863 closeMenuItem_actionPerformed();
865 else if (source == undoMenuItem)
867 undoMenuItem_actionPerformed();
869 else if (source == redoMenuItem)
871 redoMenuItem_actionPerformed();
873 else if (source == copy)
875 copy_actionPerformed();
877 else if (source == pasteNew)
879 pasteNew_actionPerformed();
881 else if (source == pasteThis)
883 pasteThis_actionPerformed();
885 else if (source == cut)
887 cut_actionPerformed();
889 else if (source == delete)
891 delete_actionPerformed();
893 else if (source == grpsFromSelection)
895 makeGrpsFromSelection_actionPerformed();
897 else if (source == deleteGroups)
899 deleteGroups_actionPerformed();
901 else if (source == selectAllSequenceMenuItem)
903 selectAllSequenceMenuItem_actionPerformed();
905 else if (source == deselectAllSequenceMenuItem)
907 deselectAllSequenceMenuItem_actionPerformed();
909 else if (source == invertSequenceMenuItem)
911 invertSequenceMenuItem_actionPerformed();
913 else if (source == invertColSel)
915 viewport.invertColumnSelection();
916 alignPanel.paintAlignment(true);
918 else if (source == remove2LeftMenuItem)
922 else if (source == remove2RightMenuItem)
924 trimAlignment(false);
926 else if (source == removeGappedColumnMenuItem)
928 removeGappedColumnMenuItem_actionPerformed();
930 else if (source == removeAllGapsMenuItem)
932 removeAllGapsMenuItem_actionPerformed();
934 else if (source == findMenuItem)
936 findMenuItem_actionPerformed();
938 else if (source == font)
940 new FontChooser(alignPanel);
942 else if (source == newView)
946 else if (source == showColumns)
948 viewport.showAllHiddenColumns();
949 alignPanel.paintAlignment(true);
951 else if (source == showSeqs)
953 viewport.showAllHiddenSeqs();
954 alignPanel.paintAlignment(true);
956 else if (source == hideColumns)
958 viewport.hideSelectedColumns();
959 alignPanel.paintAlignment(true);
961 else if (source == hideSequences
962 && viewport.getSelectionGroup() != null)
964 viewport.hideAllSelectedSeqs();
965 alignPanel.paintAlignment(true);
967 else if (source == hideAllButSelection)
969 toggleHiddenRegions(false, false);
970 alignPanel.paintAlignment(true);
972 else if (source == hideAllSelection)
974 SequenceGroup sg = viewport.getSelectionGroup();
975 viewport.expandColSelection(sg, false);
976 viewport.hideAllSelectedSeqs();
977 viewport.hideSelectedColumns();
978 alignPanel.paintAlignment(true);
980 else if (source == showAllHidden)
982 viewport.showAllHiddenColumns();
983 viewport.showAllHiddenSeqs();
984 alignPanel.paintAlignment(true);
986 else if (source == showGroupConsensus)
988 showGroupConsensus_actionPerformed();
990 else if (source == showGroupConservation)
992 showGroupConservation_actionPerformed();
994 else if (source == showSequenceLogo)
996 showSequenceLogo_actionPerformed();
998 else if (source == normSequenceLogo)
1000 normSequenceLogo_actionPerformed();
1002 else if (source == showConsensusHistogram)
1004 showConsensusHistogram_actionPerformed();
1006 else if (source == applyAutoAnnotationSettings)
1008 applyAutoAnnotationSettings_actionPerformed();
1010 else if (source == featureSettings)
1012 new FeatureSettings(alignPanel);
1014 else if (source == alProperties)
1016 StringBuffer contents = new jalview.io.AlignmentProperties(
1017 viewport.getAlignment()).formatAsString();
1018 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1019 cap.setText(contents.toString());
1020 Frame frame = new Frame();
1022 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1023 "label.alignment_properties", new String[]
1024 { getTitle() }), 400, 250);
1026 else if (source == overviewMenuItem)
1028 overviewMenuItem_actionPerformed();
1030 else if (source == noColourmenuItem)
1034 else if (source == clustalColour)
1036 abovePIDThreshold.setState(false);
1037 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1039 else if (source == zappoColour)
1041 changeColour(new ZappoColourScheme());
1043 else if (source == taylorColour)
1045 changeColour(new TaylorColourScheme());
1047 else if (source == hydrophobicityColour)
1049 changeColour(new HydrophobicColourScheme());
1051 else if (source == helixColour)
1053 changeColour(new HelixColourScheme());
1055 else if (source == strandColour)
1057 changeColour(new StrandColourScheme());
1059 else if (source == turnColour)
1061 changeColour(new TurnColourScheme());
1063 else if (source == buriedColour)
1065 changeColour(new BuriedColourScheme());
1067 else if (source == nucleotideColour)
1069 changeColour(new NucleotideColourScheme());
1071 else if (source == purinePyrimidineColour)
1073 changeColour(new PurinePyrimidineColourScheme());
1075 else if (source == RNAInteractionColour)
1077 changeColour(new RNAInteractionColourScheme());
1079 else if (source == RNAHelixColour)
1081 new RNAHelicesColourChooser(viewport, alignPanel);
1083 else if (source == modifyPID)
1085 modifyPID_actionPerformed();
1087 else if (source == modifyConservation)
1089 modifyConservation_actionPerformed();
1091 else if (source == userDefinedColour)
1093 new UserDefinedColours(alignPanel, null);
1095 else if (source == PIDColour)
1097 changeColour(new PIDColourScheme());
1099 else if (source == BLOSUM62Colour)
1101 changeColour(new Blosum62ColourScheme());
1103 else if (source == tcoffeeColour)
1105 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1107 else if (source == annotationColour)
1109 new AnnotationColourChooser(viewport, alignPanel);
1111 else if (source == sortPairwiseMenuItem)
1113 sortPairwiseMenuItem_actionPerformed();
1115 else if (source == sortIDMenuItem)
1117 sortIDMenuItem_actionPerformed();
1119 else if (source == sortLengthMenuItem)
1121 sortLengthMenuItem_actionPerformed();
1123 else if (source == sortGroupMenuItem)
1125 sortGroupMenuItem_actionPerformed();
1127 else if (source == removeRedundancyMenuItem)
1129 removeRedundancyMenuItem_actionPerformed();
1131 else if (source == pairwiseAlignmentMenuItem)
1133 pairwiseAlignmentMenuItem_actionPerformed();
1135 else if (source == PCAMenuItem)
1137 PCAMenuItem_actionPerformed();
1139 else if (source == averageDistanceTreeMenuItem)
1141 averageDistanceTreeMenuItem_actionPerformed();
1143 else if (source == neighbourTreeMenuItem)
1145 neighbourTreeMenuItem_actionPerformed();
1147 else if (source == njTreeBlosumMenuItem)
1149 njTreeBlosumMenuItem_actionPerformed();
1151 else if (source == avDistanceTreeBlosumMenuItem)
1153 avTreeBlosumMenuItem_actionPerformed();
1155 else if (source == documentation)
1157 documentation_actionPerformed();
1159 else if (source == about)
1161 about_actionPerformed();
1166 public void inputText_actionPerformed()
1168 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1169 Frame frame = new Frame();
1171 jalview.bin.JalviewLite.addFrame(frame,
1172 MessageManager.getString("label.input_cut_paste"), 500, 500);
1175 protected void outputText_actionPerformed(ActionEvent e)
1177 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1178 Frame frame = new Frame();
1180 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1181 "label.alignment_output_command", new String[]
1182 { e.getActionCommand() }), 600, 500);
1183 cap.setText(new AppletFormatAdapter().formatSequences(
1184 e.getActionCommand(), viewport.getAlignment(),
1185 viewport.showJVSuffix));
1188 public void loadAnnotations()
1190 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1191 cap.setText(MessageManager
1192 .getString("label.paste_features_annotations_Tcoffee_here"));
1193 cap.setAnnotationImport();
1194 Frame frame = new Frame();
1196 jalview.bin.JalviewLite.addFrame(frame,
1197 MessageManager.getString("action.paste_annotations"), 400, 300);
1201 public String outputAnnotations(boolean displayTextbox)
1203 String annotation = new AnnotationFile().printAnnotations(
1204 viewport.showAnnotation ? viewport.getAlignment()
1205 .getAlignmentAnnotation() : null, viewport
1206 .getAlignment().getGroups(), ((Alignment) viewport
1207 .getAlignment()).alignmentProperties);
1211 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212 Frame frame = new Frame();
1214 jalview.bin.JalviewLite.addFrame(frame,
1215 MessageManager.getString("label.annotations"), 600, 500);
1216 cap.setText(annotation);
1222 private Map<String,Object> getDisplayedFeatureCols()
1224 if (alignPanel.getFeatureRenderer() != null
1225 && viewport.getFeaturesDisplayed()!= null)
1227 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1233 public String outputFeatures(boolean displayTextbox, String format)
1236 if (format.equalsIgnoreCase("Jalview"))
1238 features = new FeaturesFile().printJalviewFormat(viewport
1239 .getAlignment().getSequencesArray(),
1240 getDisplayedFeatureCols());
1244 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1245 .getSequencesArray(), getDisplayedFeatureCols());
1250 boolean frimport = false;
1251 if (features == null || features.equals("No Features Visible"))
1253 features = "# No features visible - paste some and import them here.";
1257 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1260 cap.setAnnotationImport();
1262 Frame frame = new Frame();
1264 jalview.bin.JalviewLite.addFrame(frame,
1265 MessageManager.getString("label.features"), 600, 500);
1266 cap.setText(features);
1270 if (features == null)
1279 void launchFullApplication()
1281 StringBuffer url = new StringBuffer(jalviewServletURL);
1284 + appendProtocol(viewport.applet.getParameter("file")));
1286 if (viewport.applet.getParameter("features") != null)
1288 url.append("&features=");
1289 url.append(appendProtocol(viewport.applet.getParameter("features")));
