2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.appletgui;
23 import jalview.analysis.AlignmentSorter;
24 import jalview.api.AlignViewControllerGuiI;
25 import jalview.api.AlignViewControllerI;
26 import jalview.api.FeatureRenderer;
27 import jalview.api.SequenceStructureBinding;
28 import jalview.bin.JalviewLite;
29 import jalview.commands.CommandI;
30 import jalview.commands.EditCommand;
31 import jalview.commands.EditCommand.Action;
32 import jalview.commands.OrderCommand;
33 import jalview.commands.RemoveGapColCommand;
34 import jalview.commands.RemoveGapsCommand;
35 import jalview.commands.SlideSequencesCommand;
36 import jalview.commands.TrimRegionCommand;
37 import jalview.datamodel.Alignment;
38 import jalview.datamodel.AlignmentI;
39 import jalview.datamodel.AlignmentOrder;
40 import jalview.datamodel.ColumnSelection;
41 import jalview.datamodel.PDBEntry;
42 import jalview.datamodel.Sequence;
43 import jalview.datamodel.SequenceGroup;
44 import jalview.datamodel.SequenceI;
45 import jalview.io.AnnotationFile;
46 import jalview.io.AppletFormatAdapter;
47 import jalview.io.FeaturesFile;
48 import jalview.io.TCoffeeScoreFile;
49 import jalview.schemes.Blosum62ColourScheme;
50 import jalview.schemes.BuriedColourScheme;
51 import jalview.schemes.ClustalxColourScheme;
52 import jalview.schemes.ColourSchemeI;
53 import jalview.schemes.HelixColourScheme;
54 import jalview.schemes.HydrophobicColourScheme;
55 import jalview.schemes.NucleotideColourScheme;
56 import jalview.schemes.PIDColourScheme;
57 import jalview.schemes.PurinePyrimidineColourScheme;
58 import jalview.schemes.RNAHelicesColourChooser;
59 import jalview.schemes.RNAInteractionColourScheme;
60 import jalview.schemes.StrandColourScheme;
61 import jalview.schemes.TCoffeeColourScheme;
62 import jalview.schemes.TaylorColourScheme;
63 import jalview.schemes.TurnColourScheme;
64 import jalview.schemes.ZappoColourScheme;
65 import jalview.structure.StructureSelectionManager;
66 import jalview.structures.models.AAStructureBindingModel;
67 import jalview.util.MessageManager;
69 import java.awt.BorderLayout;
70 import java.awt.Canvas;
71 import java.awt.CheckboxMenuItem;
72 import java.awt.Color;
74 import java.awt.FontMetrics;
75 import java.awt.Frame;
76 import java.awt.Graphics;
77 import java.awt.Label;
79 import java.awt.MenuBar;
80 import java.awt.MenuItem;
81 import java.awt.event.ActionEvent;
82 import java.awt.event.ActionListener;
83 import java.awt.event.FocusEvent;
84 import java.awt.event.FocusListener;
85 import java.awt.event.ItemEvent;
86 import java.awt.event.ItemListener;
87 import java.awt.event.KeyEvent;
88 import java.awt.event.KeyListener;
89 import java.awt.event.WindowAdapter;
90 import java.awt.event.WindowEvent;
91 import java.io.IOException;
93 import java.net.URLEncoder;
94 import java.util.Arrays;
95 import java.util.Hashtable;
96 import java.util.List;
98 import java.util.StringTokenizer;
99 import java.util.Vector;
101 public class AlignFrame extends EmbmenuFrame implements ActionListener,
102 ItemListener, KeyListener, AlignViewControllerGuiI
104 public AlignViewControllerI avc;
106 public AlignmentPanel alignPanel;
108 public AlignViewport viewport;
110 int DEFAULT_WIDTH = 700;
112 int DEFAULT_HEIGHT = 500;
114 String jalviewServletURL;
116 public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet,
117 String title, boolean embedded)
121 jalviewServletURL = applet.getParameter("APPLICATION_URL");
127 } catch (Exception ex)
129 ex.printStackTrace();
131 // need to get window geometry before we calculate alignment layout
137 param = applet.getParameter("windowWidth");
140 int width = Integer.parseInt(param);
141 DEFAULT_WIDTH = width;
143 param = applet.getParameter("windowHeight");
146 int height = Integer.parseInt(param);
147 DEFAULT_HEIGHT = height;
149 } catch (Exception ex)
153 viewport = new AlignViewport(al, applet);
154 alignPanel = new AlignmentPanel(this, viewport);
155 avc = new jalview.controller.AlignViewController(this, viewport,
157 viewport.updateConservation(alignPanel);
158 viewport.updateConsensus(alignPanel);
160 annotationPanelMenuItem.setState(viewport.showAnnotation);
161 displayNonconservedMenuItem.setState(viewport.getShowUnconserved());
162 followMouseOverFlag.setState(viewport.getFollowHighlight());
163 showGroupConsensus.setState(viewport.isShowGroupConsensus());
164 showGroupConservation.setState(viewport.isShowGroupConservation());
165 showConsensusHistogram.setState(viewport.isShowConsensusHistogram());
166 showSequenceLogo.setState(viewport.isShowSequenceLogo());
167 normSequenceLogo.setState(viewport.isNormaliseSequenceLogo());
168 applyToAllGroups.setState(viewport.getColourAppliesToAllGroups());
170 seqLimits.setState(viewport.showJVSuffix);
174 String param = applet.getParameter("sortBy");
177 if (param.equalsIgnoreCase("Id"))
179 sortIDMenuItem_actionPerformed();
181 else if (param.equalsIgnoreCase("Pairwise Identity"))
183 sortPairwiseMenuItem_actionPerformed();
185 else if (param.equalsIgnoreCase("Length"))
187 sortLengthMenuItem_actionPerformed();
191 param = applet.getParameter("wrap");
194 if (param.equalsIgnoreCase("true"))
196 wrapMenuItem.setState(true);
197 wrapMenuItem_actionPerformed();
200 param = applet.getParameter("centrecolumnlabels");
203 centreColumnLabelFlag.setState(true);
204 centreColumnLabelFlag_stateChanged();
208 if (viewport.getAlignment().isNucleotide())
210 viewport.updateStrucConsensus(alignPanel);
211 if (viewport.getAlignment().hasRNAStructure())
213 RNAHelixColour.setEnabled(true);
217 RNAHelixColour.setEnabled(false);
222 RNAHelixColour.setEnabled(false);
223 purinePyrimidineColour.setEnabled(false);
225 // Some JVMS send keyevents to Top frame or lowest panel,
226 // Havent worked out why yet. So add to both this frame and seqCanvas for
228 this.addKeyListener(this);
229 alignPanel.seqPanel.seqCanvas.addKeyListener(this);
230 alignPanel.idPanel.idCanvas.addKeyListener(this);
231 alignPanel.scalePanel.addKeyListener(this);
232 alignPanel.annotationPanel.addKeyListener(this);
233 alignPanel.annotationPanelHolder.addKeyListener(this);
234 alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
235 alignPanel.alabels.addKeyListener(this);
236 createAlignFrameWindow(embedded, title);
239 alignPanel.adjustAnnotationHeight();
240 alignPanel.paintAlignment(true);
243 public AlignViewport getAlignViewport()
248 public SeqCanvas getSeqcanvas()
250 return alignPanel.seqPanel.seqCanvas;
254 * Load a features file onto the alignment
257 * file URL, content, or other resolvable path
259 * is protocol for accessing data referred to by file
262 public boolean parseFeaturesFile(String file, String type)
264 return parseFeaturesFile(file, type, true);
268 * Load a features file onto the alignment
271 * file URL, content, or other resolvable path
273 * is protocol for accessing data referred to by file
274 * @param autoenabledisplay
275 * when true, display features flag will be automatically enabled if
276 * features are loaded
277 * @return true if data parsed as a features file
279 public boolean parseFeaturesFile(String file, String type,
280 boolean autoenabledisplay)
282 // TODO: test if importing a features file onto an alignment which already
283 // has features with links overwrites the original links.
285 Hashtable featureLinks = new Hashtable();
286 boolean featuresFile = false;
289 featuresFile = new jalview.io.FeaturesFile(file, type)
290 .parse(viewport.getAlignment(), alignPanel.seqPanel.seqCanvas
291 .getFeatureRenderer().getFeatureColours(), featureLinks,
292 true, viewport.applet.getDefaultParameter(
293 "relaxedidmatch", false));
294 } catch (Exception ex)
296 ex.printStackTrace();
301 if (featureLinks.size() > 0)
303 alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureLinks = featureLinks;
305 if (autoenabledisplay)
307 viewport.setShowSequenceFeatures(true);
308 sequenceFeatures.setState(true);
310 if (alignPanel.seqPanel.seqCanvas.fr != null)
312 // update the min/max ranges where necessary
313 alignPanel.seqPanel.seqCanvas.fr.findAllFeatures(true);
315 if (viewport.featureSettings != null)
317 viewport.featureSettings.refreshTable();
319 alignPanel.paintAlignment(true);
320 statusBar.setText(MessageManager
321 .getString("label.successfully_added_features_alignment"));
327 public void keyPressed(KeyEvent evt)
329 if (viewport.cursorMode
330 && ((evt.getKeyCode() >= KeyEvent.VK_0 && evt.getKeyCode() <= KeyEvent.VK_9) || (evt
331 .getKeyCode() >= KeyEvent.VK_NUMPAD0 && evt
332 .getKeyCode() <= KeyEvent.VK_NUMPAD9))
333 && Character.isDigit(evt.getKeyChar()))
335 alignPanel.seqPanel.numberPressed(evt.getKeyChar());
338 switch (evt.getKeyCode())
340 case 27: // escape key
341 deselectAllSequenceMenuItem_actionPerformed();
343 alignPanel.alabels.cancelDrag();
346 if (evt.isControlDown() || evt.isMetaDown())
348 cut_actionPerformed();
352 if (viewport.cursorMode && !evt.isControlDown())
354 alignPanel.seqPanel.setCursorColumn();
356 if (evt.isControlDown() || evt.isMetaDown())
358 copy_actionPerformed();
362 if (evt.isControlDown())
364 paste(evt.isShiftDown());
368 if (evt.isControlDown() || evt.isMetaDown())
370 selectAllSequenceMenuItem_actionPerformed();
373 case KeyEvent.VK_DOWN:
374 if (viewport.cursorMode)
376 alignPanel.seqPanel.moveCursor(0, 1);
380 moveSelectedSequences(false);
385 if (viewport.cursorMode)
387 alignPanel.seqPanel.moveCursor(0, -1);
391 moveSelectedSequences(true);
395 case KeyEvent.VK_LEFT:
396 if (evt.isAltDown() || !viewport.cursorMode)
398 slideSequences(false, alignPanel.seqPanel.getKeyboardNo1());
402 alignPanel.seqPanel.moveCursor(-1, 0);
406 case KeyEvent.VK_RIGHT:
407 if (evt.isAltDown() || !viewport.cursorMode)
409 slideSequences(true, alignPanel.seqPanel.getKeyboardNo1());
413 alignPanel.seqPanel.moveCursor(1, 0);
417 case KeyEvent.VK_SPACE:
418 if (viewport.cursorMode)
420 alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()
421 || evt.isShiftDown() || evt.isAltDown());
425 case KeyEvent.VK_DELETE:
426 case KeyEvent.VK_BACK_SPACE:
427 if (viewport.cursorMode)
429 alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()
430 || evt.isShiftDown() || evt.isAltDown());
434 cut_actionPerformed();
435 alignPanel.seqPanel.seqCanvas.repaint();
440 if (viewport.cursorMode)
442 alignPanel.seqPanel.setCursorRow();
446 if (viewport.cursorMode)
448 alignPanel.seqPanel.setCursorPosition();
452 case KeyEvent.VK_ENTER:
453 case KeyEvent.VK_COMMA:
454 if (viewport.cursorMode)
456 alignPanel.seqPanel.setCursorRowAndColumn();
461 if (viewport.cursorMode)
463 alignPanel.seqPanel.setSelectionAreaAtCursor(true);
467 if (viewport.cursorMode)
469 alignPanel.seqPanel.setSelectionAreaAtCursor(false);
474 viewport.cursorMode = !viewport.cursorMode;
475 statusBar.setText(MessageManager.formatMessage(
476 "label.keyboard_editing_mode", new String[]
477 { (viewport.cursorMode ? "on" : "off") }));
478 if (viewport.cursorMode)
480 alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;
481 alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;
486 if (evt.isControlDown())
488 findMenuItem_actionPerformed();
494 boolean toggleSeqs = !evt.isControlDown();
495 boolean toggleCols = !evt.isShiftDown();
496 toggleHiddenRegions(toggleSeqs, toggleCols);
500 case KeyEvent.VK_PAGE_UP:
501 if (viewport.wrapAlignment)
503 alignPanel.scrollUp(true);
507 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
508 - viewport.endSeq + viewport.startSeq);
512 case KeyEvent.VK_PAGE_DOWN:
513 if (viewport.wrapAlignment)
515 alignPanel.scrollUp(false);
519 alignPanel.setScrollValues(viewport.startRes, viewport.startSeq
520 + viewport.endSeq - viewport.startSeq);
525 if (evt.isControlDown())
527 undoMenuItem_actionPerformed();
532 if (evt.isControlDown())
534 redoMenuItem_actionPerformed();
539 if (evt.isControlDown())
546 if (evt.isControlDown())
548 trimAlignment(false);
553 if (evt.isControlDown())
555 if (evt.isShiftDown())
557 this.removeAllGapsMenuItem_actionPerformed();
561 removeGappedColumnMenuItem_actionPerformed();
566 if (evt.isControlDown())
570 invertColSel_actionPerformed();
574 invertSequenceMenuItem_actionPerformed();
580 if (evt.isControlDown())
582 if (evt.isShiftDown())
584 this.unGroup_actionPerformed();
588 this.createGroup_actionPerformed();
594 if (evt.isControlDown())
596 this.deleteGroups_actionPerformed();
601 if (evt.isControlDown())
608 alignPanel.paintAlignment(true);
612 * called by key handler and the hide all/show all menu items
617 private void toggleHiddenRegions(boolean toggleSeqs, boolean toggleCols)
619 boolean hide = false;
620 SequenceGroup sg = viewport.getSelectionGroup();
621 if (!toggleSeqs && !toggleCols)
623 // Hide everything by the current selection - this is a hack - we do the
624 // invert and then hide
625 // first check that there will be visible columns after the invert.
