+ zappoColour.setText("Zappo");\r
+ zappoColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ zappoColour_actionPerformed(e);\r
+ }\r
+ });\r
+ taylorColour.setText("Taylor");\r
+ taylorColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ taylorColour_actionPerformed(e);\r
+ }\r
+ });\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ hydrophobicityColour_actionPerformed(e);\r
+ }\r
+ });\r
+ helixColour.setText("Helix Propensity");\r
+ helixColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ helixColour_actionPerformed(e);\r
+ }\r
+ });\r
+ strandColour.setText("Strand Propensity");\r
+ strandColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ strandColour_actionPerformed(e);\r
+ }\r
+ });\r
+ turnColour.setText("Turn Propensity");\r
+ turnColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ turnColour_actionPerformed(e);\r
+ }\r
+ });\r
+ buriedColour.setText("Buried Index");\r
+ buriedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ buriedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ userDefinedColour.setText("User Defined...");\r
+ userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ userDefinedColour_actionPerformed(e);\r
+ }\r
+ });\r
+ PIDColour.setText("Percentage Identity");\r
+ PIDColour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ PIDColour_actionPerformed(e);\r
+ }\r
+ });\r
+ BLOSUM62Colour.setText("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ BLOSUM62Colour_actionPerformed(e);\r
+ }\r
+ });\r
+ avDistanceTreeBlosumMenuItem.setText(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(new java.awt.event.\r
+ ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ njTreeBlosumMenuItem.setText("Neighbour Joining using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ annotationPanelMenuItem.setActionCommand("");\r
+ annotationPanelMenuItem.setText("Show Annotations");\r
+ annotationPanelMenuItem.setState( jalview.bin.Cache.getDefault("SHOW_ANNOTATIONS",true));\r
+ annotationPanelMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ annotationPanelMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ colourTextMenuItem.setText("Colour Text");\r
+ colourTextMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ colourTextMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ htmlMenuItem.setText("HTML");\r
+ htmlMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ htmlMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ overviewMenuItem.setText("Overview Window");\r
+ overviewMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ overviewMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setMnemonic('Z');\r
+ undoMenuItem.setText("Undo");\r
+ undoMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_Z,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ undoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ undoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setMnemonic('0');\r
+ redoMenuItem.setText("Redo");\r
+ redoMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ redoMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ conservationMenuItem.setText("By Conservation");\r
+ conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ conservationMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ noColourmenuItem.setText("None");\r
+ noColourmenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ noColourmenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ wrapMenuItem.setText("Wrap");\r
+ wrapMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ wrapMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ printMenuItem.setText("Print");\r
+ printMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ printMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ renderGapsMenuItem.setText("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ renderGapsMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ findMenuItem.setText("Find...");\r
+ findMenuItem.setAccelerator(javax.swing.KeyStroke.getKeyStroke(\r
+ java.awt.event.KeyEvent.VK_F,\r
+ Toolkit.getDefaultToolkit().getMenuShortcutKeyMask(), false));\r
+ findMenuItem.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ findMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
+ searchMenu.setText("Search");\r
+\r
+ abovePIDThreshold.setText("Above Identity Threshold");\r
+ abovePIDThreshold.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ abovePIDThreshold_actionPerformed(e);\r
+ }\r
+ });\r
+ showSeqFeatures.setText("Show Sequence Features");\r
+ showSeqFeatures.addActionListener(new ActionListener()\r