1292 if (viewport.applet.getParameter("annotations") != null)
1294 url.append("&annotations=");
1295 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1298 if (viewport.applet.getParameter("jnetfile") != null)
1300 url.append("&annotations=");
1301 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1304 if (viewport.applet.getParameter("defaultColour") != null)
1306 url.append("&colour="
1307 + removeWhiteSpace(viewport.applet
1308 .getParameter("defaultColour")));
1311 if (viewport.applet.getParameter("userDefinedColour") != null)
1313 url.append("&colour="
1314 + removeWhiteSpace(viewport.applet
1315 .getParameter("userDefinedColour")));
1317 if (viewport.applet.getParameter("tree") != null)
1320 + appendProtocol(viewport.applet.getParameter("tree")));
1322 if (viewport.applet.getParameter("treeFile") != null)
1325 + appendProtocol(viewport.applet.getParameter("treeFile")));
1328 showURL(url.toString(), "FULL_APP");
1331 String removeWhiteSpace(String colour)
1333 StringBuffer sb = new StringBuffer();
1334 for (int i = 0; i < colour.length(); i++)
1336 if (Character.isWhitespace(colour.charAt(i)))
1342 sb.append(colour.charAt(i));
1346 return sb.toString();
1349 String appendProtocol(String url)
1354 url = URLEncoder.encode(url);
1357 * When we finally deprecate 1.1 compatibility, we can start to use
1358 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1359 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1360 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1361 * ex.printStackTrace(); }
1363 catch (java.net.MalformedURLException ex)
1365 url = viewport.applet.getCodeBase() + url;
1370 public void closeMenuItem_actionPerformed()
1372 PaintRefresher.RemoveComponent(alignPanel);
1373 if (alignPanel.seqPanel != null
1374 && alignPanel.seqPanel.seqCanvas != null)
1376 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1378 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1380 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1383 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1398 void updateEditMenuBar()
1401 if (viewport.historyList.size() > 0)
1403 undoMenuItem.setEnabled(true);
1404 CommandI command = (CommandI) viewport.historyList.peek();
1405 undoMenuItem.setLabel(MessageManager.formatMessage(
1406 "label.undo_command", new String[]
1407 { command.getDescription() }));
1411 undoMenuItem.setEnabled(false);
1412 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1415 if (viewport.redoList.size() > 0)
1417 redoMenuItem.setEnabled(true);
1419 CommandI command = (CommandI) viewport.redoList.peek();
1420 redoMenuItem.setLabel(MessageManager.formatMessage(
1421 "label.redo_command", new String[]
1422 { command.getDescription() }));
1426 redoMenuItem.setEnabled(false);
1427 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1435 public void addHistoryItem(CommandI command)
1437 if (command.getSize() > 0)
1439 viewport.historyList.push(command);
1440 viewport.redoList.removeAllElements();
1441 updateEditMenuBar();
1442 viewport.updateHiddenColumns();
1447 * TODO: JAL-1104 DOCUMENT ME!
1452 protected void undoMenuItem_actionPerformed()
1454 if (viewport.historyList.size() < 1)
1459 CommandI command = (CommandI) viewport.historyList.pop();
1460 viewport.redoList.push(command);
1461 command.undoCommand(null);
1463 AlignViewport originalSource = getOriginatingSource(command);
1465 if (originalSource != viewport)
1468 .println("Warning: Viewport object mismatch whilst undoing");
1470 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1471 // viewport.getColumnSelection().getHiddenColumns()
1473 updateEditMenuBar();
1474 originalSource.firePropertyChange("alignment", null, originalSource
1475 .getAlignment().getSequences());
1479 * TODO: JAL-1104 DOCUMENT ME!
1484 protected void redoMenuItem_actionPerformed()
1486 if (viewport.redoList.size() < 1)
1491 CommandI command = (CommandI) viewport.redoList.pop();
1492 viewport.historyList.push(command);
1493 command.doCommand(null);
1495 AlignViewport originalSource = getOriginatingSource(command);
1497 if (originalSource != viewport)
1500 .println("Warning: Viewport object mismatch whilst re-doing");
1502 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1503 // viewport.getColumnSelection().getHiddenColumns()
1506 updateEditMenuBar();
1507 originalSource.firePropertyChange("alignment", null, originalSource
1508 .getAlignment().getSequences());
1511 AlignViewport getOriginatingSource(CommandI command)
1513 AlignViewport originalSource = null;
1514 // For sequence removal and addition, we need to fire
1515 // the property change event FROM the viewport where the
1516 // original alignment was altered
1517 AlignmentI al = null;
1518 if (command instanceof EditCommand)
1520 EditCommand editCommand = (EditCommand) command;
1521 al = editCommand.getAlignment();
1522 Vector comps = (Vector) PaintRefresher.components.get(viewport
1523 .getSequenceSetId());
1524 for (int i = 0; i < comps.size(); i++)
1526 if (comps.elementAt(i) instanceof AlignmentPanel)
1528 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1530 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1537 if (originalSource == null)
1539 // The original view is closed, we must validate
1540 // the current view against the closed view first
1543 PaintRefresher.validateSequences(al, viewport.getAlignment());
1546 originalSource = viewport;
1549 return originalSource;
1552 public void moveSelectedSequences(boolean up)
1554 SequenceGroup sg = viewport.getSelectionGroup();
1559 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1560 up ? null : viewport.getHiddenRepSequences(), up);
1561 alignPanel.paintAlignment(true);
1564 synchronized void slideSequences(boolean right, int size)
1566 List<SequenceI> sg = new Vector<SequenceI>();
1567 if (viewport.cursorMode)
1569 sg.add(viewport.getAlignment().getSequenceAt(
1570 alignPanel.seqPanel.seqCanvas.cursorY));
1572 else if (viewport.getSelectionGroup() != null
1573 && viewport.getSelectionGroup().getSize() != viewport
1574 .getAlignment().getHeight())
1576 sg = viewport.getSelectionGroup().getSequences(
1577 viewport.getHiddenRepSequences());
1585 Vector<SequenceI> invertGroup = new Vector();
1587 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1589 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1591 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1595 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1597 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1599 for (int i = 0; i < invertGroup.size(); i++)
1601 seqs2[i] = invertGroup.elementAt(i);
1604 SlideSequencesCommand ssc;
1607 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1608 size, viewport.getGapCharacter());
1612 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1613 size, viewport.getGapCharacter());
1616 int groupAdjustment = 0;
1617 if (ssc.getGapsInsertedBegin() && right)
1619 if (viewport.cursorMode)
1621 alignPanel.seqPanel.moveCursor(size, 0);
1625 groupAdjustment = size;
1628 else if (!ssc.getGapsInsertedBegin() && !right)
1630 if (viewport.cursorMode)
1632 alignPanel.seqPanel.moveCursor(-size, 0);
1636 groupAdjustment = -size;
1640 if (groupAdjustment != 0)
1642 viewport.getSelectionGroup().setStartRes(
1643 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1644 viewport.getSelectionGroup().setEndRes(
1645 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1648 boolean appendHistoryItem = false;
1649 if (viewport.historyList != null && viewport.historyList.size() > 0
1650 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1652 appendHistoryItem = ssc
1653 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1657 if (!appendHistoryItem)
1659 addHistoryItem(ssc);
1665 static StringBuffer copiedSequences;
1667 static Vector copiedHiddenColumns;
1669 protected void copy_actionPerformed()
1671 if (viewport.getSelectionGroup() == null)
1676 SequenceGroup sg = viewport.getSelectionGroup();
1677 copiedSequences = new StringBuffer();
1678 Hashtable orderedSeqs = new Hashtable();
1679 for (int i = 0; i < sg.getSize(); i++)
1681 SequenceI seq = sg.getSequenceAt(i);
1682 int index = viewport.getAlignment().findIndex(seq);
1683 orderedSeqs.put(index + "", seq);
1686 int index = 0, startRes, endRes;
1689 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1691 copiedHiddenColumns = new Vector();
1692 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1693 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1696 int[] region = (int[]) viewport.getColumnSelection()
1697 .getHiddenColumns().elementAt(i);
1699 copiedHiddenColumns.addElement(new int[]
1700 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1705 copiedHiddenColumns = null;
1708 for (int i = 0; i < sg.getSize(); i++)
1710 SequenceI seq = null;
1714 if (orderedSeqs.containsKey(index + ""))
1716 seq = (SequenceI) orderedSeqs.get(index + "");
1728 // Returns residue following index if gap
1729 startRes = seq.findPosition(sg.getStartRes());
1732 // Need to find the residue preceeding index if gap
1735 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1737 ch = seq.getCharAt(j);
1738 if (!jalview.util.Comparison.isGap((ch)))
1746 endRes += seq.getStart() - 1;
1749 copiedSequences.append(seq.getName()
1755 + seq.getSequenceAsString(sg.getStartRes(),
1756 sg.getEndRes() + 1) + "\n");
1761 protected void pasteNew_actionPerformed()
1766 protected void pasteThis_actionPerformed()
1771 void paste(boolean newAlignment)
1776 if (copiedSequences == null)