626 if ((viewport.getColumnSelection() != null
627 && viewport.getColumnSelection().getSelected() != null && viewport
628 .getColumnSelection().getSelected().size() > 0)
629 || (sg != null && sg.getSize() > 0 && sg.getStartRes() <= sg
632 // now invert the sequence set, if required - empty selection implies
633 // that no hiding is required.
636 invertSequenceMenuItem_actionPerformed();
637 sg = viewport.getSelectionGroup();
641 viewport.expandColSelection(sg, true);
642 // finally invert the column selection and get the new sequence
643 // selection and indicate it should be hidden.
644 invertColSel_actionPerformed();
651 if (sg != null && sg.getSize() != viewport.getAlignment().getHeight())
654 viewport.hideAllSelectedSeqs();
656 else if (!(toggleCols && viewport.getColumnSelection().getSelected()
659 viewport.showAllHiddenSeqs();
665 if (viewport.getColumnSelection().getSelected().size() > 0)
667 viewport.hideSelectedColumns();
670 viewport.setSelectionGroup(sg);
675 viewport.showAllHiddenColumns();
681 public void keyReleased(KeyEvent evt)
686 public void keyTyped(KeyEvent evt)
691 public void itemStateChanged(ItemEvent evt)
693 if (evt.getSource() == displayNonconservedMenuItem)
695 displayNonconservedMenuItem_actionPerformed();
697 else if (evt.getSource() == colourTextMenuItem)
699 colourTextMenuItem_actionPerformed();
701 else if (evt.getSource() == wrapMenuItem)
703 wrapMenuItem_actionPerformed();
705 else if (evt.getSource() == scaleAbove)
707 viewport.setScaleAboveWrapped(scaleAbove.getState());
709 else if (evt.getSource() == scaleLeft)
711 viewport.setScaleLeftWrapped(scaleLeft.getState());
713 else if (evt.getSource() == scaleRight)
715 viewport.setScaleRightWrapped(scaleRight.getState());
717 else if (evt.getSource() == seqLimits)
719 seqLimits_itemStateChanged();
721 else if (evt.getSource() == viewBoxesMenuItem)
723 viewport.setShowBoxes(viewBoxesMenuItem.getState());
725 else if (evt.getSource() == viewTextMenuItem)
727 viewport.setShowText(viewTextMenuItem.getState());
729 else if (evt.getSource() == renderGapsMenuItem)
731 viewport.setRenderGaps(renderGapsMenuItem.getState());
733 else if (evt.getSource() == annotationPanelMenuItem)
735 viewport.setShowAnnotation(annotationPanelMenuItem.getState());
736 alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());
738 else if (evt.getSource() == sequenceFeatures)
740 viewport.setShowSequenceFeatures(sequenceFeatures.getState());
741 alignPanel.seqPanel.seqCanvas.repaint();
743 else if (evt.getSource() == conservationMenuItem)
745 conservationMenuItem_actionPerformed();
747 else if (evt.getSource() == abovePIDThreshold)
749 abovePIDThreshold_actionPerformed();
751 else if (evt.getSource() == applyToAllGroups)
753 viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());
755 else if (evt.getSource() == autoCalculate)
757 viewport.autoCalculateConsensus = autoCalculate.getState();
759 else if (evt.getSource() == sortByTree)
761 viewport.sortByTree = sortByTree.getState();
763 else if (evt.getSource() == this.centreColumnLabelFlag)
765 centreColumnLabelFlag_stateChanged();
767 else if (evt.getSource() == this.followMouseOverFlag)
769 mouseOverFlag_stateChanged();
771 else if (evt.getSource() == showGroupConsensus)
773 showGroupConsensus_actionPerformed();
775 else if (evt.getSource() == showGroupConservation)
777 showGroupConservation_actionPerformed();
779 else if (evt.getSource() == showSequenceLogo)
781 showSequenceLogo_actionPerformed();
783 else if (evt.getSource() == normSequenceLogo)
785 normSequenceLogo_actionPerformed();
787 else if (evt.getSource() == showConsensusHistogram)
789 showConsensusHistogram_actionPerformed();
791 else if (evt.getSource() == applyAutoAnnotationSettings)
793 applyAutoAnnotationSettings_actionPerformed();
795 alignPanel.paintAlignment(true);
798 private void mouseOverFlag_stateChanged()
800 viewport.followHighlight = followMouseOverFlag.getState();
801 // TODO: could kick the scrollTo mechanism to reset view for current
805 private void centreColumnLabelFlag_stateChanged()
807 viewport.centreColumnLabels = centreColumnLabelFlag.getState();
808 this.alignPanel.annotationPanel.repaint();
812 public void actionPerformed(ActionEvent evt)
814 Object source = evt.getSource();
816 if (source == inputText)
818 inputText_actionPerformed();
820 else if (source == loadTree)
822 loadTree_actionPerformed();
824 else if (source == loadApplication)
826 launchFullApplication();
828 else if (source == loadAnnotations)
832 else if (source == outputAnnotations)
834 outputAnnotations(true);
836 else if (source == outputFeatures)
838 outputFeatures(true, "Jalview");
840 else if (source == closeMenuItem)
842 closeMenuItem_actionPerformed();
844 else if (source == copy)
846 copy_actionPerformed();
848 else if (source == undoMenuItem)
850 undoMenuItem_actionPerformed();
852 else if (source == redoMenuItem)
854 redoMenuItem_actionPerformed();
856 else if (source == inputText)
858 inputText_actionPerformed();
860 else if (source == closeMenuItem)
862 closeMenuItem_actionPerformed();
864 else if (source == undoMenuItem)
866 undoMenuItem_actionPerformed();
868 else if (source == redoMenuItem)
870 redoMenuItem_actionPerformed();
872 else if (source == copy)
874 copy_actionPerformed();
876 else if (source == pasteNew)
878 pasteNew_actionPerformed();
880 else if (source == pasteThis)
882 pasteThis_actionPerformed();
884 else if (source == cut)
886 cut_actionPerformed();
888 else if (source == delete)
890 delete_actionPerformed();
892 else if (source == grpsFromSelection)
894 makeGrpsFromSelection_actionPerformed();
896 else if (source == deleteGroups)
898 deleteGroups_actionPerformed();
900 else if (source == selectAllSequenceMenuItem)
902 selectAllSequenceMenuItem_actionPerformed();
904 else if (source == deselectAllSequenceMenuItem)
906 deselectAllSequenceMenuItem_actionPerformed();
908 else if (source == invertSequenceMenuItem)
910 invertSequenceMenuItem_actionPerformed();
912 else if (source == invertColSel)
914 viewport.invertColumnSelection();
915 alignPanel.paintAlignment(true);
917 else if (source == remove2LeftMenuItem)
921 else if (source == remove2RightMenuItem)
923 trimAlignment(false);
925 else if (source == removeGappedColumnMenuItem)
927 removeGappedColumnMenuItem_actionPerformed();
929 else if (source == removeAllGapsMenuItem)
931 removeAllGapsMenuItem_actionPerformed();
933 else if (source == findMenuItem)
935 findMenuItem_actionPerformed();
937 else if (source == font)
939 new FontChooser(alignPanel);
941 else if (source == newView)
945 else if (source == showColumns)
947 viewport.showAllHiddenColumns();
948 alignPanel.paintAlignment(true);
950 else if (source == showSeqs)
952 viewport.showAllHiddenSeqs();
953 alignPanel.paintAlignment(true);
955 else if (source == hideColumns)
957 viewport.hideSelectedColumns();
958 alignPanel.paintAlignment(true);
960 else if (source == hideSequences
961 && viewport.getSelectionGroup() != null)
963 viewport.hideAllSelectedSeqs();
964 alignPanel.paintAlignment(true);
966 else if (source == hideAllButSelection)
968 toggleHiddenRegions(false, false);
969 alignPanel.paintAlignment(true);
971 else if (source == hideAllSelection)
973 SequenceGroup sg = viewport.getSelectionGroup();
974 viewport.expandColSelection(sg, false);
975 viewport.hideAllSelectedSeqs();
976 viewport.hideSelectedColumns();
977 alignPanel.paintAlignment(true);
979 else if (source == showAllHidden)
981 viewport.showAllHiddenColumns();
982 viewport.showAllHiddenSeqs();
983 alignPanel.paintAlignment(true);
985 else if (source == showGroupConsensus)
987 showGroupConsensus_actionPerformed();
989 else if (source == showGroupConservation)
991 showGroupConservation_actionPerformed();
993 else if (source == showSequenceLogo)
995 showSequenceLogo_actionPerformed();
997 else if (source == normSequenceLogo)
999 normSequenceLogo_actionPerformed();
1001 else if (source == showConsensusHistogram)
1003 showConsensusHistogram_actionPerformed();
1005 else if (source == applyAutoAnnotationSettings)
1007 applyAutoAnnotationSettings_actionPerformed();
1009 else if (source == featureSettings)
1011 new FeatureSettings(alignPanel);
1013 else if (source == alProperties)
1015 StringBuffer contents = new jalview.io.AlignmentProperties(
1016 viewport.getAlignment()).formatAsString();
1017 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1018 cap.setText(contents.toString());
1019 Frame frame = new Frame();
1021 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1022 "label.alignment_properties", new String[]
1023 { getTitle() }), 400, 250);
1025 else if (source == overviewMenuItem)
1027 overviewMenuItem_actionPerformed();
1029 else if (source == noColourmenuItem)
1033 else if (source == clustalColour)
1035 abovePIDThreshold.setState(false);
1036 changeColour(new ClustalxColourScheme(viewport.getAlignment(), null));
1038 else if (source == zappoColour)
1040 changeColour(new ZappoColourScheme());
1042 else if (source == taylorColour)
1044 changeColour(new TaylorColourScheme());
1046 else if (source == hydrophobicityColour)
1048 changeColour(new HydrophobicColourScheme());
1050 else if (source == helixColour)
1052 changeColour(new HelixColourScheme());
1054 else if (source == strandColour)
1056 changeColour(new StrandColourScheme());
1058 else if (source == turnColour)
1060 changeColour(new TurnColourScheme());
1062 else if (source == buriedColour)
1064 changeColour(new BuriedColourScheme());
1066 else if (source == nucleotideColour)
1068 changeColour(new NucleotideColourScheme());
1070 else if (source == purinePyrimidineColour)
1072 changeColour(new PurinePyrimidineColourScheme());
1074 else if (source == RNAInteractionColour)
1076 changeColour(new RNAInteractionColourScheme());
1078 else if (source == RNAHelixColour)
1080 new RNAHelicesColourChooser(viewport, alignPanel);
1082 else if (source == modifyPID)
1084 modifyPID_actionPerformed();
1086 else if (source == modifyConservation)
1088 modifyConservation_actionPerformed();
1090 else if (source == userDefinedColour)
1092 new UserDefinedColours(alignPanel, null);
1094 else if (source == PIDColour)
1096 changeColour(new PIDColourScheme());
1098 else if (source == BLOSUM62Colour)
1100 changeColour(new Blosum62ColourScheme());
1102 else if (source == tcoffeeColour)
1104 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
1106 else if (source == annotationColour)
1108 new AnnotationColourChooser(viewport, alignPanel);
1110 else if (source == annotationColumnSelection)
1112 new AnnotationColumnChooser(viewport, alignPanel);
1114 else if (source == sortPairwiseMenuItem)
1116 sortPairwiseMenuItem_actionPerformed();
1118 else if (source == sortIDMenuItem)
1120 sortIDMenuItem_actionPerformed();
1122 else if (source == sortLengthMenuItem)
1124 sortLengthMenuItem_actionPerformed();
1126 else if (source == sortGroupMenuItem)
1128 sortGroupMenuItem_actionPerformed();
1130 else if (source == removeRedundancyMenuItem)
1132 removeRedundancyMenuItem_actionPerformed();
1134 else if (source == pairwiseAlignmentMenuItem)
1136 pairwiseAlignmentMenuItem_actionPerformed();
1138 else if (source == PCAMenuItem)
1140 PCAMenuItem_actionPerformed();
1142 else if (source == averageDistanceTreeMenuItem)
1144 averageDistanceTreeMenuItem_actionPerformed();
1146 else if (source == neighbourTreeMenuItem)
1148 neighbourTreeMenuItem_actionPerformed();
1150 else if (source == njTreeBlosumMenuItem)
1152 njTreeBlosumMenuItem_actionPerformed();
1154 else if (source == avDistanceTreeBlosumMenuItem)
1156 avTreeBlosumMenuItem_actionPerformed();
1158 else if (source == documentation)
1160 documentation_actionPerformed();
1162 else if (source == about)
1164 about_actionPerformed();
1169 public void inputText_actionPerformed()
1171 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1172 Frame frame = new Frame();
1174 jalview.bin.JalviewLite.addFrame(frame,
1175 MessageManager.getString("label.input_cut_paste"), 500, 500);
1178 protected void outputText_actionPerformed(ActionEvent e)
1180 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1181 Frame frame = new Frame();
1183 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
1184 "label.alignment_output_command", new String[]
1185 { e.getActionCommand() }), 600, 500);
1186 cap.setText(new AppletFormatAdapter().formatSequences(
1187 e.getActionCommand(), viewport.getAlignment(),
1188 viewport.showJVSuffix));
1191 public void loadAnnotations()
