2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.appletgui;
21 import jalview.analysis.AlignmentSorter;
22 import jalview.analysis.Conservation;
23 import jalview.api.AlignViewControllerGuiI;
24 import jalview.api.AlignViewControllerI;
25 import jalview.api.SequenceStructureBinding;
26 import jalview.bin.JalviewLite;
27 import jalview.commands.CommandI;
28 import jalview.commands.EditCommand;
29 import jalview.commands.OrderCommand;
30 import jalview.commands.RemoveGapColCommand;
31 import jalview.commands.RemoveGapsCommand;
32 import jalview.commands.SlideSequencesCommand;
33 import jalview.commands.TrimRegionCommand;
34 import jalview.datamodel.Alignment;
35 import jalview.datamodel.AlignmentI;
36 import jalview.datamodel.AlignmentOrder;
37 import jalview.datamodel.ColumnSelection;
38 import jalview.datamodel.PDBEntry;
39 import jalview.datamodel.Sequence;
40 import jalview.datamodel.SequenceGroup;
41 import jalview.datamodel.SequenceI;
42 import jalview.io.AnnotationFile;
43 import jalview.io.AppletFormatAdapter;
44 import jalview.io.FeaturesFile;
45 import jalview.io.TCoffeeScoreFile;
46 import jalview.schemes.Blosum62ColourScheme;
47 import jalview.schemes.BuriedColourScheme;
48 import jalview.schemes.ClustalxColourScheme;
49 import jalview.schemes.ColourSchemeI;
50 import jalview.schemes.HelixColourScheme;
51 import jalview.schemes.HydrophobicColourScheme;
52 import jalview.schemes.NucleotideColourScheme;
53 import jalview.schemes.PIDColourScheme;
54 import jalview.schemes.PurinePyrimidineColourScheme;
55 import jalview.schemes.RNAHelicesColourChooser;
56 import jalview.schemes.ResidueProperties;
57 import jalview.schemes.StrandColourScheme;
58 import jalview.schemes.TCoffeeColourScheme;
59 import jalview.schemes.TaylorColourScheme;
60 import jalview.schemes.TurnColourScheme;
61 import jalview.schemes.ZappoColourScheme;
62 import jalview.structure.StructureSelectionManager;
63 import jalview.util.MessageManager;
65 import java.awt.BorderLayout;
66 import java.awt.Canvas;
67 import java.awt.CheckboxMenuItem;
68 import java.awt.Color;
70 import java.awt.FontMetrics;
71 import java.awt.Frame;
72 import java.awt.Graphics;
73 import java.awt.Label;
75 import java.awt.MenuBar;
76 import java.awt.MenuItem;
77 import java.awt.event.ActionEvent;
78 import java.awt.event.ActionListener;
79 import java.awt.event.FocusEvent;
80 import java.awt.event.FocusListener;
81 import java.awt.event.ItemEvent;
82 import java.awt.event.ItemListener;
83 import java.awt.event.KeyEvent;
84 import java.awt.event.KeyListener;
85 import java.awt.event.WindowAdapter;
86 import java.awt.event.WindowEvent;
87 import java.io.IOException;
89 import java.net.URLEncoder;
90 import java.util.Enumeration;
91 import java.util.Hashtable;
92 import java.util.List;
93 import java.util.StringTokenizer;
94 import java.util.Vector;
96 public class AlignFrame extends EmbmenuFrame implements ActionListener,
97 ItemListener, KeyListener, AlignViewControllerGuiI
99 public AlignViewControllerI avc;
100 public AlignmentPanel alignPanel;
102 public AlignViewport viewport;
104 int DEFAULT_WIDTH = 700;
106 int DEFAULT_HEIGHT = 500;
108 String jalviewServletURL;
110 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
111 String title, boolean embedded)
115 jalviewServletURL = applet.getParameter("APPLICATION_URL");
121 } catch (Exception ex)
123 ex.printStackTrace();
125 // need to get window geometry before we calculate alignment layout
131 param = applet.getParameter("windowWidth");
134 int width = Integer.parseInt(param);
135 DEFAULT_WIDTH = width;
137 param = applet.getParameter("windowHeight");
140 int height = Integer.parseInt(param);
141 DEFAULT_HEIGHT = height;
143 } catch (Exception ex)
147 viewport = new AlignViewport(al, applet);
148 alignPanel = new AlignmentPanel(this, viewport);
149 avc = new jalview.controller.AlignViewController(this, viewport, alignPanel);
150 viewport.updateConservation(alignPanel);
151 viewport.updateConsensus(alignPanel);
153 annotationPanelMenuItem.setState(viewport.showAnnotation);
154 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
155 followMouseOverFlag.setState(viewport.getFollowHighlight());
156 showGroupConsensus.setState(viewport.isShowGroupConsensus());
157 showGroupConservation.setState(viewport.isShowGroupConservation());
158 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
159 showSequenceLogo.setState(viewport.isShowSequenceLogo());
160 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
161 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
163 seqLimits.setState(viewport.showJVSuffix);
167 String param = applet.getParameter("sortBy");
170 if (param.equalsIgnoreCase("Id"))
172 sortIDMenuItem_actionPerformed();
174 else if (param.equalsIgnoreCase("Pairwise Identity"))
176 sortPairwiseMenuItem_actionPerformed();
178 else if (param.equalsIgnoreCase("Length"))
180 sortLengthMenuItem_actionPerformed();
184 param = applet.getParameter("wrap");
187 if (param.equalsIgnoreCase("true"))
189 wrapMenuItem.setState(true);
190 wrapMenuItem_actionPerformed();
193 param = applet.getParameter("centrecolumnlabels");
196 centreColumnLabelFlag.setState(true);
197 centreColumnLabelFlag_stateChanged();
201 if (viewport.getAlignment().isNucleotide())
203 viewport.updateStrucConsensus(alignPanel);
204 if (viewport.getAlignment().hasRNAStructure())
206 RNAHelixColour.setEnabled(true);
210 RNAHelixColour.setEnabled(false);
215 RNAHelixColour.setEnabled(false);
216 purinePyrimidineColour.setEnabled(false);
218 // Some JVMS send keyevents to Top frame or lowest panel,
219 // Havent worked out why yet. So add to both this frame and seqCanvas for
221 this.addKeyListener(this);
222 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
223 alignPanel.idPanel.idCanvas.addKeyListener(this);
224 alignPanel.scalePanel.addKeyListener(this);
225 alignPanel.annotationPanel.addKeyListener(this);
226 alignPanel.annotationPanelHolder.addKeyListener(this);
227 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
228 alignPanel.alabels.addKeyListener(this);
229 createAlignFrameWindow(embedded, title);
232 alignPanel.adjustAnnotationHeight();
233 alignPanel.paintAlignment(true);
236 public AlignViewport getAlignViewport()
241 public SeqCanvas getSeqcanvas()
243 return alignPanel.seqPanel.seqCanvas;
247 * Load a features file onto the alignment
250 * file URL, content, or other resolvable path
252 * is protocol for accessing data referred to by file
255 public boolean parseFeaturesFile(String file, String type)
257 return parseFeaturesFile(file, type, true);
261 * Load a features file onto the alignment
264 * file URL, content, or other resolvable path
266 * is protocol for accessing data referred to by file
267 * @param autoenabledisplay
268 * when true, display features flag will be automatically enabled if
269 * features are loaded
270 * @return true if data parsed as a features file
272 public boolean parseFeaturesFile(String file, String type,
273 boolean autoenabledisplay)
275 // TODO: test if importing a features file onto an alignment which already
276 // has features with links overwrites the original links.
278 Hashtable featureLinks = new Hashtable();
279 boolean featuresFile = false;
282 featuresFile = new jalview.io.FeaturesFile(file, type)
283 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
284 .getFeatureRenderer().featureColours, featureLinks,
285 true, viewport.applet.getDefaultParameter(
286 "relaxedidmatch", false));
287 } catch (Exception ex)
289 ex.printStackTrace();
294 if (featureLinks.size() > 0)
296 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
298 if (autoenabledisplay)
300 viewport.showSequenceFeatures = true;
301 sequenceFeatures.setState(true);
303 if (viewport.featureSettings != null)
305 viewport.featureSettings.refreshTable();
307 alignPanel.paintAlignment(true);
308 statusBar.setText(MessageManager.getString("label.successfully_added_features_alignment"));
314 public void keyPressed(KeyEvent evt)
316 if (viewport.cursorMode
317 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
318 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
319 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
320 && Character.isDigit(evt.getKeyChar()))
321 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
323 switch (evt.getKeyCode())
325 case 27: // escape key
326 deselectAllSequenceMenuItem_actionPerformed();
328 alignPanel.alabels.cancelDrag();
331 if (evt.isControlDown() || evt.isMetaDown())
333 cut_actionPerformed();
337 if (viewport.cursorMode && !evt.isControlDown())
339 alignPanel.seqPanel.setCursorColumn();
341 if (evt.isControlDown() || evt.isMetaDown())
343 copy_actionPerformed();
347 if (evt.isControlDown())
349 paste(evt.isShiftDown());
353 if (evt.isControlDown() || evt.isMetaDown())
355 selectAllSequenceMenuItem_actionPerformed();
358 case KeyEvent.VK_DOWN:
359 if (viewport.cursorMode)
361 alignPanel.seqPanel.moveCursor(0, 1);
365 moveSelectedSequences(false);
370 if (viewport.cursorMode)
372 alignPanel.seqPanel.moveCursor(0, -1);
376 moveSelectedSequences(true);
380 case KeyEvent.VK_LEFT:
381 if (evt.isAltDown() || !viewport.cursorMode)
382 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
384 alignPanel.seqPanel.moveCursor(-1, 0);
387 case KeyEvent.VK_RIGHT:
388 if (evt.isAltDown() || !viewport.cursorMode)
389 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
391 alignPanel.seqPanel.moveCursor(1, 0);
394 case KeyEvent.VK_SPACE:
395 if (viewport.cursorMode)
397 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
398 || evt.isShiftDown() || evt.isAltDown());
402 case KeyEvent.VK_DELETE:
403 case KeyEvent.VK_BACK_SPACE:
404 if (viewport.cursorMode)
406 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
407 || evt.isShiftDown() || evt.isAltDown());
411 cut_actionPerformed();
412 alignPanel.seqPanel.seqCanvas.repaint();
417 if (viewport.cursorMode)
419 alignPanel.seqPanel.setCursorRow();
423 if (viewport.cursorMode)
425 alignPanel.seqPanel.setCursorPosition();
429 case KeyEvent.VK_ENTER:
430 case KeyEvent.VK_COMMA:
431 if (viewport.cursorMode)
433 alignPanel.seqPanel.setCursorRowAndColumn();
438 if (viewport.cursorMode)
440 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
444 if (viewport.cursorMode)
446 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
451 viewport.cursorMode = !viewport.cursorMode;
452 statusBar.setText(MessageManager.formatMessage("label.keyboard_editing_mode", new String[]{(viewport.cursorMode ? "on" : "off")}));
453 if (viewport.cursorMode)
455 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
456 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
461 if (evt.isControlDown())
463 findMenuItem_actionPerformed();
469 boolean toggleSeqs = !evt.isControlDown();
470 boolean toggleCols = !evt.isShiftDown();
471 toggleHiddenRegions(toggleSeqs, toggleCols);
475 case KeyEvent.VK_PAGE_UP:
476 if (viewport.wrapAlignment)
478 alignPanel.scrollUp(true);
482 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
483 - viewport.endSeq + viewport.startSeq);
487 case KeyEvent.VK_PAGE_DOWN:
488 if (viewport.wrapAlignment)
490 alignPanel.scrollUp(false);
494 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
495 + viewport.endSeq - viewport.startSeq);
500 if (evt.isControlDown())
502 undoMenuItem_actionPerformed();
507 if (evt.isControlDown())
509 redoMenuItem_actionPerformed();
514 if (evt.isControlDown())
521 if (evt.isControlDown())
523 trimAlignment(false);
528 if (evt.isControlDown())
530 if (evt.isShiftDown())
532 this.removeAllGapsMenuItem_actionPerformed();
536 removeGappedColumnMenuItem_actionPerformed();
541 if (evt.isControlDown())
545 invertColSel_actionPerformed();
549 invertSequenceMenuItem_actionPerformed();
555 if (evt.isControlDown())
557 if (evt.isShiftDown())
559 this.unGroup_actionPerformed();
563 this.createGroup_actionPerformed();
569 if (evt.isControlDown())
571 this.deleteGroups_actionPerformed();
576 if (evt.isControlDown())
583 alignPanel.paintAlignment(true);
587 * called by key handler and the hide all/show all menu items
592 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
594 boolean hide = false;
595 SequenceGroup sg = viewport.getSelectionGroup();
596 if (!toggleSeqs && !toggleCols)
598 // Hide everything by the current selection - this is a hack - we do the
599 // invert and then hide
600 // first check that there will be visible columns after the invert.