1781 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1782 Vector seqs = new Vector();
1783 while (st.hasMoreElements())
1785 String name = st.nextToken();
1786 int start = Integer.parseInt(st.nextToken());
1787 int end = Integer.parseInt(st.nextToken());
1788 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1790 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1791 for (int i = 0; i < seqs.size(); i++)
1793 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1798 String newtitle = MessageManager.getString("label.copied_sequences");
1799 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1801 newtitle = getTitle();
1805 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1807 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1808 viewport.applet, newtitle, false);
1809 if (copiedHiddenColumns != null)
1811 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1813 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1814 af.viewport.hideColumns(region[0], region[1]);
1818 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1823 addSequences(newSeqs);
1826 } catch (Exception ex)
1828 } // could be anything being pasted in here
1832 void addSequences(SequenceI[] seqs)
1834 for (int i = 0; i < seqs.length; i++)
1836 viewport.getAlignment().addSequence(seqs[i]);
1840 addHistoryItem(new EditCommand(
1841 MessageManager.getString("label.add_sequences"), Action.PASTE,
1842 seqs, 0, viewport.getAlignment().getWidth(),
1843 viewport.getAlignment()));
1845 viewport.setEndSeq(viewport.getAlignment().getHeight());
1846 viewport.getAlignment().getWidth();
1847 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1852 protected void cut_actionPerformed()
1854 copy_actionPerformed();
1855 delete_actionPerformed();
1858 protected void delete_actionPerformed()
1861 SequenceGroup sg = viewport.getSelectionGroup();
1867 Vector seqs = new Vector();
1869 for (int i = 0; i < sg.getSize(); i++)
1871 seq = sg.getSequenceAt(i);
1872 seqs.addElement(seq);
1875 // If the cut affects all sequences, remove highlighted columns
1876 if (sg.getSize() == viewport.getAlignment().getHeight())
1878 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1879 sg.getEndRes() + 1);
1882 SequenceI[] cut = new SequenceI[seqs.size()];
1883 for (int i = 0; i < seqs.size(); i++)
1885 cut[i] = (SequenceI) seqs.elementAt(i);
1889 * //ADD HISTORY ITEM
1891 addHistoryItem(new EditCommand(
1892 MessageManager.getString("label.cut_sequences"), Action.CUT,
1893 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1894 viewport.getAlignment()));
1896 viewport.setSelectionGroup(null);
1897 viewport.getAlignment().deleteGroup(sg);
1899 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1902 if (viewport.getAlignment().getHeight() < 1)
1904 this.setVisible(false);
1906 viewport.sendSelection();
1910 * group consensus toggled
1913 protected void showGroupConsensus_actionPerformed()
1915 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1916 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1921 * group conservation toggled.
1923 protected void showGroupConservation_actionPerformed()
1925 viewport.setShowGroupConservation(showGroupConservation.getState());
1926 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1933 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1934 * .event.ActionEvent)
1936 protected void showConsensusHistogram_actionPerformed()
1938 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1939 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1946 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1947 * .event.ActionEvent)
1949 protected void showSequenceLogo_actionPerformed()
1951 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1952 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1955 protected void normSequenceLogo_actionPerformed()
1957 showSequenceLogo.setState(true);
1958 viewport.setShowSequenceLogo(true);
1959 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1960 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1963 protected void applyAutoAnnotationSettings_actionPerformed()
1965 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1968 protected void makeGrpsFromSelection_actionPerformed()
1970 if (avc.makeGroupsFromSelection())
1972 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1973 alignPanel.updateAnnotation();
1974 alignPanel.paintAlignment(true);
1978 protected void createGroup_actionPerformed()
1983 protected void unGroup_actionPerformed()
1987 alignPanel.alignmentChanged();
1991 protected void deleteGroups_actionPerformed()
1993 if (avc.deleteGroups())
1995 alignPanel.alignmentChanged();
1999 public void selectAllSequenceMenuItem_actionPerformed()
2001 SequenceGroup sg = new SequenceGroup();
2002 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2004 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2006 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2007 viewport.setSelectionGroup(sg);
2008 alignPanel.paintAlignment(true);
2009 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2010 viewport.sendSelection();
2013 public void deselectAllSequenceMenuItem_actionPerformed()
2015 if (viewport.cursorMode)
2017 alignPanel.seqPanel.keyboardNo1 = null;
2018 alignPanel.seqPanel.keyboardNo2 = null;
2020 viewport.setSelectionGroup(null);
2021 viewport.getColumnSelection().clear();
2022 viewport.setSelectionGroup(null);
2023 alignPanel.idPanel.idCanvas.searchResults = null;
2024 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2025 alignPanel.paintAlignment(true);
2026 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2027 viewport.sendSelection();
2030 public void invertSequenceMenuItem_actionPerformed()
2032 SequenceGroup sg = viewport.getSelectionGroup();
2033 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2035 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2038 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2039 viewport.sendSelection();
2042 public void invertColSel_actionPerformed()
2044 viewport.invertColumnSelection();
2045 alignPanel.paintAlignment(true);
2046 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2047 viewport.sendSelection();
2050 void trimAlignment(boolean trimLeft)
2052 ColumnSelection colSel = viewport.getColumnSelection();
2055 if (colSel.size() > 0)
2059 column = colSel.getMin();
2063 column = colSel.getMax();
2067 if (viewport.getSelectionGroup() != null)
2069 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2070 viewport.getHiddenRepSequences());
2074 seqs = viewport.getAlignment().getSequencesArray();
2077 TrimRegionCommand trimRegion;
2080 trimRegion = new TrimRegionCommand("Remove Left",
2081 TrimRegionCommand.TRIM_LEFT, seqs, column,
2082 viewport.getAlignment(), viewport.getColumnSelection(),
2083 viewport.getSelectionGroup());
2084 viewport.setStartRes(0);
2088 trimRegion = new TrimRegionCommand("Remove Right",
2089 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2090 viewport.getAlignment(), viewport.getColumnSelection(),
2091 viewport.getSelectionGroup());
2094 statusBar.setText(MessageManager.formatMessage(
2095 "label.removed_columns", new String[]
2096 { Integer.valueOf(trimRegion.getSize()).toString() }));
2097 addHistoryItem(trimRegion);
2099 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2101 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2102 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2104 viewport.getAlignment().deleteGroup(sg);
2108 viewport.firePropertyChange("alignment", null, viewport
2109 .getAlignment().getSequences());
2113 public void removeGappedColumnMenuItem_actionPerformed()
2115 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2118 if (viewport.getSelectionGroup() != null)
2120 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2121 viewport.getHiddenRepSequences());
2122 start = viewport.getSelectionGroup().getStartRes();
2123 end = viewport.getSelectionGroup().getEndRes();
2127 seqs = viewport.getAlignment().getSequencesArray();
2130 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2131 "Remove Gapped Columns", seqs, start, end,
2132 viewport.getAlignment());
2134 addHistoryItem(removeGapCols);
2136 statusBar.setText(MessageManager.formatMessage(
2137 "label.removed_empty_columns", new String[]
2138 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2140 // This is to maintain viewport position on first residue
2141 // of first sequence
2142 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2143 int startRes = seq.findPosition(viewport.startRes);
2144 // ShiftList shifts;
2145 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2146 // edit.alColumnChanges=shifts.getInverse();
2147 // if (viewport.hasHiddenColumns)
2148 // viewport.getColumnSelection().compensateForEdits(shifts);
2149 viewport.setStartRes(seq.findIndex(startRes) - 1);
2150 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2155 public void removeAllGapsMenuItem_actionPerformed()
2157 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2160 if (viewport.getSelectionGroup() != null)
2162 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2163 viewport.getHiddenRepSequences());
2164 start = viewport.getSelectionGroup().getStartRes();
2165 end = viewport.getSelectionGroup().getEndRes();
2169 seqs = viewport.getAlignment().getSequencesArray();
2172 // This is to maintain viewport position on first residue
2173 // of first sequence
2174 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2175 int startRes = seq.findPosition(viewport.startRes);
2177 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2178 viewport.getAlignment()));