1193 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
1194 cap.setText(MessageManager
1195 .getString("label.paste_features_annotations_Tcoffee_here"));
1196 cap.setAnnotationImport();
1197 Frame frame = new Frame();
1199 jalview.bin.JalviewLite.addFrame(frame,
1200 MessageManager.getString("action.paste_annotations"), 400, 300);
1204 public String outputAnnotations(boolean displayTextbox)
1206 String annotation = new AnnotationFile()
1207 .printAnnotationsForView(viewport);
1211 CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);
1212 Frame frame = new Frame();
1214 jalview.bin.JalviewLite.addFrame(frame,
1215 MessageManager.getString("label.annotations"), 600, 500);
1216 cap.setText(annotation);
1222 private Map<String,Object> getDisplayedFeatureCols()
1224 if (alignPanel.getFeatureRenderer() != null
1225 && viewport.getFeaturesDisplayed()!= null)
1227 return alignPanel.getFeatureRenderer().getDisplayedFeatureCols();
1233 public String outputFeatures(boolean displayTextbox, String format)
1236 if (format.equalsIgnoreCase("Jalview"))
1238 features = new FeaturesFile().printJalviewFormat(viewport
1239 .getAlignment().getSequencesArray(),
1240 getDisplayedFeatureCols());
1244 features = new FeaturesFile().printGFFFormat(viewport.getAlignment()
1245 .getSequencesArray(), getDisplayedFeatureCols());
1250 boolean frimport = false;
1251 if (features == null || features.equals("No Features Visible"))
1253 features = "# No features visible - paste some and import them here.";
1257 CutAndPasteTransfer cap = new CutAndPasteTransfer(frimport, this);
1260 cap.setAnnotationImport();
1262 Frame frame = new Frame();
1264 jalview.bin.JalviewLite.addFrame(frame,
1265 MessageManager.getString("label.features"), 600, 500);
1266 cap.setText(features);
1270 if (features == null)
1279 void launchFullApplication()
1281 StringBuffer url = new StringBuffer(jalviewServletURL);
1284 + appendProtocol(viewport.applet.getParameter("file")));
1286 if (viewport.applet.getParameter("features") != null)
1288 url.append("&features=");
1289 url.append(appendProtocol(viewport.applet.getParameter("features")));
1292 if (viewport.applet.getParameter("annotations") != null)
1294 url.append("&annotations=");
1295 url.append(appendProtocol(viewport.applet.getParameter("annotations")));
1298 if (viewport.applet.getParameter("jnetfile") != null)
1300 url.append("&annotations=");
1301 url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));
1304 if (viewport.applet.getParameter("defaultColour") != null)
1306 url.append("&colour="
1307 + removeWhiteSpace(viewport.applet
1308 .getParameter("defaultColour")));
1311 if (viewport.applet.getParameter("userDefinedColour") != null)
1313 url.append("&colour="
1314 + removeWhiteSpace(viewport.applet
1315 .getParameter("userDefinedColour")));
1317 if (viewport.applet.getParameter("tree") != null)
1320 + appendProtocol(viewport.applet.getParameter("tree")));
1322 if (viewport.applet.getParameter("treeFile") != null)
1325 + appendProtocol(viewport.applet.getParameter("treeFile")));
1328 showURL(url.toString(), "FULL_APP");
1331 String removeWhiteSpace(String colour)
1333 StringBuffer sb = new StringBuffer();
1334 for (int i = 0; i < colour.length(); i++)
1336 if (Character.isWhitespace(colour.charAt(i)))
1342 sb.append(colour.charAt(i));
1346 return sb.toString();
1349 String appendProtocol(String url)
1354 url = URLEncoder.encode(url);
1357 * When we finally deprecate 1.1 compatibility, we can start to use
1358 * URLEncoder.encode(url,"UTF-8") and then we'll need this catch: catch
1359 * (UnsupportedEncodingException ex) { System.err.println("WARNING -
1360 * IMPLEMENTATION ERROR - UNSUPPORTED ENCODING EXCEPTION FOR "+url);
1361 * ex.printStackTrace(); }
1363 catch (java.net.MalformedURLException ex)
1365 url = viewport.applet.getCodeBase() + url;
1370 public void closeMenuItem_actionPerformed()
1372 PaintRefresher.RemoveComponent(alignPanel);
1373 if (alignPanel.seqPanel != null
1374 && alignPanel.seqPanel.seqCanvas != null)
1376 PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);
1378 if (alignPanel.idPanel != null && alignPanel.idPanel.idCanvas != null)
1380 PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);
1383 if (PaintRefresher.components.size() == 0 && viewport.applet == null)
1398 void updateEditMenuBar()
1401 if (viewport.historyList.size() > 0)
1403 undoMenuItem.setEnabled(true);
1404 CommandI command = (CommandI) viewport.historyList.peek();
1405 undoMenuItem.setLabel(MessageManager.formatMessage(
1406 "label.undo_command", new String[]
1407 { command.getDescription() }));
1411 undoMenuItem.setEnabled(false);
1412 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
1415 if (viewport.redoList.size() > 0)
1417 redoMenuItem.setEnabled(true);
1419 CommandI command = (CommandI) viewport.redoList.peek();
1420 redoMenuItem.setLabel(MessageManager.formatMessage(
1421 "label.redo_command", new String[]
1422 { command.getDescription() }));
1426 redoMenuItem.setEnabled(false);
1427 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
1435 public void addHistoryItem(CommandI command)
1437 if (command.getSize() > 0)
1439 viewport.historyList.push(command);
1440 viewport.redoList.removeAllElements();
1441 updateEditMenuBar();
1442 viewport.updateHiddenColumns();
1447 * TODO: JAL-1104 DOCUMENT ME!
1452 protected void undoMenuItem_actionPerformed()
1454 if (viewport.historyList.size() < 1)
1459 CommandI command = (CommandI) viewport.historyList.pop();
1460 viewport.redoList.push(command);
1461 command.undoCommand(null);
1463 AlignViewport originalSource = getOriginatingSource(command);
1465 if (originalSource != viewport)
1468 .println("Warning: Viewport object mismatch whilst undoing");
1470 originalSource.updateHiddenColumns(); // originalSource.hasHiddenColumns =
1471 // viewport.getColumnSelection().getHiddenColumns()
1473 updateEditMenuBar();
1474 originalSource.firePropertyChange("alignment", null, originalSource
1475 .getAlignment().getSequences());
1479 * TODO: JAL-1104 DOCUMENT ME!
1484 protected void redoMenuItem_actionPerformed()
1486 if (viewport.redoList.size() < 1)
1491 CommandI command = (CommandI) viewport.redoList.pop();
1492 viewport.historyList.push(command);
1493 command.doCommand(null);
1495 AlignViewport originalSource = getOriginatingSource(command);
1497 if (originalSource != viewport)
1500 .println("Warning: Viewport object mismatch whilst re-doing");
1502 originalSource.updateHiddenColumns(); // sethasHiddenColumns(); =
1503 // viewport.getColumnSelection().getHiddenColumns()
1506 updateEditMenuBar();
1507 originalSource.firePropertyChange("alignment", null, originalSource
1508 .getAlignment().getSequences());
1511 AlignViewport getOriginatingSource(CommandI command)
1513 AlignViewport originalSource = null;
1514 // For sequence removal and addition, we need to fire
1515 // the property change event FROM the viewport where the
1516 // original alignment was altered
1517 AlignmentI al = null;
1518 if (command instanceof EditCommand)
1520 EditCommand editCommand = (EditCommand) command;
1521 al = editCommand.getAlignment();
1522 Vector comps = (Vector) PaintRefresher.components.get(viewport
1523 .getSequenceSetId());
1524 for (int i = 0; i < comps.size(); i++)
1526 if (comps.elementAt(i) instanceof AlignmentPanel)
1528 if (al == ((AlignmentPanel) comps.elementAt(i)).av.getAlignment())
1530 originalSource = ((AlignmentPanel) comps.elementAt(i)).av;
1537 if (originalSource == null)
1539 // The original view is closed, we must validate
1540 // the current view against the closed view first
1543 PaintRefresher.validateSequences(al, viewport.getAlignment());
1546 originalSource = viewport;
1549 return originalSource;
1552 public void moveSelectedSequences(boolean up)
1554 SequenceGroup sg = viewport.getSelectionGroup();
1559 viewport.getAlignment().moveSelectedSequencesByOne(sg,
1560 up ? null : viewport.getHiddenRepSequences(), up);
1561 alignPanel.paintAlignment(true);
1564 synchronized void slideSequences(boolean right, int size)
1566 List<SequenceI> sg = new Vector<SequenceI>();
1567 if (viewport.cursorMode)
1569 sg.add(viewport.getAlignment().getSequenceAt(
1570 alignPanel.seqPanel.seqCanvas.cursorY));
1572 else if (viewport.getSelectionGroup() != null
1573 && viewport.getSelectionGroup().getSize() != viewport
1574 .getAlignment().getHeight())
1576 sg = viewport.getSelectionGroup().getSequences(
1577 viewport.getHiddenRepSequences());
1585 Vector<SequenceI> invertGroup = new Vector();
1587 for (int i = 0; i < viewport.getAlignment().getHeight(); i++)
1589 if (!sg.contains(viewport.getAlignment().getSequenceAt(i)))
1591 invertGroup.addElement(viewport.getAlignment().getSequenceAt(i));
1595 SequenceI[] seqs1 = sg.toArray(new SequenceI[sg.size()]);
1597 SequenceI[] seqs2 = invertGroup.toArray(new SequenceI[invertGroup
1599 for (int i = 0; i < invertGroup.size(); i++)
1601 seqs2[i] = invertGroup.elementAt(i);
1604 SlideSequencesCommand ssc;
1607 ssc = new SlideSequencesCommand("Slide Sequences", seqs2, seqs1,
1608 size, viewport.getGapCharacter());
1612 ssc = new SlideSequencesCommand("Slide Sequences", seqs1, seqs2,
1613 size, viewport.getGapCharacter());
1616 int groupAdjustment = 0;
1617 if (ssc.getGapsInsertedBegin() && right)
1619 if (viewport.cursorMode)
1621 alignPanel.seqPanel.moveCursor(size, 0);
1625 groupAdjustment = size;
1628 else if (!ssc.getGapsInsertedBegin() && !right)
1630 if (viewport.cursorMode)
1632 alignPanel.seqPanel.moveCursor(-size, 0);
1636 groupAdjustment = -size;
1640 if (groupAdjustment != 0)
1642 viewport.getSelectionGroup().setStartRes(
1643 viewport.getSelectionGroup().getStartRes() + groupAdjustment);
1644 viewport.getSelectionGroup().setEndRes(
1645 viewport.getSelectionGroup().getEndRes() + groupAdjustment);
1648 boolean appendHistoryItem = false;
1649 if (viewport.historyList != null && viewport.historyList.size() > 0
1650 && viewport.historyList.peek() instanceof SlideSequencesCommand)
1652 appendHistoryItem = ssc
1653 .appendSlideCommand((SlideSequencesCommand) viewport.historyList
1657 if (!appendHistoryItem)
1659 addHistoryItem(ssc);
1665 static StringBuffer copiedSequences;
1667 static Vector copiedHiddenColumns;
1669 protected void copy_actionPerformed()
1671 if (viewport.getSelectionGroup() == null)
1676 SequenceGroup sg = viewport.getSelectionGroup();
1677 copiedSequences = new StringBuffer();
1678 Hashtable orderedSeqs = new Hashtable();
1679 for (int i = 0; i < sg.getSize(); i++)
1681 SequenceI seq = sg.getSequenceAt(i);
1682 int index = viewport.getAlignment().findIndex(seq);
1683 orderedSeqs.put(index + "", seq);
1686 int index = 0, startRes, endRes;
1689 if (viewport.hasHiddenColumns() && viewport.getSelectionGroup() != null)
1691 copiedHiddenColumns = new Vector();
1692 int hiddenOffset = viewport.getSelectionGroup().getStartRes();
1693 for (int[] region : viewport.getColumnSelection().getHiddenColumns())
1695 copiedHiddenColumns.addElement(new int[]
1696 { region[0] - hiddenOffset, region[1] - hiddenOffset });
1701 copiedHiddenColumns = null;
1704 for (int i = 0; i < sg.getSize(); i++)
1706 SequenceI seq = null;
1710 if (orderedSeqs.containsKey(index + ""))
1712 seq = (SequenceI) orderedSeqs.get(index + "");
1724 // Returns residue following index if gap
1725 startRes = seq.findPosition(sg.getStartRes());
1728 // Need to find the residue preceeding index if gap
1731 for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)
1733 ch = seq.getCharAt(j);
1734 if (!jalview.util.Comparison.isGap((ch)))
1742 endRes += seq.getStart() - 1;
1745 copiedSequences.append(seq.getName()
1751 + seq.getSequenceAsString(sg.getStartRes(),
1752 sg.getEndRes() + 1) + "\n");
1757 protected void pasteNew_actionPerformed()
1762 protected void pasteThis_actionPerformed()
1767 void paste(boolean newAlignment)
1772 if (copiedSequences == null)
1777 StringTokenizer st = new StringTokenizer(copiedSequences.toString());
1778 Vector seqs = new Vector();
1779 while (st.hasMoreElements())
1781 String name = st.nextToken();
1782 int start = Integer.parseInt(st.nextToken());
1783 int end = Integer.parseInt(st.nextToken());
1784 seqs.addElement(new Sequence(name, st.nextToken(), start, end));
1786 SequenceI[] newSeqs = new SequenceI[seqs.size()];
1787 for (int i = 0; i < seqs.size(); i++)
1789 newSeqs[i] = (SequenceI) seqs.elementAt(i);
1794 String newtitle = MessageManager.getString("label.copied_sequences");
1795 if (getTitle().startsWith(MessageManager.getString("label.copied_sequences")))
