colours.add(BLOSUM62Colour);\r
colours.add(nucleotideColour);\r
\r
- noColourmenuItem.setSelected(true);\r
+ setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));\r
\r
- String defaultColour = jalview.bin.Cache.getDefault("DEFAULT_COLOUR", null);\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ setJMenuBar(alignFrameMenuBar);\r
+\r
+ JMenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
+ {\r
+ item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
+ elementAt(\r
+ i));\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ }\r
+\r
+ }\r
+\r
+ public void setColourSelected(String defaultColour)\r
+ {\r
\r
if (defaultColour != null)\r
{\r
\r
switch (index)\r
{\r
+ case ColourSchemeProperty.NONE:\r
+ noColourmenuItem.setSelected(true);\r
+ break;\r
case ColourSchemeProperty.CLUSTAL:\r
clustalColour.setSelected(true);\r
\r
\r
break;\r
\r
+ case ColourSchemeProperty.TAYLOR:\r
+ taylorColour.setSelected(true);\r
+ break;\r
+\r
case ColourSchemeProperty.HYDROPHOBIC:\r
hydrophobicityColour.setSelected(true);\r
\r
}\r
}\r
\r
- try\r
- {\r
- jbInit();\r
- setJMenuBar(alignFrameMenuBar);\r
-\r
- JMenuItem item;\r
-\r
- // dynamically fill save as menu with available formats\r
- for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)\r
- {\r
- item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.\r
- elementAt(\r
- i));\r
- item.addActionListener(new java.awt.event.ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- outputText_actionPerformed(e);\r
- }\r
- });\r
-\r
- outputTextboxMenu.add(item);\r
- }\r
- }\r
- catch (Exception e)\r
- {\r
- }\r
-\r
}\r
\r
private void jbInit()\r
fileMenu.setText("File");\r
saveAlignmentMenu.setMnemonic('L');\r
saveAlignmentMenu.setText("Save As");\r
+ saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.\r
+ awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));\r
saveAlignmentMenu.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
public static final int ZAPPO = 3;\r
\r
/** DOCUMENT ME!! */\r
- public static final int HYDROPHOBIC = 4;\r
+ public static final int TAYLOR = 4;\r
\r
/** DOCUMENT ME!! */\r
- public static final int HELIX = 5;\r
+ public static final int HYDROPHOBIC = 5;\r
\r
/** DOCUMENT ME!! */\r
- public static final int STRAND = 6;\r
+ public static final int HELIX = 6;\r
\r
/** DOCUMENT ME!! */\r
- public static final int TURN = 7;\r
+ public static final int STRAND = 7;\r
\r
/** DOCUMENT ME!! */\r
- public static final int BURIED = 8;\r
+ public static final int TURN = 8;\r
\r
/** DOCUMENT ME!! */\r
- public static final int NUCLEOTIDE = 9;\r
+ public static final int BURIED = 9;\r
\r
/** DOCUMENT ME!! */\r
- public static final int USER_DEFINED = 10;\r
+ public static final int NUCLEOTIDE = 10;\r
\r
/** DOCUMENT ME!! */\r
- public static final int NONE = 11;\r
+ public static final int USER_DEFINED = 11;\r
+\r
+\r
+ /** DOCUMENT ME!! */\r
+ public static final int NONE = 12;\r
\r
/**\r
* DOCUMENT ME!\r
*/\r
public static int getColourIndexFromName(String name)\r
{\r
- int ret = 11;\r
+ int ret = 12;\r
\r
if (name.equalsIgnoreCase("Clustal"))\r
{\r
{\r
ret = ZAPPO;\r
}\r
+ else if (name.equalsIgnoreCase("Taylor"))\r
+ {\r
+ ret = TAYLOR;\r
+ }\r
else if (name.equalsIgnoreCase("Hydrophobic"))\r
{\r
ret = HYDROPHOBIC;\r
cs = ((ConservationColourScheme) cs).cs;\r
}\r
\r
- int index = 11;\r
+ int index = 12;\r
\r
if (cs instanceof ClustalxColourScheme)\r
{\r
{\r
index = ZAPPO;\r
}\r
+ else if (cs instanceof TaylorColourScheme)\r
+ {\r
+ index = TAYLOR;\r
+ }\r
else if (cs instanceof HydrophobicColourScheme)\r
{\r
index = HYDROPHOBIC;\r
\r
break;\r
\r
+ case TAYLOR:\r
+ ret = "Taylor";\r
+ break;\r
+\r
case HYDROPHOBIC:\r
ret = "Hydrophobic";\r
\r
\r
break;\r
\r
+ case TAYLOR:\r
+ cs = new TaylorColourScheme();\r
+ break;\r
+\r
case HYDROPHOBIC:\r
cs = new HydrophobicColourScheme();\r
\r