2180 viewport.setStartRes(seq.findIndex(startRes) - 1);
2182 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2187 public void findMenuItem_actionPerformed()
2189 new Finder(alignPanel);
2193 * create a new view derived from the current view
2196 * @return frame for the new view
2198 public AlignFrame newView(String viewtitle)
2201 if (viewport.hasHiddenRows())
2203 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2204 .getFullAlignment().getSequencesArray());
2208 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2211 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2213 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2215 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2217 newal.addAnnotation(viewport.getAlignment()
2218 .getAlignmentAnnotation()[i]);
2223 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2225 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2226 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2227 PaintRefresher.Register(newaf.alignPanel,
2228 newaf.alignPanel.av.getSequenceSetId());
2230 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2231 newaf.alignPanel.av.getSequenceSetId());
2232 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2233 newaf.alignPanel.av.getSequenceSetId());
2235 Vector comps = (Vector) PaintRefresher.components.get(viewport
2236 .getSequenceSetId());
2238 for (int i = 0; i < comps.size(); i++)
2240 if (comps.elementAt(i) instanceof AlignmentPanel)
2246 String title = new String(this.getTitle());
2247 if (viewtitle != null)
2249 title = viewtitle + " ( " + title + ")";
2253 if (title.indexOf("(View") > -1)
2255 title = title.substring(0, title.indexOf("(View"));
2257 title += "(View " + viewSize + ")";
2260 newaf.setTitle(title.toString());
2262 newaf.viewport.historyList = viewport.historyList;
2263 newaf.viewport.redoList = viewport.redoList;
2269 * @return list of feature groups on the view
2271 public String[] getFeatureGroups()
2273 FeatureRenderer fr = null;
2274 if (alignPanel != null
2275 && (fr = alignPanel.getFeatureRenderer()) != null)
2277 List gps = fr.getFeatureGroups();
2279 String[] _gps = new String[gps.size()];
2282 _gps[p++] = gp.toString();
2290 * get sequence feature groups that are hidden or shown
2296 public String[] getFeatureGroupsOfState(boolean visible)
2298 FeatureRenderer fr = null;
2299 if (alignPanel != null
2300 && (fr = alignPanel.getFeatureRenderer()) != null)
2302 List gps = fr.getGroups(visible);
2304 String[] _gps = new String[gps.size()];
2307 _gps[p++] = gp.toString();
2315 * Change the display state for the given feature groups
2318 * list of group strings
2320 * visible or invisible
2322 public void setFeatureGroupState(String[] groups, boolean state)
2324 FeatureRenderer fr = null;
2325 this.sequenceFeatures.setState(true);
2326 viewport.setShowSequenceFeatures(true);
2327 if (alignPanel != null
2328 && (fr = alignPanel.getFeatureRenderer()) != null)
2331 fr.setGroupVisibility((List)Arrays.asList(groups), state);
2332 alignPanel.seqPanel.seqCanvas.repaint();
2333 if (alignPanel.overviewPanel != null)
2335 alignPanel.overviewPanel.updateOverviewImage();
2340 public void seqLimits_itemStateChanged()
2342 viewport.setShowJVSuffix(seqLimits.getState());
2343 alignPanel.fontChanged();
2344 alignPanel.paintAlignment(true);
2347 protected void colourTextMenuItem_actionPerformed()
2349 viewport.setColourText(colourTextMenuItem.getState());
2350 alignPanel.paintAlignment(true);
2353 protected void displayNonconservedMenuItem_actionPerformed()
2355 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2356 alignPanel.paintAlignment(true);
2359 protected void wrapMenuItem_actionPerformed()
2361 viewport.setWrapAlignment(wrapMenuItem.getState());
2362 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2363 scaleAbove.setEnabled(wrapMenuItem.getState());
2364 scaleLeft.setEnabled(wrapMenuItem.getState());
2365 scaleRight.setEnabled(wrapMenuItem.getState());
2366 alignPanel.paintAlignment(true);
2369 public void overviewMenuItem_actionPerformed()
2371 if (alignPanel.overviewPanel != null)
2376 Frame frame = new Frame();
2377 OverviewPanel overview = new OverviewPanel(alignPanel);
2378 frame.add(overview);
2379 // +50 must allow for applet frame window
2380 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2381 "label.overview_params", new String[]
2382 { this.getTitle() }), overview.getPreferredSize().width,
2383 overview.getPreferredSize().height + 50);
2386 final AlignmentPanel ap = alignPanel;
2387 frame.addWindowListener(new WindowAdapter()
2390 public void windowClosing(WindowEvent e)
2394 ap.setOverviewPanel(null);
2399 alignPanel.setOverviewPanel(overview);
2403 void changeColour(ColourSchemeI cs)
2409 if (viewport.getAbovePIDThreshold())
2411 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2415 if (viewport.getConservationSelected())
2417 cs.setConservationApplied(true);
2418 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2423 cs.setConservationApplied(false);
2426 viewport.setGlobalColourScheme(cs);
2428 if (alignPanel.getOverviewPanel() != null)
2430 alignPanel.getOverviewPanel().updateOverviewImage();
2433 jalview.structure.StructureSelectionManager
2434 .getStructureSelectionManager(viewport.applet)
2435 .sequenceColoursChanged(alignPanel);
2437 alignPanel.paintAlignment(true);
2440 protected void modifyPID_actionPerformed()
2442 if (viewport.getAbovePIDThreshold()
2443 && viewport.getGlobalColourScheme() != null)
2445 SliderPanel.setPIDSliderSource(alignPanel,
2446 viewport.getGlobalColourScheme(), "Background");
2447 SliderPanel.showPIDSlider();
2451 protected void modifyConservation_actionPerformed()
2453 if (viewport.getConservationSelected()
2454 && viewport.getGlobalColourScheme() != null)
2456 SliderPanel.setConservationSlider(alignPanel,
2457 viewport.getGlobalColourScheme(), "Background");
2458 SliderPanel.showConservationSlider();
2462 protected void conservationMenuItem_actionPerformed()
2464 viewport.setConservationSelected(conservationMenuItem.getState());
2466 viewport.setAbovePIDThreshold(false);
2467 abovePIDThreshold.setState(false);
2469 changeColour(viewport.getGlobalColourScheme());
2471 modifyConservation_actionPerformed();
2474 public void abovePIDThreshold_actionPerformed()
2476 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2478 conservationMenuItem.setState(false);
2479 viewport.setConservationSelected(false);
2481 changeColour(viewport.getGlobalColourScheme());
2483 modifyPID_actionPerformed();
2486 public void sortPairwiseMenuItem_actionPerformed()
2488 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2489 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2490 .getAlignment().getSequenceAt(0), null);
2492 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2493 viewport.getAlignment()));
2494 alignPanel.paintAlignment(true);
2497 public void sortIDMenuItem_actionPerformed()
2499 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2500 AlignmentSorter.sortByID(viewport.getAlignment());
2501 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2502 viewport.getAlignment()));
2503 alignPanel.paintAlignment(true);
2506 public void sortLengthMenuItem_actionPerformed()
2508 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2509 AlignmentSorter.sortByLength(viewport.getAlignment());
2510 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2511 viewport.getAlignment()));
2512 alignPanel.paintAlignment(true);
2515 public void sortGroupMenuItem_actionPerformed()
2517 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2518 AlignmentSorter.sortByGroup(viewport.getAlignment());
2519 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2520 viewport.getAlignment()));
2521 alignPanel.paintAlignment(true);
2525 public void removeRedundancyMenuItem_actionPerformed()
2527 new RedundancyPanel(alignPanel);
2530 public void pairwiseAlignmentMenuItem_actionPerformed()
2532 if (viewport.getSelectionGroup() != null
2533 && viewport.getSelectionGroup().getSize() > 1)
2535 Frame frame = new Frame();
2536 frame.add(new PairwiseAlignPanel(alignPanel));
2537 jalview.bin.JalviewLite.addFrame(frame,
2538 MessageManager.getString("action.pairwise_alignment"), 600,
2543 public void PCAMenuItem_actionPerformed()
2545 // are the sequences aligned?
2546 if (!viewport.getAlignment().isAligned(false))
2549 int Width = viewport.getAlignment().getWidth();
2551 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2553 current = viewport.getAlignment().getSequenceAt(i);
2555 if (current.getLength() < Width)
2557 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2560 alignPanel.paintAlignment(true);
2563 if ((viewport.getSelectionGroup() != null
2564 && viewport.getSelectionGroup().getSize() < 4 && viewport
2565 .getSelectionGroup().getSize() > 0)
2566 || viewport.getAlignment().getHeight() < 4)
2573 new PCAPanel(viewport);
2574 } catch (java.lang.OutOfMemoryError ex)
2580 public void averageDistanceTreeMenuItem_actionPerformed()
2582 NewTreePanel("AV", "PID", "Average distance tree using PID");
2585 public void neighbourTreeMenuItem_actionPerformed()
2587 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2590 protected void njTreeBlosumMenuItem_actionPerformed()
2592 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2595 protected void avTreeBlosumMenuItem_actionPerformed()
2597 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2600 void NewTreePanel(String type, String pwType, String title)
2602 // are the sequences aligned?