1797 newtitle = getTitle();
1801 newtitle = newtitle.concat(MessageManager.formatMessage("label.from_msname", new String[]{getTitle()}));
1803 AlignFrame af = new AlignFrame(new Alignment(newSeqs),
1804 viewport.applet, newtitle, false);
1805 if (copiedHiddenColumns != null)
1807 for (int i = 0; i < copiedHiddenColumns.size(); i++)
1809 int[] region = (int[]) copiedHiddenColumns.elementAt(i);
1810 af.viewport.hideColumns(region[0], region[1]);
1814 jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,
1819 addSequences(newSeqs);
1822 } catch (Exception ex)
1824 } // could be anything being pasted in here
1828 void addSequences(SequenceI[] seqs)
1830 for (int i = 0; i < seqs.length; i++)
1832 viewport.getAlignment().addSequence(seqs[i]);
1836 addHistoryItem(new EditCommand(
1837 MessageManager.getString("label.add_sequences"), Action.PASTE,
1838 seqs, 0, viewport.getAlignment().getWidth(),
1839 viewport.getAlignment()));
1841 viewport.setEndSeq(viewport.getAlignment().getHeight());
1842 viewport.getAlignment().getWidth();
1843 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1848 protected void cut_actionPerformed()
1850 copy_actionPerformed();
1851 delete_actionPerformed();
1854 protected void delete_actionPerformed()
1857 SequenceGroup sg = viewport.getSelectionGroup();
1863 Vector seqs = new Vector();
1865 for (int i = 0; i < sg.getSize(); i++)
1867 seq = sg.getSequenceAt(i);
1868 seqs.addElement(seq);
1871 // If the cut affects all sequences, remove highlighted columns
1872 if (sg.getSize() == viewport.getAlignment().getHeight())
1874 viewport.getColumnSelection().removeElements(sg.getStartRes(),
1875 sg.getEndRes() + 1);
1878 SequenceI[] cut = new SequenceI[seqs.size()];
1879 for (int i = 0; i < seqs.size(); i++)
1881 cut[i] = (SequenceI) seqs.elementAt(i);
1885 * //ADD HISTORY ITEM
1887 addHistoryItem(new EditCommand(
1888 MessageManager.getString("label.cut_sequences"), Action.CUT,
1889 cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
1890 viewport.getAlignment()));
1892 viewport.setSelectionGroup(null);
1893 viewport.getAlignment().deleteGroup(sg);
1895 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
1898 if (viewport.getAlignment().getHeight() < 1)
1900 this.setVisible(false);
1902 viewport.sendSelection();
1906 * group consensus toggled
1909 protected void showGroupConsensus_actionPerformed()
1911 viewport.setShowGroupConsensus(showGroupConsensus.getState());
1912 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1917 * group conservation toggled.
1919 protected void showGroupConservation_actionPerformed()
1921 viewport.setShowGroupConservation(showGroupConservation.getState());
1922 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1929 * jalview.jbgui.GAlignFrame#showConsensusHistogram_actionPerformed(java.awt
1930 * .event.ActionEvent)
1932 protected void showConsensusHistogram_actionPerformed()
1934 viewport.setShowConsensusHistogram(showConsensusHistogram.getState());
1935 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1942 * jalview.jbgui.GAlignFrame#showConsensusProfile_actionPerformed(java.awt
1943 * .event.ActionEvent)
1945 protected void showSequenceLogo_actionPerformed()
1947 viewport.setShowSequenceLogo(showSequenceLogo.getState());
1948 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1951 protected void normSequenceLogo_actionPerformed()
1953 showSequenceLogo.setState(true);
1954 viewport.setShowSequenceLogo(true);
1955 viewport.setNormaliseSequenceLogo(normSequenceLogo.getState());
1956 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1959 protected void applyAutoAnnotationSettings_actionPerformed()
1961 alignPanel.updateAnnotation(applyAutoAnnotationSettings.getState());
1964 protected void makeGrpsFromSelection_actionPerformed()
1966 if (avc.makeGroupsFromSelection())
1968 PaintRefresher.Refresh(this, viewport.getSequenceSetId());
1969 alignPanel.updateAnnotation();
1970 alignPanel.paintAlignment(true);
1974 protected void createGroup_actionPerformed()
1979 protected void unGroup_actionPerformed()
1983 alignPanel.alignmentChanged();
1987 protected void deleteGroups_actionPerformed()
1989 if (avc.deleteGroups())
1991 alignPanel.alignmentChanged();
1995 public void selectAllSequenceMenuItem_actionPerformed()
1997 SequenceGroup sg = new SequenceGroup();
1998 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2000 sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
2002 sg.setEndRes(viewport.getAlignment().getWidth() - 1);
2003 viewport.setSelectionGroup(sg);
2004 alignPanel.paintAlignment(true);
2005 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2006 viewport.sendSelection();
2009 public void deselectAllSequenceMenuItem_actionPerformed()
2011 if (viewport.cursorMode)
2013 alignPanel.seqPanel.keyboardNo1 = null;
2014 alignPanel.seqPanel.keyboardNo2 = null;
2016 viewport.setSelectionGroup(null);
2017 viewport.getColumnSelection().clear();
2018 viewport.setSelectionGroup(null);
2019 alignPanel.idPanel.idCanvas.searchResults = null;
2020 alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);
2021 alignPanel.paintAlignment(true);
2022 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2023 viewport.sendSelection();
2026 public void invertSequenceMenuItem_actionPerformed()
2028 SequenceGroup sg = viewport.getSelectionGroup();
2029 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2031 sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);
2034 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2035 viewport.sendSelection();
2038 public void invertColSel_actionPerformed()
2040 viewport.invertColumnSelection();
2041 alignPanel.paintAlignment(true);
2042 PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());
2043 viewport.sendSelection();
2046 void trimAlignment(boolean trimLeft)
2048 ColumnSelection colSel = viewport.getColumnSelection();
2051 if (colSel.size() > 0)
2055 column = colSel.getMin();
2059 column = colSel.getMax();
2063 if (viewport.getSelectionGroup() != null)
2065 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2066 viewport.getHiddenRepSequences());
2070 seqs = viewport.getAlignment().getSequencesArray();
2073 TrimRegionCommand trimRegion;
2076 trimRegion = new TrimRegionCommand("Remove Left",
2077 TrimRegionCommand.TRIM_LEFT, seqs, column,
2078 viewport.getAlignment(), viewport.getColumnSelection(),
2079 viewport.getSelectionGroup());
2080 viewport.setStartRes(0);
2084 trimRegion = new TrimRegionCommand("Remove Right",
2085 TrimRegionCommand.TRIM_RIGHT, seqs, column,
2086 viewport.getAlignment(), viewport.getColumnSelection(),
2087 viewport.getSelectionGroup());
2090 statusBar.setText(MessageManager.formatMessage(
2091 "label.removed_columns", new String[]
2092 { Integer.valueOf(trimRegion.getSize()).toString() }));
2093 addHistoryItem(trimRegion);
2095 for (SequenceGroup sg : viewport.getAlignment().getGroups())
2097 if ((trimLeft && !sg.adjustForRemoveLeft(column))
2098 || (!trimLeft && !sg.adjustForRemoveRight(column)))
2100 viewport.getAlignment().deleteGroup(sg);
2104 viewport.firePropertyChange("alignment", null, viewport
2105 .getAlignment().getSequences());
2109 public void removeGappedColumnMenuItem_actionPerformed()
2111 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2114 if (viewport.getSelectionGroup() != null)
2116 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2117 viewport.getHiddenRepSequences());
2118 start = viewport.getSelectionGroup().getStartRes();
2119 end = viewport.getSelectionGroup().getEndRes();
2123 seqs = viewport.getAlignment().getSequencesArray();
2126 RemoveGapColCommand removeGapCols = new RemoveGapColCommand(
2127 "Remove Gapped Columns", seqs, start, end,
2128 viewport.getAlignment());
2130 addHistoryItem(removeGapCols);
2132 statusBar.setText(MessageManager.formatMessage(
2133 "label.removed_empty_columns", new String[]
2134 { Integer.valueOf(removeGapCols.getSize()).toString() }));
2136 // This is to maintain viewport position on first residue
2137 // of first sequence
2138 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2139 int startRes = seq.findPosition(viewport.startRes);
2140 // ShiftList shifts;
2141 // viewport.getAlignment().removeGaps(shifts=new ShiftList());
2142 // edit.alColumnChanges=shifts.getInverse();
2143 // if (viewport.hasHiddenColumns)
2144 // viewport.getColumnSelection().compensateForEdits(shifts);
2145 viewport.setStartRes(seq.findIndex(startRes) - 1);
2146 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2151 public void removeAllGapsMenuItem_actionPerformed()
2153 int start = 0, end = viewport.getAlignment().getWidth() - 1;
2156 if (viewport.getSelectionGroup() != null)
2158 seqs = viewport.getSelectionGroup().getSequencesAsArray(
2159 viewport.getHiddenRepSequences());
2160 start = viewport.getSelectionGroup().getStartRes();
2161 end = viewport.getSelectionGroup().getEndRes();
2165 seqs = viewport.getAlignment().getSequencesArray();
2168 // This is to maintain viewport position on first residue
2169 // of first sequence
2170 SequenceI seq = viewport.getAlignment().getSequenceAt(0);
2171 int startRes = seq.findPosition(viewport.startRes);
2173 addHistoryItem(new RemoveGapsCommand("Remove Gaps", seqs, start, end,
2174 viewport.getAlignment()));
2176 viewport.setStartRes(seq.findIndex(startRes) - 1);
2178 viewport.firePropertyChange("alignment", null, viewport.getAlignment()
2183 public void findMenuItem_actionPerformed()
2185 new Finder(alignPanel);
2189 * create a new view derived from the current view
2192 * @return frame for the new view
2194 public AlignFrame newView(String viewtitle)
2197 if (viewport.hasHiddenRows())
2199 newal = new Alignment(viewport.getAlignment().getHiddenSequences()
2200 .getFullAlignment().getSequencesArray());
2204 newal = new Alignment(viewport.getAlignment().getSequencesArray());
2207 if (viewport.getAlignment().getAlignmentAnnotation() != null)
2209 for (int i = 0; i < viewport.getAlignment().getAlignmentAnnotation().length; i++)
2211 if (!viewport.getAlignment().getAlignmentAnnotation()[i].autoCalculated)
2213 newal.addAnnotation(viewport.getAlignment()
2214 .getAlignmentAnnotation()[i]);
2219 AlignFrame newaf = new AlignFrame(newal, viewport.applet, "", false);
2221 newaf.viewport.setSequenceSetId(alignPanel.av.getSequenceSetId());
2222 PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());
2223 PaintRefresher.Register(newaf.alignPanel,
2224 newaf.alignPanel.av.getSequenceSetId());
2226 PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,
2227 newaf.alignPanel.av.getSequenceSetId());
2228 PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,
2229 newaf.alignPanel.av.getSequenceSetId());
2231 Vector comps = (Vector) PaintRefresher.components.get(viewport
2232 .getSequenceSetId());
2234 for (int i = 0; i < comps.size(); i++)
2236 if (comps.elementAt(i) instanceof AlignmentPanel)
2242 String title = new String(this.getTitle());
2243 if (viewtitle != null)
2245 title = viewtitle + " ( " + title + ")";
2249 if (title.indexOf("(View") > -1)
2251 title = title.substring(0, title.indexOf("(View"));
2253 title += "(View " + viewSize + ")";
2256 newaf.setTitle(title.toString());
2258 newaf.viewport.historyList = viewport.historyList;
2259 newaf.viewport.redoList = viewport.redoList;
2265 * @return list of feature groups on the view
2267 public String[] getFeatureGroups()
2269 FeatureRenderer fr = null;
2270 if (alignPanel != null
2271 && (fr = alignPanel.getFeatureRenderer()) != null)
2273 List gps = fr.getFeatureGroups();
2275 String[] _gps = new String[gps.size()];
2278 _gps[p++] = gp.toString();
2286 * get sequence feature groups that are hidden or shown
2292 public String[] getFeatureGroupsOfState(boolean visible)
2294 FeatureRenderer fr = null;
2295 if (alignPanel != null
2296 && (fr = alignPanel.getFeatureRenderer()) != null)
2298 List gps = fr.getGroups(visible);
2300 String[] _gps = new String[gps.size()];
2303 _gps[p++] = gp.toString();
2311 * Change the display state for the given feature groups
2314 * list of group strings
2316 * visible or invisible
2318 public void setFeatureGroupState(String[] groups, boolean state)
2320 FeatureRenderer fr = null;
2321 this.sequenceFeatures.setState(true);
2322 viewport.setShowSequenceFeatures(true);
2323 if (alignPanel != null
2324 && (fr = alignPanel.getFeatureRenderer()) != null)
2327 fr.setGroupVisibility(Arrays.asList(groups), state);
2328 alignPanel.seqPanel.seqCanvas.repaint();
2329 if (alignPanel.overviewPanel != null)