601 if ((viewport.getColumnSelection() != null
602 && viewport.getColumnSelection().getSelected() != null && viewport
603 .getColumnSelection().getSelected().size() > 0)
604 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
607 // now invert the sequence set, if required - empty selection implies
608 // that no hiding is required.
611 invertSequenceMenuItem_actionPerformed();
612 sg = viewport.getSelectionGroup();
616 viewport.expandColSelection(sg, true);
617 // finally invert the column selection and get the new sequence
618 // selection and indicate it should be hidden.
619 invertColSel_actionPerformed();
626 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
629 viewport.hideAllSelectedSeqs();
631 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
634 viewport.showAllHiddenSeqs();
640 if (viewport.getColumnSelection().getSelected().size() > 0)
642 viewport.hideSelectedColumns();
645 viewport.setSelectionGroup(sg);
650 viewport.showAllHiddenColumns();
656 public void keyReleased(KeyEvent evt)
661 public void keyTyped(KeyEvent evt)
666 public void itemStateChanged(ItemEvent evt)
668 if (evt.getSource() == displayNonconservedMenuItem)
670 displayNonconservedMenuItem_actionPerformed();
672 else if (evt.getSource() == colourTextMenuItem)
674 colourTextMenuItem_actionPerformed();
676 else if (evt.getSource() == wrapMenuItem)
678 wrapMenuItem_actionPerformed();
680 else if (evt.getSource() == scaleAbove)
682 viewport.setScaleAboveWrapped(scaleAbove.getState());
684 else if (evt.getSource() == scaleLeft)
686 viewport.setScaleLeftWrapped(scaleLeft.getState());
688 else if (evt.getSource() == scaleRight)
690 viewport.setScaleRightWrapped(scaleRight.getState());
692 else if (evt.getSource() == seqLimits)
694 seqLimits_itemStateChanged();
696 else if (evt.getSource() == viewBoxesMenuItem)
698 viewport.setShowBoxes(viewBoxesMenuItem.getState());
700 else if (evt.getSource() == viewTextMenuItem)
702 viewport.setShowText(viewTextMenuItem.getState());
704 else if (evt.getSource() == renderGapsMenuItem)
706 viewport.setRenderGaps(renderGapsMenuItem.getState());
708 else if (evt.getSource() == annotationPanelMenuItem)
710 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
711 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
713 else if (evt.getSource() == sequenceFeatures)
715 viewport.showSequenceFeatures(sequenceFeatures.getState());
716 alignPanel.seqPanel.seqCanvas.repaint();
718 else if (evt.getSource() == conservationMenuItem)
720 conservationMenuItem_actionPerformed();
722 else if (evt.getSource() == abovePIDThreshold)
724 abovePIDThreshold_actionPerformed();
726 else if (evt.getSource() == applyToAllGroups)
728 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
730 else if (evt.getSource() == autoCalculate)
732 viewport.autoCalculateConsensus = autoCalculate.getState();
734 else if (evt.getSource() == sortByTree)
736 viewport.sortByTree = sortByTree.getState();
738 else if (evt.getSource() == this.centreColumnLabelFlag)
740 centreColumnLabelFlag_stateChanged();
742 else if (evt.getSource() == this.followMouseOverFlag)
744 mouseOverFlag_stateChanged();
746 else if (evt.getSource() == showGroupConsensus)
748 showGroupConsensus_actionPerformed();
750 else if (evt.getSource() == showGroupConservation)
752 showGroupConservation_actionPerformed();
754 else if (evt.getSource() == showSequenceLogo)
756 showSequenceLogo_actionPerformed();
758 else if (evt.getSource() == normSequenceLogo)
760 normSequenceLogo_actionPerformed();
762 else if (evt.getSource() == showConsensusHistogram)
764 showConsensusHistogram_actionPerformed();
766 else if (evt.getSource() == applyAutoAnnotationSettings)
768 applyAutoAnnotationSettings_actionPerformed();
770 alignPanel.paintAlignment(true);
773 private void mouseOverFlag_stateChanged()
775 viewport.followHighlight = followMouseOverFlag.getState();
776 // TODO: could kick the scrollTo mechanism to reset view for current
780 private void centreColumnLabelFlag_stateChanged()
782 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
783 this.alignPanel.annotationPanel.repaint();
787 public void actionPerformed(ActionEvent evt)
789 Object source = evt.getSource();
791 if (source == inputText)
793 inputText_actionPerformed();
795 else if (source == loadTree)
797 loadTree_actionPerformed();
799 else if (source == loadApplication)
801 launchFullApplication();
803 else if (source == loadAnnotations)
807 else if (source == outputAnnotations)
809 outputAnnotations(true);
811 else if (source == outputFeatures)
813 outputFeatures(true, "Jalview");
815 else if (source == closeMenuItem)
817 closeMenuItem_actionPerformed();
819 else if (source == copy)
821 copy_actionPerformed();
823 else if (source == undoMenuItem)
825 undoMenuItem_actionPerformed();
827 else if (source == redoMenuItem)
829 redoMenuItem_actionPerformed();
831 else if (source == inputText)
833 inputText_actionPerformed();
835 else if (source == closeMenuItem)
837 closeMenuItem_actionPerformed();
839 else if (source == undoMenuItem)
841 undoMenuItem_actionPerformed();
843 else if (source == redoMenuItem)
845 redoMenuItem_actionPerformed();
847 else if (source == copy)
849 copy_actionPerformed();
851 else if (source == pasteNew)
853 pasteNew_actionPerformed();
855 else if (source == pasteThis)
857 pasteThis_actionPerformed();
859 else if (source == cut)
861 cut_actionPerformed();
863 else if (source == delete)
865 delete_actionPerformed();
867 else if (source == grpsFromSelection)
869 makeGrpsFromSelection_actionPerformed();
871 else if (source == deleteGroups)
873 deleteGroups_actionPerformed();
875 else if (source == selectAllSequenceMenuItem)
877 selectAllSequenceMenuItem_actionPerformed();
879 else if (source == deselectAllSequenceMenuItem)
881 deselectAllSequenceMenuItem_actionPerformed();
883 else if (source == invertSequenceMenuItem)
885 invertSequenceMenuItem_actionPerformed();
887 else if (source == invertColSel)
889 viewport.invertColumnSelection();
890 alignPanel.paintAlignment(true);
892 else if (source == remove2LeftMenuItem)
896 else if (source == remove2RightMenuItem)
898 trimAlignment(false);
900 else if (source == removeGappedColumnMenuItem)
902 removeGappedColumnMenuItem_actionPerformed();
904 else if (source == removeAllGapsMenuItem)
906 removeAllGapsMenuItem_actionPerformed();
908 else if (source == findMenuItem)
910 findMenuItem_actionPerformed();
912 else if (source == font)
914 new FontChooser(alignPanel);
916 else if (source == newView)
920 else if (source == showColumns)
922 viewport.showAllHiddenColumns();
923 alignPanel.paintAlignment(true);
925 else if (source == showSeqs)
927 viewport.showAllHiddenSeqs();
928 alignPanel.paintAlignment(true);
930 else if (source == hideColumns)
932 viewport.hideSelectedColumns();
933 alignPanel.paintAlignment(true);
935 else if (source == hideSequences
936 && viewport.getSelectionGroup() != null)
938 viewport.hideAllSelectedSeqs();
939 alignPanel.paintAlignment(true);
941 else if (source == hideAllButSelection)
943 toggleHiddenRegions(false, false);
944 alignPanel.paintAlignment(true);
946 else if (source == hideAllSelection)
948 SequenceGroup sg = viewport.getSelectionGroup();
949 viewport.expandColSelection(sg, false);
950 viewport.hideAllSelectedSeqs();
951 viewport.hideSelectedColumns();
952 alignPanel.paintAlignment(true);
954 else if (source == showAllHidden)
956 viewport.showAllHiddenColumns();
957 viewport.showAllHiddenSeqs();
958 alignPanel.paintAlignment(true);
960 else if (source == showGroupConsensus)
962 showGroupConsensus_actionPerformed();
964 else if (source == showGroupConservation)
966 showGroupConservation_actionPerformed();
968 else if (source == showSequenceLogo)
970 showSequenceLogo_actionPerformed();
972 else if (source == normSequenceLogo)
974 normSequenceLogo_actionPerformed();
976 else if (source == showConsensusHistogram)
978 showConsensusHistogram_actionPerformed();
980 else if (source == applyAutoAnnotationSettings)
982 applyAutoAnnotationSettings_actionPerformed();
984 else if (source == featureSettings)
986 new FeatureSettings(alignPanel);
988 else if (source == alProperties)
990 StringBuffer contents = new jalview.io.AlignmentProperties(
991 viewport.getAlignment()).formatAsString();
992 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
993 cap.setText(contents.toString());
994 Frame frame = new Frame();
996 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.alignment_properties", new String[]{getTitle()}),
999 else if (source == overviewMenuItem)
1001 overviewMenuItem_actionPerformed();
1003 else if (source == noColourmenuItem)
1007 else if (source == clustalColour)
1009 abovePIDThreshold.setState(false);
1010 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1012 else if (source == zappoColour)
1014 changeColour(new ZappoColourScheme());
1016 else if (source == taylorColour)
1018 changeColour(new TaylorColourScheme());
1020 else if (source == hydrophobicityColour)
1022 changeColour(new HydrophobicColourScheme());
1024 else if (source == helixColour)
1026 changeColour(new HelixColourScheme());
1028 else if (source == strandColour)