2603 if (!viewport.getAlignment().isAligned(false))
2606 int Width = viewport.getAlignment().getWidth();
2608 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2610 current = viewport.getAlignment().getSequenceAt(i);
2612 if (current.getLength() < Width)
2614 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2617 alignPanel.paintAlignment(true);
2621 if ((viewport.getSelectionGroup() != null && viewport
2622 .getSelectionGroup().getSize() > 1)
2623 || (viewport.getAlignment().getHeight() > 1))
2625 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2627 addTreeMenuItem(tp, title);
2629 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2633 void loadTree_actionPerformed()
2635 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2636 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2637 cap.setTreeImport();
2638 Frame frame = new Frame();
2640 jalview.bin.JalviewLite.addFrame(frame,
2641 MessageManager.getString("label.paste_newick_file"), 400, 300);
2644 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2646 TreePanel tp = new TreePanel(alignPanel, treeFile,
2647 MessageManager.getString("label.load_tree_from_file"), tree);
2648 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2649 addTreeMenuItem(tp, treeFile);
2653 * sort the alignment using the given treePanel
2656 * tree used to sort view
2658 * string used for undo event name
2660 public void sortByTree(TreePanel treePanel, String title)
2662 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2664 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2665 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2666 // HistoryItem.SORT));
2667 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2668 "label.order_by_params", new String[]
2669 { title }), oldOrder, viewport.getAlignment()));
2670 alignPanel.paintAlignment(true);
2674 * Do any automatic reordering of the alignment and add the necessary bits to
2675 * the menu structure for the new tree
2680 protected void addTreeMenuItem(final TreePanel treePanel,
2683 final MenuItem item = new MenuItem(title);
2684 sortByTreeMenu.add(item);
2685 item.addActionListener(new java.awt.event.ActionListener()
2688 public void actionPerformed(ActionEvent evt)
2690 sortByTree(treePanel, title); // treePanel.getTitle());
2694 treePanel.addWindowListener(new WindowAdapter()
2697 public void windowOpened(WindowEvent e)
2699 if (viewport.sortByTree)
2701 sortByTree(treePanel, title);
2703 super.windowOpened(e);
2707 public void windowClosing(WindowEvent e)
2709 sortByTreeMenu.remove(item);
2714 public boolean sortBy(AlignmentOrder alorder, String undoname)
2716 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2717 if (viewport.applet.debug)
2719 System.err.println("Sorting " + alorder.getOrder().size()
2720 + " in alignment '" + getTitle() + "'");
2722 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2723 if (undoname != null)
2725 addHistoryItem(new OrderCommand(undoname, oldOrder,
2726 viewport.getAlignment()));
2728 alignPanel.paintAlignment(true);
2732 protected void documentation_actionPerformed()
2734 alignPanel.av.applet.openJalviewHelpUrl();
2737 protected void about_actionPerformed()
2740 class AboutPanel extends Canvas
2746 public AboutPanel(String version, String builddate)
2748 this.version = version;
2749 this.builddate = builddate;
2753 public void paint(Graphics g)
2755 g.setColor(Color.white);
2756 g.fillRect(0, 0, getSize().width, getSize().height);
2757 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2758 FontMetrics fm = g.getFontMetrics();
2759 int fh = fm.getHeight();
2761 g.setColor(Color.black);
2762 // TODO: update this text for each release or centrally store it for
2763 // lite and application
2764 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2765 g.drawString(MessageManager.formatMessage(
2766 "label.jalviewLite_release", new String[]
2767 { version }), x, y += fh);
2768 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2769 g.drawString(MessageManager.formatMessage(
2770 "label.jaview_build_date", new String[]
2771 { builddate }), x, y += fh);
2772 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2773 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2775 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2776 x + 50, y += fh + 8);
2778 MessageManager.getString("label.jalview_dev_managers"), x,
2780 g.drawString(MessageManager
2781 .getString("label.jalview_distribution_lists"), x, y += fh);
2782 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2785 MessageManager.getString("label.jalview_cite_1_authors"),
2788 MessageManager.getString("label.jalview_cite_1_title"), x,
2790 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2795 Frame frame = new Frame();
2796 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2798 jalview.bin.JalviewLite.addFrame(frame,
2799 MessageManager.getString("label.jalview"), 580, 220);
2803 public void showURL(String url, String target)
2805 if (viewport.applet == null)
2807 System.out.println("Not running as applet - no browser available.");
2811 viewport.applet.showURL(url, target);
2815 // ////////////////////////////////////////////////////////////////////////////////
2816 // JBuilder Graphics here
2818 MenuBar alignFrameMenuBar = new MenuBar();
2820 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2822 MenuItem loadApplication = new MenuItem(
2823 MessageManager.getString("label.view_full_application"));
2825 MenuItem loadTree = new MenuItem(
2826 MessageManager.getString("label.load_associated_tree"));
2828 MenuItem loadAnnotations = new MenuItem(
2829 MessageManager.getString("label.load_features_annotations"));
2831 MenuItem outputFeatures = new MenuItem(
2832 MessageManager.getString("label.export_features").concat("..."));
2834 MenuItem outputAnnotations = new MenuItem(
2835 MessageManager.getString("label.export_annotations").concat("..."));
2837 MenuItem closeMenuItem = new MenuItem(
2838 MessageManager.getString("action.close"));
2840 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2842 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2844 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2846 Menu calculateMenu = new Menu(
2847 MessageManager.getString("action.calculate"));
2849 MenuItem selectAllSequenceMenuItem = new MenuItem(
2850 MessageManager.getString("action.select_all"));
2852 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2853 MessageManager.getString("action.deselect_all"));
2855 MenuItem invertSequenceMenuItem = new MenuItem(
2856 MessageManager.getString("action.invert_selection"));
2858 MenuItem remove2LeftMenuItem = new MenuItem();
2860 MenuItem remove2RightMenuItem = new MenuItem();
2862 MenuItem removeGappedColumnMenuItem = new MenuItem();
2864 MenuItem removeAllGapsMenuItem = new MenuItem();
2866 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2868 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2870 MenuItem sortPairwiseMenuItem = new MenuItem();
2872 MenuItem sortIDMenuItem = new MenuItem();
2874 MenuItem sortLengthMenuItem = new MenuItem();
2876 MenuItem sortGroupMenuItem = new MenuItem();
2878 MenuItem removeRedundancyMenuItem = new MenuItem();
2880 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2882 MenuItem PCAMenuItem = new MenuItem();
2884 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2886 MenuItem neighbourTreeMenuItem = new MenuItem();
2888 BorderLayout borderLayout1 = new BorderLayout();
2890 public Label statusBar = new Label();
2892 Menu outputTextboxMenu = new Menu();
2894 MenuItem clustalColour = new MenuItem();
2896 MenuItem zappoColour = new MenuItem();
2898 MenuItem taylorColour = new MenuItem();
2900 MenuItem hydrophobicityColour = new MenuItem();
2902 MenuItem helixColour = new MenuItem();
2904 MenuItem strandColour = new MenuItem();
2906 MenuItem turnColour = new MenuItem();
2908 MenuItem buriedColour = new MenuItem();
2910 MenuItem purinePyrimidineColour = new MenuItem();
2912 MenuItem RNAInteractionColour = new MenuItem();
2914 MenuItem RNAHelixColour = new MenuItem();
2916 MenuItem userDefinedColour = new MenuItem();
2918 MenuItem PIDColour = new MenuItem();
2920 MenuItem BLOSUM62Colour = new MenuItem();
2922 MenuItem tcoffeeColour = new MenuItem();
2924 MenuItem njTreeBlosumMenuItem = new MenuItem();
2926 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2928 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2930 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2932 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2934 MenuItem alProperties = new MenuItem(
2935 MessageManager.getString("label.alignment_props"));
2937 MenuItem overviewMenuItem = new MenuItem();
2939 MenuItem undoMenuItem = new MenuItem();
2941 MenuItem redoMenuItem = new MenuItem();
2943 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2945 MenuItem noColourmenuItem = new MenuItem();
2947 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2949 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2951 MenuItem findMenuItem = new MenuItem();
2953 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2955 MenuItem nucleotideColour = new MenuItem();
2957 MenuItem deleteGroups = new MenuItem();
2959 MenuItem grpsFromSelection = new MenuItem();
2961 MenuItem createGroup = new MenuItem();
2963 MenuItem unGroup = new MenuItem();
2965 MenuItem delete = new MenuItem();
2967 MenuItem copy = new MenuItem();
2969 MenuItem cut = new MenuItem();
2971 Menu pasteMenu = new Menu();
2973 MenuItem pasteNew = new MenuItem();
2975 MenuItem pasteThis = new MenuItem();
2977 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2979 MenuItem font = new MenuItem();
2981 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2983 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2985 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2987 MenuItem modifyPID = new MenuItem();
2989 MenuItem modifyConservation = new MenuItem();
2991 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2992 "Autocalculate Consensus", true);
2994 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2995 "Sort Alignment With New Tree", true);
2997 Menu sortByTreeMenu = new Menu();