2331 alignPanel.overviewPanel.updateOverviewImage();
2336 public void seqLimits_itemStateChanged()
2338 viewport.setShowJVSuffix(seqLimits.getState());
2339 alignPanel.fontChanged();
2340 alignPanel.paintAlignment(true);
2343 protected void colourTextMenuItem_actionPerformed()
2345 viewport.setColourText(colourTextMenuItem.getState());
2346 alignPanel.paintAlignment(true);
2349 protected void displayNonconservedMenuItem_actionPerformed()
2351 viewport.setShowunconserved(displayNonconservedMenuItem.getState());
2352 alignPanel.paintAlignment(true);
2355 protected void wrapMenuItem_actionPerformed()
2357 viewport.setWrapAlignment(wrapMenuItem.getState());
2358 alignPanel.setWrapAlignment(wrapMenuItem.getState());
2359 scaleAbove.setEnabled(wrapMenuItem.getState());
2360 scaleLeft.setEnabled(wrapMenuItem.getState());
2361 scaleRight.setEnabled(wrapMenuItem.getState());
2362 alignPanel.paintAlignment(true);
2365 public void overviewMenuItem_actionPerformed()
2367 if (alignPanel.overviewPanel != null)
2372 Frame frame = new Frame();
2373 OverviewPanel overview = new OverviewPanel(alignPanel);
2374 frame.add(overview);
2375 // +50 must allow for applet frame window
2376 jalview.bin.JalviewLite.addFrame(frame, MessageManager.formatMessage(
2377 "label.overview_params", new String[]
2378 { this.getTitle() }), overview.getPreferredSize().width,
2379 overview.getPreferredSize().height + 50);
2382 final AlignmentPanel ap = alignPanel;
2383 frame.addWindowListener(new WindowAdapter()
2386 public void windowClosing(WindowEvent e)
2390 ap.setOverviewPanel(null);
2395 alignPanel.setOverviewPanel(overview);
2399 void changeColour(ColourSchemeI cs)
2405 if (viewport.getAbovePIDThreshold())
2407 viewport.setThreshold(SliderPanel.setPIDSliderSource(alignPanel,
2411 if (viewport.getConservationSelected())
2413 cs.setConservationApplied(true);
2414 viewport.setIncrement(SliderPanel.setConservationSlider(alignPanel,
2419 cs.setConservationApplied(false);
2422 viewport.setGlobalColourScheme(cs);
2424 if (alignPanel.getOverviewPanel() != null)
2426 alignPanel.getOverviewPanel().updateOverviewImage();
2429 jalview.structure.StructureSelectionManager
2430 .getStructureSelectionManager(viewport.applet)
2431 .sequenceColoursChanged(alignPanel);
2433 alignPanel.paintAlignment(true);
2436 protected void modifyPID_actionPerformed()
2438 if (viewport.getAbovePIDThreshold()
2439 && viewport.getGlobalColourScheme() != null)
2441 SliderPanel.setPIDSliderSource(alignPanel,
2442 viewport.getGlobalColourScheme(), "Background");
2443 SliderPanel.showPIDSlider();
2447 protected void modifyConservation_actionPerformed()
2449 if (viewport.getConservationSelected()
2450 && viewport.getGlobalColourScheme() != null)
2452 SliderPanel.setConservationSlider(alignPanel,
2453 viewport.getGlobalColourScheme(), "Background");
2454 SliderPanel.showConservationSlider();
2458 protected void conservationMenuItem_actionPerformed()
2460 viewport.setConservationSelected(conservationMenuItem.getState());
2462 viewport.setAbovePIDThreshold(false);
2463 abovePIDThreshold.setState(false);
2465 changeColour(viewport.getGlobalColourScheme());
2467 modifyConservation_actionPerformed();
2470 public void abovePIDThreshold_actionPerformed()
2472 viewport.setAbovePIDThreshold(abovePIDThreshold.getState());
2474 conservationMenuItem.setState(false);
2475 viewport.setConservationSelected(false);
2477 changeColour(viewport.getGlobalColourScheme());
2479 modifyPID_actionPerformed();
2482 public void sortPairwiseMenuItem_actionPerformed()
2484 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2485 AlignmentSorter.sortByPID(viewport.getAlignment(), viewport
2486 .getAlignment().getSequenceAt(0), null);
2488 addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,
2489 viewport.getAlignment()));
2490 alignPanel.paintAlignment(true);
2493 public void sortIDMenuItem_actionPerformed()
2495 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2496 AlignmentSorter.sortByID(viewport.getAlignment());
2497 addHistoryItem(new OrderCommand("ID Sort", oldOrder,
2498 viewport.getAlignment()));
2499 alignPanel.paintAlignment(true);
2502 public void sortLengthMenuItem_actionPerformed()
2504 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2505 AlignmentSorter.sortByLength(viewport.getAlignment());
2506 addHistoryItem(new OrderCommand("Length Sort", oldOrder,
2507 viewport.getAlignment()));
2508 alignPanel.paintAlignment(true);
2511 public void sortGroupMenuItem_actionPerformed()
2513 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2514 AlignmentSorter.sortByGroup(viewport.getAlignment());
2515 addHistoryItem(new OrderCommand("Group Sort", oldOrder,
2516 viewport.getAlignment()));
2517 alignPanel.paintAlignment(true);
2521 public void removeRedundancyMenuItem_actionPerformed()
2523 new RedundancyPanel(alignPanel);
2526 public void pairwiseAlignmentMenuItem_actionPerformed()
2528 if (viewport.getSelectionGroup() != null
2529 && viewport.getSelectionGroup().getSize() > 1)
2531 Frame frame = new Frame();
2532 frame.add(new PairwiseAlignPanel(alignPanel));
2533 jalview.bin.JalviewLite.addFrame(frame,
2534 MessageManager.getString("action.pairwise_alignment"), 600,
2539 public void PCAMenuItem_actionPerformed()
2541 // are the sequences aligned?
2542 if (!viewport.getAlignment().isAligned(false))
2545 int Width = viewport.getAlignment().getWidth();
2547 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2549 current = viewport.getAlignment().getSequenceAt(i);
2551 if (current.getLength() < Width)
2553 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2556 alignPanel.paintAlignment(true);
2559 if ((viewport.getSelectionGroup() != null
2560 && viewport.getSelectionGroup().getSize() < 4 && viewport
2561 .getSelectionGroup().getSize() > 0)
2562 || viewport.getAlignment().getHeight() < 4)
2569 new PCAPanel(viewport);
2570 } catch (java.lang.OutOfMemoryError ex)
2576 public void averageDistanceTreeMenuItem_actionPerformed()
2578 NewTreePanel("AV", "PID", "Average distance tree using PID");
2581 public void neighbourTreeMenuItem_actionPerformed()
2583 NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");
2586 protected void njTreeBlosumMenuItem_actionPerformed()
2588 NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");
2591 protected void avTreeBlosumMenuItem_actionPerformed()
2593 NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");
2596 void NewTreePanel(String type, String pwType, String title)
2598 // are the sequences aligned?
2599 if (!viewport.getAlignment().isAligned(false))
2602 int Width = viewport.getAlignment().getWidth();
2604 for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
2606 current = viewport.getAlignment().getSequenceAt(i);
2608 if (current.getLength() < Width)
2610 current.insertCharAt(Width - 1, viewport.getGapCharacter());
2613 alignPanel.paintAlignment(true);
2617 if ((viewport.getSelectionGroup() != null && viewport
2618 .getSelectionGroup().getSize() > 1)
2619 || (viewport.getAlignment().getHeight() > 1))
2621 final TreePanel tp = new TreePanel(alignPanel, type, pwType);
2623 addTreeMenuItem(tp, title);
2625 jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);
2629 void loadTree_actionPerformed()
2631 CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);
2632 cap.setText(MessageManager.getString("label.paste_newick_tree_file"));
2633 cap.setTreeImport();
2634 Frame frame = new Frame();
2636 jalview.bin.JalviewLite.addFrame(frame,
2637 MessageManager.getString("label.paste_newick_file"), 400, 300);
2640 public void loadTree(jalview.io.NewickFile tree, String treeFile)
2642 TreePanel tp = new TreePanel(alignPanel, treeFile,
2643 MessageManager.getString("label.load_tree_from_file"), tree);
2644 jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);
2645 addTreeMenuItem(tp, treeFile);
2649 * sort the alignment using the given treePanel
2652 * tree used to sort view
2654 * string used for undo event name
2656 public void sortByTree(TreePanel treePanel, String title)
2658 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2660 .sortByTree(viewport.getAlignment(), treePanel.getTree());
2661 // addHistoryItem(new HistoryItem("Sort", viewport.alignment,
2662 // HistoryItem.SORT));
2663 addHistoryItem(new OrderCommand(MessageManager.formatMessage(
2664 "label.order_by_params", new String[]
2665 { title }), oldOrder, viewport.getAlignment()));
2666 alignPanel.paintAlignment(true);
2670 * Do any automatic reordering of the alignment and add the necessary bits to
2671 * the menu structure for the new tree
2676 protected void addTreeMenuItem(final TreePanel treePanel,
2679 final MenuItem item = new MenuItem(title);
2680 sortByTreeMenu.add(item);
2681 item.addActionListener(new java.awt.event.ActionListener()
2684 public void actionPerformed(ActionEvent evt)
2686 sortByTree(treePanel, title); // treePanel.getTitle());
2690 treePanel.addWindowListener(new WindowAdapter()
2693 public void windowOpened(WindowEvent e)
2695 if (viewport.sortByTree)
2697 sortByTree(treePanel, title);
2699 super.windowOpened(e);
2703 public void windowClosing(WindowEvent e)
2705 sortByTreeMenu.remove(item);
2710 public boolean sortBy(AlignmentOrder alorder, String undoname)
2712 SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();
2713 if (viewport.applet.debug)
2715 System.err.println("Sorting " + alorder.getOrder().size()
2716 + " in alignment '" + getTitle() + "'");
2718 AlignmentSorter.sortBy(viewport.getAlignment(), alorder);
2719 if (undoname != null)
2721 addHistoryItem(new OrderCommand(undoname, oldOrder,
2722 viewport.getAlignment()));
2724 alignPanel.paintAlignment(true);
2728 protected void documentation_actionPerformed()
2730 alignPanel.av.applet.openJalviewHelpUrl();
2733 protected void about_actionPerformed()
2736 class AboutPanel extends Canvas
2742 public AboutPanel(String version, String builddate)
2744 this.version = version;
2745 this.builddate = builddate;
2749 public void paint(Graphics g)
2751 g.setColor(Color.white);
2752 g.fillRect(0, 0, getSize().width, getSize().height);
2753 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2754 FontMetrics fm = g.getFontMetrics();
2755 int fh = fm.getHeight();
2757 g.setColor(Color.black);
2758 // TODO: update this text for each release or centrally store it for
2759 // lite and application
2760 g.setFont(new Font("Helvetica", Font.BOLD, 14));
2761 g.drawString(MessageManager.formatMessage(
2762 "label.jalviewLite_release", new String[]
2763 { version }), x, y += fh);
2764 g.setFont(new Font("Helvetica", Font.BOLD, 12));
2765 g.drawString(MessageManager.formatMessage(
2766 "label.jaview_build_date", new String[]
2767 { builddate }), x, y += fh);
2768 g.setFont(new Font("Helvetica", Font.PLAIN, 12));
2769 g.drawString(MessageManager.getString("label.jalview_authors_1"),
2771 g.drawString(MessageManager.getString("label.jalview_authors_2"),
2772 x + 50, y += fh + 8);
2774 MessageManager.getString("label.jalview_dev_managers"), x,
2776 g.drawString(MessageManager
2777 .getString("label.jalview_distribution_lists"), x, y += fh);
2778 g.drawString(MessageManager.getString("label.jalview_please_cite"),
2781 MessageManager.getString("label.jalview_cite_1_authors"),
2784 MessageManager.getString("label.jalview_cite_1_title"), x,
2786 g.drawString(MessageManager.getString("label.jalview_cite_1_ref"),
2791 Frame frame = new Frame();
2792 frame.add(new AboutPanel(JalviewLite.getVersion(), JalviewLite
2794 jalview.bin.JalviewLite.addFrame(frame,
2795 MessageManager.getString("label.jalview"), 580, 220);
2799 public void showURL(String url, String target)
2801 if (viewport.applet == null)
2803 System.out.println("Not running as applet - no browser available.");
2807 viewport.applet.showURL(url, target);
2811 // ////////////////////////////////////////////////////////////////////////////////
2812 // JBuilder Graphics here
2814 MenuBar alignFrameMenuBar = new MenuBar();
2816 Menu fileMenu = new Menu(MessageManager.getString("action.file"));
2818 MenuItem loadApplication = new MenuItem(
2819 MessageManager.getString("label.view_full_application"));
2821 MenuItem loadTree = new MenuItem(
2822 MessageManager.getString("label.load_associated_tree"));
2824 MenuItem loadAnnotations = new MenuItem(
2825 MessageManager.getString("label.load_features_annotations"));
2827 MenuItem outputFeatures = new MenuItem(
2828 MessageManager.getString("label.export_features").concat("..."));