1030 changeColour(new StrandColourScheme());
1032 else if (source == turnColour)
1034 changeColour(new TurnColourScheme());
1036 else if (source == buriedColour)
1038 changeColour(new BuriedColourScheme());
1040 else if (source == nucleotideColour)
1042 changeColour(new NucleotideColourScheme());
1044 else if (source == purinePyrimidineColour)
1046 changeColour(new PurinePyrimidineColourScheme());
1048 else if (source == RNAHelixColour)
1050 new RNAHelicesColourChooser(viewport, alignPanel);
1052 else if (source == modifyPID)
1054 modifyPID_actionPerformed();
1056 else if (source == modifyConservation)
1058 modifyConservation_actionPerformed();
1060 else if (source == userDefinedColour)
1062 new UserDefinedColours(alignPanel, null);
1064 else if (source == PIDColour)
1066 changeColour(new PIDColourScheme());
1068 else if (source == BLOSUM62Colour)
1070 changeColour(new Blosum62ColourScheme());
1072 else if (source == tcoffeeColour)
1074 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1076 else if (source == annotationColour)
1078 new AnnotationColourChooser(viewport, alignPanel);
1080 else if (source == sortPairwiseMenuItem)
1082 sortPairwiseMenuItem_actionPerformed();
1084 else if (source == sortIDMenuItem)
1086 sortIDMenuItem_actionPerformed();
1088 else if (source == sortLengthMenuItem)
1090 sortLengthMenuItem_actionPerformed();
1092 else if (source == sortGroupMenuItem)
1094 sortGroupMenuItem_actionPerformed();
1096 else if (source == removeRedundancyMenuItem)
1098 removeRedundancyMenuItem_actionPerformed();
1100 else if (source == pairwiseAlignmentMenuItem)
1102 pairwiseAlignmentMenuItem_actionPerformed();
1104 else if (source == PCAMenuItem)
1106 PCAMenuItem_actionPerformed();
1108 else if (source == averageDistanceTreeMenuItem)
1110 averageDistanceTreeMenuItem_actionPerformed();
1112 else if (source == neighbourTreeMenuItem)
1114 neighbourTreeMenuItem_actionPerformed();
1116 else if (source == njTreeBlosumMenuItem)
1118 njTreeBlosumMenuItem_actionPerformed();
1120 else if (source == avDistanceTreeBlosumMenuItem)
1122 avTreeBlosumMenuItem_actionPerformed();
1124 else if (source == documentation)
1126 documentation_actionPerformed();
1128 else if (source == about)
1130 about_actionPerformed();
1135 public void inputText_actionPerformed()
1137 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1138 Frame frame = new Frame();
1140 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.input_cut_paste"), 500, 500);
1143 protected void outputText_actionPerformed(ActionEvent e)
1145 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1146 Frame frame = new Frame();
1148 jalview.bin.JalviewLite.addFrame(frame,
1149 MessageManager.formatMessage("label.alignment_output_command", new String[]{e.getActionCommand()}),600, 500);
1150 cap.setText(new AppletFormatAdapter().formatSequences(
1151 e.getActionCommand(), viewport.getAlignment(),
1152 viewport.showJVSuffix));
1155 public void loadAnnotations()
1157 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1158 cap.setText(MessageManager.getString("label.paste_features_annotations_Tcoffee_here"));
1159 cap.setAnnotationImport();
1160 Frame frame = new Frame();
1162 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.paste_annotations"), 400, 300);
1166 public String outputAnnotations(boolean displayTextbox)
1168 String annotation = new AnnotationFile().printAnnotations(
1169 viewport.showAnnotation ? viewport.getAlignment()
1170 .getAlignmentAnnotation() : null, viewport
1171 .getAlignment().getGroups(), ((Alignment) viewport
1172 .getAlignment()).alignmentProperties);
1176 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1177 Frame frame = new Frame();
1179 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.annotations"), 600, 500);
1180 cap.setText(annotation);
1186 private Hashtable getDisplayedFeatureCols()
1188 if (alignPanel.getFeatureRenderer() != null
1189 && viewport.featuresDisplayed != null)
1191 FeatureRenderer fr = alignPanel.getFeatureRenderer();
1192 Hashtable fcols = new Hashtable();
1193 Enumeration en = viewport.featuresDisplayed.keys();
1194 while (en.hasMoreElements())
1196 Object col = en.nextElement();
1197 fcols.put(col, fr.featureColours.get(col));
1204 public String outputFeatures(boolean displayTextbox, String format)
1207 if (format.equalsIgnoreCase("Jalview"))
1209 features = new FeaturesFile().printJalviewFormat(viewport
1210 .getAlignment().getSequencesArray(),
1211 getDisplayedFeatureCols());
1215 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1216 .getSequencesArray(), getDisplayedFeatureCols());
1221 boolean frimport = false;
1222 if (features == null || features.equals("No Features Visible"))
1224 features = "# No features visible - paste some and import them here.";
1228 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1231 cap.setAnnotationImport();
1233 Frame frame = new Frame();
1235 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.features"), 600, 500);
1236 cap.setText(features);
1240 if (features == null)
1247 void launchFullApplication()
1249 StringBuffer url = new StringBuffer(jalviewServletURL);
1252 + appendProtocol(viewport.applet.getParameter("file")));
1254 if (viewport.applet.getParameter("features") != null)
1256 url.append("&features=");
1257 url.append(appendProtocol(viewport.applet.getParameter("features")));
1260 if (viewport.applet.getParameter("annotations") != null)
1262 url.append("&annotations=");
1263 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1266 if (viewport.applet.getParameter("jnetfile") != null)
1268 url.append("&annotations=");
1269 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1272 if (viewport.applet.getParameter("defaultColour") != null)
1274 url.append("&colour="
1275 + removeWhiteSpace(viewport.applet
1276 .getParameter("defaultColour")));
1279 if (viewport.applet.getParameter("userDefinedColour") != null)
1281 url.append("&colour="
1282 + removeWhiteSpace(viewport.applet
1283 .getParameter("userDefinedColour")));
1285 if (viewport.applet.getParameter("tree") != null)
1288 + appendProtocol(viewport.applet.getParameter("tree")));
1290 if (viewport.applet.getParameter("treeFile") != null)
1293 + appendProtocol(viewport.applet.getParameter("treeFile")));
1296 showURL(url.toString(), "FULL_APP");
1299 String removeWhiteSpace(String colour)
1301 StringBuffer sb = new StringBuffer();
1302 for (int i = 0; i < colour.length(); i++)
1304 if (Character.isWhitespace(colour.charAt(i)))
1310 sb.append(colour.charAt(i));
1314 return sb.toString();
1317 String appendProtocol(String url)
1322 url = URLEncoder.encode(url);
1325 * When we finally deprecate 1.1 compatibility, we can start to use
1326 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1327 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1328 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1329 * ex.printStackTrace(); }
1331 catch (java.net.MalformedURLException ex)
1333 url = viewport.applet.getCodeBase() + url;
1338 public void closeMenuItem_actionPerformed()
1340 PaintRefresher.RemoveComponent(alignPanel);
1341 if (alignPanel.seqPanel != null
1342 && alignPanel.seqPanel.seqCanvas != null)
1344 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1346 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1348 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1351 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1366 void updateEditMenuBar()
1369 if (viewport.historyList.size() > 0)
1371 undoMenuItem.setEnabled(true);
1372 CommandI command = (CommandI) viewport.historyList.peek();
1373 undoMenuItem.setLabel(MessageManager.formatMessage("label.undo_command", new String[]{command.getDescription()}));
1377 undoMenuItem.setEnabled(false);
1378 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1381 if (viewport.redoList.size() > 0)
1383 redoMenuItem.setEnabled(true);
1385 CommandI command = (CommandI) viewport.redoList.peek();
1386 redoMenuItem.setLabel(MessageManager.formatMessage("label.redo_command", new String[]{command.getDescription()}));
1390 redoMenuItem.setEnabled(false);
1391 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1398 public void addHistoryItem(CommandI command)
1400 if (command.getSize() > 0)
1402 viewport.historyList.push(command);
1403 viewport.redoList.removeAllElements();
1404 updateEditMenuBar();
1405 viewport.updateHiddenColumns();
1410 * TODO: JAL-1104 DOCUMENT ME!
1415 protected void undoMenuItem_actionPerformed()
1417 if (viewport.historyList.size() < 1)
1422 CommandI command = (CommandI) viewport.historyList.pop();
1423 viewport.redoList.push(command);
1424 command.undoCommand(null);
1426 AlignViewport originalSource = getOriginatingSource(command);
1428 if (originalSource != viewport)
1431 .println("Warning: Viewport object mismatch whilst undoing");
1433 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1434 // viewport.getColumnSelection().getHiddenColumns()
1436 updateEditMenuBar();
1437 originalSource.firePropertyChange("alignment", null, originalSource
1438 .getAlignment().getSequences());
1442 * TODO: JAL-1104 DOCUMENT ME!