2999 Menu sort = new Menu();
3001 Menu calculate = new Menu();
3003 MenuItem inputText = new MenuItem();
3005 Menu helpMenu = new Menu();
3007 MenuItem documentation = new MenuItem();
3009 MenuItem about = new MenuItem();
3011 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3013 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3015 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3017 Menu autoAnnMenu = new Menu();
3019 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3021 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3023 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3025 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3027 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3029 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3031 private void jbInit() throws Exception
3034 setMenuBar(alignFrameMenuBar);
3038 // dynamically fill save as menu with available formats
3039 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3042 item = new MenuItem(
3043 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3045 item.addActionListener(new java.awt.event.ActionListener()
3048 public void actionPerformed(ActionEvent e)
3050 outputText_actionPerformed(e);
3054 outputTextboxMenu.add(item);
3056 closeMenuItem.addActionListener(this);
3057 loadApplication.addActionListener(this);
3059 loadTree.addActionListener(this);
3060 loadAnnotations.addActionListener(this);
3061 outputFeatures.addActionListener(this);
3062 outputAnnotations.addActionListener(this);
3063 selectAllSequenceMenuItem.addActionListener(this);
3064 deselectAllSequenceMenuItem.addActionListener(this);
3065 invertSequenceMenuItem.addActionListener(this);
3066 remove2LeftMenuItem.setLabel(MessageManager
3067 .getString("action.remove_left"));
3068 remove2LeftMenuItem.addActionListener(this);
3069 remove2RightMenuItem.setLabel(MessageManager
3070 .getString("action.remove_right"));
3071 remove2RightMenuItem.addActionListener(this);
3072 removeGappedColumnMenuItem.setLabel(MessageManager
3073 .getString("action.remove_empty_columns"));
3074 removeGappedColumnMenuItem.addActionListener(this);
3075 removeAllGapsMenuItem.setLabel(MessageManager
3076 .getString("action.remove_all_gaps"));
3077 removeAllGapsMenuItem.addActionListener(this);
3078 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3079 viewBoxesMenuItem.setState(true);
3080 viewBoxesMenuItem.addItemListener(this);
3081 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3082 viewTextMenuItem.setState(true);
3083 viewTextMenuItem.addItemListener(this);
3084 sortPairwiseMenuItem.setLabel(MessageManager
3085 .getString("action.by_pairwise_id"));
3086 sortPairwiseMenuItem.addActionListener(this);
3087 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3088 sortIDMenuItem.addActionListener(this);
3089 sortLengthMenuItem.setLabel(MessageManager
3090 .getString("action.by_length"));
3091 sortLengthMenuItem.addActionListener(this);
3092 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3093 sortGroupMenuItem.addActionListener(this);
3094 removeRedundancyMenuItem.setLabel(MessageManager
3095 .getString("action.remove_redundancy").concat("..."));
3096 removeRedundancyMenuItem.addActionListener(this);
3097 pairwiseAlignmentMenuItem.setLabel(MessageManager
3098 .getString("action.pairwise_alignment"));
3099 pairwiseAlignmentMenuItem.addActionListener(this);
3100 PCAMenuItem.setLabel(MessageManager
3101 .getString("label.principal_component_analysis"));
3102 PCAMenuItem.addActionListener(this);
3103 averageDistanceTreeMenuItem.setLabel(MessageManager
3104 .getString("label.average_distance_identity"));
3105 averageDistanceTreeMenuItem.addActionListener(this);
3106 neighbourTreeMenuItem.setLabel(MessageManager
3107 .getString("label.neighbour_joining_identity"));
3108 neighbourTreeMenuItem.addActionListener(this);
3109 statusBar.setBackground(Color.white);
3110 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3111 statusBar.setText(MessageManager.getString("label.status_bar"));
3112 outputTextboxMenu.setLabel(MessageManager
3113 .getString("label.out_to_textbox"));
3114 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3116 clustalColour.addActionListener(this);
3117 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3118 zappoColour.addActionListener(this);
3119 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3120 taylorColour.addActionListener(this);
3121 hydrophobicityColour.setLabel(MessageManager
3122 .getString("label.hydrophobicity"));
3123 hydrophobicityColour.addActionListener(this);
3125 .setLabel(MessageManager.getString("label.helix_propensity"));
3126 helixColour.addActionListener(this);
3127 strandColour.setLabel(MessageManager
3128 .getString("label.strand_propensity"));
3129 strandColour.addActionListener(this);
3130 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3131 turnColour.addActionListener(this);
3132 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3133 buriedColour.addActionListener(this);
3134 purinePyrimidineColour.setLabel(MessageManager
3135 .getString("label.purine_pyrimidine"));
3136 purinePyrimidineColour.addActionListener(this);
3137 RNAInteractionColour.setLabel(MessageManager
3138 .getString("label.rna_interaction"));
3139 RNAInteractionColour.addActionListener(this);
3140 RNAHelixColour.setLabel(MessageManager
3141 .getString("action.by_rna_helixes"));
3142 RNAHelixColour.addActionListener(this);
3143 userDefinedColour.setLabel(MessageManager
3144 .getString("action.user_defined"));
3145 userDefinedColour.addActionListener(this);
3146 PIDColour.setLabel(MessageManager
3147 .getString("label.percentage_identity"));
3148 PIDColour.addActionListener(this);
3149 BLOSUM62Colour.setLabel(MessageManager
3150 .getString("label.blosum62_score"));
3151 BLOSUM62Colour.addActionListener(this);
3153 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3154 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3156 tcoffeeColour.addActionListener(this);
3157 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3158 .getString("label.average_distance_bloslum62"));
3159 avDistanceTreeBlosumMenuItem.addActionListener(this);
3160 njTreeBlosumMenuItem.setLabel(MessageManager
3161 .getString("label.neighbour_blosum62"));
3162 njTreeBlosumMenuItem.addActionListener(this);
3163 annotationPanelMenuItem.setLabel(MessageManager
3164 .getString("label.show_annotations"));
3165 annotationPanelMenuItem.addItemListener(this);
3166 colourTextMenuItem.setLabel(MessageManager
3167 .getString("label.colour_text"));
3168 colourTextMenuItem.addItemListener(this);
3169 displayNonconservedMenuItem.setLabel(MessageManager
3170 .getString("label.show_non_conversed"));
3171 displayNonconservedMenuItem.addItemListener(this);
3172 alProperties.addActionListener(this);
3173 overviewMenuItem.setLabel(MessageManager
3174 .getString("label.overview_window"));
3175 overviewMenuItem.addActionListener(this);
3176 undoMenuItem.setEnabled(false);
3177 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3178 undoMenuItem.addActionListener(this);
3179 redoMenuItem.setEnabled(false);
3180 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3181 redoMenuItem.addActionListener(this);
3182 conservationMenuItem.setLabel(MessageManager
3183 .getString("action.by_conservation"));
3184 conservationMenuItem.addItemListener(this);
3185 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3186 noColourmenuItem.addActionListener(this);
3187 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3188 wrapMenuItem.addItemListener(this);
3189 renderGapsMenuItem.setLabel(MessageManager
3190 .getString("action.show_gaps"));
3191 renderGapsMenuItem.setState(true);
3192 renderGapsMenuItem.addItemListener(this);
3193 findMenuItem.setLabel(MessageManager.getString("action.find"));
3194 findMenuItem.addActionListener(this);
3195 abovePIDThreshold.setLabel(MessageManager
3196 .getString("label.above_identity_threshold"));
3197 abovePIDThreshold.addItemListener(this);
3198 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3199 nucleotideColour.addActionListener(this);
3200 deleteGroups.setLabel(MessageManager
3201 .getString("action.undefine_groups"));
3202 deleteGroups.addActionListener(this);
3203 grpsFromSelection.setLabel(MessageManager
3204 .getString("action.make_groups_selection"));
3205 grpsFromSelection.addActionListener(this);
3206 createGroup.setLabel(MessageManager.getString("action.create_group"));
3207 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3208 copy.setLabel(MessageManager.getString("action.copy"));
3209 copy.addActionListener(this);
3210 cut.setLabel(MessageManager.getString("action.cut"));
3211 cut.addActionListener(this);
3212 delete.setLabel(MessageManager.getString("action.delete"));
3213 delete.addActionListener(this);
3214 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3215 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3216 pasteNew.addActionListener(this);
3217 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3218 pasteThis.addActionListener(this);
3219 applyToAllGroups.setLabel(MessageManager
3220 .getString("label.apply_colour_to_all_groups"));
3221 applyToAllGroups.setState(true);
3222 applyToAllGroups.addItemListener(this);
3223 font.setLabel(MessageManager.getString("action.font"));
3224 font.addActionListener(this);
3225 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3226 scaleAbove.setState(true);
3227 scaleAbove.setEnabled(false);
3228 scaleAbove.addItemListener(this);
3229 scaleLeft.setEnabled(false);
3230 scaleLeft.setState(true);
3231 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3232 scaleLeft.addItemListener(this);
3233 scaleRight.setEnabled(false);
3234 scaleRight.setState(true);
3235 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3236 scaleRight.addItemListener(this);
3237 modifyPID.setLabel(MessageManager
3238 .getString("label.modify_identity_thereshold"));
3239 modifyPID.addActionListener(this);
3240 modifyConservation.setLabel(MessageManager
3241 .getString("label.modify_conservation_thereshold"));
3242 modifyConservation.addActionListener(this);
3243 sortByTreeMenu.setLabel(MessageManager