2830 MenuItem outputAnnotations = new MenuItem(
2831 MessageManager.getString("label.export_annotations").concat("..."));
2833 MenuItem closeMenuItem = new MenuItem(
2834 MessageManager.getString("action.close"));
2836 Menu editMenu = new Menu(MessageManager.getString("action.edit"));
2838 Menu viewMenu = new Menu(MessageManager.getString("action.view"));
2840 Menu colourMenu = new Menu(MessageManager.getString("action.colour"));
2842 Menu calculateMenu = new Menu(
2843 MessageManager.getString("action.calculate"));
2845 MenuItem selectAllSequenceMenuItem = new MenuItem(
2846 MessageManager.getString("action.select_all"));
2848 MenuItem deselectAllSequenceMenuItem = new MenuItem(
2849 MessageManager.getString("action.deselect_all"));
2851 MenuItem invertSequenceMenuItem = new MenuItem(
2852 MessageManager.getString("action.invert_selection"));
2854 MenuItem remove2LeftMenuItem = new MenuItem();
2856 MenuItem remove2RightMenuItem = new MenuItem();
2858 MenuItem removeGappedColumnMenuItem = new MenuItem();
2860 MenuItem removeAllGapsMenuItem = new MenuItem();
2862 CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();
2864 CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();
2866 MenuItem sortPairwiseMenuItem = new MenuItem();
2868 MenuItem sortIDMenuItem = new MenuItem();
2870 MenuItem sortLengthMenuItem = new MenuItem();
2872 MenuItem sortGroupMenuItem = new MenuItem();
2874 MenuItem removeRedundancyMenuItem = new MenuItem();
2876 MenuItem pairwiseAlignmentMenuItem = new MenuItem();
2878 MenuItem PCAMenuItem = new MenuItem();
2880 MenuItem averageDistanceTreeMenuItem = new MenuItem();
2882 MenuItem neighbourTreeMenuItem = new MenuItem();
2884 BorderLayout borderLayout1 = new BorderLayout();
2886 public Label statusBar = new Label();
2888 Menu outputTextboxMenu = new Menu();
2890 MenuItem clustalColour = new MenuItem();
2892 MenuItem zappoColour = new MenuItem();
2894 MenuItem taylorColour = new MenuItem();
2896 MenuItem hydrophobicityColour = new MenuItem();
2898 MenuItem helixColour = new MenuItem();
2900 MenuItem strandColour = new MenuItem();
2902 MenuItem turnColour = new MenuItem();
2904 MenuItem buriedColour = new MenuItem();
2906 MenuItem purinePyrimidineColour = new MenuItem();
2908 MenuItem RNAInteractionColour = new MenuItem();
2910 MenuItem RNAHelixColour = new MenuItem();
2912 MenuItem userDefinedColour = new MenuItem();
2914 MenuItem PIDColour = new MenuItem();
2916 MenuItem BLOSUM62Colour = new MenuItem();
2918 MenuItem tcoffeeColour = new MenuItem();
2920 MenuItem njTreeBlosumMenuItem = new MenuItem();
2922 MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();
2924 CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();
2926 CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();
2928 CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();
2930 MenuItem alProperties = new MenuItem(
2931 MessageManager.getString("label.alignment_props"));
2933 MenuItem overviewMenuItem = new MenuItem();
2935 MenuItem undoMenuItem = new MenuItem();
2937 MenuItem redoMenuItem = new MenuItem();
2939 CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();
2941 MenuItem noColourmenuItem = new MenuItem();
2943 CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();
2945 CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();
2947 MenuItem findMenuItem = new MenuItem();
2949 CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();
2951 MenuItem nucleotideColour = new MenuItem();
2953 MenuItem deleteGroups = new MenuItem();
2955 MenuItem grpsFromSelection = new MenuItem();
2957 MenuItem createGroup = new MenuItem();
2959 MenuItem unGroup = new MenuItem();
2961 MenuItem delete = new MenuItem();
2963 MenuItem copy = new MenuItem();
2965 MenuItem cut = new MenuItem();
2967 Menu pasteMenu = new Menu();
2969 MenuItem pasteNew = new MenuItem();
2971 MenuItem pasteThis = new MenuItem();
2973 CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();
2975 MenuItem font = new MenuItem();
2977 CheckboxMenuItem scaleAbove = new CheckboxMenuItem();
2979 CheckboxMenuItem scaleLeft = new CheckboxMenuItem();
2981 CheckboxMenuItem scaleRight = new CheckboxMenuItem();
2983 MenuItem modifyPID = new MenuItem();
2985 MenuItem modifyConservation = new MenuItem();
2987 CheckboxMenuItem autoCalculate = new CheckboxMenuItem(
2988 "Autocalculate Consensus", true);
2990 CheckboxMenuItem sortByTree = new CheckboxMenuItem(
2991 "Sort Alignment With New Tree", true);
2993 Menu sortByTreeMenu = new Menu();
2995 Menu sort = new Menu();
2997 Menu calculate = new Menu();
2999 MenuItem inputText = new MenuItem();
3001 Menu helpMenu = new Menu();
3003 MenuItem documentation = new MenuItem();
3005 MenuItem about = new MenuItem();
3007 CheckboxMenuItem seqLimits = new CheckboxMenuItem();
3009 CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();
3011 CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();
3013 Menu autoAnnMenu = new Menu();
3015 CheckboxMenuItem showSequenceLogo = new CheckboxMenuItem();
3017 CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();
3019 CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();
3021 CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();
3023 CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();
3025 CheckboxMenuItem normSequenceLogo = new CheckboxMenuItem();
3027 private void jbInit() throws Exception
3030 setMenuBar(alignFrameMenuBar);
3034 // dynamically fill save as menu with available formats
3035 for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)
3038 item = new MenuItem(
3039 jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);
3041 item.addActionListener(new java.awt.event.ActionListener()
3044 public void actionPerformed(ActionEvent e)
3046 outputText_actionPerformed(e);
3050 outputTextboxMenu.add(item);
3052 closeMenuItem.addActionListener(this);
3053 loadApplication.addActionListener(this);
3055 loadTree.addActionListener(this);
3056 loadAnnotations.addActionListener(this);
3057 outputFeatures.addActionListener(this);
3058 outputAnnotations.addActionListener(this);
3059 selectAllSequenceMenuItem.addActionListener(this);
3060 deselectAllSequenceMenuItem.addActionListener(this);
3061 invertSequenceMenuItem.addActionListener(this);
3062 remove2LeftMenuItem.setLabel(MessageManager
3063 .getString("action.remove_left"));
3064 remove2LeftMenuItem.addActionListener(this);
3065 remove2RightMenuItem.setLabel(MessageManager
3066 .getString("action.remove_right"));
3067 remove2RightMenuItem.addActionListener(this);
3068 removeGappedColumnMenuItem.setLabel(MessageManager
3069 .getString("action.remove_empty_columns"));
3070 removeGappedColumnMenuItem.addActionListener(this);
3071 removeAllGapsMenuItem.setLabel(MessageManager
3072 .getString("action.remove_all_gaps"));
3073 removeAllGapsMenuItem.addActionListener(this);
3074 viewBoxesMenuItem.setLabel(MessageManager.getString("action.boxes"));
3075 viewBoxesMenuItem.setState(true);
3076 viewBoxesMenuItem.addItemListener(this);
3077 viewTextMenuItem.setLabel(MessageManager.getString("action.text"));
3078 viewTextMenuItem.setState(true);
3079 viewTextMenuItem.addItemListener(this);
3080 sortPairwiseMenuItem.setLabel(MessageManager
3081 .getString("action.by_pairwise_id"));
3082 sortPairwiseMenuItem.addActionListener(this);
3083 sortIDMenuItem.setLabel(MessageManager.getString("action.by_id"));
3084 sortIDMenuItem.addActionListener(this);
3085 sortLengthMenuItem.setLabel(MessageManager
3086 .getString("action.by_length"));
3087 sortLengthMenuItem.addActionListener(this);
3088 sortGroupMenuItem.setLabel(MessageManager.getString("action.by_group"));
3089 sortGroupMenuItem.addActionListener(this);
3090 removeRedundancyMenuItem.setLabel(MessageManager
3091 .getString("action.remove_redundancy").concat("..."));
3092 removeRedundancyMenuItem.addActionListener(this);
3093 pairwiseAlignmentMenuItem.setLabel(MessageManager
3094 .getString("action.pairwise_alignment"));
3095 pairwiseAlignmentMenuItem.addActionListener(this);
3096 PCAMenuItem.setLabel(MessageManager
3097 .getString("label.principal_component_analysis"));
3098 PCAMenuItem.addActionListener(this);
3099 averageDistanceTreeMenuItem.setLabel(MessageManager
3100 .getString("label.average_distance_identity"));
3101 averageDistanceTreeMenuItem.addActionListener(this);
3102 neighbourTreeMenuItem.setLabel(MessageManager
3103 .getString("label.neighbour_joining_identity"));
3104 neighbourTreeMenuItem.addActionListener(this);
3105 statusBar.setBackground(Color.white);
3106 statusBar.setFont(new java.awt.Font("Verdana", 0, 11));
3107 statusBar.setText(MessageManager.getString("label.status_bar"));
3108 outputTextboxMenu.setLabel(MessageManager
3109 .getString("label.out_to_textbox"));
3110 clustalColour.setLabel(MessageManager.getString("label.clustalx"));
3112 clustalColour.addActionListener(this);
3113 zappoColour.setLabel(MessageManager.getString("label.zappo"));
3114 zappoColour.addActionListener(this);
3115 taylorColour.setLabel(MessageManager.getString("label.taylor"));
3116 taylorColour.addActionListener(this);
3117 hydrophobicityColour.setLabel(MessageManager
3118 .getString("label.hydrophobicity"));
3119 hydrophobicityColour.addActionListener(this);
3121 .setLabel(MessageManager.getString("label.helix_propensity"));
3122 helixColour.addActionListener(this);
3123 strandColour.setLabel(MessageManager
3124 .getString("label.strand_propensity"));
3125 strandColour.addActionListener(this);
3126 turnColour.setLabel(MessageManager.getString("label.turn_propensity"));
3127 turnColour.addActionListener(this);
3128 buriedColour.setLabel(MessageManager.getString("label.buried_index"));
3129 buriedColour.addActionListener(this);
3130 purinePyrimidineColour.setLabel(MessageManager
3131 .getString("label.purine_pyrimidine"));
3132 purinePyrimidineColour.addActionListener(this);
3133 RNAInteractionColour.setLabel(MessageManager
3134 .getString("label.rna_interaction"));
3135 RNAInteractionColour.addActionListener(this);
3136 RNAHelixColour.setLabel(MessageManager
3137 .getString("action.by_rna_helixes"));
3138 RNAHelixColour.addActionListener(this);
3139 userDefinedColour.setLabel(MessageManager
3140 .getString("action.user_defined"));
3141 userDefinedColour.addActionListener(this);
3142 PIDColour.setLabel(MessageManager
3143 .getString("label.percentage_identity"));
3144 PIDColour.addActionListener(this);
3145 BLOSUM62Colour.setLabel(MessageManager
3146 .getString("label.blosum62_score"));
3147 BLOSUM62Colour.addActionListener(this);
3149 .setLabel(MessageManager.getString("label.tcoffee_scores"));
3150 tcoffeeColour.setEnabled(false); // it will enabled only if a score file is
3152 tcoffeeColour.addActionListener(this);
3153 avDistanceTreeBlosumMenuItem.setLabel(MessageManager
3154 .getString("label.average_distance_bloslum62"));
3155 avDistanceTreeBlosumMenuItem.addActionListener(this);
3156 njTreeBlosumMenuItem.setLabel(MessageManager
3157 .getString("label.neighbour_blosum62"));
3158 njTreeBlosumMenuItem.addActionListener(this);
3159 annotationPanelMenuItem.setLabel(MessageManager
3160 .getString("label.show_annotations"));
3161 annotationPanelMenuItem.addItemListener(this);
3162 colourTextMenuItem.setLabel(MessageManager
3163 .getString("label.colour_text"));
3164 colourTextMenuItem.addItemListener(this);
3165 displayNonconservedMenuItem.setLabel(MessageManager
3166 .getString("label.show_non_conversed"));
3167 displayNonconservedMenuItem.addItemListener(this);
3168 alProperties.addActionListener(this);
3169 overviewMenuItem.setLabel(MessageManager
3170 .getString("label.overview_window"));
3171 overviewMenuItem.addActionListener(this);
3172 undoMenuItem.setEnabled(false);
3173 undoMenuItem.setLabel(MessageManager.getString("action.undo"));
3174 undoMenuItem.addActionListener(this);
3175 redoMenuItem.setEnabled(false);
3176 redoMenuItem.setLabel(MessageManager.getString("action.redo"));
3177 redoMenuItem.addActionListener(this);
3178 conservationMenuItem.setLabel(MessageManager
3179 .getString("action.by_conservation"));
3180 conservationMenuItem.addItemListener(this);
3181 noColourmenuItem.setLabel(MessageManager.getString("label.none"));
3182 noColourmenuItem.addActionListener(this);
3183 wrapMenuItem.setLabel(MessageManager.getString("action.wrap"));
3184 wrapMenuItem.addItemListener(this);
3185 renderGapsMenuItem.setLabel(MessageManager
3186 .getString("action.show_gaps"));
3187 renderGapsMenuItem.setState(true);
3188 renderGapsMenuItem.addItemListener(this);