1447 protected void redoMenuItem_actionPerformed()
1449 if (viewport.redoList.size() < 1)
1454 CommandI command = (CommandI) viewport.redoList.pop();
1455 viewport.historyList.push(command);
1456 command.doCommand(null);
1458 AlignViewport originalSource = getOriginatingSource(command);
1460 if (originalSource != viewport)
1463 .println("Warning: Viewport object mismatch whilst re-doing");
1465 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1466 // viewport.getColumnSelection().getHiddenColumns()
1469 updateEditMenuBar();
1470 originalSource.firePropertyChange("alignment", null, originalSource
1471 .getAlignment().getSequences());
1474 AlignViewport getOriginatingSource(CommandI command)
1476 AlignViewport originalSource = null;
1477 // For sequence removal and addition, we need to fire
1478 // the property change event FROM the viewport where the
1479 // original alignment was altered
1480 AlignmentI al = null;
1481 if (command instanceof EditCommand)
1483 EditCommand editCommand = (EditCommand) command;
1484 al = editCommand.getAlignment();
1485 Vector comps = (Vector) PaintRefresher.components.get(viewport
1486 .getSequenceSetId());
1487 for (int i = 0; i < comps.size(); i++)
1489 if (comps.elementAt(i) instanceof AlignmentPanel)
1491 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1493 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1500 if (originalSource == null)
1502 // The original view is closed, we must validate
1503 // the current view against the closed view first
1506 PaintRefresher.validateSequences(al, viewport.getAlignment());
1509 originalSource = viewport;
1512 return originalSource;
1515 public void moveSelectedSequences(boolean up)
1517 SequenceGroup sg = viewport.getSelectionGroup();
1522 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1523 up ? null : viewport.getHiddenRepSequences(), up);
1524 alignPanel.paintAlignment(true);
1527 synchronized void slideSequences(boolean right, int size)
1529 List<SequenceI> sg = new Vector<SequenceI>();
1530 if (viewport.cursorMode)
1532 sg.add(viewport.getAlignment().getSequenceAt(
1533 alignPanel.seqPanel.seqCanvas.cursorY));
1535 else if (viewport.getSelectionGroup() != null
1536 && viewport.getSelectionGroup().getSize() != viewport
1537 .getAlignment().getHeight())
1539 sg = viewport.getSelectionGroup().getSequences(
1540 viewport.getHiddenRepSequences());
1548 Vector<SequenceI> invertGroup = new Vector();
1550 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1552 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1553 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1556 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1558 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1560 for (int i = 0; i < invertGroup.size(); i++)
1561 seqs2[i] = invertGroup.elementAt(i);
1563 SlideSequencesCommand ssc;
1565 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1566 size, viewport.getGapCharacter());
1568 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1569 size, viewport.getGapCharacter());
1571 int groupAdjustment = 0;
1572 if (ssc.getGapsInsertedBegin() && right)
1574 if (viewport.cursorMode)
1575 alignPanel.seqPanel.moveCursor(size, 0);
1577 groupAdjustment = size;
1579 else if (!ssc.getGapsInsertedBegin() && !right)
1581 if (viewport.cursorMode)
1582 alignPanel.seqPanel.moveCursor(-size, 0);
1584 groupAdjustment = -size;
1587 if (groupAdjustment != 0)
1589 viewport.getSelectionGroup().setStartRes(
1590 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1591 viewport.getSelectionGroup().setEndRes(
1592 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1595 boolean appendHistoryItem = false;
1596 if (viewport.historyList != null && viewport.historyList.size() > 0
1597 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1599 appendHistoryItem = ssc
1600 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1604 if (!appendHistoryItem)
1605 addHistoryItem(ssc);
1610 static StringBuffer copiedSequences;
1612 static Vector copiedHiddenColumns;
1614 protected void copy_actionPerformed()
1616 if (viewport.getSelectionGroup() == null)
1621 SequenceGroup sg = viewport.getSelectionGroup();
1622 copiedSequences = new StringBuffer();
1623 Hashtable orderedSeqs = new Hashtable();
1624 for (int i = 0; i < sg.getSize(); i++)
1626 SequenceI seq = sg.getSequenceAt(i);
1627 int index = viewport.getAlignment().findIndex(seq);
1628 orderedSeqs.put(index + "", seq);
1631 int index = 0, startRes, endRes;
1634 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1636 copiedHiddenColumns = new Vector();
1637 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1638 for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns()
1641 int[] region = (int[]) viewport.getColumnSelection()
1642 .getHiddenColumns().elementAt(i);
1644 copiedHiddenColumns.addElement(new int[]
1645 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1650 copiedHiddenColumns = null;
1653 for (int i = 0; i < sg.getSize(); i++)
1655 SequenceI seq = null;
1659 if (orderedSeqs.containsKey(index + ""))
1661 seq = (SequenceI) orderedSeqs.get(index + "");
1673 // Returns residue following index if gap
1674 startRes = seq.findPosition(sg.getStartRes());
1677 // Need to find the residue preceeding index if gap
1680 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1682 ch = seq.getCharAt(j);
1683 if (!jalview.util.Comparison.isGap((ch)))
1691 endRes += seq.getStart() - 1;
1694 copiedSequences.append(seq.getName()
1700 + seq.getSequenceAsString(sg.getStartRes(),
1701 sg.getEndRes() + 1) + "\n");
1706 protected void pasteNew_actionPerformed()
1711 protected void pasteThis_actionPerformed()
1716 void paste(boolean newAlignment)
1721 if (copiedSequences == null)
1726 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1727 Vector seqs = new Vector();
1728 while (st.hasMoreElements())
1730 String name = st.nextToken();
1731 int start = Integer.parseInt(st.nextToken());
1732 int end = Integer.parseInt(st.nextToken());
1733 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1735 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1736 for (int i = 0; i < seqs.size(); i++)
1738 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1743 String newtitle = new String("Copied sequences");
1744 if (getTitle().startsWith("Copied sequences"))
1746 newtitle = getTitle();
1750 newtitle = newtitle.concat("- from " + getTitle());
1752 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1753 viewport.applet, newtitle, false);
1754 if (copiedHiddenColumns != null)
1756 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1758 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1759 af.viewport.hideColumns(region[0], region[1]);
1763 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1768 addSequences(newSeqs);
1771 } catch (Exception ex)
1773 } // could be anything being pasted in here
1777 void addSequences(SequenceI[] seqs)
1779 for (int i = 0; i < seqs.length; i++)
1781 viewport.getAlignment().addSequence(seqs[i]);
1785 addHistoryItem(new EditCommand("Add sequences", EditCommand.PASTE,
1786 seqs, 0, viewport.getAlignment().getWidth(),
1787 viewport.getAlignment()));
1789 viewport.setEndSeq(viewport.getAlignment().getHeight());
1790 viewport.getAlignment().getWidth();
1791 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1796 protected void cut_actionPerformed()
1798 copy_actionPerformed();
1799 delete_actionPerformed();
1802 protected void delete_actionPerformed()
1805 SequenceGroup sg = viewport.getSelectionGroup();
1811 Vector seqs = new Vector();
1813 for (int i = 0; i < sg.getSize(); i++)
1815 seq = sg.getSequenceAt(i);
1816 seqs.addElement(seq);
1819 // If the cut affects all sequences, remove highlighted columns
1820 if (sg.getSize() == viewport.getAlignment().getHeight())
1822 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1823 sg.getEndRes() + 1);
1826 SequenceI[] cut = new SequenceI[seqs.size()];
1827 for (int i = 0; i < seqs.size(); i++)
1829 cut[i] = (SequenceI) seqs.elementAt(i);
1833 * //ADD HISTORY ITEM
1835 addHistoryItem(new EditCommand("Cut Sequences", EditCommand.CUT, cut,
1836 sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1837 viewport.getAlignment()));
1839 viewport.setSelectionGroup(null);
1840 viewport.getAlignment().deleteGroup(sg);
1842 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1845 if (viewport.getAlignment().getHeight() < 1)
1847 this.setVisible(false);
1849 viewport.sendSelection();
1853 * group consensus toggled
1856 protected void showGroupConsensus_actionPerformed()
1858 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1859 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1864 * group conservation toggled.
1866 protected void showGroupConservation_actionPerformed()
1868 viewport.setShowGroupConservation(showGroupConservation.getState());
1869 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1876 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1877 * .event.ActionEvent)
1879 protected void showConsensusHistogram_actionPerformed()
1881 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1882 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1889 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1890 * .event.ActionEvent)
1892 protected void showSequenceLogo_actionPerformed()
1894 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1895 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1898 protected void normSequenceLogo_actionPerformed()
1900 showSequenceLogo.setState(true);
1901 viewport.setShowSequenceLogo(true);
1902 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1903 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1906 protected void applyAutoAnnotationSettings_actionPerformed()
1908 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1911 protected void makeGrpsFromSelection_actionPerformed()
1913 if (avc.makeGroupsFromSelection()) {
1914 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1915 alignPanel.updateAnnotation();
1916 alignPanel.paintAlignment(true);
1920 protected void createGroup_actionPerformed()
1924 protected void unGroup_actionPerformed()
1928 alignPanel.alignmentChanged();
1931 protected void deleteGroups_actionPerformed()
1933 if (avc.deleteGroups())
1935 alignPanel.alignmentChanged();
1939 public void selectAllSequenceMenuItem_actionPerformed()
1941 SequenceGroup sg = new SequenceGroup();
1942 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1944 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
1946 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
1947 viewport.setSelectionGroup(sg);
1948 alignPanel.paintAlignment(true);
1949 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1950 viewport.sendSelection();
1953 public void deselectAllSequenceMenuItem_actionPerformed()
1955 if (viewport.cursorMode)
1957 alignPanel.seqPanel.keyboardNo1 = null;
1958 alignPanel.seqPanel.keyboardNo2 = null;
1960 viewport.setSelectionGroup(null);
1961 viewport.getColumnSelection().clear();
1962 viewport.setSelectionGroup(null);
1963 alignPanel.idPanel.idCanvas.searchResults = null;
1964 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
1965 alignPanel.paintAlignment(true);
1966 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1967 viewport.sendSelection();
1970 public void invertSequenceMenuItem_actionPerformed()
1972 SequenceGroup sg = viewport.getSelectionGroup();
1973 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
1975 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
1978 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1979 viewport.sendSelection();
1982 public void invertColSel_actionPerformed()
1984 viewport.invertColumnSelection();
1985 alignPanel.paintAlignment(true);
1986 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
1987 viewport.sendSelection();
1990 void trimAlignment(boolean trimLeft)
1992 ColumnSelection colSel = viewport.getColumnSelection();
1995 if (colSel.size() > 0)
1999 column = colSel.getMin();
2003 column = colSel.getMax();
2007 if (viewport.getSelectionGroup() != null)
2009 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2010 viewport.getHiddenRepSequences());
2014 seqs = viewport.getAlignment().getSequencesArray();
2017 TrimRegionCommand trimRegion;