3244 .getString("action.by_tree_order"));
3245 sort.setLabel(MessageManager.getString("action.sort"));
3246 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3247 autoCalculate.addItemListener(this);
3248 sortByTree.addItemListener(this);
3250 .setLabel(MessageManager.getString("label.input_from_textbox"));
3251 inputText.addActionListener(this);
3252 centreColumnLabelFlag.setLabel(MessageManager
3253 .getString("label.centre_column_labels"));
3254 centreColumnLabelFlag.addItemListener(this);
3255 followMouseOverFlag.setLabel(MessageManager
3256 .getString("label.automatic_scrolling"));
3257 followMouseOverFlag.addItemListener(this);
3258 helpMenu.setLabel(MessageManager.getString("action.help"));
3259 documentation.setLabel(MessageManager.getString("label.documentation"));
3260 documentation.addActionListener(this);
3262 about.setLabel(MessageManager.getString("label.about"));
3263 about.addActionListener(this);
3264 seqLimits.setState(true);
3265 seqLimits.setLabel(MessageManager
3266 .getString("label.show_sequence_limits"));
3267 seqLimits.addItemListener(this);
3268 featureSettings.setLabel(MessageManager
3269 .getString("label.feature_settings"));
3270 featureSettings.addActionListener(this);
3271 sequenceFeatures.setLabel(MessageManager
3272 .getString("label.sequence_features"));
3273 sequenceFeatures.addItemListener(this);
3274 sequenceFeatures.setState(false);
3275 annotationColour.setLabel(MessageManager
3276 .getString("action.by_annotation"));
3277 annotationColour.addActionListener(this);
3278 invertSequenceMenuItem.setLabel(MessageManager
3279 .getString("action.invert_sequence_selection"));
3280 invertColSel.setLabel(MessageManager
3281 .getString("action.invert_column_selection"));
3282 menu1.setLabel(MessageManager.getString("action.show"));
3283 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3284 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3285 menu2.setLabel(MessageManager.getString("action.hide"));
3287 .setLabel(MessageManager.getString("label.selected_columns"));
3288 hideSequences.setLabel(MessageManager
3289 .getString("label.selected_sequences"));
3290 hideAllButSelection.setLabel(MessageManager
3291 .getString("label.all_but_selected_region"));
3292 hideAllSelection.setLabel(MessageManager
3293 .getString("label.selected_region"));
3294 showAllHidden.setLabel(MessageManager
3295 .getString("label.all_sequences_columns"));
3296 showGroupConsensus.setLabel(MessageManager
3297 .getString("label.group_consensus"));
3298 showGroupConservation.setLabel(MessageManager
3299 .getString("label.group_conservation"));
3300 showConsensusHistogram.setLabel(MessageManager
3301 .getString("label.show_consensus_histogram"));
3302 showSequenceLogo.setLabel(MessageManager
3303 .getString("label.show_consensus_logo"));
3304 normSequenceLogo.setLabel(MessageManager
3305 .getString("label.norm_consensus_logo"));
3306 applyAutoAnnotationSettings.setLabel(MessageManager
3307 .getString("label.apply_all_groups"));
3308 applyAutoAnnotationSettings.setState(true);
3309 autoAnnMenu.setLabel(MessageManager
3310 .getString("label.autocalculated_annotation"));
3312 invertColSel.addActionListener(this);
3313 showColumns.addActionListener(this);
3314 showSeqs.addActionListener(this);
3315 hideColumns.addActionListener(this);
3316 hideSequences.addActionListener(this);
3317 hideAllButSelection.addActionListener(this);
3318 hideAllSelection.addActionListener(this);
3319 showAllHidden.addActionListener(this);
3320 showGroupConsensus.addItemListener(this);
3321 showGroupConservation.addItemListener(this);
3322 showConsensusHistogram.addItemListener(this);
3323 showSequenceLogo.addItemListener(this);
3324 normSequenceLogo.addItemListener(this);
3326 applyAutoAnnotationSettings.addItemListener(this);
3327 formatMenu.setLabel(MessageManager.getString("action.format"));
3328 selectMenu.setLabel(MessageManager.getString("action.select"));
3329 newView.setLabel(MessageManager.getString("action.new_view"));
3330 newView.addActionListener(this);
3331 alignFrameMenuBar.add(fileMenu);
3332 alignFrameMenuBar.add(editMenu);
3333 alignFrameMenuBar.add(selectMenu);
3334 alignFrameMenuBar.add(viewMenu);
3335 alignFrameMenuBar.add(formatMenu);
3336 alignFrameMenuBar.add(colourMenu);
3337 alignFrameMenuBar.add(calculateMenu);
3338 alignFrameMenuBar.add(helpMenu);
3340 fileMenu.add(inputText);
3341 fileMenu.add(loadTree);
3342 fileMenu.add(loadAnnotations);
3344 fileMenu.addSeparator();
3345 fileMenu.add(outputTextboxMenu);
3346 fileMenu.add(outputFeatures);
3347 fileMenu.add(outputAnnotations);
3349 if (jalviewServletURL != null)
3351 fileMenu.add(loadApplication);
3354 fileMenu.addSeparator();
3355 fileMenu.add(closeMenuItem);
3357 editMenu.add(undoMenuItem);
3358 editMenu.add(redoMenuItem);
3361 editMenu.add(pasteMenu);
3362 editMenu.add(delete);
3363 editMenu.addSeparator();
3364 editMenu.add(remove2LeftMenuItem);
3365 editMenu.add(remove2RightMenuItem);
3366 editMenu.add(removeGappedColumnMenuItem);
3367 editMenu.add(removeAllGapsMenuItem);
3368 editMenu.add(removeRedundancyMenuItem);
3369 viewMenu.add(newView);
3370 viewMenu.addSeparator();
3371 viewMenu.add(menu1);
3372 viewMenu.add(menu2);
3373 viewMenu.addSeparator();
3374 viewMenu.add(followMouseOverFlag);
3375 viewMenu.add(annotationPanelMenuItem);
3376 autoAnnMenu.add(applyAutoAnnotationSettings);
3377 autoAnnMenu.add(showConsensusHistogram);
3378 autoAnnMenu.add(showSequenceLogo);
3379 autoAnnMenu.add(normSequenceLogo);
3380 autoAnnMenu.addSeparator();
3381 autoAnnMenu.add(showGroupConservation);
3382 autoAnnMenu.add(showGroupConsensus);
3383 viewMenu.add(autoAnnMenu);
3384 viewMenu.addSeparator();
3385 viewMenu.add(sequenceFeatures);
3386 viewMenu.add(featureSettings);
3387 viewMenu.addSeparator();
3388 viewMenu.add(alProperties);
3389 viewMenu.addSeparator();
3390 viewMenu.add(overviewMenuItem);
3391 colourMenu.add(applyToAllGroups);
3392 colourMenu.addSeparator();
3393 colourMenu.add(noColourmenuItem);
3394 colourMenu.add(clustalColour);
3395 colourMenu.add(BLOSUM62Colour);
3396 colourMenu.add(PIDColour);
3397 colourMenu.add(zappoColour);
3398 colourMenu.add(taylorColour);
3399 colourMenu.add(hydrophobicityColour);
3400 colourMenu.add(helixColour);
3401 colourMenu.add(strandColour);
3402 colourMenu.add(turnColour);
3403 colourMenu.add(buriedColour);
3404 colourMenu.add(nucleotideColour);
3405 colourMenu.add(purinePyrimidineColour);
3406 // colourMenu.add(RNAInteractionColour);
3407 colourMenu.add(tcoffeeColour);
3408 colourMenu.add(userDefinedColour);
3409 colourMenu.addSeparator();
3410 colourMenu.add(conservationMenuItem);
3411 colourMenu.add(modifyConservation);
3412 colourMenu.add(abovePIDThreshold);
3413 colourMenu.add(modifyPID);
3414 colourMenu.add(annotationColour);
3415 colourMenu.add(RNAHelixColour);
3416 calculateMenu.add(sort);
3417 calculateMenu.add(calculate);
3418 calculateMenu.addSeparator();
3419 calculateMenu.add(pairwiseAlignmentMenuItem);
3420 calculateMenu.add(PCAMenuItem);
3421 calculateMenu.add(autoCalculate);
3422 calculateMenu.add(sortByTree);
3423 this.add(statusBar, BorderLayout.SOUTH);
3424 pasteMenu.add(pasteNew);
3425 pasteMenu.add(pasteThis);
3426 sort.add(sortIDMenuItem);
3427 sort.add(sortLengthMenuItem);
3428 sort.add(sortByTreeMenu);
3429 sort.add(sortGroupMenuItem);
3430 sort.add(sortPairwiseMenuItem);
3431 calculate.add(averageDistanceTreeMenuItem);
3432 calculate.add(neighbourTreeMenuItem);
3433 calculate.add(avDistanceTreeBlosumMenuItem);
3434 calculate.add(njTreeBlosumMenuItem);
3435 helpMenu.add(documentation);
3436 helpMenu.add(about);
3437 menu1.add(showColumns);
3438 menu1.add(showSeqs);
3439 menu1.add(showAllHidden);
3440 menu2.add(hideColumns);
3441 menu2.add(hideSequences);
3442 menu2.add(hideAllSelection);
3443 menu2.add(hideAllButSelection);
3444 formatMenu.add(font);
3445 formatMenu.add(seqLimits);
3446 formatMenu.add(wrapMenuItem);
3447 formatMenu.add(scaleAbove);
3448 formatMenu.add(scaleLeft);
3449 formatMenu.add(scaleRight);
3450 formatMenu.add(viewBoxesMenuItem);
3451 formatMenu.add(viewTextMenuItem);
3452 formatMenu.add(colourTextMenuItem);
3453 formatMenu.add(displayNonconservedMenuItem);
3454 formatMenu.add(renderGapsMenuItem);
3455 formatMenu.add(centreColumnLabelFlag);
3456 selectMenu.add(findMenuItem);
3457 selectMenu.addSeparator();
3458 selectMenu.add(selectAllSequenceMenuItem);
3459 selectMenu.add(deselectAllSequenceMenuItem);
3460 selectMenu.add(invertSequenceMenuItem);
3461 selectMenu.add(invertColSel);
3462 selectMenu.add(createGroup);
3463 selectMenu.add(unGroup);
3464 selectMenu.add(grpsFromSelection);
3465 selectMenu.add(deleteGroups);
3469 public void setStatus(String string)
3471 statusBar.setText(string);
3474 MenuItem featureSettings = new MenuItem();
3476 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3478 MenuItem annotationColour = new MenuItem();
3480 MenuItem invertColSel = new MenuItem();
3482 Menu menu1 = new Menu();
3484 MenuItem showColumns = new MenuItem();
3486 MenuItem showSeqs = new MenuItem();
3488 Menu menu2 = new Menu();
3490 MenuItem hideColumns = new MenuItem();
3492 MenuItem hideSequences = new MenuItem();
3494 MenuItem hideAllButSelection = new MenuItem();
3496 MenuItem hideAllSelection = new MenuItem();
3498 MenuItem showAllHidden = new MenuItem();
3500 Menu formatMenu = new Menu();
3502 Menu selectMenu = new Menu();
3504 MenuItem newView = new MenuItem();
3507 * Attach the alignFrame panels after embedding menus, if necessary. This used
3508 * to be called setEmbedded, but is now creates the dropdown menus in a
3509 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3511 * @param reallyEmbedded
3512 * true to attach the view to the applet area on the page rather than
3515 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3520 // Explicly build the embedded menu panel for the on-page applet
3522 // view cannot be closed if its actually on the page
3523 fileMenu.remove(closeMenuItem);
3524 fileMenu.remove(3); // Remove Seperator
3525 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3526 Font.PLAIN, 11, false); // use our own fonts.