3189 findMenuItem.setLabel(MessageManager.getString("action.find"));
3190 findMenuItem.addActionListener(this);
3191 abovePIDThreshold.setLabel(MessageManager
3192 .getString("label.above_identity_threshold"));
3193 abovePIDThreshold.addItemListener(this);
3194 nucleotideColour.setLabel(MessageManager.getString("label.nucleotide"));
3195 nucleotideColour.addActionListener(this);
3196 deleteGroups.setLabel(MessageManager
3197 .getString("action.undefine_groups"));
3198 deleteGroups.addActionListener(this);
3199 grpsFromSelection.setLabel(MessageManager
3200 .getString("action.make_groups_selection"));
3201 grpsFromSelection.addActionListener(this);
3202 createGroup.setLabel(MessageManager.getString("action.create_group"));
3203 unGroup.setLabel(MessageManager.getString("action.remove_group"));
3204 copy.setLabel(MessageManager.getString("action.copy"));
3205 copy.addActionListener(this);
3206 cut.setLabel(MessageManager.getString("action.cut"));
3207 cut.addActionListener(this);
3208 delete.setLabel(MessageManager.getString("action.delete"));
3209 delete.addActionListener(this);
3210 pasteMenu.setLabel(MessageManager.getString("action.paste"));
3211 pasteNew.setLabel(MessageManager.getString("label.to_new_alignment"));
3212 pasteNew.addActionListener(this);
3213 pasteThis.setLabel(MessageManager.getString("label.to_this_alignment"));
3214 pasteThis.addActionListener(this);
3215 applyToAllGroups.setLabel(MessageManager
3216 .getString("label.apply_colour_to_all_groups"));
3217 applyToAllGroups.setState(true);
3218 applyToAllGroups.addItemListener(this);
3219 font.setLabel(MessageManager.getString("action.font"));
3220 font.addActionListener(this);
3221 scaleAbove.setLabel(MessageManager.getString("action.scale_above"));
3222 scaleAbove.setState(true);
3223 scaleAbove.setEnabled(false);
3224 scaleAbove.addItemListener(this);
3225 scaleLeft.setEnabled(false);
3226 scaleLeft.setState(true);
3227 scaleLeft.setLabel(MessageManager.getString("action.scale_left"));
3228 scaleLeft.addItemListener(this);
3229 scaleRight.setEnabled(false);
3230 scaleRight.setState(true);
3231 scaleRight.setLabel(MessageManager.getString("action.scale_right"));
3232 scaleRight.addItemListener(this);
3233 modifyPID.setLabel(MessageManager
3234 .getString("label.modify_identity_thereshold"));
3235 modifyPID.addActionListener(this);
3236 modifyConservation.setLabel(MessageManager
3237 .getString("label.modify_conservation_thereshold"));
3238 modifyConservation.addActionListener(this);
3239 sortByTreeMenu.setLabel(MessageManager
3240 .getString("action.by_tree_order"));
3241 sort.setLabel(MessageManager.getString("action.sort"));
3242 calculate.setLabel(MessageManager.getString("action.calculate_tree"));
3243 autoCalculate.addItemListener(this);
3244 sortByTree.addItemListener(this);
3246 .setLabel(MessageManager.getString("label.input_from_textbox"));
3247 inputText.addActionListener(this);
3248 centreColumnLabelFlag.setLabel(MessageManager
3249 .getString("label.centre_column_labels"));
3250 centreColumnLabelFlag.addItemListener(this);
3251 followMouseOverFlag.setLabel(MessageManager
3252 .getString("label.automatic_scrolling"));
3253 followMouseOverFlag.addItemListener(this);
3254 helpMenu.setLabel(MessageManager.getString("action.help"));
3255 documentation.setLabel(MessageManager.getString("label.documentation"));
3256 documentation.addActionListener(this);
3258 about.setLabel(MessageManager.getString("label.about"));
3259 about.addActionListener(this);
3260 seqLimits.setState(true);
3261 seqLimits.setLabel(MessageManager
3262 .getString("label.show_sequence_limits"));
3263 seqLimits.addItemListener(this);
3264 featureSettings.setLabel(MessageManager
3265 .getString("label.feature_settings"));
3266 featureSettings.addActionListener(this);
3267 sequenceFeatures.setLabel(MessageManager
3268 .getString("label.sequence_features"));
3269 sequenceFeatures.addItemListener(this);
3270 sequenceFeatures.setState(false);
3271 annotationColour.setLabel(MessageManager
3272 .getString("action.by_annotation"));
3273 annotationColour.addActionListener(this);
3275 annotationColumnSelection.setLabel("Select by Annotation");
3276 annotationColumnSelection.addActionListener(this);
3278 invertSequenceMenuItem.setLabel(MessageManager
3279 .getString("action.invert_sequence_selection"));
3280 invertColSel.setLabel(MessageManager
3281 .getString("action.invert_column_selection"));
3282 menu1.setLabel(MessageManager.getString("action.show"));
3283 showColumns.setLabel(MessageManager.getString("label.all_columns"));
3284 showSeqs.setLabel(MessageManager.getString("label.all_sequences"));
3285 menu2.setLabel(MessageManager.getString("action.hide"));
3287 .setLabel(MessageManager.getString("label.selected_columns"));
3288 hideSequences.setLabel(MessageManager
3289 .getString("label.selected_sequences"));
3290 hideAllButSelection.setLabel(MessageManager
3291 .getString("label.all_but_selected_region"));
3292 hideAllSelection.setLabel(MessageManager
3293 .getString("label.selected_region"));
3294 showAllHidden.setLabel(MessageManager
3295 .getString("label.all_sequences_columns"));
3296 showGroupConsensus.setLabel(MessageManager
3297 .getString("label.group_consensus"));
3298 showGroupConservation.setLabel(MessageManager
3299 .getString("label.group_conservation"));
3300 showConsensusHistogram.setLabel(MessageManager
3301 .getString("label.show_consensus_histogram"));
3302 showSequenceLogo.setLabel(MessageManager
3303 .getString("label.show_consensus_logo"));
3304 normSequenceLogo.setLabel(MessageManager
3305 .getString("label.norm_consensus_logo"));
3306 applyAutoAnnotationSettings.setLabel(MessageManager
3307 .getString("label.apply_all_groups"));
3308 applyAutoAnnotationSettings.setState(true);
3309 autoAnnMenu.setLabel(MessageManager
3310 .getString("label.autocalculated_annotation"));
3312 invertColSel.addActionListener(this);
3313 showColumns.addActionListener(this);
3314 showSeqs.addActionListener(this);
3315 hideColumns.addActionListener(this);
3316 hideSequences.addActionListener(this);
3317 hideAllButSelection.addActionListener(this);
3318 hideAllSelection.addActionListener(this);
3319 showAllHidden.addActionListener(this);
3320 showGroupConsensus.addItemListener(this);
3321 showGroupConservation.addItemListener(this);
3322 showConsensusHistogram.addItemListener(this);
3323 showSequenceLogo.addItemListener(this);
3324 normSequenceLogo.addItemListener(this);
3326 applyAutoAnnotationSettings.addItemListener(this);
3327 formatMenu.setLabel(MessageManager.getString("action.format"));
3328 selectMenu.setLabel(MessageManager.getString("action.select"));
3329 newView.setLabel(MessageManager.getString("action.new_view"));
3330 newView.addActionListener(this);
3331 alignFrameMenuBar.add(fileMenu);
3332 alignFrameMenuBar.add(editMenu);
3333 alignFrameMenuBar.add(selectMenu);
3334 alignFrameMenuBar.add(viewMenu);
3335 alignFrameMenuBar.add(formatMenu);
3336 alignFrameMenuBar.add(colourMenu);
3337 alignFrameMenuBar.add(calculateMenu);
3338 alignFrameMenuBar.add(helpMenu);
3340 fileMenu.add(inputText);
3341 fileMenu.add(loadTree);
3342 fileMenu.add(loadAnnotations);
3344 fileMenu.addSeparator();
3345 fileMenu.add(outputTextboxMenu);
3346 fileMenu.add(outputFeatures);
3347 fileMenu.add(outputAnnotations);
3349 if (jalviewServletURL != null)
3351 fileMenu.add(loadApplication);
3354 fileMenu.addSeparator();
3355 fileMenu.add(closeMenuItem);
3357 editMenu.add(undoMenuItem);
3358 editMenu.add(redoMenuItem);
3361 editMenu.add(pasteMenu);
3362 editMenu.add(delete);
3363 editMenu.addSeparator();
3364 editMenu.add(remove2LeftMenuItem);
3365 editMenu.add(remove2RightMenuItem);
3366 editMenu.add(removeGappedColumnMenuItem);
3367 editMenu.add(removeAllGapsMenuItem);
3368 editMenu.add(removeRedundancyMenuItem);
3369 viewMenu.add(newView);
3370 viewMenu.addSeparator();
3371 viewMenu.add(menu1);
3372 viewMenu.add(menu2);
3373 viewMenu.addSeparator();
3374 viewMenu.add(followMouseOverFlag);
3375 viewMenu.add(annotationPanelMenuItem);
3376 autoAnnMenu.add(applyAutoAnnotationSettings);
3377 autoAnnMenu.add(showConsensusHistogram);
3378 autoAnnMenu.add(showSequenceLogo);
3379 autoAnnMenu.add(normSequenceLogo);
3380 autoAnnMenu.addSeparator();
3381 autoAnnMenu.add(showGroupConservation);
3382 autoAnnMenu.add(showGroupConsensus);
3383 viewMenu.add(autoAnnMenu);
3384 viewMenu.addSeparator();
3385 viewMenu.add(sequenceFeatures);
3386 viewMenu.add(featureSettings);
3387 viewMenu.addSeparator();
3388 viewMenu.add(alProperties);
3389 viewMenu.addSeparator();
3390 viewMenu.add(overviewMenuItem);
3391 colourMenu.add(applyToAllGroups);
3392 colourMenu.addSeparator();
3393 colourMenu.add(noColourmenuItem);
3394 colourMenu.add(clustalColour);
3395 colourMenu.add(BLOSUM62Colour);
3396 colourMenu.add(PIDColour);
3397 colourMenu.add(zappoColour);
3398 colourMenu.add(taylorColour);
3399 colourMenu.add(hydrophobicityColour);
3400 colourMenu.add(helixColour);
3401 colourMenu.add(strandColour);
3402 colourMenu.add(turnColour);
3403 colourMenu.add(buriedColour);
3404 colourMenu.add(nucleotideColour);
3405 colourMenu.add(purinePyrimidineColour);
3406 // colourMenu.add(RNAInteractionColour);
3407 colourMenu.add(tcoffeeColour);
3408 colourMenu.add(userDefinedColour);
3409 colourMenu.addSeparator();
3410 colourMenu.add(conservationMenuItem);
3411 colourMenu.add(modifyConservation);
3412 colourMenu.add(abovePIDThreshold);
3413 colourMenu.add(modifyPID);
3414 colourMenu.add(annotationColour);
3415 colourMenu.add(RNAHelixColour);
3416 calculateMenu.add(sort);
3417 calculateMenu.add(calculate);
3418 calculateMenu.addSeparator();
3419 calculateMenu.add(pairwiseAlignmentMenuItem);
3420 calculateMenu.add(PCAMenuItem);
3421 calculateMenu.add(autoCalculate);
3422 calculateMenu.add(sortByTree);
3423 this.add(statusBar, BorderLayout.SOUTH);
3424 pasteMenu.add(pasteNew);
3425 pasteMenu.add(pasteThis);
3426 sort.add(sortIDMenuItem);
3427 sort.add(sortLengthMenuItem);
3428 sort.add(sortByTreeMenu);
3429 sort.add(sortGroupMenuItem);
3430 sort.add(sortPairwiseMenuItem);
3431 calculate.add(averageDistanceTreeMenuItem);
3432 calculate.add(neighbourTreeMenuItem);
3433 calculate.add(avDistanceTreeBlosumMenuItem);
3434 calculate.add(njTreeBlosumMenuItem);
3435 helpMenu.add(documentation);
3436 helpMenu.add(about);
3437 menu1.add(showColumns);
3438 menu1.add(showSeqs);
3439 menu1.add(showAllHidden);
3440 menu2.add(hideColumns);
3441 menu2.add(hideSequences);
3442 menu2.add(hideAllSelection);
3443 menu2.add(hideAllButSelection);
3444 formatMenu.add(font);
3445 formatMenu.add(seqLimits);
3446 formatMenu.add(wrapMenuItem);
3447 formatMenu.add(scaleAbove);
3448 formatMenu.add(scaleLeft);
3449 formatMenu.add(scaleRight);
3450 formatMenu.add(viewBoxesMenuItem);
3451 formatMenu.add(viewTextMenuItem);
3452 formatMenu.add(colourTextMenuItem);
3453 formatMenu.add(displayNonconservedMenuItem);
3454 formatMenu.add(renderGapsMenuItem);
3455 formatMenu.add(centreColumnLabelFlag);
3456 selectMenu.add(findMenuItem);
3457 selectMenu.addSeparator();
3458 selectMenu.add(selectAllSequenceMenuItem);
3459 selectMenu.add(deselectAllSequenceMenuItem);
3460 selectMenu.add(invertSequenceMenuItem);
3461 selectMenu.add(invertColSel);
3462 selectMenu.add(createGroup);
3463 selectMenu.add(unGroup);
3464 selectMenu.add(grpsFromSelection);
3465 selectMenu.add(deleteGroups);
3466 selectMenu.add(annotationColumnSelection);
3470 public void setStatus(String string)
3472 statusBar.setText(string);
3475 MenuItem featureSettings = new MenuItem();
3477 CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();
3479 MenuItem annotationColour = new MenuItem();
3481 MenuItem annotationColumnSelection = new MenuItem();
3483 MenuItem invertColSel = new MenuItem();
3485 Menu menu1 = new Menu();
3487 MenuItem showColumns = new MenuItem();
3489 MenuItem showSeqs = new MenuItem();
3491 Menu menu2 = new Menu();
3493 MenuItem hideColumns = new MenuItem();
3495 MenuItem hideSequences = new MenuItem();
3497 MenuItem hideAllButSelection = new MenuItem();
3499 MenuItem hideAllSelection = new MenuItem();
3501 MenuItem showAllHidden = new MenuItem();
3503 Menu formatMenu = new Menu();
3505 Menu selectMenu = new Menu();
3507 MenuItem newView = new MenuItem();
3510 * Attach the alignFrame panels after embedding menus, if necessary. This used
3511 * to be called setEmbedded, but is now creates the dropdown menus in a
3512 * platform independent manner to avoid OSX/Mac menu appendage daftness.