2020 trimRegion = new TrimRegionCommand("Remove Left",
2021 TrimRegionCommand.TRIM_LEFT, seqs, column,
2022 viewport.getAlignment(), viewport.getColumnSelection(),
2023 viewport.getSelectionGroup());
2024 viewport.setStartRes(0);
2028 trimRegion = new TrimRegionCommand("Remove Right",
2029 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2030 viewport.getAlignment(), viewport.getColumnSelection(),
2031 viewport.getSelectionGroup());
2034 statusBar.setText(MessageManager.formatMessage("label.removed_columns", new String[]{Integer.valueOf(trimRegion.getSize()).toString()}));
2035 addHistoryItem(trimRegion);
2037 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2039 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2040 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2042 viewport.getAlignment().deleteGroup(sg);
2046 viewport.firePropertyChange("alignment", null, viewport
2047 .getAlignment().getSequences());
2051 public void removeGappedColumnMenuItem_actionPerformed()
2053 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2056 if (viewport.getSelectionGroup() != null)
2058 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2059 viewport.getHiddenRepSequences());
2060 start = viewport.getSelectionGroup().getStartRes();
2061 end = viewport.getSelectionGroup().getEndRes();
2065 seqs = viewport.getAlignment().getSequencesArray();
2068 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2069 "Remove Gapped Columns", seqs, start, end,
2070 viewport.getAlignment());
2072 addHistoryItem(removeGapCols);
2074 statusBar.setText(MessageManager.formatMessage("label.removed_empty_columns", new String[]{Integer.valueOf(removeGapCols.getSize()).toString()}));
2076 // This is to maintain viewport position on first residue
2077 // of first sequence
2078 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2079 int startRes = seq.findPosition(viewport.startRes);
2080 // ShiftList shifts;
2081 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2082 // edit.alColumnChanges=shifts.getInverse();
2083 // if (viewport.hasHiddenColumns)
2084 // viewport.getColumnSelection().compensateForEdits(shifts);
2085 viewport.setStartRes(seq.findIndex(startRes) - 1);
2086 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2091 public void removeAllGapsMenuItem_actionPerformed()
2093 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2096 if (viewport.getSelectionGroup() != null)
2098 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2099 viewport.getHiddenRepSequences());
2100 start = viewport.getSelectionGroup().getStartRes();
2101 end = viewport.getSelectionGroup().getEndRes();
2105 seqs = viewport.getAlignment().getSequencesArray();
2108 // This is to maintain viewport position on first residue
2109 // of first sequence
2110 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2111 int startRes = seq.findPosition(viewport.startRes);
2113 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2114 viewport.getAlignment()));
2116 viewport.setStartRes(seq.findIndex(startRes) - 1);
2118 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2123 public void findMenuItem_actionPerformed()
2125 new Finder(alignPanel);
2129 * create a new view derived from the current view
2132 * @return frame for the new view
2134 public AlignFrame newView(String viewtitle)
2137 if (viewport.hasHiddenRows())
2139 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2140 .getFullAlignment().getSequencesArray());
2144 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2147 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2149 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2151 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2153 newal.addAnnotation(viewport.getAlignment()
2154 .getAlignmentAnnotation()[i]);
2159 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2161 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2162 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2163 PaintRefresher.Register(newaf.alignPanel,
2164 newaf.alignPanel.av.getSequenceSetId());
2166 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2167 newaf.alignPanel.av.getSequenceSetId());
2168 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2169 newaf.alignPanel.av.getSequenceSetId());
2171 Vector comps = (Vector) PaintRefresher.components.get(viewport
2172 .getSequenceSetId());
2174 for (int i = 0; i < comps.size(); i++)
2176 if (comps.elementAt(i) instanceof AlignmentPanel)
2182 String title = new String(this.getTitle());
2183 if (viewtitle != null)
2185 title = viewtitle + " ( " + title + ")";
2189 if (title.indexOf("(View") > -1)
2191 title = title.substring(0, title.indexOf("(View"));
2193 title += "(View " + viewSize + ")";
2196 newaf.setTitle(title.toString());
2198 newaf.viewport.historyList = viewport.historyList;
2199 newaf.viewport.redoList = viewport.redoList;
2205 * @return list of feature groups on the view
2207 public String[] getFeatureGroups()
2209 FeatureRenderer fr = null;
2210 if (alignPanel != null
2211 && (fr = alignPanel.getFeatureRenderer()) != null)
2213 return fr.getGroups();
2219 * get sequence feature groups that are hidden or shown
2225 public String[] getFeatureGroupsOfState(boolean visible)
2227 FeatureRenderer fr = null;
2228 if (alignPanel != null
2229 && (fr = alignPanel.getFeatureRenderer()) != null)
2231 return fr.getGroups(visible);
2237 * Change the display state for the given feature groups
2240 * list of group strings
2242 * visible or invisible
2244 public void setFeatureGroupState(String[] groups, boolean state)
2246 FeatureRenderer fr = null;
2247 this.sequenceFeatures.setState(true);
2248 viewport.showSequenceFeatures(true);
2249 if (alignPanel != null
2250 && (fr = alignPanel.getFeatureRenderer()) != null)
2252 fr.setGroupState(groups, state);
2253 alignPanel.seqPanel.seqCanvas.repaint();
2254 if (alignPanel.overviewPanel != null)
2256 alignPanel.overviewPanel.updateOverviewImage();
2261 public void seqLimits_itemStateChanged()
2263 viewport.setShowJVSuffix(seqLimits.getState());
2264 alignPanel.fontChanged();
2265 alignPanel.paintAlignment(true);
2268 protected void colourTextMenuItem_actionPerformed()
2270 viewport.setColourText(colourTextMenuItem.getState());
2271 alignPanel.paintAlignment(true);
2274 protected void displayNonconservedMenuItem_actionPerformed()
2276 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2277 alignPanel.paintAlignment(true);
2280 protected void wrapMenuItem_actionPerformed()
2282 viewport.setWrapAlignment(wrapMenuItem.getState());
2283 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2284 scaleAbove.setEnabled(wrapMenuItem.getState());
2285 scaleLeft.setEnabled(wrapMenuItem.getState());
2286 scaleRight.setEnabled(wrapMenuItem.getState());
2287 alignPanel.paintAlignment(true);
2290 public void overviewMenuItem_actionPerformed()
2292 if (alignPanel.overviewPanel != null)
2297 Frame frame = new Frame();
2298 OverviewPanel overview = new OverviewPanel(alignPanel);
2299 frame.add(overview);
2300 // +50 must allow for applet frame window
2301 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage("label.overview_params", new String[]{this.getTitle()}),
2302 overview.getPreferredSize().width,
2303 overview.getPreferredSize().height + 50);
2306 final AlignmentPanel ap = alignPanel;
2307 frame.addWindowListener(new WindowAdapter()
2310 public void windowClosing(WindowEvent e)
2314 ap.setOverviewPanel(null);
2319 alignPanel.setOverviewPanel(overview);
2323 void changeColour(ColourSchemeI cs)
2329 if (viewport.getAbovePIDThreshold())
2331 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel, cs,
2335 if (viewport.getConservationSelected())
2337 cs.setConservationApplied(true);
2338 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2343 cs.setConservationApplied(false);
2346 viewport.setGlobalColourScheme(cs);
2348 if (alignPanel.getOverviewPanel() != null)
2350 alignPanel.getOverviewPanel().updateOverviewImage();
2353 jalview.structure.StructureSelectionManager
2354 .getStructureSelectionManager(viewport.applet)
2355 .sequenceColoursChanged(alignPanel);
2357 alignPanel.paintAlignment(true);
2360 protected void modifyPID_actionPerformed()
2362 if (viewport.getAbovePIDThreshold()
2363 && viewport.getGlobalColourScheme() != null)
2365 SliderPanel.setPIDSliderSource(alignPanel,
2366 viewport.getGlobalColourScheme(), "Background");
2367 SliderPanel.showPIDSlider();
2371 protected void modifyConservation_actionPerformed()
2373 if (viewport.getConservationSelected()
2374 && viewport.getGlobalColourScheme() != null)
2376 SliderPanel.setConservationSlider(alignPanel,
2377 viewport.getGlobalColourScheme(), "Background");
2378 SliderPanel.showConservationSlider();
2382 protected void conservationMenuItem_actionPerformed()
2384 viewport.setConservationSelected(conservationMenuItem.getState());
2386 viewport.setAbovePIDThreshold(false);
2387 abovePIDThreshold.setState(false);
2389 changeColour(viewport.getGlobalColourScheme());
2391 modifyConservation_actionPerformed();
2394 public void abovePIDThreshold_actionPerformed()
2396 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2398 conservationMenuItem.setState(false);
2399 viewport.setConservationSelected(false);
2401 changeColour(viewport.getGlobalColourScheme());
2403 modifyPID_actionPerformed();
2406 public void sortPairwiseMenuItem_actionPerformed()
2408 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2409 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2410 .getAlignment().getSequenceAt(0), null);
2412 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2413 viewport.getAlignment()));
2414 alignPanel.paintAlignment(true);
2417 public void sortIDMenuItem_actionPerformed()
2419 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2420 AlignmentSorter.sortByID(viewport.getAlignment());
2421 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2422 viewport.getAlignment()));
2423 alignPanel.paintAlignment(true);
2426 public void sortLengthMenuItem_actionPerformed()
2428 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2429 AlignmentSorter.sortByLength(viewport.getAlignment());
2430 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2431 viewport.getAlignment()));
2432 alignPanel.paintAlignment(true);
2435 public void sortGroupMenuItem_actionPerformed()
2437 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2438 AlignmentSorter.sortByGroup(viewport.getAlignment());
2439 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2440 viewport.getAlignment()));
2441 alignPanel.paintAlignment(true);
2445 public void removeRedundancyMenuItem_actionPerformed()
2447 new RedundancyPanel(alignPanel);
2450 public void pairwiseAlignmentMenuItem_actionPerformed()
2452 if (viewport.getSelectionGroup() != null
2453 && viewport.getSelectionGroup().getSize() > 1)
2455 Frame frame = new Frame();
2456 frame.add(new PairwiseAlignPanel(alignPanel));
2457 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("action.pairwise_alignment"), 600,
2462 public void PCAMenuItem_actionPerformed()
2464 // are the sequences aligned?
2465 if (!viewport.getAlignment().isAligned(false))
2468 int Width = viewport.getAlignment().getWidth();
2470 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2472 current = viewport.getAlignment().getSequenceAt(i);
2474 if (current.getLength() < Width)
2476 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2479 alignPanel.paintAlignment(true);
2482 if ((viewport.getSelectionGroup() != null
2483 && viewport.getSelectionGroup().getSize() < 4 && viewport
2484 .getSelectionGroup().getSize() > 0)
2485 || viewport.getAlignment().getHeight() < 4)
2492 new PCAPanel(viewport);
2493 } catch (java.lang.OutOfMemoryError ex)
2499 public void averageDistanceTreeMenuItem_actionPerformed()
2501 NewTreePanel("AV", "PID", "Average distance tree using PID");
2504 public void neighbourTreeMenuItem_actionPerformed()
2506 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2509 protected void njTreeBlosumMenuItem_actionPerformed()
2511 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2514 protected void avTreeBlosumMenuItem_actionPerformed()
2516 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2519 void NewTreePanel(String type, String pwType, String title)
2521 // are the sequences aligned?
