Add taylor to default colour check

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 463bf70..26e5326 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -133,9 +133,41 @@ public class GAlignFrame
     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
@@ -143,6 +175,9 @@ public class GAlignFrame
 \r
       switch (index)\r
       {\r
+        case ColourSchemeProperty.NONE:\r
+              noColourmenuItem.setSelected(true);\r
+              break;\r
         case ColourSchemeProperty.CLUSTAL:\r
           clustalColour.setSelected(true);\r
 \r
@@ -163,6 +198,10 @@ public class GAlignFrame
 \r
           break;\r
 \r
+        case ColourSchemeProperty.TAYLOR:\r
+          taylorColour.setSelected(true);\r
+          break;\r
+\r
         case ColourSchemeProperty.HYDROPHOBIC:\r
           hydrophobicityColour.setSelected(true);\r
 \r
@@ -200,34 +239,6 @@ public class GAlignFrame
       }\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
@@ -237,6 +248,8 @@ public class GAlignFrame
     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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index d27dcf0..012c3a9 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -40,28 +40,32 @@ public class ColourSchemeProperty
     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
@@ -72,7 +76,7 @@ public class ColourSchemeProperty
      */\r
     public static int getColourIndexFromName(String name)\r
     {\r
-        int ret = 11;\r
+        int ret = 12;\r
 \r
         if (name.equalsIgnoreCase("Clustal"))\r
         {\r
@@ -90,6 +94,10 @@ public class ColourSchemeProperty
         {\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
@@ -136,7 +144,7 @@ public class ColourSchemeProperty
             cs = ((ConservationColourScheme) cs).cs;\r
         }\r
 \r
-        int index = 11;\r
+        int index = 12;\r
 \r
         if (cs instanceof ClustalxColourScheme)\r
         {\r
@@ -154,6 +162,10 @@ public class ColourSchemeProperty
         {\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
@@ -219,6 +231,10 @@ public class ColourSchemeProperty
 \r
             break;\r
 \r
+        case TAYLOR:\r
+            ret = "Taylor";\r
+            break;\r
+\r
         case HYDROPHOBIC:\r
             ret = "Hydrophobic";\r
 \r
@@ -328,6 +344,10 @@ public class ColourSchemeProperty
 \r
             break;\r
 \r
+        case TAYLOR:\r
+            cs = new TaylorColourScheme();\r
+            break;\r
+\r
         case HYDROPHOBIC:\r
             cs = new HydrophobicColourScheme();\r
 \r