From ef3333028b291ce92bdae34bd2f8487d35d0a0d3 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Mon, 15 Aug 2005 12:11:07 +0000
Subject: [PATCH] Add taylor to default colour check

---
 src/jalview/jbgui/GAlignFrame.java            |   73 +++++++++++++++----------
 src/jalview/schemes/ColourSchemeProperty.java |   40 ++++++++++----
 2 files changed, 73 insertions(+), 40 deletions(-)

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 463bf70..26e5326 100755
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -133,9 +133,41 @@ public class GAlignFrame
     colours.add(BLOSUM62Colour);
     colours.add(nucleotideColour);
 
-    noColourmenuItem.setSelected(true);
+    setColourSelected(jalview.bin.Cache.getDefault("DEFAULT_COLOUR", "None"));
 
-    String defaultColour = jalview.bin.Cache.getDefault("DEFAULT_COLOUR", null);
+
+    try
+    {
+      jbInit();
+      setJMenuBar(alignFrameMenuBar);
+
+      JMenuItem item;
+
+      // dynamically fill save as menu with available formats
+      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
+      {
+        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
+                             elementAt(
+                                 i));
+        item.addActionListener(new java.awt.event.ActionListener()
+        {
+          public void actionPerformed(ActionEvent e)
+          {
+            outputText_actionPerformed(e);
+          }
+        });
+
+        outputTextboxMenu.add(item);
+      }
+    }
+    catch (Exception e)
+    {
+    }
+
+  }
+
+  public void setColourSelected(String defaultColour)
+  {
 
     if (defaultColour != null)
     {
@@ -143,6 +175,9 @@ public class GAlignFrame
 
       switch (index)
       {
+        case ColourSchemeProperty.NONE:
+              noColourmenuItem.setSelected(true);
+              break;
         case ColourSchemeProperty.CLUSTAL:
           clustalColour.setSelected(true);
 
@@ -163,6 +198,10 @@ public class GAlignFrame
 
           break;
 
+        case ColourSchemeProperty.TAYLOR:
+          taylorColour.setSelected(true);
+          break;
+
         case ColourSchemeProperty.HYDROPHOBIC:
           hydrophobicityColour.setSelected(true);
 
@@ -200,34 +239,6 @@ public class GAlignFrame
       }
     }
 
-    try
-    {
-      jbInit();
-      setJMenuBar(alignFrameMenuBar);
-
-      JMenuItem item;
-
-      // dynamically fill save as menu with available formats
-      for (int i = 0; i < jalview.io.FormatAdapter.formats.size(); i++)
-      {
-        item = new JMenuItem( (String) jalview.io.FormatAdapter.formats.
-                             elementAt(
-                                 i));
-        item.addActionListener(new java.awt.event.ActionListener()
-        {
-          public void actionPerformed(ActionEvent e)
-          {
-            outputText_actionPerformed(e);
-          }
-        });
-
-        outputTextboxMenu.add(item);
-      }
-    }
-    catch (Exception e)
-    {
-    }
-
   }
 
   private void jbInit()
@@ -237,6 +248,8 @@ public class GAlignFrame
     fileMenu.setText("File");
     saveAlignmentMenu.setMnemonic('L');
     saveAlignmentMenu.setText("Save As");
+    saveAlignmentMenu.setAccelerator(javax.swing.KeyStroke.getKeyStroke(java.
+        awt.event.KeyEvent.VK_S, java.awt.event.KeyEvent.CTRL_MASK, false));
     saveAlignmentMenu.addActionListener(new ActionListener()
     {
       public void actionPerformed(ActionEvent e)
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index d27dcf0..012c3a9 100755
--- 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;
 
     /** DOCUMENT ME!! */
-    public static final int HYDROPHOBIC = 4;
+    public static final int TAYLOR = 4;
 
     /** DOCUMENT ME!! */
-    public static final int HELIX = 5;
+    public static final int HYDROPHOBIC = 5;
 
     /** DOCUMENT ME!! */
-    public static final int STRAND = 6;
+    public static final int HELIX = 6;
 
     /** DOCUMENT ME!! */
-    public static final int TURN = 7;
+    public static final int STRAND = 7;
 
     /** DOCUMENT ME!! */
-    public static final int BURIED = 8;
+    public static final int TURN = 8;
 
     /** DOCUMENT ME!! */
-    public static final int NUCLEOTIDE = 9;
+    public static final int BURIED = 9;
 
     /** DOCUMENT ME!! */
-    public static final int USER_DEFINED = 10;
+    public static final int NUCLEOTIDE = 10;
 
     /** DOCUMENT ME!! */
-    public static final int NONE = 11;
+    public static final int USER_DEFINED = 11;
+
+
+    /** DOCUMENT ME!! */
+    public static final int NONE = 12;
 
     /**
      * DOCUMENT ME!
@@ -72,7 +76,7 @@ public class ColourSchemeProperty
      */
     public static int getColourIndexFromName(String name)
     {
-        int ret = 11;
+        int ret = 12;
 
         if (name.equalsIgnoreCase("Clustal"))
         {
@@ -90,6 +94,10 @@ public class ColourSchemeProperty
         {
             ret = ZAPPO;
         }
+        else if (name.equalsIgnoreCase("Taylor"))
+        {
+          ret = TAYLOR;
+        }
         else if (name.equalsIgnoreCase("Hydrophobic"))
         {
             ret = HYDROPHOBIC;
@@ -136,7 +144,7 @@ public class ColourSchemeProperty
             cs = ((ConservationColourScheme) cs).cs;
         }
 
-        int index = 11;
+        int index = 12;
 
         if (cs instanceof ClustalxColourScheme)
         {
@@ -154,6 +162,10 @@ public class ColourSchemeProperty
         {
             index = ZAPPO;
         }
+        else if (cs instanceof TaylorColourScheme)
+        {
+            index = TAYLOR;
+        }
         else if (cs instanceof HydrophobicColourScheme)
         {
             index = HYDROPHOBIC;
@@ -219,6 +231,10 @@ public class ColourSchemeProperty
 
             break;
 
+        case TAYLOR:
+            ret = "Taylor";
+            break;
+
         case HYDROPHOBIC:
             ret = "Hydrophobic";
 
@@ -328,6 +344,10 @@ public class ColourSchemeProperty
 
             break;
 
+        case TAYLOR:
+            cs = new TaylorColourScheme();
+            break;
+
         case HYDROPHOBIC:
             cs = new HydrophobicColourScheme();
 
-- 
1.7.10.2