2522 if (!viewport.getAlignment().isAligned(false))
2525 int Width = viewport.getAlignment().getWidth();
2527 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2529 current = viewport.getAlignment().getSequenceAt(i);
2531 if (current.getLength() < Width)
2533 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2536 alignPanel.paintAlignment(true);
2540 if ((viewport.getSelectionGroup() != null && viewport
2541 .getSelectionGroup().getSize() > 1)
2542 || (viewport.getAlignment().getHeight() > 1))
2544 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2546 addTreeMenuItem(tp, title);
2548 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2552 void loadTree_actionPerformed()
2554 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2555 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2556 cap.setTreeImport();
2557 Frame frame = new Frame();
2559 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.paste_newick_file"), 400, 300);
2562 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2564 TreePanel tp = new TreePanel(alignPanel, treeFile, MessageManager.getString("label.load_tree_from_file"), tree);
2565 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2566 addTreeMenuItem(tp, treeFile);
2570 * sort the alignment using the given treePanel
2573 * tree used to sort view
2575 * string used for undo event name
2577 public void sortByTree(TreePanel treePanel, String title)
2579 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2581 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2582 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2583 // HistoryItem.SORT));
2584 addHistoryItem(new OrderCommand(MessageManager.formatMessage("label.order_by_params", new String[]{title}), oldOrder,
2585 viewport.getAlignment()));
2586 alignPanel.paintAlignment(true);
2590 * Do any automatic reordering of the alignment and add the necessary bits to
2591 * the menu structure for the new tree
2596 protected void addTreeMenuItem(final TreePanel treePanel,
2599 final MenuItem item = new MenuItem(title);
2600 sortByTreeMenu.add(item);
2601 item.addActionListener(new java.awt.event.ActionListener()
2604 public void actionPerformed(ActionEvent evt)
2606 sortByTree(treePanel, title); // treePanel.getTitle());
2610 treePanel.addWindowListener(new WindowAdapter()
2613 public void windowOpened(WindowEvent e)
2615 if (viewport.sortByTree)
2617 sortByTree(treePanel, title);
2619 super.windowOpened(e);
2623 public void windowClosing(WindowEvent e)
2625 sortByTreeMenu.remove(item);
2630 public boolean sortBy(AlignmentOrder alorder, String undoname)
2632 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2633 if (viewport.applet.debug)
2635 System.err.println("Sorting " + alorder.getOrder().size()
2636 + " in alignment '" + getTitle() + "'");
2638 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2639 if (undoname != null)
2641 addHistoryItem(new OrderCommand(undoname, oldOrder,
2642 viewport.getAlignment()));
2644 alignPanel.paintAlignment(true);
2648 protected void documentation_actionPerformed()
2650 alignPanel.av.applet.openJalviewHelpUrl();
2653 protected void about_actionPerformed()
2656 class AboutPanel extends Canvas
2662 public AboutPanel(String version, String builddate)
2664 this.version = version;
2665 this.builddate = builddate;
2669 public void paint(Graphics g)
2671 g.setColor(Color.white);
2672 g.fillRect(0, 0, getSize().width, getSize().height);
2673 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2674 FontMetrics fm = g.getFontMetrics();
2675 int fh = fm.getHeight();
2677 g.setColor(Color.black);
2678 // TODO: update this text for each release or centrally store it for
2679 // lite and application
2680 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2681 g.drawString(MessageManager.formatMessage("label.jalviewLite_release", new String[]{version}), x, y += fh);
2682 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2683 g.drawString(MessageManager.formatMessage("label.jaview_build_date", new String[]{builddate}), x, y += fh);
2684 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2686 MessageManager.getString("label.jalview_authors_1"),
2688 g.drawString(MessageManager.getString("label.jalview_authors_2"), x + 50, y += fh+8);
2690 MessageManager.getString("label.jalview_dev_managers"),
2693 MessageManager.getString("label.jalview_distribution_lists"),
2695 g.drawString(MessageManager.getString("label.jalview_please_cite"), x, y += fh + 8);
2697 MessageManager.getString("label.jalview_cite_1_authors"),
2700 MessageManager.getString("label.jalview_cite_1_title"),
2702 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2707 Frame frame = new Frame();
2708 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2710 jalview.bin.JalviewLite.addFrame(frame, MessageManager.getString("label.jalview"), 580, 220);
2714 public void showURL(String url, String target)
2716 if (viewport.applet == null)
2718 System.out.println("Not running as applet - no browser available.");
2722 viewport.applet.showURL(url, target);
2726 // ////////////////////////////////////////////////////////////////////////////////
2727 // JBuilder Graphics here
2729 MenuBar alignFrameMenuBar = new MenuBar();
2731 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2733 MenuItem loadApplication = new MenuItem(MessageManager.getString("label.view_full_application"));
2735 MenuItem loadTree = new MenuItem(MessageManager.getString("label.load_associated_tree"));
2737 MenuItem loadAnnotations = new MenuItem(MessageManager.getString("label.load_features_annotations"));
2739 MenuItem outputFeatures = new MenuItem(MessageManager.getString("label.export_features"));
2741 MenuItem outputAnnotations = new MenuItem(MessageManager.getString("label.export_annotations"));
2743 MenuItem closeMenuItem = new MenuItem(MessageManager.getString("action.close"));
2745 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2747 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2749 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2751 Menu calculateMenu = new Menu(MessageManager.getString("action.calculate"));
2753 MenuItem selectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.select_all"));
2755 MenuItem deselectAllSequenceMenuItem = new MenuItem(MessageManager.getString("action.deselect_all"));
2757 MenuItem invertSequenceMenuItem = new MenuItem(MessageManager.getString("action.invert_selection"));
2759 MenuItem remove2LeftMenuItem = new MenuItem();
2761 MenuItem remove2RightMenuItem = new MenuItem();
2763 MenuItem removeGappedColumnMenuItem = new MenuItem();
2765 MenuItem removeAllGapsMenuItem = new MenuItem();
2767 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2769 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2771 MenuItem sortPairwiseMenuItem = new MenuItem();
2773 MenuItem sortIDMenuItem = new MenuItem();
2775 MenuItem sortLengthMenuItem = new MenuItem();
2777 MenuItem sortGroupMenuItem = new MenuItem();
2779 MenuItem removeRedundancyMenuItem = new MenuItem();
2781 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2783 MenuItem PCAMenuItem = new MenuItem();
2785 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2787 MenuItem neighbourTreeMenuItem = new MenuItem();
2789 BorderLayout borderLayout1 = new BorderLayout();
2791 public Label statusBar = new Label();
2793 Menu outputTextboxMenu = new Menu();
2795 MenuItem clustalColour = new MenuItem();
2797 MenuItem zappoColour = new MenuItem();
2799 MenuItem taylorColour = new MenuItem();
2801 MenuItem hydrophobicityColour = new MenuItem();
2803 MenuItem helixColour = new MenuItem();
2805 MenuItem strandColour = new MenuItem();
2807 MenuItem turnColour = new MenuItem();
2809 MenuItem buriedColour = new MenuItem();
2811 MenuItem purinePyrimidineColour = new MenuItem();
2813 MenuItem RNAHelixColour = new MenuItem();
2815 MenuItem userDefinedColour = new MenuItem();
2817 MenuItem PIDColour = new MenuItem();
2819 MenuItem BLOSUM62Colour = new MenuItem();
2821 MenuItem tcoffeeColour = new MenuItem();
2823 MenuItem njTreeBlosumMenuItem = new MenuItem();
2825 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2827 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2829 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2831 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2833 MenuItem alProperties = new MenuItem(MessageManager.getString("label.alignment_props"));
2835 MenuItem overviewMenuItem = new MenuItem();
2837 MenuItem undoMenuItem = new MenuItem();
2839 MenuItem redoMenuItem = new MenuItem();
2841 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2843 MenuItem noColourmenuItem = new MenuItem();
2845 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2847 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2849 MenuItem findMenuItem = new MenuItem();
2851 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2853 MenuItem nucleotideColour = new MenuItem();
2855 MenuItem deleteGroups = new MenuItem();
2857 MenuItem grpsFromSelection = new MenuItem();
2859 MenuItem createGroup = new MenuItem();
2861 MenuItem unGroup = new MenuItem();
2863 MenuItem delete = new MenuItem();
2865 MenuItem copy = new MenuItem();
2867 MenuItem cut = new MenuItem();
2869 Menu pasteMenu = new Menu();
2871 MenuItem pasteNew = new MenuItem();
2873 MenuItem pasteThis = new MenuItem();
2875 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2877 MenuItem font = new MenuItem();
2879 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2881 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2883 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2885 MenuItem modifyPID = new MenuItem();
2887 MenuItem modifyConservation = new MenuItem();
2889 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2890 "Autocalculate Consensus", true);
2892 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2893 "Sort Alignment With New Tree", true);
2895 Menu sortByTreeMenu = new Menu();
2897 Menu sort = new Menu();
2899 Menu calculate = new Menu();
2901 MenuItem inputText = new MenuItem();
2903 Menu helpMenu = new Menu();
2905 MenuItem documentation = new MenuItem();
2907 MenuItem about = new MenuItem();
2909 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
2911 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
2913 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
2915 Menu autoAnnMenu = new Menu();
2917 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
2919 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
2921 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
2923 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
2925 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
2927 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
2929 private void jbInit() throws Exception
2932 setMenuBar(alignFrameMenuBar);
2936 // dynamically fill save as menu with available formats
2937 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
2940 item = new MenuItem(
2941 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
2943 item.addActionListener(new java.awt.event.ActionListener()
2946 public void actionPerformed(ActionEvent e)
2948 outputText_actionPerformed(e);
2952 outputTextboxMenu.add(item);
2954 closeMenuItem.addActionListener(this);
2955 loadApplication.addActionListener(this);
2957 loadTree.addActionListener(this);
2958 loadAnnotations.addActionListener(this);
2959 outputFeatures.addActionListener(this);
2960 outputAnnotations.addActionListener(this);
2961 selectAllSequenceMenuItem.addActionListener(this);
2962 deselectAllSequenceMenuItem.addActionListener(this);
2963 invertSequenceMenuItem.addActionListener(this);
2964 remove2LeftMenuItem.setLabel(MessageManager.getString("action.remove_left"));
2965 remove2LeftMenuItem.addActionListener(this);
2966 remove2RightMenuItem.setLabel(MessageManager.getString("action.remove_right"));
2967 remove2RightMenuItem.addActionListener(this);
2968 removeGappedColumnMenuItem.setLabel(MessageManager.getString("action.remove_empty_columns"));
2969 removeGappedColumnMenuItem.addActionListener(this);
2970 removeAllGapsMenuItem.setLabel(MessageManager.getString("action.remove_all_gaps"));
2971 removeAllGapsMenuItem.addActionListener(this);
2972 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
2973 viewBoxesMenuItem.setState(true);
2974 viewBoxesMenuItem.addItemListener(this);
2975 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
2976 viewTextMenuItem.setState(true);
2977 viewTextMenuItem.addItemListener(this);
2978 sortPairwiseMenuItem.setLabel(MessageManager.getString("action.by_pairwise_id"));
2979 sortPairwiseMenuItem.addActionListener(this);
2980 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
2981 sortIDMenuItem.addActionListener(this);
2982 sortLengthMenuItem.setLabel(MessageManager.getString("action.by_length"));
2983 sortLengthMenuItem.addActionListener(this);
