JMenuItem unGroupMenuItem = new JMenuItem();\r
JMenuItem pdbMenuItem = new JMenuItem();\r
JMenuItem outline = new JMenuItem();\r
+ JRadioButtonMenuItem nucleotideMenuItem = new JRadioButtonMenuItem();\r
\r
public PopupMenu(AlignmentPanel ap, Sequence seq)\r
{\r
outline_actionPerformed(e);\r
}\r
});\r
+ nucleotideMenuItem.setText("Nucleotide");\r
+ nucleotideMenuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ nucleotideMenuItem_actionPerformed(e);\r
+ }\r
+ });\r
add(groupMenu);\r
this.add(sequenceMenu);\r
this.add(residueMenu);\r
defineMenu.addSeparator();\r
defineMenu.add(noColourmenuItem);\r
defineMenu.add(clustalColour);\r
+ defineMenu.add(BLOSUM62Colour);\r
+ defineMenu.add(PIDColour);\r
+\r
defineMenu.add(zappoColour);\r
defineMenu.add(taylorColour);\r
defineMenu.add(hydrophobicityColour);\r
defineMenu.add(strandColour);\r
defineMenu.add(turnColour);\r
defineMenu.add(buriedColour);\r
+ defineMenu.add(nucleotideMenuItem);\r
+\r
defineMenu.add(userDefinedColour);\r
- defineMenu.add(PIDColour);\r
- defineMenu.add(BLOSUM62Colour);\r
+\r
defineMenu.addSeparator();\r
defineMenu.add(abovePIDColour);\r
defineMenu.add(conservationMenuItem);\r
clustalColour_actionPerformed(e);\r
}\r
});\r
- zappoColour.setText("Zappo colour scheme");\r
+ zappoColour.setText("Zappo");\r
zappoColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
zappoColour_actionPerformed(e);\r
}\r
});\r
- taylorColour.setText("Taylor colour scheme");\r
+ taylorColour.setText("Taylor");\r
taylorColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
taylorColour_actionPerformed(e);\r
}\r
});\r
- hydrophobicityColour.setText("By hydrophobicity");\r
+ hydrophobicityColour.setText("Hydrophobicity");\r
hydrophobicityColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
turnColour_actionPerformed(e);\r
}\r
});\r
- buriedColour.setText("Buried index");\r
+ buriedColour.setText("Buried Index");\r
buriedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
buriedColour_actionPerformed(e);\r
}\r
});\r
- abovePIDColour.setText("Above PID threshold only");\r
+ abovePIDColour.setText("Above % Identity");\r
abovePIDColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
abovePIDColour_actionPerformed(e);\r
}\r
});\r
- userDefinedColour.setText("User defined colours");\r
+ userDefinedColour.setText("User Defined");\r
userDefinedColour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
PIDColour_actionPerformed(e);\r
}\r
});\r
- BLOSUM62Colour.setText("BLOSUM62 score");\r
+ BLOSUM62Colour.setText("BLOSUM62");\r
BLOSUM62Colour.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
BLOSUM62Colour_actionPerformed(e);\r
}\r
});\r
- conservationMenuItem.setText("By conservation");\r
+ conservationMenuItem.setText("Conservation");\r
conservationMenuItem.addActionListener(new java.awt.event.ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
refresh();\r
}\r
\r
+ public void nucleotideMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ getGroup().cs = new NucleotideColourScheme();\r
+ refresh();\r
+ }\r
+\r
+\r
\r
protected void abovePIDColour_actionPerformed(ActionEvent e)\r
{\r
\r
protected void userDefinedColour_actionPerformed(ActionEvent e)\r
{\r
- JInternalFrame frame = new JInternalFrame();\r
- UserDefinedColours chooser = new UserDefinedColours( frame, ap, getGroup());\r
- frame.setContentPane(chooser);\r
- Desktop.addInternalFrame(frame,"User defined colours ("+getGroup().getName()+")", 450,540 );\r
- frame.setResizable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
-\r
+ UserDefinedColours chooser = new UserDefinedColours( ap, getGroup());\r
}\r
\r
protected void PIDColour_actionPerformed(ActionEvent e)\r