3527 // and actually add the components to the applet area
3528 viewport.applet.setLayout(new BorderLayout());
3529 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3530 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3531 alignPanel.setSize(viewport.applet.getSize().width,
3532 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3533 - statusBar.HEIGHT);
3534 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3535 final AlignFrame me = this;
3536 viewport.applet.addFocusListener(new FocusListener()
3540 public void focusLost(FocusEvent e)
3542 if (me.viewport.applet.currentAlignFrame == me)
3544 me.viewport.applet.currentAlignFrame = null;
3549 public void focusGained(FocusEvent e)
3551 me.viewport.applet.currentAlignFrame = me;
3554 viewport.applet.validate();
3559 // test and embed menu bar if necessary.
3561 if (embedMenuIfNeeded(alignPanel))
3563 // adjust for status bar height too
3564 alignPanel.setSize(getSize().width, getSize().height
3565 - statusBar.HEIGHT);
3567 add(statusBar, BorderLayout.SOUTH);
3568 add(alignPanel, BorderLayout.CENTER);
3569 // and register with the applet so it can pass external API calls to us
3570 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3576 * create a new binding between structures in an existing jmol viewer instance
3577 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3578 * this does not open a new Jmol window, or modify the display of the
3579 * structures in the original jmol window. Note This method doesn't work
3580 * without an additional javascript library to exchange messages between the
3581 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3584 * JmolViewer instance
3585 * @param sequenceIds
3586 * - sequence Ids to search for associations
3588 public SequenceStructureBinding addStructureViewInstance(
3589 Object jmolviewer, String[] sequenceIds)
3591 org.jmol.api.JmolViewer viewer = null;
3594 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3595 } catch (ClassCastException ex)
3597 System.err.println("Unsupported viewer object :"
3598 + jmolviewer.getClass());
3602 System.err.println("Can't use this object as a structure viewer:"
3603 + jmolviewer.getClass());
3606 SequenceI[] seqs = null;
3607 if (sequenceIds == null || sequenceIds.length == 0)
3609 seqs = viewport.getAlignment().getSequencesArray();
3613 Vector sqi = new Vector();
3614 AlignmentI al = viewport.getAlignment();
3615 for (int sid = 0; sid < sequenceIds.length; sid++)
3617 SequenceI sq = al.findName(sequenceIds[sid]);
3625 seqs = new SequenceI[sqi.size()];
3626 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3628 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3637 // TODO: search for a jmv that involves viewer
3639 { // create a new viewer/jalview binding.
3640 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3648 * bind a pdb file to a sequence in the current view
3651 * - sequenceId within the dataset.
3652 * @param pdbEntryString
3653 * - the short name for the PDB file
3655 * - pdb file - either a URL or a valid PDB file.
3656 * @return true if binding was as success TODO: consider making an exception
3657 * structure for indicating when PDB parsing or sequenceId location
3660 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3663 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3664 boolean needtoadd = false;
3665 if (toaddpdb != null)
3667 Vector pdbe = toaddpdb.getPDBId();
3668 PDBEntry pdbentry = null;
3669 if (pdbe != null && pdbe.size() > 0)
3671 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3673 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3674 if (!pdbentry.getId().equals(pdbEntryString)
3675 && !pdbentry.getFile().equals(pdbFile))
3685 if (pdbentry == null)
3687 pdbentry = new PDBEntry();
3688 pdbentry.setId(pdbEntryString);
3689 pdbentry.setFile(pdbFile);
3690 needtoadd = true; // add this new entry to sequence.
3692 // resolve data source
3693 // TODO: this code should be a refactored to an io package
3694 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3695 if (protocol == null)
3701 // make a note of the access mode and add
3702 if (pdbentry.getProperty() == null)
3704 pdbentry.setProperty(new Hashtable());
3706 pdbentry.getProperty().put("protocol", protocol);
3707 toaddpdb.addPDBId(pdbentry);
3708 alignPanel.getStructureSelectionManager()
3709 .registerPDBEntry(pdbentry);
3715 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3719 Vector sequences = new Vector();
3720 for (int i = 0; i < seqs.length; i++)
3722 if (seqs[i] != null)
3724 sequences.addElement(new Object[]
3725 { seqs[i], (chains != null) ? chains[i] : null });
3728 seqs = new SequenceI[sequences.size()];
3729 chains = new String[sequences.size()];
3730 for (int i = 0, isize = sequences.size(); i < isize; i++)
3732 Object[] oj = (Object[]) sequences.elementAt(i);
3734 seqs[i] = (SequenceI) oj[0];
3735 chains[i] = (String) oj[1];
3743 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3744 SequenceI[] seqs, String[] chains, String protocol)
3746 // Scrub any null sequences from the array
3747 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3748 seqs = (SequenceI[]) sqch[0];
3749 chains = (String[]) sqch[1];
3750 if (seqs == null || seqs.length == 0)
3753 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3755 if (protocol == null || protocol.trim().length() == 0
3756 || protocol.equals("null"))
3758 protocol = (String) pdb.getProperty().get("protocol");
3759 if (protocol == null)
3761 System.err.println("Couldn't work out protocol to open structure: "
3766 if (applet.useXtrnalSviewer)
3768 // register the association(s) and quit, don't create any windows.
3769 if (StructureSelectionManager.getStructureSelectionManager(applet)
3770 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3772 System.err.println("Failed to map " + pdb.getFile() + " ("
3773 + protocol + ") to any sequences");
3777 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3779 // can only do alignments with Jmol
3780 // find the last jmol window assigned to this alignment
3781 jalview.appletgui.AppletJmol ajm = null, tajm;
3782 Vector jmols = applet
3783 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3784 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3786 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3787 if (tajm.ap.alignFrame == this)
3796 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3797 // try and add the pdb structure
3802 // otherwise, create a new window
3803 if (applet.jmolAvailable)
3805 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3807 applet.lastFrameX += 40;
3808 applet.lastFrameY += 40;
3812 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3817 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3818 SequenceI[][] seqs, String[][] chains, String[] protocols)
3820 // TODO Auto-generated method stub
3821 System.err.println("Aligned Structure View: Not yet implemented.");
3825 * modify the current selection, providing the user has not made a selection
3829 * - sequences from this alignment
3831 * - columns to be selected on the alignment
3833 public void select(SequenceGroup sel, ColumnSelection csel)
3835 alignPanel.seqPanel.selection(sel, csel, null);
3838 public void scrollTo(int row, int column)
3840 alignPanel.seqPanel.scrollTo(row, column);
3843 public void scrollToRow(int row)
3845 alignPanel.seqPanel.scrollToRow(row);
3848 public void scrollToColumn(int column)
3850 alignPanel.seqPanel.scrollToColumn(column);
3854 * @return the alignments unique ID.
3856 public String getSequenceSetId()
3858 return viewport.getSequenceSetId();
3862 * Load the (T-Coffee) score file from the specified url
3865 * File/URL/T-COFFEE score file contents
3866 * @throws IOException
3867 * @return true if alignment was annotated with data from source
3869 public boolean loadScoreFile(String source) throws IOException
3872 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3873 AppletFormatAdapter.checkProtocol(source));
3874 if (!file.isValid())
3876 // TODO: raise dialog for gui
3877 System.err.println("Problems parsing T-Coffee scores: "
3878 + file.getWarningMessage());
3879 System.err.println("Origin was:\n" + source);
3884 * check that the score matrix matches the alignment dimensions
3887 if ((aln = viewport.getAlignment()) != null
3888 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3891 // TODO: raise a dialog box here rather than bomb out.
3893 .println("The scores matrix does not match the alignment dimensions");
3897 // TODO add parameter to indicate if matching should be done
3898 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3900 alignPanel.fontChanged();
3901 tcoffeeColour.setEnabled(true);
3902 // switch to this color
3903 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3908 System.err.println("Problems resolving T-Coffee scores:");
3909 if (file.getWarningMessage() != null)
3911 System.err.println(file.getWarningMessage());