2984 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
2985 sortGroupMenuItem.addActionListener(this);
2986 removeRedundancyMenuItem.setLabel(MessageManager.getString("action.remove_redundancy"));
2987 removeRedundancyMenuItem.addActionListener(this);
2988 pairwiseAlignmentMenuItem.setLabel(MessageManager.getString("action.pairwise_alignment"));
2989 pairwiseAlignmentMenuItem.addActionListener(this);
2990 PCAMenuItem.setLabel(MessageManager.getString("label.principal_component_analysis"));
2991 PCAMenuItem.addActionListener(this);
2992 averageDistanceTreeMenuItem
2993 .setLabel(MessageManager.getString("label.average_distance_identity"));
2994 averageDistanceTreeMenuItem.addActionListener(this);
2995 neighbourTreeMenuItem.setLabel(MessageManager.getString("label.neighbour_joining_identity"));
2996 neighbourTreeMenuItem.addActionListener(this);
2997 statusBar.setBackground(Color.white);
2998 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
2999 statusBar.setText(MessageManager.getString("label.status_bar"));
3000 outputTextboxMenu.setLabel(MessageManager.getString("label.out_to_textbox"));
3001 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3003 clustalColour.addActionListener(this);
3004 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3005 zappoColour.addActionListener(this);
3006 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3007 taylorColour.addActionListener(this);
3008 hydrophobicityColour.setLabel(MessageManager.getString("label.hydrophobicity"));
3009 hydrophobicityColour.addActionListener(this);
3010 helixColour.setLabel(MessageManager.getString("label.helix_propensity"));
3011 helixColour.addActionListener(this);
3012 strandColour.setLabel(MessageManager.getString("label.strand_propensity"));
3013 strandColour.addActionListener(this);
3014 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3015 turnColour.addActionListener(this);
3016 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3017 buriedColour.addActionListener(this);
3018 purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
3019 purinePyrimidineColour.addActionListener(this);
3020 RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
3021 RNAHelixColour.addActionListener(this);
3022 userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
3023 userDefinedColour.addActionListener(this);
3024 PIDColour.setLabel(MessageManager.getString("label.percentage_identity"));
3025 PIDColour.addActionListener(this);
3026 BLOSUM62Colour.setLabel(MessageManager.getString("label.blosum62_score"));
3027 BLOSUM62Colour.addActionListener(this);
3028 tcoffeeColour.setLabel(MessageManager.getString("label.tcoffee_scores"));
3029 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3031 tcoffeeColour.addActionListener(this);
3032 avDistanceTreeBlosumMenuItem
3033 .setLabel(MessageManager.getString("label.average_distance_bloslum62"));
3034 avDistanceTreeBlosumMenuItem.addActionListener(this);
3035 njTreeBlosumMenuItem.setLabel(MessageManager.getString("label.neighbour_blosum62"));
3036 njTreeBlosumMenuItem.addActionListener(this);
3037 annotationPanelMenuItem.setLabel(MessageManager.getString("label.show_annotations"));
3038 annotationPanelMenuItem.addItemListener(this);
3039 colourTextMenuItem.setLabel(MessageManager.getString("label.colour_text"));
3040 colourTextMenuItem.addItemListener(this);
3041 displayNonconservedMenuItem.setLabel(MessageManager.getString("label.show_non_conversed"));
3042 displayNonconservedMenuItem.addItemListener(this);
3043 alProperties.addActionListener(this);
3044 overviewMenuItem.setLabel(MessageManager.getString("label.overview_window"));
3045 overviewMenuItem.addActionListener(this);
3046 undoMenuItem.setEnabled(false);
3047 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3048 undoMenuItem.addActionListener(this);
3049 redoMenuItem.setEnabled(false);
3050 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3051 redoMenuItem.addActionListener(this);
3052 conservationMenuItem.setLabel(MessageManager.getString("action.by_conservation"));
3053 conservationMenuItem.addItemListener(this);
3054 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3055 noColourmenuItem.addActionListener(this);
3056 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3057 wrapMenuItem.addItemListener(this);
3058 renderGapsMenuItem.setLabel(MessageManager.getString("action.show_gaps"));
3059 renderGapsMenuItem.setState(true);
3060 renderGapsMenuItem.addItemListener(this);
3061 findMenuItem.setLabel(MessageManager.getString("action.find"));
3062 findMenuItem.addActionListener(this);
3063 abovePIDThreshold.setLabel(MessageManager.getString("label.above_identity_threshold"));
3064 abovePIDThreshold.addItemListener(this);
3065 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3066 nucleotideColour.addActionListener(this);
3067 deleteGroups.setLabel(MessageManager.getString("action.undefine_groups"));
3068 deleteGroups.addActionListener(this);
3069 grpsFromSelection.setLabel(MessageManager.getString("action.make_groups_selection"));
3070 grpsFromSelection.addActionListener(this);
3071 createGroup.setLabel(MessageManager.getString("action.create_group"));
3072 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3073 copy.setLabel(MessageManager.getString("action.copy"));
3074 copy.addActionListener(this);
3075 cut.setLabel(MessageManager.getString("action.cut"));
3076 cut.addActionListener(this);
3077 delete.setLabel(MessageManager.getString("action.delete"));
3078 delete.addActionListener(this);
3079 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3080 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3081 pasteNew.addActionListener(this);
3082 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3083 pasteThis.addActionListener(this);
3084 applyToAllGroups.setLabel(MessageManager.getString("label.apply_colour_to_all_groups"));
3085 applyToAllGroups.setState(true);
3086 applyToAllGroups.addItemListener(this);
3087 font.setLabel(MessageManager.getString("action.font"));
3088 font.addActionListener(this);
3089 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3090 scaleAbove.setState(true);
3091 scaleAbove.setEnabled(false);
3092 scaleAbove.addItemListener(this);
3093 scaleLeft.setEnabled(false);
3094 scaleLeft.setState(true);
3095 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3096 scaleLeft.addItemListener(this);
3097 scaleRight.setEnabled(false);
3098 scaleRight.setState(true);
3099 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3100 scaleRight.addItemListener(this);
3101 modifyPID.setLabel(MessageManager.getString("label.modify_identity_thereshold"));
3102 modifyPID.addActionListener(this);
3103 modifyConservation.setLabel(MessageManager.getString("label.modify_conservation_thereshold"));
3104 modifyConservation.addActionListener(this);
3105 sortByTreeMenu.setLabel(MessageManager.getString("action.by_tree_order"));
3106 sort.setLabel(MessageManager.getString("action.sort"));
3107 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3108 autoCalculate.addItemListener(this);
3109 sortByTree.addItemListener(this);
3110 inputText.setLabel(MessageManager.getString("label.input_from_textbox"));
3111 inputText.addActionListener(this);
3112 centreColumnLabelFlag.setLabel(MessageManager.getString("label.centre_column_labels"));
3113 centreColumnLabelFlag.addItemListener(this);
3114 followMouseOverFlag.setLabel(MessageManager.getString("label.automatic_scrolling"));
3115 followMouseOverFlag.addItemListener(this);
3116 helpMenu.setLabel(MessageManager.getString("action.help"));
3117 documentation.setLabel(MessageManager.getString("label.documentation"));
3118 documentation.addActionListener(this);
3120 about.setLabel(MessageManager.getString("label.about"));
3121 about.addActionListener(this);
3122 seqLimits.setState(true);
3123 seqLimits.setLabel(MessageManager.getString("label.show_sequence_limits"));
3124 seqLimits.addItemListener(this);
3125 featureSettings.setLabel(MessageManager.getString("label.feature_settings"));
3126 featureSettings.addActionListener(this);
3127 sequenceFeatures.setLabel(MessageManager.getString("label.sequence_features"));
3128 sequenceFeatures.addItemListener(this);
3129 sequenceFeatures.setState(false);
3130 annotationColour.setLabel(MessageManager.getString("action.by_annotation"));
3131 annotationColour.addActionListener(this);
3132 invertSequenceMenuItem.setLabel(MessageManager.getString("action.invert_sequence_selection"));
3133 invertColSel.setLabel(MessageManager.getString("action.invert_column_selection"));
3134 menu1.setLabel(MessageManager.getString("action.show"));
3135 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3136 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3137 menu2.setLabel(MessageManager.getString("action.hide"));
3138 hideColumns.setLabel(MessageManager.getString("label.selected_columns"));
3139 hideSequences.setLabel(MessageManager.getString("label.selected_sequences"));
3140 hideAllButSelection.setLabel(MessageManager.getString("label.all_but_selected_region"));
3141 hideAllSelection.setLabel(MessageManager.getString("label.selected_region"));
3142 showAllHidden.setLabel(MessageManager.getString("label.all_sequences_columns"));
3143 showGroupConsensus.setLabel(MessageManager.getString("label.group_consensus"));
3144 showGroupConservation.setLabel(MessageManager.getString("label.group_conservation"));
3145 showConsensusHistogram.setLabel(MessageManager.getString("label.show_consensus_histogram"));
3146 showSequenceLogo.setLabel(MessageManager.getString("label.show_consensus_logo"));
3147 normSequenceLogo.setLabel(MessageManager.getString("label.norm_consensus_logo"));
3148 applyAutoAnnotationSettings.setLabel(MessageManager.getString("label.apply_all_groups"));
3149 applyAutoAnnotationSettings.setState(true);
3150 autoAnnMenu.setLabel(MessageManager.getString("label.autocalculated_annotation"));
3152 invertColSel.addActionListener(this);
3153 showColumns.addActionListener(this);
3154 showSeqs.addActionListener(this);
3155 hideColumns.addActionListener(this);
3156 hideSequences.addActionListener(this);
3157 hideAllButSelection.addActionListener(this);
3158 hideAllSelection.addActionListener(this);
3159 showAllHidden.addActionListener(this);
3160 showGroupConsensus.addItemListener(this);
3161 showGroupConservation.addItemListener(this);
3162 showConsensusHistogram.addItemListener(this);
3163 showSequenceLogo.addItemListener(this);
3164 normSequenceLogo.addItemListener(this);
3166 applyAutoAnnotationSettings.addItemListener(this);
3167 formatMenu.setLabel(MessageManager.getString("action.format"));
3168 selectMenu.setLabel(MessageManager.getString("action.select"));
3169 newView.setLabel(MessageManager.getString("action.new_view"));
3170 newView.addActionListener(this);
3171 alignFrameMenuBar.add(fileMenu);
3172 alignFrameMenuBar.add(editMenu);
3173 alignFrameMenuBar.add(selectMenu);
3174 alignFrameMenuBar.add(viewMenu);
3175 alignFrameMenuBar.add(formatMenu);
3176 alignFrameMenuBar.add(colourMenu);
3177 alignFrameMenuBar.add(calculateMenu);
3178 alignFrameMenuBar.add(helpMenu);
3180 fileMenu.add(inputText);
3181 fileMenu.add(loadTree);
3182 fileMenu.add(loadAnnotations);
3184 fileMenu.addSeparator();
3185 fileMenu.add(outputTextboxMenu);
3186 fileMenu.add(outputFeatures);
3187 fileMenu.add(outputAnnotations);
3189 if (jalviewServletURL != null)
3191 fileMenu.add(loadApplication);
3194 fileMenu.addSeparator();
3195 fileMenu.add(closeMenuItem);
3197 editMenu.add(undoMenuItem);
3198 editMenu.add(redoMenuItem);
3201 editMenu.add(pasteMenu);
3202 editMenu.add(delete);
3203 editMenu.addSeparator();
3204 editMenu.add(remove2LeftMenuItem);
3205 editMenu.add(remove2RightMenuItem);
3206 editMenu.add(removeGappedColumnMenuItem);
3207 editMenu.add(removeAllGapsMenuItem);
3208 editMenu.add(removeRedundancyMenuItem);
3209 viewMenu.add(newView);
3210 viewMenu.addSeparator();
3211 viewMenu.add(menu1);
3212 viewMenu.add(menu2);
3213 viewMenu.addSeparator();
3214 viewMenu.add(followMouseOverFlag);
3215 viewMenu.add(annotationPanelMenuItem);
3216 autoAnnMenu.add(applyAutoAnnotationSettings);
3217 autoAnnMenu.add(showConsensusHistogram);
3218 autoAnnMenu.add(showSequenceLogo);
3219 autoAnnMenu.add(normSequenceLogo);
3220 autoAnnMenu.addSeparator();
3221 autoAnnMenu.add(showGroupConservation);
3222 autoAnnMenu.add(showGroupConsensus);
3223 viewMenu.add(autoAnnMenu);
3224 viewMenu.addSeparator();
3225 viewMenu.add(sequenceFeatures);
3226 viewMenu.add(featureSettings);
3227 viewMenu.addSeparator();
3228 viewMenu.add(alProperties);
3229 viewMenu.addSeparator();
3230 viewMenu.add(overviewMenuItem);
3231 colourMenu.add(applyToAllGroups);
3232 colourMenu.addSeparator();
3233 colourMenu.add(noColourmenuItem);
3234 colourMenu.add(clustalColour);
3235 colourMenu.add(BLOSUM62Colour);
3236 colourMenu.add(PIDColour);