3514 * @param reallyEmbedded
3515 * true to attach the view to the applet area on the page rather than
3518 public void createAlignFrameWindow(boolean reallyEmbedded, String title)
3523 // Explicly build the embedded menu panel for the on-page applet
3525 // view cannot be closed if its actually on the page
3526 fileMenu.remove(closeMenuItem);
3527 fileMenu.remove(3); // Remove Seperator
3528 embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
3529 Font.PLAIN, 11, false); // use our own fonts.
3530 // and actually add the components to the applet area
3531 viewport.applet.setLayout(new BorderLayout());
3532 viewport.applet.add(embeddedMenu, BorderLayout.NORTH);
3533 viewport.applet.add(statusBar, BorderLayout.SOUTH);
3534 alignPanel.setSize(viewport.applet.getSize().width,
3535 viewport.applet.getSize().height - embeddedMenu.HEIGHT
3536 - statusBar.HEIGHT);
3537 viewport.applet.add(alignPanel, BorderLayout.CENTER);
3538 final AlignFrame me = this;
3539 viewport.applet.addFocusListener(new FocusListener()
3543 public void focusLost(FocusEvent e)
3545 if (me.viewport.applet.currentAlignFrame == me)
3547 me.viewport.applet.currentAlignFrame = null;
3552 public void focusGained(FocusEvent e)
3554 me.viewport.applet.currentAlignFrame = me;
3557 viewport.applet.validate();
3562 // test and embed menu bar if necessary.
3564 if (embedMenuIfNeeded(alignPanel))
3566 // adjust for status bar height too
3567 alignPanel.setSize(getSize().width, getSize().height
3568 - statusBar.HEIGHT);
3570 add(statusBar, BorderLayout.SOUTH);
3571 add(alignPanel, BorderLayout.CENTER);
3572 // and register with the applet so it can pass external API calls to us
3573 jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,
3579 * create a new binding between structures in an existing jmol viewer instance
3580 * and an alignpanel with sequences that have existing PDBFile entries. Note,
3581 * this does not open a new Jmol window, or modify the display of the
3582 * structures in the original jmol window. Note This method doesn't work
3583 * without an additional javascript library to exchange messages between the
3584 * distinct applets. See http://issues.jalview.org/browse/JAL-621
3587 * JmolViewer instance
3588 * @param sequenceIds
3589 * - sequence Ids to search for associations
3591 public SequenceStructureBinding addStructureViewInstance(
3592 Object jmolviewer, String[] sequenceIds)
3594 org.jmol.api.JmolViewer viewer = null;
3597 viewer = (org.jmol.api.JmolViewer) jmolviewer;
3598 } catch (ClassCastException ex)
3600 System.err.println("Unsupported viewer object :"
3601 + jmolviewer.getClass());
3605 System.err.println("Can't use this object as a structure viewer:"
3606 + jmolviewer.getClass());
3609 SequenceI[] seqs = null;
3610 if (sequenceIds == null || sequenceIds.length == 0)
3612 seqs = viewport.getAlignment().getSequencesArray();
3616 Vector sqi = new Vector();
3617 AlignmentI al = viewport.getAlignment();
3618 for (int sid = 0; sid < sequenceIds.length; sid++)
3620 SequenceI sq = al.findName(sequenceIds[sid]);
3628 seqs = new SequenceI[sqi.size()];
3629 for (int sid = 0, sSize = sqi.size(); sid < sSize; sid++)
3631 seqs[sid] = (SequenceI) sqi.elementAt(sid);
3639 AAStructureBindingModel jmv = null;
3640 // TODO: search for a jmv that involves viewer
3642 { // create a new viewer/jalview binding.
3643 jmv = new ExtJmol(viewer, alignPanel, new SequenceI[][]
3651 * bind a pdb file to a sequence in the current view
3654 * - sequenceId within the dataset.
3655 * @param pdbEntryString
3656 * - the short name for the PDB file
3658 * - pdb file - either a URL or a valid PDB file.
3659 * @return true if binding was as success TODO: consider making an exception
3660 * structure for indicating when PDB parsing or sequenceId location
3663 public boolean addPdbFile(String sequenceId, String pdbEntryString,
3666 SequenceI toaddpdb = viewport.getAlignment().findName(sequenceId);
3667 boolean needtoadd = false;
3668 if (toaddpdb != null)
3670 Vector pdbe = toaddpdb.getPDBId();
3671 PDBEntry pdbentry = null;
3672 if (pdbe != null && pdbe.size() > 0)
3674 for (int pe = 0, peSize = pdbe.size(); pe < peSize; pe++)
3676 pdbentry = (PDBEntry) pdbe.elementAt(pe);
3677 if (!pdbentry.getId().equals(pdbEntryString)
3678 && !pdbentry.getFile().equals(pdbFile))
3688 if (pdbentry == null)
3690 pdbentry = new PDBEntry();
3691 pdbentry.setId(pdbEntryString);
3692 pdbentry.setFile(pdbFile);
3693 needtoadd = true; // add this new entry to sequence.
3695 // resolve data source
3696 // TODO: this code should be a refactored to an io package
3697 String protocol = AppletFormatAdapter.resolveProtocol(pdbFile, "PDB");
3698 if (protocol == null)
3704 // make a note of the access mode and add
3705 if (pdbentry.getProperty() == null)
3707 pdbentry.setProperty(new Hashtable());
3709 pdbentry.getProperty().put("protocol", protocol);
3710 toaddpdb.addPDBId(pdbentry);
3711 alignPanel.getStructureSelectionManager()
3712 .registerPDBEntry(pdbentry);
3718 private Object[] cleanSeqChainArrays(SequenceI[] seqs, String[] chains)
3722 Vector sequences = new Vector();
3723 for (int i = 0; i < seqs.length; i++)
3725 if (seqs[i] != null)
3727 sequences.addElement(new Object[]
3728 { seqs[i], (chains != null) ? chains[i] : null });
3731 seqs = new SequenceI[sequences.size()];
3732 chains = new String[sequences.size()];
3733 for (int i = 0, isize = sequences.size(); i < isize; i++)
3735 Object[] oj = (Object[]) sequences.elementAt(i);
3737 seqs[i] = (SequenceI) oj[0];
3738 chains[i] = (String) oj[1];
3746 public void newStructureView(JalviewLite applet, PDBEntry pdb,
3747 SequenceI[] seqs, String[] chains, String protocol)
3749 // Scrub any null sequences from the array
3750 Object[] sqch = cleanSeqChainArrays(seqs, chains);
3751 seqs = (SequenceI[]) sqch[0];
3752 chains = (String[]) sqch[1];
3753 if (seqs == null || seqs.length == 0)
3756 .println("JalviewLite.AlignFrame:newStructureView: No sequence to bind structure to.");
3758 if (protocol == null || protocol.trim().length() == 0
3759 || protocol.equals("null"))
3761 protocol = (String) pdb.getProperty().get("protocol");
3762 if (protocol == null)
3764 System.err.println("Couldn't work out protocol to open structure: "
3769 if (applet.useXtrnalSviewer)
3771 // register the association(s) and quit, don't create any windows.
3772 if (StructureSelectionManager.getStructureSelectionManager(applet)
3773 .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
3775 System.err.println("Failed to map " + pdb.getFile() + " ("
3776 + protocol + ") to any sequences");
3780 if (applet.isAlignPdbStructures() && applet.jmolAvailable)
3782 // can only do alignments with Jmol
3783 // find the last jmol window assigned to this alignment
3784 jalview.appletgui.AppletJmol ajm = null, tajm;
3785 Vector jmols = applet
3786 .getAppletWindow(jalview.appletgui.AppletJmol.class);
3787 for (int i = 0, iSize = jmols.size(); i < iSize; i++)
3789 tajm = (jalview.appletgui.AppletJmol) jmols.elementAt(i);
3790 if (tajm.ap.alignFrame == this)
3799 .println("Incremental adding and aligning structure to existing Jmol view not yet implemented.");
3800 // try and add the pdb structure
3805 // otherwise, create a new window
3806 if (applet.jmolAvailable)
3808 new jalview.appletgui.AppletJmol(pdb, seqs, chains, alignPanel,
3810 applet.lastFrameX += 40;
3811 applet.lastFrameY += 40;
3815 new MCview.AppletPDBViewer(pdb, seqs, chains, alignPanel, protocol);
3820 public void alignedStructureView(JalviewLite applet, PDBEntry[] pdb,
3821 SequenceI[][] seqs, String[][] chains, String[] protocols)
3823 // TODO Auto-generated method stub
3824 System.err.println("Aligned Structure View: Not yet implemented.");
3828 * modify the current selection, providing the user has not made a selection
3832 * - sequences from this alignment
3834 * - columns to be selected on the alignment
3836 public void select(SequenceGroup sel, ColumnSelection csel)
3838 alignPanel.seqPanel.selection(sel, csel, null);
3841 public void scrollTo(int row, int column)
3843 alignPanel.seqPanel.scrollTo(row, column);
3846 public void scrollToRow(int row)
3848 alignPanel.seqPanel.scrollToRow(row);
3851 public void scrollToColumn(int column)
3853 alignPanel.seqPanel.scrollToColumn(column);
3857 * @return the alignments unique ID.
3859 public String getSequenceSetId()
3861 return viewport.getSequenceSetId();
3865 * Load the (T-Coffee) score file from the specified url
3868 * File/URL/T-COFFEE score file contents
3869 * @throws IOException
3870 * @return true if alignment was annotated with data from source
3872 public boolean loadScoreFile(String source) throws IOException
3875 TCoffeeScoreFile file = new TCoffeeScoreFile(source,
3876 AppletFormatAdapter.checkProtocol(source));
3877 if (!file.isValid())
3879 // TODO: raise dialog for gui
3880 System.err.println("Problems parsing T-Coffee scores: "
3881 + file.getWarningMessage());
3882 System.err.println("Origin was:\n" + source);
3887 * check that the score matrix matches the alignment dimensions
3890 if ((aln = viewport.getAlignment()) != null
3891 && (aln.getHeight() != file.getHeight() || aln.getWidth() != file
3894 // TODO: raise a dialog box here rather than bomb out.
3896 .println("The scores matrix does not match the alignment dimensions");
3900 // TODO add parameter to indicate if matching should be done
3901 if (file.annotateAlignment(alignPanel.getAlignment(), false))
3903 alignPanel.fontChanged();
3904 tcoffeeColour.setEnabled(true);
3905 // switch to this color
3906 changeColour(new TCoffeeColourScheme(alignPanel.getAlignment()));
3911 System.err.println("Problems resolving T-Coffee scores:");
3912 if (file.getWarningMessage() != null)
3914 System.err.println(file.getWarningMessage());