+ viewport.applet.showURL(url, target);\r
+ }\r
+ }\r
+\r
+ // ////////////////////////////////////////////////////////////////////////////////\r
+ // JBuilder Graphics here\r
+\r
+ MenuBar alignFrameMenuBar = new MenuBar();\r
+\r
+ Menu fileMenu = new Menu("File");\r
+\r
+ MenuItem loadApplication = new MenuItem("View in Full Application");\r
+\r
+ MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+\r
+ MenuItem loadAnnotations = new MenuItem("Load Features/Annotations ...");\r
+ \r
+ MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+\r
+ MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ MenuItem closeMenuItem = new MenuItem("Close");\r
+\r
+ Menu editMenu = new Menu("Edit");\r
+\r
+ Menu viewMenu = new Menu("View");\r
+\r
+ Menu colourMenu = new Menu("Colour");\r
+\r
+ Menu calculateMenu = new Menu("Calculate");\r
+\r
+ MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+\r
+ MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+\r
+ MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+\r
+ MenuItem remove2LeftMenuItem = new MenuItem();\r
+\r
+ MenuItem remove2RightMenuItem = new MenuItem();\r
+\r
+ MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+\r
+ MenuItem removeAllGapsMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem sortPairwiseMenuItem = new MenuItem();\r
+\r
+ MenuItem sortIDMenuItem = new MenuItem();\r
+\r
+ MenuItem sortLengthMenuItem = new MenuItem();\r
+\r
+ MenuItem sortGroupMenuItem = new MenuItem();\r
+\r
+ MenuItem removeRedundancyMenuItem = new MenuItem();\r
+\r
+ MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+\r
+ MenuItem PCAMenuItem = new MenuItem();\r
+\r
+ MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+\r
+ MenuItem neighbourTreeMenuItem = new MenuItem();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ public Label statusBar = new Label();\r
+\r
+ Menu outputTextboxMenu = new Menu();\r
+\r
+ MenuItem clustalColour = new MenuItem();\r
+\r
+ MenuItem zappoColour = new MenuItem();\r
+\r
+ MenuItem taylorColour = new MenuItem();\r
+\r
+ MenuItem hydrophobicityColour = new MenuItem();\r
+\r
+ MenuItem helixColour = new MenuItem();\r
+\r
+ MenuItem strandColour = new MenuItem();\r
+\r
+ MenuItem turnColour = new MenuItem();\r
+\r
+ MenuItem buriedColour = new MenuItem();\r
+\r
+ MenuItem purinePyrimidineColour = new MenuItem();\r
+ MenuItem RNAHelixColour = new MenuItem();\r
+ \r
+ MenuItem userDefinedColour = new MenuItem();\r
+\r
+ MenuItem PIDColour = new MenuItem();\r
+\r
+ MenuItem BLOSUM62Colour = new MenuItem();\r
+ \r
+ MenuItem tcoffeeColour = new MenuItem();\r
+\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem displayNonconservedMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem alProperties = new MenuItem("Alignment Properties...");\r
+\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+\r
+ MenuItem undoMenuItem = new MenuItem();\r
+\r
+ MenuItem redoMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+\r
+ MenuItem findMenuItem = new MenuItem();\r
+\r
+ CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+\r
+ MenuItem nucleotideColour = new MenuItem();\r
+\r
+ MenuItem deleteGroups = new MenuItem();\r
+\r
+ MenuItem grpsFromSelection = new MenuItem();\r
+\r
+ MenuItem delete = new MenuItem();\r
+\r
+ MenuItem copy = new MenuItem();\r
+\r
+ MenuItem cut = new MenuItem();\r
+\r
+ Menu pasteMenu = new Menu();\r
+\r
+ MenuItem pasteNew = new MenuItem();\r
+\r
+ MenuItem pasteThis = new MenuItem();\r
+\r
+ CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+\r
+ MenuItem font = new MenuItem();\r
+\r
+ CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+\r
+ MenuItem modifyPID = new MenuItem();\r
+\r
+ MenuItem modifyConservation = new MenuItem();\r
+\r
+ CheckboxMenuItem autoCalculate = new CheckboxMenuItem(\r
+ "Autocalculate Consensus", true);\r
+\r
+ CheckboxMenuItem sortByTree = new CheckboxMenuItem(\r
+ "Sort Alignment With New Tree", true);\r
+\r
+ Menu sortByTreeMenu = new Menu();\r
+\r
+ Menu sort = new Menu();\r
+\r
+ Menu calculate = new Menu();\r
+\r
+ MenuItem inputText = new MenuItem();\r
+\r
+ Menu helpMenu = new Menu();\r
+\r
+ MenuItem documentation = new MenuItem();\r
+\r
+ MenuItem about = new MenuItem();\r
+\r
+ CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+\r
+ CheckboxMenuItem centreColumnLabelFlag = new CheckboxMenuItem();\r
+ \r
+ CheckboxMenuItem followMouseOverFlag = new CheckboxMenuItem();\r
+ Menu autoAnnMenu=new Menu();\r
+ CheckboxMenuItem showSequenceLogo= new CheckboxMenuItem();\r
+ CheckboxMenuItem applyAutoAnnotationSettings = new CheckboxMenuItem();\r
+ CheckboxMenuItem showConsensusHistogram = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConsensus = new CheckboxMenuItem();\r
+ CheckboxMenuItem showGroupConservation = new CheckboxMenuItem();\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length; i++)\r
+ {\r
+\r
+ item = new MenuItem(\r
+ jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r