3237 colourMenu.add(zappoColour);
3238 colourMenu.add(taylorColour);
3239 colourMenu.add(hydrophobicityColour);
3240 colourMenu.add(helixColour);
3241 colourMenu.add(strandColour);
3242 colourMenu.add(turnColour);
3243 colourMenu.add(buriedColour);
3244 colourMenu.add(nucleotideColour);
3245 colourMenu.add(purinePyrimidineColour);
3246 colourMenu.add(tcoffeeColour);
3247 colourMenu.add(userDefinedColour);
3248 colourMenu.addSeparator();
3249 colourMenu.add(conservationMenuItem);
3250 colourMenu.add(modifyConservation);
3251 colourMenu.add(abovePIDThreshold);
3252 colourMenu.add(modifyPID);
3253 colourMenu.add(annotationColour);
3254 colourMenu.add(RNAHelixColour);
3255 calculateMenu.add(sort);
3256 calculateMenu.add(calculate);
3257 calculateMenu.addSeparator();
3258 calculateMenu.add(pairwiseAlignmentMenuItem);
3259 calculateMenu.add(PCAMenuItem);
3260 calculateMenu.add(autoCalculate);
3261 calculateMenu.add(sortByTree);
3262 this.add(statusBar, BorderLayout.SOUTH);
3263 pasteMenu.add(pasteNew);
3264 pasteMenu.add(pasteThis);
3265 sort.add(sortIDMenuItem);
3266 sort.add(sortLengthMenuItem);
3267 sort.add(sortByTreeMenu);
3268 sort.add(sortGroupMenuItem);
3269 sort.add(sortPairwiseMenuItem);
3270 calculate.add(averageDistanceTreeMenuItem);
3271 calculate.add(neighbourTreeMenuItem);
3272 calculate.add(avDistanceTreeBlosumMenuItem);
3273 calculate.add(njTreeBlosumMenuItem);
3274 helpMenu.add(documentation);
3275 helpMenu.add(about);
3276 menu1.add(showColumns);
3277 menu1.add(showSeqs);
3278 menu1.add(showAllHidden);
3279 menu2.add(hideColumns);
3280 menu2.add(hideSequences);
3281 menu2.add(hideAllSelection);
3282 menu2.add(hideAllButSelection);
3283 formatMenu.add(font);
3284 formatMenu.add(seqLimits);
3285 formatMenu.add(wrapMenuItem);
3286 formatMenu.add(scaleAbove);
3287 formatMenu.add(scaleLeft);
3288 formatMenu.add(scaleRight);
3289 formatMenu.add(viewBoxesMenuItem);
3290 formatMenu.add(viewTextMenuItem);
3291 formatMenu.add(colourTextMenuItem);
3292 formatMenu.add(displayNonconservedMenuItem);
3293 formatMenu.add(renderGapsMenuItem);
3294 formatMenu.add(centreColumnLabelFlag);
3295 selectMenu.add(findMenuItem);
3296 selectMenu.addSeparator();
3297 selectMenu.add(selectAllSequenceMenuItem);
3298 selectMenu.add(deselectAllSequenceMenuItem);
3299 selectMenu.add(invertSequenceMenuItem);
3300 selectMenu.add(invertColSel);
3301 selectMenu.add(createGroup);
3302 selectMenu.add(unGroup);
3303 selectMenu.add(grpsFromSelection);
3304 selectMenu.add(deleteGroups);
3309 public void setStatus(String string) {
3310 statusBar.setText(string);
3313 MenuItem featureSettings = new MenuItem();
3315 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3317 MenuItem annotationColour = new MenuItem();
3319 MenuItem invertColSel = new MenuItem();
3321 Menu menu1 = new Menu();
3323 MenuItem showColumns = new MenuItem();
3325 MenuItem showSeqs = new MenuItem();
3327 Menu menu2 = new Menu();
3329 MenuItem hideColumns = new MenuItem();
3331 MenuItem hideSequences = new MenuItem();
3333 MenuItem hideAllButSelection = new MenuItem();
3335 MenuItem hideAllSelection = new MenuItem();
3337 MenuItem showAllHidden = new MenuItem();
3339 Menu formatMenu = new Menu();
3341 Menu selectMenu = new Menu();
3343 MenuItem newView = new MenuItem();
3346 * Attach the alignFrame panels after embedding menus, if necessary. This used
3347 * to be called setEmbedded, but is now creates the dropdown menus in a
3348 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3350 * @param reallyEmbedded
3351 * true to attach the view to the applet area on the page rather than
3354 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3359 // Explicly build the embedded menu panel for the on-page applet
3361 // view cannot be closed if its actually on the page
3362 fileMenu.remove(closeMenuItem);
3363 fileMenu.remove(3); // Remove Seperator
3364 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3365 Font.PLAIN, 10, false); // use our own fonts.
3366 // and actually add the components to the applet area
3367 viewport.applet.setLayout(new BorderLayout());
3368 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3369 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3370 alignPanel.setSize(viewport.applet.getSize().width,
3371 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3372 - statusBar.HEIGHT);
3373 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3374 final AlignFrame me = this;
3375 viewport.applet.addFocusListener(new FocusListener()
3379 public void focusLost(FocusEvent e)
3381 if (me.viewport.applet.currentAlignFrame == me)
3383 me.viewport.applet.currentAlignFrame = null;
3388 public void focusGained(FocusEvent e)
3390 me.viewport.applet.currentAlignFrame = me;
3393 viewport.applet.validate();
3398 // test and embed menu bar if necessary.
3400 if (embedMenuIfNeeded(alignPanel))
3402 // adjust for status bar height too
3403 alignPanel.setSize(getSize().width, getSize().height
3404 - statusBar.HEIGHT);
3406 add(statusBar, BorderLayout.SOUTH);
3407 add(alignPanel, BorderLayout.CENTER);
3408 // and register with the applet so it can pass external API calls to us
3409 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3415 * create a new binding between structures in an existing jmol viewer instance
3416 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3417 * this does not open a new Jmol window, or modify the display of the
3418 * structures in the original jmol window. Note This method doesn't work
3419 * without an additional javascript library to exchange messages between the
3420 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3423 * JmolViewer instance
3424 * @param sequenceIds
3425 * - sequence Ids to search for associations
3427 public SequenceStructureBinding addStructureViewInstance(
3428 Object jmolviewer, String[] sequenceIds)
3430 org.jmol.api.JmolViewer viewer = null;
3433 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3434 } catch (ClassCastException ex)
3436 System.err.println("Unsupported viewer object :"
3437 + jmolviewer.getClass());
3441 System.err.println("Can't use this object as a structure viewer:"
3442 + jmolviewer.getClass());
3445 SequenceI[] seqs = null;
3446 if (sequenceIds == null || sequenceIds.length == 0)
3448 seqs = viewport.getAlignment().getSequencesArray();
3452 Vector sqi = new Vector();
3453 AlignmentI al = viewport.getAlignment();
3454 for (int sid = 0; sid < sequenceIds.length; sid++)
3456 SequenceI sq = al.findName(sequenceIds[sid]);
3464 seqs = new SequenceI[sqi.size()];
3465 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3467 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3476 // TODO: search for a jmv that involves viewer
3478 { // create a new viewer/jalview binding.
3479 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3487 * bind a pdb file to a sequence in the current view
3490 * - sequenceId within the dataset.
3491 * @param pdbEntryString
3492 * - the short name for the PDB file
3494 * - pdb file - either a URL or a valid PDB file.
3495 * @return true if binding was as success TODO: consider making an exception
3496 * structure for indicating when PDB parsing or sequenceId location
3499 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3502 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3503 boolean needtoadd = false;
3504 if (toaddpdb != null)
3506 Vector pdbe = toaddpdb.getPDBId();
3507 PDBEntry pdbentry = null;
3508 if (pdbe != null && pdbe.size() > 0)
3510 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3512 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3513 if (!pdbentry.getId().equals(pdbEntryString)
3514 && !pdbentry.getFile().equals(pdbFile))
3524 if (pdbentry == null)
3526 pdbentry = new PDBEntry();
3527 pdbentry.setId(pdbEntryString);
3528 pdbentry.setFile(pdbFile);
3529 needtoadd = true; // add this new entry to sequence.
3531 // resolve data source
3532 // TODO: this code should be a refactored to an io package
3533 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3534 if (protocol == null)
3540 // make a note of the access mode and add
3541 if (pdbentry.getProperty() == null)
3543 pdbentry.setProperty(new Hashtable());
3545 pdbentry.getProperty().put("protocol", protocol);
3546 toaddpdb.addPDBId(pdbentry);
3552 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3556 Vector sequences = new Vector();
3557 for (int i = 0; i < seqs.length; i++)
3559 if (seqs[i] != null)
3561 sequences.addElement(new Object[]
3562 { seqs[i], (chains != null) ? chains[i] : null });
3565 seqs = new SequenceI[sequences.size()];
3566 chains = new String[sequences.size()];
3567 for (int i = 0, isize = sequences.size(); i < isize; i++)
3569 Object[] oj = (Object[]) sequences.elementAt(i);
3571 seqs[i] = (SequenceI) oj[0];
3572 chains[i] = (String) oj[1];
3580 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3581 SequenceI[] seqs, String[] chains, String protocol)
3583 // Scrub any null sequences from the array
3584 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3585 seqs = (SequenceI[]) sqch[0];
3586 chains = (String[]) sqch[1];
3587 if (seqs == null || seqs.length == 0)
3590 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3592 if (protocol == null || protocol.trim().length() == 0
3593 || protocol.equals("null"))
3595 protocol = (String) pdb.getProperty().get("protocol");
3596 if (protocol == null)
3598 System.err.println("Couldn't work out protocol to open structure: "
3603 if (applet.useXtrnalSviewer)
3605 // register the association(s) and quit, don't create any windows.
3606 if (StructureSelectionManager.getStructureSelectionManager(applet)
3607 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3609 System.err.println("Failed to map " + pdb.getFile() + " ("
3610 + protocol + ") to any sequences");
3614 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3616 // can only do alignments with Jmol
3617 // find the last jmol window assigned to this alignment
3618 jalview.appletgui.AppletJmol ajm = null, tajm;
3619 Vector jmols = applet
3620 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3621 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3623 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3624 if (tajm.ap.alignFrame == this)
3633 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3634 // try and add the pdb structure
3639 // otherwise, create a new window
3640 if (applet.jmolAvailable)
3642 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3644 applet.lastFrameX += 40;
3645 applet.lastFrameY += 40;
3649 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3654 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3655 SequenceI[][] seqs, String[][] chains, String[] protocols)
3657 // TODO Auto-generated method stub
3658 System.err.println("Aligned Structure View: Not yet implemented.");
3662 * modify the current selection, providing the user has not made a selection
3666 * - sequences from this alignment
3668 * - columns to be selected on the alignment
3670 public void select(SequenceGroup sel, ColumnSelection csel)
3672 alignPanel.seqPanel.selection(sel, csel, null);
3675 public void scrollTo(int row, int column)
3677 alignPanel.seqPanel.scrollTo(row, column);
3680 public void scrollToRow(int row)
3682 alignPanel.seqPanel.scrollToRow(row);
3685 public void scrollToColumn(int column)
3687 alignPanel.seqPanel.scrollToColumn(column);
3691 * @return the alignments unique ID.
3693 public String getSequenceSetId()
3695 return viewport.getSequenceSetId();
3699 * Load the (T-Coffee) score file from the specified url
3702 * File/URL/T-COFFEE score file contents
3703 * @throws IOException
3704 * @return true if alignment was annotated with data from source
3706 public boolean loadScoreFile(String source) throws IOException
3709 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3710 AppletFormatAdapter.checkProtocol(source));
3711 if (!file.isValid())
3713 // TODO: raise dialog for gui
3714 System.err.println("Problems parsing T-Coffee scores: "
3715 + file.getWarningMessage());
3716 System.err.println("Origin was:\n" + source);
3721 * check that the score matrix matches the alignment dimensions
3724 if ((aln = viewport.getAlignment()) != null
3725 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3728 // TODO: raise a dialog box here rather than bomb out.
3730 .println("The scores matrix does not match the alignment dimensions");
3734 // TODO add parameter to indicate if matching should be done
3735 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3737 alignPanel.fontChanged();
3738 tcoffeeColour.setEnabled(true);
3739 // switch to this color
3740 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3745 System.err.println("Problems resolving T-Coffee scores:");
3746 if (file.getWarningMessage() != null)
3748 System.err.println(file.getWarningMessage());